renamed module to infer_subc

ABOUT_THIS_TEMPLATE.md

@@ -32,7 +32,7 @@ Lets take a look at the structure of this template:
 ├── Makefile                 # A collection of utilities to manage the project
 ├── MANIFEST.in              # A list of files to include in a package
 ├── mkdocs.yml               # Configuration for documentation site
-├── infer_subc_2d             # The main python package for the project
+├── infer_subc             # The main python package for the project
 │   ├── base.py              # The base module for the project
 │   ├── __init__.py          # This tells Python that this is a package
 │   ├── __main__.py          # The entry point for the project
@@ -109,7 +109,7 @@ I had to do some tricks to read that version variable inside the setuptools
 I decided to keep the version in a static file because it is easier to read from
 wherever I want without the need to install the package.
 
-e.g: `cat infer_subc_2d/VERSION` will get the project version without harming
+e.g: `cat infer_subc/VERSION` will get the project version without harming
 with module imports or anything else, it is useful for CI, logs and debugging.
 
 ### Why to include `tests`, `history` and `Containerfile` as part of the release?

CONTRIBUTING.md

@@ -1,6 +1,6 @@
 # How to develop on this project
 
-infer_subc_2d welcomes contributions from the community.
+infer_subc welcomes contributions from the community.
 
 **You need PYTHON3!**
 

Containerfile

@@ -2,4 +2,4 @@ FROM python:3.7-alpine
 COPY . /app
 WORKDIR /app
 RUN pip install .
-CMD ["infer_subc_2d"]
+CMD ["infer_subc"]

MANIFEST.in

@@ -2,4 +2,4 @@ include LICENSE
 include HISTORY.md
 include Containerfile
 graft tests
-graft infer_subc_2d
+graft infer_subc

Makefile

@@ -26,20 +26,20 @@ install:          ## Install the project in dev mode.
 
 .PHONY: fmt
 fmt:              ## Format code using black & isort.
-	$(ENV_PREFIX)isort infer_subc_2d/
-	$(ENV_PREFIX)black -l 79 infer_subc_2d/
+	$(ENV_PREFIX)isort infer_subc/
+	$(ENV_PREFIX)black -l 79 infer_subc/
 	$(ENV_PREFIX)black -l 79 tests/
 
 .PHONY: lint
 lint:             ## Run pep8, black, mypy linters.
-	$(ENV_PREFIX)flake8 infer_subc_2d/
-	$(ENV_PREFIX)black -l 79 --check infer_subc_2d/
+	$(ENV_PREFIX)flake8 infer_subc/
+	$(ENV_PREFIX)black -l 79 --check infer_subc/
 	$(ENV_PREFIX)black -l 79 --check tests/
-	$(ENV_PREFIX)mypy --ignore-missing-imports infer_subc_2d/
+	$(ENV_PREFIX)mypy --ignore-missing-imports infer_subc/
 
 .PHONY: test
 test: lint        ## Run tests and generate coverage report.
-	$(ENV_PREFIX)pytest -v --cov-config .coveragerc --cov=infer_subc_2d -l --tb=short --maxfail=1 tests/
+	$(ENV_PREFIX)pytest -v --cov-config .coveragerc --cov=infer_subc -l --tb=short --maxfail=1 tests/
 	$(ENV_PREFIX)coverage xml
 	$(ENV_PREFIX)coverage html
 
@@ -78,9 +78,9 @@ virtualenv:       ## Create a virtual environment.
 release:          ## Create a new tag for release.
 	@echo "WARNING: This operation will create s version tag and push to github"
 	@read -p "Version? (provide the next x.y.z semver) : " TAG
-	@echo "$${TAG}" > infer_subc_2d/VERSION
+	@echo "$${TAG}" > infer_subc/VERSION
 	@$(ENV_PREFIX)gitchangelog > HISTORY.md
-	@git add infer_subc_2d/VERSION HISTORY.md
+	@git add infer_subc/VERSION HISTORY.md
 	@git commit -m "release: version $${TAG} 🚀"
 	@echo "creating git tag : $${TAG}"
 	@git tag $${TAG}
@@ -101,15 +101,15 @@ switch-to-poetry: ## Switch to poetry package manager.
 	@poetry init --no-interaction --name=a_flask_test --author=rochacbruno
 	@echo "" >> pyproject.toml
 	@echo "[tool.poetry.scripts]" >> pyproject.toml
-	@echo "infer_subc_2d = 'infer_subc_2d.__main__:main'" >> pyproject.toml
+	@echo "infer_subc = 'infer_subc.__main__:main'" >> pyproject.toml
 	@cat requirements.txt | while read in; do poetry add --no-interaction "$${in}"; done
 	@cat requirements-test.txt | while read in; do poetry add --no-interaction "$${in}" --dev; done
 	@poetry install --no-interaction
 	@mkdir -p .github/backup
 	@mv requirements* .github/backup
 	@mv setup.py .github/backup
 	@echo "You have switched to https://python-poetry.org/ package manager."
-	@echo "Please run 'poetry shell' or 'poetry run infer_subc_2d'"
+	@echo "Please run 'poetry shell' or 'poetry run infer_subc'"
 
 .PHONY: init
 init:             ## Initialize the project based on an application template.

README.md

@@ -1,18 +1,18 @@
-# infer_subc_2d
+# infer_subc
 
 [![codecov](https://codecov.io/gh/ergonyc/infer-subc/branch/main/graph/badge.svg?token=infer-subc_token_here)](https://codecov.io/gh/ergonyc/infer-subc)
 [![CI](https://github.com/ergonyc/infer-subc/actions/workflows/main.yml/badge.svg)](https://github.com/ergonyc/infer-subc/actions/workflows/main.yml)
 
 ## About The Project
 
-`infer_subc_2d` 
+`infer_subc` 
 - aims to create a simple, extensible, and reproducible workflow to measure (or infer) the shape, position, size, and interaction of several sub-cellular components. These data can then be applied later to better understand the spatial coordination of these structures and the interactome during key biological processes.
 
 - is part of a larger collaboration between the CZI Neurodegeneration Challenge Network [(NDCN)](https://chanzuckerberg.com/science/programs-resources/neurodegeneration-challenge/) Data Science Concierge program and the Cohen lab at UNC [(website,](https://cohenlaboratory.web.unc.edu/) [github)](https://github.com/SCohenLab) to migrate a multispectral imaging dataset of iPSCs which identifies sub-cellular components to a scalable cloud-based pipeline.  
 
 
 
-## `infer_subc_2d` Workflow
+## `infer_subc` Workflow
 
 The staring point of this workflow is a set of multichannel images, where each channel labels a different sub-cellular component. The workflow can then be completed in a _**suggested**_ series of steps, outlined in the notebooks below.
 
@@ -84,16 +84,16 @@ The following are prerequisites and should be installed prior to using the workf
 
 ### Installation
 
-`infer_subc_2d` is not yet available on `PyPI` so must be  be `pip` ionstalled from source
+`infer_subc` is not yet available on `PyPI` so must be  be `pip` ionstalled from source
 ```
 pip install git+https://github.com/ndcn/infer-subc-2D.git
 ```
 
 ## Usage
 
 ```py
-from infer_subc_2d.organelles import infer_lyso
-from infer_subc_2d.core.file_io import read_czi_image
+from infer_subc.organelles import infer_lyso
+from infer_subc.core.file_io import read_czi_image
 
 img_data,meta_dict = read_czi_image("path/to/image.czi")
 lyso_obj =  infer_lyso(img_data) 
@@ -103,9 +103,9 @@ lyso_obj =  infer_lyso(img_data)
  🚧 WIP 🚧 (🚨🚨🚨🚨 )
 > NOTE: command line capabilities not implimented
 ```bash
-$ python -m infer_subc_2d
+$ python -m infer_subc
 #or
-$ infer_subc_2d
+$ infer_subc
 ```
 
 ## Roadmap

docs/index.md

@@ -1,6 +1,6 @@
-# Welcome to infer_subc_2d
+# Welcome to infer_subc
 
- `infer_subc_2d` aims to create a simple and extensible workflow of image analysis leveraging [scipy image](link), and [napari](link) for reproducable analysis with an intuitive interface. 
+ `infer_subc` aims to create a simple and extensible workflow of image analysis leveraging [scipy image](link), and [napari](link) for reproducable analysis with an intuitive interface. 
 
 This is a simple repo to collect code and documentations from the pilot project kicking off as part of the CZI Neurodegeneration Challenge Network [(NDCN)](https://chanzuckerberg.com/science/programs-resources/neurodegeneration-challenge/) Data Science Concierge program.  The PILOT study is a collaboration with Cohen lab at UNC [(website,](https://cohenlaboratory.web.unc.edu/) [github)](https://github.com/SCohenLab) to migrate a multispectral imaging dataset of iPSCs which identifies sub-cellular components to a scalable cloud-based pipeline.  
 
@@ -47,5 +47,5 @@ Early in the develepmont we chose to leverage the Allen Cell & Structure Segment
 
 -------
 
-For full documentation visit [github.io.com/infer_subc_2d](https://ndcn.github.io/infer-subc-2D/).
+For full documentation visit [github.io.com/infer_subc](https://ndcn.github.io/infer-subc-2D/).
 Robust inference of subcellular objects:

docs/infer_subc_2d/batch.md

@@ -1,5 +1,5 @@
-# infer_subc_2d/batch
+# infer_subc/batch
 
 functions which help with processing batches of files
 
-::: infer_subc_2d.batch.batch_process
+::: infer_subc.batch.batch_process

docs/infer_subc_2d/main.md

@@ -1,6 +1,6 @@
 #
 
-## infer_subc_2d
+## infer_subc
 
 Several sub-modules organize the segmentation.
 

docs/infer_subc_2d/organelles.md

@@ -89,4 +89,4 @@ In order to leverage the A
 
 ## `organelles` submodule
 
-::: infer_subc_2d.organelles
+::: infer_subc.organelles

docs/infer_subc_2d/organelles/cytosol.md

@@ -1,3 +1,3 @@
-# infer_subc_2d/organelles/cytosol
+# infer_subc/organelles/cytosol
 
-::: infer_subc_2d.organelles.cytosol
+::: infer_subc.organelles.cytosol

docs/infer_subc_2d/organelles/er.md

@@ -1,3 +1,3 @@
-# infer_subc_2d/organelles/er
+# infer_subc/organelles/er
 
-::: infer_subc_2d.organelles.er
+::: infer_subc.organelles.er

docs/infer_subc_2d/organelles/golgi.md

@@ -1,3 +1,3 @@
-# infer_subc_2d/organelles/golgi
+# infer_subc/organelles/golgi
 
-::: infer_subc_2d.organelles.golgi
+::: infer_subc.organelles.golgi

docs/infer_subc_2d/organelles/lipid.md

@@ -1,3 +1,3 @@
-# infer_subc_2d/organelles/lipid
+# infer_subc/organelles/lipid
 
-::: infer_subc_2d.organelles.lipid
+::: infer_subc.organelles.lipid

docs/infer_subc_2d/organelles/lysosome.md

@@ -1,3 +1,3 @@
-# infer_subc_2d/organelles/lysosome
+# infer_subc/organelles/lysosome
 
-::: infer_subc_2d.organelles.lysosome
+::: infer_subc.organelles.lysosome

docs/infer_subc_2d/organelles/mitochondria.md

@@ -1,4 +1,4 @@
-# infer_subc_2d/organelles/mitochondria
+# infer_subc/organelles/mitochondria
 
-::: infer_subc_2d.organelles.mitochondria
+::: infer_subc.organelles.mitochondria
 

docs/infer_subc_2d/organelles/nuclei.md

@@ -1,3 +1,3 @@
-# infer_subc_2d/organelles/nuclei
+# infer_subc/organelles/nuclei
 
-::: infer_subc_2d.organelles.nuclei
+::: infer_subc.organelles.nuclei

docs/infer_subc_2d/organelles/peroxisome.md

@@ -1,3 +1,3 @@
-# infer_subc_2d/organelles/peroxisome
+# infer_subc/organelles/peroxisome
 
-::: infer_subc_2d.organelles.peroxisome
+::: infer_subc.organelles.peroxisome

docs/infer_subc_2d/organelles/soma.md

@@ -1,5 +1,5 @@
-# infer_subc_2d/organelles/soma
+# infer_subc/organelles/soma
 
 Routines for inference of ***soma*** for masking later organell segmentation steps.
 
-::: infer_subc_2d.organelles.soma
+::: infer_subc.organelles.soma

docs/infer_subc_2d/overview.md

@@ -1,4 +1,4 @@
-## infer_subc_2d
+## infer_subc
 
 This module contains code to segment organelles from multi-channel images generated by SCohenLab.   The "raw" data files are the output of linear unmixing of multi-spectral imaging capture in their lab.
 

docs/infer_subc_2d/utils.md

@@ -1,4 +1,4 @@
-## infer_subc_2d/utils
-# infer_subc_2d/utils
+## infer_subc/utils
+# infer_subc/utils
 
 The _utils_ are organized by _file input / output_ `file_io.py`, _image processing_ routines (`img.py`) and some _other_ (`etc`) functions.  

docs/infer_subc_2d/utils/etc.md

@@ -1,3 +1,3 @@
-# infer_subc_2d/utils
+# infer_subc/utils
 
 Also there are 'util/directories.py', 'util/filesystempy', 'util/lazy.py', and a hack from `aicsimageio` 'util/_aicsimage_reader.py'

docs/infer_subc_2d/utils/file_io.md

@@ -1,6 +1,6 @@
-# infer_subc_2d/utils/file_io
+# infer_subc/utils/file_io
 
 Helpers for file input and output
 
-::: infer_subc_2d.utils.file_io
+::: infer_subc.utils.file_io
 

docs/infer_subc_2d/utils/img.md

@@ -1,5 +1,5 @@
-# infer_subc_2d/utils/img
+# infer_subc/utils/img
 
 Image processing functions.  Most are wrappers to well known `skimage` and `scipy.ndimate` utilities as well as core routines from `aicssegmentation`
 
-::: infer_subc_2d.utils.img
+::: infer_subc.utils.img

docs/infer_subc_2d/workflow.md

@@ -1,20 +1,20 @@
-# infer_subc_2d/workflows
+# infer_subc/workflows
 
 Code for classes which interface with the sibling napari plugin repo `organelle-segmenter-plugin` documented at [ndcn.github.io/organelle-segmenter-plugin](https://ndcn.github.io/organelle-segmenter-plugin/)
 
 
-# infer_subc_2d/workflow for napari plugin
+# infer_subc/workflow for napari plugin
 
-The `workflow` sub-module is designed to interface with this repo (`infer_subc_2d`) and the sibling [napari](https://napari.org/stable/) plugin repo [organelle-segmenter-plugin](https://github.com/ndcn/organelle-segmenter-plugin)
+The `workflow` sub-module is designed to interface with this repo (`infer_subc`) and the sibling [napari](https://napari.org/stable/) plugin repo [organelle-segmenter-plugin](https://github.com/ndcn/organelle-segmenter-plugin)
 
 ### workflow sub-modules
 
-::: infer_subc_2d.workflow.workflow
+::: infer_subc.workflow.workflow
 
-::: infer_subc_2d.workflow.workflow_config
+::: infer_subc.workflow.workflow_config
 
-::: infer_subc_2d.workflow.workflow_definition
+::: infer_subc.workflow.workflow_definition
 
-::: infer_subc_2d.workflow.workflow_engine
+::: infer_subc.workflow.workflow_engine
 
-::: infer_subc_2d.workflow.workflow_step
+::: infer_subc.workflow.workflow_step

docs/nbs/overview.md

@@ -1,6 +1,6 @@
 #
 
-## infer_subc_2d
+## infer_subc
 
 This module contains code to segment organelles from multi-channel images generated by SCohenLab.   The "raw" data files are the output of linear unmixing of multi-spectral imaging capture in their lab.
 

docs/notebooks/nbs_overview.md

@@ -14,4 +14,4 @@ Robust inference of subcellular objects:
   -  8️⃣. [Infer ***endoplasmic reticulum***](https://github.com/ndcn/infer-subc-2D/tree/main/notebooks/08_endoplasmic_reticulum.ipynb)
   -  9️⃣. [Infer ***lipid body***](https://github.com/ndcn/infer-subc-2D/tree/main/notebooks/09_lipid_bodies.ipynb) 
 
-::: infer_subc_2d.organelles
+::: infer_subc.organelles

env_create.sh

@@ -15,7 +15,7 @@ pip install -e <path to organelle-segmenter-plugin>
 
 
 ##  Execute this if installing via pypi (not yet available)
-pip install infer_subc_2d
+pip install infer_subc
 pip install napari-infer-subc  
 
 # # pip install opencv-python
@@ -40,3 +40,43 @@ pip install aicssegmentation #downgrades napari and scikitlearn
 pip install napari-aicsimageio  
 
 
+
+
+
+
+conda create -n napari10 python=3.10
+conda activate napari10
+conda install -c conda-forge ipython ipykernel pip notebook napari scipy scikit-learn
+conda install matplotlib
+
+pip install aicsimageio tifffile aicspylibczi aicssegmentation napari-aicsimageio
+
+pip install aicspylibczi
+pip install aicssegmentation #downgrades napari and scikitlearn
+
+pip install napari-aicsimageio  
+
+
+
+
+
+
+
+###### TEST FOR CENTROSOME
+conda create -n cento python=3.9 -c conda-forge pip notebook napari scipy scikit-learn 
+
+conda activate cento
+
+# pip install 'napari[all]'
+# pip install scipy scikit-learn matplotlib #jupyter
+# python3 -m pip install centrosome "matplotlib >=3.1.3"
+# conda install -c bioconda centrosome
+
+pip install centrosome
+pip install aicsimageio 
+pip install aicspylibczi
+pip install aicssegmentation #downgrades napari and scikitlearn
+
+pip install napari-aicsimageio  
+
+

infer_subc_2d/__init__.py → infer_subc/__init__.py

@@ -19,7 +19,7 @@
 
 # -*- coding: utf-8 -*-
 
-"""Top-level package for infer_subc_2D."""
+"""Top-level package for infer_subc."""
 
 __author__ = "Andy Henrie"
 __email__ = "[email protected]"

infer_subc_2d/__main__.py → infer_subc/__main__.py

@@ -1,4 +1,4 @@
-"""Entry point for infer_subc_2d."""
+"""Entry point for infer_subc."""
 
 from .cli import main  # pragma: no cover