large-image-source-openslide 1.27.5.dev4__py3-none-any.whl → 1.30.7.dev10__py3-none-any.whl

large_image_source_openslide/__init__.py

@@ -47,6 +47,8 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     extensions = {
         None: SourcePriority.MEDIUM,
         'bif': SourcePriority.LOW,  # Ventana
+        'dcm': SourcePriority.LOW,  # DICOM
+        'ini': SourcePriority.LOW,  # Part of mrxs
         'mrxs': SourcePriority.PREFERRED,  # MIRAX
         'ndpi': SourcePriority.PREFERRED,  # Hamamatsu
         'scn': SourcePriority.LOW,  # Leica
@@ -92,6 +94,13 @@ 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):
@@ -153,6 +162,30 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 'svslevel': bestlevel,
                 'scale': scale,
             })
+        self._bounds = None
+        try:
+            bounds = {
+                'x': int(self._openslide.properties[openslide.PROPERTY_NAME_BOUNDS_X]),
+                'y': int(self._openslide.properties[openslide.PROPERTY_NAME_BOUNDS_Y]),
+                'width': int(self._openslide.properties[openslide.PROPERTY_NAME_BOUNDS_WIDTH]),
+                'height': int(self._openslide.properties[openslide.PROPERTY_NAME_BOUNDS_HEIGHT]),
+            }
+            if (
+                bounds['x'] >= 0 and bounds['width'] > 0 and
+                bounds['x'] + bounds['width'] <= self.sizeX and
+                bounds['y'] >= 0 and bounds['height'] > 0 and
+                bounds['y'] + bounds['height'] <= self.sizeY and
+                (bounds['width'] < self.sizeX or bounds['height'] < self.sizeY)
+            ):
+                self._bounds = bounds
+                self.sizeX, self.sizeY = bounds['width'], bounds['height']
+                prevlevels = self.levels
+                self.levels = int(math.ceil(max(
+                    math.log(float(self.sizeX) / self.tileWidth),
+                    math.log(float(self.sizeY) / self.tileHeight)) / math.log(2))) + 1
+                self._svslevels = self._svslevels[prevlevels - self.levels:]
+        except Exception:
+            pass
         self._populatedLevels = len({l['svslevel'] for l in self._svslevels})
 
     def _getTileSize(self):
@@ -291,11 +324,14 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         scale = 2 ** (self.levels - 1 - z)
         offsetx = x * self.tileWidth * scale
         offsety = y * self.tileHeight * scale
+        if self._bounds is not None:
+            offsetx += self._bounds['x'] // svslevel['scale']
+            offsety += self._bounds['y'] // svslevel['scale']
         # We ask to read an area that will cover the tile at the z level.  The
         # scale we computed in the __init__ process for this svs level tells
         # how much larger a region we need to read.
         if svslevel['scale'] > 2 ** self._maxSkippedLevels:
-            tile = self._getTileFromEmptyLevel(x, y, z, **kwargs)
+            tile, format = self._getTileFromEmptyLevel(x, y, z, **kwargs)
         else:
             retries = 3
             while retries > 0:
@@ -304,6 +340,7 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                         (offsetx, offsety), svslevel['svslevel'],
                         (self.tileWidth * svslevel['scale'],
                          self.tileHeight * svslevel['scale']))
+                    format = TILE_FORMAT_PIL
                     break
                 except openslide.lowlevel.OpenSlideError as exc:
                     self._largeImagePath = str(self._getLargeImagePath())
@@ -323,7 +360,7 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             if svslevel['scale'] != 1:
                 tile = tile.resize((self.tileWidth, self.tileHeight),
                                    getattr(PIL.Image, 'Resampling', PIL.Image).LANCZOS)
-        return self._outputTile(tile, TILE_FORMAT_PIL, x, y, z, pilImageAllowed,
+        return self._outputTile(tile, format, x, y, z, pilImageAllowed,
                                 numpyAllowed, **kwargs)
 
     def getPreferredLevel(self, level):

large_image_source_openslide-1.30.7.dev10.dist-info/METADATA

@@ -0,0 +1,47 @@
+Metadata-Version: 2.2
+Name: large-image-source-openslide
+Version: 1.30.7.dev10
+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
+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
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: large-image>=1.30.7.dev10
+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"
+Requires-Dist: openslide-bin; platform_system == "Windows" and platform_machine == "AMD64"
+Requires-Dist: openslide-bin; platform_system == "Darwin" and platform_machine == "arm64"
+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>=1.30.7.dev10; 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 Openslide tilesource for large_image.
+
+See the large-image package for more details.

large_image_source_openslide-1.30.7.dev10.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_openslide/__init__.py,sha256=O1-E-D7ZdY6Ta_ngId_HV0uqqxAbuY_J9fKTNVOFulE,20495
+large_image_source_openslide/girder_source.py,sha256=ntLgOinO7xcO85wFbjx6XEBmTgEtx5cuPZ_K6wXZzqA,1199
+large_image_source_openslide-1.30.7.dev10.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_openslide-1.30.7.dev10.dist-info/METADATA,sha256=cyvU_lZazei0R457AvXB-Kt8Zh2deJVZZ-CITnyHIAY,1858
+large_image_source_openslide-1.30.7.dev10.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+large_image_source_openslide-1.30.7.dev10.dist-info/entry_points.txt,sha256=4Z5cf63yeesvHxiR9W1dY3rfz5_V4Ck2xYhPUp4A1qA,196
+large_image_source_openslide-1.30.7.dev10.dist-info/top_level.txt,sha256=wqaQQDWQl9a_l9s6n07tTxfjeEXePtHBhz1np6aUwQE,29
+large_image_source_openslide-1.30.7.dev10.dist-info/RECORD,,

{large_image_source_openslide-1.27.5.dev4.dist-info → large_image_source_openslide-1.30.7.dev10.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_openslide-1.27.5.dev4.dist-info/METADATA

@@ -1,28 +0,0 @@
-Metadata-Version: 2.1
-Name: large-image-source-openslide
-Version: 1.27.5.dev4
-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
-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
-Requires-Python: >=3.8
-License-File: LICENSE
-Requires-Dist: large-image >=1.27.5.dev4
-Requires-Dist: openslide-python >=1.1.0
-Requires-Dist: tifftools >=1.2.0
-Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.27.5.dev4 ; extra == 'girder'
-
-An Openslide tilesource for large_image.
-
-See the large-image package for more details.

large_image_source_openslide-1.27.5.dev4.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_openslide/__init__.py,sha256=vzEx04RTBTptXUwbEMtcMMqXC2zq8lVtbenxFcdSfI8,18468
-large_image_source_openslide/girder_source.py,sha256=ntLgOinO7xcO85wFbjx6XEBmTgEtx5cuPZ_K6wXZzqA,1199
-large_image_source_openslide-1.27.5.dev4.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_openslide-1.27.5.dev4.dist-info/METADATA,sha256=jUNpNnImY3TTU26ap-psGbbqWp1Pjz0GQVklx7m-HiI,1063
-large_image_source_openslide-1.27.5.dev4.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-large_image_source_openslide-1.27.5.dev4.dist-info/entry_points.txt,sha256=4Z5cf63yeesvHxiR9W1dY3rfz5_V4Ck2xYhPUp4A1qA,196
-large_image_source_openslide-1.27.5.dev4.dist-info/top_level.txt,sha256=wqaQQDWQl9a_l9s6n07tTxfjeEXePtHBhz1np6aUwQE,29
-large_image_source_openslide-1.27.5.dev4.dist-info/RECORD,,