Fix edge case bug where grayscale image has an alpha channel, minor r…

…td fix (#1313) * Fix edge case bug where grayscale image has an alpha channel * Try doc fix * Try doc fix * Unpin spinx * Refactor color/alpha -> greyscale for clarity (Joshua's code * Fix syntax typo * Fix assignement * Test debug cleanup * Keep singleton dimension * Fix casting * Update ivadomed/loader/segmentation_pair.py Co-authored-by: Joshua Newton <joshuacwnewton@gmail.com> * Update ivadomed/loader/segmentation_pair.py Co-authored-by: Joshua Newton <joshuacwnewton@gmail.com> * Update ivadomed/loader/segmentation_pair.py Co-authored-by: Kanishk Kalra <36276423+kanishk16@users.noreply.github.com> * Revert to initial solution * Update ivadomed/loader/segmentation_pair.py Co-authored-by: Joshua Newton <joshuacwnewton@gmail.com> * Update ivadomed/loader/segmentation_pair.py Co-authored-by: Joshua Newton <joshuacwnewton@gmail.com> * Update data-testing release --------- Co-authored-by: Joshua Newton <joshuacwnewton@gmail.com> Co-authored-by: Kanishk Kalra <36276423+kanishk16@users.noreply.github.com>
ivadomed · Jan 30, 2024 · 881dc68 · 881dc68
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commit 881dc68
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diff --git a/ivadomed/loader/segmentation_pair.py b/ivadomed/loader/segmentation_pair.py
@@ -350,17 +350,19 @@ def convert_file_to_nifti(self, filename: str, extension: str, is_gt: bool = Fal
             # Note: All of these are trivially true for JPEG and PNG due to limitations of these formats.
 
             # make grayscale (treats binary as 1-bit grayscale)
-            colorspace_idx = 2 + int(props.is_batch)
+            colorspace_idx = 2
             if _img.ndim <= colorspace_idx:  # binary or gray
                 pass  # nothing to do
+            elif _img.shape[colorspace_idx] == 2:  # gray with alpha channel
+                _img = _img[:, :, 0]
             elif _img.shape[colorspace_idx] == 3:  # RGB
                 _img = np.sum(_img * (.299, .587, .114), axis=-1)
             else:  # RGBA
                 # discards alpha
                 _img = np.sum(_img * (.299, .587, .114, 0), axis=-1)
             if len(_img.shape) < 3:
                 _img = np.expand_dims(_img, axis=-1)
-        
+
             img = imageio.core.image_as_uint(_img, bitdepth=8)
 
         # Binarize ground-truth values (0-255) to 0 and 1 in uint8 with threshold 0.5

diff --git a/ivadomed/scripts/download_data.py b/ivadomed/scripts/download_data.py
@@ -23,7 +23,7 @@
             `Spine Generic <https://github.com/spine-generic/data-multi-subject>`_.
             Used for Tutorial and example in Ivadomed."""},
     "data_testing": {
-        "url": ["https://github.com/ivadomed/data-testing/archive/r20220328.zip"],
+        "url": ["https://github.com/ivadomed/data-testing/archive/r20240130.zip"],
         "description": "Data Used for integration/unit test in Ivadomed."},
     "data_multi_testing": {
         "url": ["https://github.com/MotionCorrect/data_multi-sessions-contrasts/archive/refs/tags/v2022-01-06.zip"],

diff --git a/setup.py b/setup.py
@@ -23,9 +23,9 @@
         # https://github.com/readthedocs/readthedocs.org/blob/ecac31de54bbb2c100f933e86eb22b0f4389ba84/requirements/pip.txt#L16
         'sphinx',
         'sphinx_rtd_theme',
-        'sphinx-tabs==3.2.0',
-        'sphinx-toolbox==2.15.2',
-        'sphinx-jsonschema~=1.16',
+        'sphinx-tabs',
+        'sphinx-toolbox',
+        'sphinx-jsonschema',
         'pypandoc',
     ],
     'tests': [