large-image-source-bioformats 1.33.4.dev23__py3-none-any.whl → 1.33.4.dev25__py3-none-any.whl

large_image_source_bioformats/__init__.py

@@ -339,6 +339,7 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             delattr(self, '_lastGetTileException')
         except Exception as exc:
             raise TileSourceError('Bioformats cannot read a tile: %r' % exc)
+        self._checkForOffset()
         self._populatedLevels = len([
             v for v in self._metadata['frameSeries'][0]['series'] if v is not None])
 
@@ -357,6 +358,40 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     if javabridge.get_env():
                         javabridge.detach()
 
+    def _checkForOffset(self):
+        """
+        The bioformats DICOM reader does unfortunate things to MONOCHROME1
+        16-bit images.  Store an offset to undo it, if appropriate.
+        """
+        if self._metadata.get('readerClassName') != 'loci.formats.in.DicomReader':
+            return
+        if self._metadata.get('seriesMetadata', {}).get(
+                '0028,0004 Photometric Interpretation') != 'MONOCHROME1':
+            return
+        if np.issubdtype(self.dtype, np.uint8):
+            self._fix_offset = 255
+            return
+        if not np.issubdtype(self.dtype, np.int16) and not np.issubdtype(self.dtype, '>i2'):
+            return
+        # This is bioformats behavior
+        try:
+            maxPixelRange = int(self._metadata['seriesMetadata'].get(
+                '0028,1051 Window Width', 0))
+        except Exception:
+            maxPixelRange = -1
+        try:
+            centerPixelValue = int(self._metadata['seriesMetadata'].get(
+                '0028,1050 Window Center', 0))
+        except Exception:
+            centerPixelValue = -1
+        maxPixelValue = maxPixelRange + (centerPixelValue // 2)
+        maxAllowRange = 2 ** int(self._metadata['seriesMetadata'].get(
+            '0028,0101 Bits Stored', 16)) - 1
+        if maxPixelRange == -1 or centerPixelValue < maxPixelRange // 2:
+            maxPixelValue = maxAllowRange
+        if maxPixelValue:
+            self._fix_offset = maxPixelValue
+
     def _metadataForCurrentSeries(self, rdr):
         self._metadata = getattr(self, '_metadata', {})
         self._metadata.update({
@@ -723,6 +758,8 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             retile[0:min(tile.shape[0], finalHeight), 0:min(tile.shape[1], finalWidth)] = tile[
                 0:min(tile.shape[0], finalHeight), 0:min(tile.shape[1], finalWidth)]
             tile = retile
+        if hasattr(self, '_fix_offset') and format == TILE_FORMAT_NUMPY:
+            tile = self._fix_offset - tile
         return self._outputTile(tile, format, x, y, z, pilImageAllowed, numpyAllowed, **kwargs)
 
     def getAssociatedImagesList(self):

{large_image_source_bioformats-1.33.4.dev23.dist-info → large_image_source_bioformats-1.33.4.dev25.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: large-image-source-bioformats
-Version: 1.33.4.dev23
+Version: 1.33.4.dev25
 Summary: An bioformats tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -17,10 +17,10 @@ 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.dev23
+Requires-Dist: large-image>=1.33.4.dev25
 Requires-Dist: python-bioformats>=1.5.2
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.33.4.dev23; extra == "girder"
+Requires-Dist: girder-large-image>=1.33.4.dev25; extra == "girder"
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

large_image_source_bioformats-1.33.4.dev25.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_bioformats/__init__.py,sha256=sBCg-N7s1mN29q8EIaY4Nr34ir7Oi8DINtV5mOT0cqM,36468
+large_image_source_bioformats/girder_source.py,sha256=t0X1P0m4qMsRklpdxoPH-yqgHByMvQIzFJ4qRIUykVI,1355
+large_image_source_bioformats-1.33.4.dev25.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_bioformats-1.33.4.dev25.dist-info/METADATA,sha256=Qy2A_c88BgKUvKlo7zNYd9SZO88C1DG5xYZWG2VZR6Y,1269
+large_image_source_bioformats-1.33.4.dev25.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+large_image_source_bioformats-1.33.4.dev25.dist-info/entry_points.txt,sha256=xgIbKr53QhQkyRFkr87fkagfPWweeqhHHekUEMrcpF8,202
+large_image_source_bioformats-1.33.4.dev25.dist-info/top_level.txt,sha256=e0enjlcFXwPi638IhE71Rk5-eeriA7W3M3IsQ6yH3RI,30
+large_image_source_bioformats-1.33.4.dev25.dist-info/RECORD,,

large_image_source_bioformats-1.33.4.dev23.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_bioformats/__init__.py,sha256=IWOpHHPAX3pYmqOJx3cPmEmvkHU_pMbhiTLdxXVBH3o,34872
-large_image_source_bioformats/girder_source.py,sha256=t0X1P0m4qMsRklpdxoPH-yqgHByMvQIzFJ4qRIUykVI,1355
-large_image_source_bioformats-1.33.4.dev23.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_bioformats-1.33.4.dev23.dist-info/METADATA,sha256=Kx8HtA8ZFn0z1_D7KkOdx8d_RNsNxT1oR_eGmqirOpo,1269
-large_image_source_bioformats-1.33.4.dev23.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-large_image_source_bioformats-1.33.4.dev23.dist-info/entry_points.txt,sha256=xgIbKr53QhQkyRFkr87fkagfPWweeqhHHekUEMrcpF8,202
-large_image_source_bioformats-1.33.4.dev23.dist-info/top_level.txt,sha256=e0enjlcFXwPi638IhE71Rk5-eeriA7W3M3IsQ6yH3RI,30
-large_image_source_bioformats-1.33.4.dev23.dist-info/RECORD,,