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# Minimal makefile for Sphinx documentation | ||
# | ||
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# 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 | ||
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# Put it first so that "make" without argument is like "make help". | ||
help: | ||
@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) | ||
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.PHONY: help Makefile | ||
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clean: | ||
rm -rf "$(BUILDDIR)" | ||
rm -rf $(SOURCEDIR)/api/_autogen/* | ||
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# 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) |
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API reference | ||
--------------- | ||
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.. currentmodule:: wsi | ||
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.. autoclass:: WholeSlideImage | ||
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.. automethod:: __init__ | ||
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.. rubric:: Methods | ||
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.. autosummary:: | ||
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~WholeSlideImage.__init__ | ||
~WholeSlideImage.get_thumbnail | ||
~WholeSlideImage.segment | ||
~WholeSlideImage.plot_segmentation | ||
~WholeSlideImage.save_segmentation | ||
~WholeSlideImage.load_segmentation | ||
~WholeSlideImage.tile | ||
~WholeSlideImage.plot_tile_graph | ||
~WholeSlideImage.save_tile_images | ||
~WholeSlideImage.has_tile_coords | ||
~WholeSlideImage.has_tile_images | ||
~WholeSlideImage.has_tissue_contours | ||
~WholeSlideImage.get_tile_coordinate_level_size | ||
~WholeSlideImage.get_tile_coordinates | ||
~WholeSlideImage.get_tile_graph | ||
~WholeSlideImage.get_tile_images | ||
~WholeSlideImage.get_tile_polygons | ||
~WholeSlideImage.get_tile_tissue_piece | ||
~WholeSlideImage.inference | ||
~WholeSlideImage.as_tile_bag | ||
~WholeSlideImage.as_data_loader | ||
~WholeSlideImage.as_torch_geometric_data |
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from datetime import datetime | ||
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import wsi | ||
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project = "wsi" | ||
copyright = f"{datetime.now().year}, Rendeiro Lab" | ||
author = "wsi contributors" | ||
release = wsi.__version__ | ||
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# -- General configuration --------------------------------------------------- | ||
# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration | ||
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extensions = [ | ||
"numpydoc", | ||
"sphinx.ext.autodoc", | ||
"sphinx.ext.autosummary", | ||
"sphinx.ext.autosectionlabel", | ||
"matplotlib.sphinxext.plot_directive", | ||
"sphinx.ext.intersphinx", | ||
"sphinx_design", | ||
"sphinx_copybutton", | ||
"sphinx_click", | ||
"myst_nb", | ||
] | ||
autoclass_content = "class" | ||
autodoc_docstring_signature = True | ||
autodoc_default_options = {"members": None, "undoc-members": None} | ||
autodoc_typehints = "none" | ||
# setting autosummary | ||
autosummary_generate = True | ||
numpydoc_show_class_members = False | ||
add_module_names = False | ||
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templates_path = ["_templates"] | ||
exclude_patterns = [] | ||
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html_theme = "pydata_sphinx_theme" | ||
html_sidebars = {"installation": [], "api": []} | ||
copybutton_prompt_text = r">>> |\.\.\. |\$ |In \[\d*\]: | {2,5}\.\.\.: | {5," r"8}: " | ||
copybutton_prompt_is_regexp = True | ||
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# Plot directive | ||
plot_include_source = True | ||
plot_html_show_source_link = False | ||
plot_html_show_formats = False | ||
plot_formats = [("png", 200)] | ||
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intersphinx_mapping = { | ||
"torch": ("https://pytorch.org/docs/stable/", None), | ||
"torch_geometric": ("https://pytorch-geometric.readthedocs.io/en/stable/", None), | ||
} |
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wsi | ||
=== | ||
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**wsi** is a Python library for processing whole slide images (WSI). | ||
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It is a simple library with an object-oriented interface where all operations are performed with a WholeSlideImage object. | ||
It has the goal of doing basic processing of WSIs with reasonable defaults, but high customizability. | ||
For example, to go from a slide remotely hosted to a torch geometric graph with ResNet50 features, the following lines suffice: | ||
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.. code-block:: python | ||
from wsi import WholeSlideImage | ||
slide = WholeSlideImage("https://brd.nci.nih.gov/brd/imagedownload/GTEX-O5YU-1426") | ||
slide.segment() | ||
slide.tile() | ||
data = slide.as_torch_geometric_data(model_name='resnet50') | ||
Head over to the `Installation <install.html>`_ and `API reference <api.html>`_ pages to learn more. | ||
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.. toctree:: | ||
:maxdepth: 1 | ||
:hidden: | ||
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install | ||
api | ||
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.. grid:: 1 2 2 2 | ||
:gutter: 2 | ||
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.. grid-item-card:: Installation | ||
:link: install | ||
:link-type: doc | ||
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Instructions for installation | ||
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.. grid-item-card:: API | ||
:link: api | ||
:link-type: doc | ||
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API documentation |
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Installation | ||
============ | ||
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To install the package from the GitHub repository, follow the steps below. | ||
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1. Ensure you have Python 3.10 or higher installed. | ||
2. Install the package using `pip` by running the following command: | ||
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.. code-block:: bash | ||
pip install git+https://github.com/rendeirolab/wsi.git | ||
3. Verify that the package is correctly installed by importing it in Python: | ||
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.. code-block:: python | ||
import wsi | ||
If the installation was successful, you should not encounter any errors. | ||
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For further details, please visit our `GitHub repository <https://github.com/rendeirolab/wsi>`_. |