large-image-source-tifffile 1.29.2.dev25__py3-none-any.whl → 1.29.3__py3-none-any.whl

large_image_source_tifffile/__init__.py

@@ -7,7 +7,6 @@ from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 
 import numpy as np
-import zarr
 
 import large_image
 from large_image.cache_util import LruCacheMetaclass, methodcache
@@ -16,6 +15,7 @@ from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError
 from large_image.tilesource import FileTileSource
 
 tifffile = None
+zarr = None
 
 try:
     __version__ = _importlib_version(__name__)
@@ -37,6 +37,7 @@ def _lazyImport():
     module initialization because it is slow.
     """
     global tifffile
+    global zarr
 
     if tifffile is None:
         try:
@@ -55,6 +56,8 @@ def _lazyImport():
         logging.getLogger('tifffile.tifffile').addHandler(checkForMissingDataHandler())
         logging.getLogger('tifffile').setLevel(logging.WARNING)
         logging.getLogger('tifffile').addHandler(checkForMissingDataHandler())
+    if zarr is None:
+        import zarr
 
 
 def et_findall(tag, text):
@@ -351,6 +354,63 @@ 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.

{large_image_source_tifffile-1.29.2.dev25.dist-info → large_image_source_tifffile-1.29.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tifffile
-Version: 1.29.2.dev25
+Version: 1.29.3
 Summary: A tifffile tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -17,12 +17,12 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.8
 License-File: LICENSE
-Requires-Dist: large-image >=1.29.2.dev25
+Requires-Dist: large-image >=1.29.3
 Requires-Dist: dask[array]
 Requires-Dist: tifffile[all]
 Requires-Dist: zarr
 Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.29.2.dev25 ; extra == 'girder'
+Requires-Dist: girder-large-image >=1.29.3 ; extra == 'girder'
 
 A tifffile tilesource for large_image.
 

large_image_source_tifffile-1.29.3.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_tifffile/__init__.py,sha256=f7U3_Fkaqy8G6kJL1i4sC45RhQBbpQ3JLGLIJutoWgM,26877
+large_image_source_tifffile/girder_source.py,sha256=8YsxpSK_UzbAcpjn6fIMlgKye2FchkB8_HTSQV0FpRA,1064
+large_image_source_tifffile-1.29.3.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_tifffile-1.29.3.dist-info/METADATA,sha256=fqEjj7z0QqVbkpBOoN2aYROtliv3Pk-QVaVhTWbJ3SQ,1046
+large_image_source_tifffile-1.29.3.dist-info/WHEEL,sha256=-oYQCr74JF3a37z2nRlQays_SX2MqOANoqVjBBAP2yE,91
+large_image_source_tifffile-1.29.3.dist-info/entry_points.txt,sha256=aILCN5f7-Zj8-WRXcABxCQvqJv9VLTvqRhZ_7HEyokc,190
+large_image_source_tifffile-1.29.3.dist-info/top_level.txt,sha256=feOAsix2Rzy6mjy2Ua-N0-L6tlKsgvLdRhO6Hd8_ZFs,28
+large_image_source_tifffile-1.29.3.dist-info/RECORD,,

{large_image_source_tifffile-1.29.2.dev25.dist-info → large_image_source_tifffile-1.29.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (70.3.0)
+Generator: setuptools (71.0.3)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

large_image_source_tifffile-1.29.2.dev25.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_tifffile/__init__.py,sha256=7hREWGbhyYOcz94l_vxMAOTUSJKtJY37TEIZdkvamNw,25001
-large_image_source_tifffile/girder_source.py,sha256=8YsxpSK_UzbAcpjn6fIMlgKye2FchkB8_HTSQV0FpRA,1064
-large_image_source_tifffile-1.29.2.dev25.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_tifffile-1.29.2.dev25.dist-info/METADATA,sha256=V5mA4EXX-iIJBLr7wVJ_EXkwxoALYZuj2QBRaqdIw4Y,1064
-large_image_source_tifffile-1.29.2.dev25.dist-info/WHEEL,sha256=Z4pYXqR_rTB7OWNDYFOm1qRk0RX6GFP2o8LgvP453Hk,91
-large_image_source_tifffile-1.29.2.dev25.dist-info/entry_points.txt,sha256=aILCN5f7-Zj8-WRXcABxCQvqJv9VLTvqRhZ_7HEyokc,190
-large_image_source_tifffile-1.29.2.dev25.dist-info/top_level.txt,sha256=feOAsix2Rzy6mjy2Ua-N0-L6tlKsgvLdRhO6Hd8_ZFs,28
-large_image_source_tifffile-1.29.2.dev25.dist-info/RECORD,,