large-image-source-tifffile 1.30.3__py3-none-any.whl → 1.30.3.dev3__py3-none-any.whl

large_image_source_tifffile/__init__.py

@@ -292,79 +292,6 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         except Exception:
             pass
 
-    def _handle_indica(self):
-        import xml.etree.ElementTree
-
-        import large_image.tilesource.utilities
-
-        try:
-            root = xml.etree.ElementTree.fromstring(self._tf.pages[0].description)
-            self._xml = large_image.tilesource.utilities.etreeToDict(root)
-            self._channels = [c['name'] for c in
-                              self._xml['indica']['image']['channels']['channel']]
-            if len(self._basis) == 1 and 'I' in self._basis:
-                self._basis['C'] = self._basis.pop('I')
-            self._associatedImages.clear()
-        except Exception:
-            pass
-
-    def _handle_ome(self):
-        """
-        For OME Tiff, if we didn't parse the mangification elsewhere, try to
-        parse it here.
-        """
-        import xml.etree.ElementTree
-
-        import large_image.tilesource.utilities
-
-        _omeUnitsToMeters = {
-            'Ym': 1e24,
-            'Zm': 1e21,
-            'Em': 1e18,
-            'Pm': 1e15,
-            'Tm': 1e12,
-            'Gm': 1e9,
-            'Mm': 1e6,
-            'km': 1e3,
-            'hm': 1e2,
-            'dam': 1e1,
-            'm': 1,
-            'dm': 1e-1,
-            'cm': 1e-2,
-            'mm': 1e-3,
-            '\u00b5m': 1e-6,
-            'nm': 1e-9,
-            'pm': 1e-12,
-            'fm': 1e-15,
-            'am': 1e-18,
-            'zm': 1e-21,
-            'ym': 1e-24,
-            '\u00c5': 1e-10,
-        }
-
-        try:
-            root = xml.etree.ElementTree.fromstring(self._tf.pages[0].description)
-            self._xml = large_image.tilesource.utilities.etreeToDict(root)
-        except Exception:
-            return
-        try:
-            try:
-                base = self._xml['OME']['Image'][0]['Pixels']
-            except Exception:
-                base = self._xml['OME']['Image']['Pixels']
-            if self._mm_x is None and 'PhysicalSizeX' in base:
-                self._mm_x = (
-                    float(base['PhysicalSizeX']) * 1e3 *
-                    _omeUnitsToMeters[base.get('PhysicalSizeXUnit', '\u00b5m')])
-            if self._mm_y is None and 'PhysicalSizeY' in base:
-                self._mm_y = (
-                    float(base['PhysicalSizeY']) * 1e3 *
-                    _omeUnitsToMeters[base.get('PhysicalSizeYUnit', '\u00b5m')])
-            self._mm_x = self._mm_x or self._mm_y
-            self._mm_y = self._mm_y or self._mm_x
-        except Exception:
-            pass
-
     def _handle_scn(self):  # noqa
         """
         For SCN files, parse the xml and possibly adjust how associated images
@@ -430,6 +357,63 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         except Exception:
             pass
 
+    def _handle_ome(self):
+        """
+        For OME Tiff, if we didn't parse the mangification elsewhere, try to
+        parse it here.
+        """
+        import xml.etree.ElementTree
+
+        import large_image.tilesource.utilities
+
+        _omeUnitsToMeters = {
+            'Ym': 1e24,
+            'Zm': 1e21,
+            'Em': 1e18,
+            'Pm': 1e15,
+            'Tm': 1e12,
+            'Gm': 1e9,
+            'Mm': 1e6,
+            'km': 1e3,
+            'hm': 1e2,
+            'dam': 1e1,
+            'm': 1,
+            'dm': 1e-1,
+            'cm': 1e-2,
+            'mm': 1e-3,
+            '\u00b5m': 1e-6,
+            'nm': 1e-9,
+            'pm': 1e-12,
+            'fm': 1e-15,
+            'am': 1e-18,
+            'zm': 1e-21,
+            'ym': 1e-24,
+            '\u00c5': 1e-10,
+        }
+
+        try:
+            root = xml.etree.ElementTree.fromstring(self._tf.pages[0].description)
+            self._xml = large_image.tilesource.utilities.etreeToDict(root)
+        except Exception:
+            return
+        try:
+            try:
+                base = self._xml['OME']['Image'][0]['Pixels']
+            except Exception:
+                base = self._xml['OME']['Image']['Pixels']
+            if self._mm_x is None and 'PhysicalSizeX' in base:
+                self._mm_x = (
+                    float(base['PhysicalSizeX']) * 1e3 *
+                    _omeUnitsToMeters[base.get('PhysicalSizeXUnit', '\u00b5m')])
+            if self._mm_y is None and 'PhysicalSizeY' in base:
+                self._mm_y = (
+                    float(base['PhysicalSizeY']) * 1e3 *
+                    _omeUnitsToMeters[base.get('PhysicalSizeYUnit', '\u00b5m')])
+            self._mm_x = self._mm_x or self._mm_y
+            self._mm_y = self._mm_y or self._mm_x
+        except Exception:
+            pass
+
     def getNativeMagnification(self):
         """
         Get the magnification at a particular level.
@@ -639,8 +623,6 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     sel.append(slice(series.shape[aidx]))
                     baxis += 'S'
                 else:
-                    if axis not in self._basis and axis == 'I':
-                        axis = 'C'
                     sel.append((frame // self._basis[axis][0]) % self._basis[axis][2])
             tile = bza[tuple(sel)]
             # rotate

{large_image_source_tifffile-1.30.3.dist-info → large_image_source_tifffile-1.30.3.dev3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tifffile
-Version: 1.30.3
+Version: 1.30.3.dev3
 Summary: A tifffile tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -19,12 +19,12 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.8
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.30.3
+Requires-Dist: large-image >=1.30.3.dev3
 Requires-Dist: dask[array]
 Requires-Dist: tifffile[all]
 Requires-Dist: zarr
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.3; extra == "girder"
+Requires-Dist: girder-large-image >=1.30.3.dev3 ; extra == 'girder'
 
 A tifffile tilesource for large_image.
 

large_image_source_tifffile-1.30.3.dev3.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_tifffile/__init__.py,sha256=4j4Ovb1V1xvbAKBFdm1Tbj5RvvgjRGmo_ABv4kjG2hc,27413
+large_image_source_tifffile/girder_source.py,sha256=8YsxpSK_UzbAcpjn6fIMlgKye2FchkB8_HTSQV0FpRA,1064
+large_image_source_tifffile-1.30.3.dev3.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_tifffile-1.30.3.dev3.dist-info/METADATA,sha256=nnofjz9ZvnNmT7jJOXkEBhJyDyw3WlTjW5mvCRLY-_w,1149
+large_image_source_tifffile-1.30.3.dev3.dist-info/WHEEL,sha256=OVMc5UfuAQiSplgO0_WdW7vXVGAt9Hdd6qtN4HotdyA,91
+large_image_source_tifffile-1.30.3.dev3.dist-info/entry_points.txt,sha256=aILCN5f7-Zj8-WRXcABxCQvqJv9VLTvqRhZ_7HEyokc,190
+large_image_source_tifffile-1.30.3.dev3.dist-info/top_level.txt,sha256=feOAsix2Rzy6mjy2Ua-N0-L6tlKsgvLdRhO6Hd8_ZFs,28
+large_image_source_tifffile-1.30.3.dev3.dist-info/RECORD,,

{large_image_source_tifffile-1.30.3.dist-info → large_image_source_tifffile-1.30.3.dev3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (75.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

large_image_source_tifffile-1.30.3.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_tifffile/__init__.py,sha256=DKDo0CHba44iLEi9B_Rr59iodoRaPFOdyYC8yfKFMx8,28136
-large_image_source_tifffile/girder_source.py,sha256=8YsxpSK_UzbAcpjn6fIMlgKye2FchkB8_HTSQV0FpRA,1064
-large_image_source_tifffile-1.30.3.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_tifffile-1.30.3.dist-info/METADATA,sha256=O1qT-jo5t1g0wkTZNrNMfZiC-BhI2C63OMeMxwXeQxs,1131
-large_image_source_tifffile-1.30.3.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-large_image_source_tifffile-1.30.3.dist-info/entry_points.txt,sha256=aILCN5f7-Zj8-WRXcABxCQvqJv9VLTvqRhZ_7HEyokc,190
-large_image_source_tifffile-1.30.3.dist-info/top_level.txt,sha256=feOAsix2Rzy6mjy2Ua-N0-L6tlKsgvLdRhO6Hd8_ZFs,28
-large_image_source_tifffile-1.30.3.dist-info/RECORD,,