large-image-source-openslide 1.27.1.dev65__py3-none-any.whl → 1.33.4.dev39__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
@@ -47,10 +48,13 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     extensions = {
         None: SourcePriority.MEDIUM,
         'bif': SourcePriority.LOW,  # Ventana
+        '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,
@@ -59,6 +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,
@@ -92,6 +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):
@@ -126,19 +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
@@ -152,7 +168,38 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             self._svslevels.append({
                 'svslevel': bestlevel,
                 'scale': scale,
+                'svsscale': ((svsscale / levelpow) if svsscale else 1) * 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
+        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):
@@ -202,6 +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))
@@ -210,6 +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
@@ -291,25 +343,66 @@ 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:
-            try:
-                tile = self._openslide.read_region(
-                    (offsetx, offsety), svslevel['svslevel'],
-                    (self.tileWidth * svslevel['scale'],
-                     self.tileHeight * svslevel['scale']))
-            except openslide.lowlevel.OpenSlideError as exc:
-                raise TileSourceError(
-                    'Failed to get OpenSlide region (%r).' % exc)
+            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'],
+                        (svsTileWidth, svsTileHeight))
+                    format = TILE_FORMAT_PIL
+                    break
+                except openslide.lowlevel.OpenSlideError as exc:
+                    self._largeImagePath = str(self._getLargeImagePath())
+                    msg = (
+                        'Failed to get OpenSlide region '
+                        f'({exc} on {self._largeImagePath}: {self}).')
+                    self.logger.info(msg)
+                    # Reopen handle after a lowlevel error
+                    try:
+                        self._openslide = openslide.OpenSlide(self._largeImagePath)
+                    except Exception:
+                        raise TileSourceError(msg)
+                    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),
                                    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):
@@ -381,7 +474,15 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 self._openslide = openslide.OpenSlide(self._largeImagePath)
                 return None
         tiff_buffer = io.BytesIO()
-        tifftools.write_tiff(self._tiffinfo['ifds'][images[imageKey]], tiff_buffer)
+        ifd = self._tiffinfo['ifds'][images[imageKey]]
+        if (tifftools.Tag.Photometric.value in ifd['tags'] and
+                ifd['tags'][tifftools.Tag.Photometric.value]['data'][0] ==
+                tifftools.constants.Photometric.RGB and
+                tifftools.Tag.SamplesPerPixel.value in ifd['tags'] and
+                ifd['tags'][tifftools.Tag.SamplesPerPixel.value]['data'][0] == 1):
+            ifd['tags'][tifftools.Tag.Photometric.value]['data'][
+                0] = tifftools.constants.Photometric.MinIsBlack
+        tifftools.write_tiff(ifd, tiff_buffer)
         return PIL.Image.open(tiff_buffer)
 
 

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-1.33.4.dev39.dist-info/METADATA

@@ -0,0 +1,46 @@
+Metadata-Version: 2.4
+Name: large-image-source-openslide
+Version: 1.33.4.dev39
+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-2.0
+Keywords: large_image,tile source
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Programming Language :: Python :: 3
+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: >=3.9
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: large-image>=1.33.4.dev39
+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>=1.33.4.dev39; 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.
+
+See the large-image package for more details.

large_image_source_openslide-1.33.4.dev39.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-1.33.4.dev39.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_openslide-1.33.4.dev39.dist-info/METADATA,sha256=D0LgghIyCslMY4vpBg9nqjKwpXgT3mNIWmzy454td60,1750
+large_image_source_openslide-1.33.4.dev39.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+large_image_source_openslide-1.33.4.dev39.dist-info/entry_points.txt,sha256=4Z5cf63yeesvHxiR9W1dY3rfz5_V4Ck2xYhPUp4A1qA,196
+large_image_source_openslide-1.33.4.dev39.dist-info/top_level.txt,sha256=wqaQQDWQl9a_l9s6n07tTxfjeEXePtHBhz1np6aUwQE,29
+large_image_source_openslide-1.33.4.dev39.dist-info/RECORD,,

{large_image_source_openslide-1.27.1.dev65.dist-info → large_image_source_openslide-1.33.4.dev39.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.42.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

large_image_source_openslide-1.27.1.dev65.dist-info/METADATA

@@ -1,28 +0,0 @@
-Metadata-Version: 2.1
-Name: large-image-source-openslide
-Version: 1.27.1.dev65
-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 >=1.27.1.dev65
-Requires-Dist: openslide-python >=1.1.0
-Requires-Dist: tifftools >=1.2.0
-Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.27.1.dev65 ; extra == 'girder'
-
-An Openslide tilesource for large_image.
-
-See the large-image package for more details.

large_image_source_openslide-1.27.1.dev65.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_openslide/__init__.py,sha256=OKhFazrlt2siQeqkAoWDofaA8ufDgJkdA4eyhGM_TSE,17321
-large_image_source_openslide/girder_source.py,sha256=ntLgOinO7xcO85wFbjx6XEBmTgEtx5cuPZ_K6wXZzqA,1199
-large_image_source_openslide-1.27.1.dev65.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_openslide-1.27.1.dev65.dist-info/METADATA,sha256=pXkV6EMV1i4XiTpQSvYhxlAEvIRI-EGUHozZlGx7Q4U,1066
-large_image_source_openslide-1.27.1.dev65.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-large_image_source_openslide-1.27.1.dev65.dist-info/entry_points.txt,sha256=4Z5cf63yeesvHxiR9W1dY3rfz5_V4Ck2xYhPUp4A1qA,196
-large_image_source_openslide-1.27.1.dev65.dist-info/top_level.txt,sha256=wqaQQDWQl9a_l9s6n07tTxfjeEXePtHBhz1np6aUwQE,29
-large_image_source_openslide-1.27.1.dev65.dist-info/RECORD,,