Merge 27d265c into 94b7740

histolab · Jul 27, 2020 · 6fb053a · 6fb053a
2 parents 94b7740 + 27d265c
commit 6fb053a
Show file tree

Hide file tree

Showing 16 changed files with 93 additions and 51 deletions.
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,16 +1,20 @@
 Changelog
 =========
 
+v0.0.5b
+-------
+
+ - Fix `issue #100 <https://github.com/histolab/histolab/issues/100>`_
+ - Fix `issue #108 <https://github.com/histolab/histolab/issues/108>`_
+ - `Grid Tiler <https://github.com/histolab/histolab/issues/99>`_ added
+
+
 v0.0.4b
 -------
 
  - Fix kmeans segmentation image filter default parameters
  - Fix rag threshold image filter default parameters
  - Fix check tissue on `Tile` to discard almost white tiles
 
-v0.0.5b
--------
 
- - Fix `issue #100 <https://github.com/histolab/histolab/issues/100>`_
- - Fix `issue #108 <https://github.com/histolab/histolab/issues/108>`_
- - `Grid Tiler <https://github.com/histolab/histolab/issues/99>`_ added
+.. toctree::
diff --git a/docs/api/data.rst b/docs/api/data.rst
@@ -0,0 +1,11 @@
+Data
+====================================
+
+.. toctree::
+   :caption: API Reference
+   :maxdepth: 2
+
+.. automodule:: src.histolab.data
+    :members:
+
+.. toctree::
diff --git a/docs/api/filters.rst b/docs/api/filters.rst
@@ -1,13 +1,13 @@
 Filters
 ====================================
 
-.. toctree::
-
 .. toctree::
    :maxdepth: 2
    :caption: API Reference
 
    filters/image_filters
    filters/image_filters_functional
    filters/morphological_filters
-   filters/morphological_filters_functional
+   filters/morphological_filters_functional
+
+.. toctree::
diff --git a/docs/api/filters/image_filters.rst b/docs/api/filters/image_filters.rst
@@ -1,11 +1,11 @@
 Image Filters
 ====================================
 
-.. toctree::
-
 .. toctree::
    :caption: Filters
    :maxdepth: 2
 
 .. automodule:: src.histolab.filters.image_filters
-    :members:
+    :members:
+
+.. toctree::
diff --git a/docs/api/filters/image_filters_functional.rst b/docs/api/filters/image_filters_functional.rst
@@ -1,11 +1,12 @@
 Image Filters Functional
 ====================================
 
-.. toctree::
 
 .. toctree::
    :caption: Filters
    :maxdepth: 2
 
 .. automodule:: src.histolab.filters.image_filters_functional
-    :members:
+    :members:
+
+.. toctree::
diff --git a/docs/api/filters/morphological_filters.rst b/docs/api/filters/morphological_filters.rst
@@ -1,11 +1,11 @@
 Morphological Filters
 ====================================
 
-.. toctree::
-
 .. toctree::
    :caption: Filters
    :maxdepth: 2
 
 .. automodule:: src.histolab.filters.morphological_filters
-    :members:
+    :members:
+
+.. toctree::
diff --git a/docs/api/filters/morphological_filters_functional.rst b/docs/api/filters/morphological_filters_functional.rst
@@ -1,11 +1,12 @@
 Morphological Filters Functional
 ====================================
 
-.. toctree::
-
 .. toctree::
    :caption: Filters
    :maxdepth: 2
 
 .. automodule:: src.histolab.filters.morphological_filters_functional
-    :members:
+    :members:
+
+
+.. toctree::
diff --git a/docs/api/slide.rst b/docs/api/slide.rst
@@ -1,11 +1,11 @@
 Slide
 ====================================
 
-.. toctree::
-
 .. toctree::
    :caption: API Reference
    :maxdepth: 2
 
 .. automodule:: src.histolab.slide
-    :members:
+    :members:
+
+.. toctree::
diff --git a/docs/api/tile.rst b/docs/api/tile.rst
@@ -1,11 +1,11 @@
 Tile
 ====================================
 
-.. toctree::
-
 .. toctree::
    :caption: API Reference
    :maxdepth: 2
 
 .. automodule:: src.histolab.tile
-    :members:
+    :members:
+
+.. toctree::
diff --git a/docs/api/tiler.rst b/docs/api/tiler.rst
@@ -1,12 +1,12 @@
 Tiler
 ====================================
 
-.. toctree::
-
 .. toctree::
    :caption: API Reference
    :maxdepth: 2
 
 .. automodule:: src.histolab.tiler
     :members:
-    :exclude-members: Tiler
+    :exclude-members: Tiler
+
+.. toctree::
diff --git a/docs/utils.rst → docs/api/utils.rst b/docs/utils.rst → docs/api/utils.rst
diff --git a/docs/contributing.rst b/docs/contributing.rst
@@ -208,4 +208,6 @@ Attribution
 This Code of Conduct is adapted from the `Contributor Covenant <http://contributor-covenant.org>`_\ , version 1.4,
 available at `http://contributor-covenant.org/version/1/4 <http://contributor-covenant.org/version/1/4/>`_
 
+.. toctree::
+
 .. toctree::
diff --git a/docs/index.rst b/docs/index.rst
@@ -85,7 +85,8 @@ References
    api/filters
    api/tile
    api/tiler
-   utils
+   api/data
+   api/utils
 
 
 Indices and tables

diff --git a/docs/quickstart.rst b/docs/quickstart.rst
@@ -180,4 +180,6 @@ least 80% of tissue inside.
    :alt: caption
 
 
+.. toctree::
+
 .. toctree::
diff --git a/docs/readme.rst b/docs/readme.rst
@@ -72,7 +72,7 @@ References
 
 
 .. toctree::
-  :hidden:
+
 
 .. toctree::
    :caption: API Reference

diff --git a/src/histolab/data/__init__.py b/src/histolab/data/__init__.py
@@ -215,14 +215,15 @@ def _load_svs(f: str) -> Tuple[openslide.OpenSlide, str]:
 
     Parameters
     ----------
-    f: str
-        data_filename: str
+    f : str
         Name of the file in the histolab repository
 
     Returns
     -------
-    slide : OpenSlide object
-            An OpenSlide object representing a whole-slide image.
+    slide : openslide.OpenSlide
+        An OpenSlide object representing a whole-slide image.
+    path : str
+        Path where the slide is saved
 
     Raises
     ------
@@ -241,52 +242,61 @@ def _load_svs(f: str) -> Tuple[openslide.OpenSlide, str]:
 def cmu_small_region() -> Tuple[openslide.OpenSlide, str]:
     """Carnegie Mellon University MRXS sample tissue
 
+    This image is available here
+    http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
+
     Licensed under a CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.
 
     Returns
     -------
-    cmu_mrxs_tissue : OpenSlide object
+    cmu_mrxs_tissue : openslide.OpenSlide
         Sample CMU tissue Whole-Slide-Image
+    path : str
+        Path where the slide is saved
     """
     return _load_svs("data/cmu_small_region.svs")
 
 
 def aorta_tissue() -> Tuple[openslide.OpenSlide, str]:  # pragma: no cover
     """Aorta tissue, brightfield, JPEG 2000, YCbCr
 
-    This image is avaliable here
+    This image is available here
     http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
 
     Free to use and distribute, with or without modification
 
     Returns
     -------
-    aorta_tissue : OpenSlide object
+    aorta_tissue : openslide.OpenSlide
         Aorta tissue Whole-Slide-Image
+    path : str
+        Path where the slide is saved
     """
     return _load_svs("aperio/JP2K-33003-1.svs")
 
 
 def heart_tissue() -> Tuple[openslide.OpenSlide, str]:  # pragma: no cover
     """Heart tissue, brightfield, JPEG 2000, YCbCr
 
-    This image is avaliable here
+    This image is available here
     http://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/
 
     Free to use and distribute, with or without modification
 
     Returns
     -------
-    heart_tissue : OpenSlide object
+    heart_tissue : openslide.OpenSlide
         Heart tissue Whole-Slide-Image
+    path : str
+        Path where the slide is saved
     """
     return _load_svs("aperio/JP2K-33003-2.svs")
 
 
 def breast_tissue() -> Tuple[openslide.OpenSlide, str]:  # pragma: no cover
-    """Breast tissue, TCGA-BRCA dataset
+    """Breast tissue, TCGA-BRCA dataset.
 
-    This image is avaliable here
+    This image is available here
     https://portal.gdc.cancer.gov/files/9c960533-2e58-4e54-97b2-8454dfb4b8c8
     or through the API
     https://api.gdc.cancer.gov/data/9c960533-2e58-4e54-97b2-8454dfb4b8c8
@@ -295,16 +305,18 @@ def breast_tissue() -> Tuple[openslide.OpenSlide, str]:  # pragma: no cover
 
     Returns
     -------
-    breast_tissue : OpenSlide object
+    breast_tissue : openslide.OpenSlide
         Breast tissue Whole-Slide-Image
+    path : str
+        Path where the slide is saved
     """
     return _load_svs("tcga/breast/9c960533-2e58-4e54-97b2-8454dfb4b8c8")
 
 
 def prostate_tissue() -> Tuple[openslide.OpenSlide, str]:  # pragma: no cover
-    """Prostate tissue, TCGA-
+    """Prostate tissue, TCGA-PRAD dataset.
 
-    This image is avaliable here
+    This image is available here
     https://portal.gdc.cancer.gov/files/6b725022-f1d5-4672-8c6c-de8140345210
     or through the API
     https://api.gdc.cancer.gov/data/6b725022-f1d5-4672-8c6c-de8140345210
@@ -314,8 +326,10 @@ def prostate_tissue() -> Tuple[openslide.OpenSlide, str]:  # pragma: no cover
 
     Returns
     -------
-    prostate_tissue : OpenSlide object
+    prostate_tissue : openslide.OpenSlide
         Prostate tissue Whole-Slide-Image
+    path : str
+        Path where the slide is saved
     """
     return _load_svs("tcga/prostate/6b725022-f1d5-4672-8c6c-de8140345210")
 
@@ -325,7 +339,7 @@ def breast_tissue_diagnostic_green_pen() -> Tuple[
 ]:  # pragma: no cover
     """Breast tissue, TCGA-BRCA dataset. Diagnostic slide with green pen.
 
-    This image is avaliable here
+    This image is available here
     https://portal.gdc.cancer.gov/files/da36d3aa-9b19-492a-af4f-cc028a926d96
     or through the API
     https://api.gdc.cancer.gov/data/da36d3aa-9b19-492a-af4f-cc028a926d96
@@ -334,8 +348,10 @@ def breast_tissue_diagnostic_green_pen() -> Tuple[
 
     Returns
     -------
-    breast_tissue : OpenSlide object
+    breast_tissue : openslide.OpenSlide
         Breast tissue Whole-Slide-Image
+    path : str
+        Path where the slide is saved
     """
     return _load_svs("tcga/breast/da36d3aa-9b19-492a-af4f-cc028a926d96")
 
@@ -345,7 +361,7 @@ def breast_tissue_diagnostic_red_pen() -> Tuple[
 ]:  # pragma: no cover
     """Breast tissue, TCGA-BRCA dataset. Diagnostic slide with red pen.
 
-    This image is avaliable here
+    This image is available here
     https://portal.gdc.cancer.gov/files/f8b4cee6-9149-45b4-ae53-82b0547e1e34
     or through the API
     https://api.gdc.cancer.gov/data/f8b4cee6-9149-45b4-ae53-82b0547e1e34
@@ -354,8 +370,10 @@ def breast_tissue_diagnostic_red_pen() -> Tuple[
 
     Returns
     -------
-    breast_tissue : OpenSlide object
+    breast_tissue : openslide.OpenSlide
         Breast tissue Whole-Slide-Image
+    path : str
+        Path where the slide is saved
     """
     return _load_svs("tcga/breast/f8b4cee6-9149-45b4-ae53-82b0547e1e34")
 
@@ -365,7 +383,7 @@ def breast_tissue_diagnostic_black_pen() -> Tuple[
 ]:  # pragma: no cover
     """Breast tissue, TCGA-BRCA dataset. Diagnostic slide with black pen.
 
-    This image is avaliable here
+    This image is available here
     https://portal.gdc.cancer.gov/files/31e248bf-ee24-4d18-bccb-47046fccb461
     or through the API
     https://api.gdc.cancer.gov/data/31e248bf-ee24-4d18-bccb-47046fccb461
@@ -374,7 +392,9 @@ def breast_tissue_diagnostic_black_pen() -> Tuple[
 
     Returns
     -------
-    breast_tissue : OpenSlide object
+    breast_tissue : openslide.OpenSlide
         Breast tissue Whole-Slide-Image
+    path : str
+        Path where the slide is saved
     """
     return _load_svs("tcga/breast/31e248bf-ee24-4d18-bccb-47046fccb461")