Don't read multiplane ndpi files with openslide

It explicitly only reads the focal plane at 0 and skips the others silently. Improve the tifffile source reporting of ndpi internal metadata.
girder · Jan 10, 2025 · c3ec197 · c3ec197
1 parent 840de66
commit c3ec197
Show file tree

Hide file tree

Showing 5 changed files with 31 additions and 3 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,7 @@
 
 - Better report if rasterized vector files are geospatial ([#1769](../../pull/1769))
 - Provide some latitude in vips multiframe detection ([#1770](../../pull/1770))
+- Don't read multiplane ndpi files with openslide ([#1772](../../pull/1772))
 
 ## 1.30.6
 

diff --git a/sources/openslide/large_image_source_openslide/__init__.py b/sources/openslide/large_image_source_openslide/__init__.py
@@ -94,6 +94,13 @@ def __init__(self, path, **kwargs):  # noqa
                     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):

diff --git a/sources/tifffile/large_image_source_tifffile/__init__.py b/sources/tifffile/large_image_source_tifffile/__init__.py
@@ -430,6 +430,20 @@ def _handle_svs(self):
         except Exception:
             pass
 
+    def _handle_internal_ndpi(self, intmeta):
+        try:
+            ndpi = intmeta.pop('65449')
+            intmeta['ndpi'] = {}
+            for line in ndpi.replace('\r', '\n').split('\n'):
+                if '=' in line:
+                    key, value = line.split('=', 1)
+                    key = key.strip()
+                    value = value.strip()
+                    if key and key not in intmeta['ndpi'] and value:
+                        intmeta['ndpi'][key] = value
+        except Exception:
+            pass
+
     def getNativeMagnification(self):
         """
         Get the magnification at a particular level.
@@ -499,6 +513,10 @@ def getInternalMetadata(self, **kwargs):
                                 json.dumps(result[key][subkey])
                             except Exception:
                                 del result[key][subkey]
+        for key in dir(self._tf):
+            if (key.startswith('is_') and hasattr(self, '_handle_internal_' + key[3:]) and
+                    getattr(self._tf, key)):
+                getattr(self, '_handle_internal_' + key[3:])(result)
         if hasattr(self, '_xml') and 'xml' not in result:
             result.pop('ImageDescription', None)
             result['xml'] = self._xml

diff --git a/test/datastore.py b/test/datastore.py
@@ -113,9 +113,11 @@
     '18f6378f-433c-42bf-9373-1ff9c808c118.dcm': 'sha512:36432183380eb7d44417a2210a19d550527abd1181255e19ed5c1d17695d8bb8ca42f5b426a63fa73b84e0e17b770401a377ae0c705d0ed7fdf30d571ef60e2d',  # noqa
     'a131592c-a069-4aa7-8031-398654aa8a3d.dcm': 'sha512:99bd3da4b8e11ce7b4f7ed8a294ed0c37437320667a06c40c383f4b29be85fe8e6094043e0600bee0ba879f2401de4c57285800a4a23da2caf2eb94e5b847ee0',  # noqa
     # Synthetic newer ndpi with binary data and nonblank image labelled as RGB
-    'synthetic_ndpi_2025.ndpi': 'sha512:28752f35790b62fb712eb93f370be4e2f44799d44d6bb1f34fea9d3a6f01c7b49b2c510fc34ebaa829cb1beef0bc5b12d26a4cb3060835ff49aada7d99f61e44',  # noqa
+    'synthetic_ndpi_2025.ndpi': 'sha512:b9b2c420cde9fd988786afc02efb761a7d425ce542cc68f10f5878bdc7177d61952e0d52508501c82d5664a07a87e7486ec4bb0b6634c556400cfc91fc3f52ec',  # noqa
+    # Synthetic ndpi with multiple focal planes
+    'synthetic_ndpi_multiplane_2025.ndpi': 'sha512:1025d6ddd74070d0bb2c3ab398bc5e6ae05390651f84df22c37e3dbe547bb16b4eba0a0a3cefc7ac824ff2e87320782b676b2049a602bc0d5dbb105bbc94e888',  # noqa
     # Synthetic uint16 untiled tiff that can be read with the tiff source
-    'synthetic_untiled_16.tiff': 'sha512:f4773fcfa749ba9c2db25319c9e8ad8586dd148de4366dae0393a3703906dace9f11233eafdb24418b598170d6372ef1ca861bf8d7a8212cac21a0eb8636ee77',  # noqa
+    'synthetic_untiled_16.tiff': 'sha512:1025d6ddd74070d0bb2c3ab398bc5e6ae05390651f84df22c37e3dbe547bb16b4eba0a0a3cefc7ac824ff2e87320782b676b2049a602bc0d5dbb105bbc94e888',  # noqa
     # DICOM with int16 data
     # Source: TCIA/CMB-LCA_v07_20240828/CMB-LCA/MSB-01459/
     #   12-22-1959-XR Chest-59125/1002.000000-43033/1-1.dcm

diff --git a/test/test_source_base.py b/test/test_source_base.py
@@ -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)',  # 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|multiplane.*ndpi)',  # noqa
         'skip': r'nokeyframe\.ome\.tiff|TCGA-55.*\.ome\.tiff$',
         'skipTiles': r'one_layer_missing',
     },