From 6daa8c21ec8f50cdd1193be39251e9619c03e255 Mon Sep 17 00:00:00 2001 From: lleplat Date: Wed, 17 Jul 2024 17:34:22 +0100 Subject: [PATCH] Docs --- Makefile | 20 + _static/communicating_with_qupath.html | 7987 ++++++++++++++++ _static/opening_images.html | 8238 +++++++++++++++++ _static/working_with_objects.html | 8183 ++++++++++++++++ conf.py | 37 + index.rst | 15 + make.bat | 35 + notebooks.rst | 11 + notebooks_files/communicating_with_qupath.rst | 5 + notebooks_files/opening_images.rst | 5 + notebooks_files/working_with_objects.rst | 5 + qubalab.display.rst | 10 + qubalab.images.metadata.rst | 34 + qubalab.images.rst | 82 + qubalab.objects.rst | 50 + qubalab.qupath.rst | 10 + qubalab.rst | 10 + 17 files changed, 24737 insertions(+) create mode 100644 Makefile create mode 100644 _static/communicating_with_qupath.html create mode 100644 _static/opening_images.html create mode 100644 _static/working_with_objects.html create mode 100644 conf.py create mode 100644 index.rst create mode 100644 make.bat create mode 100644 notebooks.rst create mode 100644 notebooks_files/communicating_with_qupath.rst create mode 100644 notebooks_files/opening_images.rst create mode 100644 notebooks_files/working_with_objects.rst create mode 100644 qubalab.display.rst create mode 100644 qubalab.images.metadata.rst create mode 100644 qubalab.images.rst create mode 100644 qubalab.objects.rst create mode 100644 qubalab.qupath.rst create mode 100644 qubalab.rst diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..d4bb2cb --- /dev/null +++ b/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) + +.PHONY: help Makefile + +# 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) diff --git a/_static/communicating_with_qupath.html b/_static/communicating_with_qupath.html new file mode 100644 index 0000000..612b2f6 --- /dev/null +++ b/_static/communicating_with_qupath.html @@ -0,0 +1,7987 @@ + + + + + +communicating_with_qupath + + + + + + + + + + + + +
+ + + + + + + + + + +
+ + diff --git a/_static/opening_images.html b/_static/opening_images.html new file mode 100644 index 0000000..9bf725d --- /dev/null +++ b/_static/opening_images.html @@ -0,0 +1,8238 @@ + + + + + +opening_images + + + + + + + + + + + + +
+ + + + + + + + + + + + + + +
+ + diff --git a/_static/working_with_objects.html b/_static/working_with_objects.html new file mode 100644 index 0000000..346f2f9 --- /dev/null +++ b/_static/working_with_objects.html @@ -0,0 +1,8183 @@ + + + + + +working_with_objects + + + + + + + + + + + + +
+ + + + + + + + + + + + + +
+ + diff --git a/conf.py b/conf.py new file mode 100644 index 0000000..78b95e1 --- /dev/null +++ b/conf.py @@ -0,0 +1,37 @@ +# Configuration file for the Sphinx documentation builder. +# +# For the full list of built-in configuration values, see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# Add path to code for sphinx.ext.autodoc +import sys, os +sys.path.insert(0, os.path.abspath('../qubalab')) + +# Both the class’ and the __init__ method’s docstring are concatenated and inserted +autoclass_content = "both" + +# -- Project information ----------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information + +project = 'QuBaLab' +copyright = "2024, QuPath developers, The University of Edinburgh" +author = "Pete Bankhead, Alan O'Callaghan, Léo Leplat" +release = '0.0.1' + +# -- General configuration --------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration + +extensions = [ + "sphinx.ext.autodoc", +] + +templates_path = ['_templates'] +exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store'] + + + +# -- Options for HTML output ------------------------------------------------- +# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output + +html_theme = 'sphinx_rtd_theme' +html_static_path = ['_static'] diff --git a/index.rst b/index.rst new file mode 100644 index 0000000..b26a4d5 --- /dev/null +++ b/index.rst @@ -0,0 +1,15 @@ +.. qubalab documentation master file, created by + sphinx-quickstart on Wed Jul 17 12:19:43 2024. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +QuBaLab documentation +===================== + +TODO + +.. toctree:: + :maxdepth: 3 + + notebooks + qubalab diff --git a/make.bat b/make.bat new file mode 100644 index 0000000..32bb245 --- /dev/null +++ b/make.bat @@ -0,0 +1,35 @@ +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=. +set BUILDDIR=_build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/notebooks.rst b/notebooks.rst new file mode 100644 index 0000000..faa8c6a --- /dev/null +++ b/notebooks.rst @@ -0,0 +1,11 @@ +Notebooks +=============================== + +TODO + +.. toctree:: + :maxdepth: 1 + + notebooks_files/opening_images + notebooks_files/communicating_with_qupath + notebooks_files/working_with_objects \ No newline at end of file diff --git a/notebooks_files/communicating_with_qupath.rst b/notebooks_files/communicating_with_qupath.rst new file mode 100644 index 0000000..f31f6c9 --- /dev/null +++ b/notebooks_files/communicating_with_qupath.rst @@ -0,0 +1,5 @@ +Communicating with QuPath +=============================== + +.. raw:: html + :file: ../_static/communicating_with_qupath.html \ No newline at end of file diff --git a/notebooks_files/opening_images.rst b/notebooks_files/opening_images.rst new file mode 100644 index 0000000..4a25c94 --- /dev/null +++ b/notebooks_files/opening_images.rst @@ -0,0 +1,5 @@ +Opening images +=============================== + +.. raw:: html + :file: ../_static/opening_images.html \ No newline at end of file diff --git a/notebooks_files/working_with_objects.rst b/notebooks_files/working_with_objects.rst new file mode 100644 index 0000000..ff7ff71 --- /dev/null +++ b/notebooks_files/working_with_objects.rst @@ -0,0 +1,5 @@ +Working with objects +=============================== + +.. raw:: html + :file: ../_static/working_with_objects.html \ No newline at end of file diff --git a/qubalab.display.rst b/qubalab.display.rst new file mode 100644 index 0000000..e271d53 --- /dev/null +++ b/qubalab.display.rst @@ -0,0 +1,10 @@ +qubalab.display package +======================= + +qubalab.display.plot module +--------------------------- + +.. automodule:: qubalab.display.plot + :members: + :undoc-members: + :show-inheritance: diff --git a/qubalab.images.metadata.rst b/qubalab.images.metadata.rst new file mode 100644 index 0000000..14c7b0e --- /dev/null +++ b/qubalab.images.metadata.rst @@ -0,0 +1,34 @@ +qubalab.images.metadata package +=============================== + +qubalab.images.metadata.image\_channel module +--------------------------------------------- + +.. automodule:: qubalab.images.metadata.image_channel + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.metadata.image\_metadata module +---------------------------------------------- + +.. automodule:: qubalab.images.metadata.image_metadata + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.metadata.image\_shape module +------------------------------------------- + +.. automodule:: qubalab.images.metadata.image_shape + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.metadata.pixel\_calibration module +------------------------------------------------- + +.. automodule:: qubalab.images.metadata.pixel_calibration + :members: + :undoc-members: + :show-inheritance: diff --git a/qubalab.images.rst b/qubalab.images.rst new file mode 100644 index 0000000..dcf13fc --- /dev/null +++ b/qubalab.images.rst @@ -0,0 +1,82 @@ +qubalab.images package +====================== + +qubalab.images.aicsimageio\_server module +----------------------------------------- + +.. automodule:: qubalab.images.aicsimageio_server + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.icc\_profile\_server module +------------------------------------------ + +.. automodule:: qubalab.images.icc_profile_server + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.image\_server module +----------------------------------- + +.. automodule:: qubalab.images.image_server + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.labeled\_server module +------------------------------------- + +.. automodule:: qubalab.images.labeled_server + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.openslide\_server module +--------------------------------------- + +.. automodule:: qubalab.images.openslide_server + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.qupath\_server module +------------------------------------ + +.. automodule:: qubalab.images.qupath_server + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.region\_2d module +-------------------------------- + +.. automodule:: qubalab.images.region_2d + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.utils module +--------------------------- + +.. automodule:: qubalab.images.utils + :members: + :undoc-members: + :show-inheritance: + +qubalab.images.wrapped\_image\_server module +-------------------------------------------- + +.. automodule:: qubalab.images.wrapped_image_server + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + :maxdepth: 3 + + qubalab.images.metadata \ No newline at end of file diff --git a/qubalab.objects.rst b/qubalab.objects.rst new file mode 100644 index 0000000..b7cfce0 --- /dev/null +++ b/qubalab.objects.rst @@ -0,0 +1,50 @@ +qubalab.objects package +======================= + +qubalab.objects.classification module +------------------------------------- + +.. automodule:: qubalab.objects.classification + :members: + :undoc-members: + :show-inheritance: + +qubalab.objects.draw module +--------------------------- + +.. automodule:: qubalab.objects.draw + :members: + :undoc-members: + :show-inheritance: + +qubalab.objects.geojson module +------------------------------ + +.. automodule:: qubalab.objects.geojson + :members: + :undoc-members: + :show-inheritance: + +qubalab.objects.geometry module +------------------------------- + +.. automodule:: qubalab.objects.geometry + :members: + :undoc-members: + :show-inheritance: + +qubalab.objects.image\_feature module +------------------------------------- + +.. automodule:: qubalab.objects.image_feature + :members: + :undoc-members: + :show-inheritance: + +qubalab.objects.object\_type module +----------------------------------- + +.. automodule:: qubalab.objects.object_type + :members: + :undoc-members: + :show-inheritance: diff --git a/qubalab.qupath.rst b/qubalab.qupath.rst new file mode 100644 index 0000000..f9631a9 --- /dev/null +++ b/qubalab.qupath.rst @@ -0,0 +1,10 @@ +qubalab.qupath package +====================== + +qubalab.qupath.qupath\_gateway module +------------------------------------- + +.. automodule:: qubalab.qupath.qupath_gateway + :members: + :undoc-members: + :show-inheritance: diff --git a/qubalab.rst b/qubalab.rst new file mode 100644 index 0000000..dd774eb --- /dev/null +++ b/qubalab.rst @@ -0,0 +1,10 @@ +API documentation +================= + +.. toctree:: + :maxdepth: 4 + + qubalab.images + qubalab.qupath + qubalab.objects + qubalab.display