TEST: Add test for mask, imports

.github/workflows/build-test-package.yml

@@ -12,7 +12,7 @@ jobs:
 
         include:
           - flake8-python-git-tag: ""
-          - itk-python-git-tag: ""
+          - pooch-python-git-tag: ""
           - pytest-python-git-tag: ""
 
     steps:
@@ -36,7 +36,7 @@ jobs:
           sudo apt update
           sudo apt install openslide-tools python3-openslide
           python -m pip install --upgrade pip setuptools wheel
-          pip install 'flake8${{ matrix.flake8-python-git-tag }}' 'pytest${{ matrix.pytest-python-git-tag }}' 'itk${{ matrix.itk-python-git-tag }}' 'tensorflow'
+          pip install 'flake8${{ matrix.flake8-python-git-tag }}' 'pooch${{ matrix.pooch-python-git-tag }}' 'pytest${{ matrix.pytest-python-git-tag }}'
           pip install 'large-image[bioformats,ometiff,openjpeg,openslide,tiff]' 'scikit_image' --find-links https://girder.github.io/large_image_wheels
 
       - name: Install histomics_stream

histomics_stream/configure.py

@@ -27,7 +27,7 @@
 import numpy as np
 import random
 import re
-import scipy
+import scipy.interpolate
 
 
 class _TilesByCommon:

test/test_find_itk.py → test/test_find_imports.py

@@ -19,12 +19,19 @@
 # =========================================================================
 
 
-def test_itk_can_be_found():
-    """Purpose: Test to check that ITK can be found"""
+def test_imports_can_be_found():
+    """Purpose: Test to check that each import can be found"""
 
     # Import succeeds
+    import imagecodecs
     import itk
+    import numcodecs
+    import numpy
+    import scipy.interpolate
+    import tensorflow
+    import torch
+    import zarr
 
 
 if __name__ == "__main__":
-    test_itk_can_be_found()
+    test_imports_can_be_found()

test/test_mask.py

@@ -0,0 +1,130 @@
+#!/usr/bin/env python3
+
+# =========================================================================
+#
+#   Copyright NumFOCUS
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#          https://www.apache.org/licenses/LICENSE-2.0.txt
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+# =========================================================================
+
+
+def test_mask_threshold():
+    import histomics_stream as hs
+    import os
+    import pooch
+
+    wsi_path = pooch.retrieve(
+        fname="TCGA-AN-A0G0-01Z-00-DX1.svs",
+        url=(
+            "https://drive.google.com/uc"
+            "?export=download"
+            "&id=19agE_0cWY582szhOVxp9h3kozRfB4CvV"
+            "&confirm=t"
+            "&uuid=6f2d51e7-9366-4e98-abc7-4f77427dd02c"
+            "&at=ALgDtswlqJJw1KU7P3Z1tZNcE01I:1679111148632"
+        ),
+        known_hash="d046f952759ff6987374786768fc588740eef1e54e4e295a684f3bd356c8528f",
+        path=str(pooch.os_cache("pooch")) + os.sep + "wsi",
+    )
+    print(f"Have {wsi_path}")
+
+    # download binary mask image
+    mask_path = pooch.retrieve(
+        fname="TCGA-AN-A0G0-01Z-00-DX1.mask.png",
+        url=(
+            "https://drive.google.com/uc"
+            "?export=download"
+            "&id=17GOOHbL8Bo3933rdIui82akr7stbRfta"
+        ),
+        known_hash="bb657ead9fd3b8284db6ecc1ca8a1efa57a0e9fd73d2ea63ce6053fbd3d65171",
+        path=str(pooch.os_cache("pooch")) + os.sep + "wsi",
+    )
+    print(f"Have {mask_path}")
+
+    my_study = dict(
+        version="version-1",
+        tile_width=5471,
+        tile_height=5743,
+        overlap_width=127,
+        overlap_height=101,
+        slides=dict(
+            Slide_0=dict(
+                filename=wsi_path,
+                slide_name=os.path.splitext(os.path.split(wsi_path)[1])[0],
+                slide_group="test_mask_threshold",
+                chunk_width=31,
+                chunk_height=37,
+            )
+        ),
+    )
+    find_slide_resolution = hs.configure.FindResolutionForSlide(
+        my_study, target_magnification=20, magnification_source="native"
+    )
+    for slide in my_study["slides"].values():
+        find_slide_resolution(slide)
+
+    tiler_thresholds = (0.00, 0.20, 0.50, 0.80, 1.00)
+    tilers = [
+        hs.configure.TilesByGridAndMask(
+            my_study, mask_filename=mask_path, mask_threshold=threshold
+        )
+        for threshold in tiler_thresholds
+    ]
+
+    def run_tiler(study, tiler):
+        for slide in study["slides"].values():
+            tiler(slide)
+        return tiler.get_tiles(my_study)
+
+    found_tiles = [run_tiler(my_study, tiler) for tiler in tilers]
+
+    # print(f"    expected_tiles = {repr(found_tiles)}")
+    expected_tiles = [
+        [
+            (
+                wsi_path,
+                [(0, 10688), (0, 16032), (0, 21376)]
+                + [(5642, 5344), (5642, 10688), (5642, 16032), (5642, 21376)]
+                + [(11284, 5344), (11284, 10688), (11284, 16032), (11284, 21376)],
+            )
+        ],
+        [
+            (
+                wsi_path,
+                [(0, 16032), (0, 21376)]
+                + [(5642, 5344), (5642, 10688), (5642, 16032), (5642, 21376)]
+                + [(11284, 5344), (11284, 10688), (11284, 16032), (11284, 21376)],
+            )
+        ],
+        [
+            (
+                wsi_path,
+                [(0, 16032), (0, 21376)]
+                + [(5642, 10688), (5642, 16032), (5642, 21376)]
+                + [(11284, 10688), (11284, 16032)],
+            )
+        ],
+        [(wsi_path, [(5642, 10688), (5642, 16032), (11284, 10688), (11284, 16032)])],
+        [(wsi_path, [(5642, 16032), (11284, 16032)])],
+    ]
+
+    for i in range(len(found_tiles) - 1):
+        assert set(found_tiles[i + 1][0][1]).issubset(set(found_tiles[i + 1][0][1]))
+    for i in range(len(found_tiles)):
+        assert found_tiles[i] == expected_tiles[i]
+    print("Test succeeded")
+
+
+if __name__ == "__main__":
+    test_mask_threshold()