large-image-source-tifffile 1.30.3.dev17__tar.gz → 1.30.3.dev21__tar.gz

{large_image_source_tifffile-1.30.3.dev17 → large_image_source_tifffile-1.30.3.dev21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tifffile
-Version: 1.30.3.dev17
+Version: 1.30.3.dev21
 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.dev17
+Requires-Dist: large-image>=1.30.3.dev21
 Requires-Dist: dask[array]
 Requires-Dist: tifffile[all]
 Requires-Dist: zarr
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.3.dev17; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.3.dev21; extra == "girder"
 
 A tifffile tilesource for large_image.
 

{large_image_source_tifffile-1.30.3.dev17 → large_image_source_tifffile-1.30.3.dev21}/large_image_source_tifffile/__init__.py

@@ -292,68 +292,19 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         except Exception:
             pass
 
-    def _handle_scn(self):  # noqa
-        """
-        For SCN files, parse the xml and possibly adjust how associated images
-        are labelled.
-        """
+    def _handle_indica(self):
         import xml.etree.ElementTree
 
         import large_image.tilesource.utilities
 
-        root = xml.etree.ElementTree.fromstring(self._tf.pages[0].description)
-        self._xml = large_image.tilesource.utilities.etreeToDict(root)
-        for collection in et_findall(root, 'collection'):
-            sizeX = collection.attrib.get('sizeX')
-            sizeY = collection.attrib.get('sizeY')
-            for supplementalImage in et_findall(collection, 'supplementalImage'):
-                name = supplementalImage.attrib.get('type', '').lower()
-                ifd = supplementalImage.attrib.get('ifd', '')
-                oldname = 'image_%s' % ifd
-                if (name and ifd and oldname in self._associatedImages and
-                        name not in self._associatedImages):
-                    self._associatedImages[name] = self._associatedImages[oldname]
-                    self._associatedImages.pop(oldname, None)
-            for image in et_findall(collection, 'image'):
-                name = image.attrib.get('name', 'Unknown')
-                for view in et_findall(image, 'view'):
-                    if (sizeX and view.attrib.get('sizeX') == sizeX and
-                            sizeY and view.attrib.get('sizeY') == sizeY and
-                            not int(view.attrib.get('offsetX')) and
-                            not int(view.attrib.get('offsetY')) and
-                            name.lower() in self._associatedImages and
-                            'macro' not in self._associatedImages):
-                        self._associatedImages['macro'] = self._associatedImages[name.lower()]
-                        self._associatedImages.pop(name.lower(), None)
-                if name != self._baseSeries.name:
-                    continue
-                for scanSettings in et_findall(image, 'scanSettings'):
-                    for objectiveSettings in et_findall(scanSettings, 'objectiveSettings'):
-                        for objective in et_findall(objectiveSettings, 'objective'):
-                            if not hasattr(self, '_magnification') and float(objective.text) > 0:
-                                self._magnification = float(objective.text)
-                    for channelSettings in et_findall(scanSettings, 'channelSettings'):
-                        channels = {}
-                        for channel in et_findall(channelSettings, 'channel'):
-                            channels[int(channel.attrib.get('index', 0))] = (
-                                large_image.tilesource.utilities.etreeToDict(channel)['channel'])
-                        self._channelInfo = channels
-                        try:
-                            self._channels = [
-                                channels.get(idx)['name'].split('|')[0]
-                                for idx in range(len(channels))]
-                        except Exception:
-                            pass
-
-    def _handle_svs(self):
-        """
-        For SVS files, parse the magnification and pixel size.
-        """
         try:
-            meta = self._tf.pages[0].description
-            self._magnification = float(meta.split('AppMag = ')[1].split('|')[0].strip())
-            self._mm_x = self._mm_y = float(
-                meta.split('|MPP = ', 1)[1].split('|')[0].strip()) * 0.001
+            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
 
@@ -414,6 +365,71 @@ class TifffileFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         except Exception:
             pass
 
+    def _handle_scn(self):  # noqa
+        """
+        For SCN files, parse the xml and possibly adjust how associated images
+        are labelled.
+        """
+        import xml.etree.ElementTree
+
+        import large_image.tilesource.utilities
+
+        root = xml.etree.ElementTree.fromstring(self._tf.pages[0].description)
+        self._xml = large_image.tilesource.utilities.etreeToDict(root)
+        for collection in et_findall(root, 'collection'):
+            sizeX = collection.attrib.get('sizeX')
+            sizeY = collection.attrib.get('sizeY')
+            for supplementalImage in et_findall(collection, 'supplementalImage'):
+                name = supplementalImage.attrib.get('type', '').lower()
+                ifd = supplementalImage.attrib.get('ifd', '')
+                oldname = 'image_%s' % ifd
+                if (name and ifd and oldname in self._associatedImages and
+                        name not in self._associatedImages):
+                    self._associatedImages[name] = self._associatedImages[oldname]
+                    self._associatedImages.pop(oldname, None)
+            for image in et_findall(collection, 'image'):
+                name = image.attrib.get('name', 'Unknown')
+                for view in et_findall(image, 'view'):
+                    if (sizeX and view.attrib.get('sizeX') == sizeX and
+                            sizeY and view.attrib.get('sizeY') == sizeY and
+                            not int(view.attrib.get('offsetX')) and
+                            not int(view.attrib.get('offsetY')) and
+                            name.lower() in self._associatedImages and
+                            'macro' not in self._associatedImages):
+                        self._associatedImages['macro'] = self._associatedImages[name.lower()]
+                        self._associatedImages.pop(name.lower(), None)
+                if name != self._baseSeries.name:
+                    continue
+                for scanSettings in et_findall(image, 'scanSettings'):
+                    for objectiveSettings in et_findall(scanSettings, 'objectiveSettings'):
+                        for objective in et_findall(objectiveSettings, 'objective'):
+                            if not hasattr(self, '_magnification') and float(objective.text) > 0:
+                                self._magnification = float(objective.text)
+                    for channelSettings in et_findall(scanSettings, 'channelSettings'):
+                        channels = {}
+                        for channel in et_findall(channelSettings, 'channel'):
+                            channels[int(channel.attrib.get('index', 0))] = (
+                                large_image.tilesource.utilities.etreeToDict(channel)['channel'])
+                        self._channelInfo = channels
+                        try:
+                            self._channels = [
+                                channels.get(idx)['name'].split('|')[0]
+                                for idx in range(len(channels))]
+                        except Exception:
+                            pass
+
+    def _handle_svs(self):
+        """
+        For SVS files, parse the magnification and pixel size.
+        """
+        try:
+            meta = self._tf.pages[0].description
+            self._magnification = float(meta.split('AppMag = ')[1].split('|')[0].strip())
+            self._mm_x = self._mm_y = float(
+                meta.split('|MPP = ', 1)[1].split('|')[0].strip()) * 0.001
+        except Exception:
+            pass
+
     def getNativeMagnification(self):
         """
         Get the magnification at a particular level.
@@ -623,6 +639,8 @@ 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.dev17 → large_image_source_tifffile-1.30.3.dev21}/large_image_source_tifffile.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-tifffile
-Version: 1.30.3.dev17
+Version: 1.30.3.dev21
 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.dev17
+Requires-Dist: large-image>=1.30.3.dev21
 Requires-Dist: dask[array]
 Requires-Dist: tifffile[all]
 Requires-Dist: zarr
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.3.dev17; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.3.dev21; extra == "girder"
 
 A tifffile tilesource for large_image.
 

large_image_source_tifffile-1.30.3.dev21/large_image_source_tifffile.egg-info/requires.txt

@@ -0,0 +1,7 @@
+large-image>=1.30.3.dev21
+dask[array]
+tifffile[all]
+zarr
+
+[girder]
+girder-large-image>=1.30.3.dev21

large_image_source_tifffile-1.30.3.dev17/large_image_source_tifffile.egg-info/requires.txt

@@ -1,7 +0,0 @@
-large-image>=1.30.3.dev17
-dask[array]
-tifffile[all]
-zarr
-
-[girder]
-girder-large-image>=1.30.3.dev17