Fix bioformats processing of MONOCHROME1 dicom data

Bioformats ignores the rescale=false option with MONOCHROME1 dicom data. Further, not only does it invert the pixel value direction, but it offsets 16 bit data incorrectly. This undoes these effects so that the raw pixel data is returned. Fixes #1823.
girder · Feb 20, 2025 · 496c331 · 496c331
1 parent 44eeb86
commit 496c331
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Showing 4 changed files with 56 additions and 4 deletions.
diff --git a/sources/bioformats/large_image_source_bioformats/__init__.py b/sources/bioformats/large_image_source_bioformats/__init__.py
@@ -332,6 +332,7 @@ def __init__(self, path, **kwargs):  # noqa
             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])
 
@@ -348,6 +349,40 @@ def __del__(self):
                 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({
@@ -710,6 +745,8 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
             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):

diff --git a/test/datastore.py b/test/datastore.py
@@ -129,6 +129,10 @@
     # --rgb --quality=0.015 --compression='JPEG-2000 Lossy' parameters to make
     # the file small
     'TCGA-55-8207-01Z-00-DX1.ome.tiff': 'sha512:50cf63f0e8bfa3054d3532b7dd0237b66aeb4c7609da874639a28bc068dbd157f786e84d3eb76a3b0e6636a042c56c3b96d3be2ad66f7589d0542a5d20cecdb4',  # noqa
+    # Extracted from a sample dicom file from issue #1823 on github
+    # This is a dicom with monochrome1 format data that bioformats incorrectly
+    # inverts and offsets
+    'monochrome1.dcm': 'sha512:a67c38a5e26aba31b68e40eec0f260acf0ba638f0bf7fd99d41c3e16ddd8fd43b2737aeb3759ce92f2c4a10a81995bdae3b93b101ebcaa59543ea6eff7a4c8f2',  # noqa
 }
 
 

diff --git a/test/test_source_base.py b/test/test_source_base.py
@@ -33,7 +33,7 @@
     'deepzoom': {},
     'dicom': {
         'read': r'\.dcm$',
-        'noread': r'tcia.*\.dcm$',
+        'noread': r'(tcia.*|monochrome1)\.dcm$',
     },
     'dummy': {'any': True, 'skipTiles': r''},
     'gdal': {
@@ -63,7 +63,7 @@
     'openjpeg': {'read': r'\.(jp2)$'},
     'openslide': {
         'read': r'\.(ptif|svs|ndpi|tif.*|qptiff|dcm)$',
-        'noread': r'(oahu|DDX58_AXL|huron\.image2_jpeg2k|landcover_sample|d042-353\.crop|US_Geo\.|extraoverview|imagej|bad_axes|synthetic_untiled|indica|tcia.*dcm|multiplane.*ndpi)',  # noqa
+        'noread': r'(oahu|DDX58_AXL|huron\.image2_jpeg2k|landcover_sample|d042-353\.crop|US_Geo\.|extraoverview|imagej|bad_axes|synthetic_untiled|indica|tcia.*dcm|monochrome1.dcm|multiplane.*ndpi)',  # noqa
         'skip': r'nokeyframe\.ome\.tiff|TCGA-55.*\.ome\.tiff$',
         'skipTiles': r'one_layer_missing',
     },
@@ -83,14 +83,14 @@
         'skipTiles': r'(sample_image\.ptif|one_layer_missing_tiles)'},
     'tifffile': {
         'read': r'',
-        'noread': r'((\.(nc|nd2|yml|yaml|json|czi|png|jpg|jpeg|jp2|zarr\.db|zarr\.zip)|(nokeyframe\.ome\.tiff|XY01\.ome\.tif|level.*\.dcm|tcia.*dcm)$)' +  # noqa
+        'noread': r'((\.(nc|nd2|yml|yaml|json|czi|png|jpg|jpeg|jp2|zarr\.db|zarr\.zip)|(nokeyframe\.ome\.tiff|XY01\.ome\.tif|level.*\.dcm|tcia.*dcm|monochrome1.dcm)$)' +  # noqa
                   (r'|bad_axes' if sys.version_info < (3, 9) else '') +
                   r')',
         'skip': r'indica' if sys.version_info < (3, 9) else '^$',
     },
     'vips': {
         'read': r'',
-        'noread': r'(\.(nc|nd2|yml|yaml|json|czi|png|svs|scn|zarr\.db|zarr\.zip)|tcia.*dcm)$',
+        'noread': r'(\.(nc|nd2|yml|yaml|json|czi|png|svs|scn|zarr\.db|zarr\.zip)|tcia.*dcm|monochrome1.dcm)$',  # noqa
         'skipTiles': r'(sample_image\.ptif|one_layer_missing_tiles|JK-kidney_B-gal_H3_4C_1-500sec\.jp2|extraoverview|synthetic_untiled)',  # noqa
     },
     'zarr': {'read': r'\.(zarr|zgroup|zattrs|db|zarr\.zip)$'},

diff --git a/test/test_source_bioformats.py b/test/test_source_bioformats.py
@@ -1,3 +1,5 @@
+import large_image
+
 from . import utilities
 from .datastore import datastore
 
@@ -31,3 +33,12 @@ def testBioformatsJarVersion():
     import large_image_source_bioformats
 
     assert '.' in large_image_source_bioformats._getBioformatsVersion()
+
+
+def testBioformatsDicomMonochome1():
+    import large_image_source_bioformats
+
+    imagePath = datastore.fetch('monochrome1.dcm')
+    source = large_image_source_bioformats.open(imagePath)
+    img, _ = source.getRegion(format=large_image.constants.TILE_FORMAT_NUMPY)
+    assert img[255, 191, 0] == 618