Merge pull request #1705 from girder/zarr-channel-data

Don't compute channel window in zarr sinks
girder · Oct 28, 2024 · 9cc086d · 9cc086d
2 parents 99405bb + 7de60f5
commit 9cc086d
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -12,6 +12,10 @@
 - Better handle images with signed pixel data ([#1695](../../pull/1695))
 - Reduce loading geojs when switching views in Girder ([#1699](../../pull/1699))
 
+### Bug Fixes
+
+- Don't compute channel window in zarr sinks ([#1705](../../pull/1705))
+
 ## 1.30.1
 
 ### Improvements

diff --git a/sources/zarr/large_image_source_zarr/__init__.py b/sources/zarr/large_image_source_zarr/__init__.py
@@ -872,21 +872,21 @@ def _writeInternalMetadata(self):
                         'inverted': False,
                         'label': f'Band {c + 1}',
                     }
-                    slicing = tuple(
-                        slice(None)
-                        if k != ('c' if 'c' in self._axes else 's')
-                        else c
-                        for k, v in self._axes.items()
-                    )
-                    channel_data = base_array[slicing]
-                    channel_min = np.min(channel_data)
-                    channel_max = np.max(channel_data)
-                    channel_metadata['window'] = {
-                        'end': channel_max,
-                        'max': channel_max,
-                        'min': channel_min,
-                        'start': channel_min,
-                    }
+                    # slicing = tuple(
+                    #     slice(None)
+                    #     if k != ('c' if 'c' in self._axes else 's')
+                    #     else c
+                    #     for k, v in self._axes.items()
+                    # )
+                    # channel_data = base_array[slicing]
+                    # channel_min = np.min(channel_data)
+                    # channel_max = np.max(channel_data)
+                    # channel_metadata['window'] = {
+                    #     'end': channel_max,
+                    #     'max': channel_max,
+                    #     'min': channel_min,
+                    #     'start': channel_min,
+                    # }
                     if len(self._channelNames) > c:
                         channel_metadata['label'] = self._channelNames[c]
                     if len(self._channelColors) > c:

diff --git a/test/test_sink.py b/test/test_sink.py
@@ -1,4 +1,3 @@
-import math
 import subprocess
 from multiprocessing.pool import Pool, ThreadPool
 from os import sys
@@ -419,13 +418,13 @@ def testMetadata(tmp_path):
         assert c.get('family') == 'linear'
         assert not c.get('inverted')
         assert c.get('label') == channel_names[i]
-        window = c.get('window')
-        assert window is not None
-        # max should be nearly 1 and min should be nearly 0
-        assert math.ceil(window.get('end')) == 1
-        assert math.ceil(window.get('max')) == 1
-        assert math.floor(window.get('start')) == 0
-        assert math.floor(window.get('min')) == 0
+        # window = c.get('window')
+        # assert window is not None
+        # # max should be nearly 1 and min should be nearly 0
+        # assert math.ceil(window.get('end')) == 1
+        # assert math.ceil(window.get('max')) == 1
+        # assert math.floor(window.get('start')) == 0
+        # assert math.floor(window.get('min')) == 0
 
     rdefs = omero.get('rdefs')
     assert rdefs is not None