diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
new file mode 100644
index 00000000..0877a905
--- /dev/null
+++ b/.github/workflows/ci.yml
@@ -0,0 +1,36 @@
+name: CI
+
+on:
+ workflow_dispatch:
+ push:
+ branches:
+ - main
+ - develop
+ pull_request:
+ branches:
+ - main
+ - develop
+
+jobs:
+ test:
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ py: [ 3.9, 3.8, 3.7 ]
+ steps:
+ - uses: actions/checkout@v2
+ - name: Install Python ${{ matrix.py }}
+ uses: actions/setup-python@v2
+ with:
+ python-version: ${{ matrix.py }}
+ - name: Get full Python version
+ shell: bash
+ run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+ - name: Install dependencies
+ shell: bash
+ run: |
+ python -m pip install --upgrade pip
+ python -m pip install -e .[test]
+ - name: Run unittest
+ shell: bash
+ run: python -m unittest discover -q
\ No newline at end of file
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
new file mode 100644
index 00000000..725843c5
--- /dev/null
+++ b/.github/workflows/release.yml
@@ -0,0 +1,31 @@
+name: release
+
+on:
+ push:
+ tags:
+ - '*.*.*'
+
+jobs:
+ release:
+ runs-on: ubuntu-latest
+ steps:
+ - uses: actions/checkout@v2
+ - name: Install Python 3.7
+ uses: actions/setup-python@v2
+ with:
+ python-version: 3.7
+ - name: Get full Python version
+ shell: bash
+ run: echo ::set-output name=version::$(python -c "import sys; print('-'.join(str(v) for v in sys.version_info))")
+ - name: Build project for distribution
+ shell: bash
+ run: |
+ python -m pip install -q build
+ python -m build
+ - name: Create Release
+ uses: ncipollo/release-action@v1
+ with:
+ artifacts: "dist/*"
+ token: ${{ secrets.GITHUB_TOKEN }}
+ draft: false
+ prerelease: steps.check-version.outputs.prerelease == 'true'
\ No newline at end of file
diff --git a/.gitignore b/.gitignore
index 9ab22dc7..92b1bbe1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -112,6 +112,7 @@ dask-worker-space
# osx
.DS_Store
-# R
-.RData
-.Rhistory
+# Github codespaces
+pythonenv3.8
+
+.vscode
diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 2ef73b4c..00000000
--- a/.travis.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-language: python
-python: '3.6'
-install:
- - python setup.py install
- - pip install mockito PyHamcrest
-script: python -m unittest discover
diff --git a/Makefile b/Makefile
index e650b479..1bcd80bb 100644
--- a/Makefile
+++ b/Makefile
@@ -1,26 +1,20 @@
-# Minimal makefile for Sphinx documentation
-#
+install:
+ @python setup.py build install
-# You can set these variables from the command line.
-SPHINXOPTS =
-SPHINXBUILD = sphinx-build
-SPHINXPROJ = jMetalPy
-SOURCEDIR = docs/source
-BUILDDIR = build
+install-dependencies:
+ @python -m pip install -e .[all]
-# Put it first so that "make" without argument is like "make help".
-help:
- @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+clean:
+ @rm -rf build dist .eggs *.egg-info
+ @find . -type d -name '.mypy_cache' -exec rm -rf {} +
+ @find . -type d -name '__pycache__' -exec rm -rf {} +
-.PHONY: help Makefile
+black: clean
+ @isort --profile black jmetal/ examples/
+ @black jmetal/ examples/
-# "make github" option to build gh-pages
-github:
- @make html
- @cp -a $(BUILDDIR)/html/. docs
- @rm -r $(BUILDDIR)
+lint:
+ @mypy jmetal/ examples/ --show-error-codes
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
- @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+tests:
+ @python -m unittest discover -q
\ No newline at end of file
diff --git a/README.md b/README.md
index ae4391e8..b2d62330 100644
--- a/README.md
+++ b/README.md
@@ -1,10 +1,10 @@
![jMetalPy](docs/source/jmetalpy.png)
-[![Build Status](https://img.shields.io/travis/jMetal/jMetalPy/master.svg?style=flat-square)](https://travis-ci.org/jMetal/jMetalPy)
-[![Documentation](https://img.shields.io/badge/docs-online-success?style=flat-square)](https://jmetal.github.io/jMetalPy/index.html)
-[![PyPI License](https://img.shields.io/pypi/l/jMetalPy.svg?style=flat-square)]()
-[![PyPI version](https://img.shields.io/pypi/v/jMetalPy.svg?style=flat-square)]()
-[![PyPI Python version](https://img.shields.io/pypi/pyversions/jMetalPy.svg?style=flat-square)]()
+[![CI](https://github.com/jMetal/jMetalPy/actions/workflows/ci.yml/badge.svg)](https://github.com/jMetal/jMetalPy/actions/workflows/ci.yml)
+[![PyPI Python version](https://img.shields.io/pypi/pyversions/jMetalPy.svg)]()
+[![DOI](https://img.shields.io/badge/DOI-10.1016%2Fj.swevo.2019.100598-blue)](https://doi.org/10.1016/j.swevo.2019.100598)
+[![PyPI License](https://img.shields.io/pypi/l/jMetalPy.svg)]()
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
A paper introducing jMetalPy is available at: https://doi.org/10.1016/j.swevo.2019.100598
@@ -43,7 +43,7 @@ pip install "jmetalpy[core]"
Other supported commands are listed next:
```console
-pip install "jmetalpy[docs]" # Install requirements for building docs
+pip install "jmetalpy[dev]" # Install requirements for development
pip install "jmetalpy[distributed]" # Install requirements for parallel/distributed computing
pip install "jmetalpy[complete]" # Install all requirements
```
@@ -78,10 +78,10 @@ algorithm.run()
We can then proceed to explore the results:
```python
-from jmetal.util.solution import get_non_dominated_solutions, print_function_values_to_file, \
+from jmetal.util.solution import get_non_dominated_solutions, print_function_values_to_file,
print_variables_to_file
-front = get_non_dominated_solutions(algorithm.get_result())
+front = get_non_dominated_solutions(algorithm.result())
# save to files
print_function_values_to_file(front, 'FUN.NSGAII.ZDT1')
@@ -100,11 +100,15 @@ plot_front.plot(front, label='NSGAII-ZDT1', filename='NSGAII-ZDT1', format='png'
## Features
-The current release of jMetalPy (v1.5.5) contains the following components:
+<<<<<<< HEAD
+The current release of jMetalPy (v1.5.7) contains the following components:
+=======
+The current release of jMetalPy (v1.5.4) contains the following components:
+>>>>>>> 8c0a6cf (Feature/mixed solution (#73))
* Algorithms: local search, genetic algorithm, evolution strategy, simulated annealing, random search, NSGA-II, NSGA-III, SMPSO, OMOPSO, MOEA/D, MOEA/D-DRA, MOEA/D-IEpsilon, GDE3, SPEA2, HYPE, IBEA. Preference articulation-based algorithms (G-NSGA-II, G-GDE3, G-SPEA2, SMPSO/RP); Dynamic versions of NSGA-II, SMPSO, and GDE3.
* Parallel computing based on Apache Spark and Dask.
-* Benchmark problems: ZDT1-6, DTLZ1-2, FDA, LZ09, LIR-CMOP, unconstrained (Kursawe, Fonseca, Schaffer, Viennet2), constrained (Srinivas, Tanaka).
+* Benchmark problems: ZDT1-6, DTLZ1-2, FDA, LZ09, LIR-CMOP, RWA, unconstrained (Kursawe, Fonseca, Schaffer, Viennet2), constrained (Srinivas, Tanaka).
* Encodings: real, binary, permutations.
* Operators: selection (binary tournament, ranking and crowding distance, random, nary random, best solution), crossover (single-point, SBX), mutation (bit-blip, polynomial, uniform, random).
* Quality indicators: hypervolume, additive epsilon, GD, IGD.
@@ -118,9 +122,14 @@ The current release of jMetalPy (v1.5.5) contains the following components:
## Changelog
+* [v1.6.1] Add RWA benchmark, refactor classes BinarySolution and BinaryProblem.
+* [v1.6.0] Refactor class Problem, the single-objective genetic algorithm can solve constrained problems, performance improvements in NSGA-II, generation of Latex tables summarizing the results of the Wilcoxon rank sum test, added a notebook folder with examples.
+* [v1.5.7] Use of linters for catching errors and formatters to fix style, minor bug fixes.
+* [v1.5.6] Removed warnings when using Python 3.8.
* [v1.5.5] Minor bug fixes.
* [v1.5.4] Refactored quality indicators to accept numpy array as input parameter.
* [v1.5.4] Added [CompositeSolution](https://github.com/jMetal/jMetalPy/blob/master/jmetal/core/solution.py#L111) class to support mixed combinatorial problems. [#69](https://github.com/jMetal/jMetalPy/issues/69)
## License
+
This project is licensed under the terms of the MIT - see the [LICENSE](LICENSE) file for details.
\ No newline at end of file
diff --git a/docs/_sources/contributing.rst.txt b/docs/_sources/contributing.rst.txt
index 5ddc89f8..c603b14e 100644
--- a/docs/_sources/contributing.rst.txt
+++ b/docs/_sources/contributing.rst.txt
@@ -11,10 +11,10 @@ We have a set of branches on the remote Git server.
Some branches are temporary, and others are constant throughout the life of the repository.
* Branches always present in the repository:
- * *master*: You have the latest released to production, receive merges from the develop branch, or merge from a *hotfix* branch (emergency).
- * Do I have to put a TAG when doing a merge from develop to master? yes
- * Do I have to put a TAG when doing a merge from a hotfix branch to master? yes
- * After merge from a hotfix to master, do I have to merge from master to develop? yes
+ * *main*: You have the latest released to production, receive merges from the develop branch, or merge from a *hotfix* branch (emergency).
+ * Do I have to put a TAG when doing a merge from develop to main? yes
+ * Do I have to put a TAG when doing a merge from a hotfix branch to main? yes
+ * After merge from a hotfix to main, do I have to merge from main to develop? yes
* *develop*: It is considered the "Next Release", receives merges from branches of each developer, either corrections (*fix*) or new features (*feature*).
* Temporary branches:
@@ -27,8 +27,8 @@ Some branches are temporary, and others are constant throughout the life of the
* When I finish the correction in my fix branch, which branch to merge into?: You always merge feature branch into develop branch
* *hotfix/\\-\*: When we are correcting an emergency incidence in production, we create a local branch with the prefix "hotfix/", then only if there is a task id, we indicate it and we add a hyphen. The following we indicate a description according to the functionality that we are correcting. The words are separated by hyphens.
- * Where does this branch emerge?: This branch always emerge from the master branch
- * When I finish the correction in my hotfix branch, which branch to merge into?: This branch always emerge from the master and develop branch
+ * Where does this branch emerge?: This branch always emerge from the main branch
+ * When I finish the correction in my hotfix branch, which branch to merge into?: This branch always emerge from the main and develop branch
* Steps to follow when you are creating or going to work on a branch of any kind (feature / fix / hotfix):
1. After you create your branch (feature / fix / hotfix) locally, upload it to the remote Git server. The integration system will verify your code from the outset.
@@ -200,4 +200,4 @@ And the produced output doc will be:
.. image:: contributing/method_way_sphinx.png
-As you may notice, if you don't use any docstring, the method documentation will be empty.
\ No newline at end of file
+As you may notice, if you don't use any docstring, the method documentation will be empty.
diff --git a/docs/contributing.rst b/docs/contributing.rst
index 5ddc89f8..c603b14e 100644
--- a/docs/contributing.rst
+++ b/docs/contributing.rst
@@ -11,10 +11,10 @@ We have a set of branches on the remote Git server.
Some branches are temporary, and others are constant throughout the life of the repository.
* Branches always present in the repository:
- * *master*: You have the latest released to production, receive merges from the develop branch, or merge from a *hotfix* branch (emergency).
- * Do I have to put a TAG when doing a merge from develop to master? yes
- * Do I have to put a TAG when doing a merge from a hotfix branch to master? yes
- * After merge from a hotfix to master, do I have to merge from master to develop? yes
+ * *main*: You have the latest released to production, receive merges from the develop branch, or merge from a *hotfix* branch (emergency).
+ * Do I have to put a TAG when doing a merge from develop to main? yes
+ * Do I have to put a TAG when doing a merge from a hotfix branch to main? yes
+ * After merge from a hotfix to main, do I have to merge from main to develop? yes
* *develop*: It is considered the "Next Release", receives merges from branches of each developer, either corrections (*fix*) or new features (*feature*).
* Temporary branches:
@@ -27,8 +27,8 @@ Some branches are temporary, and others are constant throughout the life of the
* When I finish the correction in my fix branch, which branch to merge into?: You always merge feature branch into develop branch
* *hotfix/\\-\*: When we are correcting an emergency incidence in production, we create a local branch with the prefix "hotfix/", then only if there is a task id, we indicate it and we add a hyphen. The following we indicate a description according to the functionality that we are correcting. The words are separated by hyphens.
- * Where does this branch emerge?: This branch always emerge from the master branch
- * When I finish the correction in my hotfix branch, which branch to merge into?: This branch always emerge from the master and develop branch
+ * Where does this branch emerge?: This branch always emerge from the main branch
+ * When I finish the correction in my hotfix branch, which branch to merge into?: This branch always emerge from the main and develop branch
* Steps to follow when you are creating or going to work on a branch of any kind (feature / fix / hotfix):
1. After you create your branch (feature / fix / hotfix) locally, upload it to the remote Git server. The integration system will verify your code from the outset.
@@ -200,4 +200,4 @@ And the produced output doc will be:
.. image:: contributing/method_way_sphinx.png
-As you may notice, if you don't use any docstring, the method documentation will be empty.
\ No newline at end of file
+As you may notice, if you don't use any docstring, the method documentation will be empty.
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 2de98813..2ce056bb 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -2,6 +2,7 @@
import os
import sys
+
sys.path.insert(0, os.path.abspath('../../'))
# -- Project information -----------------------------------------------------
diff --git a/examples/experiment/QualityIndicatorSummary.csv b/examples/experiment/QualityIndicatorSummary.csv
index 4b8cf80e..29ae3962 100644
--- a/examples/experiment/QualityIndicatorSummary.csv
+++ b/examples/experiment/QualityIndicatorSummary.csv
@@ -1 +1,31851 @@
-Algorithm,Problem,ExecutionId,IndicatorName,IndicatorValue
+Algorithm,Problem,IndicatorName,ExecutionId,IndicatorValue
+NSGAII,ZDT1,EP,0,0.020829126426465366
+NSGAII,ZDT1,EP,1,0.02141113073233196
+NSGAII,ZDT1,EP,2,0.02063580911122953
+NSGAII,ZDT1,EP,3,0.02334369883946802
+NSGAII,ZDT1,EP,4,0.025894227553437316
+NSGAII,ZDT1,EP,5,0.03131364976248252
+NSGAII,ZDT1,EP,6,0.021718806077531183
+NSGAII,ZDT1,EP,7,0.023027227215041524
+NSGAII,ZDT1,EP,8,0.029105136520303665
+NSGAII,ZDT1,EP,9,0.028168910648695755
+NSGAII,ZDT1,EP,10,0.028591869055156205
+NSGAII,ZDT1,EP,11,0.028829101166133325
+NSGAII,ZDT1,EP,12,0.026158773171380045
+NSGAII,ZDT1,EP,13,0.023713132604175957
+NSGAII,ZDT1,EP,14,0.025805754634406736
+NSGAII,ZDT1,EP,15,0.0246252362900522
+NSGAII,ZDT1,EP,16,0.027738393467528266
+NSGAII,ZDT1,EP,17,0.030153133754990263
+NSGAII,ZDT1,EP,18,0.020779949444387463
+NSGAII,ZDT1,EP,19,0.027355240409925027
+NSGAII,ZDT1,EP,20,0.022352790589545243
+NSGAII,ZDT1,EP,21,0.026140818240545427
+NSGAII,ZDT1,EP,22,0.02430357141328987
+NSGAII,ZDT1,EP,23,0.024703565449628484
+NSGAII,ZDT1,EP,24,0.030834793239977898
+NSGAII,ZDT2,EP,0,0.04724522684087913
+NSGAII,ZDT2,EP,1,0.10116729014132775
+NSGAII,ZDT2,EP,2,0.04313815284341144
+NSGAII,ZDT2,EP,3,0.9168386866894864
+NSGAII,ZDT2,EP,4,0.9493865716780141
+NSGAII,ZDT2,EP,5,0.0849789721855184
+NSGAII,ZDT2,EP,6,0.08771367920491385
+NSGAII,ZDT2,EP,7,0.79786378063766
+NSGAII,ZDT2,EP,8,0.04682542156014008
+NSGAII,ZDT2,EP,9,0.05572063348915534
+NSGAII,ZDT2,EP,10,0.8218823055962623
+NSGAII,ZDT2,EP,11,0.05854234843135804
+NSGAII,ZDT2,EP,12,0.05546943862133298
+NSGAII,ZDT2,EP,13,0.05205274239279724
+NSGAII,ZDT2,EP,14,0.04305855294287332
+NSGAII,ZDT2,EP,15,0.05571797475983325
+NSGAII,ZDT2,EP,16,0.8037897910514717
+NSGAII,ZDT2,EP,17,0.6051920983678831
+NSGAII,ZDT2,EP,18,0.7752577765434107
+NSGAII,ZDT2,EP,19,0.04490968570611845
+NSGAII,ZDT2,EP,20,0.10284807946549077
+NSGAII,ZDT2,EP,21,0.10727103424910757
+NSGAII,ZDT2,EP,22,0.9098628657528467
+NSGAII,ZDT2,EP,23,0.04734961070355123
+NSGAII,ZDT2,EP,24,0.03515686673493227
+NSGAII,ZDT3,EP,0,0.026676360547485234
+NSGAII,ZDT3,EP,1,0.025492637893048675
+NSGAII,ZDT3,EP,2,0.017457503078392778
+NSGAII,ZDT3,EP,3,0.02256567081727967
+NSGAII,ZDT3,EP,4,0.026705834626690295
+NSGAII,ZDT3,EP,5,0.022494750218764126
+NSGAII,ZDT3,EP,6,0.02209386716061368
+NSGAII,ZDT3,EP,7,0.020237381632524754
+NSGAII,ZDT3,EP,8,0.023197389667788837
+NSGAII,ZDT3,EP,9,0.021859705043649202
+NSGAII,ZDT3,EP,10,0.019729589801497638
+NSGAII,ZDT3,EP,11,0.022504767236888323
+NSGAII,ZDT3,EP,12,0.021398336829035136
+NSGAII,ZDT3,EP,13,0.02116621444505551
+NSGAII,ZDT3,EP,14,0.01536724024590208
+NSGAII,ZDT3,EP,15,0.020118851163259177
+NSGAII,ZDT3,EP,16,0.19461690806262544
+NSGAII,ZDT3,EP,17,0.016181361791488436
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+OMOPSO,ZDT3,NHV,5,0.3910921476531193
+OMOPSO,ZDT3,NHV,6,0.2457711103561293
+OMOPSO,ZDT3,NHV,7,0.07773965028834628
+OMOPSO,ZDT3,NHV,8,0.26182100679863074
+OMOPSO,ZDT3,NHV,9,0.04980404204162092
+OMOPSO,ZDT3,NHV,10,0.2774153600784727
+OMOPSO,ZDT3,NHV,11,0.27829139258183677
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+OMOPSO,ZDT3,NHV,20,0.012044590531619659
+OMOPSO,ZDT3,NHV,21,0.168798303059836
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+OMOPSO,ZDT4,NHV,2,1.0
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+OMOPSO,ZDT6,NHV,0,0.011283298285399757
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+OMOPSO,DTLZ1,NHV,0,0.5531597301640763
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+AutoMOPSOZ,WFG9,IGD+,19,0.006621154726917907
+AutoMOPSOZ,WFG9,IGD+,20,0.004800434652957739
+AutoMOPSOZ,WFG9,IGD+,21,0.004889581259493455
+AutoMOPSOZ,WFG9,IGD+,22,0.003992197480091924
+AutoMOPSOZ,WFG9,IGD+,23,0.004745486181265039
+AutoMOPSOZ,WFG9,IGD+,24,0.0032146269084663494
+AutoMOPSOZ,RE21,IGD+,0,0.0022308891779125027
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+AutoMOPSOZ,RE21,IGD+,2,0.002271768153387178
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+AutoMOPSOZ,RE21,IGD+,4,0.0022804544335494176
+AutoMOPSOZ,RE21,IGD+,5,0.002238805042048279
+AutoMOPSOZ,RE21,IGD+,6,0.0022489044005358253
+AutoMOPSOZ,RE21,IGD+,7,0.0022970647924421338
+AutoMOPSOZ,RE21,IGD+,8,0.0022792495508352313
+AutoMOPSOZ,RE21,IGD+,9,0.0022730596944812043
+AutoMOPSOZ,RE21,IGD+,10,0.0022603139852652265
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+AutoMOPSOZ,RE21,IGD+,12,0.002293357370802947
+AutoMOPSOZ,RE21,IGD+,13,0.002289652426537784
+AutoMOPSOZ,RE21,IGD+,14,0.0022732675817712794
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+AutoMOPSOZ,RE21,IGD+,17,0.002278279477775797
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+AutoMOPSOZ,RE21,IGD+,24,0.002247692489319765
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+AutoMOPSOZ,RE22,IGD+,1,0.0023396104169013552
+AutoMOPSOZ,RE22,IGD+,2,0.0023607413050799188
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+AutoMOPSOZ,RE22,IGD+,8,0.0023993676013040963
+AutoMOPSOZ,RE22,IGD+,9,0.002379152239131205
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+AutoMOPSOZ,RE22,IGD+,17,0.0023435713708040173
+AutoMOPSOZ,RE22,IGD+,18,0.002340250700042938
+AutoMOPSOZ,RE22,IGD+,19,0.0023468183881786334
+AutoMOPSOZ,RE22,IGD+,20,0.002327725861161014
+AutoMOPSOZ,RE22,IGD+,21,0.0023485615890838736
+AutoMOPSOZ,RE22,IGD+,22,0.0023887473238546155
+AutoMOPSOZ,RE22,IGD+,23,0.00237899493161414
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+AutoMOPSOZ,RE23,IGD+,0,0.0017090565037761925
+AutoMOPSOZ,RE23,IGD+,1,0.0030089418452866677
+AutoMOPSOZ,RE23,IGD+,2,0.0019565815173104542
+AutoMOPSOZ,RE23,IGD+,3,0.0027116124617639135
+AutoMOPSOZ,RE23,IGD+,4,0.0036227812822603143
+AutoMOPSOZ,RE23,IGD+,5,0.001957578852631335
+AutoMOPSOZ,RE23,IGD+,6,0.002674222084138073
+AutoMOPSOZ,RE23,IGD+,7,0.002310210637714443
+AutoMOPSOZ,RE23,IGD+,8,0.003731328570719683
+AutoMOPSOZ,RE23,IGD+,9,0.002626183395829358
+AutoMOPSOZ,RE23,IGD+,10,0.0014536816818177677
+AutoMOPSOZ,RE23,IGD+,11,0.004353545750106923
+AutoMOPSOZ,RE23,IGD+,12,0.0031438092604017588
+AutoMOPSOZ,RE23,IGD+,13,0.002699794388455214
+AutoMOPSOZ,RE23,IGD+,14,0.005766866227489159
+AutoMOPSOZ,RE23,IGD+,15,0.0031948014384404963
+AutoMOPSOZ,RE23,IGD+,16,0.0020549244919155774
+AutoMOPSOZ,RE23,IGD+,17,0.002102103074400144
+AutoMOPSOZ,RE23,IGD+,18,0.002635950353060808
+AutoMOPSOZ,RE23,IGD+,19,0.001984477590646495
+AutoMOPSOZ,RE23,IGD+,20,0.005603358740751495
+AutoMOPSOZ,RE23,IGD+,21,0.0020854553188637717
+AutoMOPSOZ,RE23,IGD+,22,0.00331618671852569
+AutoMOPSOZ,RE23,IGD+,23,0.003841624267893459
+AutoMOPSOZ,RE23,IGD+,24,0.002162563764994441
+AutoMOPSOZ,RE24,IGD+,0,4.583969731908632E-4
+AutoMOPSOZ,RE24,IGD+,1,4.5928999643938693E-4
+AutoMOPSOZ,RE24,IGD+,2,4.664459311900191E-4
+AutoMOPSOZ,RE24,IGD+,3,4.6428369001645225E-4
+AutoMOPSOZ,RE24,IGD+,4,4.6014359436700406E-4
+AutoMOPSOZ,RE24,IGD+,5,4.6581546387103616E-4
+AutoMOPSOZ,RE24,IGD+,6,4.6327414370081883E-4
+AutoMOPSOZ,RE24,IGD+,7,4.6127170579238116E-4
+AutoMOPSOZ,RE24,IGD+,8,4.650149832602554E-4
+AutoMOPSOZ,RE24,IGD+,9,4.613921530139209E-4
+AutoMOPSOZ,RE24,IGD+,10,4.6041401961381635E-4
+AutoMOPSOZ,RE24,IGD+,11,4.5904230626081277E-4
+AutoMOPSOZ,RE24,IGD+,12,4.6179959281777153E-4
+AutoMOPSOZ,RE24,IGD+,13,4.592907839161069E-4
+AutoMOPSOZ,RE24,IGD+,14,4.6578734311502576E-4
+AutoMOPSOZ,RE24,IGD+,15,4.6528719852799373E-4
+AutoMOPSOZ,RE24,IGD+,16,4.632754853551924E-4
+AutoMOPSOZ,RE24,IGD+,17,4.6793656211808376E-4
+AutoMOPSOZ,RE24,IGD+,18,4.524934690258512E-4
+AutoMOPSOZ,RE24,IGD+,19,4.6308248443826985E-4
+AutoMOPSOZ,RE24,IGD+,20,4.593115763740723E-4
+AutoMOPSOZ,RE24,IGD+,21,4.6080844554317657E-4
+AutoMOPSOZ,RE24,IGD+,22,4.607515776822765E-4
+AutoMOPSOZ,RE24,IGD+,23,4.630426146765165E-4
+AutoMOPSOZ,RE24,IGD+,24,4.604112832714483E-4
+AutoMOPSOZ,RE25,IGD+,0,1.1516472562857684E-7
+AutoMOPSOZ,RE25,IGD+,1,7.690801544261661E-8
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+AutoMOPSOZ,RE25,IGD+,3,9.191504969943573E-8
+AutoMOPSOZ,RE25,IGD+,4,3.4794606711115944E-8
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+AutoMOPSOZ,RE25,IGD+,12,6.350733556646743E-8
+AutoMOPSOZ,RE25,IGD+,13,9.683409024185853E-8
+AutoMOPSOZ,RE25,IGD+,14,7.381024647048223E-8
+AutoMOPSOZ,RE25,IGD+,15,8.276629184795755E-8
+AutoMOPSOZ,RE25,IGD+,16,7.217205674480561E-8
+AutoMOPSOZ,RE25,IGD+,17,4.216974119664328E-8
+AutoMOPSOZ,RE25,IGD+,18,1.1077134778261169E-7
+AutoMOPSOZ,RE25,IGD+,19,1.2435453871549566E-7
+AutoMOPSOZ,RE25,IGD+,20,3.565452511400274E-8
+AutoMOPSOZ,RE25,IGD+,21,7.454757559577025E-8
+AutoMOPSOZ,RE25,IGD+,22,1.2435453871549566E-7
+AutoMOPSOZ,RE25,IGD+,23,3.372466904065783E-8
+AutoMOPSOZ,RE25,IGD+,24,1.2246642369196306E-7
diff --git a/examples/experiment/comparison.py b/examples/experiment/comparison.py
index 5b654d7a..614a5b24 100644
--- a/examples/experiment/comparison.py
+++ b/examples/experiment/comparison.py
@@ -21,12 +21,13 @@ def configure_experiment(problems: dict, n_run: int):
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables,
- distribution_index=20),
+ mutation=PolynomialMutation(
+ probability=1.0 / problem.number_of_variables, distribution_index=20
+ ),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
),
- algorithm_tag='NSGAII',
+ algorithm_tag="NSGAII",
problem_tag=problem_tag,
run=run,
)
@@ -38,9 +39,9 @@ def configure_experiment(problems: dict, n_run: int):
population_size=100,
cr=0.5,
f=0.5,
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
),
- algorithm_tag='GDE3',
+ algorithm_tag="GDE3",
problem_tag=problem_tag,
run=run,
)
@@ -50,12 +51,13 @@ def configure_experiment(problems: dict, n_run: int):
algorithm=SMPSO(
problem=problem,
swarm_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables,
- distribution_index=20),
+ mutation=PolynomialMutation(
+ probability=1.0 / problem.number_of_variables, distribution_index=20
+ ),
leaders=CrowdingDistanceArchive(100),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
),
- algorithm_tag='SMPSO',
+ algorithm_tag="SMPSO",
problem_tag=problem_tag,
run=run,
)
@@ -64,12 +66,12 @@ def configure_experiment(problems: dict, n_run: int):
return jobs
-if __name__ == '__main__':
+if __name__ == "__main__":
# Configure the experiments
- jobs = configure_experiment(problems={'ZDT1': ZDT1(), 'ZDT2': ZDT2(), 'ZDT3': ZDT3()}, n_run=25)
+ jobs = configure_experiment(problems={"ZDT1": ZDT1(), "ZDT2": ZDT2(), "ZDT3": ZDT3()}, n_run=2)
# Run the study
- output_directory = 'data'
+ output_directory = "data"
experiment = Experiment(output_dir=output_directory, jobs=jobs)
experiment.run()
@@ -77,6 +79,6 @@ def configure_experiment(problems: dict, n_run: int):
# Generate summary file
generate_summary_from_experiment(
input_dir=output_directory,
- reference_fronts='resources/reference_front',
- quality_indicators=[GenerationalDistance(), EpsilonIndicator(), HyperVolume([1.0, 1.0])]
+ reference_fronts="resources/reference_front",
+ quality_indicators=[GenerationalDistance(), EpsilonIndicator(), HyperVolume([1.0, 1.0])],
)
diff --git a/examples/experiment/generateKolmogorovSmirnovLatexTables.py b/examples/experiment/generateKolmogorovSmirnovLatexTables.py
new file mode 100644
index 00000000..32e85cb9
--- /dev/null
+++ b/examples/experiment/generateKolmogorovSmirnovLatexTables.py
@@ -0,0 +1,10 @@
+from jmetal.lab.experiment import (
+ generate_kolmogorov_smirnov_latex_tables,
+)
+
+if __name__ == "__main__":
+ """
+ Generate Latex tables with the results of the Kolmogorov-Smirnov test. The last algorithm is considered as
+ the reference algorithm, and the cells include a symbol with the p-value < 0.05.
+ """
+ generate_kolmogorov_smirnov_latex_tables(filename="QualityIndicatorSummary.csv")
diff --git a/examples/experiment/generateMedianAndWilcoxonLatexTables.py b/examples/experiment/generateMedianAndWilcoxonLatexTables.py
new file mode 100644
index 00000000..d036a078
--- /dev/null
+++ b/examples/experiment/generateMedianAndWilcoxonLatexTables.py
@@ -0,0 +1,11 @@
+from jmetal.lab.experiment import (
+ generate_median_and_wilcoxon_latex_tables,
+)
+
+if __name__ == "__main__":
+ """
+ Generate Latex tables including medians and IQRs. Additionally, the last algorithm is considered as the reference
+ algorithm, and the cells include a symbol indicating whether the differences with the reference algorithm
+ are significant or not according to the Wilcoxon rank sum test.
+ """
+ generate_median_and_wilcoxon_latex_tables(filename="QualityIndicatorSummary.csv")
diff --git a/examples/experiment/statistical_analysis.py b/examples/experiment/statistical_analysis.py
index a1691676..3830dcb1 100644
--- a/examples/experiment/statistical_analysis.py
+++ b/examples/experiment/statistical_analysis.py
@@ -1,68 +1,75 @@
-from jmetal.lab.experiment import generate_boxplot, generate_latex_tables, compute_mean_indicator, compute_wilcoxon
+from jmetal.lab.experiment import (
+ compute_mean_indicator,
+ compute_wilcoxon,
+ generate_boxplot,
+ generate_latex_tables,
+)
from jmetal.lab.statistical_test.bayesian import *
from jmetal.lab.statistical_test.functions import *
from jmetal.lab.visualization import CDplot, plot_posterior
-if __name__ == '__main__':
+if __name__ == "__main__":
# Generate Median & IQR tables
- generate_latex_tables(filename='QualityIndicatorSummary.csv')
+ generate_latex_tables(filename="QualityIndicatorSummary.csv")
# Generate boxplots
- generate_boxplot(filename='QualityIndicatorSummary.csv')
+ generate_boxplot(filename="QualityIndicatorSummary.csv")
# Wilcoxon
- compute_wilcoxon(filename='QualityIndicatorSummary.csv')
+ compute_wilcoxon(filename="QualityIndicatorSummary.csv")
# Statistical lab
- avg = compute_mean_indicator(filename='QualityIndicatorSummary.csv', indicator_name='HV')
+ avg = compute_mean_indicator(filename="QualityIndicatorSummary.csv", indicator_name="HV")
print(avg)
# Non-parametric test
- print('-------- Sign Test --------')
- print(sign_test(avg[['NSGAII', 'SMPSO']]))
- print('-------- Friedman Test --------')
+ print("-------- Sign Test --------")
+ print(sign_test(avg[["NSGAII", "SMPSO"]]))
+ print("-------- Friedman Test --------")
print(friedman_test(avg))
- print('-------- Friedman Aligned Rank Test --------')
+ print("-------- Friedman Aligned Rank Test --------")
print(friedman_aligned_rank_test(avg))
- print('-------- Quade Test --------')
+ print("-------- Quade Test --------")
print(quade_test(avg))
# Post-hoc tests
- print('-------- Friedman Post-Hoc Test --------')
- z, p_val, adj_pval = friedman_ph_test(avg, control=0, apv_procedure='Bonferroni')
- print('z values \n', z)
- print('p-values \n', p_val)
- print('adjusted p-values \n', adj_pval)
- print('-------- Friedman Aligned Rank Post-Hoc Test --------')
- z, p_val, adj_pval = friedman_aligned_ph_test(avg, apv_procedure='Shaffer')
- print('z values \n', z)
- print('p-values \n', p_val)
- print('adjusted p-values \n', adj_pval)
- print('-------- QuadeTest Post-Hoc Test --------')
- z, p_val, adj_pval = quade_ph_test(avg, apv_procedure='Holm')
- print('z values \n', z)
- print('p-values \n', p_val)
- print('adjusted p-values \n', adj_pval)
+ print("-------- Friedman Post-Hoc Test --------")
+ z, p_val, adj_pval = friedman_ph_test(avg, control=0, apv_procedure="Bonferroni")
+ print("z values \n", z)
+ print("p-values \n", p_val)
+ print("adjusted p-values \n", adj_pval)
+ print("-------- Friedman Aligned Rank Post-Hoc Test --------")
+ z, p_val, adj_pval = friedman_aligned_ph_test(avg, apv_procedure="Shaffer")
+ print("z values \n", z)
+ print("p-values \n", p_val)
+ print("adjusted p-values \n", adj_pval)
+ print("-------- QuadeTest Post-Hoc Test --------")
+ z, p_val, adj_pval = quade_ph_test(avg, apv_procedure="Holm")
+ print("z values \n", z)
+ print("p-values \n", p_val)
+ print("adjusted p-values \n", adj_pval)
# Plot critical distance
CDplot(avg.T, alpha=0.15, higher_is_better=True)
- print('-------- Bayesian Sign Test --------')
- bst, DProcess = bayesian_sign_test(avg[['NSGAII', 'SMPSO']], rope_limits=[-0.002, 0.002],
- prior_strength=0.5, return_sample=True)
- plot_posterior(DProcess, higher_is_better=True, alg_names=['NSGAII', 'SMPSO'])
+ print("-------- Bayesian Sign Test --------")
+ bst, DProcess = bayesian_sign_test(
+ avg[["NSGAII", "SMPSO"]], rope_limits=[-0.002, 0.002], prior_strength=0.5, return_sample=True
+ )
+ plot_posterior(DProcess, higher_is_better=True, alg_names=["NSGAII", "SMPSO"])
- print('Pr(NSGAII < SMPSO) = %.3f' % bst[0])
- print('Pr(NSGAII ~= SMPSO) = %.3f' % bst[1])
- print('Pr(NSGAII > SMPSO) = %.3f' % bst[2])
+ print("Pr(NSGAII < SMPSO) = %.3f" % bst[0])
+ print("Pr(NSGAII ~= SMPSO) = %.3f" % bst[1])
+ print("Pr(NSGAII > SMPSO) = %.3f" % bst[2])
- print('-------- Bayesian Signed Rank Test --------')
- bst, DProcess = bayesian_signed_rank_test(avg[['NSGAII', 'SMPSO']], rope_limits=[-0.002, 0.002],
- prior_strength=0.5, return_sample=True)
- plot_posterior(DProcess, higher_is_better=True, alg_names=['NSGAII', 'SMPSO'])
+ print("-------- Bayesian Signed Rank Test --------")
+ bst, DProcess = bayesian_signed_rank_test(
+ avg[["NSGAII", "SMPSO"]], rope_limits=[-0.002, 0.002], prior_strength=0.5, return_sample=True
+ )
+ plot_posterior(DProcess, higher_is_better=True, alg_names=["NSGAII", "SMPSO"])
- print('Pr(NSGAII < SMPSO) = %.3f' % bst[0])
- print('Pr(NSGAII ~= SMPSO) = %.3f' % bst[1])
- print('Pr(NSGAII > SMPSO) = %.3f' % bst[2])
+ print("Pr(NSGAII < SMPSO) = %.3f" % bst[0])
+ print("Pr(NSGAII ~= SMPSO) = %.3f" % bst[1])
+ print("Pr(NSGAII > SMPSO) = %.3f" % bst[2])
diff --git a/examples/multiobjective/gde3/dynamic_gde3.py b/examples/multiobjective/gde3/dynamic_gde3.py
index cd92568f..ccf4478a 100644
--- a/examples/multiobjective/gde3/dynamic_gde3.py
+++ b/examples/multiobjective/gde3/dynamic_gde3.py
@@ -1,10 +1,10 @@
from jmetal.algorithm.multiobjective.gde3 import DynamicGDE3
from jmetal.problem.multiobjective.fda import FDA2
from jmetal.util.observable import TimeCounter
-from jmetal.util.observer import WriteFrontToFileObserver, PlotFrontToFileObserver
+from jmetal.util.observer import PlotFrontToFileObserver, WriteFrontToFileObserver
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = FDA2()
time_counter = TimeCounter(delay=1)
@@ -16,10 +16,10 @@
population_size=100,
cr=0.5,
f=0.5,
- termination_criterion=StoppingByEvaluations(max_evaluations=500)
+ termination_criterion=StoppingByEvaluations(max_evaluations=500),
)
- algorithm.observable.register(observer=PlotFrontToFileObserver('dynamic_front_vis'))
- algorithm.observable.register(observer=WriteFrontToFileObserver('dynamic_front'))
+ algorithm.observable.register(observer=PlotFrontToFileObserver("dynamic_front_vis"))
+ algorithm.observable.register(observer=WriteFrontToFileObserver("dynamic_front"))
algorithm.run()
diff --git a/examples/multiobjective/gde3/gde3_spark_evaluator.py b/examples/multiobjective/gde3/gde3_spark_evaluator.py
index 7f47ca66..c7e16e85 100644
--- a/examples/multiobjective/gde3/gde3_spark_evaluator.py
+++ b/examples/multiobjective/gde3/gde3_spark_evaluator.py
@@ -4,7 +4,7 @@
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1Modified()
algorithm = GDE3(
@@ -13,16 +13,16 @@
cr=0.5,
f=0.5,
termination_criterion=StoppingByEvaluations(max_evaluations=100),
- population_evaluator=SparkEvaluator()
+ population_evaluator=SparkEvaluator(),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.get_name() + "." + problem.get_name())
- print_variables_to_file(front, 'VAR.' + algorithm.get_name() + "." + problem.get_name())
+ print_function_values_to_file(front, "FUN." + algorithm.get_name() + "." + problem.name())
+ print_variables_to_file(front, "VAR." + algorithm.get_name() + "." + problem.name())
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print(f"Algorithm (continuous problem): {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/gde3/gde3_zdt1.py b/examples/multiobjective/gde3/gde3_zdt1.py
index 4b7bfcca..54f758e7 100644
--- a/examples/multiobjective/gde3/gde3_zdt1.py
+++ b/examples/multiobjective/gde3/gde3_zdt1.py
@@ -1,27 +1,25 @@
from jmetal.algorithm.multiobjective.gde3 import GDE3
from jmetal.problem import ZDT1
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByKeyboard
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
- algorithm = GDE3(
- problem=problem,
- population_size=100,
- cr=0.5,
- f=0.5,
- termination_criterion=StoppingByKeyboard()
- )
+ algorithm = GDE3(problem=problem, population_size=100, cr=0.5, f=0.5, termination_criterion=StoppingByKeyboard())
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/gde3/ggde3_zdt2.py b/examples/multiobjective/gde3/ggde3_zdt2.py
index ed3564cf..5bd1aa86 100644
--- a/examples/multiobjective/gde3/ggde3_zdt2.py
+++ b/examples/multiobjective/gde3/ggde3_zdt2.py
@@ -1,12 +1,16 @@
from jmetal.algorithm.multiobjective.gde3 import GDE3
from jmetal.problem import ZDT2
from jmetal.util.comparator import GDominanceComparator
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT2()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT2.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT2.pf")
max_evaluations = 25000
reference_point = [0.2, 0.5]
@@ -17,16 +21,16 @@
cr=0.5,
f=0.5,
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
- dominance_comparator=GDominanceComparator(reference_point)
+ dominance_comparator=GDominanceComparator(reference_point),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/hype/hype_zdt1.py b/examples/multiobjective/hype/hype_zdt1.py
index 6c10153f..3423aa92 100644
--- a/examples/multiobjective/hype/hype_zdt1.py
+++ b/examples/multiobjective/hype/hype_zdt1.py
@@ -1,34 +1,42 @@
from jmetal.algorithm.multiobjective.hype import HYPE
from jmetal.core.solution import FloatSolution
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import ZDT1
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
- reference_point = FloatSolution([0], [1], problem.number_of_objectives, )
- reference_point.objectives = [1., 1.] # Mandatory for HYPE
+ reference_point = FloatSolution(
+ [0],
+ [1],
+ problem.number_of_objectives(),
+ )
+ reference_point.objectives = [1.0, 1.0] # Mandatory for HYPE
algorithm = HYPE(
problem=problem,
reference_point=reference_point,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(25000)
+ termination_criterion=StoppingByEvaluations(25000),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/ibea/ibea_zdt1.py b/examples/multiobjective/ibea/ibea_zdt1.py
index ad2b71ad..d059be0e 100644
--- a/examples/multiobjective/ibea/ibea_zdt1.py
+++ b/examples/multiobjective/ibea/ibea_zdt1.py
@@ -1,30 +1,34 @@
from jmetal.algorithm.multiobjective.ibea import IBEA
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import ZDT1
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
algorithm = IBEA(
problem=problem,
- kappa=1.,
+ kappa=1.0,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=25000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=25000),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/mocell/mocell_zdt1.py b/examples/multiobjective/mocell/mocell_zdt1.py
index 617b72d1..4f6cbfe3 100644
--- a/examples/multiobjective/mocell/mocell_zdt1.py
+++ b/examples/multiobjective/mocell/mocell_zdt1.py
@@ -1,16 +1,19 @@
-from jmetal.util.solution_list import print_function_values_to_file, print_variables_to_file
-
from jmetal.algorithm.multiobjective.mocell import MOCell
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import ZDT1
from jmetal.util.archive import CrowdingDistanceArchive
from jmetal.util.neighborhood import C9
-from jmetal.util.solution import read_solutions
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
+
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT4.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
max_evaluations = 25000
algorithm = MOCell(
@@ -18,18 +21,18 @@
population_size=100,
neighborhood=C9(10, 10),
archive=CrowdingDistanceArchive(100),
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/moead/moead_dtlz2.py b/examples/multiobjective/moead/moead_dtlz2.py
index 8770b47b..4573b3ea 100644
--- a/examples/multiobjective/moead/moead_dtlz2.py
+++ b/examples/multiobjective/moead/moead_dtlz2.py
@@ -1,40 +1,45 @@
from jmetal.algorithm.multiobjective.moead import MOEAD
-from jmetal.core.quality_indicator import HyperVolume, InvertedGenerationalDistance
-from jmetal.operator import PolynomialMutation, DifferentialEvolutionCrossover
+from jmetal.core.quality_indicator import HyperVolume
+from jmetal.operator import DifferentialEvolutionCrossover, PolynomialMutation
from jmetal.problem import DTLZ2
-from jmetal.util.aggregative_function import Tschebycheff
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.aggregation_function import PenaltyBoundaryIntersection
+
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = DTLZ2()
- problem.reference_front = read_solutions(filename='resources/reference_front/DTLZ2.3D.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/DTLZ2.3D.pf")
max_evaluations = 50000
algorithm = MOEAD(
problem=problem,
- population_size=300,
+ population_size=91,
crossover=DifferentialEvolutionCrossover(CR=1.0, F=0.5),
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
- aggregative_function=Tschebycheff(dimension=problem.number_of_objectives),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
+ aggregation_function=PenaltyBoundaryIntersection(dimension=problem.number_of_objectives()),
neighbor_size=20,
neighbourhood_selection_probability=0.9,
max_number_of_replaced_solutions=2,
- weight_files_path='resources/MOEAD_weights',
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ weight_files_path="resources/MOEAD_weights",
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
hypervolume = HyperVolume([1.0, 1.0, 1.0])
print("Hypervolume: " + str(hypervolume.compute([front[i].objectives for i in range(len(front))])))
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/moead/moead_iepsilon_lircmop1.py b/examples/multiobjective/moead/moead_iepsilon_lircmop1.py
index 3f517a11..c3a9616b 100644
--- a/examples/multiobjective/moead/moead_iepsilon_lircmop1.py
+++ b/examples/multiobjective/moead/moead_iepsilon_lircmop1.py
@@ -1,14 +1,18 @@
from jmetal.algorithm.multiobjective.moead import MOEADIEpsilon
-from jmetal.operator import PolynomialMutation, DifferentialEvolutionCrossover
+from jmetal.operator import DifferentialEvolutionCrossover, PolynomialMutation
from jmetal.problem.multiobjective.lircmop import LIRCMOP2
-from jmetal.util.aggregative_function import Tschebycheff
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.aggregation_function import Tschebycheff
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = LIRCMOP2()
- problem.reference_front = read_solutions(filename='resources/reference_front/LIRCMOP2.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/LIRCMOP2.pf")
max_evaluations = 300000
@@ -16,22 +20,22 @@
problem=problem,
population_size=300,
crossover=DifferentialEvolutionCrossover(CR=1.0, F=0.5),
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
- aggregative_function=Tschebycheff(dimension=problem.number_of_objectives),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
+ aggregation_function=Tschebycheff(dimension=problem.number_of_objectives()),
neighbor_size=20,
neighbourhood_selection_probability=0.9,
max_number_of_replaced_solutions=2,
- weight_files_path='resources/MOEAD_weights',
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ weight_files_path="resources/MOEAD_weights",
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/moead/moead_lz09.py b/examples/multiobjective/moead/moead_lz09.py
index e0bf3c10..3ce28316 100644
--- a/examples/multiobjective/moead/moead_lz09.py
+++ b/examples/multiobjective/moead/moead_lz09.py
@@ -1,14 +1,18 @@
from jmetal.algorithm.multiobjective.moead import MOEAD
-from jmetal.operator import PolynomialMutation, DifferentialEvolutionCrossover
+from jmetal.operator import DifferentialEvolutionCrossover, PolynomialMutation
from jmetal.problem import LZ09_F2
-from jmetal.util.aggregative_function import Tschebycheff
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.aggregation_function import Tschebycheff
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = LZ09_F2()
- problem.reference_front = read_solutions(filename='resources/reference_front/LZ09_F2.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/LZ09_F2.pf")
max_evaluations = 150000
@@ -16,22 +20,22 @@
problem=problem,
population_size=300,
crossover=DifferentialEvolutionCrossover(CR=1.0, F=0.5),
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
- aggregative_function=Tschebycheff(dimension=problem.number_of_objectives),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
+ aggregation_function=Tschebycheff(dimension=problem.number_of_objectives()),
neighbor_size=20,
neighbourhood_selection_probability=0.9,
max_number_of_replaced_solutions=2,
- weight_files_path='resources/MOEAD_weights',
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ weight_files_path="resources/MOEAD_weights",
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.get_name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/moead/moeaddra_lz09.py b/examples/multiobjective/moead/moeaddra_lz09.py
index ea0aba9d..ac25463d 100644
--- a/examples/multiobjective/moead/moeaddra_lz09.py
+++ b/examples/multiobjective/moead/moeaddra_lz09.py
@@ -1,15 +1,19 @@
from jmetal.algorithm.multiobjective.moead import MOEAD_DRA
-from jmetal.operator import PolynomialMutation, DifferentialEvolutionCrossover
-from jmetal.problem import LZ09_F2
+from jmetal.core.quality_indicator import HyperVolume
+from jmetal.operator import DifferentialEvolutionCrossover, PolynomialMutation
+from jmetal.problem.multiobjective.lz09 import LZ09_F1
from jmetal.problem.multiobjective.uf import UF1
-from jmetal.util.aggregative_function import Tschebycheff
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.aggregation_function import Tschebycheff
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-from jmetal.core.quality_indicator import HyperVolume, InvertedGenerationalDistance
-if __name__ == '__main__':
- problem = UF1()
- problem.reference_front = read_solutions(filename='resources/reference_front/UF1.pf')
+if __name__ == "__main__":
+ problem = LZ09_F1()
+ problem.reference_front = read_solutions(filename="resources/reference_front/LZ09_F1.pf")
max_evaluations = 300000
@@ -17,27 +21,25 @@
problem=problem,
population_size=600,
crossover=DifferentialEvolutionCrossover(CR=1.0, F=0.5),
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
- aggregative_function=Tschebycheff(dimension=problem.number_of_objectives),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
+ aggregation_function=Tschebycheff(dimension=problem.number_of_objectives()),
neighbor_size=20,
neighbourhood_selection_probability=0.9,
max_number_of_replaced_solutions=2,
- weight_files_path='resources/MOEAD_weights',
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ weight_files_path="resources/MOEAD_weights",
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
hypervolume = HyperVolume([2.0, 2.0])
print("Hypervolume: " + str(hypervolume.compute([front[i].objectives for i in range(len(front))])))
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
-
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
-
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/distributed_nsgaii_with_dask.py b/examples/multiobjective/nsgaii/distributed_nsgaii_with_dask.py
index 1b266b51..b289e52d 100644
--- a/examples/multiobjective/nsgaii/distributed_nsgaii_with_dask.py
+++ b/examples/multiobjective/nsgaii/distributed_nsgaii_with_dask.py
@@ -10,14 +10,14 @@
Distributed (asynchronous) version of NSGA-II using Dask.
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1Modified()
# setup Dask client
client = Client(LocalCluster(n_workers=24))
ncores = sum(client.ncores().values())
- print(f'{ncores} cores available')
+ print(f"{ncores} cores available")
# creates the algorithm
max_evaluations = 25000
@@ -29,13 +29,12 @@
crossover=SBXCrossover(probability=1.0, distribution_index=20),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
number_of_cores=ncores,
- client=client
+ client=client,
)
algorithm.run()
- front = algorithm.get_result()
-
- print('Algorithm: ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ front = algorithm.result()
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.get_name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/distributed_nsgaii_with_dask_evaluator.py b/examples/multiobjective/nsgaii/distributed_nsgaii_with_dask_evaluator.py
index 4230b469..d022cea5 100644
--- a/examples/multiobjective/nsgaii/distributed_nsgaii_with_dask_evaluator.py
+++ b/examples/multiobjective/nsgaii/distributed_nsgaii_with_dask_evaluator.py
@@ -1,4 +1,5 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.operator import SBXCrossover, PolynomialMutation
from jmetal.problem.multiobjective.zdt import ZDT1Modified
from jmetal.util.evaluator import DaskEvaluator
@@ -8,7 +9,7 @@
"""
Distributed (synchronous) version of NSGA-II using Dask.
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1Modified()
max_evaluations = 100
@@ -20,17 +21,16 @@
mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
population_evaluator=DaskEvaluator(),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
-
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/distributed_nsgaii_with_spark_evaluator.py b/examples/multiobjective/nsgaii/distributed_nsgaii_with_spark_evaluator.py
index 1d585d24..b856d344 100644
--- a/examples/multiobjective/nsgaii/distributed_nsgaii_with_spark_evaluator.py
+++ b/examples/multiobjective/nsgaii/distributed_nsgaii_with_spark_evaluator.py
@@ -1,5 +1,5 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem.multiobjective.zdt import ZDT1Modified
from jmetal.util.evaluator import SparkEvaluator
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
@@ -9,7 +9,7 @@
Distributed (synchronous) version of NSGA-II using Apache Spark.
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1Modified()
max_evaluations = 100
@@ -21,16 +21,16 @@
mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
population_evaluator=SparkEvaluator(),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.get_name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/dynamic_nsgaii_solving_fda2.py b/examples/multiobjective/nsgaii/dynamic_nsgaii_solving_fda2.py
index 6ba30bc3..b61a7db1 100644
--- a/examples/multiobjective/nsgaii/dynamic_nsgaii_solving_fda2.py
+++ b/examples/multiobjective/nsgaii/dynamic_nsgaii_solving_fda2.py
@@ -5,7 +5,7 @@
from jmetal.util.observer import PlotFrontToFileObserver, WriteFrontToFileObserver
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = FDA2()
time_counter = TimeCounter(delay=1)
@@ -19,10 +19,10 @@
offspring_population_size=100,
mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
- algorithm.observable.register(observer=PlotFrontToFileObserver('dynamic_front_vis'))
- algorithm.observable.register(observer=WriteFrontToFileObserver('dynamic_front'))
+ algorithm.observable.register(observer=PlotFrontToFileObserver("dynamic_front_vis"))
+ algorithm.observable.register(observer=WriteFrontToFileObserver("dynamic_front"))
algorithm.run()
diff --git a/examples/multiobjective/nsgaii/gnsgaii_solving_zdt2_with_reference_point.py b/examples/multiobjective/nsgaii/gnsgaii_solving_zdt2_with_reference_point.py
index b84dd8e1..62ae4a86 100644
--- a/examples/multiobjective/nsgaii/gnsgaii_solving_zdt2_with_reference_point.py
+++ b/examples/multiobjective/nsgaii/gnsgaii_solving_zdt2_with_reference_point.py
@@ -34,7 +34,7 @@
observer=VisualizerObserver(reference_front=problem.reference_front, reference_point=reference_point))
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Plot front
plot_front = Plot(title='Pareto front approximation. Problem: ' + problem.get_name(),
diff --git a/examples/multiobjective/nsgaii/nsgaii_defining_schaffer_problem_on_the_fly.py b/examples/multiobjective/nsgaii/nsgaii_defining_schaffer_problem_on_the_fly.py
index 7c0a8a51..e78cdc2b 100644
--- a/examples/multiobjective/nsgaii/nsgaii_defining_schaffer_problem_on_the_fly.py
+++ b/examples/multiobjective/nsgaii/nsgaii_defining_schaffer_problem_on_the_fly.py
@@ -1,15 +1,18 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
from jmetal.core.problem import OnTheFlyFloatProblem
-from jmetal.operator import SBXCrossover, PolynomialMutation
-from jmetal.util.solution import get_non_dominated_solutions, read_solutions, print_function_values_to_file, \
- print_variables_to_file
+from jmetal.operator import PolynomialMutation, SBXCrossover
+from jmetal.util.solution import (
+ get_non_dominated_solutions,
+ print_function_values_to_file,
+ print_variables_to_file,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
"""
Program to configure and run the NSGA-II algorithm configured with standard settings.
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
# Defining problem Schaffer on the fly
def f1(x: [float]):
return x[0] * x[0]
@@ -18,32 +21,25 @@ def f2(x: [float]):
return (x[0] - 2) * (x[0] - 2)
problem = OnTheFlyFloatProblem()
- problem \
- .set_name('Schaffer') \
- .add_variable(-10000.0, 10000.0) \
- .add_function(f1) \
- .add_function(f2)
-
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.set_name("Schaffer").add_variable(-1000.0, 1000.0).add_function(f1).add_function(f2)
max_evaluations = 25000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = get_non_dominated_solutions(algorithm.get_result())
+ front = get_non_dominated_solutions(algorithm.result())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
-
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_defining_srinivas_problem_on_the_fly.py b/examples/multiobjective/nsgaii/nsgaii_defining_srinivas_problem_on_the_fly.py
index a017bfcd..7861f7c0 100644
--- a/examples/multiobjective/nsgaii/nsgaii_defining_srinivas_problem_on_the_fly.py
+++ b/examples/multiobjective/nsgaii/nsgaii_defining_srinivas_problem_on_the_fly.py
@@ -1,61 +1,64 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
from jmetal.core.problem import OnTheFlyFloatProblem
-from jmetal.operator import SBXCrossover, PolynomialMutation
-from jmetal.util.solution import get_non_dominated_solutions, read_solutions, print_function_values_to_file, \
- print_variables_to_file
+from jmetal.operator import PolynomialMutation, SBXCrossover
+from jmetal.util.comparator import DominanceWithConstraintsComparator
+from jmetal.util.solution import (
+ get_non_dominated_solutions,
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
"""
Program to configure and run the NSGA-II algorithm configured with standard settings.
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
# Defining problem Srinivas on the fly
def f1(x: [float]):
return 2.0 + (x[0] - 2.0) * (x[0] - 2.0) + (x[1] - 1.0) * (x[1] - 1.0)
-
def f2(x: [float]):
return 9.0 * x[0] - (x[1] - 1.0) * (x[1] - 1.0)
-
def c1(x: [float]):
return 1.0 - (x[0] * x[0] + x[1] * x[1]) / 225.0
-
def c2(x: [float]):
return (3.0 * x[1] - x[0]) / 10.0 - 1.0
-
- problem = OnTheFlyFloatProblem() \
- .set_name('Srinivas') \
- .add_variable(-20.0, 20.0) \
- .add_variable(-20.0, 20.0) \
- .add_function(f1) \
- .add_function(f2) \
- .add_constraint(c1) \
+ problem = (
+ OnTheFlyFloatProblem()
+ .set_name("Srinivas")
+ .add_variable(-20.0, 20.0)
+ .add_variable(-20.0, 20.0)
+ .add_function(f1)
+ .add_function(f2)
+ .add_constraint(c1)
.add_constraint(c2)
+ )
- problem.reference_front = read_solutions(filename='resources/reference_front/Srinivas.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/Srinivas.pf")
max_evaluations = 25000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
+ dominance_comparator=DominanceWithConstraintsComparator()
)
algorithm.run()
- front = get_non_dominated_solutions(algorithm.get_result())
+ front = get_non_dominated_solutions(algorithm.result())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
-
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_solving_3D_problem.py b/examples/multiobjective/nsgaii/nsgaii_solving_3D_problem.py
index c8dcb7bd..7861f7c0 100644
--- a/examples/multiobjective/nsgaii/nsgaii_solving_3D_problem.py
+++ b/examples/multiobjective/nsgaii/nsgaii_solving_3D_problem.py
@@ -1,32 +1,64 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
-from jmetal.operator import SBXCrossover, PolynomialMutation
-from jmetal.problem import DTLZ2
-from jmetal.util.comparator import DominanceComparator
-from jmetal.util.solution import print_function_values_to_file, print_variables_to_file, read_solutions
+from jmetal.core.problem import OnTheFlyFloatProblem
+from jmetal.operator import PolynomialMutation, SBXCrossover
+from jmetal.util.comparator import DominanceWithConstraintsComparator
+from jmetal.util.solution import (
+ get_non_dominated_solutions,
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
- problem = DTLZ2()
- problem.reference_front = read_solutions(filename='resources/reference_front/DTLZ2.3D.pf')
+"""
+Program to configure and run the NSGA-II algorithm configured with standard settings.
+"""
+
+if __name__ == "__main__":
+ # Defining problem Srinivas on the fly
+ def f1(x: [float]):
+ return 2.0 + (x[0] - 2.0) * (x[0] - 2.0) + (x[1] - 1.0) * (x[1] - 1.0)
+
+ def f2(x: [float]):
+ return 9.0 * x[0] - (x[1] - 1.0) * (x[1] - 1.0)
+
+ def c1(x: [float]):
+ return 1.0 - (x[0] * x[0] + x[1] * x[1]) / 225.0
+
+ def c2(x: [float]):
+ return (3.0 * x[1] - x[0]) / 10.0 - 1.0
+
+ problem = (
+ OnTheFlyFloatProblem()
+ .set_name("Srinivas")
+ .add_variable(-20.0, 20.0)
+ .add_variable(-20.0, 20.0)
+ .add_function(f1)
+ .add_function(f2)
+ .add_constraint(c1)
+ .add_constraint(c2)
+ )
+
+ problem.reference_front = read_solutions(filename="resources/reference_front/Srinivas.pf")
max_evaluations = 25000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
- dominance_comparator=DominanceComparator()
+ dominance_comparator=DominanceWithConstraintsComparator()
)
algorithm.run()
- front = algorithm.get_result()
+ front = get_non_dominated_solutions(algorithm.result())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_solving_ZDT5.py b/examples/multiobjective/nsgaii/nsgaii_solving_ZDT5.py
new file mode 100644
index 00000000..bdf6e2bc
--- /dev/null
+++ b/examples/multiobjective/nsgaii/nsgaii_solving_ZDT5.py
@@ -0,0 +1,35 @@
+from jmetal.algorithm.multiobjective.nsgaii import NSGAII
+from jmetal.operator import BitFlipMutation, SPXCrossover
+from jmetal.problem import ZDT5, OneMax
+from jmetal.problem.multiobjective.unconstrained import OneZeroMax
+from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
+from jmetal.util.termination_criterion import StoppingByEvaluations
+
+"""
+Program to configure and run the NSGA-II algorithm configured to solve a binary problem, OneZeroMax, which is
+multiobjective version of the ONE_MAX problem where the numbers of 1s and 0s have to be maximized at the same time.
+"""
+
+if __name__ == "__main__":
+ problem = ZDT5()
+
+ max_evaluations = 30000
+ algorithm = NSGAII(
+ problem=problem,
+ population_size=100,
+ offspring_population_size=100,
+ mutation=BitFlipMutation(probability=1.0 / problem.total_number_of_bits()),
+ crossover=SPXCrossover(probability=1.0),
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
+ )
+
+ algorithm.run()
+ front = algorithm.result()
+
+ # Save results to file
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_solving_binary_problem.py b/examples/multiobjective/nsgaii/nsgaii_solving_binary_problem.py
index 73bacf7f..7e3a7308 100644
--- a/examples/multiobjective/nsgaii/nsgaii_solving_binary_problem.py
+++ b/examples/multiobjective/nsgaii/nsgaii_solving_binary_problem.py
@@ -9,27 +9,27 @@
multiobjective version of the ONE_MAX problem where the numbers of 1s and 0s have to be maximized at the same time.
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
binary_string_length = 512
problem = OneZeroMax(binary_string_length)
- max_evaluations = 50000
+ max_evaluations = 30000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=100,
mutation=BitFlipMutation(probability=1.0 / binary_string_length),
crossover=SPXCrossover(probability=1.0),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_solving_constrained_srinivas_problem.py b/examples/multiobjective/nsgaii/nsgaii_solving_constrained_srinivas_problem.py
index 180a5f53..ed4ea391 100644
--- a/examples/multiobjective/nsgaii/nsgaii_solving_constrained_srinivas_problem.py
+++ b/examples/multiobjective/nsgaii/nsgaii_solving_constrained_srinivas_problem.py
@@ -1,32 +1,35 @@
from jmetal.algorithm.multiobjective import NSGAII
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import Srinivas
-from jmetal.util.comparator import DominanceComparator
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.comparator import DominanceWithConstraintsComparator
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = Srinivas()
- problem.reference_front = read_solutions(filename='resources/reference_front/Srinivas.pf')
+ #problem.reference_front = read_solutions(filename="resources/reference_front/Srinivas.pf")
max_evaluations = 25000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
- dominance_comparator=DominanceComparator()
+ dominance_comparator=DominanceWithConstraintsComparator(),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_solving_mixed_encoding_problem.py b/examples/multiobjective/nsgaii/nsgaii_solving_mixed_encoding_problem.py
index b859d11d..3b53f814 100644
--- a/examples/multiobjective/nsgaii/nsgaii_solving_mixed_encoding_problem.py
+++ b/examples/multiobjective/nsgaii/nsgaii_solving_mixed_encoding_problem.py
@@ -1,13 +1,16 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
-from jmetal.operator import SBXCrossover, PolynomialMutation, IntegerPolynomialMutation
+from jmetal.operator import IntegerPolynomialMutation, PolynomialMutation, SBXCrossover
from jmetal.operator.crossover import CompositeCrossover, IntegerSBXCrossover
from jmetal.operator.mutation import CompositeMutation
from jmetal.problem.multiobjective.unconstrained import MixedIntegerFloatProblem
-from jmetal.util.solution import get_non_dominated_solutions, print_function_values_to_file, \
- print_variables_to_file
+from jmetal.util.solution import (
+ get_non_dominated_solutions,
+ print_function_values_to_file,
+ print_variables_to_file,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = MixedIntegerFloatProblem(10, 10, 100, -100, -1000, 1000)
max_evaluations = 25000
@@ -16,18 +19,22 @@
population_size=100,
offspring_population_size=100,
mutation=CompositeMutation([IntegerPolynomialMutation(0.01, 20), PolynomialMutation(0.01, 20.0)]),
- crossover=CompositeCrossover([IntegerSBXCrossover(probability=1.0, distribution_index=20),
- SBXCrossover(probability=1.0, distribution_index=20)]),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ crossover=CompositeCrossover(
+ [
+ IntegerSBXCrossover(probability=1.0, distribution_index=20),
+ SBXCrossover(probability=1.0, distribution_index=20),
+ ]
+ ),
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = get_non_dominated_solutions(algorithm.get_result())
+ front = get_non_dominated_solutions(algorithm.result())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.' + algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_ssp.py b/examples/multiobjective/nsgaii/nsgaii_ssp.py
index 7e40df07..b391e430 100644
--- a/examples/multiobjective/nsgaii/nsgaii_ssp.py
+++ b/examples/multiobjective/nsgaii/nsgaii_ssp.py
@@ -4,23 +4,138 @@
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
C = 300500
- W = [2902, 5235, 357, 6058, 4846, 8280, 1295, 181, 3264,
- 7285, 8806, 2344, 9203, 6806, 1511, 2172, 843, 4697,
- 3348, 1866, 5800, 4094, 2751, 64, 7181, 9167, 5579,
- 9461, 3393, 4602, 1796, 8174, 1691, 8854, 5902, 4864,
- 5488, 1129, 1111, 7597, 5406, 2134, 7280, 6465, 4084,
- 8564, 2593, 9954, 4731, 1347, 8984, 5057, 3429, 7635,
- 1323, 1146, 5192, 6547, 343, 7584, 3765, 8660, 9318,
- 5098, 5185, 9253, 4495, 892, 5080, 5297, 9275, 7515,
- 9729, 6200, 2138, 5480, 860, 8295, 8327, 9629, 4212,
- 3087, 5276, 9250, 1835, 9241, 1790, 1947, 8146, 8328,
- 973, 1255, 9733, 4314, 6912, 8007, 8911, 6802, 5102,
- 5451, 1026, 8029, 6628, 8121, 5509, 3603, 6094, 4447,
- 683, 6996, 3304, 3130, 2314, 7788, 8689, 3253, 5920,
- 3660, 2489, 8153, 2822, 6132, 7684, 3032, 9949, 59,
- 6669, 6334]
+ W = [
+ 2902,
+ 5235,
+ 357,
+ 6058,
+ 4846,
+ 8280,
+ 1295,
+ 181,
+ 3264,
+ 7285,
+ 8806,
+ 2344,
+ 9203,
+ 6806,
+ 1511,
+ 2172,
+ 843,
+ 4697,
+ 3348,
+ 1866,
+ 5800,
+ 4094,
+ 2751,
+ 64,
+ 7181,
+ 9167,
+ 5579,
+ 9461,
+ 3393,
+ 4602,
+ 1796,
+ 8174,
+ 1691,
+ 8854,
+ 5902,
+ 4864,
+ 5488,
+ 1129,
+ 1111,
+ 7597,
+ 5406,
+ 2134,
+ 7280,
+ 6465,
+ 4084,
+ 8564,
+ 2593,
+ 9954,
+ 4731,
+ 1347,
+ 8984,
+ 5057,
+ 3429,
+ 7635,
+ 1323,
+ 1146,
+ 5192,
+ 6547,
+ 343,
+ 7584,
+ 3765,
+ 8660,
+ 9318,
+ 5098,
+ 5185,
+ 9253,
+ 4495,
+ 892,
+ 5080,
+ 5297,
+ 9275,
+ 7515,
+ 9729,
+ 6200,
+ 2138,
+ 5480,
+ 860,
+ 8295,
+ 8327,
+ 9629,
+ 4212,
+ 3087,
+ 5276,
+ 9250,
+ 1835,
+ 9241,
+ 1790,
+ 1947,
+ 8146,
+ 8328,
+ 973,
+ 1255,
+ 9733,
+ 4314,
+ 6912,
+ 8007,
+ 8911,
+ 6802,
+ 5102,
+ 5451,
+ 1026,
+ 8029,
+ 6628,
+ 8121,
+ 5509,
+ 3603,
+ 6094,
+ 4447,
+ 683,
+ 6996,
+ 3304,
+ 3130,
+ 2314,
+ 7788,
+ 8689,
+ 3253,
+ 5920,
+ 3660,
+ 2489,
+ 8153,
+ 2822,
+ 6132,
+ 7684,
+ 3032,
+ 9949,
+ 59,
+ 6669,
+ 6334,
+ ]
problem = SubsetSum(C, W)
@@ -30,16 +145,16 @@
offspring_population_size=100,
mutation=BitFlipMutation(probability=0.5),
crossover=SPXCrossover(probability=0.8),
- termination_criterion=StoppingByEvaluations(max_evaluations=25000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=25000),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_standard_settings.py b/examples/multiobjective/nsgaii/nsgaii_standard_settings.py
index 1c711c03..09d5fe2f 100644
--- a/examples/multiobjective/nsgaii/nsgaii_standard_settings.py
+++ b/examples/multiobjective/nsgaii/nsgaii_standard_settings.py
@@ -1,37 +1,38 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
-from jmetal.operator import SBXCrossover, PolynomialMutation
-from jmetal.problem import ZDT1
-from jmetal.util.solution import get_non_dominated_solutions, read_solutions, print_function_values_to_file, \
- print_variables_to_file
+from jmetal.operator import PolynomialMutation, SBXCrossover
+from jmetal.problem import Fonseca, ZDT4
+from jmetal.util.solution import (
+ get_non_dominated_solutions,
+ print_function_values_to_file,
+ print_variables_to_file, read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-
"""
-Program to configure and run the NSGA-II algorithm configured with standard settings.
+ Program to configure and run the NSGA-II algorithm configured with standard settings.
"""
+if __name__ == "__main__":
+ problem = ZDT4()
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT4.pf")
-if __name__ == '__main__':
- problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
-
- max_evaluations = 25000
+ max_evaluations = 20000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 * 1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = get_non_dominated_solutions(algorithm.get_result())
- # Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ front = get_non_dominated_solutions(algorithm.result())
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ # Save results to file
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_standard_settings_with_real_time_plotting.py b/examples/multiobjective/nsgaii/nsgaii_standard_settings_with_real_time_plotting.py
index bd968147..381b537e 100644
--- a/examples/multiobjective/nsgaii/nsgaii_standard_settings_with_real_time_plotting.py
+++ b/examples/multiobjective/nsgaii/nsgaii_standard_settings_with_real_time_plotting.py
@@ -1,48 +1,59 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
-from jmetal.lab.visualization import Plot, InteractivePlot
-from jmetal.operator import SBXCrossover, PolynomialMutation
-from jmetal.problem import ZDT1
+from jmetal.lab.visualization import InteractivePlot, Plot
+from jmetal.operator import PolynomialMutation, SBXCrossover
+from jmetal.problem import ZDT6, ZDT1
from jmetal.util.observer import ProgressBarObserver, VisualizerObserver
-from jmetal.util.solution import read_solutions, print_function_values_to_file, \
- print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
"""
Program to configure and run the NSGA-II algorithm configured with standard settings.
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
- max_evaluations = 25000
+ max_evaluations = 10000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.observable.register(observer=ProgressBarObserver(max=max_evaluations))
algorithm.observable.register(observer=VisualizerObserver(reference_front=problem.reference_front))
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Plot front
- plot_front = Plot(title='Pareto front approximation. Problem: ' + problem.get_name(), reference_front=problem.reference_front, axis_labels=problem.obj_labels)
+ plot_front = Plot(
+ title="Pareto front approximation. Problem: " + problem.name(),
+ reference_front=problem.reference_front,
+ axis_labels=problem.obj_labels,
+ )
plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
# Plot interactive front
- plot_front = InteractivePlot(title='Pareto front approximation. Problem: ' + problem.get_name(), reference_front=problem.reference_front, axis_labels=problem.obj_labels)
+ plot_front = InteractivePlot(
+ title="Pareto front approximation. Problem: " + problem.name(),
+ reference_front=problem.reference_front,
+ axis_labels=problem.obj_labels,
+ )
plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
\ No newline at end of file
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_steady_state.py b/examples/multiobjective/nsgaii/nsgaii_steady_state.py
index 2101c506..153102c1 100644
--- a/examples/multiobjective/nsgaii/nsgaii_steady_state.py
+++ b/examples/multiobjective/nsgaii/nsgaii_steady_state.py
@@ -1,36 +1,39 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import ZDT1
-from jmetal.util.solution import get_non_dominated_solutions, read_solutions, print_function_values_to_file, \
- print_variables_to_file
+from jmetal.util.solution import (
+ get_non_dominated_solutions,
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
"""
Program to configure and run a steady-state version of the NSGA-II algorithm (configured with standard settings).
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
max_evaluations = 25000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=1,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = get_non_dominated_solutions(algorithm.get_result())
+ front = get_non_dominated_solutions(algorithm.result())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
-
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/nsgaii_steady_state_with_real_time_plotting.py b/examples/multiobjective/nsgaii/nsgaii_steady_state_with_real_time_plotting.py
index 17304b10..49b64482 100644
--- a/examples/multiobjective/nsgaii/nsgaii_steady_state_with_real_time_plotting.py
+++ b/examples/multiobjective/nsgaii/nsgaii_steady_state_with_real_time_plotting.py
@@ -1,10 +1,13 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
from jmetal.lab.visualization import InteractivePlot, Plot
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import ZDT1
from jmetal.util.observer import ProgressBarObserver, VisualizerObserver
-from jmetal.util.solution import read_solutions, print_function_values_to_file, \
- print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
"""
@@ -12,43 +15,48 @@
update frequency is set to 100 evaluations.
"""
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
max_evaluations = 25000
algorithm = NSGAII(
problem=problem,
population_size=100,
offspring_population_size=1,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.observable.register(observer=ProgressBarObserver(max=max_evaluations))
algorithm.observable.register(
- observer=VisualizerObserver(reference_front=problem.reference_front, display_frequency=100))
+ observer=VisualizerObserver(reference_front=problem.reference_front, display_frequency=100)
+ )
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Plot front
- plot_front = Plot(title='Pareto front approximation. Problem: ' + problem.get_name(),
- reference_front=problem.reference_front,
- axis_labels=problem.obj_labels)
+ plot_front = Plot(
+ title="Pareto front approximation. Problem: " + problem.name(),
+ reference_front=problem.reference_front,
+ axis_labels=problem.obj_labels,
+ )
plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
# Plot interactive front
- plot_front = InteractivePlot(title='Pareto front approximation. Problem: ' + problem.get_name(),
- reference_front=problem.reference_front,
- axis_labels=problem.obj_labels)
+ plot_front = InteractivePlot(
+ title="Pareto front approximation. Problem: " + problem.name(),
+ reference_front=problem.reference_front,
+ axis_labels=problem.obj_labels,
+ )
plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.' + algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaii/parallel_nsgaii_with_multiprocess_evaluator.py b/examples/multiobjective/nsgaii/parallel_nsgaii_with_multiprocess_evaluator.py
index eb7f4615..a931e899 100644
--- a/examples/multiobjective/nsgaii/parallel_nsgaii_with_multiprocess_evaluator.py
+++ b/examples/multiobjective/nsgaii/parallel_nsgaii_with_multiprocess_evaluator.py
@@ -1,11 +1,11 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem.multiobjective.zdt import ZDT1Modified
from jmetal.util.evaluator import MultiprocessEvaluator
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1Modified()
max_evaluations = 100
@@ -15,19 +15,18 @@
problem=problem,
population_size=10,
offspring_population_size=10,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
-
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/nsgaiii/nsgaiii_dtlz2.py b/examples/multiobjective/nsgaiii/nsgaiii_dtlz2.py
index 1ffb9059..673e6c97 100644
--- a/examples/multiobjective/nsgaiii/nsgaiii_dtlz2.py
+++ b/examples/multiobjective/nsgaiii/nsgaiii_dtlz2.py
@@ -1,12 +1,20 @@
-from jmetal.algorithm.multiobjective.nsgaiii import NSGAIII, UniformReferenceDirectionFactory
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.algorithm.multiobjective.nsgaiii import (
+ NSGAIII,
+ UniformReferenceDirectionFactory,
+)
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import DTLZ2
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.solution import (
+ get_non_dominated_solutions,
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = DTLZ2()
- problem.reference_front = read_solutions(filename='resources/reference_front/DTLZ2.3D.pf')
+ reference_front = read_solutions(filename="resources/reference_front/DTLZ2.3D.pf")
max_evaluations = 25000
@@ -14,18 +22,18 @@
problem=problem,
population_size=92,
reference_directions=UniformReferenceDirectionFactory(3, n_points=91),
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=30),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = get_non_dominated_solutions(algorithm.result())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/omopso/omopso_spark_evaluator.py b/examples/multiobjective/omopso/omopso_spark_evaluator.py
index 16b52115..337b71d0 100644
--- a/examples/multiobjective/omopso/omopso_spark_evaluator.py
+++ b/examples/multiobjective/omopso/omopso_spark_evaluator.py
@@ -4,13 +4,17 @@
from jmetal.problem.multiobjective.zdt import ZDT1Modified
from jmetal.util.archive import CrowdingDistanceArchive
from jmetal.util.evaluator import SparkEvaluator
-from jmetal.util.solution import print_function_values_to_file, print_variables_to_file, read_solutions
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1Modified()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
- mutation_probability = 1.0 / problem.number_of_variables
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
+ mutation_probability = 1.0 / problem.number_of_variables()
max_evaluations = 100
swarm_size = 10
@@ -19,20 +23,21 @@
swarm_size=swarm_size,
epsilon=0.0075,
uniform_mutation=UniformMutation(probability=mutation_probability, perturbation=0.5),
- non_uniform_mutation=NonUniformMutation(mutation_probability, perturbation=0.5,
- max_iterations=max_evaluations / swarm_size),
+ non_uniform_mutation=NonUniformMutation(
+ mutation_probability, perturbation=0.5, max_iterations=max_evaluations / swarm_size
+ ),
leaders=CrowdingDistanceArchive(10),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
swarm_evaluator=SparkEvaluator(),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.get_name() + "." + problem.get_name())
- print_variables_to_file(front, 'VAR.' + algorithm.get_name() + "." + problem.get_name())
+ print_function_values_to_file(front, "FUN." + algorithm.get_name() + "." + problem.name())
+ print_variables_to_file(front, "VAR." + algorithm.get_name() + "." + problem.name())
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/omopso/omopso_zdt1.py b/examples/multiobjective/omopso/omopso_zdt1.py
index 9bf19f5a..65b6f02f 100644
--- a/examples/multiobjective/omopso/omopso_zdt1.py
+++ b/examples/multiobjective/omopso/omopso_zdt1.py
@@ -3,15 +3,18 @@
from jmetal.operator.mutation import NonUniformMutation
from jmetal.problem import ZDT1
from jmetal.util.archive import CrowdingDistanceArchive
-from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
-from jmetal.util.solution import read_solutions
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
- mutation_probability = 1.0 / problem.number_of_variables
+ mutation_probability = 1.0 / problem.number_of_variables()
max_evaluations = 25000
swarm_size = 100
@@ -20,19 +23,20 @@
swarm_size=swarm_size,
epsilon=0.0075,
uniform_mutation=UniformMutation(probability=mutation_probability, perturbation=0.5),
- non_uniform_mutation=NonUniformMutation(mutation_probability, perturbation=0.5,
- max_iterations=int(max_evaluations / swarm_size)),
+ non_uniform_mutation=NonUniformMutation(
+ mutation_probability, perturbation=0.5, max_iterations=int(max_evaluations / swarm_size)
+ ),
leaders=CrowdingDistanceArchive(100),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/preferences/__init__.py b/examples/multiobjective/preferences/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/examples/multiobjective/preferences/ggde3_zdt2.py b/examples/multiobjective/preferences/ggde3_zdt2.py
index 76ded1e6..13a1d4a0 100644
--- a/examples/multiobjective/preferences/ggde3_zdt2.py
+++ b/examples/multiobjective/preferences/ggde3_zdt2.py
@@ -1,18 +1,17 @@
-from jmetal.util.solutions import read_solutions, print_function_values_to_file, print_variables_to_file
-from jmetal.util.solutions.comparator import GDominanceComparator
-
from jmetal.algorithm.multiobjective.gde3 import GDE3
-from jmetal.lab.visualization import Plot, InteractivePlot
+from jmetal.lab.visualization import InteractivePlot, Plot
from jmetal.problem import ZDT2
+from jmetal.util.comparator import GDominanceComparator
from jmetal.util.observer import VisualizerObserver
+from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT2()
- problem.reference_front = read_solutions(filename='resources/reference_front/{}.pf'.format(problem.get_name()))
+ reference_front = read_solutions(filename="resources/reference_front/{}.pf".format(problem.name()))
max_evaluations = 25000
- reference_point = [0.2, 0.5]
+ reference_point = [0.4, 0.6]
algorithm = GDE3(
problem=problem,
@@ -20,26 +19,32 @@
cr=0.5,
f=0.5,
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
- dominance_comparator=GDominanceComparator(reference_point)
+ dominance_comparator=GDominanceComparator(reference_point),
)
- algorithm.observable.register(observer=VisualizerObserver(reference_front=problem.reference_front, reference_point=reference_point))
+ algorithm.observable.register(
+ observer=VisualizerObserver(reference_front=reference_front, reference_point=reference_point)
+ )
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Plot front
- plot_front = Plot(plot_title='Pareto front approximation', reference_front=problem.reference_front, axis_labels=problem.obj_labels)
+ plot_front = Plot(
+ plot_title="Pareto front approximation", reference_front=reference_front, axis_labels=problem.obj_labels
+ )
plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
# Plot interactive front
- plot_front = InteractivePlot(plot_title='Pareto front approximation', reference_front=problem.reference_front, axis_labels=problem.obj_labels)
+ plot_front = InteractivePlot(
+ plot_title="Pareto front approximation", reference_front=reference_front, axis_labels=problem.obj_labels
+ )
plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
\ No newline at end of file
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/preferences/gnsgaii_solving_zdt2_with_reference_point.py b/examples/multiobjective/preferences/gnsgaii_solving_zdt2_with_reference_point.py
new file mode 100644
index 00000000..863250b9
--- /dev/null
+++ b/examples/multiobjective/preferences/gnsgaii_solving_zdt2_with_reference_point.py
@@ -0,0 +1,66 @@
+from jmetal.algorithm.multiobjective.nsgaii import NSGAII
+from jmetal.lab.visualization import InteractivePlot, Plot
+from jmetal.operator import PolynomialMutation, SBXCrossover
+from jmetal.problem import ZDT2
+from jmetal.util.comparator import GDominanceComparator
+from jmetal.util.observer import ProgressBarObserver, VisualizerObserver
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
+from jmetal.util.termination_criterion import StoppingByEvaluations
+
+"""
+Program to configure and run G-NSGA-II (NSGA-II with G-Dominance) to solve problem ZDT2 with
+reference point = [0.2, 0.5].
+"""
+
+if __name__ == "__main__":
+ problem = ZDT2()
+ reference_front = read_solutions(filename="resources/reference_front/ZDT2.pf")
+
+ reference_point = [0.3, 0.5]
+
+ max_evaluations = 25000
+ algorithm = NSGAII(
+ problem=problem,
+ population_size=100,
+ offspring_population_size=100,
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
+ crossover=SBXCrossover(probability=1.0, distribution_index=20),
+ dominance_comparator=GDominanceComparator(reference_point),
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
+ )
+
+ algorithm.observable.register(observer=ProgressBarObserver(max=max_evaluations))
+ algorithm.observable.register(
+ observer=VisualizerObserver(reference_front=reference_front, reference_point=reference_point)
+ )
+
+ algorithm.run()
+ front = algorithm.result()
+
+ # Plot front
+ plot_front = Plot(
+ title="Pareto front approximation. Problem: " + problem.name(),
+ reference_front=reference_front,
+ axis_labels=problem.obj_labels,
+ )
+ plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
+
+ # Plot interactive front
+ plot_front = InteractivePlot(
+ title="Pareto front approximation. Problem: " + problem.name(),
+ reference_front=reference_front,
+ axis_labels=problem.obj_labels,
+ )
+ plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
+
+ # Save results to file
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/random_search/random_search_zdt1.py b/examples/multiobjective/random_search/random_search_zdt1.py
index 8d7a3106..5a6bd6a1 100644
--- a/examples/multiobjective/random_search/random_search_zdt1.py
+++ b/examples/multiobjective/random_search/random_search_zdt1.py
@@ -1,11 +1,13 @@
from jmetal.algorithm.multiobjective.random_search import RandomSearch
from jmetal.problem import ZDT1
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
max_evaluations = 1000
algorithm = RandomSearch(
@@ -14,12 +16,12 @@
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/smpso/dynamic_smpso.py b/examples/multiobjective/smpso/dynamic_smpso.py
index 7cfb6ecf..d90186bb 100644
--- a/examples/multiobjective/smpso/dynamic_smpso.py
+++ b/examples/multiobjective/smpso/dynamic_smpso.py
@@ -3,14 +3,10 @@
from jmetal.problem.multiobjective.fda import FDA2
from jmetal.util.archive import CrowdingDistanceArchive
from jmetal.util.observable import TimeCounter
-<<<<<<< HEAD
from jmetal.util.observer import PlotFrontToFileObserver, WriteFrontToFileObserver
-=======
-
->>>>>>> master
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = FDA2()
time_counter = TimeCounter(delay=15)
@@ -23,10 +19,14 @@
swarm_size=100,
mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
leaders=CrowdingDistanceArchive(100),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
- algorithm.observable.register(observer=PlotFrontToFileObserver('dynamic_front_vis'))
- algorithm.observable.register(observer=WriteFrontToFileObserver('dynamic_front'))
+ algorithm.observable.register(observer=PlotFrontToFileObserver("dynamic_front_vis"))
+ algorithm.observable.register(observer=WriteFrontToFileObserver("dynamic_front"))
algorithm.run()
+
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.get_name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/smpso/smpso_schaffer_on_the_fly.py b/examples/multiobjective/smpso/smpso_schaffer_on_the_fly.py
index 39a61cc3..bc82cfb4 100644
--- a/examples/multiobjective/smpso/smpso_schaffer_on_the_fly.py
+++ b/examples/multiobjective/smpso/smpso_schaffer_on_the_fly.py
@@ -5,7 +5,7 @@
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
# Defining problem Schaffer on the fly
def f1(x: [float]):
@@ -15,29 +15,25 @@ def f2(x: [float]):
return (x[0] - 2) * (x[0] - 2)
problem = OnTheFlyFloatProblem()
- problem \
- .set_name('Schaffer') \
- .add_variable(-10000.0, 10000.0) \
- .add_function(f1) \
- .add_function(f2)
+ problem.set_name("Schaffer").add_variable(-10000.0, 10000.0).add_function(f1).add_function(f2)
max_evaluations = 25000
algorithm = SMPSO(
problem=problem,
swarm_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
leaders=CrowdingDistanceArchive(100),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/smpso/smpso_spark_evaluator.py b/examples/multiobjective/smpso/smpso_spark_evaluator.py
index fd790a2c..0fdd661a 100644
--- a/examples/multiobjective/smpso/smpso_spark_evaluator.py
+++ b/examples/multiobjective/smpso/smpso_spark_evaluator.py
@@ -4,31 +4,34 @@
from jmetal.operator import PolynomialMutation
from jmetal.util.archive import CrowdingDistanceArchive
from jmetal.util.evaluator import SparkEvaluator
-from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
-from jmetal.util.solution import read_solutions
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1Modified()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ problem.reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
max_evaluations = 100
algorithm = SMPSO(
problem=problem,
swarm_size=10,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
leaders=CrowdingDistanceArchive(10),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
swarm_evaluator=SparkEvaluator(),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.get_name() + "." + problem.get_name())
- print_variables_to_file(front, 'VAR.'+ algorithm.get_name() + "." + problem.get_name())
+ print_function_values_to_file(front, "FUN." + algorithm.get_name() + "." + problem.get_name())
+ print_variables_to_file(front, "VAR." + algorithm.get_name() + "." + problem.get_name())
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/smpso/smpso_srinivas.py b/examples/multiobjective/smpso/smpso_srinivas.py
index 5480245e..6d257875 100644
--- a/examples/multiobjective/smpso/smpso_srinivas.py
+++ b/examples/multiobjective/smpso/smpso_srinivas.py
@@ -14,18 +14,18 @@
algorithm = SMPSO(
problem=problem,
swarm_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
leaders=CrowdingDistanceArchive(100),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
print_function_values_to_file(front, 'FUN.' + algorithm.label)
print_variables_to_file(front, 'VAR.'+ algorithm.label)
print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
+ print(f'Problem: ${problem.name()}')
print(f'Computing time: ${algorithm.total_computing_time}')
diff --git a/examples/multiobjective/smpso/smpso_srinivas_on_the_fly.py b/examples/multiobjective/smpso/smpso_srinivas_on_the_fly.py
index 0083df06..407a3545 100644
--- a/examples/multiobjective/smpso/smpso_srinivas_on_the_fly.py
+++ b/examples/multiobjective/smpso/smpso_srinivas_on_the_fly.py
@@ -2,52 +2,52 @@
from jmetal.core.problem import OnTheFlyFloatProblem
from jmetal.operator import PolynomialMutation
from jmetal.util.archive import CrowdingDistanceArchive
+from jmetal.util.comparator import DominanceWithConstraintsComparator
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
# Defining problem Srinivas on the fly
def f1(x: [float]):
return 2.0 + (x[0] - 2.0) * (x[0] - 2.0) + (x[1] - 1.0) * (x[1] - 1.0)
-
def f2(x: [float]):
return 9.0 * x[0] - (x[1] - 1.0) * (x[1] - 1.0)
-
def c1(x: [float]):
return 1.0 - (x[0] * x[0] + x[1] * x[1]) / 225.0
-
def c2(x: [float]):
return (3.0 * x[1] - x[0]) / 10.0 - 1.0
-
- problem = OnTheFlyFloatProblem() \
- .set_name('Srinivas') \
- .add_variable(-20.0, 20.0) \
- .add_variable(-20.0, 20.0) \
- .add_function(f1) \
- .add_function(f2) \
- .add_constraint(c1) \
+ problem = (
+ OnTheFlyFloatProblem()
+ .set_name("Srinivas")
+ .add_variable(-20.0, 20.0)
+ .add_variable(-20.0, 20.0)
+ .add_function(f1)
+ .add_function(f2)
+ .add_constraint(c1)
.add_constraint(c2)
+ )
max_evaluations = 25000
algorithm = SMPSO(
problem=problem,
swarm_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
- leaders=CrowdingDistanceArchive(100),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
+ leaders=CrowdingDistanceArchive(100, dominance_comparator = DominanceWithConstraintsComparator()),
+ dominance_comparator=DominanceWithConstraintsComparator(),
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/smpso/smpso_tanaka.py b/examples/multiobjective/smpso/smpso_tanaka.py
new file mode 100644
index 00000000..4065096a
--- /dev/null
+++ b/examples/multiobjective/smpso/smpso_tanaka.py
@@ -0,0 +1,36 @@
+from jmetal.algorithm.multiobjective.smpso import SMPSO
+from jmetal.operator import PolynomialMutation
+from jmetal.problem import Tanaka
+from jmetal.util.archive import CrowdingDistanceArchive
+from jmetal.util.comparator import DominanceWithConstraintsComparator
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
+from jmetal.util.termination_criterion import StoppingByEvaluations
+
+if __name__ == "__main__":
+ problem = Tanaka()
+ reference_front = read_solutions(filename="resources/reference_front/Tanaka.pf")
+
+ max_evaluations = 25000
+ algorithm = SMPSO(
+ problem=problem,
+ swarm_size=100,
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
+ leaders=CrowdingDistanceArchive(100, dominance_comparator = DominanceWithConstraintsComparator()),
+ dominance_comparator=DominanceWithConstraintsComparator(),
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
+ )
+
+ algorithm.run()
+ front = algorithm.result()
+
+ # Save results to file
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
+
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/smpso/smpso_zdt4.py b/examples/multiobjective/smpso/smpso_zdt4.py
index 19c77523..71720464 100644
--- a/examples/multiobjective/smpso/smpso_zdt4.py
+++ b/examples/multiobjective/smpso/smpso_zdt4.py
@@ -2,30 +2,31 @@
from jmetal.operator import PolynomialMutation
from jmetal.problem import ZDT4
from jmetal.util.archive import CrowdingDistanceArchive
-from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
-from jmetal.util.solution import read_solutions
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT4()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT4.pf')
max_evaluations = 25000
algorithm = SMPSO(
problem=problem,
swarm_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
leaders=CrowdingDistanceArchive(100),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/smpso/smpsorp_zdt4.py b/examples/multiobjective/smpso/smpsorp_zdt4.py
index e2f4c7d0..00460f50 100644
--- a/examples/multiobjective/smpso/smpsorp_zdt4.py
+++ b/examples/multiobjective/smpso/smpsorp_zdt4.py
@@ -1,22 +1,23 @@
-from jmetal.lab.visualization import Plot, InteractivePlot
-from jmetal.util.observer import ProgressBarObserver, VisualizerObserver
-from jmetal.util.solution import print_function_values_to_file, print_variables_to_file, read_solutions
-
-from jmetal.util.termination_criterion import StoppingByEvaluations
-
from jmetal.algorithm.multiobjective.smpso import SMPSORP
+from jmetal.lab.visualization import InteractivePlot, Plot
from jmetal.operator import PolynomialMutation
-from jmetal.problem import ZDT4, ZDT1
+from jmetal.problem import ZDT1
from jmetal.util.archive import CrowdingDistanceArchiveWithReferencePoint
+from jmetal.util.observer import VisualizerObserver
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
+from jmetal.util.termination_criterion import StoppingByEvaluations
-
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
+ reference_front = read_solutions(filename="resources/reference_front/ZDT1.pf")
swarm_size = 100
- reference_point = [[0.1, 0.8],[0.6, 0.1]]
+ reference_point = [[0.1, 0.8], [0.6, 0.1]]
archives_with_reference_points = []
for point in reference_point:
@@ -28,32 +29,39 @@
algorithm = SMPSORP(
problem=problem,
swarm_size=swarm_size,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
reference_points=reference_point,
leaders=archives_with_reference_points,
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.observable.register(
- observer=VisualizerObserver(reference_front=problem.reference_front, reference_point=reference_point))
+ observer=VisualizerObserver(reference_front=reference_front, reference_point=reference_point)
+ )
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Plot front
- plot_front = Plot(title='Pareto front approximation. Problem: ' + problem.get_name(),
- reference_front=problem.reference_front, axis_labels=problem.obj_labels)
+ plot_front = Plot(
+ title="Pareto front approximation. Problem: " + problem.name(),
+ reference_front=reference_front,
+ axis_labels=problem.obj_labels,
+ )
plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
# Plot interactive front
- plot_front = InteractivePlot(title='Pareto front approximation. Problem: ' + problem.get_name(),
- reference_front=problem.reference_front, axis_labels=problem.obj_labels)
+ plot_front = InteractivePlot(
+ title="Pareto front approximation. Problem: " + problem.name(),
+ reference_front=reference_front,
+ axis_labels=problem.obj_labels,
+ )
plot_front.plot(front, label=algorithm.label, filename=algorithm.get_name())
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.' + algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/spea2/gspea2_zdt1.py b/examples/multiobjective/spea2/gspea2_zdt1.py
index d2bd2441..3ac19460 100644
--- a/examples/multiobjective/spea2/gspea2_zdt1.py
+++ b/examples/multiobjective/spea2/gspea2_zdt1.py
@@ -1,13 +1,15 @@
from jmetal.algorithm.multiobjective.spea2 import SPEA2
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import ZDT1
from jmetal.util.comparator import GDominanceComparator
-from jmetal.util.solution import print_function_values_to_file, print_variables_to_file, read_solutions
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
reference_point = [0.4, 0.6]
@@ -16,19 +18,19 @@
problem=problem,
population_size=40,
offspring_population_size=40,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
- dominance_comparator=GDominanceComparator(reference_point)
+ dominance_comparator=GDominanceComparator(reference_point),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/spea2/spea2_dtlz1.py b/examples/multiobjective/spea2/spea2_dtlz1.py
index 1f58a3b4..a643af6d 100644
--- a/examples/multiobjective/spea2/spea2_dtlz1.py
+++ b/examples/multiobjective/spea2/spea2_dtlz1.py
@@ -1,30 +1,32 @@
from jmetal.algorithm.multiobjective.spea2 import SPEA2
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import DTLZ2
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = DTLZ2()
- problem.reference_front = read_solutions(filename='resources/reference_front/DTLZ2.3D.pf')
max_evaluations = 20000
algorithm = SPEA2(
problem=problem,
population_size=20,
offspring_population_size=20,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.'+ algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/multiobjective/spea2/spea2_zdt1.py b/examples/multiobjective/spea2/spea2_zdt1.py
index 1f010bff..c445bf13 100644
--- a/examples/multiobjective/spea2/spea2_zdt1.py
+++ b/examples/multiobjective/spea2/spea2_zdt1.py
@@ -1,30 +1,32 @@
from jmetal.algorithm.multiobjective.spea2 import SPEA2
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem import ZDT1
-from jmetal.util.solution import read_solutions, print_function_values_to_file, print_variables_to_file
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+)
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = ZDT1()
- problem.reference_front = read_solutions(filename='resources/reference_front/ZDT1.pf')
max_evaluations = 20000
algorithm = SPEA2(
problem=problem,
population_size=40,
offspring_population_size=40,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.label)
- print_variables_to_file(front, 'VAR.' + algorithm.label)
+ print_function_values_to_file(front, "FUN." + algorithm.label)
+ print_variables_to_file(front, "VAR." + algorithm.label)
- print(f'Algorithm: ${algorithm.get_name()}')
- print(f'Problem: ${problem.get_name()}')
- print(f'Computing time: ${algorithm.total_computing_time}')
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Problem: {problem.name()}")
+ print(f"Computing time: {algorithm.total_computing_time}")
diff --git a/examples/singleobjective/evolution_strategy/evolution_strategy_binary.py b/examples/singleobjective/evolution_strategy/evolution_strategy_binary.py
index a6766639..ffd977d5 100644
--- a/examples/singleobjective/evolution_strategy/evolution_strategy_binary.py
+++ b/examples/singleobjective/evolution_strategy/evolution_strategy_binary.py
@@ -3,7 +3,7 @@
from jmetal.problem import OneMax
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = OneMax(number_of_bits=512)
algorithm = EvolutionStrategy(
@@ -12,14 +12,14 @@
lambda_=10,
mutation=BitFlipMutation(probability=1.0 / problem.number_of_bits),
elitist=True,
- termination_criterion=StoppingByEvaluations(max_evaluations=25000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=25000),
)
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
- print('Algorithm: ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Solution: ' + str(result.variables[0]))
- print('Fitness: ' + str(result.objectives[0]))
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm: " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Solution: " + str(result.variables[0]))
+ print("Fitness: " + str(result.objectives[0]))
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/evolution_strategy/evolution_strategy_float.py b/examples/singleobjective/evolution_strategy/evolution_strategy_float.py
index 3a1c3833..b5f00858 100644
--- a/examples/singleobjective/evolution_strategy/evolution_strategy_float.py
+++ b/examples/singleobjective/evolution_strategy/evolution_strategy_float.py
@@ -3,7 +3,7 @@
from jmetal.problem import Sphere
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = Sphere(number_of_variables=10)
algorithm = EvolutionStrategy(
@@ -12,14 +12,14 @@
lambda_=10,
elitist=True,
mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables),
- termination_criterion=StoppingByEvaluations(max_evaluations=25000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=25000),
)
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
- print('Algorithm: ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Solution: ' + str(result.variables[0]))
- print('Fitness: ' + str(result.objectives[0]))
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm: " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Solution: " + str(result.variables[0]))
+ print("Fitness: " + str(result.objectives[0]))
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/evolution_strategy/evolution_strategy_permutation.py b/examples/singleobjective/evolution_strategy/evolution_strategy_permutation.py
new file mode 100644
index 00000000..a41b8419
--- /dev/null
+++ b/examples/singleobjective/evolution_strategy/evolution_strategy_permutation.py
@@ -0,0 +1,27 @@
+from jmetal.algorithm.singleobjective.evolution_strategy import EvolutionStrategy
+from jmetal.operator.mutation import PermutationSwapMutation
+from jmetal.problem.singleobjective.tsp import TSP
+from jmetal.util.termination_criterion import StoppingByTime
+
+if __name__ == "__main__":
+ problem = TSP(instance="resources/TSP_instances/kroA100.tsp")
+
+ print(f"Solving TSP problem with {problem.number_of_cities} cities.")
+
+ algorithm = EvolutionStrategy(
+ problem=problem,
+ mu=1,
+ lambda_=10,
+ mutation=PermutationSwapMutation(1.0 / problem.number_of_cities),
+ elitist=False,
+ termination_criterion=StoppingByTime(10),
+ )
+
+ algorithm.run()
+ result = algorithm.result()
+
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Solution: {result.variables}")
+ print(f"The shortest path length: {result.objectives[0]}")
+ print(f"Computing time: {algorithm.total_computing_time}")
+ print(f"Number of evaluations: {algorithm.evaluations}")
diff --git a/examples/singleobjective/gde3/gde3_single_objective.py b/examples/singleobjective/gde3/gde3_single_objective.py
index 1ecd2743..de19e2d1 100644
--- a/examples/singleobjective/gde3/gde3_single_objective.py
+++ b/examples/singleobjective/gde3/gde3_single_objective.py
@@ -3,24 +3,20 @@
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = Rastrigin(10)
algorithm = GDE3(
- problem=problem,
- population_size=100,
- cr=0.5,
- f=0.5,
- termination_criterion=StoppingByEvaluations(50000)
+ problem=problem, population_size=100, cr=0.5, f=0.5, termination_criterion=StoppingByEvaluations(100000)
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.' + algorithm.get_name() + "." + problem.get_name())
- print_variables_to_file(front, 'VAR.' + algorithm.get_name() + "." + problem.get_name())
+ print_function_values_to_file(front, "FUN." + algorithm.get_name() + "." + problem.get_name())
+ print_variables_to_file(front, "VAR." + algorithm.get_name() + "." + problem.get_name())
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm (continuous problem): " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_binary.py b/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_binary.py
index d205175a..e8908293 100644
--- a/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_binary.py
+++ b/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_binary.py
@@ -1,26 +1,28 @@
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
-from jmetal.operator import BitFlipMutation, SPXCrossover, BinaryTournamentSelection
+from jmetal.operator import BitFlipMutation, SPXCrossover
from jmetal.problem import OneMax
+from jmetal.util.observer import PrintObjectivesObserver
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
- problem = OneMax(number_of_bits=1024)
+if __name__ == "__main__":
+ problem = OneMax(number_of_bits=512)
algorithm = GeneticAlgorithm(
problem=problem,
- population_size=100,
- offspring_population_size=100,
- mutation=BitFlipMutation(1.0 / problem.number_of_bits),
+ population_size=40,
+ offspring_population_size=40,
+ mutation=BitFlipMutation(1.0 / problem.total_number_of_bits()),
crossover=SPXCrossover(1.0),
- selection=BinaryTournamentSelection(),
- termination_criterion=StoppingByEvaluations(max_evaluations=20000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=20000),
)
+ algorithm.observable.register(observer=PrintObjectivesObserver(100))
+
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
- print('Algorithm: {}'.format(algorithm.get_name()))
- print('Problem: {}'.format(problem.get_name()))
- print('Solution: ' + result.get_binary_string())
- print('Fitness: ' + str(result.objectives[0]))
- print('Computing time: {}'.format(algorithm.total_computing_time))
+ print("Algorithm: {}".format(algorithm.get_name()))
+ print("Problem: {}".format(problem.name()))
+ print("Solution: " + result.get_binary_string())
+ print("Fitness: " + str(result.objectives[0]))
+ print("Computing time: {}".format(algorithm.total_computing_time))
diff --git a/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_float.py b/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_float.py
index e3aff749..9dabc4b6 100644
--- a/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_float.py
+++ b/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_float.py
@@ -1,26 +1,25 @@
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
-from jmetal.operator import BinaryTournamentSelection, PolynomialMutation, SBXCrossover
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem.singleobjective.unconstrained import Rastrigin
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = Rastrigin(10)
algorithm = GeneticAlgorithm(
problem=problem,
population_size=100,
- offspring_population_size=100,
- mutation=PolynomialMutation(1.0 / problem.number_of_variables, 20.0),
- crossover=SBXCrossover(0.9, 20.0),
- selection=BinaryTournamentSelection(),
- termination_criterion=StoppingByEvaluations(max_evaluations=500000)
+ offspring_population_size=1,
+ mutation=PolynomialMutation(1.0 / problem.number_of_variables(), 20.0),
+ crossover=SBXCrossover(0.9, 5.0),
+ termination_criterion=StoppingByEvaluations(max_evaluations=150000),
)
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
- print('Algorithm: {}'.format(algorithm.get_name()))
- print('Problem: {}'.format(problem.get_name()))
- print('Solution: {}'.format(result.variables))
- print('Fitness: {}'.format(result.objectives[0]))
- print('Computing time: {}'.format(algorithm.total_computing_time))
+ print("Algorithm: {}".format(algorithm.get_name()))
+ print("Problem: {}".format(problem.name()))
+ print("Solution: {}".format(result.variables))
+ print("Fitness: {}".format(result.objectives[0]))
+ print("Computing time: {}".format(algorithm.total_computing_time))
diff --git a/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_tsp.py b/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_tsp.py
index e0b076ee..8e88d43c 100644
--- a/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_tsp.py
+++ b/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_tsp.py
@@ -1,35 +1,31 @@
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
-from jmetal.operator import BinaryTournamentSelection
from jmetal.operator.crossover import PMXCrossover
from jmetal.operator.mutation import PermutationSwapMutation
from jmetal.problem.singleobjective.tsp import TSP
-from jmetal.util.comparator import MultiComparator
-from jmetal.util.density_estimator import CrowdingDistance
-from jmetal.util.ranking import FastNonDominatedRanking
+from jmetal.util.observer import PrintObjectivesObserver
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
- problem = TSP(instance='resources/TSP_instances/kroA100.tsp')
+if __name__ == "__main__":
+ problem = TSP(instance="resources/TSP_instances/kroA100.tsp")
- print('Cities: ', problem.number_of_variables)
+ print("Cities: ", problem.number_of_variables())
algorithm = GeneticAlgorithm(
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PermutationSwapMutation(1.0 / problem.number_of_variables),
+ mutation=PermutationSwapMutation(1.0 / problem.number_of_variables()),
crossover=PMXCrossover(0.8),
- selection=BinaryTournamentSelection(
- MultiComparator([FastNonDominatedRanking.get_comparator(),
- CrowdingDistance.get_comparator()])),
- termination_criterion=StoppingByEvaluations(max_evaluations=2500000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=250000),
)
+ algorithm.observable.register(observer=PrintObjectivesObserver(5000))
+
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
- print('Algorithm: {}'.format(algorithm.get_name()))
- print('Problem: {}'.format(problem.get_name()))
- print('Solution: {}'.format(result.variables))
- print('Fitness: {}'.format(result.objectives[0]))
- print('Computing time: {}'.format(algorithm.total_computing_time))
+ print("Algorithm: {}".format(algorithm.get_name()))
+ print("Problem: {}".format(problem.name()))
+ print("Solution: {}".format(result.variables))
+ print("Fitness: {}".format(result.objectives[0]))
+ print("Computing time: {}".format(algorithm.total_computing_time))
diff --git a/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_tsp_with_contraints.py b/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_tsp_with_contraints.py
new file mode 100644
index 00000000..70f60770
--- /dev/null
+++ b/examples/singleobjective/genetic_algorithm/generational_genetic_algorithm_tsp_with_contraints.py
@@ -0,0 +1,61 @@
+from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
+from jmetal.core.solution import PermutationSolution
+from jmetal.operator import BinaryTournamentSelection
+from jmetal.operator.crossover import PMXCrossover
+from jmetal.operator.mutation import PermutationSwapMutation
+from jmetal.problem.singleobjective.tsp import TSP
+from jmetal.util.comparator import MultiComparator, OverallConstraintViolationComparator, ObjectiveComparator
+from jmetal.util.observer import PrintObjectivesObserver
+from jmetal.util.termination_criterion import StoppingByEvaluations
+
+if __name__ == "__main__":
+ class TSPWithConstraints(TSP):
+ def __init__(self, instance: str):
+ super(TSPWithConstraints, self).__init__(instance)
+
+ def number_of_constraints(self) -> int:
+ return 1
+
+ def evaluate(self, solution: PermutationSolution) -> PermutationSolution:
+ super().evaluate(solution)
+ self.__evaluate_constraints__(solution)
+
+ return solution
+
+ def __evaluate_constraints__(self, solution: PermutationSolution):
+ """ Constraint: city 17 must be in the first position of the tour
+ """
+ city = 17
+ position = solution.variables.index(city)
+
+ constraint = 0 - position
+
+ solution.constraints = [constraint]
+
+ return solution
+
+
+ problem = TSPWithConstraints(instance="resources/TSP_instances/kroA100.tsp")
+
+ solution_comparator = MultiComparator([OverallConstraintViolationComparator(), ObjectiveComparator(0)])
+ algorithm = GeneticAlgorithm(
+ problem=problem,
+ population_size=100,
+ offspring_population_size=100,
+ mutation=PermutationSwapMutation(1.0 / problem.number_of_variables()),
+ crossover=PMXCrossover(0.9),
+ selection=BinaryTournamentSelection(solution_comparator),
+ termination_criterion=StoppingByEvaluations(max_evaluations=10000),
+ solution_comparator=solution_comparator
+ )
+
+ algorithm.observable.register(observer=PrintObjectivesObserver(1000))
+
+ algorithm.run()
+ result = algorithm.result()
+
+ print("Algorithm: {}".format(algorithm.get_name()))
+ print("Problem: {}".format(problem.name()))
+ print("Solution: {}".format(result.variables))
+ print("Fitness: {}".format(result.objectives[0]))
+ print("Computing time: {}".format(algorithm.total_computing_time))
diff --git a/examples/singleobjective/genetic_algorithm/steady_state_genetic_algorithm.py b/examples/singleobjective/genetic_algorithm/steady_state_genetic_algorithm.py
index e2337f19..ad0e5b0d 100644
--- a/examples/singleobjective/genetic_algorithm/steady_state_genetic_algorithm.py
+++ b/examples/singleobjective/genetic_algorithm/steady_state_genetic_algorithm.py
@@ -1,25 +1,140 @@
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
-from jmetal.operator import SPXCrossover, BitFlipMutation, BinaryTournamentSelection
+from jmetal.operator import BinaryTournamentSelection, BitFlipMutation, SPXCrossover
from jmetal.problem.singleobjective.unconstrained import SubsetSum
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
C = 300500
- W = [2902, 5235, 357, 6058, 4846, 8280, 1295, 181, 3264,
- 7285, 8806, 2344, 9203, 6806, 1511, 2172, 843, 4697,
- 3348, 1866, 5800, 4094, 2751, 64, 7181, 9167, 5579,
- 9461, 3393, 4602, 1796, 8174, 1691, 8854, 5902, 4864,
- 5488, 1129, 1111, 7597, 5406, 2134, 7280, 6465, 4084,
- 8564, 2593, 9954, 4731, 1347, 8984, 5057, 3429, 7635,
- 1323, 1146, 5192, 6547, 343, 7584, 3765, 8660, 9318,
- 5098, 5185, 9253, 4495, 892, 5080, 5297, 9275, 7515,
- 9729, 6200, 2138, 5480, 860, 8295, 8327, 9629, 4212,
- 3087, 5276, 9250, 1835, 9241, 1790, 1947, 8146, 8328,
- 973, 1255, 9733, 4314, 6912, 8007, 8911, 6802, 5102,
- 5451, 1026, 8029, 6628, 8121, 5509, 3603, 6094, 4447,
- 683, 6996, 3304, 3130, 2314, 7788, 8689, 3253, 5920,
- 3660, 2489, 8153, 2822, 6132, 7684, 3032, 9949, 59,
- 6669, 6334]
+ W = [
+ 2902,
+ 5235,
+ 357,
+ 6058,
+ 4846,
+ 8280,
+ 1295,
+ 181,
+ 3264,
+ 7285,
+ 8806,
+ 2344,
+ 9203,
+ 6806,
+ 1511,
+ 2172,
+ 843,
+ 4697,
+ 3348,
+ 1866,
+ 5800,
+ 4094,
+ 2751,
+ 64,
+ 7181,
+ 9167,
+ 5579,
+ 9461,
+ 3393,
+ 4602,
+ 1796,
+ 8174,
+ 1691,
+ 8854,
+ 5902,
+ 4864,
+ 5488,
+ 1129,
+ 1111,
+ 7597,
+ 5406,
+ 2134,
+ 7280,
+ 6465,
+ 4084,
+ 8564,
+ 2593,
+ 9954,
+ 4731,
+ 1347,
+ 8984,
+ 5057,
+ 3429,
+ 7635,
+ 1323,
+ 1146,
+ 5192,
+ 6547,
+ 343,
+ 7584,
+ 3765,
+ 8660,
+ 9318,
+ 5098,
+ 5185,
+ 9253,
+ 4495,
+ 892,
+ 5080,
+ 5297,
+ 9275,
+ 7515,
+ 9729,
+ 6200,
+ 2138,
+ 5480,
+ 860,
+ 8295,
+ 8327,
+ 9629,
+ 4212,
+ 3087,
+ 5276,
+ 9250,
+ 1835,
+ 9241,
+ 1790,
+ 1947,
+ 8146,
+ 8328,
+ 973,
+ 1255,
+ 9733,
+ 4314,
+ 6912,
+ 8007,
+ 8911,
+ 6802,
+ 5102,
+ 5451,
+ 1026,
+ 8029,
+ 6628,
+ 8121,
+ 5509,
+ 3603,
+ 6094,
+ 4447,
+ 683,
+ 6996,
+ 3304,
+ 3130,
+ 2314,
+ 7788,
+ 8689,
+ 3253,
+ 5920,
+ 3660,
+ 2489,
+ 8153,
+ 2822,
+ 6132,
+ 7684,
+ 3032,
+ 9949,
+ 59,
+ 6669,
+ 6334,
+ ]
problem = SubsetSum(C, W)
@@ -30,14 +145,14 @@
mutation=BitFlipMutation(probability=0.1),
crossover=SPXCrossover(probability=0.8),
selection=BinaryTournamentSelection(),
- termination_criterion=StoppingByEvaluations(max_evaluations=25000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=25000),
)
algorithm.run()
- subset = algorithm.get_result()
+ subset = algorithm.result()
- print('Algorithm: {}'.format(algorithm.get_name()))
- print('Problem: {}'.format(problem.get_name()))
- print('Solution: {}'.format(subset.variables))
- print('Fitness: {}'.format(subset.objectives[0]))
- print('Computing time: {}'.format(algorithm.total_computing_time))
+ print("Algorithm: {}".format(algorithm.get_name()))
+ print("Problem: {}".format(problem.name()))
+ print("Solution: {}".format(subset.variables))
+ print("Fitness: {}".format(subset.objectives[0]))
+ print("Computing time: {}".format(algorithm.total_computing_time))
diff --git a/examples/singleobjective/genetic_algorithm/steady_state_genetic_algorithm_with_knapsack_problem.py b/examples/singleobjective/genetic_algorithm/steady_state_genetic_algorithm_with_knapsack_problem.py
index a8dd133d..ee5d5b98 100644
--- a/examples/singleobjective/genetic_algorithm/steady_state_genetic_algorithm_with_knapsack_problem.py
+++ b/examples/singleobjective/genetic_algorithm/steady_state_genetic_algorithm_with_knapsack_problem.py
@@ -1,10 +1,10 @@
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
-from jmetal.operator import SPXCrossover, BitFlipMutation, BinaryTournamentSelection
+from jmetal.operator import BinaryTournamentSelection, BitFlipMutation, SPXCrossover
from jmetal.problem.singleobjective.knapsack import Knapsack
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
- problem = Knapsack(from_file=True, filename='resources/Knapsack_instances/KnapsackInstance_50_0_0.kp')
+if __name__ == "__main__":
+ problem = Knapsack(from_file=True, filename="resources/Knapsack_instances/KnapsackInstance_50_0_0.kp")
algorithm = GeneticAlgorithm(
problem=problem,
@@ -13,15 +13,15 @@
mutation=BitFlipMutation(probability=0.1),
crossover=SPXCrossover(probability=0.8),
selection=BinaryTournamentSelection(),
- termination_criterion=StoppingByEvaluations(max_evaluations=25000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=25000),
)
algorithm.run()
- subset = algorithm.get_result()
+ subset = algorithm.result()
- print('Algorithm: {}'.format(algorithm.get_name()))
- print('Problem: {}'.format(problem.get_name()))
- print('Solution: {}'.format(subset.variables))
- print('Fitness: {}'.format(-subset.objectives[0]))
- print('Computing time: {}'.format(algorithm.total_computing_time))
+ print("Algorithm: {}".format(algorithm.get_name()))
+ print("Problem: {}".format(problem.name()))
+ print("Solution: {}".format(subset.variables))
+ print("Fitness: {}".format(-subset.objectives[0]))
+ print("Computing time: {}".format(algorithm.total_computing_time))
print(f"Problem Maximum Capacity: {problem.capacity}")
diff --git a/examples/singleobjective/local_search/local_search_binary.py b/examples/singleobjective/local_search/local_search_binary.py
index cb4ec22f..981b9fe3 100644
--- a/examples/singleobjective/local_search/local_search_binary.py
+++ b/examples/singleobjective/local_search/local_search_binary.py
@@ -1,28 +1,31 @@
from jmetal.algorithm.singleobjective.local_search import LocalSearch
from jmetal.operator import BitFlipMutation
from jmetal.problem import OneMax
+from jmetal.util.observer import PrintObjectivesObserver
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
- problem = OneMax(number_of_bits=1024)
+if __name__ == "__main__":
+ problem = OneMax(number_of_bits=512)
max_evaluations = 10000
algorithm = LocalSearch(
problem=problem,
mutation=BitFlipMutation(probability=1.0 / problem.number_of_bits),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
+ algorithm.observable.register(observer=PrintObjectivesObserver(100))
+
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
# Save results to file
- print_function_values_to_file(result, 'FUN.'+ algorithm.get_name() + "." + problem.get_name())
- print_variables_to_file(result, 'VAR.' + algorithm.get_name() + "." + problem.get_name())
+ print_function_values_to_file(result, "FUN." + algorithm.get_name() + "." + problem.get_name())
+ print_variables_to_file(result, "VAR." + algorithm.get_name() + "." + problem.get_name())
- print('Algorithm: ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Solution: ' + result.get_binary_string())
- print('Fitness: ' + str(result.objectives[0]))
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm: " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Solution: " + result.get_binary_string())
+ print("Fitness: " + str(result.objectives[0]))
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/local_search/local_search_float.py b/examples/singleobjective/local_search/local_search_float.py
index 73db5a24..70aa1edc 100644
--- a/examples/singleobjective/local_search/local_search_float.py
+++ b/examples/singleobjective/local_search/local_search_float.py
@@ -1,29 +1,29 @@
from jmetal.algorithm.singleobjective.local_search import LocalSearch
from jmetal.operator import PolynomialMutation
-from jmetal.problem.singleobjective.unconstrained import Sphere
+from jmetal.problem.singleobjective.unconstrained import Rastrigin
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
- problem = Sphere(10)
+if __name__ == "__main__":
+ problem = Rastrigin(10)
- max_evaluations = 1000000
+ max_evaluations = 100000
algorithm = LocalSearch(
problem=problem,
mutation=PolynomialMutation(1.0 / problem.number_of_variables, 20.0),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
# Save results to file
- print_function_values_to_file(result, 'FUN.'+ algorithm.get_name() + "." + problem.get_name())
- print_variables_to_file(result, 'VAR.' + algorithm.get_name() + "." + problem.get_name())
+ print_function_values_to_file(result, "FUN." + algorithm.get_name() + "." + problem.get_name())
+ print_variables_to_file(result, "VAR." + algorithm.get_name() + "." + problem.get_name())
- print('Algorithm: ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Solution: ' + str(result.variables))
- print('Fitness: ' + str(result.objectives[0]))
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm: " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Solution: " + str(result.variables))
+ print("Fitness: " + str(result.objectives[0]))
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/nsgaii/nsgaii_single_objective_binary.py b/examples/singleobjective/nsgaii/nsgaii_single_objective_binary.py
index 587ba1ce..3de31c78 100644
--- a/examples/singleobjective/nsgaii/nsgaii_single_objective_binary.py
+++ b/examples/singleobjective/nsgaii/nsgaii_single_objective_binary.py
@@ -2,10 +2,11 @@
from jmetal.operator import BitFlipMutation, SPXCrossover
from jmetal.problem import OneMax
from jmetal.util.comparator import DominanceComparator
+from jmetal.util.observer import ProgressBarObserver
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
binary_string_length = 512
problem = OneMax(binary_string_length)
@@ -14,20 +15,22 @@
algorithm = NSGAII(
problem=problem,
population_size=100,
- offspring_population_size=1,
+ offspring_population_size=100,
mutation=BitFlipMutation(probability=1.0 / binary_string_length),
crossover=SPXCrossover(probability=1.0),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
- dominance_comparator=DominanceComparator()
+ dominance_comparator=DominanceComparator(),
)
+ algorithm.observable.register(observer=ProgressBarObserver(max=max_evaluations))
+
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.'+ algorithm.get_name()+"-"+problem.get_name())
- print_variables_to_file(front, 'VAR.' + algorithm.get_name()+"-"+problem.get_name())
+ print_function_values_to_file(front, "FUN." + algorithm.get_name() + "-" + problem.get_name())
+ print_variables_to_file(front, "VAR." + algorithm.get_name() + "-" + problem.get_name())
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm (continuous problem): " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/nsgaii/nsgaii_single_objective_float.py b/examples/singleobjective/nsgaii/nsgaii_single_objective_float.py
index 3679a6d4..e1bf5919 100644
--- a/examples/singleobjective/nsgaii/nsgaii_single_objective_float.py
+++ b/examples/singleobjective/nsgaii/nsgaii_single_objective_float.py
@@ -1,11 +1,11 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
-from jmetal.operator import SBXCrossover, PolynomialMutation
+from jmetal.operator import PolynomialMutation, SBXCrossover
from jmetal.problem.singleobjective.unconstrained import Rastrigin
from jmetal.util.comparator import DominanceComparator
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = Rastrigin(10)
max_evaluations = 50000
@@ -16,16 +16,16 @@
mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20.0),
crossover=SBXCrossover(probability=0.9, distribution_index=20.0),
termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
- dominance_comparator=DominanceComparator()
+ dominance_comparator=DominanceComparator(),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
# Save results to file
- print_function_values_to_file(front, 'FUN.'+ algorithm.get_name()+"-"+problem.get_name())
- print_variables_to_file(front, 'VAR.' + algorithm.get_name()+"-"+problem.get_name())
+ print_function_values_to_file(front, "FUN." + algorithm.get_name() + "-" + problem.get_name())
+ print_variables_to_file(front, "VAR." + algorithm.get_name() + "-" + problem.get_name())
- print('Algorithm (continuous problem): ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm (continuous problem): " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/simulated_annealing/simulated_annealing_binary.py b/examples/singleobjective/simulated_annealing/simulated_annealing_binary.py
index 7320448e..56026d97 100644
--- a/examples/singleobjective/simulated_annealing/simulated_annealing_binary.py
+++ b/examples/singleobjective/simulated_annealing/simulated_annealing_binary.py
@@ -4,26 +4,26 @@
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
- problem = OneMax(number_of_bits=1024)
+if __name__ == "__main__":
+ problem = OneMax(number_of_bits=512)
- max_evaluations = 20000
+ max_evaluations = 10000
algorithm = SimulatedAnnealing(
problem=problem,
mutation=BitFlipMutation(probability=1.0 / problem.number_of_bits),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
# Save results to file
- print_function_values_to_file(result, 'FUN.'+ algorithm.get_name() + "." + problem.get_name())
- print_variables_to_file(result, 'VAR.' + algorithm.get_name() + "." + problem.get_name())
+ print_function_values_to_file(result, "FUN." + algorithm.get_name() + "." + problem.get_name())
+ print_variables_to_file(result, "VAR." + algorithm.get_name() + "." + problem.get_name())
- print('Algorithm: ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Solution: ' + result.get_binary_string())
- print('Fitness: ' + str(result.objectives[0]))
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm: " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Solution: " + result.get_binary_string())
+ print("Fitness: " + str(result.objectives[0]))
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/simulated_annealing/simulated_annealing_float.py b/examples/singleobjective/simulated_annealing/simulated_annealing_float.py
index 23b40432..c83d210c 100644
--- a/examples/singleobjective/simulated_annealing/simulated_annealing_float.py
+++ b/examples/singleobjective/simulated_annealing/simulated_annealing_float.py
@@ -4,26 +4,26 @@
from jmetal.util.solution import print_function_values_to_file, print_variables_to_file
from jmetal.util.termination_criterion import StoppingByEvaluations
-if __name__ == '__main__':
+if __name__ == "__main__":
problem = Rastrigin(10)
- max_evaluations = 250000
+ max_evaluations = 100000
algorithm = SimulatedAnnealing(
problem=problem,
mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20.0),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- result = algorithm.get_result()
+ result = algorithm.result()
# Save results to file
- print_function_values_to_file(result, 'FUN.'+ algorithm.get_name() + "." + problem.get_name())
- print_variables_to_file(result, 'VAR.' + algorithm.get_name() + "." + problem.get_name())
+ print_function_values_to_file(result, "FUN." + algorithm.get_name() + "." + problem.get_name())
+ print_variables_to_file(result, "VAR." + algorithm.get_name() + "." + problem.get_name())
- print('Algorithm: ' + algorithm.get_name())
- print('Problem: ' + problem.get_name())
- print('Solution: ' + str(result.variables[0]))
- print('Fitness: ' + str(result.objectives[0]))
- print('Computing time: ' + str(algorithm.total_computing_time))
+ print("Algorithm: " + algorithm.get_name())
+ print("Problem: " + problem.get_name())
+ print("Solution: " + str(result.variables[0]))
+ print("Fitness: " + str(result.objectives[0]))
+ print("Computing time: " + str(algorithm.total_computing_time))
diff --git a/examples/singleobjective/simulated_annealing/simulated_annealing_permutation.py b/examples/singleobjective/simulated_annealing/simulated_annealing_permutation.py
new file mode 100644
index 00000000..0a136e95
--- /dev/null
+++ b/examples/singleobjective/simulated_annealing/simulated_annealing_permutation.py
@@ -0,0 +1,24 @@
+from jmetal.algorithm.singleobjective.simulated_annealing import SimulatedAnnealing
+from jmetal.operator import ScrambleMutation
+from jmetal.problem import TSP
+from jmetal.util.termination_criterion import StoppingByTime
+
+if __name__ == "__main__":
+ problem = TSP(instance="resources/TSP_instances/kroA100.tsp")
+
+ print(f"Solving TSP problem with {problem.number_of_cities} cities.")
+
+ algorithm = SimulatedAnnealing(
+ problem=problem,
+ mutation=ScrambleMutation(probability=1.0 / problem.number_of_cities),
+ termination_criterion=StoppingByTime(max_seconds=10),
+ )
+
+ algorithm.run()
+ result = algorithm.result()
+
+ print(f"Algorithm: {algorithm.get_name()}")
+ print(f"Solution: {result.variables}")
+ print(f"The shortest path length: {str(result.objectives[0])}")
+ print(f"Computing time: {str(algorithm.total_computing_time)}")
+ print(f"Problem evaluations: {str(algorithm.evaluations)}")
diff --git a/jmetal/__init__.py b/jmetal/__init__.py
index 70baa3db..3db5537e 100644
--- a/jmetal/__init__.py
+++ b/jmetal/__init__.py
@@ -1,25 +1,7 @@
-import logging
+from jmetal import algorithm, core, operator, problem
+from jmetal.logger import configure_logging
-from jmetal import algorithm
-from jmetal import core
-from jmetal import operator
-from jmetal import problem
+configure_logging()
-__all__ = ['core', 'algorithm', 'operator', 'problem']
-
-logger = logging.getLogger('jmetal')
-logger.setLevel(logging.INFO)
-
-# create a file handler
-file_handler = logging.FileHandler('jmetalpy.log', delay=True)
-file_handler.setLevel(logging.INFO)
-stream_handler = logging.StreamHandler()
-
-# create a logging format
-formatter = logging.Formatter('%(asctime)s [%(threadName)-12.12s] [%(levelname)-5.5s] %(message)s')
-file_handler.setFormatter(formatter)
-stream_handler.setFormatter(formatter)
-
-# add the handlers to the logger
-logger.addHandler(file_handler)
-logger.addHandler(stream_handler)
+__all__ = ["core", "algorithm", "operator", "problem"]
+__version__ = "1.6.0"
diff --git a/jmetal/algorithm/multiobjective/gde3.py b/jmetal/algorithm/multiobjective/gde3.py
index 7dd1da69..09b1b7f1 100644
--- a/jmetal/algorithm/multiobjective/gde3.py
+++ b/jmetal/algorithm/multiobjective/gde3.py
@@ -1,36 +1,39 @@
-from typing import TypeVar, List
+from typing import List, TypeVar
from jmetal.config import store
-from jmetal.core.algorithm import EvolutionaryAlgorithm, DynamicAlgorithm
-from jmetal.core.problem import Problem, DynamicProblem
+from jmetal.core.algorithm import DynamicAlgorithm, EvolutionaryAlgorithm
+from jmetal.core.problem import DynamicProblem, Problem
from jmetal.core.solution import FloatSolution
-from jmetal.operator import DifferentialEvolutionCrossover, RankingAndCrowdingDistanceSelection
+from jmetal.operator import (
+ DifferentialEvolutionCrossover,
+ RankingAndCrowdingDistanceSelection,
+)
from jmetal.operator.selection import DifferentialEvolutionSelection
from jmetal.util.comparator import Comparator, DominanceComparator
from jmetal.util.evaluator import Evaluator
from jmetal.util.generator import Generator
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
+S = TypeVar("S")
R = List[S]
class GDE3(EvolutionaryAlgorithm[FloatSolution, FloatSolution]):
-
- def __init__(self,
- problem: Problem,
- population_size: int,
- cr: float,
- f: float,
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- k: float = 0.5,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator,
- dominance_comparator: Comparator = store.default_comparator):
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ cr: float,
+ f: float,
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ k: float = 0.5,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ dominance_comparator: Comparator = store.default_comparator,
+ ):
super(GDE3, self).__init__(
- problem=problem,
- population_size=population_size,
- offspring_population_size=population_size)
+ problem=problem, population_size=population_size, offspring_population_size=population_size
+ )
self.dominance_comparator = dominance_comparator
self.selection_operator = DifferentialEvolutionSelection()
self.crossover_operator = DifferentialEvolutionCrossover(cr, f, k)
@@ -57,7 +60,7 @@ def reproduction(self, mating_pool: List[S]) -> List[S]:
for solution in self.solutions:
self.crossover_operator.current_individual = solution
- parents = mating_pool[first_parent_index:first_parent_index + 3]
+ parents = mating_pool[first_parent_index : first_parent_index + 3]
first_parent_index += 3
offspring_population.append(self.crossover_operator.execute(parents)[0])
@@ -92,28 +95,37 @@ def evaluate(self, solution_list: List[FloatSolution]) -> List[FloatSolution]:
def stopping_condition_is_met(self) -> bool:
return self.termination_criterion.is_met
- def get_result(self) -> List[FloatSolution]:
+ def result(self) -> List[FloatSolution]:
return self.solutions
def get_name(self) -> str:
- return 'GDE3'
+ return "GDE3"
class DynamicGDE3(GDE3, DynamicAlgorithm):
-
- def __init__(self,
- problem: DynamicProblem,
- population_size: int,
- cr: float,
- f: float,
- termination_criterion: TerminationCriterion,
- k: float = 0.5,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator,
- dominance_comparator: Comparator = DominanceComparator()):
+ def __init__(
+ self,
+ problem: DynamicProblem,
+ population_size: int,
+ cr: float,
+ f: float,
+ termination_criterion: TerminationCriterion,
+ k: float = 0.5,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ dominance_comparator: Comparator = DominanceComparator(),
+ ):
super(DynamicGDE3, self).__init__(
- problem, population_size, cr, f, termination_criterion, k,
- population_generator, population_evaluator, dominance_comparator)
+ problem,
+ population_size,
+ cr,
+ f,
+ termination_criterion,
+ k,
+ population_generator,
+ population_evaluator,
+ dominance_comparator,
+ )
self.completed_iterations = 0
@@ -125,14 +137,14 @@ def update_progress(self):
self.restart()
self.problem.clear_changed()
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
self.evaluations += self.offspring_population_size
def stopping_condition_is_met(self):
if self.termination_criterion.is_met:
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
self.restart()
diff --git a/jmetal/algorithm/multiobjective/hype.py b/jmetal/algorithm/multiobjective/hype.py
index 4fc997ec..b508b664 100644
--- a/jmetal/algorithm/multiobjective/hype.py
+++ b/jmetal/algorithm/multiobjective/hype.py
@@ -1,36 +1,36 @@
-from typing import TypeVar, List
+from typing import List, TypeVar
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
from jmetal.config import store
-from jmetal.core.operator import Mutation, Crossover
+from jmetal.core.operator import Crossover, Mutation
from jmetal.core.problem import Problem
from jmetal.core.solution import Solution
from jmetal.operator import BinaryTournamentSelection
from jmetal.operator.selection import RankingAndFitnessSelection
-from jmetal.util.comparator import Comparator
-from jmetal.util.comparator import SolutionAttributeComparator
+from jmetal.util.comparator import Comparator, SolutionAttributeComparator
from jmetal.util.evaluator import Evaluator
from jmetal.util.generator import Generator
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
class HYPE(GeneticAlgorithm[S, R]):
-
- def __init__(self,
- problem: Problem,
- reference_point: Solution,
- population_size: int,
- offspring_population_size: int,
- mutation: Mutation,
- crossover: Crossover,
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator,
- dominance_comparator: Comparator = store.default_comparator):
- """ This is an implementation of the Hypervolume Estimation Algorithm for Multi-objective Optimization
+ def __init__(
+ self,
+ problem: Problem,
+ reference_point: Solution,
+ population_size: int,
+ offspring_population_size: int,
+ mutation: Mutation,
+ crossover: Crossover,
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ dominance_comparator: Comparator = store.default_comparator,
+ ):
+ """This is an implementation of the Hypervolume Estimation Algorithm for Multi-objective Optimization
proposed in:
* J. Bader and E. Zitzler. HypE: An Algorithm for Fast Hypervolume-Based Many-Objective
@@ -49,10 +49,11 @@ def __init__(self,
"""
selection = BinaryTournamentSelection(
- comparator=SolutionAttributeComparator(key='fitness', lowest_is_best=False))
- self.ranking_fitness = RankingAndFitnessSelection(population_size,
- dominance_comparator=dominance_comparator,
- reference_point=reference_point)
+ comparator=SolutionAttributeComparator(key="fitness", lowest_is_best=False)
+ )
+ self.ranking_fitness = RankingAndFitnessSelection(
+ population_size, dominance_comparator=dominance_comparator, reference_point=reference_point
+ )
self.reference_point = reference_point
self.dominance_comparator = dominance_comparator
@@ -65,21 +66,22 @@ def __init__(self,
selection=selection,
termination_criterion=termination_criterion,
population_evaluator=population_evaluator,
- population_generator=population_generator
+ population_generator=population_generator,
)
def evaluate(self, population: List[S]):
population = self.population_evaluator.evaluate(population, self.problem)
- population = self.ranking_fitness.compute_hypervol_fitness_values(population, self.reference_point,
- len(population))
+ population = self.ranking_fitness.compute_hypervol_fitness_values(
+ population, self.reference_point, len(population)
+ )
return population
def replacement(self, population: List[S], offspring_population: List[S]) -> List[List[S]]:
join_population = population + offspring_population
return self.ranking_fitness.execute(join_population)
- def get_result(self) -> R:
+ def result(self) -> R:
return self.solutions
def get_name(self) -> str:
- return 'HYPE'
+ return "HYPE"
diff --git a/jmetal/algorithm/multiobjective/ibea.py b/jmetal/algorithm/multiobjective/ibea.py
index 12ca0d30..cd59a954 100644
--- a/jmetal/algorithm/multiobjective/ibea.py
+++ b/jmetal/algorithm/multiobjective/ibea.py
@@ -1,10 +1,10 @@
-from typing import TypeVar, List
+from typing import List, TypeVar
import numpy as np
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
from jmetal.config import store
-from jmetal.core.operator import Mutation, Crossover
+from jmetal.core.operator import Crossover, Mutation
from jmetal.core.problem import Problem
from jmetal.core.quality_indicator import EpsilonIndicator
from jmetal.operator import BinaryTournamentSelection
@@ -13,23 +13,24 @@
from jmetal.util.generator import Generator
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
class IBEA(GeneticAlgorithm[S, R]):
-
- def __init__(self,
- problem: Problem,
- population_size: int,
- offspring_population_size: int,
- mutation: Mutation,
- crossover: Crossover,
- kappa: float,
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator):
- """ Epsilon IBEA implementation as described in
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ offspring_population_size: int,
+ mutation: Mutation,
+ crossover: Crossover,
+ kappa: float,
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ ):
+ """Epsilon IBEA implementation as described in
* Zitzler, Eckart, and Simon Künzli. "Indicator-based selection in multiobjective search."
In International Conference on Parallel Problem Solving from Nature, pp. 832-842. Springer,
@@ -50,7 +51,8 @@ def __init__(self,
"""
selection = BinaryTournamentSelection(
- comparator=SolutionAttributeComparator(key='fitness', lowest_is_best=False))
+ comparator=SolutionAttributeComparator(key="fitness", lowest_is_best=False)
+ )
self.kappa = kappa
super(IBEA, self).__init__(
@@ -62,17 +64,18 @@ def __init__(self,
selection=selection,
termination_criterion=termination_criterion,
population_evaluator=population_evaluator,
- population_generator=population_generator
+ population_generator=population_generator,
)
def compute_fitness_values(self, population: List[S], kappa: float) -> List[S]:
for i in range(len(population)):
- population[i].attributes['fitness'] = 0
+ population[i].attributes["fitness"] = 0
for j in range(len(population)):
if j != i:
- population[i].attributes['fitness'] += -np.exp(
- -EpsilonIndicator([population[i].objectives]).compute([population[j].objectives]) / self.kappa)
+ population[i].attributes["fitness"] += -np.exp(
+ -EpsilonIndicator([population[i].objectives]).compute([population[j].objectives]) / self.kappa
+ )
return population
def create_initial_solutions(self) -> List[S]:
@@ -87,20 +90,24 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
join_population = self.compute_fitness_values(join_population, self.kappa)
while join_population_size > self.population_size:
- current_fitnesses = [individual.attributes['fitness'] for individual in join_population]
+ current_fitnesses = [individual.attributes["fitness"] for individual in join_population]
index_worst = current_fitnesses.index(min(current_fitnesses))
for i in range(join_population_size):
- join_population[i].attributes['fitness'] += np.exp(
- - EpsilonIndicator([join_population[i].objectives]).compute([join_population[index_worst].objectives]) / self.kappa)
+ join_population[i].attributes["fitness"] += np.exp(
+ -EpsilonIndicator([join_population[i].objectives]).compute(
+ [join_population[index_worst].objectives]
+ )
+ / self.kappa
+ )
join_population.pop(index_worst)
join_population_size = join_population_size - 1
return join_population
- def get_result(self) -> R:
+ def result(self) -> R:
return self.solutions
def get_name(self) -> str:
- return 'Epsilon-IBEA'
+ return "Epsilon-IBEA"
diff --git a/jmetal/algorithm/multiobjective/mocell.py b/jmetal/algorithm/multiobjective/mocell.py
index fd6c282f..d384c254 100644
--- a/jmetal/algorithm/multiobjective/mocell.py
+++ b/jmetal/algorithm/multiobjective/mocell.py
@@ -1,10 +1,10 @@
import copy
from functools import cmp_to_key
-from typing import TypeVar, List
+from typing import List, TypeVar
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
from jmetal.config import store
-from jmetal.core.operator import Mutation, Crossover, Selection
+from jmetal.core.operator import Crossover, Mutation, Selection
from jmetal.core.problem import Problem
from jmetal.operator import BinaryTournamentSelection
from jmetal.util.archive import BoundedArchive
@@ -16,8 +16,8 @@
from jmetal.util.ranking import FastNonDominatedRanking, Ranking
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: MOCell
@@ -28,21 +28,22 @@
class MOCell(GeneticAlgorithm[S, R]):
-
- def __init__(self,
- problem: Problem,
- population_size: int,
- neighborhood: Neighborhood,
- archive: BoundedArchive,
- mutation: Mutation,
- crossover: Crossover,
- selection: Selection = BinaryTournamentSelection(
- MultiComparator([FastNonDominatedRanking.get_comparator(),
- CrowdingDistance.get_comparator()])),
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator,
- dominance_comparator: Comparator = store.default_comparator):
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ neighborhood: Neighborhood,
+ archive: BoundedArchive,
+ mutation: Mutation,
+ crossover: Crossover,
+ selection: Selection = BinaryTournamentSelection(
+ MultiComparator([FastNonDominatedRanking.get_comparator(), CrowdingDistance.get_comparator()])
+ ),
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ dominance_comparator: Comparator = store.default_comparator,
+ ):
"""
MOCEll implementation as described in:
@@ -61,7 +62,7 @@ def __init__(self,
selection=selection,
termination_criterion=termination_criterion,
population_evaluator=population_evaluator,
- population_generator=population_generator
+ population_generator=population_generator,
)
self.dominance_comparator = dominance_comparator
self.neighborhood = neighborhood
@@ -69,8 +70,7 @@ def __init__(self,
self.current_individual = 0
self.current_neighbors = []
- self.comparator = MultiComparator([FastNonDominatedRanking.get_comparator(),
- CrowdingDistance.get_comparator()])
+ self.comparator = MultiComparator([FastNonDominatedRanking.get_comparator(), CrowdingDistance.get_comparator()])
def init_progress(self) -> None:
super().init_progress()
@@ -99,10 +99,10 @@ def reproduction(self, mating_population: List[S]) -> List[S]:
number_of_parents_to_combine = self.crossover_operator.get_number_of_parents()
if len(mating_population) % number_of_parents_to_combine != 0:
- raise Exception('Wrong number of parents')
+ raise Exception("Wrong number of parents")
offspring_population = self.crossover_operator.execute(mating_population)
- self.mutation_operator.execute(offspring_population[0])
+ offspring_population[0] = self.mutation_operator.execute(offspring_population[0])
return [offspring_population[0]]
@@ -111,7 +111,7 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
if result == 1: # the offspring individual dominates the current one
population[self.current_individual] = offspring_population[0]
- self.archive.add(offspring_population[0])
+ self.archive.add(copy.deepcopy(offspring_population[0]))
elif result == 0: # the offspring and current individuals are non-dominated
new_individual = offspring_population[0]
@@ -127,14 +127,14 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
self.current_neighbors.sort(key=cmp_to_key(self.comparator.compare))
worst_solution = self.current_neighbors[-1]
- self.archive.add(new_individual)
+ self.archive.add(copy.deepcopy(new_individual))
if worst_solution != new_individual:
population[self.current_individual] = new_individual
return population
- def get_result(self) -> R:
+ def result(self) -> R:
return self.archive.solution_list
def get_name(self) -> str:
- return 'MOCell'
+ return "MOCell"
diff --git a/jmetal/algorithm/multiobjective/moead.py b/jmetal/algorithm/multiobjective/moead.py
index c2e39669..d073918c 100644
--- a/jmetal/algorithm/multiobjective/moead.py
+++ b/jmetal/algorithm/multiobjective/moead.py
@@ -1,7 +1,7 @@
import copy
import random
from math import ceil
-from typing import TypeVar, List, Generator
+from typing import Generator, List, TypeVar
import numpy as np
@@ -10,34 +10,41 @@
from jmetal.core.operator import Mutation
from jmetal.core.problem import Problem
from jmetal.operator import DifferentialEvolutionCrossover, NaryRandomSolutionSelection
-from jmetal.util.aggregative_function import AggregativeFunction
-from jmetal.util.constraint_handling import feasibility_ratio, \
- overall_constraint_violation_degree, is_feasible
+from jmetal.util.aggregation_function import AggregationFunction
+from jmetal.util.constraint_handling import (
+ feasibility_ratio,
+ is_feasible,
+ overall_constraint_violation_degree,
+)
from jmetal.util.density_estimator import CrowdingDistance
from jmetal.util.evaluator import Evaluator
from jmetal.util.neighborhood import WeightVectorNeighborhood
from jmetal.util.ranking import FastNonDominatedRanking
-from jmetal.util.termination_criterion import TerminationCriterion, StoppingByEvaluations
+from jmetal.util.termination_criterion import (
+ StoppingByEvaluations,
+ TerminationCriterion,
+)
-S = TypeVar('S')
+S = TypeVar("S")
R = List[S]
class MOEAD(GeneticAlgorithm):
-
- def __init__(self,
- problem: Problem,
- population_size: int,
- mutation: Mutation,
- crossover: DifferentialEvolutionCrossover,
- aggregative_function: AggregativeFunction,
- neighbourhood_selection_probability: float,
- max_number_of_replaced_solutions: int,
- neighbor_size: int,
- weight_files_path: str,
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator):
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ mutation: Mutation,
+ crossover: DifferentialEvolutionCrossover,
+ aggregation_function: AggregationFunction,
+ neighbourhood_selection_probability: float,
+ max_number_of_replaced_solutions: int,
+ neighbor_size: int,
+ weight_files_path: str,
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ ):
"""
:param max_number_of_replaced_solutions: (eta in Zhang & Li paper).
:param neighbourhood_selection_probability: Probability of mating with a solution in the neighborhood rather
@@ -52,15 +59,15 @@ def __init__(self,
selection=NaryRandomSolutionSelection(2),
population_evaluator=population_evaluator,
population_generator=population_generator,
- termination_criterion=termination_criterion
+ termination_criterion=termination_criterion,
)
self.max_number_of_replaced_solutions = max_number_of_replaced_solutions
- self.fitness_function = aggregative_function
+ self.fitness_function = aggregation_function
self.neighbourhood = WeightVectorNeighborhood(
number_of_weight_vectors=population_size,
neighborhood_size=neighbor_size,
- weight_vector_size=problem.number_of_objectives,
- weights_path=weight_files_path
+ weight_vector_size=problem.number_of_objectives(),
+ weights_path=weight_files_path,
)
self.neighbourhood_selection_probability = neighbourhood_selection_probability
self.permutation = None
@@ -74,14 +81,14 @@ def init_progress(self) -> None:
self.permutation = Permutation(self.population_size)
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
def selection(self, population: List[S]):
self.current_subproblem = self.permutation.get_next_value()
self.neighbor_type = self.choose_neighbor_type()
- if self.neighbor_type == 'NEIGHBOR':
+ if self.neighbor_type == "NEIGHBOR":
neighbors = self.neighbourhood.get_neighbors(self.current_subproblem, population)
mating_population = self.selection_operator.execute(neighbors)
else:
@@ -128,7 +135,7 @@ def update_current_subproblem_neighborhood(self, new_solution, population):
return population
def generate_permutation_of_neighbors(self, subproblem_id):
- if self.neighbor_type == 'NEIGHBOR':
+ if self.neighbor_type == "NEIGHBOR":
neighbors = self.neighbourhood.get_neighborhood()[subproblem_id]
permuted_array = copy.deepcopy(neighbors.tolist())
else:
@@ -140,30 +147,49 @@ def choose_neighbor_type(self):
rnd = random.random()
if rnd < self.neighbourhood_selection_probability:
- neighbor_type = 'NEIGHBOR'
+ neighbor_type = "NEIGHBOR"
else:
- neighbor_type = 'POPULATION'
+ neighbor_type = "POPULATION"
return neighbor_type
def get_name(self):
- return 'MOEAD'
+ return "MOEAD"
- def get_result(self):
+ def result(self):
return self.solutions
class MOEAD_DRA(MOEAD):
- def __init__(self, problem, population_size, mutation, crossover, aggregative_function,
- neighbourhood_selection_probability, max_number_of_replaced_solutions, neighbor_size,
- weight_files_path, termination_criterion=store.default_termination_criteria,
- population_generator=store.default_generator, population_evaluator=store.default_evaluator):
- super(MOEAD_DRA, self).__init__(problem, population_size, mutation, crossover, aggregative_function,
- neighbourhood_selection_probability, max_number_of_replaced_solutions,
- neighbor_size, weight_files_path,
- termination_criterion=termination_criterion,
- population_generator=population_generator,
- population_evaluator=population_evaluator)
+ def __init__(
+ self,
+ problem,
+ population_size,
+ mutation,
+ crossover,
+ aggregation_function,
+ neighbourhood_selection_probability,
+ max_number_of_replaced_solutions,
+ neighbor_size,
+ weight_files_path,
+ termination_criterion=store.default_termination_criteria,
+ population_generator=store.default_generator,
+ population_evaluator=store.default_evaluator,
+ ):
+ super(MOEAD_DRA, self).__init__(
+ problem,
+ population_size,
+ mutation,
+ crossover,
+ aggregation_function,
+ neighbourhood_selection_probability,
+ max_number_of_replaced_solutions,
+ neighbor_size,
+ weight_files_path,
+ termination_criterion=termination_criterion,
+ population_generator=population_generator,
+ population_evaluator=population_evaluator,
+ )
self.saved_values = []
self.utility = [1.0 for _ in range(population_size)]
@@ -183,7 +209,7 @@ def init_progress(self):
self.order = self.__tour_selection(10)
self.current_order_index = 0
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
def update_progress(self):
@@ -205,7 +231,7 @@ def selection(self, population: List[S]):
self.neighbor_type = self.choose_neighbor_type()
- if self.neighbor_type == 'NEIGHBOR':
+ if self.neighbor_type == "NEIGHBOR":
neighbors = self.neighbourhood.get_neighbors(self.current_subproblem, population)
mating_population = self.selection_operator.execute(neighbors)
else:
@@ -216,7 +242,7 @@ def selection(self, population: List[S]):
return mating_population
def get_name(self):
- return 'MOEAD-DRA'
+ return "MOEAD-DRA"
def __utility_function(self):
for i in range(len(self.solutions)):
@@ -232,8 +258,8 @@ def __utility_function(self):
self.saved_values[i] = copy.copy(self.solutions[i])
def __tour_selection(self, depth):
- selected = [i for i in range(self.problem.number_of_objectives)]
- candidate = [i for i in range(self.problem.number_of_objectives, self.population_size)]
+ selected = [i for i in range(self.problem.number_of_objectives())]
+ candidate = [i for i in range(self.problem.number_of_objectives(), self.population_size)]
while len(selected) < int(self.population_size / 5.0):
best_idd = int(random.random() * len(candidate))
@@ -251,19 +277,21 @@ def __tour_selection(self, depth):
class MOEADIEpsilon(MOEAD):
- def __init__(self,
- problem: Problem,
- population_size: int,
- mutation: Mutation,
- crossover: DifferentialEvolutionCrossover,
- aggregative_function: AggregativeFunction,
- neighbourhood_selection_probability: float,
- max_number_of_replaced_solutions: int,
- neighbor_size: int,
- weight_files_path: str,
- termination_criterion: TerminationCriterion = StoppingByEvaluations(300000),
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator):
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ mutation: Mutation,
+ crossover: DifferentialEvolutionCrossover,
+ aggregation_function: AggregationFunction,
+ neighbourhood_selection_probability: float,
+ max_number_of_replaced_solutions: int,
+ neighbor_size: int,
+ weight_files_path: str,
+ termination_criterion: TerminationCriterion = StoppingByEvaluations(300000),
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ ):
"""
:param max_number_of_replaced_solutions: (eta in Zhang & Li paper).
:param neighbourhood_selection_probability: Probability of mating with a solution in the neighborhood rather
@@ -274,14 +302,14 @@ def __init__(self,
population_size=population_size,
mutation=mutation,
crossover=crossover,
- aggregative_function=aggregative_function,
+ aggregation_function=aggregation_function,
neighbourhood_selection_probability=neighbourhood_selection_probability,
max_number_of_replaced_solutions=max_number_of_replaced_solutions,
neighbor_size=neighbor_size,
weight_files_path=weight_files_path,
population_evaluator=population_evaluator,
population_generator=population_generator,
- termination_criterion=termination_criterion
+ termination_criterion=termination_criterion,
)
self.constraints = []
self.epsilon_k = 0
@@ -298,8 +326,9 @@ def init_progress(self) -> None:
# for i in range(self.population_size):
# self.constraints[i] = get_overall_constraint_violation_degree(self.permutation[i])
- self.constraints = [overall_constraint_violation_degree(self.solutions[i])
- for i in range(0, self.population_size)]
+ self.constraints = [
+ overall_constraint_violation_degree(self.solutions[i]) for i in range(0, self.population_size)
+ ]
sorted(self.constraints)
self.epsilon_zero = abs(self.constraints[int(ceil(0.05 * self.population_size))])
@@ -378,20 +407,20 @@ def update_external_archive(self):
crowding_distance = CrowdingDistance()
while len(first_rank_solutions) > self.population_size:
crowding_distance.compute_density_estimator(first_rank_solutions)
- first_rank_solutions = sorted(first_rank_solutions, key=lambda x: x.attributes['crowding_distance'],
- reverse=True)
+ first_rank_solutions = sorted(
+ first_rank_solutions, key=lambda x: x.attributes["crowding_distance"], reverse=True
+ )
first_rank_solutions.pop()
self.archive = []
for solution in first_rank_solutions:
self.archive.append(copy.deepcopy(solution))
- def get_result(self):
+ def result(self):
return self.archive
class Permutation:
-
def __init__(self, length: int):
self.counter = 0
self.length = length
diff --git a/jmetal/algorithm/multiobjective/nsgaii.py b/jmetal/algorithm/multiobjective/nsgaii.py
index 5606bdeb..581db207 100644
--- a/jmetal/algorithm/multiobjective/nsgaii.py
+++ b/jmetal/algorithm/multiobjective/nsgaii.py
@@ -1,27 +1,30 @@
import time
-from typing import TypeVar, List, Generator
+from typing import Generator, List, TypeVar
try:
import dask
- from distributed import as_completed, Client
+ from distributed import Client, as_completed
except ImportError:
pass
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
from jmetal.config import store
-from jmetal.core.algorithm import DynamicAlgorithm, Algorithm
-from jmetal.core.operator import Mutation, Crossover, Selection
-from jmetal.core.problem import Problem, DynamicProblem
+from jmetal.core.algorithm import Algorithm, DynamicAlgorithm
+from jmetal.core.operator import Crossover, Mutation, Selection
+from jmetal.core.problem import DynamicProblem, Problem
from jmetal.operator import BinaryTournamentSelection
+from jmetal.util.comparator import Comparator, DominanceComparator, MultiComparator
from jmetal.util.density_estimator import CrowdingDistance
from jmetal.util.evaluator import Evaluator
from jmetal.util.ranking import FastNonDominatedRanking
-from jmetal.util.replacement import RankingAndDensityEstimatorReplacement, RemovalPolicyType
-from jmetal.util.comparator import DominanceComparator, Comparator, MultiComparator
+from jmetal.util.replacement import (
+ RankingAndDensityEstimatorReplacement,
+ RemovalPolicyType,
+)
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: NSGA-II
@@ -33,20 +36,21 @@
class NSGAII(GeneticAlgorithm[S, R]):
-
- def __init__(self,
- problem: Problem,
- population_size: int,
- offspring_population_size: int,
- mutation: Mutation,
- crossover: Crossover,
- selection: Selection = BinaryTournamentSelection(
- MultiComparator([FastNonDominatedRanking.get_comparator(),
- CrowdingDistance.get_comparator()])),
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator,
- dominance_comparator: Comparator = store.default_comparator):
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ offspring_population_size: int,
+ mutation: Mutation,
+ crossover: Crossover,
+ selection: Selection = BinaryTournamentSelection(
+ MultiComparator([FastNonDominatedRanking.get_comparator(), CrowdingDistance.get_comparator()])
+ ),
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ dominance_comparator: Comparator = store.default_comparator,
+ ):
"""
NSGA-II implementation as described in
@@ -64,7 +68,6 @@ def __init__(self,
:param population_size: Size of the population.
:param mutation: Mutation operator (see :py:mod:`jmetal.operator.mutation`).
:param crossover: Crossover operator (see :py:mod:`jmetal.operator.crossover`).
- :param selection: Selection operator (see :py:mod:`jmetal.operator.selection`).
"""
super(NSGAII, self).__init__(
problem=problem,
@@ -75,12 +78,12 @@ def __init__(self,
selection=selection,
termination_criterion=termination_criterion,
population_evaluator=population_evaluator,
- population_generator=population_generator
+ population_generator=population_generator,
)
self.dominance_comparator = dominance_comparator
def replacement(self, population: List[S], offspring_population: List[S]) -> List[List[S]]:
- """ This method joins the current and offspring populations to produce the population of the next generation
+ """This method joins the current and offspring populations to produce the population of the next generation
by applying the ranking and crowding distance selection.
:param population: Parent population.
@@ -95,28 +98,29 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
return solutions
- def get_result(self) -> R:
+ def result(self) -> R:
return self.solutions
def get_name(self) -> str:
- return 'NSGAII'
+ return "NSGAII"
class DynamicNSGAII(NSGAII[S, R], DynamicAlgorithm):
-
- def __init__(self,
- problem: DynamicProblem[S],
- population_size: int,
- offspring_population_size: int,
- mutation: Mutation,
- crossover: Crossover,
- selection: Selection = BinaryTournamentSelection(
- MultiComparator([FastNonDominatedRanking.get_comparator(),
- CrowdingDistance.get_comparator()])),
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator,
- dominance_comparator: DominanceComparator = DominanceComparator()):
+ def __init__(
+ self,
+ problem: DynamicProblem[S],
+ population_size: int,
+ offspring_population_size: int,
+ mutation: Mutation,
+ crossover: Crossover,
+ selection: Selection = BinaryTournamentSelection(
+ MultiComparator([FastNonDominatedRanking.get_comparator(), CrowdingDistance.get_comparator()])
+ ),
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ dominance_comparator: DominanceComparator = DominanceComparator(),
+ ):
super(DynamicNSGAII, self).__init__(
problem=problem,
population_size=population_size,
@@ -127,7 +131,8 @@ def __init__(self,
population_evaluator=population_evaluator,
population_generator=population_generator,
termination_criterion=termination_criterion,
- dominance_comparator=dominance_comparator)
+ dominance_comparator=dominance_comparator,
+ )
self.completed_iterations = 0
self.start_computing_time = 0
self.total_computing_time = 0
@@ -140,15 +145,15 @@ def update_progress(self):
self.restart()
self.problem.clear_changed()
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
self.evaluations += self.offspring_population_size
def stopping_condition_is_met(self):
if self.termination_criterion.is_met:
- observable_data = self.get_observable_data()
- observable_data['TERMINATION_CRITERIA_IS_MET'] = True
+ observable_data = self.observable_data()
+ observable_data["TERMINATION_CRITERIA_IS_MET"] = True
self.observable.notify_all(**observable_data)
self.restart()
@@ -158,19 +163,20 @@ def stopping_condition_is_met(self):
class DistributedNSGAII(Algorithm[S, R]):
-
- def __init__(self,
- problem: Problem,
- population_size: int,
- mutation: Mutation,
- crossover: Crossover,
- number_of_cores: int,
- client,
- selection: Selection = BinaryTournamentSelection(
- MultiComparator([FastNonDominatedRanking.get_comparator(),
- CrowdingDistance.get_comparator()])),
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- dominance_comparator: DominanceComparator = DominanceComparator()):
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ mutation: Mutation,
+ crossover: Crossover,
+ number_of_cores: int,
+ client,
+ selection: Selection = BinaryTournamentSelection(
+ MultiComparator([FastNonDominatedRanking.get_comparator(), CrowdingDistance.get_comparator()])
+ ),
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ dominance_comparator: DominanceComparator = DominanceComparator(),
+ ):
super(DistributedNSGAII, self).__init__()
self.problem = problem
self.population_size = population_size
@@ -194,29 +200,31 @@ def evaluate(self, solutions: List[S]) -> List[S]:
def stopping_condition_is_met(self) -> bool:
return self.termination_criterion.is_met
- def get_observable_data(self) -> dict:
+ def observable_data(self) -> dict:
ctime = time.time() - self.start_computing_time
- return {'PROBLEM': self.problem,
- 'EVALUATIONS': self.evaluations,
- 'SOLUTIONS': self.get_result(),
- 'COMPUTING_TIME': ctime}
+ return {
+ "PROBLEM": self.problem,
+ "EVALUATIONS": self.evaluations,
+ "SOLUTIONS": self.result(),
+ "COMPUTING_TIME": ctime,
+ }
def init_progress(self) -> None:
self.evaluations = self.number_of_cores
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
def step(self) -> None:
pass
def update_progress(self):
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
def run(self):
- """ Execute the algorithm. """
+ """Execute the algorithm."""
self.start_computing_time = time.time()
create_solution = dask.delayed(self.problem.create_solution)
@@ -273,8 +281,9 @@ def run(self):
mating_population.append(solution)
# Reproduction and evaluation
- new_task = self.client.submit(reproduction, mating_population, self.problem,
- self.crossover_operator, self.mutation_operator)
+ new_task = self.client.submit(
+ reproduction, mating_population, self.problem, self.crossover_operator, self.mutation_operator
+ )
task_pool.add(new_task)
# update progress
@@ -292,11 +301,11 @@ def run(self):
for future, _ in task_pool:
future.cancel()
- def get_result(self) -> R:
+ def result(self) -> R:
return self.solutions
def get_name(self) -> str:
- return 'dNSGA-II'
+ return "dNSGA-II"
def reproduction(mating_population: List[S], problem, crossover_operator, mutation_operator) -> S:
diff --git a/jmetal/algorithm/multiobjective/nsgaiii.py b/jmetal/algorithm/multiobjective/nsgaiii.py
index 1b8de042..fa80bc02 100644
--- a/jmetal/algorithm/multiobjective/nsgaiii.py
+++ b/jmetal/algorithm/multiobjective/nsgaiii.py
@@ -1,5 +1,5 @@
-from abc import abstractmethod, ABC
-from typing import TypeVar, List
+from abc import ABC, abstractmethod
+from typing import List, TypeVar
import numpy as np
from numpy.linalg import LinAlgError
@@ -7,7 +7,7 @@
from jmetal.algorithm.multiobjective.nsgaii import NSGAII
from jmetal.config import store
-from jmetal.core.operator import Mutation, Crossover, Selection
+from jmetal.core.operator import Crossover, Mutation, Selection
from jmetal.core.problem import Problem
from jmetal.operator import BinaryTournamentSelection
from jmetal.util.comparator import Comparator, MultiComparator
@@ -17,8 +17,8 @@
from jmetal.util.ranking import FastNonDominatedRanking
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: NSGA-III
@@ -30,7 +30,6 @@
class ReferenceDirectionFactory(ABC):
-
def __init__(self, n_dim: int, scaling=None) -> None:
self.n_dim = n_dim
self.scaling = scaling
@@ -50,7 +49,6 @@ def _compute(self):
class UniformReferenceDirectionFactory(ReferenceDirectionFactory):
-
def __init__(self, n_dim: int, scaling=None, n_points: int = None, n_partitions: int = None) -> None:
super().__init__(n_dim, scaling)
if n_points is not None:
@@ -77,8 +75,7 @@ def __uniform_reference_directions(self, ref_dirs, ref_dir, n_partitions: int, b
else:
for i in range(beta + 1):
ref_dir[depth] = 1.0 * i / (1.0 * n_partitions)
- self.__uniform_reference_directions(ref_dirs, np.copy(ref_dir), n_partitions, beta - i,
- depth + 1)
+ self.__uniform_reference_directions(ref_dirs, np.copy(ref_dir), n_partitions, beta - i, depth + 1)
@staticmethod
def get_partition_closest_to_points(n_points, n_dim):
@@ -100,7 +97,7 @@ def get_n_points(n_partitions, n_dim):
def get_extreme_points(F, n_objs, ideal_point, extreme_points=None):
- """ Calculate the Achievement Scalarization Function which is used for the extreme point decomposition. """
+ """Calculate the Achievement Scalarization Function which is used for the extreme point decomposition."""
asf = np.eye(n_objs)
asf[asf == 0] = 1e6
@@ -122,7 +119,7 @@ def get_extreme_points(F, n_objs, ideal_point, extreme_points=None):
def get_nadir_point(extreme_points, ideal_point, worst_point, worst_of_front, worst_of_population):
- """ Calculate the axis intersects for a set of individuals and its extremes (construct hyperplane). """
+ """Calculate the axis intersects for a set of individuals and its extremes (construct hyperplane)."""
try:
# find the intercepts using gaussian elimination
M = extreme_points - ideal_point
@@ -181,7 +178,7 @@ def niching(pop: List[S], n_remaining: int, niche_count, niche_of_individuals, d
# add the selected individual to the survivors
mask[next_ind] = False
- pop[next_ind].attributes['is_closest'] = is_closest
+ pop[next_ind].attributes["is_closest"] = is_closest
survivors.append(int(next_ind))
# increase the corresponding niche count
@@ -191,7 +188,7 @@ def niching(pop: List[S], n_remaining: int, niche_count, niche_of_individuals, d
def associate_to_niches(F, niches, ideal_point, nadir_point, utopian_epsilon: float = 0.0):
- """ Associate each solution to a reference point. """
+ """Associate each solution to a reference point."""
utopian_point = ideal_point - utopian_epsilon
denom = nadir_point - utopian_point
@@ -230,26 +227,27 @@ def compute_niche_count(n_niches: int, niche_of_individuals):
class NSGAIII(NSGAII):
-
- def __init__(self,
- reference_directions,
- problem: Problem,
- mutation: Mutation,
- crossover: Crossover,
- population_size: int = None,
- selection: Selection = BinaryTournamentSelection(
- MultiComparator([FastNonDominatedRanking.get_comparator(),
- CrowdingDistance.get_comparator()])),
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator,
- dominance_comparator: Comparator = store.default_comparator):
+ def __init__(
+ self,
+ reference_directions,
+ problem: Problem,
+ mutation: Mutation,
+ crossover: Crossover,
+ population_size: int = None,
+ selection: Selection = BinaryTournamentSelection(
+ MultiComparator([FastNonDominatedRanking.get_comparator(), CrowdingDistance.get_comparator()])
+ ),
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ dominance_comparator: Comparator = store.default_comparator,
+ ):
self.reference_directions = reference_directions.compute()
if not population_size:
population_size = len(self.reference_directions)
- if self.reference_directions.shape[1] != problem.number_of_objectives:
- raise Exception('Dimensionality of reference points must be equal to the number of objectives')
+ if self.reference_directions.shape[1] != problem.number_of_objectives():
+ raise Exception("Dimensionality of reference points must be equal to the number of objectives")
super(NSGAIII, self).__init__(
problem=problem,
@@ -261,15 +259,15 @@ def __init__(self,
termination_criterion=termination_criterion,
population_evaluator=population_evaluator,
population_generator=population_generator,
- dominance_comparator=dominance_comparator
+ dominance_comparator=dominance_comparator,
)
self.extreme_points = None
- self.ideal_point = np.full(self.problem.number_of_objectives, np.inf)
- self.worst_point = np.full(self.problem.number_of_objectives, -np.inf)
+ self.ideal_point = np.full(self.problem.number_of_objectives(), np.inf)
+ self.worst_point = np.full(self.problem.number_of_objectives(), -np.inf)
def replacement(self, population: List[S], offspring_population: List[S]) -> List[S]:
- """ Implements NSGA-III environmental selection based on reference points as described in:
+ """Implements NSGA-III environmental selection based on reference points as described in:
* Deb, K., & Jain, H. (2014). An Evolutionary Many-Objective Optimization
Algorithm Using Reference-Point-Based Nondominated Sorting Approach,
@@ -290,20 +288,24 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
fronts, non_dominated = ranking.ranked_sublists, ranking.get_subfront(0)
# find the extreme points for normalization
- self.extreme_points = get_extreme_points(F=np.array([s.objectives for s in non_dominated]),
- n_objs=self.problem.number_of_objectives,
- ideal_point=self.ideal_point,
- extreme_points=self.extreme_points)
+ self.extreme_points = get_extreme_points(
+ F=np.array([s.objectives for s in non_dominated]),
+ n_objs=self.problem.number_of_objectives(),
+ ideal_point=self.ideal_point,
+ extreme_points=self.extreme_points,
+ )
# find the intercepts for normalization and do backup if gaussian elimination fails
worst_of_population = np.max(F, axis=0)
worst_of_front = np.max(np.array([s.objectives for s in non_dominated]), axis=0)
- nadir_point = get_nadir_point(extreme_points=self.extreme_points,
- ideal_point=self.ideal_point,
- worst_point=self.worst_point,
- worst_of_population=worst_of_population,
- worst_of_front=worst_of_front)
+ nadir_point = get_nadir_point(
+ extreme_points=self.extreme_points,
+ ideal_point=self.ideal_point,
+ worst_point=self.worst_point,
+ worst_of_population=worst_of_population,
+ worst_of_front=worst_of_front,
+ )
# consider only the population until we come to the splitting front
pop = np.concatenate(ranking.ranked_sublists)
@@ -318,10 +320,9 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
last_front = np.array(fronts[-1])
# associate individuals to niches
- niche_of_individuals, dist_to_niche = associate_to_niches(F=F,
- niches=self.reference_directions,
- ideal_point=self.ideal_point,
- nadir_point=nadir_point)
+ niche_of_individuals, dist_to_niche = associate_to_niches(
+ F=F, niches=self.reference_directions, ideal_point=self.ideal_point, nadir_point=nadir_point
+ )
# if we need to select individuals to survive
if len(pop) > self.population_size:
@@ -333,27 +334,30 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
# if some individuals already survived
else:
until_last_front = np.concatenate(fronts[:-1])
- niche_count = compute_niche_count(len(self.reference_directions),
- niche_of_individuals[until_last_front])
+ niche_count = compute_niche_count(
+ len(self.reference_directions), niche_of_individuals[until_last_front]
+ )
n_remaining = self.population_size - len(until_last_front)
- S_idx = niching(pop=pop[last_front],
- n_remaining=n_remaining,
- niche_count=niche_count,
- niche_of_individuals=niche_of_individuals[last_front],
- dist_to_niche=dist_to_niche[last_front])
+ S_idx = niching(
+ pop=pop[last_front],
+ n_remaining=n_remaining,
+ niche_count=niche_count,
+ niche_of_individuals=niche_of_individuals[last_front],
+ dist_to_niche=dist_to_niche[last_front],
+ )
survivors_idx = np.concatenate((until_last_front, last_front[S_idx].tolist()))
pop = pop[survivors_idx]
return list(pop)
- def get_result(self):
- """ Return only non dominated solutions."""
+ def result(self):
+ """Return only non dominated solutions."""
ranking = FastNonDominatedRanking(self.dominance_comparator)
ranking.compute_ranking(self.solutions, k=self.population_size)
return ranking.get_subfront(0)
def get_name(self) -> str:
- return 'NSGAIII'
+ return "NSGAIII"
diff --git a/jmetal/algorithm/multiobjective/omopso.py b/jmetal/algorithm/multiobjective/omopso.py
index fb07555e..ab6b6727 100644
--- a/jmetal/algorithm/multiobjective/omopso.py
+++ b/jmetal/algorithm/multiobjective/omopso.py
@@ -1,7 +1,6 @@
import random
from copy import copy
-from math import sqrt
-from typing import TypeVar, List, Optional
+from typing import List, Optional, TypeVar
import numpy
@@ -17,7 +16,7 @@
from jmetal.util.generator import Generator
from jmetal.util.termination_criterion import TerminationCriterion
-R = TypeVar('R')
+R = TypeVar("R")
"""
.. module:: OMOPSO
@@ -29,18 +28,19 @@
class OMOPSO(ParticleSwarmOptimization):
-
- def __init__(self,
- problem: FloatProblem,
- swarm_size: int,
- uniform_mutation: UniformMutation,
- non_uniform_mutation: NonUniformMutation,
- leaders: Optional[BoundedArchive],
- epsilon: float,
- termination_criterion: TerminationCriterion,
- swarm_generator: Generator = store.default_generator,
- swarm_evaluator: Evaluator = store.default_evaluator):
- """ This class implements the OMOPSO algorithm as described in
+ def __init__(
+ self,
+ problem: FloatProblem,
+ swarm_size: int,
+ uniform_mutation: UniformMutation,
+ non_uniform_mutation: NonUniformMutation,
+ leaders: Optional[BoundedArchive],
+ epsilon: float,
+ termination_criterion: TerminationCriterion,
+ swarm_generator: Generator = store.default_generator,
+ swarm_evaluator: Evaluator = store.default_evaluator,
+ ):
+ """This class implements the OMOPSO algorithm as described in
todo Update this reference
* SMPSO: A new PSO-based metaheuristic for multi-objective optimization
@@ -52,9 +52,7 @@ def __init__(self,
:param swarm_size: Size of the swarm.
:param leaders: Archive for leaders.
"""
- super(OMOPSO, self).__init__(
- problem=problem,
- swarm_size=swarm_size)
+ super(OMOPSO, self).__init__(problem=problem, swarm_size=swarm_size)
self.swarm_generator = swarm_generator
self.swarm_evaluator = swarm_evaluator
@@ -84,7 +82,7 @@ def __init__(self,
self.dominance_comparator = DominanceComparator()
- self.speed = numpy.zeros((self.swarm_size, self.problem.number_of_variables), dtype=float)
+ self.speed = numpy.zeros((self.swarm_size, self.problem.number_of_variables()), dtype=float)
def create_initial_solutions(self) -> List[FloatSolution]:
return [self.swarm_generator.new(self.problem) for _ in range(self.swarm_size)]
@@ -102,16 +100,16 @@ def initialize_global_best(self, swarm: List[FloatSolution]) -> None:
def initialize_particle_best(self, swarm: List[FloatSolution]) -> None:
for particle in swarm:
- particle.attributes['local_best'] = copy(particle)
+ particle.attributes["local_best"] = copy(particle)
def initialize_velocity(self, swarm: List[FloatSolution]) -> None:
for i in range(self.swarm_size):
- for j in range(self.problem.number_of_variables):
+ for j in range(self.problem.number_of_variables()):
self.speed[i][j] = 0.0
def update_velocity(self, swarm: List[FloatSolution]) -> None:
for i in range(self.swarm_size):
- best_particle = copy(swarm[i].attributes['local_best'])
+ best_particle = copy(swarm[i].attributes["local_best"])
best_global = self.select_global_best()
r1 = round(random.uniform(self.r1_min, self.r1_max), 1)
@@ -121,9 +119,11 @@ def update_velocity(self, swarm: List[FloatSolution]) -> None:
w = round(random.uniform(self.weight_min, self.weight_max), 1)
for var in range(swarm[i].number_of_variables):
- self.speed[i][var] = w * self.speed[i][var] \
- + (c1 * r1 * (best_particle.variables[var] - swarm[i].variables[var])) \
- + (c2 * r2 * (best_global.variables[var] - swarm[i].variables[var]))
+ self.speed[i][var] = (
+ w * self.speed[i][var]
+ + (c1 * r1 * (best_particle.variables[var] - swarm[i].variables[var]))
+ + (c2 * r2 * (best_global.variables[var] - swarm[i].variables[var]))
+ )
def update_position(self, swarm: List[FloatSolution]) -> None:
for i in range(self.swarm_size):
@@ -147,11 +147,9 @@ def update_global_best(self, swarm: List[FloatSolution]) -> None:
def update_particle_best(self, swarm: List[FloatSolution]) -> None:
for i in range(self.swarm_size):
- flag = self.dominance_comparator.compare(
- swarm[i],
- swarm[i].attributes['local_best'])
+ flag = self.dominance_comparator.compare(swarm[i], swarm[i].attributes["local_best"])
if flag != 1:
- swarm[i].attributes['local_best'] = copy(swarm[i])
+ swarm[i].attributes["local_best"] = copy(swarm[i])
def perturbation(self, swarm: List[FloatSolution]) -> None:
self.non_uniform_mutation.set_current_iteration(self.evaluations / self.swarm_size)
@@ -176,27 +174,6 @@ def select_global_best(self) -> FloatSolution:
return best_global
- def __velocity_constriction(self, value: float, delta_max: [], delta_min: [], variable_index: int) -> float:
- result = value
- if value > delta_max[variable_index]:
- result = delta_max[variable_index]
- if value < delta_min[variable_index]:
- result = delta_min[variable_index]
-
- return result
-
- def __inertia_weight(self, wmax: float):
- return wmax
-
- def __constriction_coefficient(self, c1: float, c2: float) -> float:
- rho = c1 + c2
- if rho <= 4:
- result = 1.0
- else:
- result = 2.0 / (2.0 - rho - sqrt(pow(rho, 2.0) - 4.0 * rho))
-
- return result
-
def init_progress(self) -> None:
self.evaluations = self.swarm_size
self.leaders.compute_density_estimator()
@@ -209,12 +186,12 @@ def update_progress(self) -> None:
self.evaluations += self.swarm_size
self.leaders.compute_density_estimator()
- observable_data = self.get_observable_data()
- observable_data['SOLUTIONS'] = self.epsilon_archive.solution_list
+ observable_data = self.observable_data()
+ observable_data["SOLUTIONS"] = self.epsilon_archive.solution_list
self.observable.notify_all(**observable_data)
- def get_result(self) -> List[FloatSolution]:
+ def result(self) -> List[FloatSolution]:
return self.epsilon_archive.solution_list
def get_name(self) -> str:
- return 'OMOPSO'
+ return "OMOPSO"
diff --git a/jmetal/algorithm/multiobjective/random_search.py b/jmetal/algorithm/multiobjective/random_search.py
index 867167a8..f37af534 100644
--- a/jmetal/algorithm/multiobjective/random_search.py
+++ b/jmetal/algorithm/multiobjective/random_search.py
@@ -1,5 +1,5 @@
import time
-from typing import TypeVar, List
+from typing import List, TypeVar
from jmetal.config import store
from jmetal.core.algorithm import Algorithm
@@ -7,8 +7,8 @@
from jmetal.util.archive import NonDominatedSolutionsArchive
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: RamdomSearch
@@ -20,10 +20,9 @@
class RandomSearch(Algorithm[S, R]):
-
- def __init__(self,
- problem: Problem[S],
- termination_criterion: TerminationCriterion = store.default_termination_criteria):
+ def __init__(
+ self, problem: Problem[S], termination_criterion: TerminationCriterion = store.default_termination_criteria
+ ):
super().__init__()
self.problem = problem
self.termination_criterion = termination_criterion
@@ -31,10 +30,14 @@ def __init__(self,
self.archive = NonDominatedSolutionsArchive()
- def get_observable_data(self) -> dict:
+ def observable_data(self) -> dict:
ctime = time.time() - self.start_computing_time
- return {'PROBLEM': self.problem, 'EVALUATIONS': self.evaluations, 'SOLUTIONS': self.get_result(),
- 'COMPUTING_TIME': ctime}
+ return {
+ "PROBLEM": self.problem,
+ "EVALUATIONS": self.evaluations,
+ "SOLUTIONS": self.result(),
+ "COMPUTING_TIME": ctime,
+ }
def create_initial_solutions(self) -> List[S]:
return [self.problem.create_solution()]
@@ -45,7 +48,7 @@ def evaluate(self, solution_list: List[S]) -> List[S]:
def init_progress(self) -> None:
self.evaluations = 1
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
def stopping_condition_is_met(self) -> bool:
@@ -59,15 +62,15 @@ def step(self) -> None:
def update_progress(self) -> None:
self.evaluations += 1
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
- def get_result(self) -> List[S]:
+ def result(self) -> List[S]:
return self.archive.solution_list
def get_name(self) -> str:
- return 'Random Search'
+ return "Random Search"
@property
def label(self) -> str:
- return f'{self.get_name()}.{self.problem.get_name()}'
\ No newline at end of file
+ return f"{self.get_name()}.{self.problem.name()}"
diff --git a/jmetal/algorithm/multiobjective/smpso.py b/jmetal/algorithm/multiobjective/smpso.py
index 4e50d914..bcfac7b2 100644
--- a/jmetal/algorithm/multiobjective/smpso.py
+++ b/jmetal/algorithm/multiobjective/smpso.py
@@ -2,22 +2,22 @@
import threading
from copy import copy
from math import sqrt
-from typing import TypeVar, List, Optional
+from typing import List, Optional, TypeVar
import numpy
from jmetal.config import store
-from jmetal.core.algorithm import ParticleSwarmOptimization, DynamicAlgorithm
+from jmetal.core.algorithm import DynamicAlgorithm, ParticleSwarmOptimization
from jmetal.core.operator import Mutation
-from jmetal.core.problem import FloatProblem, DynamicProblem
+from jmetal.core.problem import DynamicProblem, FloatProblem
from jmetal.core.solution import FloatSolution
-from jmetal.util.archive import BoundedArchive, ArchiveWithReferencePoint
-from jmetal.util.comparator import DominanceComparator
+from jmetal.util.archive import ArchiveWithReferencePoint, BoundedArchive
+from jmetal.util.comparator import DominanceComparator, Comparator
from jmetal.util.evaluator import Evaluator
from jmetal.util.generator import Generator
from jmetal.util.termination_criterion import TerminationCriterion
-R = TypeVar('R')
+R = TypeVar("R")
"""
.. module:: SMPSO
@@ -29,16 +29,18 @@
class SMPSO(ParticleSwarmOptimization):
-
- def __init__(self,
- problem: FloatProblem,
- swarm_size: int,
- mutation: Mutation,
- leaders: Optional[BoundedArchive],
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- swarm_generator: Generator = store.default_generator,
- swarm_evaluator: Evaluator = store.default_evaluator):
- """ This class implements the SMPSO algorithm as described in
+ def __init__(
+ self,
+ problem: FloatProblem,
+ swarm_size: int,
+ mutation: Mutation,
+ leaders: Optional[BoundedArchive],
+ dominance_comparator: Comparator = DominanceComparator(),
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ swarm_generator: Generator = store.default_generator,
+ swarm_evaluator: Evaluator = store.default_evaluator,
+ ):
+ """This class implements the SMPSO algorithm as described in
* SMPSO: A new PSO-based metaheuristic for multi-objective optimization
* MCDM 2009. DOI: ``_.
@@ -52,9 +54,7 @@ def __init__(self,
:param mutation: Mutation operator (see :py:mod:`jmetal.operator.mutation`).
:param leaders: Archive for leaders.
"""
- super(SMPSO, self).__init__(
- problem=problem,
- swarm_size=swarm_size)
+ super(SMPSO, self).__init__(problem=problem, swarm_size=swarm_size)
self.swarm_generator = swarm_generator
self.swarm_evaluator = swarm_evaluator
self.termination_criterion = termination_criterion
@@ -75,11 +75,13 @@ def __init__(self,
self.change_velocity1 = -1
self.change_velocity2 = -1
- self.dominance_comparator = DominanceComparator()
+ self.dominance_comparator = dominance_comparator
- self.speed = numpy.zeros((self.swarm_size, self.problem.number_of_variables), dtype=float)
- self.delta_max, self.delta_min = numpy.empty(problem.number_of_variables), \
- numpy.empty(problem.number_of_variables)
+ self.speed = numpy.zeros((self.swarm_size, self.problem.number_of_variables()), dtype=float)
+ self.delta_max, self.delta_min = (
+ numpy.empty(problem.number_of_variables()),
+ numpy.empty(problem.number_of_variables()),
+ )
def create_initial_solutions(self) -> List[FloatSolution]:
return [self.swarm_generator.new(self.problem) for _ in range(self.swarm_size)]
@@ -96,17 +98,17 @@ def initialize_global_best(self, swarm: List[FloatSolution]) -> None:
def initialize_particle_best(self, swarm: List[FloatSolution]) -> None:
for particle in swarm:
- particle.attributes['local_best'] = copy(particle)
+ particle.attributes["local_best"] = copy(particle)
def initialize_velocity(self, swarm: List[FloatSolution]) -> None:
- for i in range(self.problem.number_of_variables):
+ for i in range(self.problem.number_of_variables()):
self.delta_max[i] = (self.problem.upper_bound[i] - self.problem.lower_bound[i]) / 2.0
self.delta_min = -1.0 * self.delta_max
def update_velocity(self, swarm: List[FloatSolution]) -> None:
for i in range(self.swarm_size):
- best_particle = copy(swarm[i].attributes['local_best'])
+ best_particle = copy(swarm[i].attributes["local_best"])
best_global = self.select_global_best()
r1 = round(random.uniform(self.r1_min, self.r1_max), 1)
@@ -116,22 +118,24 @@ def update_velocity(self, swarm: List[FloatSolution]) -> None:
wmax = self.max_weight
wmin = self.min_weight
- for var in range(swarm[i].number_of_variables):
- self.speed[i][var] = \
- self.__velocity_constriction(
- self.__constriction_coefficient(c1, c2) *
- ((self.__inertia_weight(wmax)
- * self.speed[i][var])
- + (c1 * r1 * (best_particle.variables[var] - swarm[i].variables[var]))
- + (c2 * r2 * (best_global.variables[var] - swarm[i].variables[var]))
- ),
- self.delta_max, self.delta_min, var)
+ for var in range(len(swarm[i].variables)):
+ self.speed[i][var] = self.__velocity_constriction(
+ self.__constriction_coefficient(c1, c2)
+ * (
+ (self.__inertia_weight(wmax) * self.speed[i][var])
+ + (c1 * r1 * (best_particle.variables[var] - swarm[i].variables[var]))
+ + (c2 * r2 * (best_global.variables[var] - swarm[i].variables[var]))
+ ),
+ self.delta_max,
+ self.delta_min,
+ var,
+ )
def update_position(self, swarm: List[FloatSolution]) -> None:
for i in range(self.swarm_size):
particle = swarm[i]
- for j in range(particle.number_of_variables):
+ for j in range(len(particle.variables)):
particle.variables[j] += self.speed[i][j]
if particle.variables[j] < self.problem.lower_bound[j]:
@@ -148,11 +152,9 @@ def update_global_best(self, swarm: List[FloatSolution]) -> None:
def update_particle_best(self, swarm: List[FloatSolution]) -> None:
for i in range(self.swarm_size):
- flag = self.dominance_comparator.compare(
- swarm[i],
- swarm[i].attributes['local_best'])
+ flag = self.dominance_comparator.compare(swarm[i], swarm[i].attributes["local_best"])
if flag != 1:
- swarm[i].attributes['local_best'] = copy(swarm[i])
+ swarm[i].attributes["local_best"] = copy(swarm[i])
def perturbation(self, swarm: List[FloatSolution]) -> None:
for i in range(self.swarm_size):
@@ -207,27 +209,28 @@ def update_progress(self) -> None:
self.evaluations += self.swarm_size
self.leaders.compute_density_estimator()
- observable_data = self.get_observable_data()
- observable_data['SOLUTIONS'] = self.leaders.solution_list
+ observable_data = self.observable_data()
+ observable_data["SOLUTIONS"] = self.leaders.solution_list
self.observable.notify_all(**observable_data)
- def get_result(self) -> List[FloatSolution]:
+ def result(self) -> List[FloatSolution]:
return self.leaders.solution_list
def get_name(self) -> str:
- return 'SMPSO'
+ return "SMPSO"
class DynamicSMPSO(SMPSO, DynamicAlgorithm):
-
- def __init__(self,
- problem: DynamicProblem[FloatSolution],
- swarm_size: int,
- mutation: Mutation,
- leaders: BoundedArchive,
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- swarm_generator: Generator = store.default_generator,
- swarm_evaluator: Evaluator = store.default_evaluator):
+ def __init__(
+ self,
+ problem: DynamicProblem[FloatSolution],
+ swarm_size: int,
+ mutation: Mutation,
+ leaders: BoundedArchive,
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ swarm_generator: Generator = store.default_generator,
+ swarm_evaluator: Evaluator = store.default_evaluator,
+ ):
super(DynamicSMPSO, self).__init__(
problem=problem,
swarm_size=swarm_size,
@@ -235,7 +238,8 @@ def __init__(self,
leaders=leaders,
termination_criterion=termination_criterion,
swarm_generator=swarm_generator,
- swarm_evaluator=swarm_evaluator)
+ swarm_evaluator=swarm_evaluator,
+ )
self.completed_iterations = 0
def restart(self) -> None:
@@ -255,7 +259,7 @@ def update_progress(self):
self.restart()
self.problem.clear_changed()
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
self.evaluations += self.swarm_size
@@ -263,8 +267,8 @@ def update_progress(self):
def stopping_condition_is_met(self):
if self.termination_criterion.is_met:
- observable_data = self.get_observable_data()
- observable_data['termination_criterion_is_met'] = True
+ observable_data = self.observable_data()
+ observable_data["termination_criterion_is_met"] = True
self.observable.notify_all(**observable_data)
self.restart()
@@ -273,17 +277,18 @@ def stopping_condition_is_met(self):
class SMPSORP(SMPSO):
-
- def __init__(self,
- problem: FloatProblem,
- swarm_size: int,
- mutation: Mutation,
- reference_points: List[List[float]],
- leaders: List[ArchiveWithReferencePoint],
- termination_criterion: TerminationCriterion,
- swarm_generator: Generator = store.default_generator,
- swarm_evaluator: Evaluator = store.default_evaluator):
- """ This class implements the SMPSORP algorithm.
+ def __init__(
+ self,
+ problem: FloatProblem,
+ swarm_size: int,
+ mutation: Mutation,
+ reference_points: List[List[float]],
+ leaders: List[ArchiveWithReferencePoint],
+ termination_criterion: TerminationCriterion,
+ swarm_generator: Generator = store.default_generator,
+ swarm_evaluator: Evaluator = store.default_evaluator,
+ ):
+ """This class implements the SMPSORP algorithm.
:param problem: The problem to solve.
:param swarm_size:
@@ -298,7 +303,8 @@ def __init__(self,
leaders=None,
swarm_generator=swarm_generator,
swarm_evaluator=swarm_evaluator,
- termination_criterion=termination_criterion)
+ termination_criterion=termination_criterion,
+ )
self.leaders = leaders
self.reference_points = reference_points
self.lock = threading.Lock()
@@ -356,8 +362,8 @@ def update_progress(self) -> None:
leader.filter()
leader.compute_density_estimator()
- observable_data = self.get_observable_data()
- observable_data['REFERENCE_POINT'] = self.get_reference_point()
+ observable_data = self.observable_data()
+ observable_data["REFERENCE_POINT"] = self.get_reference_point()
self.observable.notify_all(**observable_data)
def update_reference_point(self, new_reference_points: list):
@@ -371,7 +377,7 @@ def get_reference_point(self):
with self.lock:
return self.reference_points
- def get_result(self) -> List[FloatSolution]:
+ def result(self) -> List[FloatSolution]:
result = []
for leader in self.leaders:
@@ -381,22 +387,21 @@ def get_result(self) -> List[FloatSolution]:
return result
def get_name(self) -> str:
- return 'SMPSO/RP'
+ return "SMPSO/RP"
def _change_reference_point(algorithm: SMPSORP):
- """ Auxiliar function to read new reference points from the keyboard for the SMPSO/RP algorithm
- """
+ """Auxiliar function to read new reference points from the keyboard for the SMPSO/RP algorithm"""
number_of_reference_points = len(algorithm.reference_points)
number_of_objectives = algorithm.problem.number_of_objectives
while True:
- print(f'Enter {number_of_reference_points}-points of dimension {number_of_objectives}: ')
+ print(f"Enter {number_of_reference_points}-points of dimension {number_of_objectives}: ")
read = [float(x) for x in input().split()]
# Update reference points
reference_points = []
for i in range(0, len(read), number_of_objectives):
- reference_points.append(read[i:i + number_of_objectives])
+ reference_points.append(read[i : i + number_of_objectives])
algorithm.update_reference_point(reference_points)
diff --git a/jmetal/algorithm/multiobjective/spea2.py b/jmetal/algorithm/multiobjective/spea2.py
index 5b7dea5f..40cc0f1c 100644
--- a/jmetal/algorithm/multiobjective/spea2.py
+++ b/jmetal/algorithm/multiobjective/spea2.py
@@ -1,8 +1,8 @@
-from typing import TypeVar, List
+from typing import List, TypeVar
from jmetal.algorithm.singleobjective.genetic_algorithm import GeneticAlgorithm
from jmetal.config import store
-from jmetal.core.operator import Mutation, Crossover
+from jmetal.core.operator import Crossover, Mutation
from jmetal.core.problem import Problem
from jmetal.operator import BinaryTournamentSelection
from jmetal.util.comparator import Comparator, MultiComparator
@@ -13,8 +13,8 @@
from jmetal.util.replacement import RankingAndDensityEstimatorReplacement, RemovalPolicyType
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: SPEA2
@@ -33,25 +33,27 @@
class SPEA2(GeneticAlgorithm[S, R]):
-
- def __init__(self,
- problem: Problem,
- population_size: int,
- offspring_population_size: int,
- mutation: Mutation,
- crossover: Crossover,
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator,
- dominance_comparator: Comparator = store.default_comparator):
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ offspring_population_size: int,
+ mutation: Mutation,
+ crossover: Crossover,
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ dominance_comparator: Comparator = store.default_comparator,
+ ):
"""
:param problem: The problem to solve.
:param population_size: Size of the population.
:param mutation: Mutation operator (see :py:mod:`jmetal.operator.mutation`).
:param crossover: Crossover operator (see :py:mod:`jmetal.operator.crossover`).
"""
- multi_comparator = MultiComparator([StrengthRanking.get_comparator(),
- KNearestNeighborDensityEstimator.get_comparator()])
+ multi_comparator = MultiComparator(
+ [StrengthRanking.get_comparator(), KNearestNeighborDensityEstimator.get_comparator()]
+ )
selection = BinaryTournamentSelection(comparator=multi_comparator)
super(SPEA2, self).__init__(
@@ -63,12 +65,12 @@ def __init__(self,
selection=selection,
termination_criterion=termination_criterion,
population_evaluator=population_evaluator,
- population_generator=population_generator
+ population_generator=population_generator,
)
self.dominance_comparator = dominance_comparator
def replacement(self, population: List[S], offspring_population: List[S]) -> List[List[S]]:
- """ This method joins the current and offspring populations to produce the population of the next generation
+ """This method joins the current and offspring populations to produce the population of the next generation
by applying the ranking and crowding distance selection.
:param population: Parent population.
@@ -83,8 +85,8 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
return solutions
- def get_result(self) -> R:
+ def result(self) -> R:
return self.solutions
def get_name(self) -> str:
- return 'SPEA2'
+ return "SPEA2"
diff --git a/jmetal/algorithm/singleobjective/evolution_strategy.py b/jmetal/algorithm/singleobjective/evolution_strategy.py
index 2f52a543..0e989c4d 100644
--- a/jmetal/algorithm/singleobjective/evolution_strategy.py
+++ b/jmetal/algorithm/singleobjective/evolution_strategy.py
@@ -1,16 +1,16 @@
from copy import copy
-from typing import TypeVar, List
+from typing import List, TypeVar
from jmetal.core.algorithm import EvolutionaryAlgorithm
from jmetal.core.operator import Mutation
from jmetal.core.problem import Problem
+from jmetal.util.constraint_handling import overall_constraint_violation_degree
from jmetal.util.evaluator import Evaluator, SequentialEvaluator
from jmetal.util.generator import Generator, RandomGenerator
from jmetal.util.termination_criterion import TerminationCriterion
-from jmetal.util.constraint_handling import overall_constraint_violation_degree
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: evolutionary_algorithm
@@ -22,20 +22,18 @@
class EvolutionStrategy(EvolutionaryAlgorithm[S, R]):
-
- def __init__(self,
- problem: Problem,
- mu: int,
- lambda_: int,
- elitist: bool,
- mutation: Mutation,
- termination_criterion: TerminationCriterion,
- population_generator: Generator = RandomGenerator(),
- population_evaluator: Evaluator = SequentialEvaluator()):
- super(EvolutionStrategy, self).__init__(
- problem=problem,
- population_size=mu,
- offspring_population_size=lambda_)
+ def __init__(
+ self,
+ problem: Problem,
+ mu: int,
+ lambda_: int,
+ elitist: bool,
+ mutation: Mutation,
+ termination_criterion: TerminationCriterion,
+ population_generator: Generator = RandomGenerator(),
+ population_evaluator: Evaluator = SequentialEvaluator(),
+ ):
+ super(EvolutionStrategy, self).__init__(problem=problem, population_size=mu, offspring_population_size=lambda_)
self.mu = mu
self.lambda_ = lambda_
self.elitist = elitist
@@ -49,8 +47,7 @@ def __init__(self,
self.observable.register(termination_criterion)
def create_initial_solutions(self) -> List[S]:
- return [self.population_generator.new(self.problem)
- for _ in range(self.population_size)]
+ return [self.population_generator.new(self.problem) for _ in range(self.population_size)]
def evaluate(self, solution_list: List[S]):
return self.population_evaluator.evaluate(solution_list, self.problem)
@@ -87,8 +84,8 @@ def replacement(self, population: List[S], offspring_population: List[S]) -> Lis
return new_population
- def get_result(self) -> R:
+ def result(self) -> R:
return self.solutions[0]
def get_name(self) -> str:
- return 'Elitist evolution Strategy'
+ return "Elitist evolution Strategy"
diff --git a/jmetal/algorithm/singleobjective/genetic_algorithm.py b/jmetal/algorithm/singleobjective/genetic_algorithm.py
index 8216625d..5656ee50 100644
--- a/jmetal/algorithm/singleobjective/genetic_algorithm.py
+++ b/jmetal/algorithm/singleobjective/genetic_algorithm.py
@@ -1,15 +1,18 @@
-from typing import TypeVar, List
+from functools import cmp_to_key
+from typing import List, TypeVar
from jmetal.config import store
from jmetal.core.algorithm import EvolutionaryAlgorithm
-from jmetal.core.operator import Mutation, Crossover, Selection
+from jmetal.core.operator import Crossover, Mutation, Selection
from jmetal.core.problem import Problem
+from jmetal.operator import BinaryTournamentSelection
+from jmetal.util.comparator import Comparator, ObjectiveComparator
from jmetal.util.evaluator import Evaluator
from jmetal.util.generator import Generator
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: genetic_algorithm
@@ -20,23 +23,26 @@
class GeneticAlgorithm(EvolutionaryAlgorithm[S, R]):
-
- def __init__(self,
- problem: Problem,
- population_size: int,
- offspring_population_size: int,
- mutation: Mutation,
- crossover: Crossover,
- selection: Selection,
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- population_generator: Generator = store.default_generator,
- population_evaluator: Evaluator = store.default_evaluator):
+ def __init__(
+ self,
+ problem: Problem,
+ population_size: int,
+ offspring_population_size: int,
+ mutation: Mutation,
+ crossover: Crossover,
+ selection: Selection = BinaryTournamentSelection(ObjectiveComparator(0)),
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ population_generator: Generator = store.default_generator,
+ population_evaluator: Evaluator = store.default_evaluator,
+ solution_comparator: Comparator = ObjectiveComparator(0)
+ ):
super(GeneticAlgorithm, self).__init__(
- problem=problem,
- population_size=population_size,
- offspring_population_size=offspring_population_size)
+ problem=problem, population_size=population_size, offspring_population_size=offspring_population_size
+ )
self.mutation_operator = mutation
self.crossover_operator = crossover
+ self.solution_comparator = solution_comparator
+
self.selection_operator = selection
self.population_generator = population_generator
@@ -45,16 +51,17 @@ def __init__(self,
self.termination_criterion = termination_criterion
self.observable.register(termination_criterion)
- self.mating_pool_size = \
- self.offspring_population_size * \
- self.crossover_operator.get_number_of_parents() // self.crossover_operator.get_number_of_children()
+ self.mating_pool_size = (
+ self.offspring_population_size
+ * self.crossover_operator.get_number_of_parents()
+ // self.crossover_operator.get_number_of_children()
+ )
if self.mating_pool_size < self.crossover_operator.get_number_of_children():
self.mating_pool_size = self.crossover_operator.get_number_of_children()
def create_initial_solutions(self) -> List[S]:
- return [self.population_generator.new(self.problem)
- for _ in range(self.population_size)]
+ return [self.population_generator.new(self.problem) for _ in range(self.population_size)]
def evaluate(self, population: List[S]):
return self.population_evaluator.evaluate(population, self.problem)
@@ -65,7 +72,7 @@ def stopping_condition_is_met(self) -> bool:
def selection(self, population: List[S]):
mating_population = []
- for i in range(self.mating_pool_size):
+ for _ in range(self.mating_pool_size):
solution = self.selection_operator.execute(population)
mating_population.append(solution)
@@ -75,7 +82,7 @@ def reproduction(self, mating_population: List[S]) -> List[S]:
number_of_parents_to_combine = self.crossover_operator.get_number_of_parents()
if len(mating_population) % number_of_parents_to_combine != 0:
- raise Exception('Wrong number of parents')
+ raise Exception("Wrong number of parents")
offspring_population = []
for i in range(0, self.offspring_population_size, number_of_parents_to_combine):
@@ -96,12 +103,12 @@ def reproduction(self, mating_population: List[S]) -> List[S]:
def replacement(self, population: List[S], offspring_population: List[S]) -> List[S]:
population.extend(offspring_population)
- population.sort(key=lambda s: s.objectives[0])
+ population.sort(key=cmp_to_key(self.solution_comparator.compare))
- return population[:self.population_size]
+ return population[: self.population_size]
- def get_result(self) -> R:
+ def result(self) -> R:
return self.solutions[0]
def get_name(self) -> str:
- return 'Genetic algorithm'
+ return "Genetic algorithm"
diff --git a/jmetal/algorithm/singleobjective/local_search.py b/jmetal/algorithm/singleobjective/local_search.py
index 53b2c146..1774e804 100644
--- a/jmetal/algorithm/singleobjective/local_search.py
+++ b/jmetal/algorithm/singleobjective/local_search.py
@@ -2,7 +2,7 @@
import random
import threading
import time
-from typing import TypeVar, List
+from typing import List, TypeVar
from jmetal.config import store
from jmetal.core.algorithm import Algorithm
@@ -12,8 +12,8 @@
from jmetal.util.comparator import Comparator
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: local_search
@@ -25,12 +25,13 @@
class LocalSearch(Algorithm[S, R], threading.Thread):
-
- def __init__(self,
- problem: Problem[S],
- mutation: Mutation,
- termination_criterion: TerminationCriterion = store.default_termination_criteria,
- comparator: Comparator = store.default_comparator):
+ def __init__(
+ self,
+ problem: Problem[S],
+ mutation: Mutation,
+ termination_criterion: TerminationCriterion = store.default_termination_criteria,
+ comparator: Comparator = store.default_comparator,
+ ):
super(LocalSearch, self).__init__()
self.comparator = comparator
self.problem = problem
@@ -68,16 +69,20 @@ def step(self) -> None:
def update_progress(self) -> None:
self.evaluations += 1
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
- def get_observable_data(self) -> dict:
+ def observable_data(self) -> dict:
ctime = time.time() - self.start_computing_time
- return {'PROBLEM': self.problem, 'EVALUATIONS': self.evaluations, 'SOLUTIONS': self.get_result(),
- 'COMPUTING_TIME': ctime}
-
- def get_result(self) -> R:
+ return {
+ "PROBLEM": self.problem,
+ "EVALUATIONS": self.evaluations,
+ "SOLUTIONS": self.result(),
+ "COMPUTING_TIME": ctime,
+ }
+
+ def result(self) -> R:
return self.solutions[0]
def get_name(self) -> str:
- return 'LS'
+ return "LS"
diff --git a/jmetal/algorithm/singleobjective/simulated_annealing.py b/jmetal/algorithm/singleobjective/simulated_annealing.py
index 7d36f7c0..a546730d 100644
--- a/jmetal/algorithm/singleobjective/simulated_annealing.py
+++ b/jmetal/algorithm/singleobjective/simulated_annealing.py
@@ -2,7 +2,7 @@
import random
import threading
import time
-from typing import TypeVar, List
+from typing import List, TypeVar
import numpy
@@ -14,8 +14,8 @@
from jmetal.util.generator import Generator
from jmetal.util.termination_criterion import TerminationCriterion
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: simulated_annealing
@@ -27,12 +27,13 @@
class SimulatedAnnealing(Algorithm[S, R], threading.Thread):
-
- def __init__(self,
- problem: Problem[S],
- mutation: Mutation,
- termination_criterion: TerminationCriterion,
- solution_generator: Generator = store.default_generator):
+ def __init__(
+ self,
+ problem: Problem[S],
+ mutation: Mutation,
+ termination_criterion: TerminationCriterion,
+ solution_generator: Generator = store.default_generator,
+ ):
super(SimulatedAnnealing, self).__init__()
self.problem = problem
self.mutation = mutation
@@ -62,9 +63,8 @@ def step(self) -> None:
mutated_solution = self.evaluate([mutated_solution])[0]
acceptance_probability = self.compute_acceptance_probability(
- self.solutions[0].objectives[0],
- mutated_solution.objectives[0],
- self.temperature)
+ self.solutions[0].objectives[0], mutated_solution.objectives[0], self.temperature
+ )
if acceptance_probability > random.random():
self.solutions[0] = mutated_solution
@@ -82,16 +82,20 @@ def compute_acceptance_probability(self, current: float, new: float, temperature
def update_progress(self) -> None:
self.evaluations += 1
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
- def get_observable_data(self) -> dict:
+ def observable_data(self) -> dict:
ctime = time.time() - self.start_computing_time
- return {'PROBLEM': self.problem, 'EVALUATIONS': self.evaluations, 'SOLUTIONS': self.get_result(),
- 'COMPUTING_TIME': ctime}
-
- def get_result(self) -> R:
+ return {
+ "PROBLEM": self.problem,
+ "EVALUATIONS": self.evaluations,
+ "SOLUTIONS": self.result(),
+ "COMPUTING_TIME": ctime,
+ }
+
+ def result(self) -> R:
return self.solutions[0]
def get_name(self) -> str:
- return 'Simulated Annealing'
+ return "Simulated Annealing"
diff --git a/jmetal/algorithm/test/ittest_algorithm.py b/jmetal/algorithm/test/ittest_algorithm.py
index 9a7c5415..11bd461e 100644
--- a/jmetal/algorithm/test/ittest_algorithm.py
+++ b/jmetal/algorithm/test/ittest_algorithm.py
@@ -10,14 +10,13 @@
class RunningAlgorithmsTestCases(unittest.TestCase):
-
def setUp(self):
self.problem = ZDT1()
self.population_size = 100
self.offspring_size = 100
self.mating_pool_size = 100
self.max_evaluations = 100
- self.mutation = PolynomialMutation(probability=1.0 / self.problem.number_of_variables, distribution_index=20)
+ self.mutation = PolynomialMutation(probability=1.0 / self.problem.number_of_variables(), distribution_index=20)
self.crossover = SBXCrossover(probability=1.0, distribution_index=20)
def test_NSGAII(self):
@@ -27,7 +26,7 @@ def test_NSGAII(self):
offspring_population_size=self.offspring_size,
mutation=self.mutation,
crossover=self.crossover,
- termination_criterion=StoppingByEvaluations(max_evaluations=1000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=1000),
).run()
def test_SMPSO(self):
@@ -36,12 +35,11 @@ def test_SMPSO(self):
swarm_size=self.population_size,
mutation=self.mutation,
leaders=CrowdingDistanceArchive(100),
- termination_criterion=StoppingByEvaluations(max_evaluations=1000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=1000),
).run()
class IntegrationTestCases(unittest.TestCase):
-
def test_should_NSGAII_work_when_solving_problem_ZDT1_with_standard_settings(self):
problem = ZDT1()
@@ -51,13 +49,13 @@ def test_should_NSGAII_work_when_solving_problem_ZDT1_with_standard_settings(sel
problem=problem,
population_size=100,
offspring_population_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
crossover=SBXCrossover(probability=1.0, distribution_index=20),
- termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations)
+ termination_criterion=StoppingByEvaluations(max_evaluations=max_evaluations),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
hv = HyperVolume(reference_point=[1, 1])
value = hv.compute([front[i].objectives for i in range(len(front))])
@@ -70,13 +68,13 @@ def test_should_SMPSO_work_when_solving_problem_ZDT1_with_standard_settings(self
algorithm = SMPSO(
problem=problem,
swarm_size=100,
- mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables, distribution_index=20),
+ mutation=PolynomialMutation(probability=1.0 / problem.number_of_variables(), distribution_index=20),
leaders=CrowdingDistanceArchive(100),
- termination_criterion=StoppingByEvaluations(max_evaluations=25000)
+ termination_criterion=StoppingByEvaluations(max_evaluations=25000),
)
algorithm.run()
- front = algorithm.get_result()
+ front = algorithm.result()
hv = HyperVolume(reference_point=[1, 1])
value = hv.compute([front[i].objectives for i in range(len(front))])
@@ -84,5 +82,5 @@ def test_should_SMPSO_work_when_solving_problem_ZDT1_with_standard_settings(self
self.assertTrue(value >= 0.655)
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/jmetal/config.py b/jmetal/config.py
index 51597da3..76a58182 100644
--- a/jmetal/config.py
+++ b/jmetal/config.py
@@ -1,19 +1,19 @@
-from jmetal.operator import PolynomialMutation, BitFlipMutation
+from jmetal.core.observer import Observable
+from jmetal.operator import BitFlipMutation, PolynomialMutation
from jmetal.util.comparator import DominanceComparator
-from jmetal.util.evaluator import SequentialEvaluator
+from jmetal.util.evaluator import Evaluator, SequentialEvaluator
from jmetal.util.generator import RandomGenerator
from jmetal.util.observable import DefaultObservable
from jmetal.util.termination_criterion import StoppingByEvaluations
class _Store:
-
@property
- def default_observable(self):
+ def default_observable(self) -> Observable:
return DefaultObservable()
@property
- def default_evaluator(self):
+ def default_evaluator(self) -> Evaluator:
return SequentialEvaluator()
@property
@@ -30,10 +30,7 @@ def default_comparator(self):
@property
def default_mutation(self):
- return {
- 'real': PolynomialMutation(probability=0.15, distribution_index=20),
- 'binary': BitFlipMutation(0.15)
- }
+ return {"real": PolynomialMutation(probability=0.15, distribution_index=20), "binary": BitFlipMutation(0.15)}
store = _Store()
diff --git a/jmetal/core/algorithm.py b/jmetal/core/algorithm.py
index ea602b54..2c7e960c 100644
--- a/jmetal/core/algorithm.py
+++ b/jmetal/core/algorithm.py
@@ -1,17 +1,17 @@
-import logging
import threading
import time
-from abc import abstractmethod, ABC
-from typing import TypeVar, Generic, List
+from abc import ABC, abstractmethod
+from typing import Generic, List, TypeVar
from jmetal.config import store
from jmetal.core.problem import Problem
from jmetal.core.solution import FloatSolution
+from jmetal.logger import get_logger
-LOGGER = logging.getLogger('jmetal')
+logger = get_logger(__name__)
-S = TypeVar('S')
-R = TypeVar('R')
+S = TypeVar("S")
+R = TypeVar("R")
"""
.. module:: algorithm
@@ -23,7 +23,6 @@
class Algorithm(Generic[S, R], threading.Thread, ABC):
-
def __init__(self):
threading.Thread.__init__(self)
@@ -36,58 +35,63 @@ def __init__(self):
@abstractmethod
def create_initial_solutions(self) -> List[S]:
- """ Creates the initial list of solutions of a metaheuristic. """
+ """Creates the initial list of solutions of a metaheuristic."""
pass
@abstractmethod
def evaluate(self, solution_list: List[S]) -> List[S]:
- """ Evaluates a solution list. """
+ """Evaluates a solution list."""
pass
@abstractmethod
def init_progress(self) -> None:
- """ Initialize the algorithm. """
+ """Initialize the algorithm."""
pass
@abstractmethod
def stopping_condition_is_met(self) -> bool:
- """ The stopping condition is met or not. """
+ """The stopping condition is met or not."""
pass
@abstractmethod
def step(self) -> None:
- """ Performs one iteration/step of the algorithm's loop. """
+ """Performs one iteration/step of the algorithm's loop."""
pass
@abstractmethod
def update_progress(self) -> None:
- """ Update the progress after each iteration. """
+ """Update the progress after each iteration."""
pass
@abstractmethod
- def get_observable_data(self) -> dict:
- """ Get observable data, with the information that will be send to all observers each time. """
+ def observable_data(self) -> dict:
+ """Get observable data, with the information that will be seng to all observers each time."""
pass
def run(self):
- """ Execute the algorithm. """
+ """Execute the algorithm."""
self.start_computing_time = time.time()
+ logger.debug("Creating initial set of solutions...")
self.solutions = self.create_initial_solutions()
+
+ logger.debug("Evaluating solutions...")
self.solutions = self.evaluate(self.solutions)
- LOGGER.debug('Initializing progress')
+ logger.debug("Initializing progress...")
self.init_progress()
- LOGGER.debug('Running main loop until termination criteria is met')
+ logger.debug("Running main loop until termination criteria is met")
while not self.stopping_condition_is_met():
self.step()
self.update_progress()
+ logger.debug("Finished!")
+
self.total_computing_time = time.time() - self.start_computing_time
@abstractmethod
- def get_result(self) -> R:
+ def result(self) -> R:
pass
@abstractmethod
@@ -96,18 +100,13 @@ def get_name(self) -> str:
class DynamicAlgorithm(Algorithm[S, R], ABC):
-
@abstractmethod
def restart(self) -> None:
pass
class EvolutionaryAlgorithm(Algorithm[S, R], ABC):
-
- def __init__(self,
- problem: Problem[S],
- population_size: int,
- offspring_population_size: int):
+ def __init__(self, problem: Problem[S], population_size: int, offspring_population_size: int):
super(EvolutionaryAlgorithm, self).__init__()
self.problem = problem
self.population_size = population_size
@@ -115,29 +114,31 @@ def __init__(self,
@abstractmethod
def selection(self, population: List[S]) -> List[S]:
- """ Select the best-fit individuals for reproduction (parents). """
+ """Select the best-fit individuals for reproduction (parents)."""
pass
@abstractmethod
def reproduction(self, population: List[S]) -> List[S]:
- """ Breed new individuals through crossover and mutation operations to give birth to offspring. """
+ """Breed new individuals through crossover and mutation operations to give birth to offspring."""
pass
@abstractmethod
def replacement(self, population: List[S], offspring_population: List[S]) -> List[S]:
- """ Replace least-fit population with new individuals. """
+ """Replace least-fit population with new individuals."""
pass
- def get_observable_data(self) -> dict:
- return {'PROBLEM': self.problem,
- 'EVALUATIONS': self.evaluations,
- 'SOLUTIONS': self.get_result(),
- 'COMPUTING_TIME': time.time() - self.start_computing_time}
+ def observable_data(self) -> dict:
+ return {
+ "PROBLEM": self.problem,
+ "EVALUATIONS": self.evaluations,
+ "SOLUTIONS": self.result(),
+ "COMPUTING_TIME": time.time() - self.start_computing_time,
+ }
def init_progress(self) -> None:
self.evaluations = self.population_size
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
def step(self):
@@ -150,19 +151,16 @@ def step(self):
def update_progress(self) -> None:
self.evaluations += self.offspring_population_size
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
@property
def label(self) -> str:
- return f'{self.get_name()}.{self.problem.get_name()}'
+ return f"{self.get_name()}.{self.problem.name()}"
class ParticleSwarmOptimization(Algorithm[FloatSolution, List[FloatSolution]], ABC):
-
- def __init__(self,
- problem: Problem[S],
- swarm_size: int):
+ def __init__(self, problem: Problem[S], swarm_size: int):
super(ParticleSwarmOptimization, self).__init__()
self.problem = problem
self.swarm_size = swarm_size
@@ -199,11 +197,13 @@ def update_position(self, swarm: List[FloatSolution]) -> None:
def perturbation(self, swarm: List[FloatSolution]) -> None:
pass
- def get_observable_data(self) -> dict:
- return {'PROBLEM': self.problem,
- 'EVALUATIONS': self.evaluations,
- 'SOLUTIONS': self.get_result(),
- 'COMPUTING_TIME': time.time() - self.start_computing_time}
+ def observable_data(self) -> dict:
+ return {
+ "PROBLEM": self.problem,
+ "EVALUATIONS": self.evaluations,
+ "SOLUTIONS": self.result(),
+ "COMPUTING_TIME": time.time() - self.start_computing_time,
+ }
def init_progress(self) -> None:
self.evaluations = self.swarm_size
@@ -212,7 +212,7 @@ def init_progress(self) -> None:
self.initialize_particle_best(self.solutions)
self.initialize_global_best(self.solutions)
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
def step(self):
@@ -226,9 +226,9 @@ def step(self):
def update_progress(self) -> None:
self.evaluations += self.swarm_size
- observable_data = self.get_observable_data()
+ observable_data = self.observable_data()
self.observable.notify_all(**observable_data)
@property
def label(self) -> str:
- return f'{self.get_name()}.{self.problem.get_name()}'
+ return f"{self.get_name()}.{self.problem.name()}"
diff --git a/jmetal/core/observer.py b/jmetal/core/observer.py
index a8c36730..b2a0be99 100644
--- a/jmetal/core/observer.py
+++ b/jmetal/core/observer.py
@@ -1,4 +1,4 @@
-from abc import abstractmethod, ABC
+from abc import ABC, abstractmethod
"""
.. module:: Observable
@@ -10,16 +10,13 @@
class Observer(ABC):
-
@abstractmethod
def update(self, *args, **kwargs):
- """ Update method.
- """
+ """Update method."""
pass
class Observable(ABC):
-
@abstractmethod
def register(self, observer):
pass
@@ -35,5 +32,3 @@ def deregister_all(self):
@abstractmethod
def notify_all(self, *args, **kwargs):
pass
-
-
diff --git a/jmetal/core/operator.py b/jmetal/core/operator.py
index d68f18d6..7a96543c 100644
--- a/jmetal/core/operator.py
+++ b/jmetal/core/operator.py
@@ -1,8 +1,10 @@
from abc import ABC, abstractmethod
-from typing import TypeVar, Generic, List
+from typing import Generic, List, TypeVar
-S = TypeVar('S')
-R = TypeVar('R')
+from jmetal.core.solution import Solution
+
+S = TypeVar("S", bound=Solution)
+R = TypeVar("R", bound=Solution)
"""
.. module:: Operator
@@ -14,7 +16,7 @@
class Operator(Generic[S, R], ABC):
- """ Class representing operator """
+ """Class representing operator"""
@abstractmethod
def execute(self, source: S) -> R:
@@ -28,17 +30,18 @@ def get_name(self) -> str:
def check_valid_probability_value(func):
def func_wrapper(self, probability: float):
if probability > 1.0:
- raise Exception('The probability is greater than one: {}'.format(probability))
+ raise Exception("The probability is greater than one: {}".format(probability))
elif probability < 0.0:
- raise Exception('The probability is lower than zero: {}'.format(probability))
+ raise Exception("The probability is lower than zero: {}".format(probability))
res = func(self, probability)
return res
+
return func_wrapper
class Mutation(Operator[S, S], ABC):
- """ Class representing mutation operator. """
+ """Class representing mutation operator."""
@check_valid_probability_value
def __init__(self, probability: float):
@@ -46,7 +49,7 @@ def __init__(self, probability: float):
class Crossover(Operator[List[S], List[R]], ABC):
- """ Class representing crossover operator. """
+ """Class representing crossover operator."""
@check_valid_probability_value
def __init__(self, probability: float):
@@ -62,7 +65,7 @@ def get_number_of_children(self) -> int:
class Selection(Operator[S, R], ABC):
- """ Class representing selection operator. """
+ """Class representing selection operator."""
def __init__(self):
pass
diff --git a/jmetal/core/problem.py b/jmetal/core/problem.py
index 9519fac5..ecf0b5e5 100644
--- a/jmetal/core/problem.py
+++ b/jmetal/core/problem.py
@@ -1,54 +1,66 @@
-import logging
import random
from abc import ABC, abstractmethod
-from typing import Generic, TypeVar, List
+from typing import Generic, List, TypeVar
from jmetal.core.observer import Observer
-from jmetal.core.solution import BinarySolution, FloatSolution, IntegerSolution, PermutationSolution
+from jmetal.core.solution import (
+ BinarySolution,
+ FloatSolution,
+ IntegerSolution,
+ PermutationSolution,
+)
+from jmetal.logger import get_logger
-LOGGER = logging.getLogger('jmetal')
-S = TypeVar('S')
+logger = get_logger(__name__)
+
+S = TypeVar("S")
class Problem(Generic[S], ABC):
- """ Class representing problems. """
+ """Class representing problems."""
MINIMIZE = -1
MAXIMIZE = 1
def __init__(self):
- self.number_of_variables: int = 0
- self.number_of_objectives: int = 0
- self.number_of_constraints: int = 0
-
self.reference_front: List[S] = []
-
self.directions: List[int] = []
self.labels: List[str] = []
+ @abstractmethod
+ def number_of_variables(self) -> int:
+ pass
+
+ @abstractmethod
+ def number_of_objectives(self) -> int:
+ pass
+
+ @abstractmethod
+ def number_of_constraints(self) -> int:
+ pass
+
@abstractmethod
def create_solution(self) -> S:
- """ Creates a random_search solution to the problem.
+ """Creates a random_search solution to the problem.
- :return: Solution. """
+ :return: Solution."""
pass
@abstractmethod
def evaluate(self, solution: S) -> S:
- """ Evaluate a solution. For any new problem inheriting from :class:`Problem`, this method should be
- replaced. Note that this framework ASSUMES minimization, thus solutions must be evaluated in consequence.
+ """Evaluate a solution. For any new problem inheriting from :class:`Problem`, this method should be replaced.
+ Note that this framework ASSUMES minimization, thus solutions must be evaluated in consequence.
- :return: Evaluated solution. """
+ :return: Evaluated solution."""
pass
@abstractmethod
- def get_name(self) -> str:
+ def name(self) -> str:
pass
class DynamicProblem(Problem[S], Observer, ABC):
-
@abstractmethod
def the_problem_has_changed(self) -> bool:
pass
@@ -59,56 +71,68 @@ def clear_changed(self) -> None:
class BinaryProblem(Problem[BinarySolution], ABC):
- """ Class representing binary problems. """
+ """Class representing binary problems."""
def __init__(self):
super(BinaryProblem, self).__init__()
+ self.number_of_bits_per_variable = []
+
+ def number_of_bits_per_variable_list(self):
+ return self.number_of_bits_per_variable
+
+ def total_number_of_bits(self):
+ return sum(self.number_of_bits_per_variable)
+
class FloatProblem(Problem[FloatSolution], ABC):
- """ Class representing float problems. """
+ """Class representing float problems."""
def __init__(self):
super(FloatProblem, self).__init__()
self.lower_bound = []
self.upper_bound = []
+ def number_of_variables(self) -> int:
+ return len(self.lower_bound)
+
def create_solution(self) -> FloatSolution:
new_solution = FloatSolution(
- self.lower_bound,
- self.upper_bound,
- self.number_of_objectives,
- self.number_of_constraints)
- new_solution.variables = \
- [random.uniform(self.lower_bound[i] * 1.0, self.upper_bound[i] * 1.0) for i in
- range(self.number_of_variables)]
+ self.lower_bound, self.upper_bound, self.number_of_objectives(), self.number_of_constraints()
+ )
+ new_solution.variables = [
+ random.uniform(self.lower_bound[i] * 1.0, self.upper_bound[i] * 1.0)
+ for i in range(self.number_of_variables())
+ ]
return new_solution
class IntegerProblem(Problem[IntegerSolution], ABC):
- """ Class representing integer problems. """
+ """Class representing integer problems."""
def __init__(self):
super(IntegerProblem, self).__init__()
- self.lower_bound = None
- self.upper_bound = None
+ self.lower_bound = []
+ self.upper_bound = []
+
+ def number_of_variables(self) -> int:
+ return len(self.lower_bound)
def create_solution(self) -> IntegerSolution:
new_solution = IntegerSolution(
- self.lower_bound,
- self.upper_bound,
- self.number_of_objectives,
- self.number_of_constraints)
- new_solution.variables = \
- [int(random.uniform(self.lower_bound[i] * 1.0, self.upper_bound[i] * 1.0))
- for i in range(self.number_of_variables)]
+ self.lower_bound, self.upper_bound, self.number_of_objectives(), self.number_of_constraints()
+ )
+ new_solution.variables = [
+ round(random.uniform(self.lower_bound[i] * 1.0, self.upper_bound[i] * 1.0))
+ for i in range(self.number_of_variables())
+ ]
return new_solution
class PermutationProblem(Problem[PermutationSolution], ABC):
- """ Class representing permutation problems. """
+ """Class representing permutation problems."""
def __init__(self):
super(PermutationProblem, self).__init__()
@@ -146,38 +170,41 @@ def __init__(self):
super(OnTheFlyFloatProblem, self).__init__()
self.functions = []
self.constraints = []
- self.name = None
+ self.problem_name = None
- def set_name(self, name):
- self.name = name
+ def set_name(self, name) -> "OnTheFlyFloatProblem":
+ self.problem_name = name
return self
- def add_function(self, function):
+ def add_function(self, function) -> "OnTheFlyFloatProblem":
self.functions.append(function)
- self.number_of_objectives += 1
return self
- def add_constraint(self, constraint):
+ def add_constraint(self, constraint) -> "OnTheFlyFloatProblem":
self.constraints.append(constraint)
- self.number_of_constraints += 1
return self
- def add_variable(self, lower_bound, upper_bound):
+ def add_variable(self, lower_bound, upper_bound) -> "OnTheFlyFloatProblem":
self.lower_bound.append(lower_bound)
self.upper_bound.append(upper_bound)
- self.number_of_variables += 1
return self
- def evaluate(self, solution: FloatSolution):
- for i in range(self.number_of_objectives):
+ def number_of_objectives(self) -> int:
+ return len(self.functions)
+
+ def number_of_constraints(self) -> int:
+ return len(self.constraints)
+
+ def evaluate(self, solution: FloatSolution) -> None:
+ for i in range(self.number_of_objectives()):
solution.objectives[i] = self.functions[i](solution.variables)
- for i in range(self.number_of_constraints):
+ for i in range(self.number_of_constraints()):
solution.constraints[i] = self.constraints[i](solution.variables)
- def get_name(self) -> str:
- return self.name
+ def name(self) -> str:
+ return self.problem_name
diff --git a/jmetal/core/quality_indicator.py b/jmetal/core/quality_indicator.py
index 809ca247..152ed8fa 100644
--- a/jmetal/core/quality_indicator.py
+++ b/jmetal/core/quality_indicator.py
@@ -1,11 +1,11 @@
from abc import ABC, abstractmethod
+from typing import Iterable
import numpy as np
from scipy import spatial
class QualityIndicator(ABC):
-
def __init__(self, is_minimization: bool):
self.is_minimization = is_minimization
@@ -40,10 +40,10 @@ def compute(self, solutions: np.array):
return mean
def get_name(self) -> str:
- return 'Fitness'
+ return "Fitness"
def get_short_name(self) -> str:
- return 'Fitness'
+ return "Fitness"
class GenerationalDistance(QualityIndicator):
@@ -57,17 +57,17 @@ def __init__(self, reference_front: np.array = None):
def compute(self, solutions: np.array):
if self.reference_front is None:
- raise Exception('Reference front is none')
+ raise Exception("Reference front is none")
distances = spatial.distance.cdist(solutions, self.reference_front)
return np.mean(np.min(distances, axis=1))
def get_short_name(self) -> str:
- return 'GD'
+ return "GD"
def get_name(self) -> str:
- return 'Generational Distance'
+ return "Generational Distance"
class InvertedGenerationalDistance(QualityIndicator):
@@ -77,17 +77,17 @@ def __init__(self, reference_front: np.array = None):
def compute(self, solutions: np.array):
if self.reference_front is None:
- raise Exception('Reference front is none')
+ raise Exception("Reference front is none")
distances = spatial.distance.cdist(self.reference_front, solutions)
return np.mean(np.min(distances, axis=1))
def get_short_name(self) -> str:
- return 'IGD'
+ return "IGD"
def get_name(self) -> str:
- return 'Inverted Generational Distance'
+ return "Inverted Generational Distance"
class EpsilonIndicator(QualityIndicator):
@@ -96,18 +96,17 @@ def __init__(self, reference_front: np.array = None):
self.reference_front = reference_front
def compute(self, front: np.array) -> float:
- return max([min(
- [max([s2[k] - s1[k] for k in range(len(s2))]) for s2 in front]) for s1 in self.reference_front])
+ return max([min([max([s2[k] - s1[k] for k in range(len(s2))]) for s2 in front]) for s1 in self.reference_front])
def get_short_name(self) -> str:
- return 'EP'
+ return "EP"
def get_name(self) -> str:
return "Additive Epsilon"
class HyperVolume(QualityIndicator):
- """ Hypervolume computation based on variant 3 of the algorithm in the paper:
+ """Hypervolume computation based on variant 3 of the algorithm in the paper:
* C. M. Fonseca, L. Paquete, and M. Lopez-Ibanez. An improved dimension-sweep
algorithm for the hypervolume indicator. In IEEE Congress on Evolutionary
@@ -192,7 +191,8 @@ def _hv_recursive(self, dim_index: int, length: int, bounds: list):
q = q.prev[dim_index]
q = p.prev[dim_index]
while length > 1 and (
- q.cargo[dim_index] > bounds[dim_index] or q.prev[dim_index].cargo[dim_index] >= bounds[dim_index]):
+ q.cargo[dim_index] > bounds[dim_index] or q.prev[dim_index].cargo[dim_index] >= bounds[dim_index]
+ ):
p = q
remove(p, dim_index, bounds)
q = p.prev[dim_index]
@@ -202,10 +202,11 @@ def _hv_recursive(self, dim_index: int, length: int, bounds: list):
q_prev_dim_index = q.prev[dim_index]
if length > 1:
hvol = q_prev_dim_index.volume[dim_index] + q_prev_dim_index.area[dim_index] * (
- q_cargo[dim_index] - q_prev_dim_index.cargo[dim_index])
+ q_cargo[dim_index] - q_prev_dim_index.cargo[dim_index]
+ )
else:
q_area[0] = 1
- q_area[1:dim_index + 1] = [q_area[i] * -q_cargo[i] for i in range(dim_index)]
+ q_area[1 : dim_index + 1] = [q_area[i] * -q_cargo[i] for i in range(dim_index)]
q.volume[dim_index] = hvol
if q.ignore >= dim_index:
q_area[dim_index] = q_prev_dim_index.area[dim_index]
@@ -251,7 +252,7 @@ def _sort_by_dimension(self, nodes, i):
nodes[:] = [node for (_, node) in decorated]
def get_short_name(self) -> str:
- return 'HV'
+ return "HV"
def get_name(self) -> str:
return "Hypervolume (Fonseca et al. implementation)"
@@ -265,7 +266,6 @@ class MultiList:
"""
class Node:
-
def __init__(self, number_lists, cargo=None):
self.cargo = cargo
self.next = [None] * number_lists
@@ -278,8 +278,7 @@ def __str__(self):
return str(self.cargo)
def __init__(self, number_lists):
- """ Builds 'numberLists' doubly linked lists.
- """
+ """Builds 'numberLists' doubly linked lists."""
self.number_lists = number_lists
self.sentinel = MultiList.Node(number_lists)
self.sentinel.next = [self.sentinel] * number_lists
@@ -314,7 +313,7 @@ def get_length(self, i):
return length
def append(self, node, index):
- """ Appends a node to the end of the list at the given index."""
+ """Appends a node to the end of the list at the given index."""
last_but_one = self.sentinel.prev[index]
node.next[index] = self.sentinel
node.prev[index] = last_but_one
@@ -323,7 +322,7 @@ def append(self, node, index):
last_but_one.next[index] = node
def extend(self, nodes, index):
- """ Extends the list at the given index with the nodes."""
+ """Extends the list at the given index with the nodes."""
sentinel = self.sentinel
for node in nodes:
last_but_one = sentinel.prev[index]
@@ -334,7 +333,7 @@ def extend(self, nodes, index):
last_but_one.next[index] = node
def remove(self, node, index, bounds):
- """ Removes and returns 'node' from all lists in [0, 'index'[."""
+ """Removes and returns 'node' from all lists in [0, 'index'[."""
for i in range(index):
predecessor = node.prev[i]
successor = node.next[i]
@@ -345,7 +344,7 @@ def remove(self, node, index, bounds):
return node
def reinsert(self, node, index, bounds):
- """ Inserts 'node' at the position it had in all lists in [0, 'index'[
+ """Inserts 'node' at the position it had in all lists in [0, 'index'[
before it was removed. This method assumes that the next and previous
nodes of the node that is reinserted are in the list.
"""
@@ -354,3 +353,33 @@ def reinsert(self, node, index, bounds):
node.next[i].prev[i] = node
if bounds[i] > node.cargo[i]:
bounds[i] = node.cargo[i]
+
+
+class NormalizedHyperVolume(QualityIndicator):
+ """Implementation of the normalized hypervolume, which is calculated as follows:
+
+ relative hypervolume = 1 - (HV of the front / HV of the reference front).
+
+ Minimization is implicitly assumed here!
+ """
+
+ def __init__(self, reference_point: Iterable[float], reference_front: np.array):
+ """Delegates the computation of the HyperVolume to `jMetal.core.quality_indicator.HyperVolume`.
+
+ Fails if the HV of the reference front is zero."""
+ self.reference_point = reference_point
+ self._hv = HyperVolume(reference_point=reference_point)
+ self._reference_hypervolume = self._hv.compute(reference_front)
+
+ assert self._reference_hypervolume != 0, "Hypervolume of reference front is zero"
+
+ def compute(self, solutions: np.array) -> float:
+ hv = self._hv.compute(solutions=solutions)
+
+ return 1 - (hv / self._reference_hypervolume)
+
+ def get_short_name(self) -> str:
+ return "NHV"
+
+ def get_name(self) -> str:
+ return "Normalized Hypervolume"
diff --git a/jmetal/core/solution.py b/jmetal/core/solution.py
index 6d8a994f..44abdd0a 100644
--- a/jmetal/core/solution.py
+++ b/jmetal/core/solution.py
@@ -1,22 +1,19 @@
from abc import ABC
-from typing import List, Generic, TypeVar
+from typing import Generic, List, TypeVar
from jmetal.util.ckecking import Check
BitSet = List[bool]
-S = TypeVar('S')
+S = TypeVar("S")
class Solution(Generic[S], ABC):
- """ Class representing solutions """
+ """Class representing solutions"""
def __init__(self, number_of_variables: int, number_of_objectives: int, number_of_constraints: int = 0):
- self.number_of_variables = number_of_variables
- self.number_of_objectives = number_of_objectives
- self.number_of_constraints = number_of_constraints
- self.variables = [[] for _ in range(self.number_of_variables)]
- self.objectives = [0.0 for _ in range(self.number_of_objectives)]
- self.constraints = [0.0 for _ in range(self.number_of_constraints)]
+ self.variables = [[] for _ in range(number_of_variables)]
+ self.objectives = [0.0 for _ in range(number_of_objectives)]
+ self.constraints = [0.0 for _ in range(number_of_constraints)]
self.attributes = {}
def __eq__(self, solution) -> bool:
@@ -25,24 +22,27 @@ def __eq__(self, solution) -> bool:
return False
def __str__(self) -> str:
- return 'Solution(variables={},objectives={},constraints={})'.format(self.variables, self.objectives,
- self.constraints)
+ return "Solution(variables={},objectives={},constraints={})".format(
+ self.variables, self.objectives, self.constraints
+ )
class BinarySolution(Solution[BitSet]):
- """ Class representing float solutions """
+ """Class representing float solutions"""
def __init__(self, number_of_variables: int, number_of_objectives: int, number_of_constraints: int = 0):
super(BinarySolution, self).__init__(number_of_variables, number_of_objectives, number_of_constraints)
+ self.bits_per_variable = []
+
def __copy__(self):
- new_solution = BinarySolution(
- self.number_of_variables,
- self.number_of_objectives)
+ new_solution = BinarySolution(len(self.variables), len(self.objectives), len(self.constraints))
new_solution.objectives = self.objectives[:]
new_solution.variables = self.variables[:]
+ new_solution.constraints = self.constraints[:]
new_solution.attributes = self.attributes.copy()
+ new_solution.bits_per_variable = self.bits_per_variable
return new_solution
@@ -56,60 +56,75 @@ def get_total_number_of_bits(self) -> int:
def get_binary_string(self) -> str:
string = ""
for bit in self.variables[0]:
- string += '1' if bit else '0'
+ string += "1" if bit else "0"
return string
+ def cardinality(self, variable_index) -> int:
+ return sum(1 for _ in self.variables[variable_index] if _)
-class FloatSolution(Solution[float]):
- """ Class representing float solutions """
- def __init__(self, lower_bound: List[float], upper_bound: List[float], number_of_objectives: int,
- number_of_constraints: int = 0):
+class FloatSolution(Solution[float]):
+ """Class representing float solutions"""
+
+ def __init__(
+ self,
+ lower_bound: List[float],
+ upper_bound: List[float],
+ number_of_objectives: int,
+ number_of_constraints: int = 0
+ ):
super(FloatSolution, self).__init__(len(lower_bound), number_of_objectives, number_of_constraints)
self.lower_bound = lower_bound
self.upper_bound = upper_bound
def __copy__(self):
new_solution = FloatSolution(
- self.lower_bound,
- self.upper_bound,
- self.number_of_objectives,
- self.number_of_constraints)
+ self.lower_bound, self.upper_bound, len(self.objectives), len(self.constraints)
+ )
new_solution.objectives = self.objectives[:]
new_solution.variables = self.variables[:]
new_solution.constraints = self.constraints[:]
+ new_solution.lower_bound = self.lower_bound
+ new_solution.upper_bound = self.upper_bound
+
new_solution.attributes = self.attributes.copy()
return new_solution
class IntegerSolution(Solution[int]):
- """ Class representing integer solutions """
-
- def __init__(self, lower_bound: List[int], upper_bound: List[int], number_of_objectives: int,
- number_of_constraints: int = 0):
+ """Class representing integer solutions"""
+
+ def __init__(
+ self,
+ lower_bound: List[int],
+ upper_bound: List[int],
+ number_of_objectives: int,
+ number_of_constraints: int = 0
+ ):
super(IntegerSolution, self).__init__(len(lower_bound), number_of_objectives, number_of_constraints)
self.lower_bound = lower_bound
self.upper_bound = upper_bound
def __copy__(self):
new_solution = IntegerSolution(
- self.lower_bound,
- self.upper_bound,
- self.number_of_objectives,
- self.number_of_constraints)
+ self.lower_bound, self.upper_bound, len(self.objectives), len(self.constraints)
+ )
new_solution.objectives = self.objectives[:]
new_solution.variables = self.variables[:]
new_solution.constraints = self.constraints[:]
+ new_solution.lower_bound = self.lower_bound
+ new_solution.upper_bound = self.upper_bound
+
new_solution.attributes = self.attributes.copy()
return new_solution
class CompositeSolution(Solution):
- """ Class representing solutions composed of a list of solutions. The idea is that each decision variable can
+ """Class representing solutions composed of a list of solutions. The idea is that each decision variable can
be a solution of any type, so we can create mixed solutions (e.g., solutions combining any of the existing
encodings). The adopted approach has the advantage of easing the reuse of existing variation operators, but all the
solutions in the list will need to have the same function and constraint violation values.
@@ -118,18 +133,23 @@ class CompositeSolution(Solution):
"""
def __init__(self, solutions: List[Solution]):
- super(CompositeSolution, self).__init__(len(solutions), solutions[0].number_of_objectives,
- solutions[0].number_of_constraints)
+ super(CompositeSolution, self).__init__(
+ len(solutions), len(solutions[0].objectives), len(solutions[0].constraints)
+ )
Check.is_not_none(solutions)
Check.collection_is_not_empty(solutions)
for solution in solutions:
- Check.that(solution.number_of_objectives == solutions[0].number_of_objectives,
- "The solutions in the list must have the same number of objectives: " + str(
- solutions[0].number_of_objectives))
- Check.that(solution.number_of_constraints == solutions[0].number_of_constraints,
- "The solutions in the list must have the same number of constraints: " + str(
- solutions[0].number_of_constraints))
+ Check.that(
+ len(solution.objectives) == len(solutions[0].objectives),
+ "The solutions in the list must have the same number of objectives: "
+ + str(len(solutions[0].objectives)),
+ )
+ Check.that(
+ len(solution.constraints) == len(solutions[0].constraints),
+ "The solutions in the list must have the same number of constraints: "
+ + str(len(solutions[0].constraints)),
+ )
self.variables = solutions
@@ -144,17 +164,16 @@ def __copy__(self):
class PermutationSolution(Solution):
- """ Class representing permutation solutions """
+ """Class representing permutation solutions"""
def __init__(self, number_of_variables: int, number_of_objectives: int, number_of_constraints: int = 0):
super(PermutationSolution, self).__init__(number_of_variables, number_of_objectives, number_of_constraints)
def __copy__(self):
- new_solution = PermutationSolution(
- self.number_of_variables,
- self.number_of_objectives)
+ new_solution = PermutationSolution(len(self.variables), len(self.objectives), len(self.constraints))
new_solution.objectives = self.objectives[:]
new_solution.variables = self.variables[:]
+ new_solution.constraints = self.constraints[:]
new_solution.attributes = self.attributes.copy()
diff --git a/jmetal/core/test/test_observable.py b/jmetal/core/test/test_observable.py
index 6ef40ea1..874799d3 100644
--- a/jmetal/core/test/test_observable.py
+++ b/jmetal/core/test/test_observable.py
@@ -4,16 +4,15 @@
from jmetal.util.observable import DefaultObservable
-class ObservableTestCases(unittest.TestCase):
-
- class DummyObserver(Observer):
+class DummyObserver(Observer):
+ def update(self, *args, **kwargs):
+ pass
- def update(self, *args, **kwargs):
- pass
+class ObservableTestCases(unittest.TestCase):
def setUp(self):
self.observable = DefaultObservable()
- self.observer = self.DummyObserver()
+ self.observer = DummyObserver()
def test_should_register_add_one_observer(self):
self.observable.register(self.observer)
@@ -21,7 +20,7 @@ def test_should_register_add_one_observer(self):
self.assertEqual(1, len(self.observable.observers))
def test_should_register_add_two_observers(self):
- observer_two = self.DummyObserver()
+ observer_two = DummyObserver()
self.observable.register(self.observer)
self.observable.register(observer_two)
@@ -29,7 +28,7 @@ def test_should_register_add_two_observers(self):
self.assertEqual(2, len(self.observable.observers))
def test_should_deregister_remove_the_observer_if_it_is_registered(self):
- observer_two = self.DummyObserver()
+ observer_two = DummyObserver()
self.observable.register(self.observer)
self.observable.register(observer_two)
@@ -38,7 +37,7 @@ def test_should_deregister_remove_the_observer_if_it_is_registered(self):
self.assertEqual(1, len(self.observable.observers))
def test_should_deregister_not_remove_the_observer_if_it_is_not_registered(self):
- observer_two = self.DummyObserver()
+ observer_two = DummyObserver()
self.observable.register(self.observer)
self.observable.deregister(observer_two)
diff --git a/jmetal/core/test/test_operator.py b/jmetal/core/test/test_operator.py
index 6604bca9..8b7bbe53 100644
--- a/jmetal/core/test/test_operator.py
+++ b/jmetal/core/test/test_operator.py
@@ -1,39 +1,32 @@
import unittest
-from typing import TypeVar
-from jmetal.core.operator import Mutation, Crossover
+from jmetal.core.operator import Crossover, Mutation
from jmetal.core.solution import Solution
-S = TypeVar('S')
-R = TypeVar('R')
-
-
-class DummyMutation(Mutation[Solution]):
+class DummyMutation(Mutation):
def __init__(self, probability: float):
super(DummyMutation, self).__init__(probability=probability)
- def execute(self, source: Solution) -> Solution:
- return None
+ def execute(self, source: Solution) -> None:
+ pass
def get_name(self) -> str:
- return ""
+ pass
-class DummyCrossover(Crossover[Solution, Solution]):
-
+class DummyCrossover(Crossover):
def __init__(self, probability: float):
super(DummyCrossover, self).__init__(probability=probability)
- def execute(self, source: Solution) -> Solution:
- return None
+ def execute(self, source: Solution) -> None:
+ pass
def get_name(self) -> str:
- return ""
+ pass
class OperatorTestCase(unittest.TestCase):
-
def test_should_mutation_constructor_raises_an_exception_is_probability_is_negative(self) -> None:
with self.assertRaises(Exception):
DummyMutation(-1)
@@ -51,5 +44,5 @@ def test_should_crossover_constructor_raises_an_exception_is_probability_is_high
DummyMutation(1.1)
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/jmetal/core/test/test_problem.py b/jmetal/core/test/test_problem.py
index ed8c5472..7af301e1 100644
--- a/jmetal/core/test/test_problem.py
+++ b/jmetal/core/test/test_problem.py
@@ -5,55 +5,57 @@
class DummyIntegerProblem(IntegerProblem):
-
def __init__(self):
super(DummyIntegerProblem, self).__init__()
+ def number_of_objectives(self) -> int:
+ return 2
+
+ def number_of_constraints(self) -> int:
+ return 0
+
def evaluate(self, solution: IntegerSolution) -> IntegerSolution:
- pass
+ return solution
- def get_name(self) -> str:
- pass
+ def name(self) -> str:
+ return "Dummy integer problem"
class DummyFloatProblem(FloatProblem):
-
def __init__(self):
super(DummyFloatProblem, self).__init__()
+ def number_of_objectives(self) -> int:
+ return 2
+
+ def number_of_constraints(self) -> int:
+ return 0
+
def evaluate(self, solution: FloatSolution) -> FloatSolution:
- pass
+ return solution
- def get_name(self) -> str:
- pass
+ def name(self) -> str:
+ return "Dummy float problem"
class FloatProblemTestCases(unittest.TestCase):
-
- def test_should_default_constructor_create_a_valid_problem(self) -> None:
- number_of_objectives = 2
- number_of_constraints = 0
+ def test_should_default_constructor_create_a_valid_problem(self):
lower_bound = [-1.0]
upper_bound = [1.0]
problem = DummyFloatProblem()
problem.lower_bound = lower_bound
problem.upper_bound = upper_bound
- problem.number_of_constraints = number_of_constraints
- problem.number_of_objectives = number_of_objectives
- problem.number_of_variables = len(lower_bound)
- self.assertEqual(1, problem.number_of_variables)
- self.assertEqual(2, problem.number_of_objectives)
- self.assertEqual(0, problem.number_of_constraints)
+ self.assertEqual(1, problem.number_of_variables())
+ self.assertEqual(2, problem.number_of_objectives())
+ self.assertEqual(0, problem.number_of_constraints())
self.assertEqual([-1], problem.lower_bound)
self.assertEqual([1], problem.upper_bound)
- def test_should_create_solution_create_a_valid_solution(self) -> None:
+ def test_should_create_solution_create_a_valid_solution(self):
problem = DummyFloatProblem()
- problem.number_of_variables = 2
- problem.number_of_objectives = 2
- problem.number_of_constraints = 0
+
problem.lower_bound = [-1.0, -2.0]
problem.upper_bound = [1.0, 2.0]
@@ -64,34 +66,31 @@ def test_should_create_solution_create_a_valid_solution(self) -> None:
class IntegerProblemTestCases(unittest.TestCase):
-
- def test_should_default_constructor_create_a_valid_problem(self) -> None:
+ def test_should_default_constructor_create_a_valid_problem(self):
problem = DummyIntegerProblem()
- problem.number_of_variables = 1
- problem.number_of_objectives = 2
- problem.number_of_constraints = 0
+
problem.lower_bound = [-1]
problem.upper_bound = [1]
- self.assertEqual(1, problem.number_of_variables)
- self.assertEqual(2, problem.number_of_objectives)
- self.assertEqual(0, problem.number_of_constraints)
+ self.assertEqual(1, problem.number_of_variables())
+ self.assertEqual(2, problem.number_of_objectives())
+ self.assertEqual(0, problem.number_of_constraints())
self.assertEqual([-1], problem.lower_bound)
self.assertEqual([1], problem.upper_bound)
- def test_should_create_solution_create_a_valid_solution(self) -> None:
+ def test_should_create_solution_create_a_valid_solution(self):
problem = DummyIntegerProblem()
- problem.number_of_variables = 2
- problem.number_of_objectives = 2
- problem.number_of_constraints = 0
+
problem.lower_bound = [-1, -2]
problem.upper_bound = [1, 2]
+ print(problem.number_of_variables())
+
solution = problem.create_solution()
self.assertNotEqual(None, solution)
self.assertTrue(-1 <= solution.variables[0] <= 1)
self.assertTrue(-2 <= solution.variables[1] <= 2)
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/jmetal/core/test/test_quality_indicator.py b/jmetal/core/test/test_quality_indicator.py
index f1c82048..109b10ce 100644
--- a/jmetal/core/test/test_quality_indicator.py
+++ b/jmetal/core/test/test_quality_indicator.py
@@ -1,16 +1,18 @@
+import os
import unittest
-from os.path import dirname, join
from pathlib import Path
import numpy as np
-from jmetal.core.quality_indicator import GenerationalDistance, InvertedGenerationalDistance, EpsilonIndicator, \
- HyperVolume
+from jmetal.core.quality_indicator import (EpsilonIndicator,
+ GenerationalDistance, HyperVolume,
+ InvertedGenerationalDistance,
+ NormalizedHyperVolume)
+
+DIRNAME = os.path.dirname(os.path.abspath(__file__))
-class GenerationalDistanceTestCases(unittest.TestCase):
- """ Class including unit tests for class GenerationalDistance
- """
+class GenerationalDistanceTestCases(unittest.TestCase):
def test_should_constructor_create_a_non_null_object(self) -> None:
indicator = GenerationalDistance([])
self.assertIsNotNone(indicator)
@@ -132,9 +134,6 @@ def test_case7(self):
class InvertedGenerationalDistanceTestCases(unittest.TestCase):
- """ Class including unit tests for class InvertedGenerationalDistance
- """
-
def test_should_constructor_create_a_non_null_object(self) -> None:
indicator = InvertedGenerationalDistance([])
self.assertIsNotNone(indicator)
@@ -231,19 +230,12 @@ def test_case5(self):
class EpsilonIndicatorTestCases(unittest.TestCase):
- """ Class including unit tests for class EpsilonIndicator
- """
-
def test_should_constructor_create_a_non_null_object(self) -> None:
indicator = EpsilonIndicator(np.array([[1.0, 1.0], [2.0, 2.0]]))
self.assertIsNotNone(indicator)
class HyperVolumeTestCases(unittest.TestCase):
-
- def setUp(self):
- self.file_path = dirname(join(dirname(__file__)))
-
def test_should_hypervolume_return_5_0(self):
reference_point = [2, 2, 2]
@@ -255,15 +247,13 @@ def test_should_hypervolume_return_5_0(self):
self.assertEqual(5.0, value)
def test_should_hypervolume_return_the_correct_value_when_applied_to_the_ZDT1_reference_front(self):
- filename = 'jmetal/core/test/ZDT1.pf'
+ filepath = Path(DIRNAME, "ZDT1.pf")
front = []
- if Path(filename).is_file():
- with open(filename) as file:
- for line in file:
- vector = [float(x) for x in line.split()]
- front.append(vector)
- else:
- print("error")
+
+ with open(filepath) as file:
+ for line in file:
+ vector = [float(x) for x in line.split()]
+ front.append(vector)
reference_point = [1, 1]
@@ -273,5 +263,35 @@ def test_should_hypervolume_return_the_correct_value_when_applied_to_the_ZDT1_re
self.assertAlmostEqual(0.666, value, delta=0.001)
-if __name__ == '__main__':
+class NormalizedHyperVolumeTestCases(unittest.TestCase):
+ @classmethod
+ def setUpClass(cls):
+ filepath = Path(DIRNAME, "ZDT1.pf")
+ front = []
+
+ with open(filepath) as file:
+ for line in file:
+ vector = [float(x) for x in line.split()]
+ front.append(vector)
+
+ cls._front = np.array(front)
+
+ def test_should_hypervolume_return_zero_when_providing_reference_front(self):
+ reference_point = [1, 1]
+ reference_front = self._front
+
+ hv = NormalizedHyperVolume(reference_point, reference_front=reference_front)
+ value = hv.compute(reference_front)
+
+ self.assertAlmostEqual(0, value, delta=0.001)
+
+ def test_should_raise_AssertionError_when_reference_front_hv_is_zero(self):
+ reference_point = [0, 0]
+ reference_front = self._front
+
+ with self.assertRaises(AssertionError):
+ _ = NormalizedHyperVolume(reference_point, reference_front=reference_front)
+
+
+if __name__ == "__main__":
unittest.main()
diff --git a/jmetal/core/test/test_solution.py b/jmetal/core/test/test_solution.py
index 2b005bee..7df19924 100644
--- a/jmetal/core/test/test_solution.py
+++ b/jmetal/core/test/test_solution.py
@@ -1,39 +1,44 @@
import copy
import unittest
-from jmetal.core.solution import BinarySolution, FloatSolution, IntegerSolution, Solution, CompositeSolution
+from jmetal.core.solution import (
+ BinarySolution,
+ CompositeSolution,
+ FloatSolution,
+ IntegerSolution,
+ Solution,
+)
from jmetal.util.ckecking import InvalidConditionException
class SolutionTestCase(unittest.TestCase):
-
- def test_should_default_constructor_create_a_valid_solution(self) -> None:
+ def test_should_default_constructor_create_a_valid_solution(self):
solution = Solution(2, 3)
- self.assertEqual(2, solution.number_of_variables)
- self.assertEqual(3, solution.number_of_objectives)
+ self.assertEqual(2, len(solution.variables))
+ self.assertEqual(3, len(solution.objectives))
self.assertEqual(0, len(solution.attributes))
self.assertEqual(2, len(solution.variables))
self.assertEqual(3, len(solution.objectives))
class BinarySolutionTestCase(unittest.TestCase):
- def test_should_default_constructor_create_a_valid_solution(self) -> None:
+ def test_should_default_constructor_create_a_valid_solution(self):
solution = BinarySolution(2, 3)
- self.assertEqual(2, solution.number_of_variables)
- self.assertEqual(3, solution.number_of_objectives)
+ self.assertEqual(2, len(solution.variables))
+ self.assertEqual(3, len(solution.objectives))
- def test_should_constructor_create_a_valid_solution(self) -> None:
+ def test_should_constructor_create_a_valid_solution(self):
solution = BinarySolution(number_of_variables=2, number_of_objectives=3)
solution.variables[0] = [True, False]
solution.variables[1] = [False]
- self.assertEqual(2, solution.number_of_variables)
- self.assertEqual(3, solution.number_of_objectives)
+ self.assertEqual(2, len(solution.variables))
+ self.assertEqual(3, len(solution.objectives))
self.assertEqual(2, len(solution.variables))
self.assertEqual(3, len(solution.objectives))
self.assertEqual([True, False], solution.variables[0])
self.assertEqual([False], solution.variables[1])
- def test_should_get_total_number_of_bits_return_zero_if_the_object_variables_are_not_initialized(self) -> None:
+ def test_should_get_total_number_of_bits_return_zero_if_the_object_variables_are_not_initialized(self):
solution = BinarySolution(number_of_variables=2, number_of_objectives=3)
self.assertEqual(0, solution.get_total_number_of_bits())
@@ -45,16 +50,15 @@ def test_should_get_total_number_of_bits_return_the_right_value(self) -> None:
class FloatSolutionTestCase(unittest.TestCase):
-
- def test_should_constructor_create_a_non_null_object(self) -> None:
+ def test_should_constructor_create_a_non_null_object(self):
solution = FloatSolution([], [], 2)
self.assertIsNotNone(solution)
- def test_should_default_constructor_create_a_valid_solution(self) -> None:
+ def test_should_default_constructor_create_a_valid_solution(self):
solution = FloatSolution([0.0, 0.5], [1.0, 2.0], 3)
- self.assertEqual(2, solution.number_of_variables)
- self.assertEqual(3, solution.number_of_objectives)
+ self.assertEqual(2, len(solution.variables))
+ self.assertEqual(3, len(solution.objectives))
self.assertEqual(2, len(solution.variables))
self.assertEqual(3, len(solution.objectives))
self.assertEqual([0.0, 0.5], solution.lower_bound)
@@ -69,8 +73,8 @@ def test_should_copy_work_properly(self) -> None:
new_solution = copy.copy(solution)
- self.assertEqual(solution.number_of_variables, new_solution.number_of_variables)
- self.assertEqual(solution.number_of_objectives, new_solution.number_of_objectives)
+ self.assertEqual(len(solution.variables), len(new_solution.variables))
+ self.assertEqual(len(solution.objectives), len(new_solution.objectives))
self.assertEqual(solution.variables, new_solution.variables)
self.assertEqual(solution.objectives, new_solution.objectives)
self.assertEqual(solution.lower_bound, new_solution.lower_bound)
@@ -82,23 +86,22 @@ def test_should_copy_work_properly(self) -> None:
class IntegerSolutionTestCase(unittest.TestCase):
-
- def test_should_constructor_create_a_non_null_object(self) -> None:
+ def test_should_constructor_create_a_non_null_object(self):
solution = IntegerSolution([], [], 2)
self.assertIsNotNone(solution)
- def test_should_default_constructor_create_a_valid_solution(self) -> None:
+ def test_should_default_constructor_create_a_valid_solution(self):
solution = IntegerSolution([0, 5], [1, 2], 3, 0)
- self.assertEqual(2, solution.number_of_variables)
- self.assertEqual(3, solution.number_of_objectives)
+ self.assertEqual(2, len(solution.variables))
+ self.assertEqual(3, len(solution.objectives))
self.assertEqual(2, len(solution.variables))
self.assertEqual(3, len(solution.objectives))
self.assertEqual(0, len(solution.constraints))
self.assertEqual([0, 5], solution.lower_bound)
self.assertEqual([1, 2], solution.upper_bound)
- def test_should_copy_work_properly(self) -> None:
+ def test_should_copy_work_properly(self):
solution = IntegerSolution([0, 5], [1, 2], 3, 1)
solution.variables = [1, 2]
solution.objectives = [0.16, -2.34, 9.25]
@@ -107,8 +110,8 @@ def test_should_copy_work_properly(self) -> None:
new_solution = copy.copy(solution)
- self.assertEqual(solution.number_of_variables, new_solution.number_of_variables)
- self.assertEqual(solution.number_of_objectives, new_solution.number_of_objectives)
+ self.assertEqual(len(solution.variables), len(new_solution.variables))
+ self.assertEqual(len(solution.objectives), len(new_solution.objectives))
self.assertEqual(solution.variables, new_solution.variables)
self.assertEqual(solution.objectives, new_solution.objectives)
self.assertEqual(solution.lower_bound, new_solution.lower_bound)
@@ -125,8 +128,8 @@ def test_should_constructor_create_a_valid_not_none_composite_solution_composed_
self.assertIsNotNone(composite_solution)
def test_should_constructor_raise_an_exception_if_the_number_of_objectives_is_not_coherent(self):
- float_solution: FloatSolution = FloatSolution([1.0], [3.0], 3)
- integer_solution: IntegerSolution = IntegerSolution([2], [4], 2)
+ float_solution = FloatSolution([1.0], [3.0], 3)
+ integer_solution = IntegerSolution([2], [4], 2)
with self.assertRaises(InvalidConditionException):
CompositeSolution([float_solution, integer_solution])
@@ -134,37 +137,38 @@ def test_should_constructor_raise_an_exception_if_the_number_of_objectives_is_no
def test_should_constructor_create_a_valid_soltion_composed_of_a_float_and_an_integer_solutions(self):
number_of_objectives = 3
number_of_constraints = 1
- float_solution: FloatSolution = FloatSolution([1.0], [3.0], number_of_objectives, number_of_constraints)
- integer_solution: IntegerSolution = IntegerSolution([2], [4], number_of_objectives, number_of_constraints)
- solution: CompositeSolution = CompositeSolution([float_solution, integer_solution])
+ float_solution = FloatSolution([1.0], [3.0], number_of_objectives, number_of_constraints)
+ integer_solution = IntegerSolution([2], [4], number_of_objectives, number_of_constraints)
+
+ solution = CompositeSolution([float_solution, integer_solution])
self.assertIsNotNone(solution)
- self.assertEqual(2, solution.number_of_variables)
- self.assertEqual(number_of_objectives, solution.number_of_objectives)
- self.assertEqual(number_of_constraints, solution.number_of_constraints)
- self.assertEqual(number_of_objectives, solution.variables[0].number_of_objectives)
- self.assertEqual(number_of_objectives, solution.variables[1].number_of_objectives)
- self.assertEqual(number_of_constraints, solution.variables[0].number_of_constraints)
- self.assertEqual(number_of_constraints, solution.variables[1].number_of_constraints)
+ self.assertEqual(2, len(solution.variables))
+ self.assertEqual(number_of_objectives, len(solution.objectives))
+ self.assertEqual(number_of_constraints, len(solution.constraints))
+ self.assertEqual(number_of_objectives, len(solution.variables[0].objectives))
+ self.assertEqual(number_of_objectives, len(solution.variables[1].objectives))
+ self.assertEqual(number_of_constraints, len(solution.variables[0].constraints))
+ self.assertEqual(number_of_constraints, len(solution.variables[1].constraints))
self.assertTrue(type(solution.variables[0] is FloatSolution))
self.assertTrue(type(solution.variables[1] is IntegerSolution))
def test_should_copy_work_properly(self):
number_of_objectives = 3
number_of_constraints = 1
- float_solution: FloatSolution = FloatSolution([1.0], [3.0], number_of_objectives, number_of_constraints)
- integer_solution: IntegerSolution = IntegerSolution([2], [4], number_of_objectives, number_of_constraints)
+ float_solution = FloatSolution([1.0], [3.0], number_of_objectives, number_of_constraints)
+ integer_solution = IntegerSolution([2], [4], number_of_objectives, number_of_constraints)
- solution: CompositeSolution = CompositeSolution([float_solution, integer_solution])
- new_solution: CompositeSolution = copy.deepcopy(solution)
+ solution = CompositeSolution([float_solution, integer_solution])
+ new_solution = copy.deepcopy(solution)
- self.assertEqual(solution.number_of_variables, new_solution.number_of_variables)
- self.assertEqual(solution.number_of_objectives, new_solution.number_of_objectives)
- self.assertEqual(solution.number_of_constraints, new_solution.number_of_constraints)
+ self.assertEqual(len(solution.variables), len(new_solution.variables))
+ self.assertEqual(len(solution.objectives), len(new_solution.objectives))
+ self.assertEqual(len(solution.constraints), len(new_solution.constraints))
- self.assertEqual(solution.variables[0].number_of_variables, new_solution.variables[0].number_of_variables)
- self.assertEqual(solution.variables[1].number_of_variables, new_solution.variables[1].number_of_variables)
+ self.assertEqual(len(solution.variables[0].variables), len(new_solution.variables[0].variables))
+ self.assertEqual(len(solution.variables[1].variables), len(new_solution.variables[1].variables))
self.assertEqual(solution.variables[0], new_solution.variables[0])
self.assertEqual(solution.variables[1], new_solution.variables[1])
@@ -172,5 +176,5 @@ def test_should_copy_work_properly(self):
self.assertEqual(solution.variables[1].variables, new_solution.variables[1].variables)
-if __name__ == '__main__':
+if __name__ == "__main__":
unittest.main()
diff --git a/jmetal/lab/experiment.py b/jmetal/lab/experiment.py
index 8beb2a40..dc8de35a 100644
--- a/jmetal/lab/experiment.py
+++ b/jmetal/lab/experiment.py
@@ -1,5 +1,4 @@
import io
-import logging
import os
from concurrent.futures import ProcessPoolExecutor
from pathlib import Path
@@ -9,13 +8,18 @@
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
-from scipy.stats import mannwhitneyu
+from scipy.stats import mannwhitneyu, iqr, ks_2samp
from jmetal.core.algorithm import Algorithm
from jmetal.core.quality_indicator import QualityIndicator
-from jmetal.util.solution import print_function_values_to_file, print_variables_to_file, read_solutions
+from jmetal.logger import get_logger
+from jmetal.util.solution import (
+ print_function_values_to_file,
+ print_variables_to_file,
+ read_solutions,
+)
-LOGGER = logging.getLogger('jmetal')
+logger = get_logger(__name__)
"""
.. module:: laboratory
@@ -27,32 +31,33 @@
class Job:
-
def __init__(self, algorithm: Algorithm, algorithm_tag: str, problem_tag: str, run: int):
self.algorithm = algorithm
self.algorithm_tag = algorithm_tag
self.problem_tag = problem_tag
self.run_tag = run
- def execute(self, output_path: str = ''):
+ def execute(self, output_path: str = ""):
self.algorithm.run()
if output_path:
- file_name = os.path.join(output_path, 'FUN.{}.tsv'.format(self.run_tag))
- print_function_values_to_file(self.algorithm.get_result(), filename=file_name)
+ file_name = os.path.join(output_path, "FUN.{}.tsv".format(self.run_tag))
+ print_function_values_to_file(self.algorithm.result(), filename=file_name)
- file_name = os.path.join(output_path, 'VAR.{}.tsv'.format(self.run_tag))
- print_variables_to_file(self.algorithm.get_result(), filename=file_name)
+ file_name = os.path.join(output_path, "VAR.{}.tsv".format(self.run_tag))
+ print_variables_to_file(self.algorithm.result(), filename=file_name)
- file_name = os.path.join(output_path, 'TIME.{}'.format(self.run_tag))
- with open(file_name, 'w+') as of:
+ file_name = os.path.join(output_path, "TIME.{}".format(self.run_tag))
+ with open(file_name, "w+") as of:
of.write(str(self.algorithm.total_computing_time))
+ def get_algorithm_data(self):
+ return self.algorithm.observable_data()
-class Experiment:
+class Experiment:
def __init__(self, output_dir: str, jobs: List[Job], m_workers: int = 6):
- """ Run an experiment to execute a list of jobs.
+ """Run an experiment to execute a list of jobs.
:param output_dir: Base directory where each job will save its results.
:param jobs: List of Jobs (from :py:mod:`jmetal.util.laboratory)`) to be executed.
@@ -61,17 +66,20 @@ def __init__(self, output_dir: str, jobs: List[Job], m_workers: int = 6):
self.jobs = jobs
self.m_workers = m_workers
self.output_dir = output_dir
+ self.job_data = []
def run(self) -> None:
with ProcessPoolExecutor(max_workers=self.m_workers) as executor:
for job in self.jobs:
output_path = os.path.join(self.output_dir, job.algorithm_tag, job.problem_tag)
executor.submit(job.execute(output_path))
+ self.job_data.append(job.get_algorithm_data())
-def generate_summary_from_experiment(input_dir: str, quality_indicators: List[QualityIndicator],
- reference_fronts: str = ''):
- """ Compute a list of quality indicators. The input data directory *must* met the following structure (this is generated
+def generate_summary_from_experiment(
+ input_dir: str, quality_indicators: List[QualityIndicator], reference_fronts: str = ""
+):
+ """Compute a list of quality indicators. The input data directory *must* met the following structure (this is generated
automatically by the Experiment class):
*
@@ -95,36 +103,36 @@ def generate_summary_from_experiment(input_dir: str, quality_indicators: List[Qu
if not quality_indicators:
quality_indicators = []
- with open('QualityIndicatorSummary.csv', 'w+') as of:
- of.write('Algorithm,Problem,ExecutionId,IndicatorName,IndicatorValue\n')
+ with open("QualityIndicatorSummary.csv", "w+") as of:
+ of.write("Algorithm,Problem,ExecutionId,IndicatorName,IndicatorValue\n")
for dirname, _, filenames in os.walk(input_dir):
for filename in filenames:
try:
# Linux filesystem
- algorithm, problem = dirname.split('/')[-2:]
+ algorithm, problem = dirname.split("/")[-2:]
except ValueError:
# Windows filesystem
- algorithm, problem = dirname.split('\\')[-2:]
+ algorithm, problem = dirname.split("\\")[-2:]
- if 'TIME' in filename:
- run_tag = [s for s in filename.split('.') if s.isdigit()].pop()
+ if "TIME" in filename:
+ run_tag = [s for s in filename.split(".") if s.isdigit()].pop()
- with open(os.path.join(dirname, filename), 'r') as content_file:
+ with open(os.path.join(dirname, filename), "r") as content_file:
content = content_file.read()
- with open('QualityIndicatorSummary.csv', 'a+') as of:
- of.write(','.join([algorithm, problem, run_tag, 'Time', str(content)]))
- of.write('\n')
+ with open("QualityIndicatorSummary.csv", "a+") as of:
+ of.write(",".join([algorithm, problem, run_tag, "Time", str(content)]))
+ of.write("\n")
- if 'FUN' in filename:
+ if "FUN" in filename:
solutions = read_solutions(os.path.join(dirname, filename))
- run_tag = [s for s in filename.split('.') if s.isdigit()].pop()
+ run_tag = [s for s in filename.split(".") if s.isdigit()].pop()
for indicator in quality_indicators:
- reference_front_file = os.path.join(reference_fronts, problem + '.pf')
+ reference_front_file = os.path.join(reference_fronts, problem + ".pf")
# Add reference front if any
- if hasattr(indicator, 'reference_front'):
+ if hasattr(indicator, "reference_front"):
if Path(reference_front_file).is_file():
reference_front = []
with open(reference_front_file) as file:
@@ -133,18 +141,18 @@ def generate_summary_from_experiment(input_dir: str, quality_indicators: List[Qu
indicator.reference_front = reference_front
else:
- LOGGER.warning('Reference front not found at', reference_front_file)
+ logger.warning("Reference front not found at", reference_front_file)
result = indicator.compute([solutions[i].objectives for i in range(len(solutions))])
# Save quality indicator value to file
- with open('QualityIndicatorSummary.csv', 'a+') as of:
- of.write(','.join([algorithm, problem, run_tag, indicator.get_short_name(), str(result)]))
- of.write('\n')
+ with open("QualityIndicatorSummary.csv", "a+") as of:
+ of.write(",".join([algorithm, problem, run_tag, indicator.get_short_name(), str(result)]))
+ of.write("\n")
-def generate_boxplot(filename: str, output_dir: str = 'boxplot'):
- """ Generate boxplot diagrams.
+def generate_boxplot(filename: str, output_dir: str = "boxplot"):
+ """Generate boxplot diagrams.
:param filename: Input filename (summary).
:param output_dir: Output path.
@@ -152,31 +160,32 @@ def generate_boxplot(filename: str, output_dir: str = 'boxplot'):
df = pd.read_csv(filename, skipinitialspace=True)
if len(set(df.columns.tolist())) != 5:
- raise Exception('Wrong number of columns')
+ raise Exception("Wrong number of columns")
if Path(output_dir).is_dir():
- LOGGER.warning('Directory {} exists. Removing contents.'.format(output_dir))
+ logger.warning("Directory {} exists. Removing contents.".format(output_dir))
for file in os.listdir(output_dir):
- os.remove('{0}/{1}'.format(output_dir, file))
+ os.remove("{0}/{1}".format(output_dir, file))
else:
- LOGGER.warning('Directory {} does not exist. Creating it.'.format(output_dir))
+ logger.warning("Directory {} does not exist. Creating it.".format(output_dir))
Path(output_dir).mkdir(parents=True)
- algorithms = pd.unique(df['Algorithm'])
- problems = pd.unique(df['Problem'])
- indicators = pd.unique(df['IndicatorName'])
+ algorithms = pd.unique(df["Algorithm"])
+ problems = pd.unique(df["Problem"])
+ indicators = pd.unique(df["IndicatorName"])
# We consider the quality indicator indicator_name
for indicator_name in indicators:
- data = df[df['IndicatorName'] == indicator_name]
+ data = df[df["IndicatorName"] == indicator_name]
for pr in problems:
data_to_plot = []
for alg in algorithms:
- data_to_plot.append(data['IndicatorValue'][np.logical_and(
- data['Algorithm'] == alg, data['Problem'] == pr)])
+ data_to_plot.append(
+ data["IndicatorValue"][np.logical_and(data["Algorithm"] == alg, data["Problem"] == pr)]
+ )
# Create a figure instance
fig = plt.figure(1, figsize=(9, 6))
@@ -188,13 +197,13 @@ def generate_boxplot(filename: str, output_dir: str = 'boxplot'):
ax.set_xticklabels(algorithms)
ax.tick_params(labelsize=20)
- plt.savefig(os.path.join(output_dir, 'boxplot-{}-{}.png'.format(pr, indicator_name)), bbox_inches='tight')
- plt.savefig(os.path.join(output_dir, 'boxplot-{}-{}.eps'.format(pr, indicator_name)), bbox_inches='tight')
+ plt.savefig(os.path.join(output_dir, "boxplot-{}-{}.png".format(pr, indicator_name)), bbox_inches="tight")
+ plt.savefig(os.path.join(output_dir, "boxplot-{}-{}.eps".format(pr, indicator_name)), bbox_inches="tight")
plt.close(fig)
-def generate_latex_tables(filename: str, output_dir: str = 'latex/statistical'):
- """ Computes a number of statistical values (mean, median, standard deviation, interquartile range).
+def generate_latex_tables(filename: str, output_dir: str = "latex/statistical"):
+ """Computes a number of statistical values (mean, median, standard deviation, interquartile range).
:param filename: Input filename (summary).
:param output_dir: Output path.
@@ -202,24 +211,24 @@ def generate_latex_tables(filename: str, output_dir: str = 'latex/statistical'):
df = pd.read_csv(filename, skipinitialspace=True)
if len(set(df.columns.tolist())) != 5:
- raise Exception('Wrong number of columns')
+ raise Exception("Wrong number of columns")
if Path(output_dir).is_dir():
- LOGGER.warning('Directory {} exists. Removing contents.'.format(output_dir))
+ logger.warning("Directory {} exists. Removing contents.".format(output_dir))
for file in os.listdir(output_dir):
- os.remove('{0}/{1}'.format(output_dir, file))
+ os.remove("{0}/{1}".format(output_dir, file))
else:
- LOGGER.warning('Directory {} does not exist. Creating it.'.format(output_dir))
+ logger.warning("Directory {} does not exist. Creating it.".format(output_dir))
Path(output_dir).mkdir(parents=True)
# Generate median & iqr tables
median, iqr = pd.DataFrame(), pd.DataFrame()
mean, std = pd.DataFrame(), pd.DataFrame()
- for algorithm_name, subset in df.groupby('Algorithm', sort=False):
- subset = subset.drop('Algorithm', axis=1)
- subset = subset.rename(columns={'IndicatorValue': algorithm_name})
- subset = subset.set_index(['Problem', 'IndicatorName', 'ExecutionId'])
+ for algorithm_name, subset in df.groupby("Algorithm", sort=False):
+ subset = subset.drop("Algorithm", axis=1)
+ subset = subset.rename(columns={"IndicatorValue": algorithm_name})
+ subset = subset.set_index(["Problem", "IndicatorName", "ExecutionId"])
# Compute Median and Interquartile range
median_ = subset.groupby(level=[0, 1]).median()
@@ -236,63 +245,63 @@ def generate_latex_tables(filename: str, output_dir: str = 'latex/statistical'):
std = pd.concat([std, std_], axis=1)
# Generate mean & std tables
- for indicator_name, subset in std.groupby('IndicatorName', sort=False):
- subset = median.groupby('IndicatorName', sort=False).get_group(indicator_name)
+ for indicator_name, subset in std.groupby("IndicatorName", sort=False):
+ subset = median.groupby("IndicatorName", sort=False).get_group(indicator_name)
subset.index = subset.index.droplevel(1)
- subset.to_csv(os.path.join(output_dir, 'Median-{}.csv'.format(indicator_name)), sep='\t', encoding='utf-8')
+ subset.to_csv(os.path.join(output_dir, "Median-{}.csv".format(indicator_name)), sep="\t", encoding="utf-8")
- subset = iqr.groupby('IndicatorName', sort=False).get_group(indicator_name)
+ subset = iqr.groupby("IndicatorName", sort=False).get_group(indicator_name)
subset.index = subset.index.droplevel(1)
- subset.to_csv(os.path.join(output_dir, 'IQR-{}.csv'.format(indicator_name)), sep='\t', encoding='utf-8')
+ subset.to_csv(os.path.join(output_dir, "IQR-{}.csv".format(indicator_name)), sep="\t", encoding="utf-8")
- subset = mean.groupby('IndicatorName', sort=False).get_group(indicator_name)
+ subset = mean.groupby("IndicatorName", sort=False).get_group(indicator_name)
subset.index = subset.index.droplevel(1)
- subset.to_csv(os.path.join(output_dir, 'Mean-{}.csv'.format(indicator_name)), sep='\t', encoding='utf-8')
+ subset.to_csv(os.path.join(output_dir, "Mean-{}.csv".format(indicator_name)), sep="\t", encoding="utf-8")
- subset = std.groupby('IndicatorName', sort=False).get_group(indicator_name)
+ subset = std.groupby("IndicatorName", sort=False).get_group(indicator_name)
subset.index = subset.index.droplevel(1)
- subset.to_csv(os.path.join(output_dir, 'Std-{}.csv'.format(indicator_name)), sep='\t', encoding='utf-8')
+ subset.to_csv(os.path.join(output_dir, "Std-{}.csv".format(indicator_name)), sep="\t", encoding="utf-8")
# Generate LaTeX tables
- for indicator_name in df.groupby('IndicatorName', sort=False).groups.keys():
+ for indicator_name in df.groupby("IndicatorName", sort=False).groups.keys():
# Median & IQR
- md = median.groupby('IndicatorName', sort=False).get_group(indicator_name)
+ md = median.groupby("IndicatorName", sort=False).get_group(indicator_name)
md.index = md.index.droplevel(1)
- i = iqr.groupby('IndicatorName', sort=False).get_group(indicator_name)
+ i = iqr.groupby("IndicatorName", sort=False).get_group(indicator_name)
i.index = i.index.droplevel(1)
- with open(os.path.join(output_dir, 'MedianIQR-{}.tex'.format(indicator_name)), 'w') as latex:
+ with open(os.path.join(output_dir, "MedianIQR-{}.tex".format(indicator_name)), "w") as latex:
latex.write(
__averages_to_latex(
md,
i,
- caption='Median and Interquartile Range of the {} quality indicator.'.format(indicator_name),
+ caption="Median and Interquartile Range of the {} quality indicator.".format(indicator_name),
minimization=check_minimization(indicator_name),
- label='table:{}'.format(indicator_name)
+ label="table:{}".format(indicator_name),
)
)
# Mean & Std
- mn = mean.groupby('IndicatorName', sort=False).get_group(indicator_name)
+ mn = mean.groupby("IndicatorName", sort=False).get_group(indicator_name)
mn.index = mn.index.droplevel(1)
- s = std.groupby('IndicatorName', sort=False).get_group(indicator_name)
+ s = std.groupby("IndicatorName", sort=False).get_group(indicator_name)
s.index = s.index.droplevel(1)
- with open(os.path.join(output_dir, 'MeanStd-{}.tex'.format(indicator_name)), 'w') as latex:
+ with open(os.path.join(output_dir, "MeanStd-{}.tex".format(indicator_name)), "w") as latex:
latex.write(
__averages_to_latex(
mn,
s,
- caption='Mean and Standard Deviation of the {} quality indicator.'.format(indicator_name),
+ caption="Mean and Standard Deviation of the {} quality indicator.".format(indicator_name),
minimization=check_minimization(indicator_name),
- label='table:{}'.format(indicator_name)
+ label="table:{}".format(indicator_name),
)
)
-def compute_wilcoxon(filename: str, output_dir: str = 'latex/wilcoxon'):
+def compute_wilcoxon(filename: str, output_dir: str = "latex/wilcoxon"):
"""
:param filename: Input filename (summary).
:param output_dir: Output path.
@@ -300,19 +309,19 @@ def compute_wilcoxon(filename: str, output_dir: str = 'latex/wilcoxon'):
df = pd.read_csv(filename, skipinitialspace=True)
if len(set(df.columns.tolist())) != 5:
- raise Exception('Wrong number of columns')
+ raise Exception("Wrong number of columns")
if Path(output_dir).is_dir():
- LOGGER.warning('Directory {} exists. Removing contents.'.format(output_dir))
+ logger.warning("Directory {} exists. Removing contents.".format(output_dir))
for file in os.listdir(output_dir):
- os.remove('{0}/{1}'.format(output_dir, file))
+ os.remove("{0}/{1}".format(output_dir, file))
else:
- LOGGER.warning('Directory {} does not exist. Creating it.'.format(output_dir))
+ logger.warning("Directory {} does not exist. Creating it.".format(output_dir))
Path(output_dir).mkdir(parents=True)
- algorithms = pd.unique(df['Algorithm'])
- problems = pd.unique(df['Problem'])
- indicators = pd.unique(df['IndicatorName'])
+ algorithms = pd.unique(df["Algorithm"])
+ problems = pd.unique(df["Problem"])
+ indicators = pd.unique(df["IndicatorName"])
table = pd.DataFrame(index=algorithms[0:-1], columns=algorithms[1:])
@@ -324,10 +333,16 @@ def compute_wilcoxon(filename: str, output_dir: str = 'latex/wilcoxon'):
if i <= j:
for problem in problems:
- df1 = df[(df["Algorithm"] == row_algorithm) & (df["Problem"] == problem) & (
- df["IndicatorName"] == indicator_name)]
- df2 = df[(df["Algorithm"] == col_algorithm) & (df["Problem"] == problem) & (
- df["IndicatorName"] == indicator_name)]
+ df1 = df[
+ (df["Algorithm"] == row_algorithm)
+ & (df["Problem"] == problem)
+ & (df["IndicatorName"] == indicator_name)
+ ]
+ df2 = df[
+ (df["Algorithm"] == col_algorithm)
+ & (df["Problem"] == problem)
+ & (df["IndicatorName"] == indicator_name)
+ ]
data1 = df1["IndicatorValue"]
data2 = df2["IndicatorValue"]
@@ -340,49 +355,51 @@ def compute_wilcoxon(filename: str, output_dir: str = 'latex/wilcoxon'):
if p <= 0.05:
if check_minimization(indicator_name):
if median1 <= median2:
- line.append('+')
+ line.append("+")
else:
- line.append('o')
+ line.append("o")
else:
if median1 >= median2:
- line.append('+')
+ line.append("+")
else:
- line.append('o')
+ line.append("o")
else:
- line.append('-')
- wilcoxon.append(''.join(line))
+ line.append("-")
+ wilcoxon.append("".join(line))
- if len(wilcoxon) < len(algorithms): wilcoxon = [''] * (len(algorithms) - len(wilcoxon) - 1) + wilcoxon
+ if len(wilcoxon) < len(algorithms):
+ wilcoxon = [""] * (len(algorithms) - len(wilcoxon) - 1) + wilcoxon
table.loc[row_algorithm] = wilcoxon
- table.to_csv(os.path.join(output_dir, 'Wilcoxon-{}.csv'.format(indicator_name)), sep='\t', encoding='utf-8')
+ table.to_csv(os.path.join(output_dir, "Wilcoxon-{}.csv".format(indicator_name)), sep="\t", encoding="utf-8")
- with open(os.path.join(output_dir, 'Wilcoxon-{}.tex'.format(indicator_name)), 'w') as latex:
+ with open(os.path.join(output_dir, "Wilcoxon-{}.tex".format(indicator_name)), "w") as latex:
latex.write(
__wilcoxon_to_latex(
table,
- caption='Wilcoxon values of the {} quality indicator ({}).'.format(indicator_name,
- ', '.join(problems)),
- label='table:{}'.format(indicator_name)
+ caption="Wilcoxon values of the {} quality indicator ({}).".format(
+ indicator_name, ", ".join(problems)
+ ),
+ label="table:{}".format(indicator_name),
)
)
def compute_mean_indicator(filename: str, indicator_name: str):
- """ Compute the mean values of an indicator.
+ """Compute the mean values of an indicator.
:param filename:
:param indicator_name: Quality indicator name.
"""
df = pd.read_csv(filename, skipinitialspace=True)
if len(set(df.columns.tolist())) != 5:
- raise Exception('Wrong number of columns')
+ raise Exception("Wrong number of columns")
- algorithms = pd.unique(df['Algorithm'])
- problems = pd.unique(df['Problem'])
+ algorithms = pd.unique(df["Algorithm"])
+ problems = pd.unique(df["Problem"])
# We consider the quality indicator indicator_name
- data = df[df['IndicatorName'] == indicator_name]
+ data = df[df["IndicatorName"] == indicator_name]
# Compute for each pair algorithm/problem the average of IndicatorValue
average_values = np.zeros((problems.size, algorithms.size))
@@ -390,8 +407,9 @@ def compute_mean_indicator(filename: str, indicator_name: str):
for alg in algorithms:
i = 0
for pr in problems:
- average_values[i, j] = data['IndicatorValue'][np.logical_and(
- data['Algorithm'] == alg, data['Problem'] == pr)].mean()
+ average_values[i, j] = data["IndicatorValue"][
+ np.logical_and(data["Algorithm"] == alg, data["Problem"] == pr)
+ ].mean()
i += 1
j += 1
@@ -402,9 +420,164 @@ def compute_mean_indicator(filename: str, indicator_name: str):
return df
-def __averages_to_latex(central_tendency: pd.DataFrame, dispersion: pd.DataFrame,
- caption: str, label: str, minimization=True, alignment: str = 'c'):
- """ Convert a pandas DataFrame to a LaTeX tabular. Prints labels in bold and does use math mode.
+def generate_median_and_wilcoxon_latex_tables(filename: str, output_dir: str = "latex/meansAndWilcoxon"):
+ """Generate Latex tables including medians and IQRs. Additionally, the last algorithm is considered as the reference
+ algorithm, and the cells include a symbol indicating whether the differences with the reference algorithm
+ are significant or not according to the Wilcoxon rank sum test.
+
+ :param filename: Input filename (summary).
+ :param output_dir: Output path.
+ """
+ data = pd.read_csv(filename, skipinitialspace=True)
+
+ if len(set(data.columns.tolist())) != 5:
+ raise Exception("Wrong number of columns")
+
+ if Path(output_dir).is_dir():
+ logger.warning("Directory {} exists. Removing contents.".format(output_dir))
+ for file in os.listdir(output_dir):
+ os.remove("{0}/{1}".format(output_dir, file))
+ else:
+ logger.warning("Directory {} does not exist. Creating it.".format(output_dir))
+ Path(output_dir).mkdir(parents=True)
+
+ algorithms = pd.unique(data["Algorithm"])
+ problems = pd.unique(data["Problem"])
+ indicators = pd.unique(data["IndicatorName"])
+
+ control_algorithm = algorithms[-1]
+
+ # Compute medians and IQRs
+ medians = data.groupby(["Algorithm", "Problem", "IndicatorName"])["IndicatorValue"].median()
+ iqrs = data.groupby(["Algorithm", "Problem", "IndicatorName"])["IndicatorValue"].apply(lambda x: iqr(x))
+
+ # Create data frame to store the Wilcoxon test results
+ wilcoxon_data = pd.DataFrame(columns=["Indicator", "Algorithm", "Problem", "PValue", "Median", "TestResult"])
+
+ for indicator in indicators:
+ for algorithm in algorithms:
+ for problem in problems:
+ algorithm_data = data[(data["Problem"] == problem) & (data["Algorithm"] == algorithm) & (
+ data["IndicatorName"] == indicator)]
+ ref_data = data[(data["Problem"] == problem) & (data["Algorithm"] == control_algorithm) & (
+ data["IndicatorName"] == indicator)]
+ stat, p_value = mannwhitneyu(algorithm_data["IndicatorValue"], ref_data["IndicatorValue"])
+
+ test_result = ""
+ if p_value <= 0.05:
+ if check_minimization(indicator):
+ if medians[algorithm][problem][indicator] <= medians[control_algorithm][problem][indicator]:
+ test_result = '+'
+ else:
+ test_result = '-'
+ else:
+ if medians[algorithm][problem][indicator] >= medians[control_algorithm][problem][indicator]:
+ test_result = '+'
+ else:
+ test_result = '-'
+ else:
+ test_result = '='
+
+ new_row = {'Indicator': indicator, 'Algorithm': algorithm, "Problem": problem,
+ "PValue": p_value,
+ "Median": medians[algorithm][problem][indicator],
+ "IQR": iqrs[algorithm][problem][indicator],
+ "TestResult": test_result
+ }
+ wilcoxon_data = wilcoxon_data._append(new_row, ignore_index=True)
+
+ # Generate LaTeX tables
+ caption = "Median and interquartile range (IQR) of the results of the {} quality indicator. " + \
+ "Cells with dark and light gray background highlights, respectively, the best and second best indicator values. " + \
+ "The algorithm in the last column is the reference " + \
+ "algorithm, and the symbols $+$, $-$ and $\\approx$ indicate that the differences with the reference " + \
+ "algorithm are significantly better, worse, or there is no difference according to the Wilcoxon rank " + \
+ "sum test (confidence level: 95\%)."
+ for indicator_name in indicators:
+ with open(os.path.join(output_dir, "MedianIQRWilcoxon-{}.tex".format(indicator_name)), "w") as latex:
+ latex.write(
+ __median_wilcoxon_to_latex(
+ indicator_name,
+ wilcoxon_data,
+ caption=caption.format(indicator_name),
+ label="table:{}".format(indicator_name),
+ )
+ )
+
+
+def generate_kolmogorov_smirnov_latex_tables(filename: str, output_dir: str = "latex/KolmogorovSmirnov"):
+ """Generate Latex tables with the results of the Kolmogorov-Smirnov test. The last algorithm is considered as
+ the reference algorithm, and the cells include a symbol with the p-value < 0.05.
+
+ :param filename: Input filename (summary).
+ :param output_dir: Output path.
+ """
+ data = pd.read_csv(filename, skipinitialspace=True)
+
+ if len(set(data.columns.tolist())) != 5:
+ raise Exception("Wrong number of columns")
+
+ if Path(output_dir).is_dir():
+ logger.warning("Directory {} exists. Removing contents.".format(output_dir))
+ for file in os.listdir(output_dir):
+ os.remove("{0}/{1}".format(output_dir, file))
+ else:
+ logger.warning("Directory {} does not exist. Creating it.".format(output_dir))
+ Path(output_dir).mkdir(parents=True)
+
+ algorithms = pd.unique(data["Algorithm"])
+ problems = pd.unique(data["Problem"])
+ indicators = pd.unique(data["IndicatorName"])
+
+ control_algorithm = algorithms[-1]
+
+ # Create data frame to store the Kolmogorov Smirnov test results
+ test_data = pd.DataFrame(columns=["Indicator", "Algorithm", "Problem", "PValue", "TestResult"])
+
+ for indicator in indicators:
+ for algorithm in algorithms:
+ for problem in problems:
+ algorithm_data = data[(data["Problem"] == problem) & (data["Algorithm"] == algorithm) & (
+ data["IndicatorName"] == indicator)]
+ ref_data = data[(data["Problem"] == problem) & (data["Algorithm"] == control_algorithm) & (
+ data["IndicatorName"] == indicator)]
+ stat, p_value = ks_2samp(algorithm_data["IndicatorValue"], ref_data["IndicatorValue"])
+
+ test_result = stat
+
+ new_row = {'Indicator': indicator, 'Algorithm': algorithm, "Problem": problem,
+ "PValue": p_value,
+ "TestResult": test_result
+ }
+ test_data = test_data._append(new_row, ignore_index=True)
+
+ # Generate LaTeX tables
+ caption = "Kolmogorov-Smirnov Test of the {} quality indicator. " \
+ "The algorithm in the last column is the reference " + \
+ "algorithm and each cell contain the p-value obtained when applying the test with the reference " \
+ "algorithm. Cells with gray background highlight p-values less than 0.05 (i.e., the null hypothesis" \
+ " -- the two distributions are identical -- is rejected)."
+ for indicator_name in indicators:
+ with open(os.path.join(output_dir, "KolmogorovSmirnov-{}.tex".format(indicator_name)), "w") as latex:
+ latex.write(
+ __kolmogorov_smirnov_to_latex(
+ indicator_name,
+ test_data,
+ caption=caption.format(indicator_name),
+ label="table:{}".format(indicator_name),
+ )
+ )
+
+
+def __averages_to_latex(
+ central_tendency: pd.DataFrame,
+ dispersion: pd.DataFrame,
+ caption: str,
+ label: str,
+ minimization=True,
+ alignment: str = "c",
+):
+ """Convert a pandas DataFrame to a LaTeX tabular. Prints labels in bold and does use math mode.
:param caption: LaTeX table caption.
:param label: LaTeX table label.
@@ -413,40 +586,40 @@ def __averages_to_latex(central_tendency: pd.DataFrame, dispersion: pd.DataFrame
num_columns, num_rows = central_tendency.shape[1], central_tendency.shape[0]
output = io.StringIO()
- col_format = '{}|{}'.format(alignment, alignment * num_columns)
- column_labels = ['\\textbf{{{0}}}'.format(label.replace('_', '\\_')) for label in central_tendency.columns]
+ col_format = "{}|{}".format(alignment, alignment * num_columns)
+ column_labels = ["\\textbf{{{0}}}".format(label.replace("_", "\\_")) for label in central_tendency.columns]
# Write header
- output.write('\\documentclass{article}\n')
+ output.write("\\documentclass{article}\n")
- output.write('\\usepackage[utf8]{inputenc}\n')
- output.write('\\usepackage{tabularx}\n')
- output.write('\\usepackage{colortbl}\n')
- output.write('\\usepackage[table*]{xcolor}\n')
+ output.write("\\usepackage[utf8]{inputenc}\n")
+ output.write("\\usepackage{tabularx}\n")
+ output.write("\\usepackage{colortbl}\n")
+ output.write("\\usepackage[table*]{xcolor}\n")
- output.write('\\xdefinecolor{gray95}{gray}{0.65}\n')
- output.write('\\xdefinecolor{gray25}{gray}{0.8}\n')
+ output.write("\\xdefinecolor{gray95}{gray}{0.65}\n")
+ output.write("\\xdefinecolor{gray25}{gray}{0.8}\n")
- output.write('\\title{Median and IQR}\n')
- output.write('\\author{}\n')
+ output.write("\\title{Median and IQR}\n")
+ output.write("\\author{}\n")
- output.write('\\begin{document}\n')
- output.write('\\maketitle\n')
+ output.write("\\begin{document}\n")
+ output.write("\\maketitle\n")
- output.write('\\section{Table}\n')
+ output.write("\\section{Table}\n")
- output.write('\\begin{table}[!htp]\n')
- output.write(' \\caption{{{}}}\n'.format(caption))
- output.write(' \\label{{{}}}\n'.format(label))
- output.write(' \\centering\n')
- output.write(' \\begin{scriptsize}\n')
- output.write(' \\begin{tabular}{%s}\n' % col_format)
- output.write(' & {} \\\\\\hline\n'.format(' & '.join(column_labels)))
+ output.write("\\begin{table}[!htp]\n")
+ output.write(" \\caption{{{}}}\n".format(caption))
+ output.write(" \\label{{{}}}\n".format(label))
+ output.write(" \\centering\n")
+ output.write(" \\begin{scriptsize}\n")
+ output.write(" \\begin{tabular}{%s}\n" % col_format)
+ output.write(" & {} \\\\\\hline\n".format(" & ".join(column_labels)))
# Write data lines
for i in range(num_rows):
- central_values = [v for v in central_tendency.ix[i]]
- dispersion_values = [v for v in dispersion.ix[i]]
+ central_values = [v for v in central_tendency.iloc[i]]
+ dispersion_values = [v for v in dispersion.iloc[i]]
# Sort mean/median values (the lower the better if minimization)
# Note that mean/median values could be the same: in that case, sort by Std/IQR (the lower the better)
@@ -460,29 +633,32 @@ def __averages_to_latex(central_tendency: pd.DataFrame, dispersion: pd.DataFrame
second_best, best = sorted_values[-1][2], sorted_values[-2][2]
# Compose cell
- values = ['{:.2e}_{{{:.2e}}}'.format(central_values[i], dispersion_values[i]) for i in
- range(len(central_values))]
+ values = [
+ "{:.2e}_{{{:.2e}}}".format(central_values[i], dispersion_values[i]) for i in range(len(central_values))
+ ]
# Highlight values
- values[best] = '\\cellcolor{gray25} ' + values[best]
- values[second_best] = '\\cellcolor{gray95} ' + values[second_best]
+ values[best] = "\\cellcolor{gray25} " + values[best]
+ values[second_best] = "\\cellcolor{gray95} " + values[second_best]
- output.write(' \\textbf{{{0}}} & ${1}$ \\\\\n'.format(
- central_tendency.index[i], ' $ & $ '.join([str(val) for val in values]))
+ output.write(
+ " \\textbf{{{0}}} & ${1}$ \\\\\n".format(
+ central_tendency.index[i], " $ & $ ".join([str(val) for val in values])
+ )
)
# Write footer
- output.write(' \\end{tabular}\n')
- output.write(' \\end{scriptsize}\n')
- output.write('\\end{table}\n')
+ output.write(" \\end{tabular}\n")
+ output.write(" \\end{scriptsize}\n")
+ output.write("\\end{table}\n")
- output.write('\\end{document}')
+ output.write("\\end{document}")
return output.getvalue()
-def __wilcoxon_to_latex(df: pd.DataFrame, caption: str, label: str, minimization=True, alignment: str = 'c'):
- """ Convert a pandas DataFrame to a LaTeX tabular. Prints labels in bold and does use math mode.
+def __wilcoxon_to_latex(df: pd.DataFrame, caption: str, label: str, minimization=True, alignment: str = "c"):
+ """Convert a pandas DataFrame to a LaTeX tabular. Prints labels in bold and does use math mode.
:param df: Pandas dataframe.
:param caption: LaTeX table caption.
@@ -492,58 +668,242 @@ def __wilcoxon_to_latex(df: pd.DataFrame, caption: str, label: str, minimization
num_columns, num_rows = df.shape[1], df.shape[0]
output = io.StringIO()
- col_format = '{}|{}'.format(alignment, alignment * num_columns)
- column_labels = ['\\textbf{{{0}}}'.format(label.replace('_', '\\_')) for label in df.columns]
+ col_format = "{}|{}".format(alignment, alignment * num_columns)
+ column_labels = ["\\textbf{{{0}}}".format(label.replace("_", "\\_")) for label in df.columns]
# Write header
- output.write('\\documentclass{article}\n')
+ output.write("\\documentclass{article}\n")
- output.write('\\usepackage[utf8]{inputenc}\n')
- output.write('\\usepackage{tabularx}\n')
- output.write('\\usepackage{amssymb}\n')
- output.write('\\usepackage{amsmath}\n')
+ output.write("\\usepackage[utf8]{inputenc}\n")
+ output.write("\\usepackage{tabularx}\n")
+ output.write("\\usepackage{amssymb}\n")
+ output.write("\\usepackage{amsmath}\n")
- output.write('\\title{Wilcoxon - Mann-Whitney rank sum test}\n')
- output.write('\\author{}\n')
+ output.write("\\title{Wilcoxon - Mann-Whitney rank sum test}\n")
+ output.write("\\author{}\n")
- output.write('\\begin{document}\n')
- output.write('\\maketitle\n')
+ output.write("\\begin{document}\n")
+ output.write("\\maketitle\n")
- output.write('\\section{Table}\n')
+ output.write("\\section{Table}\n")
- output.write('\\begin{table}[!htp]\n')
- output.write(' \\caption{{{}}}\n'.format(caption))
- output.write(' \\label{{{}}}\n'.format(label))
- output.write(' \\centering\n')
- output.write(' \\begin{scriptsize}\n')
- output.write(' \\begin{tabular}{%s}\n' % col_format)
- output.write(' & {} \\\\\\hline\n'.format(' & '.join(column_labels)))
+ output.write("\\begin{table}[!htp]\n")
+ output.write(" \\caption{{{}}}\n".format(caption))
+ output.write(" \\label{{{}}}\n".format(label))
+ output.write(" \\centering\n")
+ output.write(" \\begin{scriptsize}\n")
+ output.write(" \\begin{tabular}{%s}\n" % col_format)
+ output.write(" & {} \\\\\\hline\n".format(" & ".join(column_labels)))
- symbolo = '\\triangledown\ '
- symbolplus = '\\blacktriangle\ '
+ symbolo = "\\triangledown\ "
+ symbolplus = "\\blacktriangle\ "
if not minimization:
symbolo, symbolplus = symbolplus, symbolo
# Write data lines
for i in range(num_rows):
- values = [val.replace('-', '\\text{--}\ ').replace('o', symbolo).replace('+', symbolplus) for val in df.ix[i]]
- output.write(' \\textbf{{{0}}} & ${1}$ \\\\\n'.format(
- df.index[i], ' $ & $ '.join([str(val) for val in values]))
+ values = [val.replace("-", "\\text{--}\ ").replace("o", symbolo).replace("+", symbolplus) for val in df.iloc[i]]
+ output.write(
+ " \\textbf{{{0}}} & ${1}$ \\\\\n".format(df.index[i], " $ & $ ".join([str(val) for val in values]))
+ )
+
+ # Write footer
+ output.write(" \\end{tabular}\n")
+ output.write(" \\end{scriptsize}\n")
+ output.write("\\end{table}\n")
+
+ output.write("\\end{document}")
+
+ return output.getvalue()
+
+
+def __median_wilcoxon_to_latex(
+ indicator_name: str,
+ wilcoxon_data: pd.DataFrame,
+ caption: str,
+ label):
+ indicator_data = wilcoxon_data[wilcoxon_data["Indicator"] == indicator_name]
+
+ problems = pd.unique(indicator_data["Problem"])
+ algorithms = pd.unique(indicator_data["Algorithm"])
+
+ num_columns = len(algorithms)
+ columns = algorithms
+
+ alignment = "c"
+ col_format = "{}|{}".format(alignment, alignment * num_columns)
+ column_labels = ["\\textbf{{{0}}}".format(label.replace("_", "\\_")) for label in columns]
+
+ output = io.StringIO()
+
+ output.write("\\documentclass{article}\n")
+
+ output.write("\\usepackage[utf8]{inputenc}\n")
+ output.write("\\usepackage{tabularx}\n")
+ output.write("\\usepackage{colortbl}\n")
+ output.write("\\usepackage[table*]{xcolor}\n")
+
+ output.write("\\xdefinecolor{gray95}{gray}{0.65}\n")
+ output.write("\\xdefinecolor{gray25}{gray}{0.8}\n")
+
+ output.write("\\title{Median and Wilcoxon}\n")
+ output.write("\\author{}\n")
+
+ output.write("\\begin{document}\n")
+ output.write("\\maketitle\n")
+
+ output.write("\\section{Table}\n")
+
+ output.write("\\begin{table}[!htp]\n")
+ output.write(" \\caption{{{}}}\n".format(caption))
+ output.write(" \\label{{{}}}\n".format(label))
+ output.write(" \\centering\n")
+ output.write(" \\begin{tiny}\n")
+ output.write(" \\begin{tabular}{%s}\n" % col_format)
+ output.write(" & {} \\\\\\hline\n".format(" & ".join(column_labels)))
+
+ # Counts the number of times that an algorithm performs better, worse or equal than the reference algorithm
+ counters = {}
+ for algorithm in algorithms:
+ counters[algorithm] = [0, 0, 0] # best, equal, worse
+
+ for problem in problems:
+ values = []
+
+ for algorithm in algorithms:
+ row = indicator_data[(indicator_data["Problem"] == problem) & (indicator_data["Algorithm"] == algorithm)]
+ value = "{:.2e}({:.2e})".format(row["Median"].tolist()[0], row["IQR"].tolist()[0])
+
+ # Include the symbol according to the Wilcoxon rank sum test with the reference algorithm
+ if algorithm != algorithms[-1]:
+ if row["TestResult"].tolist()[0] == "-":
+ value = "{{{}-}}".format(value)
+ counters[algorithm][2] = counters[algorithm][2] + 1
+ elif row["TestResult"].tolist()[0] == "+":
+ value = "{{{}+}}".format(value)
+ counters[algorithm][0] = counters[algorithm][0] + 1
+ else:
+ value = "{{{}\\approx}}".format(value)
+ counters[algorithm][1] = counters[algorithm][1] + 1
+ values.append(value)
+
+ # Find the best and second best values
+ medians = indicator_data[(indicator_data["Problem"] == problem)]["Median"]
+ iqrs = indicator_data[(indicator_data["Problem"] == problem)]["IQR"]
+ pairs = list(zip(medians, iqrs))
+ indexes = sorted(range(len(pairs)), key=lambda x: pairs[x])
+
+ if check_minimization(indicator_name):
+ best = indexes[0]
+ second_best = indexes[1]
+ else:
+ best = indexes[-1]
+ second_best = indexes[-2]
+
+ values[best] = "\\cellcolor{gray95} " + values[best]
+ values[second_best] = "\\cellcolor{gray25} " + values[second_best]
+
+ output.write(
+ "\\textbf{{{0}}} & ${1}$ \\\\\n".format(problem, " $ & $ ".join(
+ [str(val).replace("e-", "e\makebox[0.1cm]{-}").replace("e+", "e\makebox[0.1cm]{+}") for val in values])
+ )
)
+ # Select all but the last counter
+ counter_summary = []
+ for algorithm in algorithms[:-1]:
+ counter_summary.append(counters[algorithm])
+
+ output.write(" \\hline\n")
+ output.write(
+ "\\textbf{{{0}}} & ${1}$ \\\\\n".format("$+/\\approx/-$", " $ & $ ".join(
+ [str(val[0]) + "/" + str(val[1]) + "/" + str(val[2]) for val in counter_summary])))
+
+ # Write footer
+ output.write(" \\end{tabular}\n")
+ output.write(" \\end{tiny}\n")
+ output.write("\\end{table}\n")
+
+ output.write("\\end{document}")
+
+ return output.getvalue()
+
+
+def __kolmogorov_smirnov_to_latex(indicator_name: str, test_data: pd.DataFrame, caption: str, label: str):
+ indicator_data = test_data[test_data["Indicator"] == indicator_name]
+
+ problems = pd.unique(indicator_data["Problem"])
+ algorithms = pd.unique(indicator_data["Algorithm"])
+
+ num_columns = len(algorithms)
+ columns = algorithms
+
+ alignment = "c"
+ col_format = "{}|{}".format(alignment, alignment * num_columns)
+ column_labels = ["\\textbf{{{0}}}".format(label.replace("_", "\\_")) for label in columns]
+
+ output = io.StringIO()
+
+ output.write("\\documentclass{article}\n")
+
+ output.write("\\usepackage[utf8]{inputenc}\n")
+ output.write("\\usepackage{tabularx}\n")
+ output.write("\\usepackage{colortbl}\n")
+ output.write("\\usepackage[table*]{xcolor}\n")
+
+ output.write("\\xdefinecolor{gray95}{gray}{0.65}\n")
+ output.write("\\xdefinecolor{gray25}{gray}{0.8}\n")
+
+ output.write("\\title{Kolmogorov-Smirnov Test}\n")
+ output.write("\\author{}\n")
+
+ output.write("\\begin{document}\n")
+ output.write("\\maketitle\n")
+
+ output.write("\\section{Table}\n")
+
+ output.write("\\begin{table}[!htp]\n")
+ output.write(" \\caption{{{}}}\n".format(caption))
+ output.write(" \\label{{{}}}\n".format(label))
+ output.write(" \\centering\n")
+ output.write(" \\begin{tiny}\n")
+ output.write(" \\begin{tabular}{%s}\n" % col_format)
+ output.write(" & {} \\\\\\hline\n".format(" & ".join(column_labels)))
+
+ for problem in problems:
+ values = []
+
+ for algorithm in algorithms[:-1]:
+ row = indicator_data[(indicator_data["Problem"] == problem) & (indicator_data["Algorithm"] == algorithm)]
+ value = "{:.2e}".format(row["PValue"].tolist()[0])
+
+ if (row["PValue"].tolist()[0] < 0.05):
+ value = "\\cellcolor{gray25} " + value
+
+ values.append(value)
+ values.append("-")
+
+ output.write(
+ "\\textbf{{{0}}} & ${1}$ \\\\\n".format(problem, " $ & $ ".join(
+ [str(val).replace("e-", "e\makebox[0.1cm]{-}").replace("e+", "e\makebox[0.1cm]{+}") for val in values])
+ )
+ )
+
+ output.write(" \\hline\n")
+
# Write footer
- output.write(' \\end{tabular}\n')
- output.write(' \\end{scriptsize}\n')
- output.write('\\end{table}\n')
+ output.write(" \\end{tabular}\n")
+ output.write(" \\end{tiny}\n")
+ output.write("\\end{table}\n")
- output.write('\\end{document}')
+ output.write("\\end{document}")
return output.getvalue()
def check_minimization(indicator) -> bool:
- if indicator == 'HV':
+ if indicator == "HV":
return False
else:
return True
diff --git a/jmetal/lab/statistical_test/apv_procedures.py b/jmetal/lab/statistical_test/apv_procedures.py
index 3aa7cb37..d0c8d235 100644
--- a/jmetal/lab/statistical_test/apv_procedures.py
+++ b/jmetal/lab/statistical_test/apv_procedures.py
@@ -21,14 +21,12 @@ def bonferroni_dunn(p_values, control):
algorithms = p_values.columns
p_values = p_values.values
elif type(p_values) == np.ndarray:
- algorithms = np.array(
- ['Alg%d' % alg for alg in range(p_values.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(p_values.shape[1])])
if type(control) == str:
control = int(np.where(algorithms == control)[0])
if control is None:
- raise ValueError(
- 'Initialization ERROR. Incorrect value for control.')
+ raise ValueError("Initialization ERROR. Incorrect value for control.")
k = p_values.shape[1]
@@ -38,10 +36,9 @@ def bonferroni_dunn(p_values, control):
APVs = np.zeros((k - 1, 1))
comparison = []
for i in range(k - 1):
- comparison.append(algorithms[control] +
- ' vs ' + algorithms[argsorted_pvals[i]])
+ comparison.append(algorithms[control] + " vs " + algorithms[argsorted_pvals[i]])
APVs[i, 0] = np.min([(k - 1) * p_values[0, argsorted_pvals[i]], 1])
- return pd.DataFrame(data=APVs, index=comparison, columns=['Bonferroni'])
+ return pd.DataFrame(data=APVs, index=comparison, columns=["Bonferroni"])
def holland(p_values, control):
@@ -63,14 +60,12 @@ def holland(p_values, control):
algorithms = p_values.columns
p_values = p_values.values
elif type(p_values) == np.ndarray:
- algorithms = np.array(
- ['Alg%d' % alg for alg in range(p_values.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(p_values.shape[1])])
if type(control) == str:
control = int(np.where(algorithms == control)[0])
if control is None:
- raise ValueError(
- 'Initialization ERROR. Incorrect value for control.')
+ raise ValueError("Initialization ERROR. Incorrect value for control.")
# --------------------------------------------------------------------------
# ------------------------------- Procedure --------------------------------
@@ -83,12 +78,11 @@ def holland(p_values, control):
APVs = np.zeros((k - 1, 1))
comparison = []
for i in range(k - 1):
- comparison.append(algorithms[control] +
- ' vs ' + algorithms[argsorted_pvals[i]])
+ comparison.append(algorithms[control] + " vs " + algorithms[argsorted_pvals[i]])
aux = k - 1 - np.arange(i + 1)
- v = np.max(1 - (1 - p_values[0, argsorted_pvals[:(i + 1)]]) ** aux)
+ v = np.max(1 - (1 - p_values[0, argsorted_pvals[: (i + 1)]]) ** aux)
APVs[i, 0] = np.min([v, 1])
- return pd.DataFrame(data=APVs, index=comparison, columns=['Holland'])
+ return pd.DataFrame(data=APVs, index=comparison, columns=["Holland"])
def finner(p_values, control):
@@ -110,14 +104,12 @@ def finner(p_values, control):
algorithms = p_values.columns
p_values = p_values.values
elif type(p_values) == np.ndarray:
- algorithms = np.array(
- ['Alg%d' % alg for alg in range(p_values.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(p_values.shape[1])])
if type(control) == str:
control = int(np.where(algorithms == control)[0])
if control is None:
- raise ValueError(
- 'Initialization ERROR. Incorrect value for control.')
+ raise ValueError("Initialization ERROR. Incorrect value for control.")
k = p_values.shape[1]
@@ -127,12 +119,11 @@ def finner(p_values, control):
APVs = np.zeros((k - 1, 1))
comparison = []
for i in range(k - 1):
- comparison.append(algorithms[control] +
- ' vs ' + algorithms[argsorted_pvals[i]])
+ comparison.append(algorithms[control] + " vs " + algorithms[argsorted_pvals[i]])
aux = float(k - 1) / (np.arange(i + 1) + 1)
- v = np.max(1 - (1 - p_values[0, argsorted_pvals[:(i + 1)]]) ** aux)
+ v = np.max(1 - (1 - p_values[0, argsorted_pvals[: (i + 1)]]) ** aux)
APVs[i, 0] = np.min([v, 1])
- return pd.DataFrame(data=APVs, index=comparison, columns=['Finner'])
+ return pd.DataFrame(data=APVs, index=comparison, columns=["Finner"])
def hochberg(p_values, control):
@@ -154,14 +145,12 @@ def hochberg(p_values, control):
algorithms = p_values.columns
p_values = p_values.values
elif type(p_values) == np.ndarray:
- algorithms = np.array(
- ['Alg%d' % alg for alg in range(p_values.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(p_values.shape[1])])
if type(control) == str:
control = int(np.where(algorithms == control)[0])
if control is None:
- raise ValueError(
- 'Initialization ERROR. Incorrect value for control.')
+ raise ValueError("Initialization ERROR. Incorrect value for control.")
k = p_values.shape[1]
@@ -171,12 +160,11 @@ def hochberg(p_values, control):
APVs = np.zeros((k - 1, 1))
comparison = []
for i in range(k - 1):
- comparison.append(algorithms[control] +
- ' vs ' + algorithms[argsorted_pvals[i]])
+ comparison.append(algorithms[control] + " vs " + algorithms[argsorted_pvals[i]])
aux = np.arange(k, i, -1).astype(np.uint8)
v = np.max(p_values[0, argsorted_pvals[aux - 1]] * (k - aux))
APVs[i, 0] = np.min([v, 1])
- return pd.DataFrame(data=APVs, index=comparison, columns=['Hochberg'])
+ return pd.DataFrame(data=APVs, index=comparison, columns=["Hochberg"])
def li(p_values, control):
@@ -200,14 +188,12 @@ def li(p_values, control):
algorithms = p_values.columns
p_values = p_values.values
elif type(p_values) == np.ndarray:
- algorithms = np.array(
- ['Alg%d' % alg for alg in range(p_values.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(p_values.shape[1])])
if type(control) == str:
control = int(np.where(algorithms == control)[0])
if control is None:
- raise ValueError(
- 'Initialization ERROR. Incorrect value for control.')
+ raise ValueError("Initialization ERROR. Incorrect value for control.")
k = p_values.shape[1]
@@ -217,11 +203,15 @@ def li(p_values, control):
APVs = np.zeros((k - 1, 1))
comparison = []
for i in range(k - 1):
- comparison.append(algorithms[control] +
- ' vs ' + algorithms[argsorted_pvals[i]])
- APVs[i, 0] = np.min([p_values[0, argsorted_pvals[-2]], p_values[0, argsorted_pvals[i]] / (
- p_values[0, argsorted_pvals[i]] + 1 - p_values[0, argsorted_pvals[-2]])])
- return pd.DataFrame(data=APVs, index=comparison, columns=['Li'])
+ comparison.append(algorithms[control] + " vs " + algorithms[argsorted_pvals[i]])
+ APVs[i, 0] = np.min(
+ [
+ p_values[0, argsorted_pvals[-2]],
+ p_values[0, argsorted_pvals[i]]
+ / (p_values[0, argsorted_pvals[i]] + 1 - p_values[0, argsorted_pvals[-2]]),
+ ]
+ )
+ return pd.DataFrame(data=APVs, index=comparison, columns=["Li"])
def holm(p_values, control=None):
@@ -245,8 +235,7 @@ def holm(p_values, control=None):
algorithms = p_values.columns
p_values = p_values.values
elif type(p_values) == np.ndarray:
- algorithms = np.array(
- ['Alg%d' % alg for alg in range(p_values.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(p_values.shape[1])])
if type(control) == str:
control = int(np.where(algorithms == control)[0])
@@ -261,9 +250,8 @@ def holm(p_values, control=None):
comparison = []
for i in range(k - 1):
aux = k - 1 - np.arange(i + 1)
- comparison.append(
- algorithms[control] + ' vs ' + algorithms[argsorted_pvals[i]])
- v = np.max(aux * p_values[0, argsorted_pvals[:(i + 1)]])
+ comparison.append(algorithms[control] + " vs " + algorithms[argsorted_pvals[i]])
+ v = np.max(aux * p_values[0, argsorted_pvals[: (i + 1)]])
APVs[i, 0] = np.min([v, 1])
elif control is None:
@@ -281,10 +269,10 @@ def holm(p_values, control=None):
for i in range(m):
row = pairs_index[0][pairs_sorted[i]]
col = pairs_index[1][pairs_sorted[i]]
- comparison.append(algorithms[row] + ' vs ' + algorithms[col])
- v = np.max(aux[:i + 1])
+ comparison.append(algorithms[row] + " vs " + algorithms[col])
+ v = np.max(aux[: i + 1])
APVs[i, 0] = np.min([v, 1])
- return pd.DataFrame(data=APVs, index=comparison, columns=['Holm'])
+ return pd.DataFrame(data=APVs, index=comparison, columns=["Holm"])
def shaffer(p_values):
@@ -320,8 +308,7 @@ def S(k):
TrueHset = [0]
if k > 1:
for j in np.arange(k, 0, -1, dtype=int):
- TrueHset = list(set(TrueHset) | set(
- [binomial(j, 2) + x for x in S(k - j)]))
+ TrueHset = list(set(TrueHset) | set([binomial(j, 2) + x for x in S(k - j)]))
return TrueHset
# Initial Checking
@@ -329,15 +316,12 @@ def S(k):
algorithms = p_values.columns
p_values = p_values.values
elif type(p_values) == np.ndarray:
- algorithms = np.array(
- ['Alg%d' % alg for alg in range(p_values.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(p_values.shape[1])])
if p_values.ndim != 2:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions.')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions.")
elif p_values.shape[0] != p_values.shape[1]:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions.')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions.")
# define parameters
k = p_values.shape[0]
@@ -356,15 +340,15 @@ def S(k):
# Adjust p-values
APVs = np.zeros((m, 1))
- aux = (pairs_pvals[pairs_sorted] * t)
+ aux = pairs_pvals[pairs_sorted] * t
comparison = []
for i in range(m):
row = pairs_index[0][pairs_sorted[i]]
col = pairs_index[1][pairs_sorted[i]]
- comparison.append(algorithms[row] + ' vs ' + algorithms[col])
- v = np.max(aux[:i + 1])
+ comparison.append(algorithms[row] + " vs " + algorithms[col])
+ v = np.max(aux[: i + 1])
APVs[i, 0] = np.min([v, 1])
- return pd.DataFrame(data=APVs, index=comparison, columns=['Shaffer'])
+ return pd.DataFrame(data=APVs, index=comparison, columns=["Shaffer"])
def nemenyi(p_values):
@@ -385,15 +369,12 @@ def nemenyi(p_values):
algorithms = p_values.columns
p_values = p_values.values
elif type(p_values) == np.ndarray:
- algorithms = np.array(
- ['Alg%d' % alg for alg in range(p_values.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(p_values.shape[1])])
if p_values.ndim != 2:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions.')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions.")
elif p_values.shape[0] != p_values.shape[1]:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions.')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions.")
# define parameters
k = p_values.shape[0]
@@ -410,6 +391,6 @@ def nemenyi(p_values):
for i in range(m):
row = pairs_index[0][pairs_sorted[i]]
col = pairs_index[1][pairs_sorted[i]]
- comparison.append(algorithms[row] + ' vs ' + algorithms[col])
+ comparison.append(algorithms[row] + " vs " + algorithms[col])
APVs[i, 0] = np.min([pairs_pvals[pairs_sorted[i]] * m, 1])
- return pd.DataFrame(data=APVs, index=comparison, columns=['Nemenyi'])
+ return pd.DataFrame(data=APVs, index=comparison, columns=["Nemenyi"])
diff --git a/jmetal/lab/statistical_test/bayesian.py b/jmetal/lab/statistical_test/bayesian.py
index c3924624..c79eda6e 100644
--- a/jmetal/lab/statistical_test/bayesian.py
+++ b/jmetal/lab/statistical_test/bayesian.py
@@ -2,9 +2,10 @@
import pandas as pd
-def bayesian_sign_test(data, rope_limits=[-0.01, 0.01], prior_strength=0.5, prior_place='rope', sample_size=50000,
- return_sample=False):
- """ Bayesian version of the sign test.
+def bayesian_sign_test(
+ data, rope_limits=[-0.01, 0.01], prior_strength=0.5, prior_place="rope", sample_size=50000, return_sample=False
+):
+ """Bayesian version of the sign test.
:param data: An (n x 2) array or DataFrame contaning the results. In data, each column represents an algorithm and, and each row a problem.
:param rope_limits: array_like. Default [-0.01, 0.01]. Limits of the practical equivalence.
@@ -27,16 +28,13 @@ def bayesian_sign_test(data, rope_limits=[-0.01, 0.01], prior_strength=0.5, prio
sample1, sample2 = data[:, 0], data[:, 1]
n = data.shape[0]
else:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of dimensions for axis 1')
+ raise ValueError("Initialization ERROR. Incorrect number of dimensions for axis 1")
if prior_strength <= 0:
- raise ValueError(
- 'Initialization ERROR. prior_strength mustb be a positive float')
+ raise ValueError("Initialization ERROR. prior_strength mustb be a positive float")
- if prior_place not in ['left', 'rope', 'right']:
- raise ValueError(
- 'Initialization ERROR. Incorrect value fro prior_place')
+ if prior_place not in ["left", "rope", "right"]:
+ raise ValueError("Initialization ERROR. Incorrect value fro prior_place")
# Compute the differences
Z = sample1 - sample2
@@ -53,7 +51,7 @@ def bayesian_sign_test(data, rope_limits=[-0.01, 0.01], prior_strength=0.5, prio
# Parameters of the Dirichlet distribution
alpha = np.array([Nleft, Nequiv, Nright], dtype=float) + 1e-6
- alpha[['left', 'rope', 'right'].index(prior_place)] += prior_strength
+ alpha[["left", "rope", "right"].index(prior_place)] += prior_strength
# Simulate dirichlet process
Dprocess = np.random.dirichlet(alpha, sample_size)
@@ -69,10 +67,10 @@ def bayesian_sign_test(data, rope_limits=[-0.01, 0.01], prior_strength=0.5, prio
return np.array([win_left, win_rope, win_rifht]) / float(sample_size)
-def bayesian_signed_rank_test(data, rope_limits=[-0.01, 0.01], prior_strength=1.0, prior_place='rope',
- sample_size=10000,
- return_sample=False):
- """ Bayesian version of the signed rank test.
+def bayesian_signed_rank_test(
+ data, rope_limits=[-0.01, 0.01], prior_strength=1.0, prior_place="rope", sample_size=10000, return_sample=False
+):
+ """Bayesian version of the signed rank test.
:param data: An (n x 2) array or DataFrame contaning the results. In data, each column represents an algorithm and, and each row a problem.
:param rope_limits: array_like. Default [-0.01, 0.01]. Limits of the practical equivalence.
@@ -98,21 +96,17 @@ def weights(n, s):
sample1, sample2 = data[:, 0], data[:, 1]
n = data.shape[0]
else:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of dimensions for axis 1')
+ raise ValueError("Initialization ERROR. Incorrect number of dimensions for axis 1")
if prior_strength <= 0:
- raise ValueError(
- 'Initialization ERROR. prior_strength must be a positive float')
+ raise ValueError("Initialization ERROR. prior_strength must be a positive float")
- if prior_place not in ['left', 'rope', 'right']:
- raise ValueError(
- 'Initialization ERROR. Incorrect value for prior_place')
+ if prior_place not in ["left", "rope", "right"]:
+ raise ValueError("Initialization ERROR. Incorrect value for prior_place")
# Compute the differences
Z = sample1 - sample2
- Z0 = [-float('Inf'), 0.0, float('Inf')][['left',
- 'rope', 'right'].index(prior_place)]
+ Z0 = [-float("Inf"), 0.0, float("Inf")][["left", "rope", "right"].index(prior_place)]
Z = np.concatenate(([Z0], Z), axis=None)
# compute the the probabilities that the mean difference of accuracy is in
diff --git a/jmetal/lab/statistical_test/critical_distance.py b/jmetal/lab/statistical_test/critical_distance.py
index d03891c6..954c4832 100644
--- a/jmetal/lab/statistical_test/critical_distance.py
+++ b/jmetal/lab/statistical_test/critical_distance.py
@@ -7,7 +7,7 @@
def NemenyiCD(alpha: float, num_alg, num_dataset):
- """ Computes Nemenyi's critical difference:
+ """Computes Nemenyi's critical difference:
* CD = q_alpha * sqrt(num_alg*(num_alg + 1)/(6*num_prob))
where q_alpha is the critical value, of the Studentized range statistic divided by sqrt(2).
:param alpha: {0.1, 0.999}. Significance level.
@@ -24,8 +24,14 @@ def NemenyiCD(alpha: float, num_alg, num_dataset):
return cd
-def CDplot(results, alpha: float = 0.05, higher_is_better: bool=False, alg_names: list = None, output_filename: str = 'cdplot.eps'):
- """ CDgraph plots the critical difference graph show in Janez Demsar's 2006 work:
+def CDplot(
+ results,
+ alpha: float = 0.05,
+ higher_is_better: bool = False,
+ alg_names: list = None,
+ output_filename: str = "cdplot.eps",
+):
+ """CDgraph plots the critical difference graph show in Janez Demsar's 2006 work:
* Statistical Comparisons of Classifiers over Multiple Data Sets.
:param results: A 2-D array containing results from each algorithm. Each row of 'results' represents an algorithm, and each column a dataset.
:param alpha: {0.1, 0.999}. Significance level for the critical difference.
@@ -40,8 +46,7 @@ def _join_alg(avranks, num_alg, cd):
# get all pairs
sets = (-1) * np.ones((num_alg, 2))
for i in range(num_alg):
- elements = np.where(np.logical_and(
- avranks - avranks[i] > 0, avranks - avranks[i] < cd))[0]
+ elements = np.where(np.logical_and(avranks - avranks[i] > 0, avranks - avranks[i] < cd))[0]
if elements.size > 0:
sets[i, :] = [avranks[i], avranks[elements[-1]]]
sets = np.delete(sets, np.where(sets[:, 0] < 0)[0], axis=0)
@@ -59,14 +64,12 @@ def _join_alg(avranks, num_alg, cd):
alg_names = results.index
results = results.values
elif type(results) == np.ndarray and alg_names is None:
- alg_names = np.array(
- ['Alg%d' % alg for alg in range(results.shape[1])])
+ alg_names = np.array(["Alg%d" % alg for alg in range(results.shape[1])])
if results.ndim == 2:
num_alg, num_dataset = results.shape
else:
- raise ValueError(
- 'Initialization ERROR: In CDplot(...) results must be 2-D array')
+ raise ValueError("Initialization ERROR: In CDplot(...) results must be 2-D array")
# Get the critical difference
cd = NemenyiCD(alpha, num_alg, num_dataset)
@@ -90,7 +93,7 @@ def _join_alg(avranks, num_alg, cd):
highest = np.ceil(np.max(avranks)).astype(np.uint8) # highest shown rank
lowest = np.floor(np.min(avranks)).astype(np.uint8) # lowest shown rank
width = 6 # default figure width (in inches)
- height = (0.575 * (rows + 1)) # figure height
+ height = 0.575 * (rows + 1) # figure height
"""
FIGURE
@@ -118,60 +121,79 @@ def _join_alg(avranks, num_alg, cd):
lline = sright - sleft
# Initialize figure
- fig = plt.figure(figsize=(width, height), facecolor='white')
+ fig = plt.figure(figsize=(width, height), facecolor="white")
ax = fig.add_axes([0, 0, 1, 1])
ax.set_xlim(0, 1)
ax.set_ylim(0, 1)
ax.set_axis_off()
# Main horizontal axis
- ax.hlines(stop, sleft, sright, color='black', linewidth=0.7)
+ ax.hlines(stop, sleft, sright, color="black", linewidth=0.7)
for xi in range(highest - lowest + 1):
# Plot mayor ticks
- ax.vlines(x=sleft + (lline * xi) / (highest - lowest),
- ymin=stop, ymax=stop + 0.05, color='black', linewidth=0.7)
+ ax.vlines(
+ x=sleft + (lline * xi) / (highest - lowest), ymin=stop, ymax=stop + 0.05, color="black", linewidth=0.7
+ )
# Mayor ticks labels
- ax.text(x=sleft + (lline * xi) / (highest - lowest),
- y=stop + 0.06,
- s=str(lowest + xi), ha='center', va='bottom')
+ ax.text(
+ x=sleft + (lline * xi) / (highest - lowest), y=stop + 0.06, s=str(lowest + xi), ha="center", va="bottom"
+ )
# Minor ticks
if xi < highest - lowest:
- ax.vlines(x=sleft + (lline * (xi + 0.5)) / (highest - lowest),
- ymin=stop, ymax=stop + 0.025, color='black', linewidth=0.7)
+ ax.vlines(
+ x=sleft + (lline * (xi + 0.5)) / (highest - lowest),
+ ymin=stop,
+ ymax=stop + 0.025,
+ color="black",
+ linewidth=0.7,
+ )
# Plot lines/names for left models
vspace = 0.5 * (stop - sbottom) / (spoint + 1)
for i in range(spoint):
- ax.vlines(x=sleft + (lline * (leftalg[i] - lowest)) / (highest - lowest),
- ymin=sbottom + (spoint - 1 - i) * vspace, ymax=stop, color='black', linewidth=0.7)
- ax.hlines(y=sbottom + (spoint - 1 - i) * vspace, xmin=sleft,
- xmax=sleft +
- (lline * (leftalg[i] - lowest)) / (highest - lowest),
- color='black', linewidth=0.7)
- ax.text(x=sleft - 0.01, y=sbottom + (spoint - 1 - i) * vspace,
- s=alg_names[indices][i], ha='right', va='center')
+ ax.vlines(
+ x=sleft + (lline * (leftalg[i] - lowest)) / (highest - lowest),
+ ymin=sbottom + (spoint - 1 - i) * vspace,
+ ymax=stop,
+ color="black",
+ linewidth=0.7,
+ )
+ ax.hlines(
+ y=sbottom + (spoint - 1 - i) * vspace,
+ xmin=sleft,
+ xmax=sleft + (lline * (leftalg[i] - lowest)) / (highest - lowest),
+ color="black",
+ linewidth=0.7,
+ )
+ ax.text(x=sleft - 0.01, y=sbottom + (spoint - 1 - i) * vspace, s=alg_names[indices][i], ha="right", va="center")
# Plot lines/names for right models
vspace = 0.5 * (stop - sbottom) / (num_alg - spoint + 1)
for i in range(num_alg - spoint):
- ax.vlines(x=sleft + (lline * (rightalg[i] - lowest)) / (highest - lowest),
- ymin=sbottom + i * vspace, ymax=stop, color='black', linewidth=0.7)
- ax.hlines(y=sbottom + i * vspace,
- xmin=sleft +
- (lline * (rightalg[i] - lowest)) / (highest - lowest),
- xmax=sright, color='black', linewidth=0.7)
- ax.text(x=sright + 0.01, y=sbottom + i * vspace,
- s=alg_names[indices][spoint + i], ha='left', va='center')
+ ax.vlines(
+ x=sleft + (lline * (rightalg[i] - lowest)) / (highest - lowest),
+ ymin=sbottom + i * vspace,
+ ymax=stop,
+ color="black",
+ linewidth=0.7,
+ )
+ ax.hlines(
+ y=sbottom + i * vspace,
+ xmin=sleft + (lline * (rightalg[i] - lowest)) / (highest - lowest),
+ xmax=sright,
+ color="black",
+ linewidth=0.7,
+ )
+ ax.text(x=sright + 0.01, y=sbottom + i * vspace, s=alg_names[indices][spoint + i], ha="left", va="center")
# Plot critical difference rule
if sleft + (cd * lline) / (highest - lowest) <= sright:
- ax.hlines(y=stop + 0.2, xmin=sleft, xmax=sleft +
- (cd * lline) / (highest - lowest), linewidth=1.5)
- ax.text(x=sleft + 0.5 * (cd * lline) /
- (highest - lowest), y=stop + 0.21, s='CD=%.3f' % cd, ha='center', va='bottom')
+ ax.hlines(y=stop + 0.2, xmin=sleft, xmax=sleft + (cd * lline) / (highest - lowest), linewidth=1.5)
+ ax.text(
+ x=sleft + 0.5 * (cd * lline) / (highest - lowest), y=stop + 0.21, s="CD=%.3f" % cd, ha="center", va="bottom"
+ )
else:
- ax.text(x=(sleft + sright) / 2, y=stop + 0.2, s='CD=%.3f' %
- cd, ha='center', va='bottom')
+ ax.text(x=(sleft + sright) / 2, y=stop + 0.2, s="CD=%.3f" % cd, ha="center", va="bottom")
# Get pair of non-significant methods
nonsig = _join_alg(avranks, num_alg, cd)
@@ -180,29 +202,31 @@ def _join_alg(avranks, num_alg, cd):
left_lines = np.reshape(nonsig[0, :], (1, 2))
right_lines = np.reshape(nonsig[1, :], (1, 2))
else:
- left_lines = nonsig[:np.round(
- nonsig.shape[0] / 2.0).astype(np.uint8), :]
- right_lines = nonsig[np.round(
- nonsig.shape[0] / 2.0).astype(np.uint8):, :]
+ left_lines = nonsig[: np.round(nonsig.shape[0] / 2.0).astype(np.uint8), :]
+ right_lines = nonsig[np.round(nonsig.shape[0] / 2.0).astype(np.uint8) :, :]
else:
left_lines = np.reshape(nonsig, (1, nonsig.shape[0]))
# plot from the left
vspace = 0.5 * (stop - sbottom) / (left_lines.shape[0] + 1)
for i in range(left_lines.shape[0]):
- ax.hlines(y=stop - (i + 1) * vspace,
- xmin=sleft + lline * (left_lines[i, 0] -
- lowest - 0.025) / (highest - lowest),
- xmax=sleft + lline * (left_lines[i, 1] - lowest + 0.025) / (highest - lowest), linewidth=2)
+ ax.hlines(
+ y=stop - (i + 1) * vspace,
+ xmin=sleft + lline * (left_lines[i, 0] - lowest - 0.025) / (highest - lowest),
+ xmax=sleft + lline * (left_lines[i, 1] - lowest + 0.025) / (highest - lowest),
+ linewidth=2,
+ )
# plot from the rigth
if nonsig.ndim == 2:
vspace = 0.5 * (stop - sbottom) / (left_lines.shape[0])
for i in range(right_lines.shape[0]):
- ax.hlines(y=stop - (i + 1) * vspace,
- xmin=sleft + lline * (right_lines[i, 0] -
- lowest - 0.025) / (highest - lowest),
- xmax=sleft + lline * (right_lines[i, 1] - lowest + 0.025) / (highest - lowest), linewidth=2)
-
- plt.savefig(output_filename, bbox_inches='tight')
+ ax.hlines(
+ y=stop - (i + 1) * vspace,
+ xmin=sleft + lline * (right_lines[i, 0] - lowest - 0.025) / (highest - lowest),
+ xmax=sleft + lline * (right_lines[i, 1] - lowest + 0.025) / (highest - lowest),
+ linewidth=2,
+ )
+
+ plt.savefig(output_filename, bbox_inches="tight")
plt.show()
diff --git a/jmetal/lab/statistical_test/functions.py b/jmetal/lab/statistical_test/functions.py
index 6f5d47da..f1e9b5c9 100644
--- a/jmetal/lab/statistical_test/functions.py
+++ b/jmetal/lab/statistical_test/functions.py
@@ -1,10 +1,10 @@
-from scipy.stats import chi2, f, binom, norm
+from scipy.stats import binom, chi2, f, norm
from jmetal.lab.statistical_test.apv_procedures import *
def ranks(data: np.array, descending=False):
- """ Computes the rank of the elements in data.
+ """Computes the rank of the elements in data.
:param data: 2-D matrix
:param descending: boolean (default False). If true, rank is sorted in descending order.
@@ -17,23 +17,27 @@ def ranks(data: np.array, descending=False):
ranks = np.ones(data.shape)
for i in range(data.shape[0]):
values, indices, rep = np.unique(
- (-1) ** s * np.sort((-1) ** s * data[i, :]), return_index=True, return_counts=True, )
+ (-1) ** s * np.sort((-1) ** s * data[i, :]),
+ return_index=True,
+ return_counts=True,
+ )
for j in range(data.shape[1]):
- ranks[i, j] += indices[values == data[i, j]] + \
- 0.5 * (rep[values == data[i, j]] - 1)
+ ranks[i, j] += indices[values == data[i, j]] + 0.5 * (rep[values == data[i, j]] - 1)
return ranks
elif data.ndim == 1:
ranks = np.ones((data.size,))
values, indices, rep = np.unique(
- (-1) ** s * np.sort((-1) ** s * data), return_index=True, return_counts=True, )
+ (-1) ** s * np.sort((-1) ** s * data),
+ return_index=True,
+ return_counts=True,
+ )
for i in range(data.size):
- ranks[i] += indices[values == data[i]] + \
- 0.5 * (rep[values == data[i]] - 1)
+ ranks[i] += indices[values == data[i]] + 0.5 * (rep[values == data[i]] - 1)
return ranks
def sign_test(data):
- """ Given the results drawn from two algorithms/methods X and Y, the sign test analyses if
+ """Given the results drawn from two algorithms/methods X and Y, the sign test analyses if
there is a difference between X and Y.
.. note:: Null Hypothesis: Pr(XY', 'p-value'],
- columns=['Results'])
+ return pd.DataFrame(
+ data=np.array([Wminus, Wplus, p_value]), index=["Num XY", "p-value"], columns=["Results"]
+ )
def friedman_test(data):
- """ Friedman ranking test.
+ """Friedman ranking test.
..note:: Null Hypothesis: In a set of k (>=2) treaments (or tested algorithms), all the treatments are equivalent, so their average ranks should be equal.
@@ -88,11 +92,9 @@ def friedman_test(data):
if data.ndim == 2:
n_samples, k = data.shape
else:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions")
if k < 2:
- raise ValueError(
- 'Initialization Error. Incorrect number of dimensions for axis 1.')
+ raise ValueError("Initialization Error. Incorrect number of dimensions for axis 1.")
# Compute ranks.
datarank = ranks(data)
@@ -101,18 +103,18 @@ def friedman_test(data):
avranks = np.mean(datarank, axis=0)
# Get Friedman statistics
- friedman_stat = (12.0 * n_samples) / (k * (k + 1.0)) * \
- (np.sum(avranks ** 2) - (k * (k + 1) ** 2) / 4.0)
+ friedman_stat = (12.0 * n_samples) / (k * (k + 1.0)) * (np.sum(avranks**2) - (k * (k + 1) ** 2) / 4.0)
# Compute p-value
- p_value = (1.0 - chi2.cdf(friedman_stat, df=(k - 1)))
+ p_value = 1.0 - chi2.cdf(friedman_stat, df=(k - 1))
- return pd.DataFrame(data=np.array([friedman_stat, p_value]), index=['Friedman-statistic', 'p-value'],
- columns=['Results'])
+ return pd.DataFrame(
+ data=np.array([friedman_stat, p_value]), index=["Friedman-statistic", "p-value"], columns=["Results"]
+ )
def friedman_aligned_rank_test(data):
- """ Method of aligned ranks for the Friedman test.
+ """Method of aligned ranks for the Friedman test.
..note:: Null Hypothesis: In a set of k (>=2) treaments (or tested algorithms), all the treatments are equivalent, so their average ranks should be equal.
@@ -128,11 +130,9 @@ def friedman_aligned_rank_test(data):
if data.ndim == 2:
n_samples, k = data.shape
else:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions")
if k < 2:
- raise ValueError(
- 'Initialization Error. Incorrect number of dimensions for axis 1.')
+ raise ValueError("Initialization Error. Incorrect number of dimensions for axis 1.")
# Compute the average value achieved by all algorithms in each problem
control = np.mean(data, axis=1)
@@ -140,27 +140,28 @@ def friedman_aligned_rank_test(data):
diff = [data[:, j] - control for j in range(data.shape[1])]
# rank diff
alignedRanks = ranks(np.ravel(diff))
- alignedRanks = np.reshape(alignedRanks, newshape=(n_samples, k), order='F')
+ alignedRanks = np.reshape(alignedRanks, newshape=(n_samples, k), order="F")
# Compute statistic
Rhat_i = np.sum(alignedRanks, axis=1)
Rhat_j = np.sum(alignedRanks, axis=0)
- si, sj = np.sum(Rhat_i ** 2), np.sum(Rhat_j ** 2)
+ si, sj = np.sum(Rhat_i**2), np.sum(Rhat_j**2)
- A = sj - (k * n_samples ** 2 / 4.0) * (k * n_samples + 1) ** 2
- B1 = (k * n_samples * (k * n_samples + 1) * (2 * k * n_samples + 1) / 6.0)
+ A = sj - (k * n_samples**2 / 4.0) * (k * n_samples + 1) ** 2
+ B1 = k * n_samples * (k * n_samples + 1) * (2 * k * n_samples + 1) / 6.0
B2 = si / float(k)
alignedRanks_stat = ((k - 1) * A) / (B1 - B2)
p_value = 1 - chi2.cdf(alignedRanks_stat, df=k - 1)
- return pd.DataFrame(data=np.array([alignedRanks_stat, p_value]), index=['Aligned Rank stat', 'p-value'],
- columns=['Results'])
+ return pd.DataFrame(
+ data=np.array([alignedRanks_stat, p_value]), index=["Aligned Rank stat", "p-value"], columns=["Results"]
+ )
def quade_test(data):
- """ Quade test.
+ """Quade test.
..note:: Null Hypothesis: In a set of k (>=2) treaments (or tested algorithms), all the treatments are equivalent, so their average ranks should be equal.
@@ -176,11 +177,9 @@ def quade_test(data):
if data.ndim == 2:
n_samples, k = data.shape
else:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions")
if k < 2:
- raise ValueError(
- 'Initialization Error. Incorrect number of dimensions for axis 1.')
+ raise ValueError("Initialization Error. Incorrect number of dimensions for axis 1.")
# Compute ranks.
datarank = ranks(data)
@@ -197,8 +196,8 @@ def quade_test(data):
Salg = np.sum(S_stat, axis=0)
# Compute Fq (Quade Test statistic) and associated p_value
- A = np.sum(S_stat ** 2)
- B = np.sum(Salg ** 2) / float(n_samples)
+ A = np.sum(S_stat**2)
+ B = np.sum(Salg**2) / float(n_samples)
if A == B:
Fq = np.Inf
@@ -207,11 +206,11 @@ def quade_test(data):
Fq = (n_samples - 1.0) * B / (A - B)
p_value = 1 - f.cdf(Fq, k - 1, (k - 1) * (n_samples - 1))
- return pd.DataFrame(data=np.array([Fq, p_value]), index=['Quade Test statistic', 'p-value'], columns=['Results'])
+ return pd.DataFrame(data=np.array([Fq, p_value]), index=["Quade Test statistic", "p-value"], columns=["Results"])
def friedman_ph_test(data, control=None, apv_procedure=None):
- """ Friedman post-hoc test.
+ """Friedman post-hoc test.
:param data: An (n x 2) array or DataFrame contaning the results. In data, each column represents an algorithm and, and each row a problem.
:param control: optional int or string. Default None. Index or Name of the control algorithm. If control = None all FriedmanPosHocTest considers all possible comparisons among algorithms.
@@ -233,7 +232,7 @@ def friedman_ph_test(data, control=None, apv_procedure=None):
algorithms = data.columns
data = data.values
elif type(data) == np.ndarray:
- algorithms = np.array(['Alg%d' % alg for alg in range(data.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(data.shape[1])])
if control is None:
index = algorithms
@@ -245,24 +244,29 @@ def friedman_ph_test(data, control=None, apv_procedure=None):
if data.ndim == 2:
n_samples, k = data.shape
else:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions.')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions.")
if k < 2:
- raise ValueError(
- 'Initialization Error. Incorrect number of dimensions for axis 1.')
+ raise ValueError("Initialization Error. Incorrect number of dimensions for axis 1.")
if control is not None:
if type(control) == int and control >= data.shape[1]:
- raise ValueError('Initialization ERROR. control is out of bounds')
+ raise ValueError("Initialization ERROR. control is out of bounds")
if type(control) == str and control not in algorithms:
- raise ValueError(
- 'Initialization ERROR. %s is not a column name of data' % control)
+ raise ValueError("Initialization ERROR. %s is not a column name of data" % control)
if apv_procedure is not None:
- if apv_procedure not in ['Bonferroni', 'Holm', 'Hochberg', 'Hommel', 'Holland', 'Finner', 'Li', 'Shaffer',
- 'Nemenyi']:
- raise ValueError(
- 'Initialization ERROR. Incorrect value for APVprocedure.')
+ if apv_procedure not in [
+ "Bonferroni",
+ "Holm",
+ "Hochberg",
+ "Hommel",
+ "Holland",
+ "Finner",
+ "Li",
+ "Shaffer",
+ "Nemenyi",
+ ]:
+ raise ValueError("Initialization ERROR. Incorrect value for APVprocedure.")
# Compute ranks.
datarank = ranks(data)
@@ -294,28 +298,28 @@ def friedman_ph_test(data, control=None, apv_procedure=None):
if apv_procedure is None:
return zvalues_df, pvalues_df
else:
- if apv_procedure == 'Bonferroni':
+ if apv_procedure == "Bonferroni":
ap_vs_df = bonferroni_dunn(pvalues_df, control=control)
- elif apv_procedure == 'Holm':
+ elif apv_procedure == "Holm":
ap_vs_df = holm(pvalues_df, control=control)
- elif apv_procedure == 'Hochberg':
+ elif apv_procedure == "Hochberg":
ap_vs_df = hochberg(pvalues_df, control=control)
- elif apv_procedure == 'Holland':
+ elif apv_procedure == "Holland":
ap_vs_df = holland(pvalues_df, control=control)
- elif apv_procedure == 'Finner':
+ elif apv_procedure == "Finner":
ap_vs_df = finner(pvalues_df, control=control)
- elif apv_procedure == 'Li':
+ elif apv_procedure == "Li":
ap_vs_df = li(pvalues_df, control=control)
- elif apv_procedure == 'Shaffer':
+ elif apv_procedure == "Shaffer":
ap_vs_df = shaffer(pvalues_df)
- elif apv_procedure == 'Nemenyi':
+ elif apv_procedure == "Nemenyi":
ap_vs_df = nemenyi(pvalues_df)
return zvalues_df, pvalues_df, ap_vs_df
def friedman_aligned_ph_test(data, control=None, apv_procedure=None):
- """ Friedman Aligned Ranks post-hoc test.
+ """Friedman Aligned Ranks post-hoc test.
:param data: An (n x 2) array or DataFrame contaning the results. In data, each column represents an algorithm and, and each row a problem.
:param control: optional int or string. Default None. Index or Name of the control algorithm. If control = None all FriedmanPosHocTest considers all possible comparisons among algorithms.
@@ -337,7 +341,7 @@ def friedman_aligned_ph_test(data, control=None, apv_procedure=None):
algorithms = data.columns
data = data.values
elif type(data) == np.ndarray:
- algorithms = np.array(['Alg%d' % alg for alg in range(data.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(data.shape[1])])
if control is None:
index = algorithms
@@ -349,18 +353,15 @@ def friedman_aligned_ph_test(data, control=None, apv_procedure=None):
if data.ndim == 2:
n_samples, k = data.shape
else:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions.')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions.")
if k < 2:
- raise ValueError(
- 'Initialization Error. Incorrect number of dimensions for axis 1.')
+ raise ValueError("Initialization Error. Incorrect number of dimensions for axis 1.")
if control is not None:
if type(control) == int and control >= data.shape[1]:
- raise ValueError('Initialization ERROR. control is out of bounds')
+ raise ValueError("Initialization ERROR. control is out of bounds")
if type(control) == str and control not in algorithms:
- raise ValueError(
- 'Initialization ERROR. %s is not a column name of data' % control)
+ raise ValueError("Initialization ERROR. %s is not a column name of data" % control)
# Compute the average value achieved by all algorithms in each problem
problemmean = np.mean(data, axis=1)
@@ -399,28 +400,28 @@ def friedman_aligned_ph_test(data, control=None, apv_procedure=None):
if apv_procedure is None:
return zvalues_df, pvalues_df
else:
- if apv_procedure == 'Bonferroni':
+ if apv_procedure == "Bonferroni":
ap_vs_df = bonferroni_dunn(pvalues_df, control=control)
- elif apv_procedure == 'Holm':
+ elif apv_procedure == "Holm":
ap_vs_df = holm(pvalues_df, control=control)
- elif apv_procedure == 'Hochberg':
+ elif apv_procedure == "Hochberg":
ap_vs_df = hochberg(pvalues_df, control=control)
- elif apv_procedure == 'Holland':
+ elif apv_procedure == "Holland":
ap_vs_df = holland(pvalues_df, control=control)
- elif apv_procedure == 'Finner':
+ elif apv_procedure == "Finner":
ap_vs_df = finner(pvalues_df, control=control)
- elif apv_procedure == 'Li':
+ elif apv_procedure == "Li":
ap_vs_df = li(pvalues_df, control=control)
- elif apv_procedure == 'Shaffer':
+ elif apv_procedure == "Shaffer":
ap_vs_df = shaffer(pvalues_df)
- elif apv_procedure == 'Nemenyi':
+ elif apv_procedure == "Nemenyi":
ap_vs_df = nemenyi(pvalues_df)
return zvalues_df, pvalues_df, ap_vs_df
def quade_ph_test(data, control=None, apv_procedure=None):
- """ Quade post-hoc test.
+ """Quade post-hoc test.
:param data: An (n x 2) array or DataFrame contaning the results. In data, each column represents an algorithm and, and each row a problem.
:param control: optional int or string. Default None. Index or Name of the control algorithm. If control = None all FriedmanPosHocTest considers all possible comparisons among algorithms.
@@ -442,7 +443,7 @@ def quade_ph_test(data, control=None, apv_procedure=None):
algorithms = data.columns
data = data.values
elif type(data) == np.ndarray:
- algorithms = np.array(['Alg%d' % alg for alg in range(data.shape[1])])
+ algorithms = np.array(["Alg%d" % alg for alg in range(data.shape[1])])
if control is None:
index = algorithms
@@ -454,18 +455,15 @@ def quade_ph_test(data, control=None, apv_procedure=None):
if data.ndim == 2:
n_samples, k = data.shape
else:
- raise ValueError(
- 'Initialization ERROR. Incorrect number of array dimensions.')
+ raise ValueError("Initialization ERROR. Incorrect number of array dimensions.")
if k < 2:
- raise ValueError(
- 'Initialization Error. Incorrect number of dimensions for axis 1.')
+ raise ValueError("Initialization Error. Incorrect number of dimensions for axis 1.")
if control is not None:
if type(control) == int and control >= data.shape[1]:
- raise ValueError('Initialization ERROR. control is out of bounds')
+ raise ValueError("Initialization ERROR. control is out of bounds")
if type(control) == str and control not in algorithms:
- raise ValueError(
- 'Initialization ERROR. %s is not a column name of data' % control)
+ raise ValueError("Initialization ERROR. %s is not a column name of data" % control)
# Compute ranks.
datarank = ranks(data)
@@ -480,8 +478,7 @@ def quade_ph_test(data, control=None, apv_procedure=None):
W[i, :] = problemRank[i] * datarank[i, :]
avranks = 2 * np.sum(W, axis=0) / (n_samples * (n_samples + 1))
# Compute test statistics
- aux = 1.0 / np.sqrt(k * (k + 1) * (2 * n_samples + 1) * (k - 1) /
- (18.0 * n_samples * (n_samples + 1)))
+ aux = 1.0 / np.sqrt(k * (k + 1) * (2 * n_samples + 1) * (k - 1) / (18.0 * n_samples * (n_samples + 1)))
if control is None:
z = np.zeros((k, k))
for i in range(k):
@@ -504,21 +501,21 @@ def quade_ph_test(data, control=None, apv_procedure=None):
if apv_procedure is None:
return zvalues_df, pvalues_df
else:
- if apv_procedure == 'Bonferroni':
+ if apv_procedure == "Bonferroni":
ap_vs_df = bonferroni_dunn(pvalues_df, control=control)
- elif apv_procedure == 'Holm':
+ elif apv_procedure == "Holm":
ap_vs_df = holm(pvalues_df, control=control)
- elif apv_procedure == 'Hochberg':
+ elif apv_procedure == "Hochberg":
ap_vs_df = hochberg(pvalues_df, control=control)
- elif apv_procedure == 'Holland':
+ elif apv_procedure == "Holland":
ap_vs_df = holland(pvalues_df, control=control)
- elif apv_procedure == 'Finner':
+ elif apv_procedure == "Finner":
ap_vs_df = finner(pvalues_df, control=control)
- elif apv_procedure == 'Li':
+ elif apv_procedure == "Li":
ap_vs_df = li(pvalues_df, control=control)
- elif apv_procedure == 'Shaffer':
+ elif apv_procedure == "Shaffer":
ap_vs_df = shaffer(pvalues_df)
- elif apv_procedure == 'Nemenyi':
+ elif apv_procedure == "Nemenyi":
ap_vs_df = nemenyi(pvalues_df)
return zvalues_df, pvalues_df, ap_vs_df
diff --git a/jmetal/lab/visualization/__init__.py b/jmetal/lab/visualization/__init__.py
index 42ecc322..1cc15dd1 100644
--- a/jmetal/lab/visualization/__init__.py
+++ b/jmetal/lab/visualization/__init__.py
@@ -1,9 +1,8 @@
from jmetal.lab.statistical_test.critical_distance import CDplot
+
from .interactive import InteractivePlot
from .plotting import Plot
from .posterior import plot_posterior
from .streaming import StreamingPlot
-__all__ = [
- 'Plot', 'InteractivePlot', 'StreamingPlot', 'CDplot', 'plot_posterior'
-]
+__all__ = ["Plot", "InteractivePlot", "StreamingPlot", "CDplot", "plot_posterior"]
diff --git a/jmetal/lab/visualization/chord_plot.py b/jmetal/lab/visualization/chord_plot.py
index de69a0dd..59415ea4 100644
--- a/jmetal/lab/visualization/chord_plot.py
+++ b/jmetal/lab/visualization/chord_plot.py
@@ -14,30 +14,41 @@ def polar_to_cartesian(r, theta):
return np.array([r * np.cos(theta), r * np.sin(theta)])
-def draw_sector(start_angle=0, end_angle=60, radius=1.0, width=0.2, lw=2, ls='-', ax=None, fc=(1, 0, 0), ec=(0, 0, 0),
- z_order=1):
+def draw_sector(
+ start_angle=0, end_angle=60, radius=1.0, width=0.2, lw=2, ls="-", ax=None, fc=(1, 0, 0), ec=(0, 0, 0), z_order=1
+):
if start_angle > end_angle:
start_angle, end_angle = end_angle, start_angle
- start_angle *= np.pi / 180.
- end_angle *= np.pi / 180.
+ start_angle *= np.pi / 180.0
+ end_angle *= np.pi / 180.0
# https://stackoverflow.com/questions/1734745/how-to-create-circle-with-b%C3%A9zier-curves
- opt = 4. / 3. * np.tan((end_angle - start_angle) / 4.) * radius
+ opt = 4.0 / 3.0 * np.tan((end_angle - start_angle) / 4.0) * radius
inner = radius * (1 - width)
- vertsPath = [polar_to_cartesian(radius, start_angle),
- polar_to_cartesian(radius, start_angle) + polar_to_cartesian(opt, start_angle + 0.5 * np.pi),
- polar_to_cartesian(radius, end_angle) + polar_to_cartesian(opt, end_angle - 0.5 * np.pi),
- polar_to_cartesian(radius, end_angle),
- polar_to_cartesian(inner, end_angle),
- polar_to_cartesian(inner, end_angle) + polar_to_cartesian(opt * (1 - width), end_angle - 0.5 * np.pi),
- polar_to_cartesian(inner, start_angle) + polar_to_cartesian(opt * (1 - width),
- start_angle + 0.5 * np.pi),
- polar_to_cartesian(inner, start_angle),
- polar_to_cartesian(radius, start_angle)]
-
- codesPaths = [Path.MOVETO, Path.CURVE4, Path.CURVE4, Path.CURVE4, Path.LINETO, Path.CURVE4, Path.CURVE4,
- Path.CURVE4, Path.CLOSEPOLY]
+ vertsPath = [
+ polar_to_cartesian(radius, start_angle),
+ polar_to_cartesian(radius, start_angle) + polar_to_cartesian(opt, start_angle + 0.5 * np.pi),
+ polar_to_cartesian(radius, end_angle) + polar_to_cartesian(opt, end_angle - 0.5 * np.pi),
+ polar_to_cartesian(radius, end_angle),
+ polar_to_cartesian(inner, end_angle),
+ polar_to_cartesian(inner, end_angle) + polar_to_cartesian(opt * (1 - width), end_angle - 0.5 * np.pi),
+ polar_to_cartesian(inner, start_angle) + polar_to_cartesian(opt * (1 - width), start_angle + 0.5 * np.pi),
+ polar_to_cartesian(inner, start_angle),
+ polar_to_cartesian(radius, start_angle),
+ ]
+
+ codesPaths = [
+ Path.MOVETO,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.LINETO,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CLOSEPOLY,
+ ]
if ax is None:
return vertsPath, codesPaths
@@ -45,38 +56,64 @@ def draw_sector(start_angle=0, end_angle=60, radius=1.0, width=0.2, lw=2, ls='-'
path = Path(vertsPath, codesPaths)
patch = patches.PathPatch(path, facecolor=fc, edgecolor=ec, lw=lw, linestyle=ls, zorder=z_order)
ax.add_patch(patch)
- return (patch)
-
-
-def draw_chord(start_angle1=0, end_angle1=60, start_angle2=180, end_angle2=240, radius=1.0, chord_width=0.7, ax=None,
- color=(1, 0, 0), z_order=1):
+ return patch
+
+
+def draw_chord(
+ start_angle1=0,
+ end_angle1=60,
+ start_angle2=180,
+ end_angle2=240,
+ radius=1.0,
+ chord_width=0.7,
+ ax=None,
+ color=(1, 0, 0),
+ z_order=1,
+):
if start_angle1 > end_angle1:
start_angle1, end_angle1 = end_angle1, start_angle1
if start_angle2 > end_angle2:
start_angle2, end_angle2 = end_angle2, start_angle2
- start_angle1 *= np.pi / 180.
- end_angle1 *= np.pi / 180.
- start_angle2 *= np.pi / 180.
- end_angle2 *= np.pi / 180.
+ start_angle1 *= np.pi / 180.0
+ end_angle1 *= np.pi / 180.0
+ start_angle2 *= np.pi / 180.0
+ end_angle2 *= np.pi / 180.0
- optAngle1 = 4. / 3. * np.tan((end_angle1 - start_angle1) / 4.) * radius
- optAngle2 = 4. / 3. * np.tan((end_angle2 - start_angle2) / 4.) * radius
+ optAngle1 = 4.0 / 3.0 * np.tan((end_angle1 - start_angle1) / 4.0) * radius
+ optAngle2 = 4.0 / 3.0 * np.tan((end_angle2 - start_angle2) / 4.0) * radius
rchord = radius * (1 - chord_width)
- vertsPath = [polar_to_cartesian(radius, start_angle1),
- polar_to_cartesian(radius, start_angle1) + polar_to_cartesian(optAngle1, start_angle1 + 0.5 * np.pi),
- polar_to_cartesian(radius, end_angle1) + polar_to_cartesian(optAngle1, end_angle1 - 0.5 * np.pi),
- polar_to_cartesian(radius, end_angle1),
- polar_to_cartesian(rchord, end_angle1), polar_to_cartesian(rchord, start_angle2),
- polar_to_cartesian(radius, start_angle2),
- polar_to_cartesian(radius, start_angle2) + polar_to_cartesian(optAngle2, start_angle2 + 0.5 * np.pi),
- polar_to_cartesian(radius, end_angle2) + polar_to_cartesian(optAngle2, end_angle2 - 0.5 * np.pi),
- polar_to_cartesian(radius, end_angle2),
- polar_to_cartesian(rchord, end_angle2), polar_to_cartesian(rchord, start_angle1),
- polar_to_cartesian(radius, start_angle1)]
-
- codesPath = [Path.MOVETO, Path.CURVE4, Path.CURVE4, Path.CURVE4, Path.CURVE4, Path.CURVE4, Path.CURVE4,
- Path.CURVE4, Path.CURVE4, Path.CURVE4, Path.CURVE4, Path.CURVE4, Path.CURVE4]
+ vertsPath = [
+ polar_to_cartesian(radius, start_angle1),
+ polar_to_cartesian(radius, start_angle1) + polar_to_cartesian(optAngle1, start_angle1 + 0.5 * np.pi),
+ polar_to_cartesian(radius, end_angle1) + polar_to_cartesian(optAngle1, end_angle1 - 0.5 * np.pi),
+ polar_to_cartesian(radius, end_angle1),
+ polar_to_cartesian(rchord, end_angle1),
+ polar_to_cartesian(rchord, start_angle2),
+ polar_to_cartesian(radius, start_angle2),
+ polar_to_cartesian(radius, start_angle2) + polar_to_cartesian(optAngle2, start_angle2 + 0.5 * np.pi),
+ polar_to_cartesian(radius, end_angle2) + polar_to_cartesian(optAngle2, end_angle2 - 0.5 * np.pi),
+ polar_to_cartesian(radius, end_angle2),
+ polar_to_cartesian(rchord, end_angle2),
+ polar_to_cartesian(rchord, start_angle1),
+ polar_to_cartesian(radius, start_angle1),
+ ]
+
+ codesPath = [
+ Path.MOVETO,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ Path.CURVE4,
+ ]
if ax == None:
return vertsPath, codesPath
@@ -84,7 +121,7 @@ def draw_chord(start_angle1=0, end_angle1=60, start_angle2=180, end_angle2=240,
path = Path(vertsPath, codesPath)
patch = patches.PathPatch(path, facecolor=color + (0.5,), edgecolor=color + (0.4,), lw=2, alpha=0.5)
ax.add_patch(patch)
- return (patch)
+ return patch
def hover_over_bin(event, handle_tickers, handle_plots, colors, fig):
@@ -109,8 +146,14 @@ def hover_over_bin(event, handle_tickers, handle_plots, colors, fig):
fig.canvas.draw_idle()
-def chord_diagram(solutions: List[FloatSolution], nbins='auto', ax=None, obj_labels=None,
- prop_labels=dict(fontsize=13, ha='center', va='center'), pad=6):
+def chord_diagram(
+ solutions: List[FloatSolution],
+ nbins="auto",
+ ax=None,
+ obj_labels=None,
+ prop_labels=dict(fontsize=13, ha="center", va="center"),
+ pad=6,
+):
points_matrix = np.array([s.objectives for s in solutions])
(NPOINTS, NOBJ) = np.shape(points_matrix)
@@ -119,13 +162,13 @@ def chord_diagram(solutions: List[FloatSolution], nbins='auto', ax=None, obj_lab
if ax is None:
fig = plt.figure(figsize=(6, 6))
- ax = plt.axes([0, 0, 1, 1], aspect='equal')
+ ax = plt.axes([0, 0, 1, 1], aspect="equal")
ax.set_xlim(-2.3, 2.3)
ax.set_ylim(-2.3, 2.3)
- ax.axis('off')
+ ax.axis("off")
- y = np.array([1. / NOBJ] * NOBJ) * (360 - pad * NOBJ)
+ y = np.array([1.0 / NOBJ] * NOBJ) * (360 - pad * NOBJ)
sector_angles = []
labels_pos_and_ros = []
@@ -145,9 +188,13 @@ def chord_diagram(solutions: List[FloatSolution], nbins='auto', ax=None, obj_lab
angleText -= 270
labels_pos_and_ros.append(
- tuple(polar_to_cartesian(1.0, 0.5 * (start_angle + end_angle) * np.pi / 180.)) + (angle_diff,) +
- tuple(polar_to_cartesian(0.725, (start_angle - 2.5) * np.pi / 180.)) + (angleText,) +
- tuple(polar_to_cartesian(0.85, (start_angle - 2.5) * np.pi / 180.)) + (angleText,))
+ tuple(polar_to_cartesian(1.0, 0.5 * (start_angle + end_angle) * np.pi / 180.0))
+ + (angle_diff,)
+ + tuple(polar_to_cartesian(0.725, (start_angle - 2.5) * np.pi / 180.0))
+ + (angleText,)
+ + tuple(polar_to_cartesian(0.85, (start_angle - 2.5) * np.pi / 180.0))
+ + (angleText,)
+ )
start_angle = end_angle + pad
arc_points = []
@@ -164,15 +211,41 @@ def chord_diagram(solutions: List[FloatSolution], nbins='auto', ax=None, obj_lab
handle_tickers = []
handle_plots = []
- for iobj in tqdm(range(NOBJ), ascii=True, desc='Chord diagram'):
- draw_sector(start_angle=sector_angles[iobj][0], end_angle=sector_angles[iobj][1], radius=0.925, width=0.225,
- ax=ax,
- fc=(1, 1, 1, 0.0), ec=(0, 0, 0), lw=2, z_order=10)
- draw_sector(start_angle=sector_angles[iobj][0], end_angle=sector_angles[iobj][1], radius=0.925, width=0.05,
- ax=ax,
- fc=colors[iobj], ec=(0, 0, 0), lw=2, z_order=10)
- draw_sector(start_angle=sector_angles[iobj][0], end_angle=sector_angles[iobj][1], radius=0.7 + 0.15, width=0.0,
- ax=ax, fc=colors[iobj], ec=colors[iobj], lw=2, ls=':', z_order=5)
+ for iobj in tqdm(range(NOBJ), ascii=True, desc="Chord diagram"):
+ draw_sector(
+ start_angle=sector_angles[iobj][0],
+ end_angle=sector_angles[iobj][1],
+ radius=0.925,
+ width=0.225,
+ ax=ax,
+ fc=(1, 1, 1, 0.0),
+ ec=(0, 0, 0),
+ lw=2,
+ z_order=10,
+ )
+ draw_sector(
+ start_angle=sector_angles[iobj][0],
+ end_angle=sector_angles[iobj][1],
+ radius=0.925,
+ width=0.05,
+ ax=ax,
+ fc=colors[iobj],
+ ec=(0, 0, 0),
+ lw=2,
+ z_order=10,
+ )
+ draw_sector(
+ start_angle=sector_angles[iobj][0],
+ end_angle=sector_angles[iobj][1],
+ radius=0.7 + 0.15,
+ width=0.0,
+ ax=ax,
+ fc=colors[iobj],
+ ec=colors[iobj],
+ lw=2,
+ ls=":",
+ z_order=5,
+ )
histValues, binsDim = np.histogram(points_matrix[:, iobj], bins=nbins)
relativeHeightBinPre = 0.025
@@ -181,70 +254,122 @@ def chord_diagram(solutions: List[FloatSolution], nbins='auto', ax=None, obj_lab
handle_plots.append([])
for indexBin in range(len(histValues)):
- startAngleBin = sector_angles[iobj][0] + (sector_angles[iobj][1] - sector_angles[iobj][0]) * binsDim[
- indexBin]
- endAngleBin = sector_angles[iobj][0] + (sector_angles[iobj][1] - sector_angles[iobj][0]) * binsDim[
- indexBin + 1]
+ startAngleBin = (
+ sector_angles[iobj][0] + (sector_angles[iobj][1] - sector_angles[iobj][0]) * binsDim[indexBin]
+ )
+ endAngleBin = (
+ sector_angles[iobj][0] + (sector_angles[iobj][1] - sector_angles[iobj][0]) * binsDim[indexBin + 1]
+ )
relativeHeightBin = 0.15 * histValues[indexBin] / max(histValues)
handle_tickers[-1].append(
- draw_sector(start_angle=startAngleBin, end_angle=endAngleBin, radius=0.69, width=0.08, ax=ax, lw=1,
- fc=(1, 1, 1), ec=(0, 0, 0)))
+ draw_sector(
+ start_angle=startAngleBin,
+ end_angle=endAngleBin,
+ radius=0.69,
+ width=0.08,
+ ax=ax,
+ lw=1,
+ fc=(1, 1, 1),
+ ec=(0, 0, 0),
+ )
+ )
handle_plots[-1].append([])
if histValues[indexBin] > 0:
- draw_sector(start_angle=startAngleBin, end_angle=endAngleBin, radius=0.7 + relativeHeightBin, width=0,
- ax=ax, lw=1, fc=colors[iobj], ec=colors[iobj])
- plotPoint1 = polar_to_cartesian(0.7 + relativeHeightBinPre, startAngleBin * np.pi / 180.)
- plotPoint2 = polar_to_cartesian(0.7 + relativeHeightBin, startAngleBin * np.pi / 180.)
+ draw_sector(
+ start_angle=startAngleBin,
+ end_angle=endAngleBin,
+ radius=0.7 + relativeHeightBin,
+ width=0,
+ ax=ax,
+ lw=1,
+ fc=colors[iobj],
+ ec=colors[iobj],
+ )
+ plotPoint1 = polar_to_cartesian(0.7 + relativeHeightBinPre, startAngleBin * np.pi / 180.0)
+ plotPoint2 = polar_to_cartesian(0.7 + relativeHeightBin, startAngleBin * np.pi / 180.0)
plt.plot([plotPoint1[0], plotPoint2[0]], [plotPoint1[1], plotPoint2[1]], c=colors[iobj], lw=1)
relativeHeightBinPre = relativeHeightBin
else:
- plotPoint1 = polar_to_cartesian(0.7 + relativeHeightBinPre, startAngleBin * np.pi / 180.)
- plotPoint2 = polar_to_cartesian(0.725 + relativeHeightBin, startAngleBin * np.pi / 180.)
+ plotPoint1 = polar_to_cartesian(0.7 + relativeHeightBinPre, startAngleBin * np.pi / 180.0)
+ plotPoint2 = polar_to_cartesian(0.725 + relativeHeightBin, startAngleBin * np.pi / 180.0)
plt.plot([plotPoint1[0], plotPoint2[0]], [plotPoint1[1], plotPoint2[1]], c=colors[iobj], lw=1)
relativeHeightBinPre = 0.025
if indexBin == len(histValues) - 1:
- plotPoint1 = polar_to_cartesian(0.7 + relativeHeightBin, endAngleBin * np.pi / 180.)
- plotPoint2 = polar_to_cartesian(0.725, endAngleBin * np.pi / 180.)
+ plotPoint1 = polar_to_cartesian(0.7 + relativeHeightBin, endAngleBin * np.pi / 180.0)
+ plotPoint2 = polar_to_cartesian(0.725, endAngleBin * np.pi / 180.0)
plt.plot([plotPoint1[0], plotPoint2[0]], [plotPoint1[1], plotPoint2[1]], c=colors[iobj], lw=1)
for ipoint in range(len(points_matrix)):
- plotPoint1 = polar_to_cartesian(0.6, arc_points[ipoint][iobj][0] * np.pi / 180.)
- plotPoint2 = polar_to_cartesian(0.6, arc_points[ipoint][iobj][0] * np.pi / 180.)
- plt.plot([plotPoint1[0], plotPoint2[0]], [plotPoint1[1], plotPoint2[1]], marker='o', markersize=3,
- c=colors[iobj], lw=2)
-
- if binsDim[indexBin] < points_matrix[ipoint, iobj] <= binsDim[
- indexBin + 1]:
+ plotPoint1 = polar_to_cartesian(0.6, arc_points[ipoint][iobj][0] * np.pi / 180.0)
+ plotPoint2 = polar_to_cartesian(0.6, arc_points[ipoint][iobj][0] * np.pi / 180.0)
+ plt.plot(
+ [plotPoint1[0], plotPoint2[0]],
+ [plotPoint1[1], plotPoint2[1]],
+ marker="o",
+ markersize=3,
+ c=colors[iobj],
+ lw=2,
+ )
+
+ if binsDim[indexBin] < points_matrix[ipoint, iobj] <= binsDim[indexBin + 1]:
for jdim in range(NOBJ):
if jdim >= 1:
handle_plots[iobj][indexBin].append(
- draw_chord(arc_points[ipoint][jdim - 1][0], arc_points[ipoint][jdim - 1][1],
- arc_points[ipoint][jdim][0], arc_points[ipoint][jdim][1], radius=0.55,
- color=colors[iobj], chord_width=1, ax=ax))
+ draw_chord(
+ arc_points[ipoint][jdim - 1][0],
+ arc_points[ipoint][jdim - 1][1],
+ arc_points[ipoint][jdim][0],
+ arc_points[ipoint][jdim][1],
+ radius=0.55,
+ color=colors[iobj],
+ chord_width=1,
+ ax=ax,
+ )
+ )
handle_plots[iobj][indexBin][-1].set_visible(False)
handle_plots[iobj][indexBin].append(
- draw_chord(arc_points[ipoint][-1][0], arc_points[ipoint][-1][1], arc_points[ipoint][0][0],
- arc_points[ipoint][0][1], radius=0.55, color=colors[iobj], chord_width=1, ax=ax))
+ draw_chord(
+ arc_points[ipoint][-1][0],
+ arc_points[ipoint][-1][1],
+ arc_points[ipoint][0][0],
+ arc_points[ipoint][0][1],
+ radius=0.55,
+ color=colors[iobj],
+ chord_width=1,
+ ax=ax,
+ )
+ )
handle_plots[iobj][indexBin][-1].set_visible(False)
if obj_labels is None:
- obj_labels = ['$f_{' + str(i) + '}(\mathbf{x})$' for i in range(NOBJ)]
+ obj_labels = ["$f_{" + str(i) + "}(\mathbf{x})$" for i in range(NOBJ)]
- prop_legend_bins = dict(fontsize=9, ha='center', va='center')
+ prop_legend_bins = dict(fontsize=9, ha="center", va="center")
for i in range(NOBJ):
- p0, p1 = polar_to_cartesian(0.975, sector_angles[i][0] * np.pi / 180.)
- ax.text(p0, p1, '0', **prop_legend_bins)
- p0, p1 = polar_to_cartesian(0.975, sector_angles[i][1] * np.pi / 180.)
- ax.text(p0, p1, '1', **prop_legend_bins)
- ax.text(labels_pos_and_ros[i][0], labels_pos_and_ros[i][1], obj_labels[i], rotation=labels_pos_and_ros[i][2],
- **prop_labels)
- ax.text(labels_pos_and_ros[i][3], labels_pos_and_ros[i][4], '0', **prop_legend_bins, color=colors[i])
- ax.text(labels_pos_and_ros[i][6], labels_pos_and_ros[i][7], str(max_hist_values[i]), **prop_legend_bins,
- color=colors[i])
+ p0, p1 = polar_to_cartesian(0.975, sector_angles[i][0] * np.pi / 180.0)
+ ax.text(p0, p1, "0", **prop_legend_bins)
+ p0, p1 = polar_to_cartesian(0.975, sector_angles[i][1] * np.pi / 180.0)
+ ax.text(p0, p1, "1", **prop_legend_bins)
+ ax.text(
+ labels_pos_and_ros[i][0],
+ labels_pos_and_ros[i][1],
+ obj_labels[i],
+ rotation=labels_pos_and_ros[i][2],
+ **prop_labels
+ )
+ ax.text(labels_pos_and_ros[i][3], labels_pos_and_ros[i][4], "0", **prop_legend_bins, color=colors[i])
+ ax.text(
+ labels_pos_and_ros[i][6],
+ labels_pos_and_ros[i][7],
+ str(max_hist_values[i]),
+ **prop_legend_bins,
+ color=colors[i]
+ )
plt.axis([-1.2, 1.2, -1.2, 1.2])
- fig.canvas.mpl_connect("motion_notify_event",
- lambda event: hover_over_bin(event, handle_tickers, handle_plots, colors, fig))
+ fig.canvas.mpl_connect(
+ "motion_notify_event", lambda event: hover_over_bin(event, handle_tickers, handle_plots, colors, fig)
+ )
plt.show()
diff --git a/jmetal/lab/visualization/interactive.py b/jmetal/lab/visualization/interactive.py
index 00d78d42..673ee005 100644
--- a/jmetal/lab/visualization/interactive.py
+++ b/jmetal/lab/visualization/interactive.py
@@ -1,5 +1,5 @@
import logging
-from typing import TypeVar, List
+from typing import List, TypeVar
import pandas as pd
from plotly import graph_objs as go
@@ -8,25 +8,26 @@
from jmetal.lab.visualization.plotting import Plot
-LOGGER = logging.getLogger('jmetal')
+logger = logging.getLogger(__name__)
-S = TypeVar('S')
+S = TypeVar("S")
class InteractivePlot(Plot):
-
- def __init__(self,
- title: str = 'Pareto front approximation',
- reference_front: List[S] = None,
- reference_point: list = None,
- axis_labels: list = None):
+ def __init__(
+ self,
+ title: str = "Pareto front approximation",
+ reference_front: List[S] = None,
+ reference_point: list = None,
+ axis_labels: list = None,
+ ):
super(InteractivePlot, self).__init__(title, reference_front, reference_point, axis_labels)
self.figure = None
self.layout = None
self.data = []
- def plot(self, front, label=None, normalize: bool = False, filename: str = None, format: str = 'HTML'):
- """ Plot a front of solutions (2D, 3D or parallel coordinates).
+ def plot(self, front, label=None, normalize: bool = False, filename: str = None, format: str = "HTML"):
+ """Plot a front of solutions (2D, 3D or parallel coordinates).
:param front: List of solutions.
:param label: Front name.
@@ -39,50 +40,57 @@ def plot(self, front, label=None, normalize: bool = False, filename: str = None,
self.layout = go.Layout(
margin=dict(l=80, r=80, b=80, t=150),
height=800,
- title='{}
{}'.format(self.plot_title, label[0]),
+ title="{}
{}".format(self.plot_title, label[0]),
scene=dict(
xaxis=dict(title=self.axis_labels[0:1][0] if self.axis_labels[0:1] else None),
yaxis=dict(title=self.axis_labels[1:2][0] if self.axis_labels[1:2] else None),
- zaxis=dict(title=self.axis_labels[2:3][0] if self.axis_labels[2:3] else None)
+ zaxis=dict(title=self.axis_labels[2:3][0] if self.axis_labels[2:3] else None),
),
- hovermode='closest'
+ hovermode="closest",
)
# If any reference front, plot
if self.reference_front:
points, _ = self.get_points(self.reference_front)
- trace = self.__generate_trace(points=points, legend='Reference front', normalize=normalize,
- color='black', size=2)
+ trace = self.__generate_trace(
+ points=points, legend="Reference front", normalize=normalize, color="black", size=2
+ )
self.data.append(trace)
# If any reference point, plot
if self.reference_point:
points = pd.DataFrame(self.reference_point)
- trace = self.__generate_trace(points=points, legend='Reference point', color='red', size=8)
+ trace = self.__generate_trace(points=points, legend="Reference point", color="red", size=8)
self.data.append(trace)
# Get points and metadata
points, _ = self.get_points(front)
metadata = list(solution.__str__() for solution in front)
- trace = self.__generate_trace(points=points, metadata=metadata, legend='Front approximation',
- normalize=normalize)
+ trace = self.__generate_trace(
+ points=points, metadata=metadata, legend="Front approximation", normalize=normalize
+ )
self.data.append(trace)
self.figure = go.Figure(data=self.data, layout=self.layout)
# Plot the figure
if filename:
- if format == 'HTML':
+ if format == "HTML":
self.export_to_html(filename)
+ logger.info("Figure {_filename} exported to HTML file")
else:
- pio.write_image(self.figure, filename + '.' + format)
+ _filename = filename + "." + format
+
+ pio.write_image(self.figure, _filename)
+ logger.info("Figure {_filename} saved to file")
def export_to_html(self, filename: str) -> str:
- """ Export the graph to an interactive HTML (solutions can be selected to show some metadata).
+ """Export the graph to an interactive HTML (solutions can be selected to show some metadata).
:param filename: Output file name.
- :return: Script as string. """
- html_string = '''
+ :return: Script as string."""
+ html_string = (
+ """
@@ -92,7 +100,9 @@ def export_to_html(self, filename: str) -> str:
- ''' + self.export_to_div(filename=None, include_plotlyjs=False) + '''
+ """
+ + self.export_to_div(filename=None, include_plotlyjs=False)
+ + """
- '''
+