large-image-source-ometiff 1.27.5.dev6__py3-none-any.whl → 1.30.7.dev12__py3-none-any.whl

large_image_source_ometiff/__init__.py

@@ -105,6 +105,7 @@ class OMETiffFileTileSource(TiffFileTileSource, metaclass=LruCacheMetaclass):
             msg = 'Not a recognized OME Tiff'
             raise TileSourceError(msg)
         info = getattr(base, '_description_record', None)
+        self._associatedImages = {}
         if not info or not info.get('OME'):
             msg = 'Not an OME Tiff'
             raise TileSourceError(msg)
@@ -115,6 +116,7 @@ class OMETiffFileTileSource(TiffFileTileSource, metaclass=LruCacheMetaclass):
         except KeyError:
             msg = 'Not a recognized OME Tiff'
             raise TileSourceError(msg)
+        usesSubIfds = self._checkForSubIfds(base)
         omeimages = [
             entry['Pixels'] for entry in self._omeinfo['Image'] if
             len(entry['Pixels']['TiffData']) == len(self._omebase['TiffData'])]
@@ -125,10 +127,16 @@ class OMETiffFileTileSource(TiffFileTileSource, metaclass=LruCacheMetaclass):
         omebylevel = dict(zip(levels, omeimages))
         self._omeLevels = [omebylevel.get(key) for key in range(max(omebylevel.keys()) + 1)]
         if base._tiffInfo.get('istiled'):
+            if usesSubIfds:
+                self._omeLevels = [None] * max(usesSubIfds) + [self._omeLevels[-1]]
             self._tiffDirectories = [
                 self.getTiffDir(int(entry['TiffData'][0].get('IFD', 0)))
                 if entry else None
                 for entry in self._omeLevels]
+            if usesSubIfds:
+                for lvl in usesSubIfds:
+                    if self._tiffDirectories[lvl] is None:
+                        self._tiffDirectories[lvl] = False
         else:
             self._tiffDirectories = [
                 self.getTiffDir(0, mustBeTiled=None)
@@ -149,7 +157,6 @@ class OMETiffFileTileSource(TiffFileTileSource, metaclass=LruCacheMetaclass):
         # We can get the embedded images, but we don't currently use non-tiled
         # images as associated images.  This would require enumerating tiff
         # directories not mentioned by the ome list.
-        self._associatedImages = {}
         self._checkForInefficientDirectories()
 
     def _checkForOMEZLoop(self):
@@ -199,10 +206,47 @@ class OMETiffFileTileSource(TiffFileTileSource, metaclass=LruCacheMetaclass):
         info['Image']['Pixels']['PlanesFromZloop'] = 'true'
         info['Image']['Pixels']['SizeZ'] = str(zloop)
 
+    def _checkForSubIfds(self, base):
+        """
+        Check if the first ifd has sub-ifds.  If so, expect lower resolutions
+        to be in subifds, not in primary ifds.
+
+        :param base: base tiff directory
+        :returns: either False if no subifds are lower resolution, or a
+            dictionary of levels (keys) and values that are subifd numbers.
+        """
+        try:
+            levels = int(max(0, math.ceil(max(
+                math.log(float(base.imageWidth) / base.tileWidth),
+                math.log(float(base.imageHeight) / base.tileHeight)) / math.log(2))) + 1)
+            filled = {}
+            for z in range(levels - 2, -1, -1):
+                subdir = levels - 1 - z
+                scale = int(2 ** subdir)
+                try:
+                    dir = self.getTiffDir(0, mustBeTiled=True, subDirectoryNum=subdir)
+                except Exception:
+                    continue
+                if (dir is not None and
+                        (dir.tileWidth in {base.tileWidth, dir.imageWidth}) and
+                        (dir.tileHeight in {base.tileHeight, dir.imageHeight}) and
+                        abs(dir.imageWidth * scale - base.imageWidth) <= scale and
+                        abs(dir.imageHeight * scale - base.imageHeight) <= scale):
+                    filled[z] = subdir
+            if not len(filled):
+                return False
+            filled[levels - 1] = 0
+            return filled
+        except TiffError:
+            return False
+
     def _parseOMEInfo(self):  # noqa
         if isinstance(self._omeinfo['Image'], dict):
             self._omeinfo['Image'] = [self._omeinfo['Image']]
         for img in self._omeinfo['Image']:
+            if isinstance(img['Pixels'], list):
+                msg = 'OME Tiff has multiple pixels'
+                raise TileSourceError(msg)
             if isinstance(img['Pixels'].get('TiffData'), dict):
                 img['Pixels']['TiffData'] = [img['Pixels']['TiffData']]
             if isinstance(img['Pixels'].get('Plane'), dict):
@@ -241,6 +285,32 @@ class OMETiffFileTileSource(TiffFileTileSource, metaclass=LruCacheMetaclass):
                     for entry in self._omebase['TiffData']}) > 1:
                 msg = 'OME Tiff references multiple files'
                 raise TileSourceError(msg)
+            if (len(self._omebase['TiffData']) ==
+                    int(self._omebase['SizeT']) * int(self._omebase['SizeZ'])):
+                self._omebase['SizeC'] = 1
+                for img in self._omeinfo['Image'][1:]:
+                    try:
+                        if img['Name'] and img['Pixels']['TiffData'][0]['IFD']:
+                            self._addAssociatedImage(
+                                int(img['Pixels']['TiffData'][0]['IFD']),
+                                None, None, img['Name'].split()[0])
+                    except Exception:
+                        pass
+            elif len(self._omeinfo['Image']) > 1:
+                multiple = False
+                for img in self._omeinfo['Image'][1:]:
+                    try:
+                        bpix = self._omeinfo['Image'][0]['Pixels']
+                        imgpix = img['Pixels']
+                        if imgpix['SizeX'] == bpix['SizeX'] and imgpix['SizeY'] == bpix['SizeY']:
+                            multiple = True
+                            break
+                    except Exception:
+                        multiple = True
+                if multiple:
+                    # We should handle this as SizeXY
+                    msg = 'OME Tiff references multiple images'
+                    raise TileSourceError(msg)
             if (len(self._omebase['TiffData']) != int(self._omebase['SizeC']) *
                     int(self._omebase['SizeT']) * int(self._omebase['SizeZ']) or
                     len(self._omebase['TiffData']) != len(
@@ -343,8 +413,8 @@ class OMETiffFileTileSource(TiffFileTileSource, metaclass=LruCacheMetaclass):
         if subdir:
             scale = int(2 ** subdir)
             if (dir is None or
-                    (dir.tileWidth != self.tileWidth and dir.tileWidth != dir.imageWidth) or
-                    (dir.tileHeight != self.tileHeight and dir.tileHeight != dir.imageHeight) or
+                    (dir.tileWidth not in {self.tileWidth, dir.imageWidth}) or
+                    (dir.tileHeight not in {self.tileHeight, dir.imageHeight}) or
                     abs(dir.imageWidth * scale - self.sizeX) > scale or
                     abs(dir.imageHeight * scale - self.sizeY) > scale):
                 return super().getTile(

{large_image_source_ometiff-1.27.5.dev6.dist-info → large_image_source_ometiff-1.30.7.dev12.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: large-image-source-ometiff
-Version: 1.27.5.dev6
+Version: 1.30.7.dev12
 Summary: An OMETiff tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -15,12 +15,26 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image >=1.27.5.dev6
-Requires-Dist: large-image-source-tiff >=1.27.5.dev6
+Requires-Dist: large-image>=1.30.7.dev12
+Requires-Dist: large-image-source-tiff>=1.30.7.dev12
 Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.27.5.dev6 ; extra == 'girder'
+Requires-Dist: girder-large-image>=1.30.7.dev12; extra == "girder"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 An OMETiff tilesource for large_image.
 

large_image_source_ometiff-1.30.7.dev12.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_ometiff/__init__.py,sha256=r3Ii965r6Y8m9D7eRnYmyG58aLkXyXULMIv8XV9Y_lQ,20634
+large_image_source_ometiff/girder_source.py,sha256=QotYLsC_JY3pOixVOXZ_wwtHJABSuWw_f_8Q5pDnNWo,1047
+large_image_source_ometiff-1.30.7.dev12.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_ometiff-1.30.7.dev12.dist-info/METADATA,sha256=SoWIIh7cakdNmptH0fo6msVPd7S2_z4v3NGCsIxpZfo,1381
+large_image_source_ometiff-1.30.7.dev12.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+large_image_source_ometiff-1.30.7.dev12.dist-info/entry_points.txt,sha256=-xiaxFJTzRayHYwLkPsBXF0grk8j5nQy5cizSazP404,184
+large_image_source_ometiff-1.30.7.dev12.dist-info/top_level.txt,sha256=Me0pziNZRmyYLdGAKu9zgDHHINn_7ayKLLYxTGXv5lo,27
+large_image_source_ometiff-1.30.7.dev12.dist-info/RECORD,,

{large_image_source_ometiff-1.27.5.dev6.dist-info → large_image_source_ometiff-1.30.7.dev12.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

large_image_source_ometiff-1.27.5.dev6.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_ometiff/__init__.py,sha256=ufxVdvDPSk1QwoIBSAyfwB6EHI78FnDnQPqO9Lx1PYU,17350
-large_image_source_ometiff/girder_source.py,sha256=QotYLsC_JY3pOixVOXZ_wwtHJABSuWw_f_8Q5pDnNWo,1047
-large_image_source_ometiff-1.27.5.dev6.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_ometiff-1.27.5.dev6.dist-info/METADATA,sha256=eUR9Pnq1KdvrtXNhnpd6L1Xqsxwp7iLaAm1Y_MHL6hM,1037
-large_image_source_ometiff-1.27.5.dev6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-large_image_source_ometiff-1.27.5.dev6.dist-info/entry_points.txt,sha256=-xiaxFJTzRayHYwLkPsBXF0grk8j5nQy5cizSazP404,184
-large_image_source_ometiff-1.27.5.dev6.dist-info/top_level.txt,sha256=Me0pziNZRmyYLdGAKu9zgDHHINn_7ayKLLYxTGXv5lo,27
-large_image_source_ometiff-1.27.5.dev6.dist-info/RECORD,,