Updated documentation for version 0.0.2 (#9)

* Integration of CI/CD practices (#2) * Integration CI/CD pipeline to this project * Corrected github actions test workflow * Install the package before test it * Created empty __init__.py inside tests to record coverage * Changed name of sample_images_generator.py to utils.py for clarity * Updated test workflow to use a non-supported workaround for the multiple OpenMP runtime library issue * Updated test workflow to report coverage * Moved non-pytorch compatibility test to last position * Added test for datasets with zero expected samples * Changed PatchSampler to take as base the patche size instead of the input image's chunk sizes * Reverted change in the computation when masks elements are relative smaller than patch sizes * Fixed spatial chunk size computation when patch sizes are grater than the chunk size * Fixed missing patches from chunks smaller than the input image chunk size * Padding and stride added to PatchSampler and ImageBase classes to allow overlapping patches extraction * Added tests for stride and pad parameters of PatchSampler class * Fixed patch slices generation in PatchSampler to always retrieve patches of the defined shape * Standardized patch sampling method to handle smaller and bigger mask scales than image scale * Added example notebook to documentation * Fix offset (#8) * Changed PatchSampler to take as base the patche size instead of the input image's chunk sizes * Reverted change in the computation when masks elements are relative smaller than patch sizes * Fixed spatial chunk size computation when patch sizes are grater than the chunk size * Fixed missing patches from chunks smaller than the input image chunk size * Padding and stride added to PatchSampler and ImageBase classes to allow overlapping patches extraction * Added tests for stride and pad parameters of PatchSampler class * Fixed patch slices generation in PatchSampler to always retrieve patches of the defined shape * Standardized patch sampling method to handle smaller and bigger mask scales than image scale * Added example notebook to documentation * Fixed incorrect sampling of patches on masked regions * Updated documentation for version 0.0.2 * Updated tests/utils.py to use an example image from a public S3 bucket
TheJacksonLaboratory · Aug 29, 2024 · fe19cf4 · fe19cf4
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diff --git a/.github/workflows/putblish_to_test_pypi.yml b/.github/workflows/putblish_to_test_pypi.yml
@@ -0,0 +1,29 @@
+name: Release to Test PyPI
+
+on:
+  release:
+    types: [ released, prereleased ]
+
+jobs:
+  release:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.9
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install Tools
+      run: |
+        python -m pip install --upgrade pip
+        pip install setuptools wheel twine
+    - name: Package and Upload
+      env:
+        VERSION: ${{ github.event.release.tag_name }}
+        TWINE_USERNAME: __token__
+        TWINE_PASSWORD: ${{ secrets.TEST_PYPI_API_TOKEN }}
+      run: |
+        python setup.py sdist bdist_wheel
+        twine upload --repository-url https://test.pypi.org/legacy/ dist/* --verbose
diff --git a/.gitignore b/.gitignore
@@ -137,3 +137,6 @@ tests/test_zarrs/*
 tests/test_tiffs/*
 tests/*.png
 .vscode/settings.json
+
+/docs_build/
+/jupyter_execute/
diff --git a/docs/.buildinfo b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5704830082c07750dd4f65112d73bff2
+config: ca6db5e3c63f8be4f91f3b82db3b81cf
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/.doctrees/autoapi/index.doctree b/docs/.doctrees/autoapi/index.doctree
diff --git a/docs/.doctrees/autoapi/zarrdataset/_augs/index.doctree b/docs/.doctrees/autoapi/zarrdataset/_augs/index.doctree
diff --git a/docs/.doctrees/autoapi/zarrdataset/_imageloaders/index.doctree b/docs/.doctrees/autoapi/zarrdataset/_imageloaders/index.doctree
diff --git a/docs/.doctrees/autoapi/zarrdataset/_maskfuncs/index.doctree b/docs/.doctrees/autoapi/zarrdataset/_maskfuncs/index.doctree
diff --git a/docs/.doctrees/autoapi/zarrdataset/_samplers/index.doctree b/docs/.doctrees/autoapi/zarrdataset/_samplers/index.doctree
diff --git a/docs/.doctrees/autoapi/zarrdataset/_utils/index.doctree b/docs/.doctrees/autoapi/zarrdataset/_utils/index.doctree
diff --git a/docs/.doctrees/autoapi/zarrdataset/_zarrdataset/index.doctree b/docs/.doctrees/autoapi/zarrdataset/_zarrdataset/index.doctree
diff --git a/docs/.doctrees/autoapi/zarrdataset/index.doctree b/docs/.doctrees/autoapi/zarrdataset/index.doctree
diff --git a/docs/.doctrees/environment.pickle b/docs/.doctrees/environment.pickle
diff --git a/docs/.doctrees/examples/advanced_example_pytorch.doctree b/docs/.doctrees/examples/advanced_example_pytorch.doctree
diff --git a/docs/.doctrees/examples/advanced_example_pytorch_inference.doctree b/docs/.doctrees/examples/advanced_example_pytorch_inference.doctree
diff --git a/docs/.doctrees/examples/advanced_masked_datasets_example.doctree b/docs/.doctrees/examples/advanced_masked_datasets_example.doctree
diff --git a/docs/.doctrees/examples/basic_example.doctree b/docs/.doctrees/examples/basic_example.doctree
diff --git a/docs/.doctrees/examples/basic_example_pytorch.doctree b/docs/.doctrees/examples/basic_example_pytorch.doctree
diff --git a/docs/.doctrees/examples/basic_example_tensorflow.doctree b/docs/.doctrees/examples/basic_example_tensorflow.doctree
diff --git a/docs/.doctrees/examples/basic_labeled_datasets_example.doctree b/docs/.doctrees/examples/basic_labeled_datasets_example.doctree
diff --git a/docs/.doctrees/examples/basic_masked_datasets_example.doctree b/docs/.doctrees/examples/basic_masked_datasets_example.doctree
diff --git a/docs/.doctrees/index.doctree b/docs/.doctrees/index.doctree
diff --git a/docs/.doctrees/license_link.doctree b/docs/.doctrees/license_link.doctree
diff --git a/docs/.doctrees/readme_link.doctree b/docs/.doctrees/readme_link.doctree
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diff --git a/docs/_images/efb0e0c981a2a37c61e11c54650023abd22cd8217f80b9af551ca2c50a0ee414.png b/docs/_images/efb0e0c981a2a37c61e11c54650023abd22cd8217f80b9af551ca2c50a0ee414.png
diff --git a/docs/_images/f99c6c24479005965377053093c7c4b95248d8010913dabe394641feeb087266.png b/docs/_images/f99c6c24479005965377053093c7c4b95248d8010913dabe394641feeb087266.png
diff --git a/docs/_images/fad1bda0fb99150f350bad3eb2d11531e570bf1fb182fda50859b693662a8898.png b/docs/_images/fad1bda0fb99150f350bad3eb2d11531e570bf1fb182fda50859b693662a8898.png
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
@@ -6,7 +6,7 @@
   <title>Overview: module code &mdash; ZarrDataset  documentation</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css" />
+      <link rel="stylesheet" type="text/css" href="../_static/mystnb.4510f1fc1dee50b3e5859aac5469c37c29e427902b24a333a5f9fcb2f0b3ac41.css?v=be8a1c11" />
       <link rel="stylesheet" type="text/css" href="../_static/graphviz.css?v=fd3f3429" />
 
 

diff --git a/docs/_modules/zarrdataset/_samplers.html b/docs/_modules/zarrdataset/_samplers.html
diff --git a/docs/_sources/autoapi/zarrdataset/_augs/index.rst.txt b/docs/_sources/autoapi/zarrdataset/_augs/index.rst.txt
@@ -1,32 +1,34 @@
-:py:mod:`zarrdataset._augs`
-===========================
+zarrdataset._augs
+=================
 
 .. py:module:: zarrdataset._augs
 
 
-Module Contents
----------------
-
 Classes
-~~~~~~~
+-------
 
 .. autoapisummary::
 
    zarrdataset._augs.ToDtype
 
 
-
+Module Contents
+---------------
 
 .. py:class:: ToDtype(dtype: numpy.dtype)
 
-
    Bases: :py:obj:`object`
 
+
    Converted a numpy NDArray to the specified data type.
 
    :param dtype: The data type to cast the input array.
    :type dtype: numpy.dtype
 
+
+   .. py:attribute:: _dtype
+
+
    .. py:method:: __call__(image: numpy.ndarray) -> numpy.ndarray
 
       Casts the type of `image` to the data type specified with `dtype`.
@@ -38,6 +40,7 @@ Classes
       :rtype: numpy.ndarray
 
 
+
    .. py:method:: __repr__() -> str
 
       Return repr(self).

diff --git a/docs/_sources/autoapi/zarrdataset/_imageloaders/index.rst.txt b/docs/_sources/autoapi/zarrdataset/_imageloaders/index.rst.txt
@@ -1,14 +1,19 @@
-:py:mod:`zarrdataset._imageloaders`
-===================================
+zarrdataset._imageloaders
+=========================
 
 .. py:module:: zarrdataset._imageloaders
 
 
-Module Contents
----------------
+Attributes
+----------
+
+.. autoapisummary::
+
+   zarrdataset._imageloaders.TIFFFILE_SUPPORT
+
 
 Classes
-~~~~~~~
+-------
 
 .. autoapisummary::
 
@@ -17,28 +22,20 @@ Classes
    zarrdataset._imageloaders.ImageCollection
 
 
-
 Functions
-~~~~~~~~~
+---------
 
 .. autoapisummary::
 
    zarrdataset._imageloaders.image2array
 
 
-
-Attributes
-~~~~~~~~~~
-
-.. autoapisummary::
-
-   zarrdataset._imageloaders.TIFFFILE_SUPPORT
-
+Module Contents
+---------------
 
 .. py:data:: TIFFFILE_SUPPORT
    :value: True
 
-
 
 .. py:function:: image2array(arr_src: Union[str, zarr.Group, zarr.Array, numpy.ndarray], data_group: Union[str, int, None] = None, zarr_store: Union[zarr.storage.Store, None] = None)
 
@@ -62,88 +59,91 @@ Attributes
 
 .. py:class:: ImageBase(shape: Iterable[int], chunk_size: Union[Iterable[int], None] = None, source_axes: str = '', mode: str = '')
 
-
    Bases: :py:obj:`object`
 
-   .. py:property:: shape
-      :type: Iterable[int]
-
-
-   .. py:property:: chunk_size
-      :type: Iterable[int]
-
-
-   .. py:property:: scale
-      :type: dict
-
 
    .. py:attribute:: arr
+      :value: None
+
 
-      
 
    .. py:attribute:: spatial_axes
       :value: 'ZYX'
 
-      
+
 
    .. py:attribute:: source_axes
+      :value: None
+
 
-      
 
    .. py:attribute:: axes
+      :value: None
+
 
-      
 
    .. py:attribute:: mode
       :value: ''
 
-      
+
 
    .. py:attribute:: permute_order
+      :value: None
+
 
-      
 
    .. py:attribute:: _store
+      :value: None
+
 
-      
 
    .. py:attribute:: _new_axes
       :value: ''
 
-      
+
 
    .. py:attribute:: _drop_axes
       :value: ''
 
-      
+
 
    .. py:attribute:: _scale
+      :value: None
+
 
-      
 
    .. py:attribute:: _shape
+      :value: None
+
 
-      
 
    .. py:attribute:: _spatial_reference_shape
+      :value: None
+
 
-      
 
    .. py:attribute:: _spatial_reference_axes
+      :value: None
+
 
-      
 
    .. py:attribute:: _chunk_size
+      :value: None
+
 
-      
 
    .. py:attribute:: _cached_coords
+      :value: None
+
 
-      
 
    .. py:attribute:: _image_func
+      :value: None
+
+
+
+   .. py:attribute:: roi
 
-      
 
    .. py:method:: _iscached(coords)
 
@@ -169,11 +169,26 @@ Attributes
 
 
 
-.. py:class:: ImageLoader(filename: str, source_axes: str, data_group: Union[str, None] = None, axes: Union[str, None] = None, roi: Union[str, slice, Iterable[slice], None] = None, image_func: Union[Callable, None] = None, zarr_store: Union[zarr.storage.Store, None] = None, spatial_axes: str = 'ZYX', mode: str = '')
+   .. py:property:: shape
+      :type: Iterable[int]
+
+
+
+   .. py:property:: chunk_size
+      :type: Iterable[int]
+
+
+
+   .. py:property:: scale
+      :type: dict
+
 
 
+.. py:class:: ImageLoader(filename: str, source_axes: str, data_group: Union[str, None] = None, axes: Union[str, None] = None, roi: Union[str, slice, Iterable[slice], None] = None, image_func: Union[Callable, None] = None, zarr_store: Union[zarr.storage.Store, None] = None, spatial_axes: str = 'ZYX', mode: str = '')
+
    Bases: :py:obj:`ImageBase`
 
+
    Image lazy loader class.
 
    Opens the zarr file, or any image that can be open by TiffFile or PIL, as a
@@ -198,15 +213,36 @@ Attributes
    :param mode:
    :type mode: str
 
-   .. py:method:: __del__()
 
+   .. py:attribute:: mode
 
 
-.. py:class:: ImageCollection(collection_args: dict, spatial_axes: str = 'ZYX')
+   .. py:attribute:: spatial_axes
+
+
+   .. py:attribute:: roi_slices
 
 
+   .. py:attribute:: roi
+
+
+   .. py:attribute:: source_axes
+
+
+   .. py:attribute:: axes
+
+
+   .. py:attribute:: _image_func
+
+
+   .. py:method:: __del__()
+
+
+.. py:class:: ImageCollection(collection_args: dict, spatial_axes: str = 'ZYX')
+
    Bases: :py:obj:`object`
 
+
    A class to contain a collection of inputs from different modalities.
 
    This is used to match images with their respective labels and masks.
@@ -218,6 +254,16 @@ Attributes
                         modalities using as reference these axes from the `images` collection.
    :type spatial_axes: str
 
+
+   .. py:attribute:: reference_mode
+
+
+   .. py:attribute:: spatial_axes
+
+
+   .. py:attribute:: collection
+
+
    .. py:method:: _generate_mask()
 
 
@@ -227,7 +273,7 @@ Attributes
       collection shape on the `spatial_axes` only.
 
 
-   .. py:method:: __getitem__(index)
 
+   .. py:method:: __getitem__(index)