Merge pull request #1196 from girder/better-dicom-detection

Improve dicom multi level detection

CHANGELOG.md

@@ -2,13 +2,16 @@
 
 ## 1.22.3
 
+### Improvements
+- Better DICOM multi-level detection ([#1196](../../pull/1196))
+
 ### Changes
 - Change how extensions and fallback priorities interact ([#1192](../../pull/1192))
 - Refactor reading the .large_image_config.yaml file on the girder client ([#1193](../../pull/1193))
 - Refactor of the which-folders-have-annotations pipeline ([#1194](../../pull/1194))
 
 ### Bug Fixes
-- Fix an issue converting multiframe files that vips reads as single frame  ([#1195](../../pull/1195))
+- Fix an issue converting multiframe files that vips reads as single frame ([#1195](../../pull/1195))
 
 ## 1.22.2
 

large_image/tilesource/__init__.py

@@ -1,4 +1,5 @@
 import os
+import re
 import uuid
 
 try:
@@ -77,7 +78,8 @@ def getSortedSourceList(availableSources, pathOrUri, mimeType=None, *args, **kwa
     """
     uriWithoutProtocol = str(pathOrUri).split('://', 1)[-1]
     isLargeImageUri = str(pathOrUri).startswith('large_image://')
-    extensions = [ext.lower() for ext in os.path.basename(uriWithoutProtocol).split('.')[1:]]
+    baseName = os.path.basename(uriWithoutProtocol)
+    extensions = [ext.lower() for ext in baseName.split('.')[1:]]
     properties = {
         '_geospatial_source': isGeospatial(pathOrUri),
     }
@@ -90,6 +92,10 @@ def getSortedSourceList(availableSources, pathOrUri, mimeType=None, *args, **kwa
                 mimeType in availableSources[sourceName].mimeTypes):
             fallback = False
             priority = min(priority, availableSources[sourceName].mimeTypes[mimeType])
+        for regex in getattr(availableSources[sourceName], 'nameMatches', {}):
+            if re.match(regex, baseName):
+                fallback = False
+                priority = min(priority, availableSources[sourceName].nameMatches[regex])
         for ext in extensions:
             if ext in sourceExtensions:
                 fallback = False

large_image/tilesource/base.py

@@ -30,23 +30,29 @@
 
 
 class TileSource:
-    #: Name of the tile source
+    # Name of the tile source
     name = None
 
-    #: A dictionary of known file extensions and the ``SourcePriority`` given
-    #: to each.  It must contain a None key with a priority for the tile source
-    #: when the extension does not match.
+    # A dictionary of known file extensions and the ``SourcePriority`` given
+    # to each.  It must contain a None key with a priority for the tile source
+    # when the extension does not match.
     extensions = {
         None: SourcePriority.FALLBACK
     }
 
-    #: A dictionary of common mime-types handled by the source and the
-    #: ``SourcePriority`` given to each.  This are used in place of or in
-    #: additional to extensions.
+    # A dictionary of common mime-types handled by the source and the
+    # ``SourcePriority`` given to each.  This are used in place of or in
+    # additional to extensions.
     mimeTypes = {
         None: SourcePriority.FALLBACK
     }
 
+    # A dictionary with regex strings as the keys and the ``SourcePriority``
+    # given to names that match that expression.  This is used in addition to
+    # extensions and mimeTypes, with the highest priority match taken.
+    nameMatches = {
+    }
+
     geospatial = False
 
     def __init__(self, encoding='JPEG', jpegQuality=95, jpegSubsampling=0,

sources/dicom/large_image_source_dicom/__init__.py

@@ -92,6 +92,9 @@ class DICOMFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         None: SourcePriority.FALLBACK,
         'application/dicom': SourcePriority.PREFERRED,
     }
+    nameMatches = {
+        r'DCM_\d+$': SourcePriority.MEDIUM,
+    }
 
     _minTileSize = 64
     _maxTileSize = 4096
@@ -156,6 +159,8 @@ def _pathMightBeDicom(self, path):
             return True
         if re.match(r'^([1-9][0-9]*|0)(\.([1-9][0-9]*|0))+$', path) and len(path) <= 64:
             return True
+        if re.match(r'^DCM_\d+$', path):
+            return True
         return False
 
     def getNativeMagnification(self):