Merge pull request #1374 from girder/fix-ometiff-style

Fix an issue with apply a frame style to ome tiffs

CHANGELOG.md

@@ -19,6 +19,7 @@
 - Default to "None" for the DICOM assetstore limit ([#1359](../../pull/1359))
 - Fix series detection for some bioformats files ([#1365](../../pull/1365), [#1367](../../pull/1367))
 - Fix time comparison in annotation history check ([#1369](../../pull/1369))
+- Fix an issue with apply a frame style to ome tiffs ([#1374](../../pull/1374))
 
 ## 1.26.0
 

sources/ometiff/large_image_source_ometiff/__init__.py

@@ -318,8 +318,9 @@ def getNativeMagnification(self):
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
                 sparseFallback=False, **kwargs):
-        if (z < 0 or z >= len(self._omeLevels) or (
-                self._omeLevels[z] is not None and kwargs.get('frame') in (None, 0, '0', ''))):
+        if ((z < 0 or z >= len(self._omeLevels) or (
+                self._omeLevels[z] is not None and kwargs.get('frame') in (None, 0, '0', ''))) and
+                not getattr(self, '_style', None)):
             return super().getTile(
                 x, y, z, pilImageAllowed=pilImageAllowed,
                 numpyAllowed=numpyAllowed, sparseFallback=sparseFallback,

test/test_source_ometiff.py

@@ -204,4 +204,6 @@ def testXMLParsing():
 def testFrameStyleOMETiff():
     imagePath = datastore.fetch('DDX58_AXL_EGFR_well2_XY01.ome.tif')
     source = large_image_source_ometiff.open(imagePath, style={'bands': [{'frame': 4}]})
-    assert source.getTile(0, 0, 2)
+    tile1 = source.getTile(0, 0, 2)
+    tile2 = source.getTile(0, 0, 2, frame=1)
+    assert tile1 == tile2

tox.ini

@@ -254,7 +254,8 @@ exclude =
 ignore = D100,D101,D102,D103,D104,D105,D106,D107,D200,D205,D400,D401,E741,W504,B017
 
 [pytest]
-addopts = --verbose --strict-markers --showlocals --cov-report="term" --cov-report="xml" --cov-report="html" --cov --ignore test/utils --cov-context=test
+addopts = --verbose --strict-markers --showlocals --cov-report="term" --cov-report="xml" --cov-report="html" --cov --ignore test/utils
+# --cov-context=test
 cache_dir = build/pytest_cache
 testpaths =
   test
@@ -322,7 +323,7 @@ parallel = True
 [coverage:html]
 directory = build/test/artifacts/python_coverage
 title = Large image Coverage Report
-show_contexts = True
+# show_contexts = True
 
 [coverage:xml]
 output = build/test/coverage/py_coverage.xml