From e91e0c50946de5c3a925511b3c890e5fc5801fff Mon Sep 17 00:00:00 2001 From: Rakesh Rathod <112565618+rakesh9177@users.noreply.github.com> Date: Mon, 8 Jan 2024 17:49:01 +0530 Subject: [PATCH] Added readthedocs documentation support (#339) * readthedocs config added * index.rst change * a * a * rst files * a * a * all * all * all * all * all * all * all * all * all * readthedocs configured * reformatting using black * mypy updates * mypy updates * doc update * doc update * doc update * doc update * doc update * doc update * doc update * doc updates * doc updatess * doc updates * doc updates * doc updates * black changes * conf update * path updates to conf.py * module updates * conf update --- .readthedocs.yaml | 13 ++ Makefile | 20 ++ docs/Makefile | 20 ++ docs/make.bat | 35 ++++ docs/requirements.txt | 4 + docs/source/conf.py | 186 ++++++++++++++++++ docs/source/fuse.data.datasets.caching.rst | 37 ++++ .../fuse.data.datasets.caching.tests.rst | 21 ++ docs/source/fuse.data.datasets.rst | 54 +++++ docs/source/fuse.data.datasets.tests.rst | 37 ++++ docs/source/fuse.data.ops.rst | 101 ++++++++++ docs/source/fuse.data.ops.tests.rst | 53 +++++ docs/source/fuse.data.pipelines.rst | 29 +++ docs/source/fuse.data.pipelines.tests.rst | 21 ++ docs/source/fuse.data.rst | 49 +++++ docs/source/fuse.data.tests.rst | 21 ++ docs/source/fuse.data.utils.rst | 61 ++++++ docs/source/fuse.data.utils.tests.rst | 37 ++++ docs/source/fuse.dl.lightning.rst | 37 ++++ docs/source/fuse.dl.losses.rst | 61 ++++++ docs/source/fuse.dl.losses.segmentation.rst | 21 ++ docs/source/fuse.dl.models.backbones.rst | 69 +++++++ docs/source/fuse.dl.models.heads.rst | 53 +++++ docs/source/fuse.dl.models.rst | 62 ++++++ docs/source/fuse.dl.rst | 22 +++ docs/source/fuse.dl.templates.rst | 21 ++ docs/source/fuse.dl.tests.rst | 37 ++++ docs/source/fuse.eval.examples.rst | 45 +++++ docs/source/fuse.eval.metrics.libs.rst | 85 ++++++++ docs/source/fuse.eval.metrics.rst | 47 +++++ .../source/fuse.eval.metrics.segmentation.rst | 29 +++ docs/source/fuse.eval.metrics.survival.rst | 21 ++ docs/source/fuse.eval.rst | 31 +++ docs/source/fuse.eval.tests.rst | 21 ++ docs/source/fuse.rst | 34 ++++ docs/source/fuse.utils.config_tools.rst | 29 +++ docs/source/fuse.utils.config_tools.tests.rst | 45 +++++ docs/source/fuse.utils.cpu_profiling.rst | 37 ++++ .../source/fuse.utils.cpu_profiling.tests.rst | 29 +++ docs/source/fuse.utils.data.rst | 29 +++ docs/source/fuse.utils.data.tests.rst | 21 ++ docs/source/fuse.utils.file_io.rst | 53 +++++ docs/source/fuse.utils.file_io.tests.rst | 21 ++ docs/source/fuse.utils.multiprocessing.rst | 29 +++ docs/source/fuse.utils.rand.rst | 37 ++++ docs/source/fuse.utils.rand.tests.rst | 29 +++ docs/source/fuse.utils.remote_execution.rst | 29 +++ docs/source/fuse.utils.rst | 76 +++++++ docs/source/fuse.utils.tests.rst | 29 +++ ...les.imaging.classification.bright.eval.rst | 21 ++ ...examples.imaging.classification.bright.rst | 18 ++ ...e_examples.imaging.classification.cmmd.rst | 21 ++ ...e_examples.imaging.classification.isic.rst | 29 +++ ...les.imaging.classification.knight.eval.rst | 21 ++ ...examples.imaging.classification.knight.rst | 37 ++++ ..._examples.imaging.classification.mnist.rst | 37 ++++ .../fuse_examples.imaging.classification.rst | 23 +++ ...xamples.imaging.classification.stoic21.rst | 29 +++ .../fuse_examples.imaging.hello_world.rst | 21 ++ docs/source/fuse_examples.imaging.rst | 19 ++ ...examples.multimodality.ehr_transformer.rst | 45 +++++ ..._examples.multimodality.image_clinical.rst | 21 ++ docs/source/fuse_examples.multimodality.rst | 19 ++ docs/source/fuse_examples.rst | 20 ++ docs/source/fuse_examples.tests.rst | 77 ++++++++ docs/source/fuseimg.data.ops.rst | 69 +++++++ docs/source/fuseimg.data.ops.tests.rst | 29 +++ docs/source/fuseimg.data.rst | 18 ++ docs/source/fuseimg.datasets.rst | 77 ++++++++ docs/source/fuseimg.datasets.tests.rst | 21 ++ docs/source/fuseimg.eval.rst | 21 ++ docs/source/fuseimg.rst | 20 ++ docs/source/fuseimg.utils.align.rst | 29 +++ docs/source/fuseimg.utils.rst | 29 +++ docs/source/index.rst | 26 +++ docs/source/modules.rst | 9 + docs/source/run_all_unit_tests.rst | 7 + docs/source/setup.rst | 7 + fuse/data/ops/op_base.py | 1 - fuse/data/ops/ops_cast.py | 1 - fuse/data/pipelines/pipeline_default.py | 3 +- fuse/data/utils/collates.py | 1 - fuse/data/utils/split.py | 1 - fuse/dl/cross_validation/pipeline.py | 3 - .../backbones/backbone_inception_resnet_v2.py | 1 - fuse/dl/models/backbones/backbone_mlp.py | 1 - .../dl/models/backbones/backbone_resnet_3d.py | 2 - fuse/dl/models/heads/heads_1D.py | 1 - fuse/dl/models/model_ensemble.py | 1 - fuse/dl/models/model_multistream.py | 1 - fuse/eval/evaluator.py | 2 - fuse/utils/data/collate.py | 2 - fuse/utils/multiprocessing/helpers.py | 1 - fuse/utils/ndict.py | 2 - .../mnist/simple_mnist_starter.py | 1 - .../multimodality/ehr_transformer/dataset.py | 8 - .../ehr_transformer/main_train.py | 1 - fuse_examples/tests/test_ehr_transformer.py | 2 - fuseimg/data/ops/color.py | 1 - fuseimg/data/ops/image_loader.py | 1 - fuseimg/datasets/tests/test_datasets.py | 1 - fuseimg/utils/align/utils_align_ecc.py | 1 - make.bat | 35 ++++ 103 files changed, 2844 insertions(+), 39 deletions(-) create mode 100644 .readthedocs.yaml create mode 100644 Makefile create mode 100644 docs/Makefile create mode 100644 docs/make.bat create mode 100644 docs/requirements.txt create mode 100644 docs/source/conf.py create mode 100644 docs/source/fuse.data.datasets.caching.rst create mode 100644 docs/source/fuse.data.datasets.caching.tests.rst create mode 100644 docs/source/fuse.data.datasets.rst create mode 100644 docs/source/fuse.data.datasets.tests.rst create mode 100644 docs/source/fuse.data.ops.rst create mode 100644 docs/source/fuse.data.ops.tests.rst create mode 100644 docs/source/fuse.data.pipelines.rst create mode 100644 docs/source/fuse.data.pipelines.tests.rst create mode 100644 docs/source/fuse.data.rst create mode 100644 docs/source/fuse.data.tests.rst create mode 100644 docs/source/fuse.data.utils.rst create mode 100644 docs/source/fuse.data.utils.tests.rst create mode 100644 docs/source/fuse.dl.lightning.rst create mode 100644 docs/source/fuse.dl.losses.rst create mode 100644 docs/source/fuse.dl.losses.segmentation.rst create mode 100644 docs/source/fuse.dl.models.backbones.rst create mode 100644 docs/source/fuse.dl.models.heads.rst create mode 100644 docs/source/fuse.dl.models.rst create mode 100644 docs/source/fuse.dl.rst create mode 100644 docs/source/fuse.dl.templates.rst create mode 100644 docs/source/fuse.dl.tests.rst create mode 100644 docs/source/fuse.eval.examples.rst create mode 100644 docs/source/fuse.eval.metrics.libs.rst create mode 100644 docs/source/fuse.eval.metrics.rst create mode 100644 docs/source/fuse.eval.metrics.segmentation.rst create mode 100644 docs/source/fuse.eval.metrics.survival.rst create mode 100644 docs/source/fuse.eval.rst create mode 100644 docs/source/fuse.eval.tests.rst create mode 100644 docs/source/fuse.rst create mode 100644 docs/source/fuse.utils.config_tools.rst create mode 100644 docs/source/fuse.utils.config_tools.tests.rst create mode 100644 docs/source/fuse.utils.cpu_profiling.rst create mode 100644 docs/source/fuse.utils.cpu_profiling.tests.rst create mode 100644 docs/source/fuse.utils.data.rst create mode 100644 docs/source/fuse.utils.data.tests.rst create mode 100644 docs/source/fuse.utils.file_io.rst create mode 100644 docs/source/fuse.utils.file_io.tests.rst create mode 100644 docs/source/fuse.utils.multiprocessing.rst create mode 100644 docs/source/fuse.utils.rand.rst create mode 100644 docs/source/fuse.utils.rand.tests.rst create mode 100644 docs/source/fuse.utils.remote_execution.rst create mode 100644 docs/source/fuse.utils.rst create mode 100644 docs/source/fuse.utils.tests.rst create mode 100644 docs/source/fuse_examples.imaging.classification.bright.eval.rst create mode 100644 docs/source/fuse_examples.imaging.classification.bright.rst create mode 100644 docs/source/fuse_examples.imaging.classification.cmmd.rst create mode 100644 docs/source/fuse_examples.imaging.classification.isic.rst create mode 100644 docs/source/fuse_examples.imaging.classification.knight.eval.rst create mode 100644 docs/source/fuse_examples.imaging.classification.knight.rst create mode 100644 docs/source/fuse_examples.imaging.classification.mnist.rst create mode 100644 docs/source/fuse_examples.imaging.classification.rst create mode 100644 docs/source/fuse_examples.imaging.classification.stoic21.rst create mode 100644 docs/source/fuse_examples.imaging.hello_world.rst create mode 100644 docs/source/fuse_examples.imaging.rst create mode 100644 docs/source/fuse_examples.multimodality.ehr_transformer.rst create mode 100644 docs/source/fuse_examples.multimodality.image_clinical.rst create mode 100644 docs/source/fuse_examples.multimodality.rst create mode 100644 docs/source/fuse_examples.rst create mode 100644 docs/source/fuse_examples.tests.rst create mode 100644 docs/source/fuseimg.data.ops.rst create mode 100644 docs/source/fuseimg.data.ops.tests.rst create mode 100644 docs/source/fuseimg.data.rst create mode 100644 docs/source/fuseimg.datasets.rst create mode 100644 docs/source/fuseimg.datasets.tests.rst create mode 100644 docs/source/fuseimg.eval.rst create mode 100644 docs/source/fuseimg.rst create mode 100644 docs/source/fuseimg.utils.align.rst create mode 100644 docs/source/fuseimg.utils.rst create mode 100644 docs/source/index.rst create mode 100644 docs/source/modules.rst create mode 100644 docs/source/run_all_unit_tests.rst create mode 100644 docs/source/setup.rst create mode 100644 make.bat diff --git a/.readthedocs.yaml b/.readthedocs.yaml new file mode 100644 index 00000000..3a7e5af6 --- /dev/null +++ b/.readthedocs.yaml @@ -0,0 +1,13 @@ +version: "2" + +build: + os: "ubuntu-22.04" + tools: + python: "3.10" + +python: + install: + - requirements: docs/requirements.txt + +sphinx: + configuration: docs/source/conf.py \ No newline at end of file diff --git a/Makefile b/Makefile new file mode 100644 index 00000000..d0c3cbf1 --- /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 = source +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) $(O) diff --git a/docs/Makefile b/docs/Makefile new file mode 100644 index 00000000..d4bb2cbb --- /dev/null +++ b/docs/Makefile @@ -0,0 +1,20 @@ +# Minimal makefile for Sphinx documentation +# + +# You can set these variables from the command line, and also +# from the environment for the first two. +SPHINXOPTS ?= +SPHINXBUILD ?= sphinx-build +SOURCEDIR = . +BUILDDIR = _build + +# Put it first so that "make" without argument is like "make help". +help: + @$(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/docs/make.bat b/docs/make.bat new file mode 100644 index 00000000..32bb2452 --- /dev/null +++ b/docs/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/docs/requirements.txt b/docs/requirements.txt new file mode 100644 index 00000000..4dfbd070 --- /dev/null +++ b/docs/requirements.txt @@ -0,0 +1,4 @@ +sphinx==7.1.2 +sphinx-rtd-theme==1.3.0rc1 +m2r2 + diff --git a/docs/source/conf.py b/docs/source/conf.py new file mode 100644 index 00000000..95269e10 --- /dev/null +++ b/docs/source/conf.py @@ -0,0 +1,186 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# http://www.sphinx-doc.org/en/master/config + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +import os +import sys + +sys.path.insert(0, os.path.abspath(os.path.join("..", ".."))) + + +# -- Project information ----------------------------------------------------- + + +# Take from setup.py file +def grep_value_from_setup(key: str) -> str: + import re + + setup_file = os.path.normpath( + os.path.join(os.path.dirname(os.path.abspath(__file__)), "..", "..", "setup.py") + ) + with open(setup_file, "r") as setup_file: + for line in setup_file.readlines(): + value = re.search(".*{key}=(.*),*".format(key=key), line) + if value: + value = value.group(1) + value = re.sub(r"^\W+", "", value) # lstrip non alphanumeric + value = re.sub(r"\W+$", "", value) # rstrip non alphanumeric + return value + + +project = grep_value_from_setup("name") +copyright = "2023" +author = grep_value_from_setup("author") + +# The full version, including alpha/beta/rc tags + +release = "latest" + + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "sphinx.ext.autodoc", + "sphinx.ext.doctest", + "sphinx.ext.coverage", + "sphinx.ext.viewcode", + "sphinx.ext.intersphinx", # link to other documentations + # 'nbsphinx', # work with jupyter notebook. requires pip install nbsphinx + # 'sphinx.ext.mathjax', # required for math in Jupyter Notebook + "m2r2", # work with markdown files. requires pip install m2r2 + "sphinx.ext.napoleon", # parse Google/numpy docstring + # 'sphinx.ext.autosummary', # Automated index.rst toctreee +] + +# autosummary_generate = True # create api docs with autosummary + + +intersphinx_mapping = { + "numpy": ("http://docs.scipy.org/doc/numpy/", None), + "scipy": ("http://docs.scipy.org/doc/scipy/reference/", None), + "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None), + "python": ("https://docs.python.org/{}.{}".format(*sys.version_info), None), +} + +autoclass_content = "both" + +numpydoc_show_class_members = False # Suppress sphinx warnings when building numpy-doc + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# The suffix(es) of source filenames. +# You can specify multiple suffix as a list of string: +source_suffix = { + ".rst": "restructuredtext", + ".txt": "restructuredtext", + ".md": "markdown", +} + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [ + "*estimation.*_.rst", # estimation old files which kept locally + "*tests.*", # remove tests from documentation +] + +# https://www.sphinx-doc.org/en/master/usage/configuration.html?highlight=master_doc#confval-master_doc +master_doc = "index" # what file includes the root toctree. Needed explicitly for readthedocs.org + + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +# +on_rtd = os.environ.get("READTHEDOCS") == "True" +if on_rtd: + html_theme = "sphinx_rtd_theme" +else: + html_theme = "classic" + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] + +# # Add content to the navigation side bar: +html_sidebars = { + "**": ["localtoc.html", "sourcelink.html", "searchbox.html", "globaltoc.html"] +} + + +# -- Custom scripts ------------------------------------------------- + + +# Add module's README for each module HTML page +def add_modules_readme() -> str: + def get_rst_file_name_from_package_source(package_source_path: str) -> str: + rst_source_path = os.path.relpath(package_source_path, os.getcwd()) + rst_file_name = rst_source_path.split(os.sep) + rst_file_name = [ + directory for directory in rst_file_name if not directory.startswith(".") + ] + rst_file_name += ["rst"] + rst_file_name = ".".join(rst_file_name) + rst_file_name = os.path.join(source_html_dir, rst_file_name) + return rst_file_name + + def get_edited_rast_file( + rst_source_path: str, include_text: str, remove_original_header: bool = True + ) -> str: + with open(rst_source_path, "r") as fh: + rst_source_lines = fh.read().splitlines() + if not any([include_text in line for line in rst_source_lines]): + # Add link to readme only if not already exists + rst_source_lines.insert(3, include_text) + if remove_original_header: + rst_source_lines = rst_source_lines[2:] # remove existing header + + return rst_source_lines + + INCLUDE_TEXT = ".. mdinclude:: " + + README_FILE_NAME = "README.md" + + # source_code_dir = os.path.join("..", "..", "fuse-med-ml") + source_html_dir = os.getcwd() + "/docs/source/" # sphinx's docs source directory + + for dir_name, subdir_list, file_names in os.walk(os.getcwd()): + if README_FILE_NAME in file_names: # Current dir has a readme file + # Get README file path: + # source_path = os.path.relpath(dir_name, os.path.join(source_code_dir, "..")) + source_path = os.path.normpath(dir_name) + + readme_file_path = os.path.join(source_path, README_FILE_NAME) + + # Construct the corresponding module rst file: + rst_source_file = get_rst_file_name_from_package_source(source_path) + + # Edit the rst file to include the path to the readme: + path_to_be_added = os.path.relpath(readme_file_path, os.getcwd()) + + try: + include_text = INCLUDE_TEXT + "../../" + path_to_be_added + "\n" + content = get_edited_rast_file(rst_source_file, include_text, True) + + with open(rst_source_file, "w") as f: + for line in content: + f.write("{}\n".format(line)) + + except FileNotFoundError: + print("Could not find file {}".format(rst_source_file)) + + +add_modules_readme() diff --git a/docs/source/fuse.data.datasets.caching.rst b/docs/source/fuse.data.datasets.caching.rst new file mode 100644 index 00000000..4d645ac2 --- /dev/null +++ b/docs/source/fuse.data.datasets.caching.rst @@ -0,0 +1,37 @@ +fuse.data.datasets.caching package +================================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.data.datasets.caching.tests + +Submodules +---------- + +fuse.data.datasets.caching.object\_caching\_handlers module +----------------------------------------------------------- + +.. automodule:: fuse.data.datasets.caching.object_caching_handlers + :members: + :undoc-members: + :show-inheritance: + +fuse.data.datasets.caching.samples\_cacher module +------------------------------------------------- + +.. automodule:: fuse.data.datasets.caching.samples_cacher + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.datasets.caching + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.datasets.caching.tests.rst b/docs/source/fuse.data.datasets.caching.tests.rst new file mode 100644 index 00000000..6a7ea3f2 --- /dev/null +++ b/docs/source/fuse.data.datasets.caching.tests.rst @@ -0,0 +1,21 @@ +fuse.data.datasets.caching.tests package +======================================== + +Submodules +---------- + +fuse.data.datasets.caching.tests.test\_sample\_caching module +------------------------------------------------------------- + +.. automodule:: fuse.data.datasets.caching.tests.test_sample_caching + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.datasets.caching.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.datasets.rst b/docs/source/fuse.data.datasets.rst new file mode 100644 index 00000000..0ff3b256 --- /dev/null +++ b/docs/source/fuse.data.datasets.rst @@ -0,0 +1,54 @@ +fuse.data.datasets package +========================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.data.datasets.caching + fuse.data.datasets.tests + +Submodules +---------- + +fuse.data.datasets.dataset\_base module +--------------------------------------- + +.. automodule:: fuse.data.datasets.dataset_base + :members: + :undoc-members: + :show-inheritance: + +fuse.data.datasets.dataset\_default module +------------------------------------------ + +.. automodule:: fuse.data.datasets.dataset_default + :members: + :undoc-members: + :show-inheritance: + +fuse.data.datasets.dataset\_wrap\_seq\_to\_dict module +------------------------------------------------------ + +.. automodule:: fuse.data.datasets.dataset_wrap_seq_to_dict + :members: + :undoc-members: + :show-inheritance: + +fuse.data.datasets.sample\_caching\_audit module +------------------------------------------------ + +.. automodule:: fuse.data.datasets.sample_caching_audit + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.datasets + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.datasets.tests.rst b/docs/source/fuse.data.datasets.tests.rst new file mode 100644 index 00000000..5cd5702d --- /dev/null +++ b/docs/source/fuse.data.datasets.tests.rst @@ -0,0 +1,37 @@ +fuse.data.datasets.tests package +================================ + +Submodules +---------- + +fuse.data.datasets.tests.test\_dataset\_default module +------------------------------------------------------ + +.. automodule:: fuse.data.datasets.tests.test_dataset_default + :members: + :undoc-members: + :show-inheritance: + +fuse.data.datasets.tests.test\_dataset\_default\_audit\_feature module +---------------------------------------------------------------------- + +.. automodule:: fuse.data.datasets.tests.test_dataset_default_audit_feature + :members: + :undoc-members: + :show-inheritance: + +fuse.data.datasets.tests.test\_dataset\_wrap\_seq\_to\_dict module +------------------------------------------------------------------ + +.. automodule:: fuse.data.datasets.tests.test_dataset_wrap_seq_to_dict + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.datasets.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.ops.rst b/docs/source/fuse.data.ops.rst new file mode 100644 index 00000000..537a8760 --- /dev/null +++ b/docs/source/fuse.data.ops.rst @@ -0,0 +1,101 @@ +fuse.data.ops package +===================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.data.ops.tests + +Submodules +---------- + +fuse.data.ops.caching\_tools module +----------------------------------- + +.. automodule:: fuse.data.ops.caching_tools + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.hashable\_class module +------------------------------------ + +.. automodule:: fuse.data.ops.hashable_class + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.op\_base module +----------------------------- + +.. automodule:: fuse.data.ops.op_base + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.ops\_aug\_common module +------------------------------------- + +.. automodule:: fuse.data.ops.ops_aug_common + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.ops\_aug\_tabular module +-------------------------------------- + +.. automodule:: fuse.data.ops.ops_aug_tabular + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.ops\_cast module +------------------------------ + +.. automodule:: fuse.data.ops.ops_cast + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.ops\_common module +-------------------------------- + +.. automodule:: fuse.data.ops.ops_common + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.ops\_common\_for\_testing module +---------------------------------------------- + +.. automodule:: fuse.data.ops.ops_common_for_testing + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.ops\_debug module +------------------------------- + +.. automodule:: fuse.data.ops.ops_debug + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.ops\_read module +------------------------------ + +.. automodule:: fuse.data.ops.ops_read + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.ops + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.ops.tests.rst b/docs/source/fuse.data.ops.tests.rst new file mode 100644 index 00000000..1b151625 --- /dev/null +++ b/docs/source/fuse.data.ops.tests.rst @@ -0,0 +1,53 @@ +fuse.data.ops.tests package +=========================== + +Submodules +---------- + +fuse.data.ops.tests.test\_op\_base module +----------------------------------------- + +.. automodule:: fuse.data.ops.tests.test_op_base + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.tests.test\_ops\_aug\_common module +------------------------------------------------- + +.. automodule:: fuse.data.ops.tests.test_ops_aug_common + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.tests.test\_ops\_cast module +------------------------------------------ + +.. automodule:: fuse.data.ops.tests.test_ops_cast + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.tests.test\_ops\_common module +-------------------------------------------- + +.. automodule:: fuse.data.ops.tests.test_ops_common + :members: + :undoc-members: + :show-inheritance: + +fuse.data.ops.tests.test\_ops\_read module +------------------------------------------ + +.. automodule:: fuse.data.ops.tests.test_ops_read + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.ops.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.pipelines.rst b/docs/source/fuse.data.pipelines.rst new file mode 100644 index 00000000..f81d76ef --- /dev/null +++ b/docs/source/fuse.data.pipelines.rst @@ -0,0 +1,29 @@ +fuse.data.pipelines package +=========================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.data.pipelines.tests + +Submodules +---------- + +fuse.data.pipelines.pipeline\_default module +-------------------------------------------- + +.. automodule:: fuse.data.pipelines.pipeline_default + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.pipelines + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.pipelines.tests.rst b/docs/source/fuse.data.pipelines.tests.rst new file mode 100644 index 00000000..4e3103f7 --- /dev/null +++ b/docs/source/fuse.data.pipelines.tests.rst @@ -0,0 +1,21 @@ +fuse.data.pipelines.tests package +================================= + +Submodules +---------- + +fuse.data.pipelines.tests.test\_pipeline\_default module +-------------------------------------------------------- + +.. automodule:: fuse.data.pipelines.tests.test_pipeline_default + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.pipelines.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.rst b/docs/source/fuse.data.rst new file mode 100644 index 00000000..918a84db --- /dev/null +++ b/docs/source/fuse.data.rst @@ -0,0 +1,49 @@ + +.. mdinclude:: ../../fuse/data/README.md + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.data.datasets + fuse.data.ops + fuse.data.pipelines + fuse.data.tests + fuse.data.utils + +Submodules +---------- + +fuse.data.key\_types module +--------------------------- + +.. automodule:: fuse.data.key_types + :members: + :undoc-members: + :show-inheritance: + +fuse.data.key\_types\_for\_testing module +----------------------------------------- + +.. automodule:: fuse.data.key_types_for_testing + :members: + :undoc-members: + :show-inheritance: + +fuse.data.patterns module +------------------------- + +.. automodule:: fuse.data.patterns + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.tests.rst b/docs/source/fuse.data.tests.rst new file mode 100644 index 00000000..68b8f679 --- /dev/null +++ b/docs/source/fuse.data.tests.rst @@ -0,0 +1,21 @@ +fuse.data.tests package +======================= + +Submodules +---------- + +fuse.data.tests.test\_version module +------------------------------------ + +.. automodule:: fuse.data.tests.test_version + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.utils.rst b/docs/source/fuse.data.utils.rst new file mode 100644 index 00000000..ced807c0 --- /dev/null +++ b/docs/source/fuse.data.utils.rst @@ -0,0 +1,61 @@ +fuse.data.utils package +======================= + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.data.utils.tests + +Submodules +---------- + +fuse.data.utils.collates module +------------------------------- + +.. automodule:: fuse.data.utils.collates + :members: + :undoc-members: + :show-inheritance: + +fuse.data.utils.export module +----------------------------- + +.. automodule:: fuse.data.utils.export + :members: + :undoc-members: + :show-inheritance: + +fuse.data.utils.sample module +----------------------------- + +.. automodule:: fuse.data.utils.sample + :members: + :undoc-members: + :show-inheritance: + +fuse.data.utils.samplers module +------------------------------- + +.. automodule:: fuse.data.utils.samplers + :members: + :undoc-members: + :show-inheritance: + +fuse.data.utils.split module +---------------------------- + +.. automodule:: fuse.data.utils.split + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.data.utils.tests.rst b/docs/source/fuse.data.utils.tests.rst new file mode 100644 index 00000000..1d479948 --- /dev/null +++ b/docs/source/fuse.data.utils.tests.rst @@ -0,0 +1,37 @@ +fuse.data.utils.tests package +============================= + +Submodules +---------- + +fuse.data.utils.tests.test\_collates module +------------------------------------------- + +.. automodule:: fuse.data.utils.tests.test_collates + :members: + :undoc-members: + :show-inheritance: + +fuse.data.utils.tests.test\_dataset\_export module +-------------------------------------------------- + +.. automodule:: fuse.data.utils.tests.test_dataset_export + :members: + :undoc-members: + :show-inheritance: + +fuse.data.utils.tests.test\_samplers module +------------------------------------------- + +.. automodule:: fuse.data.utils.tests.test_samplers + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.data.utils.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.lightning.rst b/docs/source/fuse.dl.lightning.rst new file mode 100644 index 00000000..191e0ebf --- /dev/null +++ b/docs/source/fuse.dl.lightning.rst @@ -0,0 +1,37 @@ +fuse.dl.lightning package +========================= + +Submodules +---------- + +fuse.dl.lightning.pl\_epoch\_summary module +------------------------------------------- + +.. automodule:: fuse.dl.lightning.pl_epoch_summary + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.lightning.pl\_funcs module +---------------------------------- + +.. automodule:: fuse.dl.lightning.pl_funcs + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.lightning.pl\_module module +----------------------------------- + +.. automodule:: fuse.dl.lightning.pl_module + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.dl.lightning + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.losses.rst b/docs/source/fuse.dl.losses.rst new file mode 100644 index 00000000..888697bf --- /dev/null +++ b/docs/source/fuse.dl.losses.rst @@ -0,0 +1,61 @@ +fuse.dl.losses package +====================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.dl.losses.segmentation + +Submodules +---------- + +fuse.dl.losses.loss\_base module +-------------------------------- + +.. automodule:: fuse.dl.losses.loss_base + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.losses.loss\_default module +----------------------------------- + +.. automodule:: fuse.dl.losses.loss_default + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.losses.loss\_extract module +----------------------------------- + +.. automodule:: fuse.dl.losses.loss_extract + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.losses.loss\_warm\_up module +------------------------------------ + +.. automodule:: fuse.dl.losses.loss_warm_up + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.losses.loss\_wrap\_to\_dict module +------------------------------------------ + +.. automodule:: fuse.dl.losses.loss_wrap_to_dict + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.dl.losses + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.losses.segmentation.rst b/docs/source/fuse.dl.losses.segmentation.rst new file mode 100644 index 00000000..a06e425a --- /dev/null +++ b/docs/source/fuse.dl.losses.segmentation.rst @@ -0,0 +1,21 @@ +fuse.dl.losses.segmentation package +=================================== + +Submodules +---------- + +fuse.dl.losses.segmentation.loss\_dice module +--------------------------------------------- + +.. automodule:: fuse.dl.losses.segmentation.loss_dice + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.dl.losses.segmentation + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.models.backbones.rst b/docs/source/fuse.dl.models.backbones.rst new file mode 100644 index 00000000..89d44c89 --- /dev/null +++ b/docs/source/fuse.dl.models.backbones.rst @@ -0,0 +1,69 @@ +fuse.dl.models.backbones package +================================ + +Submodules +---------- + +fuse.dl.models.backbones.backbone\_inception\_resnet\_v2 module +--------------------------------------------------------------- + +.. automodule:: fuse.dl.models.backbones.backbone_inception_resnet_v2 + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.backbones.backbone\_mlp module +--------------------------------------------- + +.. automodule:: fuse.dl.models.backbones.backbone_mlp + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.backbones.backbone\_mvit module +---------------------------------------------- + +.. automodule:: fuse.dl.models.backbones.backbone_mvit + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.backbones.backbone\_resnet module +------------------------------------------------ + +.. automodule:: fuse.dl.models.backbones.backbone_resnet + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.backbones.backbone\_resnet\_3d module +---------------------------------------------------- + +.. automodule:: fuse.dl.models.backbones.backbone_resnet_3d + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.backbones.backbone\_transformer module +----------------------------------------------------- + +.. automodule:: fuse.dl.models.backbones.backbone_transformer + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.backbones.backbone\_vit module +--------------------------------------------- + +.. automodule:: fuse.dl.models.backbones.backbone_vit + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.dl.models.backbones + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.models.heads.rst b/docs/source/fuse.dl.models.heads.rst new file mode 100644 index 00000000..85f41e74 --- /dev/null +++ b/docs/source/fuse.dl.models.heads.rst @@ -0,0 +1,53 @@ +fuse.dl.models.heads package +============================ + +Submodules +---------- + +fuse.dl.models.heads.common module +---------------------------------- + +.. automodule:: fuse.dl.models.heads.common + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.heads.head\_dense\_segmentation module +----------------------------------------------------- + +.. automodule:: fuse.dl.models.heads.head_dense_segmentation + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.heads.head\_global\_pooling\_classifier module +------------------------------------------------------------- + +.. automodule:: fuse.dl.models.heads.head_global_pooling_classifier + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.heads.heads\_1D module +------------------------------------- + +.. automodule:: fuse.dl.models.heads.heads_1D + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.heads.heads\_3D module +------------------------------------- + +.. automodule:: fuse.dl.models.heads.heads_3D + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.dl.models.heads + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.models.rst b/docs/source/fuse.dl.models.rst new file mode 100644 index 00000000..125c3272 --- /dev/null +++ b/docs/source/fuse.dl.models.rst @@ -0,0 +1,62 @@ +fuse.dl.models package +====================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.dl.models.backbones + fuse.dl.models.heads + +Submodules +---------- + +fuse.dl.models.model\_ensemble module +------------------------------------- + +.. automodule:: fuse.dl.models.model_ensemble + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.model\_multihead module +-------------------------------------- + +.. automodule:: fuse.dl.models.model_multihead + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.model\_multistream module +---------------------------------------- + +.. automodule:: fuse.dl.models.model_multistream + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.model\_siamese module +------------------------------------ + +.. automodule:: fuse.dl.models.model_siamese + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.models.model\_wrapper module +------------------------------------ + +.. automodule:: fuse.dl.models.model_wrapper + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.dl.models + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.rst b/docs/source/fuse.dl.rst new file mode 100644 index 00000000..3a3ec006 --- /dev/null +++ b/docs/source/fuse.dl.rst @@ -0,0 +1,22 @@ + +.. mdinclude:: ../../fuse/dl/README.md + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.dl.lightning + fuse.dl.losses + fuse.dl.models + fuse.dl.templates + fuse.dl.tests + +Module contents +--------------- + +.. automodule:: fuse.dl + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.templates.rst b/docs/source/fuse.dl.templates.rst new file mode 100644 index 00000000..b8d3b7fe --- /dev/null +++ b/docs/source/fuse.dl.templates.rst @@ -0,0 +1,21 @@ +fuse.dl.templates package +========================= + +Submodules +---------- + +fuse.dl.templates.walkthrough\_template module +---------------------------------------------- + +.. automodule:: fuse.dl.templates.walkthrough_template + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.dl.templates + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.dl.tests.rst b/docs/source/fuse.dl.tests.rst new file mode 100644 index 00000000..d164ec18 --- /dev/null +++ b/docs/source/fuse.dl.tests.rst @@ -0,0 +1,37 @@ +fuse.dl.tests package +===================== + +Submodules +---------- + +fuse.dl.tests.test\_cat module +------------------------------ + +.. automodule:: fuse.dl.tests.test_cat + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.tests.test\_loss\_wrapper module +---------------------------------------- + +.. automodule:: fuse.dl.tests.test_loss_wrapper + :members: + :undoc-members: + :show-inheritance: + +fuse.dl.tests.test\_vit module +------------------------------ + +.. automodule:: fuse.dl.tests.test_vit + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.dl.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.eval.examples.rst b/docs/source/fuse.eval.examples.rst new file mode 100644 index 00000000..01098112 --- /dev/null +++ b/docs/source/fuse.eval.examples.rst @@ -0,0 +1,45 @@ +fuse.eval.examples package +========================== + +Submodules +---------- + +fuse.eval.examples.examples module +---------------------------------- + +.. automodule:: fuse.eval.examples.examples + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.examples.examples\_segmentation module +------------------------------------------------ + +.. automodule:: fuse.eval.examples.examples_segmentation + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.examples.examples\_seq\_gen module +-------------------------------------------- + +.. automodule:: fuse.eval.examples.examples_seq_gen + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.examples.examples\_stats module +----------------------------------------- + +.. automodule:: fuse.eval.examples.examples_stats + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.eval.examples + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.eval.metrics.libs.rst b/docs/source/fuse.eval.metrics.libs.rst new file mode 100644 index 00000000..717dcac0 --- /dev/null +++ b/docs/source/fuse.eval.metrics.libs.rst @@ -0,0 +1,85 @@ +fuse.eval.metrics.libs package +============================== + +Submodules +---------- + +fuse.eval.metrics.libs.calibration module +----------------------------------------- + +.. automodule:: fuse.eval.metrics.libs.calibration + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.libs.classification module +-------------------------------------------- + +.. automodule:: fuse.eval.metrics.libs.classification + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.libs.ensembling module +---------------------------------------- + +.. automodule:: fuse.eval.metrics.libs.ensembling + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.libs.instance\_segmentation module +---------------------------------------------------- + +.. automodule:: fuse.eval.metrics.libs.instance_segmentation + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.libs.model\_comparison module +----------------------------------------------- + +.. automodule:: fuse.eval.metrics.libs.model_comparison + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.libs.segmentation module +------------------------------------------ + +.. automodule:: fuse.eval.metrics.libs.segmentation + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.libs.stat module +---------------------------------- + +.. automodule:: fuse.eval.metrics.libs.stat + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.libs.survival module +-------------------------------------- + +.. automodule:: fuse.eval.metrics.libs.survival + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.libs.thresholding module +------------------------------------------ + +.. automodule:: fuse.eval.metrics.libs.thresholding + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.eval.metrics.libs + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.eval.metrics.rst b/docs/source/fuse.eval.metrics.rst new file mode 100644 index 00000000..13d5f1bf --- /dev/null +++ b/docs/source/fuse.eval.metrics.rst @@ -0,0 +1,47 @@ +fuse.eval.metrics package +========================= + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.eval.metrics.libs + fuse.eval.metrics.segmentation + fuse.eval.metrics.survival + +Submodules +---------- + +fuse.eval.metrics.metrics\_common module +---------------------------------------- + +.. automodule:: fuse.eval.metrics.metrics_common + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.metrics\_model\_comparison module +--------------------------------------------------- + +.. automodule:: fuse.eval.metrics.metrics_model_comparison + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.utils module +------------------------------ + +.. automodule:: fuse.eval.metrics.utils + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.eval.metrics + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.eval.metrics.segmentation.rst b/docs/source/fuse.eval.metrics.segmentation.rst new file mode 100644 index 00000000..1261afc4 --- /dev/null +++ b/docs/source/fuse.eval.metrics.segmentation.rst @@ -0,0 +1,29 @@ +fuse.eval.metrics.segmentation package +====================================== + +Submodules +---------- + +fuse.eval.metrics.segmentation.metrics\_instance\_segmentation\_common module +----------------------------------------------------------------------------- + +.. automodule:: fuse.eval.metrics.segmentation.metrics_instance_segmentation_common + :members: + :undoc-members: + :show-inheritance: + +fuse.eval.metrics.segmentation.metrics\_segmentation\_common module +------------------------------------------------------------------- + +.. automodule:: fuse.eval.metrics.segmentation.metrics_segmentation_common + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.eval.metrics.segmentation + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.eval.metrics.survival.rst b/docs/source/fuse.eval.metrics.survival.rst new file mode 100644 index 00000000..f84d0df7 --- /dev/null +++ b/docs/source/fuse.eval.metrics.survival.rst @@ -0,0 +1,21 @@ +fuse.eval.metrics.survival package +================================== + +Submodules +---------- + +fuse.eval.metrics.survival.metrics\_survival module +--------------------------------------------------- + +.. automodule:: fuse.eval.metrics.survival.metrics_survival + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.eval.metrics.survival + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.eval.rst b/docs/source/fuse.eval.rst new file mode 100644 index 00000000..d8620dbf --- /dev/null +++ b/docs/source/fuse.eval.rst @@ -0,0 +1,31 @@ + +.. mdinclude:: ../../fuse/eval/README.md + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.eval.examples + fuse.eval.metrics + fuse.eval.tests + +Submodules +---------- + +fuse.eval.evaluator module +-------------------------- + +.. automodule:: fuse.eval.evaluator + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.eval + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.eval.tests.rst b/docs/source/fuse.eval.tests.rst new file mode 100644 index 00000000..243740bb --- /dev/null +++ b/docs/source/fuse.eval.tests.rst @@ -0,0 +1,21 @@ +fuse.eval.tests package +======================= + +Submodules +---------- + +fuse.eval.tests.test\_eval module +--------------------------------- + +.. automodule:: fuse.eval.tests.test_eval + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.eval.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.rst b/docs/source/fuse.rst new file mode 100644 index 00000000..a8ff6895 --- /dev/null +++ b/docs/source/fuse.rst @@ -0,0 +1,34 @@ +.. mdinclude:: ../../fuse/dl/README.md + +fuse package +============ + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.data + fuse.dl + fuse.eval + fuse.utils + +Submodules +---------- + +fuse.version module +------------------- + +.. automodule:: fuse.version + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.config_tools.rst b/docs/source/fuse.utils.config_tools.rst new file mode 100644 index 00000000..e8ab3bf6 --- /dev/null +++ b/docs/source/fuse.utils.config_tools.rst @@ -0,0 +1,29 @@ +fuse.utils.config\_tools package +================================ + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.utils.config_tools.tests + +Submodules +---------- + +fuse.utils.config\_tools.config\_tools module +--------------------------------------------- + +.. automodule:: fuse.utils.config_tools.config_tools + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.config_tools + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.config_tools.tests.rst b/docs/source/fuse.utils.config_tools.tests.rst new file mode 100644 index 00000000..8b1e3cd2 --- /dev/null +++ b/docs/source/fuse.utils.config_tools.tests.rst @@ -0,0 +1,45 @@ +fuse.utils.config\_tools.tests package +====================================== + +Submodules +---------- + +fuse.utils.config\_tools.tests.base\_conf\_example module +--------------------------------------------------------- + +.. automodule:: fuse.utils.config_tools.tests.base_conf_example + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.config\_tools.tests.some\_conf\_internal\_include module +------------------------------------------------------------------- + +.. automodule:: fuse.utils.config_tools.tests.some_conf_internal_include + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.config\_tools.tests.some\_conf\_no\_include module +------------------------------------------------------------- + +.. automodule:: fuse.utils.config_tools.tests.some_conf_no_include + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.config\_tools.tests.test\_config module +-------------------------------------------------- + +.. automodule:: fuse.utils.config_tools.tests.test_config + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.config_tools.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.cpu_profiling.rst b/docs/source/fuse.utils.cpu_profiling.rst new file mode 100644 index 00000000..b51614e2 --- /dev/null +++ b/docs/source/fuse.utils.cpu_profiling.rst @@ -0,0 +1,37 @@ +fuse.utils.cpu\_profiling package +================================= + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.utils.cpu_profiling.tests + +Submodules +---------- + +fuse.utils.cpu\_profiling.profiler module +----------------------------------------- + +.. automodule:: fuse.utils.cpu_profiling.profiler + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.cpu\_profiling.timer module +-------------------------------------- + +.. automodule:: fuse.utils.cpu_profiling.timer + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.cpu_profiling + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.cpu_profiling.tests.rst b/docs/source/fuse.utils.cpu_profiling.tests.rst new file mode 100644 index 00000000..8f8c3a33 --- /dev/null +++ b/docs/source/fuse.utils.cpu_profiling.tests.rst @@ -0,0 +1,29 @@ +fuse.utils.cpu\_profiling.tests package +======================================= + +Submodules +---------- + +fuse.utils.cpu\_profiling.tests.test\_profiler module +----------------------------------------------------- + +.. automodule:: fuse.utils.cpu_profiling.tests.test_profiler + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.cpu\_profiling.tests.test\_timer module +-------------------------------------------------- + +.. automodule:: fuse.utils.cpu_profiling.tests.test_timer + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.cpu_profiling.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.data.rst b/docs/source/fuse.utils.data.rst new file mode 100644 index 00000000..5b9e255c --- /dev/null +++ b/docs/source/fuse.utils.data.rst @@ -0,0 +1,29 @@ +fuse.utils.data package +======================= + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.utils.data.tests + +Submodules +---------- + +fuse.utils.data.collate module +------------------------------ + +.. automodule:: fuse.utils.data.collate + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.data + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.data.tests.rst b/docs/source/fuse.utils.data.tests.rst new file mode 100644 index 00000000..4a0a55d2 --- /dev/null +++ b/docs/source/fuse.utils.data.tests.rst @@ -0,0 +1,21 @@ +fuse.utils.data.tests package +============================= + +Submodules +---------- + +fuse.utils.data.tests.test\_collate module +------------------------------------------ + +.. automodule:: fuse.utils.data.tests.test_collate + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.data.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.file_io.rst b/docs/source/fuse.utils.file_io.rst new file mode 100644 index 00000000..216c1816 --- /dev/null +++ b/docs/source/fuse.utils.file_io.rst @@ -0,0 +1,53 @@ +fuse.utils.file\_io package +=========================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.utils.file_io.tests + +Submodules +---------- + +fuse.utils.file\_io.atomic\_file module +--------------------------------------- + +.. automodule:: fuse.utils.file_io.atomic_file + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.file\_io.compressed module +------------------------------------- + +.. automodule:: fuse.utils.file_io.compressed + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.file\_io.file\_io module +----------------------------------- + +.. automodule:: fuse.utils.file_io.file_io + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.file\_io.path module +------------------------------- + +.. automodule:: fuse.utils.file_io.path + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.file_io + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.file_io.tests.rst b/docs/source/fuse.utils.file_io.tests.rst new file mode 100644 index 00000000..013795dc --- /dev/null +++ b/docs/source/fuse.utils.file_io.tests.rst @@ -0,0 +1,21 @@ +fuse.utils.file\_io.tests package +================================= + +Submodules +---------- + +fuse.utils.file\_io.tests.test\_hdf5 module +------------------------------------------- + +.. automodule:: fuse.utils.file_io.tests.test_hdf5 + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.file_io.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.multiprocessing.rst b/docs/source/fuse.utils.multiprocessing.rst new file mode 100644 index 00000000..8ef656ab --- /dev/null +++ b/docs/source/fuse.utils.multiprocessing.rst @@ -0,0 +1,29 @@ +fuse.utils.multiprocessing package +================================== + +Submodules +---------- + +fuse.utils.multiprocessing.helpers module +----------------------------------------- + +.. automodule:: fuse.utils.multiprocessing.helpers + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.multiprocessing.run\_multiprocessed module +----------------------------------------------------- + +.. automodule:: fuse.utils.multiprocessing.run_multiprocessed + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.multiprocessing + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.rand.rst b/docs/source/fuse.utils.rand.rst new file mode 100644 index 00000000..00971e3d --- /dev/null +++ b/docs/source/fuse.utils.rand.rst @@ -0,0 +1,37 @@ +fuse.utils.rand package +======================= + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.utils.rand.tests + +Submodules +---------- + +fuse.utils.rand.param\_sampler module +------------------------------------- + +.. automodule:: fuse.utils.rand.param_sampler + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.rand.seed module +--------------------------- + +.. automodule:: fuse.utils.rand.seed + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.rand + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.rand.tests.rst b/docs/source/fuse.utils.rand.tests.rst new file mode 100644 index 00000000..f96b854c --- /dev/null +++ b/docs/source/fuse.utils.rand.tests.rst @@ -0,0 +1,29 @@ +fuse.utils.rand.tests package +============================= + +Submodules +---------- + +fuse.utils.rand.tests.test\_param\_sampler module +------------------------------------------------- + +.. automodule:: fuse.utils.rand.tests.test_param_sampler + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.rand.tests.test\_seed module +--------------------------------------- + +.. automodule:: fuse.utils.rand.tests.test_seed + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.rand.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.remote_execution.rst b/docs/source/fuse.utils.remote_execution.rst new file mode 100644 index 00000000..c96753c0 --- /dev/null +++ b/docs/source/fuse.utils.remote_execution.rst @@ -0,0 +1,29 @@ +fuse.utils.remote\_execution package +==================================== + +Submodules +---------- + +fuse.utils.remote\_execution.remote\_execution module +----------------------------------------------------- + +.. automodule:: fuse.utils.remote_execution.remote_execution + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.remote\_execution.shell\_handler module +-------------------------------------------------- + +.. automodule:: fuse.utils.remote_execution.shell_handler + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.remote_execution + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.rst b/docs/source/fuse.utils.rst new file mode 100644 index 00000000..ecccf374 --- /dev/null +++ b/docs/source/fuse.utils.rst @@ -0,0 +1,76 @@ + +.. mdinclude:: ../../fuse/utils/README.md + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse.utils.config_tools + fuse.utils.cpu_profiling + fuse.utils.data + fuse.utils.file_io + fuse.utils.multiprocessing + fuse.utils.rand + fuse.utils.remote_execution + fuse.utils.tests + +Submodules +---------- + +fuse.utils.add\_preamble module +------------------------------- + +.. automodule:: fuse.utils.add_preamble + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.gpu module +--------------------- + +.. automodule:: fuse.utils.gpu + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.ndict module +----------------------- + +.. automodule:: fuse.utils.ndict + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.utils\_debug module +------------------------------ + +.. automodule:: fuse.utils.utils_debug + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.utils\_hierarchical\_dict module +------------------------------------------- + +.. automodule:: fuse.utils.utils_hierarchical_dict + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.utils\_logger module +------------------------------- + +.. automodule:: fuse.utils.utils_logger + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse.utils.tests.rst b/docs/source/fuse.utils.tests.rst new file mode 100644 index 00000000..7a52e738 --- /dev/null +++ b/docs/source/fuse.utils.tests.rst @@ -0,0 +1,29 @@ +fuse.utils.tests package +======================== + +Submodules +---------- + +fuse.utils.tests.test\_ndict module +----------------------------------- + +.. automodule:: fuse.utils.tests.test_ndict + :members: + :undoc-members: + :show-inheritance: + +fuse.utils.tests.test\_utils\_hierarchical\_dict module +------------------------------------------------------- + +.. automodule:: fuse.utils.tests.test_utils_hierarchical_dict + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse.utils.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.bright.eval.rst b/docs/source/fuse_examples.imaging.classification.bright.eval.rst new file mode 100644 index 00000000..c397ff4b --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.bright.eval.rst @@ -0,0 +1,21 @@ +fuse\_examples.imaging.classification.bright.eval package +========================================================= + +Submodules +---------- + +fuse\_examples.imaging.classification.bright.eval.eval module +------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.bright.eval.eval + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification.bright.eval + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.bright.rst b/docs/source/fuse_examples.imaging.classification.bright.rst new file mode 100644 index 00000000..4c209746 --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.bright.rst @@ -0,0 +1,18 @@ + +.. mdinclude:: ../../fuse_examples/imaging/classification/bright/README.md + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse_examples.imaging.classification.bright.eval + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification.bright + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.cmmd.rst b/docs/source/fuse_examples.imaging.classification.cmmd.rst new file mode 100644 index 00000000..9e3a4a09 --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.cmmd.rst @@ -0,0 +1,21 @@ + +.. mdinclude:: ../../fuse_examples/imaging/classification/cmmd/README.md + +Submodules +---------- + +fuse\_examples.imaging.classification.cmmd.runner module +-------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.cmmd.runner + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification.cmmd + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.isic.rst b/docs/source/fuse_examples.imaging.classification.isic.rst new file mode 100644 index 00000000..3f70c154 --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.isic.rst @@ -0,0 +1,29 @@ + +.. mdinclude:: ../../fuse_examples/imaging/classification/isic/README.md + +Submodules +---------- + +fuse\_examples.imaging.classification.isic.golden\_members module +----------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.isic.golden_members + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.imaging.classification.isic.isic\_runner module +-------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.isic.isic_runner + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification.isic + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.knight.eval.rst b/docs/source/fuse_examples.imaging.classification.knight.eval.rst new file mode 100644 index 00000000..82511f34 --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.knight.eval.rst @@ -0,0 +1,21 @@ +fuse\_examples.imaging.classification.knight.eval package +========================================================= + +Submodules +---------- + +fuse\_examples.imaging.classification.knight.eval.eval module +------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.knight.eval.eval + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification.knight.eval + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.knight.rst b/docs/source/fuse_examples.imaging.classification.knight.rst new file mode 100644 index 00000000..ddc11d39 --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.knight.rst @@ -0,0 +1,37 @@ + +.. mdinclude:: ../../fuse_examples/imaging/classification/knight/README.md + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse_examples.imaging.classification.knight.eval + +Submodules +---------- + +fuse\_examples.imaging.classification.knight.make\_predictions\_file module +--------------------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.knight.make_predictions_file + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.imaging.classification.knight.make\_targets\_file module +----------------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.knight.make_targets_file + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification.knight + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.mnist.rst b/docs/source/fuse_examples.imaging.classification.mnist.rst new file mode 100644 index 00000000..04b63258 --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.mnist.rst @@ -0,0 +1,37 @@ +fuse\_examples.imaging.classification.mnist package +=================================================== + +Submodules +---------- + +fuse\_examples.imaging.classification.mnist.lenet module +-------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.mnist.lenet + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.imaging.classification.mnist.run\_mnist\_custom\_pl\_imp module +------------------------------------------------------------------------------ + +.. automodule:: fuse_examples.imaging.classification.mnist.run_mnist_custom_pl_imp + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.imaging.classification.mnist.simple\_mnist\_starter module +------------------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.mnist.simple_mnist_starter + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification.mnist + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.rst b/docs/source/fuse_examples.imaging.classification.rst new file mode 100644 index 00000000..efbd75a5 --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.rst @@ -0,0 +1,23 @@ +fuse\_examples.imaging.classification package +============================================= + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse_examples.imaging.classification.bright + fuse_examples.imaging.classification.cmmd + fuse_examples.imaging.classification.isic + fuse_examples.imaging.classification.knight + fuse_examples.imaging.classification.mnist + fuse_examples.imaging.classification.stoic21 + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.classification.stoic21.rst b/docs/source/fuse_examples.imaging.classification.stoic21.rst new file mode 100644 index 00000000..a4e8c50a --- /dev/null +++ b/docs/source/fuse_examples.imaging.classification.stoic21.rst @@ -0,0 +1,29 @@ + +.. mdinclude:: ../../fuse_examples/imaging/classification/stoic21/README.md + +Submodules +---------- + +fuse\_examples.imaging.classification.stoic21.dataset module +------------------------------------------------------------ + +.. automodule:: fuse_examples.imaging.classification.stoic21.dataset + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.imaging.classification.stoic21.runner\_stoic21 module +-------------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.classification.stoic21.runner_stoic21 + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.classification.stoic21 + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.hello_world.rst b/docs/source/fuse_examples.imaging.hello_world.rst new file mode 100644 index 00000000..fe49db50 --- /dev/null +++ b/docs/source/fuse_examples.imaging.hello_world.rst @@ -0,0 +1,21 @@ +fuse\_examples.imaging.hello\_world package +=========================================== + +Submodules +---------- + +fuse\_examples.imaging.hello\_world.hello\_world\_utils module +-------------------------------------------------------------- + +.. automodule:: fuse_examples.imaging.hello_world.hello_world_utils + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging.hello_world + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.imaging.rst b/docs/source/fuse_examples.imaging.rst new file mode 100644 index 00000000..b4c3388b --- /dev/null +++ b/docs/source/fuse_examples.imaging.rst @@ -0,0 +1,19 @@ +fuse\_examples.imaging package +============================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse_examples.imaging.classification + fuse_examples.imaging.hello_world + +Module contents +--------------- + +.. automodule:: fuse_examples.imaging + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.multimodality.ehr_transformer.rst b/docs/source/fuse_examples.multimodality.ehr_transformer.rst new file mode 100644 index 00000000..af24c5ca --- /dev/null +++ b/docs/source/fuse_examples.multimodality.ehr_transformer.rst @@ -0,0 +1,45 @@ + +.. mdinclude:: ../../fuse_examples/multimodality/ehr_transformer/README.md + +Submodules +---------- + +fuse\_examples.multimodality.ehr\_transformer.dataset module +------------------------------------------------------------ + +.. automodule:: fuse_examples.multimodality.ehr_transformer.dataset + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.multimodality.ehr\_transformer.main\_train module +---------------------------------------------------------------- + +.. automodule:: fuse_examples.multimodality.ehr_transformer.main_train + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.multimodality.ehr\_transformer.model module +---------------------------------------------------------- + +.. automodule:: fuse_examples.multimodality.ehr_transformer.model + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.multimodality.ehr\_transformer.utils module +---------------------------------------------------------- + +.. automodule:: fuse_examples.multimodality.ehr_transformer.utils + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.multimodality.ehr_transformer + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.multimodality.image_clinical.rst b/docs/source/fuse_examples.multimodality.image_clinical.rst new file mode 100644 index 00000000..fc854c48 --- /dev/null +++ b/docs/source/fuse_examples.multimodality.image_clinical.rst @@ -0,0 +1,21 @@ +fuse\_examples.multimodality.image\_clinical package +==================================================== + +Submodules +---------- + +fuse\_examples.multimodality.image\_clinical.dataset module +----------------------------------------------------------- + +.. automodule:: fuse_examples.multimodality.image_clinical.dataset + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.multimodality.image_clinical + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.multimodality.rst b/docs/source/fuse_examples.multimodality.rst new file mode 100644 index 00000000..8ef45e9c --- /dev/null +++ b/docs/source/fuse_examples.multimodality.rst @@ -0,0 +1,19 @@ +fuse\_examples.multimodality package +==================================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse_examples.multimodality.ehr_transformer + fuse_examples.multimodality.image_clinical + +Module contents +--------------- + +.. automodule:: fuse_examples.multimodality + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.rst b/docs/source/fuse_examples.rst new file mode 100644 index 00000000..ab9076da --- /dev/null +++ b/docs/source/fuse_examples.rst @@ -0,0 +1,20 @@ +fuse\_examples package +====================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuse_examples.imaging + fuse_examples.multimodality + fuse_examples.tests + +Module contents +--------------- + +.. automodule:: fuse_examples + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuse_examples.tests.rst b/docs/source/fuse_examples.tests.rst new file mode 100644 index 00000000..26fde469 --- /dev/null +++ b/docs/source/fuse_examples.tests.rst @@ -0,0 +1,77 @@ +fuse\_examples.tests package +============================ + +Submodules +---------- + +fuse\_examples.tests.test\_classification\_cmmd module +------------------------------------------------------ + +.. automodule:: fuse_examples.tests.test_classification_cmmd + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.tests.test\_classification\_isic module +------------------------------------------------------ + +.. automodule:: fuse_examples.tests.test_classification_isic + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.tests.test\_classification\_knight module +-------------------------------------------------------- + +.. automodule:: fuse_examples.tests.test_classification_knight + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.tests.test\_classification\_mnist module +------------------------------------------------------- + +.. automodule:: fuse_examples.tests.test_classification_mnist + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.tests.test\_classification\_stoic21 module +--------------------------------------------------------- + +.. automodule:: fuse_examples.tests.test_classification_stoic21 + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.tests.test\_ehr\_transformer module +-------------------------------------------------- + +.. automodule:: fuse_examples.tests.test_ehr_transformer + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.tests.test\_notebook\_hello\_world module +-------------------------------------------------------- + +.. automodule:: fuse_examples.tests.test_notebook_hello_world + :members: + :undoc-members: + :show-inheritance: + +fuse\_examples.tests.test\_segmentation\_picai module +----------------------------------------------------- + +.. automodule:: fuse_examples.tests.test_segmentation_picai + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuse_examples.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.data.ops.rst b/docs/source/fuseimg.data.ops.rst new file mode 100644 index 00000000..5c0cbd40 --- /dev/null +++ b/docs/source/fuseimg.data.ops.rst @@ -0,0 +1,69 @@ +fuseimg.data.ops package +======================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuseimg.data.ops.tests + +Submodules +---------- + +fuseimg.data.ops.color module +----------------------------- + +.. automodule:: fuseimg.data.ops.color + :members: + :undoc-members: + :show-inheritance: + +fuseimg.data.ops.debug\_ops module +---------------------------------- + +.. automodule:: fuseimg.data.ops.debug_ops + :members: + :undoc-members: + :show-inheritance: + +fuseimg.data.ops.image\_loader module +------------------------------------- + +.. automodule:: fuseimg.data.ops.image_loader + :members: + :undoc-members: + :show-inheritance: + +fuseimg.data.ops.ops\_common\_imaging module +-------------------------------------------- + +.. automodule:: fuseimg.data.ops.ops_common_imaging + :members: + :undoc-members: + :show-inheritance: + +fuseimg.data.ops.ops\_debug module +---------------------------------- + +.. automodule:: fuseimg.data.ops.ops_debug + :members: + :undoc-members: + :show-inheritance: + +fuseimg.data.ops.shape\_ops module +---------------------------------- + +.. automodule:: fuseimg.data.ops.shape_ops + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuseimg.data.ops + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.data.ops.tests.rst b/docs/source/fuseimg.data.ops.tests.rst new file mode 100644 index 00000000..3fb5754e --- /dev/null +++ b/docs/source/fuseimg.data.ops.tests.rst @@ -0,0 +1,29 @@ +fuseimg.data.ops.tests package +============================== + +Submodules +---------- + +fuseimg.data.ops.tests.test\_ops module +--------------------------------------- + +.. automodule:: fuseimg.data.ops.tests.test_ops + :members: + :undoc-members: + :show-inheritance: + +fuseimg.data.ops.tests.test\_pipeline\_caching module +----------------------------------------------------- + +.. automodule:: fuseimg.data.ops.tests.test_pipeline_caching + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuseimg.data.ops.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.data.rst b/docs/source/fuseimg.data.rst new file mode 100644 index 00000000..db2aacd5 --- /dev/null +++ b/docs/source/fuseimg.data.rst @@ -0,0 +1,18 @@ +fuseimg.data package +==================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuseimg.data.ops + +Module contents +--------------- + +.. automodule:: fuseimg.data + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.datasets.rst b/docs/source/fuseimg.datasets.rst new file mode 100644 index 00000000..8af9200c --- /dev/null +++ b/docs/source/fuseimg.datasets.rst @@ -0,0 +1,77 @@ +fuseimg.datasets package +======================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuseimg.datasets.tests + +Submodules +---------- + +fuseimg.datasets.cmmd module +---------------------------- + +.. automodule:: fuseimg.datasets.cmmd + :members: + :undoc-members: + :show-inheritance: + +fuseimg.datasets.isic module +---------------------------- + +.. automodule:: fuseimg.datasets.isic + :members: + :undoc-members: + :show-inheritance: + +fuseimg.datasets.kits21 module +------------------------------ + +.. automodule:: fuseimg.datasets.kits21 + :members: + :undoc-members: + :show-inheritance: + +fuseimg.datasets.knight module +------------------------------ + +.. automodule:: fuseimg.datasets.knight + :members: + :undoc-members: + :show-inheritance: + +fuseimg.datasets.mnist module +----------------------------- + +.. automodule:: fuseimg.datasets.mnist + :members: + :undoc-members: + :show-inheritance: + +fuseimg.datasets.picai module +----------------------------- + +.. automodule:: fuseimg.datasets.picai + :members: + :undoc-members: + :show-inheritance: + +fuseimg.datasets.stoic21 module +------------------------------- + +.. automodule:: fuseimg.datasets.stoic21 + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuseimg.datasets + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.datasets.tests.rst b/docs/source/fuseimg.datasets.tests.rst new file mode 100644 index 00000000..d061eabc --- /dev/null +++ b/docs/source/fuseimg.datasets.tests.rst @@ -0,0 +1,21 @@ +fuseimg.datasets.tests package +============================== + +Submodules +---------- + +fuseimg.datasets.tests.test\_datasets module +-------------------------------------------- + +.. automodule:: fuseimg.datasets.tests.test_datasets + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuseimg.datasets.tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.eval.rst b/docs/source/fuseimg.eval.rst new file mode 100644 index 00000000..49ab2200 --- /dev/null +++ b/docs/source/fuseimg.eval.rst @@ -0,0 +1,21 @@ +fuseimg.eval package +==================== + +Submodules +---------- + +fuseimg.eval.metrics\_vis\_2d module +------------------------------------ + +.. automodule:: fuseimg.eval.metrics_vis_2d + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuseimg.eval + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.rst b/docs/source/fuseimg.rst new file mode 100644 index 00000000..e1e6d480 --- /dev/null +++ b/docs/source/fuseimg.rst @@ -0,0 +1,20 @@ + +.. mdinclude:: ../../fuseimg/README.md + +----------- + +.. toctree:: + :maxdepth: 4 + + fuseimg.data + fuseimg.datasets + fuseimg.eval + fuseimg.utils + +Module contents +--------------- + +.. automodule:: fuseimg + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.utils.align.rst b/docs/source/fuseimg.utils.align.rst new file mode 100644 index 00000000..5246826d --- /dev/null +++ b/docs/source/fuseimg.utils.align.rst @@ -0,0 +1,29 @@ +fuseimg.utils.align package +=========================== + +Submodules +---------- + +fuseimg.utils.align.utils\_align\_base module +--------------------------------------------- + +.. automodule:: fuseimg.utils.align.utils_align_base + :members: + :undoc-members: + :show-inheritance: + +fuseimg.utils.align.utils\_align\_ecc module +-------------------------------------------- + +.. automodule:: fuseimg.utils.align.utils_align_ecc + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuseimg.utils.align + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/fuseimg.utils.rst b/docs/source/fuseimg.utils.rst new file mode 100644 index 00000000..8c265035 --- /dev/null +++ b/docs/source/fuseimg.utils.rst @@ -0,0 +1,29 @@ +fuseimg.utils package +===================== + +Subpackages +----------- + +.. toctree:: + :maxdepth: 4 + + fuseimg.utils.align + +Submodules +---------- + +fuseimg.utils.image\_processing module +-------------------------------------- + +.. automodule:: fuseimg.utils.image_processing + :members: + :undoc-members: + :show-inheritance: + +Module contents +--------------- + +.. automodule:: fuseimg.utils + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/index.rst b/docs/source/index.rst new file mode 100644 index 00000000..f71610d3 --- /dev/null +++ b/docs/source/index.rst @@ -0,0 +1,26 @@ +.. Fuse-Med-ML documentation master file, created by + sphinx-quickstart on Thu Dec 21 03:47:44 2023. + You can adapt this file completely to your liking, but it should at least + contain the root `toctree` directive. + +Welcome to Fuse-Med-ML's documentation! +===================================== +.. mdinclude:: ../../README.md + + +fuse-med-ml +=========== + +.. toctree:: + :maxdepth: 4 + + fuse + fuseimg + fuse_examples + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` diff --git a/docs/source/modules.rst b/docs/source/modules.rst new file mode 100644 index 00000000..9dfdf29e --- /dev/null +++ b/docs/source/modules.rst @@ -0,0 +1,9 @@ +fuse-med-ml +=========== + +.. toctree:: + :maxdepth: 4 + + fuse + fuseimg + fuse_examples diff --git a/docs/source/run_all_unit_tests.rst b/docs/source/run_all_unit_tests.rst new file mode 100644 index 00000000..c2416d63 --- /dev/null +++ b/docs/source/run_all_unit_tests.rst @@ -0,0 +1,7 @@ +run\_all\_unit\_tests module +============================ + +.. automodule:: run_all_unit_tests + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/setup.rst b/docs/source/setup.rst new file mode 100644 index 00000000..552eb49d --- /dev/null +++ b/docs/source/setup.rst @@ -0,0 +1,7 @@ +setup module +============ + +.. automodule:: setup + :members: + :undoc-members: + :show-inheritance: diff --git a/fuse/data/ops/op_base.py b/fuse/data/ops/op_base.py index 85660cf5..04dc9c98 100644 --- a/fuse/data/ops/op_base.py +++ b/fuse/data/ops/op_base.py @@ -106,7 +106,6 @@ def reverse( def op_call( op: OpBase, sample_dict: NDict, op_id: str, **kwargs: dict ) -> Union[None, dict, List[dict]]: - if inspect.isclass(op): raise Exception( f"Error: expected an instance object, not a class object for {op}\n" diff --git a/fuse/data/ops/ops_cast.py b/fuse/data/ops/ops_cast.py index 51915044..d1c64eca 100644 --- a/fuse/data/ops/ops_cast.py +++ b/fuse/data/ops/ops_cast.py @@ -226,7 +226,6 @@ class OpToNumpy(OpCast): """ def _cast(self, value: Any, dtype: Optional[np.dtype] = None) -> np.ndarray: - return Cast.to_numpy(value, dtype) diff --git a/fuse/data/pipelines/pipeline_default.py b/fuse/data/pipelines/pipeline_default.py index d29601bf..da6bbe21 100644 --- a/fuse/data/pipelines/pipeline_default.py +++ b/fuse/data/pipelines/pipeline_default.py @@ -103,7 +103,7 @@ def get_name(self) -> str: def __str__(self) -> str: text = [] - for (op_id, op_kwargs) in zip(self._op_ids, self._ops_and_kwargs): + for op_id, op_kwargs in zip(self._op_ids, self._ops_and_kwargs): op, kwargs = op_kwargs text.append( str(op_id) @@ -146,7 +146,6 @@ def __call__( samples_to_process_next = [] for sample in samples_to_process: - sample = op_call(op, sample, f"{op_id}.{sub_op_id}", **op_kwargs) # three options for return value: diff --git a/fuse/data/utils/collates.py b/fuse/data/utils/collates.py index d4bf2fee..ea5a0049 100644 --- a/fuse/data/utils/collates.py +++ b/fuse/data/utils/collates.py @@ -80,7 +80,6 @@ def __call__(self, samples: List[Dict]) -> Dict: # collect values for key in keys: - # skip keys if key in self._skip_keys: continue diff --git a/fuse/data/utils/split.py b/fuse/data/utils/split.py index 63a1053f..5beb712c 100644 --- a/fuse/data/utils/split.py +++ b/fuse/data/utils/split.py @@ -137,7 +137,6 @@ def dataset_balanced_division_to_folds( verify_folds_total_size: bool = True, **kwargs: dict, ) -> dict: - """ Split dataset to folds. Support balancing, exclusion and radom seed (with a small improvement could support no mixture criterion). diff --git a/fuse/dl/cross_validation/pipeline.py b/fuse/dl/cross_validation/pipeline.py index 21dd5be5..9c0dfa18 100644 --- a/fuse/dl/cross_validation/pipeline.py +++ b/fuse/dl/cross_validation/pipeline.py @@ -81,7 +81,6 @@ def train_wrapper( func: Callable, params: dict, ) -> None: - paths_train = paths.copy() # set parameters specific to this fold: @@ -118,7 +117,6 @@ def infer_wrapper( func: Callable, params: dict, ) -> None: - paths_infer = paths.copy() # set parameters specific to this fold, and generate data: @@ -156,7 +154,6 @@ def eval_wrapper( func: Callable, params: dict, ) -> None: - paths_eval = paths.copy() if sample_ids_per_fold is None: # test mode diff --git a/fuse/dl/models/backbones/backbone_inception_resnet_v2.py b/fuse/dl/models/backbones/backbone_inception_resnet_v2.py index a7abaadf..a8746835 100644 --- a/fuse/dl/models/backbones/backbone_inception_resnet_v2.py +++ b/fuse/dl/models/backbones/backbone_inception_resnet_v2.py @@ -275,7 +275,6 @@ def __init__( str ] = "http://data.lip6.fr/cadene/pretrainedmodels/inceptionresnetv2-520b38e4.pth", ) -> None: - super().__init__() self.logical_units_num = logical_units_num self.intra_block_cut_level = intra_block_cut_level diff --git a/fuse/dl/models/backbones/backbone_mlp.py b/fuse/dl/models/backbones/backbone_mlp.py index cf3b7e7c..b95606d7 100644 --- a/fuse/dl/models/backbones/backbone_mlp.py +++ b/fuse/dl/models/backbones/backbone_mlp.py @@ -49,7 +49,6 @@ def __init__( self.mlp = nn.ModuleList(mlp_layers) def forward(self, input_tensor: torch.Tensor) -> torch.Tensor: - for layer in self.mlp: input_tensor = layer(input_tensor) return input_tensor diff --git a/fuse/dl/models/backbones/backbone_resnet_3d.py b/fuse/dl/models/backbones/backbone_resnet_3d.py index eaacbfc3..9c5e074d 100644 --- a/fuse/dl/models/backbones/backbone_resnet_3d.py +++ b/fuse/dl/models/backbones/backbone_resnet_3d.py @@ -31,7 +31,6 @@ def __init__( stride: int = 1, padding: int = 1, ) -> None: - super().__init__( in_channels=in_planes, out_channels=out_planes, @@ -47,7 +46,6 @@ def get_downsample_stride(stride: int) -> Tuple[int, int, int]: class BasicBlock(nn.Module): - expansion = 1 def __init__( diff --git a/fuse/dl/models/heads/heads_1D.py b/fuse/dl/models/heads/heads_1D.py index 6289ea02..17a5029d 100644 --- a/fuse/dl/models/heads/heads_1D.py +++ b/fuse/dl/models/heads/heads_1D.py @@ -92,7 +92,6 @@ def __init__( ) def forward(self, batch_dict: Dict) -> Dict: - conv_input = torch.cat( [batch_dict[conv_input[0]] for conv_input in self.conv_inputs], dim=1 ) diff --git a/fuse/dl/models/model_ensemble.py b/fuse/dl/models/model_ensemble.py index 552bca3d..a92ed7e7 100644 --- a/fuse/dl/models/model_ensemble.py +++ b/fuse/dl/models/model_ensemble.py @@ -51,7 +51,6 @@ def eval(self) -> None: net.eval() def load_state_dict(self, *net_state_dicts: List[Dict], strict: bool) -> None: - for idx, net_state_dict in enumerate(net_state_dicts): self.nets[idx].load_state_dict(net_state_dict, strict=strict) diff --git a/fuse/dl/models/model_multistream.py b/fuse/dl/models/model_multistream.py index c756f304..e3bd7212 100644 --- a/fuse/dl/models/model_multistream.py +++ b/fuse/dl/models/model_multistream.py @@ -66,7 +66,6 @@ def __init__( self.add_module("heads", self.heads) def forward(self, batch_dict: NDict) -> Dict: - # Forward pass through multiple streams # ------------------------------------- if self.split_logic is None: diff --git a/fuse/eval/evaluator.py b/fuse/eval/evaluator.py index 602c88cd..e96f2c02 100644 --- a/fuse/eval/evaluator.py +++ b/fuse/eval/evaluator.py @@ -206,7 +206,6 @@ def read_data( result_data = result_data.set_index(keys=id_key, drop=False) elif isinstance(data, str): # data is path to a file - result_data = read_dataframe(data) # make sure "id" column exist and set it as index if id_key not in result_data.keys(): @@ -233,7 +232,6 @@ def read_data( df_list = [] all_ids = set() for key, data_elem in data.items(): - try: data_elem_df = self.read_data(data_elem, ids_df, id_key=id_key) all_ids = all_ids.union(set(data_elem_df.index)) diff --git a/fuse/utils/data/collate.py b/fuse/utils/data/collate.py index dc25e873..c1fd8ced 100644 --- a/fuse/utils/data/collate.py +++ b/fuse/utils/data/collate.py @@ -55,7 +55,6 @@ def __call__(self, samples: List[Dict]) -> Dict: # collect values for key in keys: - # skip keys if key in self._skip_keys: continue @@ -142,7 +141,6 @@ def uncollate(batch: Dict) -> List[Dict]: for key in batch.keys(): values = batch[key] for sample_index in range(batch_size): - if isinstance(values, (np.ndarray, torch.Tensor, list)): try: samples[sample_index][key] = values[sample_index] diff --git a/fuse/utils/multiprocessing/helpers.py b/fuse/utils/multiprocessing/helpers.py index e434c8f6..6c3d6ef1 100644 --- a/fuse/utils/multiprocessing/helpers.py +++ b/fuse/utils/multiprocessing/helpers.py @@ -4,7 +4,6 @@ def num_available_cores(verbose: bool = True) -> int: - if hasattr(os, "sched_getaffinity"): try: ans = len(os.sched_getaffinity(0)) diff --git a/fuse/utils/ndict.py b/fuse/utils/ndict.py index 565ce2d6..a145f711 100644 --- a/fuse/utils/ndict.py +++ b/fuse/utils/ndict.py @@ -326,7 +326,6 @@ def __repr__(self) -> str: return repr(self._stored) def __contains__(self, key: str) -> bool: - if key in self._stored: return True @@ -375,7 +374,6 @@ def unflatten(self) -> dict: @staticmethod def _unflatten_static(data_dict: NDict) -> dict: - res = dict() for top_key in data_dict.top_level_keys(): value = data_dict[top_key] diff --git a/fuse_examples/imaging/classification/mnist/simple_mnist_starter.py b/fuse_examples/imaging/classification/mnist/simple_mnist_starter.py index 56a07aa4..d63c5366 100644 --- a/fuse_examples/imaging/classification/mnist/simple_mnist_starter.py +++ b/fuse_examples/imaging/classification/mnist/simple_mnist_starter.py @@ -189,7 +189,6 @@ def run_train( lr: float = 1e-4, weight_decay: float = 0.001, ) -> None: - # initialize model model = FuseLitLenet( model_dir=None, diff --git a/fuse_examples/multimodality/ehr_transformer/dataset.py b/fuse_examples/multimodality/ehr_transformer/dataset.py index 8e2aa124..18bf76c4 100644 --- a/fuse_examples/multimodality/ehr_transformer/dataset.py +++ b/fuse_examples/multimodality/ehr_transformer/dataset.py @@ -59,14 +59,12 @@ class OpAddBMI(OpBase): """ def __init__(self, key_in_height: str, key_in_weight: str, key_out_bmi: str): - super().__init__() self._key_height = key_in_height self._key_weight = key_in_weight self._key_bmi = key_out_bmi def __call__(self, sample_dict: NDict) -> Any: - if (self._key_height in sample_dict["StaticDetails"]) & ( self._key_weight in sample_dict["StaticDetails"] ): @@ -89,13 +87,11 @@ class OpConvertVisitToSentence(OpBase): """ def __call__(self, sample_dict: NDict) -> Any: - df_visits = sample_dict["Visits"] d_visit_sentences = OrderedDict() for visit_time, df_visit in df_visits.groupby("Time", sort=True): - d_visit_sentences[visit_time] = [] d_visit_sentences[visit_time].extend(df_visit["Value"].to_list()) @@ -124,7 +120,6 @@ def __init__( embed_static_in_all_visits: int, static_variables_to_embed: list, ): - super().__init__() self._max_len = max_len self._vocab = vocab @@ -132,7 +127,6 @@ def __init__( self._embed_static_in_all_visits = embed_static_in_all_visits def __call__(self, sample_dict: NDict) -> Any: - d_visits_sentences = sample_dict["VisitSentences"] n_visits = len(d_visits_sentences) @@ -208,7 +202,6 @@ class OpMapToCategorical(OpBase): """ def __call__(self, sample_dict: NDict, bins: dict) -> Any: - # convert continuous measurements to categorical ones based # on defined bins mapping static clinical characteristics # (Age, Gender, ICU type, Height, etc) @@ -323,7 +316,6 @@ def _drop_bad_patients( count_dropped_short_time = 0 count_dropped_min_visits = 0 for pat_id, df_pat_records in df.groupby("PatientId"): - hours = df_pat_records["Time"].str.split(":", n=1, expand=True)[0].values if max(hours.astype(int)) < min_hours: df_fixed.drop(df_pat_records.index, inplace=True) diff --git a/fuse_examples/multimodality/ehr_transformer/main_train.py b/fuse_examples/multimodality/ehr_transformer/main_train.py index f0184e9d..63410fde 100644 --- a/fuse_examples/multimodality/ehr_transformer/main_train.py +++ b/fuse_examples/multimodality/ehr_transformer/main_train.py @@ -107,7 +107,6 @@ def model( aux_next_vis_classification: bool, classifier_next_vis_head: dict, ) -> torch.nn.Module: - """ Create transformer based model with 3 classification heads :param embed: arguments for Embed constructor diff --git a/fuse_examples/tests/test_ehr_transformer.py b/fuse_examples/tests/test_ehr_transformer.py index b0a1b5db..a3648388 100644 --- a/fuse_examples/tests/test_ehr_transformer.py +++ b/fuse_examples/tests/test_ehr_transformer.py @@ -42,7 +42,6 @@ def init_test_environment(root: str) -> DictConfig: - with open(TEST_PARAMS["CONFIG_PATH"], "r") as file: cfg = yaml.safe_load(file) @@ -58,7 +57,6 @@ def init_test_environment(root: str) -> DictConfig: def run_ehr_transformer(cfg: DictConfig) -> None: - try: main_train(cfg) diff --git a/fuseimg/data/ops/color.py b/fuseimg/data/ops/color.py index b7205ec0..8d4f6826 100644 --- a/fuseimg/data/ops/color.py +++ b/fuseimg/data/ops/color.py @@ -114,7 +114,6 @@ def __call__( from_range: Tuple[float, float], to_range: Tuple[float, float], ) -> NDict: - from_range_start = from_range[0] from_range_end = from_range[1] to_range_start = to_range[0] diff --git a/fuseimg/data/ops/image_loader.py b/fuseimg/data/ops/image_loader.py index bc2f8144..bb777639 100644 --- a/fuseimg/data/ops/image_loader.py +++ b/fuseimg/data/ops/image_loader.py @@ -39,7 +39,6 @@ def __call__( if (format == "infer" and img_filename_suffix in ["nii"]) or ( format in ["nii", "nib"] ): - img = nib.load(img_filename) img_np = img.get_fdata() sample_dict[key_out] = img_np diff --git a/fuseimg/datasets/tests/test_datasets.py b/fuseimg/datasets/tests/test_datasets.py index 2385f682..3c003c79 100644 --- a/fuseimg/datasets/tests/test_datasets.py +++ b/fuseimg/datasets/tests/test_datasets.py @@ -110,7 +110,6 @@ def test_stoic21(self) -> None: self.assertTrue(5 in dict(results["metrics.age"])) def test_isic(self) -> None: - create_dir(self.isic_cache_dir) dataset = ISIC.dataset( self.isic_data_dir, diff --git a/fuseimg/utils/align/utils_align_ecc.py b/fuseimg/utils/align/utils_align_ecc.py index 988e6ddf..333c7d48 100644 --- a/fuseimg/utils/align/utils_align_ecc.py +++ b/fuseimg/utils/align/utils_align_ecc.py @@ -41,7 +41,6 @@ def __init__( self.img2_aligned = None def align(self, img1, img2, mask=None): - if self.transformation_type == "affine": transformation = cv2.MOTION_AFFINE M = np.eye(2, 3, dtype=np.float32) diff --git a/make.bat b/make.bat new file mode 100644 index 00000000..747ffb7b --- /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=source +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