large-image-source-openslide 1.30.3.dev35__py3-none-any.whl → 1.33.6a165__py3-none-any.whl

large_image_source_openslide/__init__.py

@@ -20,6 +20,7 @@ import os
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 
+import numpy as np
 import openslide
 import PIL
 import tifftools
@@ -47,12 +48,13 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     extensions = {
         None: SourcePriority.MEDIUM,
         'bif': SourcePriority.LOW,  # Ventana
-        'dcm': SourcePriority.LOW,  # DICOM
+        'czi': SourcePriority.PREFERRED,
+        'dcm': SourcePriority.MEDIUM,  # DICOM
         'ini': SourcePriority.LOW,  # Part of mrxs
         'mrxs': SourcePriority.PREFERRED,  # MIRAX
         'ndpi': SourcePriority.PREFERRED,  # Hamamatsu
         'scn': SourcePriority.LOW,  # Leica
-        'svs': SourcePriority.PREFERRED,
+        'svs': SourcePriority.HIGH,
         'svslide': SourcePriority.PREFERRED,
         'tif': SourcePriority.MEDIUM,
         'tiff': SourcePriority.MEDIUM,
@@ -61,6 +63,8 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     }
     mimeTypes = {
         None: SourcePriority.FALLBACK,
+        'image/czi': SourcePriority.PREFERRED,
+        'application/dicom': SourcePriority.MEDIUM,
         'image/mirax': SourcePriority.PREFERRED,  # MIRAX
         'image/tiff': SourcePriority.MEDIUM,
         'image/x-tiff': SourcePriority.MEDIUM,
@@ -94,6 +98,13 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     tifftools.Tag.ICCProfile.value]['data']]
         except Exception:
             pass
+        if hasattr(self, '_tiffinfo'):
+            for ifd in self._tiffinfo['ifds']:
+                if (tifftools.Tag.NDPI_FOCAL_PLANE.value in ifd['tags'] and
+                        ifd['tags'][tifftools.Tag.NDPI_FOCAL_PLANE.value]['data'][0] != 0):
+                    msg = ('File will not be opened via OpenSlide; '
+                           'non-zero focal planes would be missed.')
+                    raise TileSourceError(msg)
 
         svsAvailableLevels = self._getAvailableLevels(self._largeImagePath)
         if not len(svsAvailableLevels):
@@ -128,19 +139,22 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         # load an appropriate area and scale it to the tile size later.
         maxSize = 16384   # This should probably be based on available memory
         for level in range(self.levels):
-            levelW = max(1, self.sizeX / 2 ** (self.levels - 1 - level))
-            levelH = max(1, self.sizeY / 2 ** (self.levels - 1 - level))
+            levelpow = 2 ** (self.levels - 1 - level)
+            levelW = max(1, self.sizeX / levelpow)
+            levelH = max(1, self.sizeY / levelpow)
             # bestlevel and scale will be the picked svs level and the scale
             # between that level and what we really wanted.  We expect scale to
             # always be a positive integer power of two.
             bestlevel = svsAvailableLevels[0]['level']
             scale = 1
+            svsscale = 0
             for svslevel in range(len(svsAvailableLevels)):
                 if (svsAvailableLevels[svslevel]['width'] < levelW - 1 or
                         svsAvailableLevels[svslevel]['height'] < levelH - 1):
                     break
                 bestlevel = svsAvailableLevels[svslevel]['level']
                 scale = int(round(svsAvailableLevels[svslevel]['width'] / levelW))
+                svsscale = svsAvailableLevels[svslevel].get('downsample', 0)
             # If there are no tiles at a particular level, we have to read a
             # larger area of a higher resolution level.  If such an area would
             # be excessively large, we could have memory issues, so raise an
@@ -154,6 +168,7 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             self._svslevels.append({
                 'svslevel': bestlevel,
                 'scale': scale,
+                'svsscale': ((svsscale / levelpow) if svsscale else 1) * scale,
             })
         self._bounds = None
         try:
@@ -179,6 +194,12 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 self._svslevels = self._svslevels[prevlevels - self.levels:]
         except Exception:
             pass
+        try:
+            self._background = tuple(int(
+                self._openslide.properties['openslide.background-color']
+                [i * 2:i * 2 + 2], 16) for i in range(3))
+        except Exception:
+            self._background = None
         self._populatedLevels = len({l['svslevel'] for l in self._svslevels})
 
     def _getTileSize(self):
@@ -228,6 +249,7 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         """
         levels = []
         svsLevelDimensions = self._openslide.level_dimensions
+
         for svslevel in range(len(svsLevelDimensions)):
             try:
                 self._openslide.read_region((0, 0), svslevel, (1, 1))
@@ -236,6 +258,10 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     'width': svsLevelDimensions[svslevel][0],
                     'height': svsLevelDimensions[svslevel][1],
                 }
+                try:
+                    level['downsample'] = self._openslide.level_downsamples[svslevel]
+                except Exception:
+                    pass
                 if level['width'] > 0 and level['height'] > 0:
                     # add to the list so that we can sort by resolution and
                     # then by earlier entries
@@ -327,12 +353,31 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             tile, format = self._getTileFromEmptyLevel(x, y, z, **kwargs)
         else:
             retries = 3
+            svsTileWidth = self.tileWidth * svslevel['scale']
+            svsTileHeight = self.tileHeight * svslevel['scale']
+            # Peculiarly, openslide has a "downsample" factor which isn't the
+            # power of 2 one would expect.  This is computed based on the
+            # actual dimensions of levels, but since higher-resolution levels
+            # are not fully populated at the right and bottom, this ends up
+            # with not the actual downsampling, but some slightly higher number
+            # (e.g., 16.0018 rather than 16).  Internally, when asking for a
+            # region for anything other than the maximum resolution lever, the
+            # openslide library is passed coordinates in what _seems_ to be
+            # base image coordinates, but is actually inflated by the ratio of
+            # their downsample value and the actual downsample value (e.g.,
+            # 16.0018 / 16).  We multiple our values by this ratio so when
+            # openslide misapplies its downsampling we get the region we
+            # actually want
+            if svslevel['svsscale'] != 1:
+                offsetx = int(round(offsetx * svslevel['svsscale']))
+                offsety = int(round(offsety * svslevel['svsscale']))
+                svsTileWidth = int(round(svsTileWidth * svslevel['svsscale']))
+                svsTileHeight = int(round(svsTileHeight * svslevel['svsscale']))
             while retries > 0:
                 try:
                     tile = self._openslide.read_region(
                         (offsetx, offsety), svslevel['svslevel'],
-                        (self.tileWidth * svslevel['scale'],
-                         self.tileHeight * svslevel['scale']))
+                        (svsTileWidth, svsTileHeight))
                     format = TILE_FORMAT_PIL
                     break
                 except openslide.lowlevel.OpenSlideError as exc:
@@ -349,6 +394,10 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     retries -= 1
                     if retries <= 0:
                         raise TileSourceError(msg)
+            if tile.mode == 'RGBA' and self._background:
+                tile = np.array(tile)
+                tile[tile[:, :, -1] == 0, :3] = self._background
+                tile = PIL.Image.fromarray(tile, 'RGBA')
             # Always scale to the svs level 0 tile size.
             if svslevel['scale'] != 1:
                 tile = tile.resize((self.tileWidth, self.tileHeight),

large_image_source_openslide/girder_source.py

@@ -28,5 +28,5 @@ class OpenslideGirderTileSource(OpenslideFileTileSource, GirderTileSource):
     cacheName = 'tilesource'
     name = 'openslide'
 
-    extensionsWithAdjacentFiles = {'mrxs'}
-    mimeTypesWithAdjacentFiles = {'image/mirax'}
+    extensionsWithAdjacentFiles = {'mrxs', 'dcm', 'dicom'}
+    mimeTypesWithAdjacentFiles = {'image/mirax', 'application/dicom'}

{large_image_source_openslide-1.30.3.dev35.dist-info → large_image_source_openslide-1.33.6a165.dist-info}/METADATA

@@ -1,25 +1,24 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: large-image-source-openslide
-Version: 1.30.3.dev35
+Version: 1.33.6a165
 Summary: An Openslide tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
 Author-email: kitware@kitware.com
-License: Apache Software License 2.0
+License: Apache-2.0
 Keywords: large_image,tile source
 Classifier: Development Status :: 5 - Production/Stable
-Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 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
+Classifier: Programming Language :: Python :: 3.14
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.30.3.dev35
+Requires-Dist: large-image>=1.33.6.a165
 Requires-Dist: openslide-python>=1.4.1
 Requires-Dist: openslide-bin; platform_system == "Linux" and platform_machine == "x86_64"
 Requires-Dist: openslide-bin; platform_system == "Linux" and platform_machine == "aarch64"
@@ -28,7 +27,20 @@ Requires-Dist: openslide-bin; platform_system == "Darwin" and platform_machine =
 Requires-Dist: openslide-bin; platform_system == "Darwin" and platform_machine == "x86_64"
 Requires-Dist: tifftools>=1.2.0
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.3.dev35; extra == "girder"
+Requires-Dist: girder-large-image>=1.33.6.a165; extra == "girder"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 An Openslide tilesource for large_image.
 

large_image_source_openslide-1.33.6a165.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_openslide/__init__.py,sha256=CEfTufsAco3V87GHdRtJz7KbIuLrgu1vGyc5-dtOXd4,22822
+large_image_source_openslide/girder_source.py,sha256=wPa7xBoJ5-PKHMVy9joUNSUHTN6HCZKyR45lhR0SsRc,1236
+large_image_source_openslide-1.33.6a165.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_openslide-1.33.6a165.dist-info/METADATA,sha256=XApXY6AO8gL5WbeS8nvvWYjrUSQQEgGc9Qe2avit_mM,1797
+large_image_source_openslide-1.33.6a165.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+large_image_source_openslide-1.33.6a165.dist-info/entry_points.txt,sha256=4Z5cf63yeesvHxiR9W1dY3rfz5_V4Ck2xYhPUp4A1qA,196
+large_image_source_openslide-1.33.6a165.dist-info/top_level.txt,sha256=wqaQQDWQl9a_l9s6n07tTxfjeEXePtHBhz1np6aUwQE,29
+large_image_source_openslide-1.33.6a165.dist-info/RECORD,,

{large_image_source_openslide-1.30.3.dev35.dist-info → large_image_source_openslide-1.33.6a165.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.6.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

large_image_source_openslide-1.30.3.dev35.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_openslide/__init__.py,sha256=Ql2nXz2XuIySbrEse0gf-oRBmKD0ugQztLAVjOj5UF0,20056
-large_image_source_openslide/girder_source.py,sha256=ntLgOinO7xcO85wFbjx6XEBmTgEtx5cuPZ_K6wXZzqA,1199
-large_image_source_openslide-1.30.3.dev35.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_openslide-1.30.3.dev35.dist-info/METADATA,sha256=DXzCXqED-xYQ4VqsLViWr4t6bTLfZiTIZzw9I-TyeNk,1602
-large_image_source_openslide-1.30.3.dev35.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
-large_image_source_openslide-1.30.3.dev35.dist-info/entry_points.txt,sha256=4Z5cf63yeesvHxiR9W1dY3rfz5_V4Ck2xYhPUp4A1qA,196
-large_image_source_openslide-1.30.3.dev35.dist-info/top_level.txt,sha256=wqaQQDWQl9a_l9s6n07tTxfjeEXePtHBhz1np6aUwQE,29
-large_image_source_openslide-1.30.3.dev35.dist-info/RECORD,,