Merge pull request #1561 from girder/folder-item-images

Better handle images that are composed of a folder and an item.
girder · Jun 27, 2024 · af42659 · af42659
2 parents 8949886 + 43f29d8
commit af42659
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Showing 5 changed files with 53 additions and 6 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,7 @@
 
 ### Improvements
 - Show a loading spinner on the image display in geojs in girder ([#1559](../../pull/1559))
+-
 
 ### Bug Fixes
 - Fix a compositing error in transformed multi source images ([#1560](../../pull/1560))

diff --git a/girder/girder_large_image/__init__.py b/girder/girder_large_image/__init__.py
@@ -158,7 +158,7 @@ def _updateJob(event):
                      datetime.timedelta(seconds=30)))
 
 
-def checkForLargeImageFiles(event):
+def checkForLargeImageFiles(event):  # noqa
     file = event.info
     logger.info('Handling file %s (%s)', file['_id'], file['name'])
     possible = False
@@ -178,10 +178,51 @@ def checkForLargeImageFiles(event):
         return
     try:
         ImageItem().createImageItem(item, file, createJob=False)
+        return
     except Exception:
-        # We couldn't automatically set this as a large image
-        girder.logger.info(
-            'Saved file %s cannot be automatically used as a largeImage' % str(file['_id']))
+        pass
+    # Check for files that are from folder/image style images.  This is custom
+    # per folder/image format
+    imageFolderRecords = {
+        'mrxs': {
+            'match': r'^Slidedat.ini$',
+            'up': 1,
+            'folder': r'^(.*)$',
+            'image': '\\1.mrxs',
+        },
+        'vsi': {
+            'match': r'^.*\.ets$',
+            'up': 2,
+            'folder': r'^_(\.*)_$',
+            'image': '\\1.vsi',
+        },
+    }
+    for check in imageFolderRecords.values():
+        if re.match(check['match'], file['name']):
+            try:
+                folderId = item['folderId']
+                folder = None
+                for _ in range(check['up']):
+                    folder = Folder().load(folderId, force=True)
+                    if not folder:
+                        break
+                    folderId = folder['parentId']
+                if not folder or not re.match(check['folder'], folder['name']):
+                    continue
+                imageName = re.sub(check['folder'], check['image'], folder['name'])
+                parentItem = Item().findOne({'folderId': folder['parentId'], 'name': imageName})
+                if not parentItem:
+                    continue
+                files = list(Item().childFiles(item=parentItem, limit=2))
+                if len(files) == 1:
+                    parentFile = files[0]
+                    ImageItem().createImageItem(parentItem, parentFile, createJob=False)
+                    return
+            except Exception:
+                pass
+    # We couldn't automatically set this as a large image
+    girder.logger.info(
+        'Saved file %s cannot be automatically used as a largeImage' % str(file['_id']))
 
 
 def removeThumbnails(event):

diff --git a/girder/girder_large_image/girder_tilesource.py b/girder/girder_large_image/girder_tilesource.py
@@ -5,7 +5,7 @@
 from girder.exceptions import FilePathException, ValidationException
 from girder.models.file import File
 from girder.models.item import Item
-from large_image import tilesource
+from large_image import config, tilesource
 from large_image.constants import SourcePriority
 from large_image.exceptions import TileSourceAssetstoreError, TileSourceError
 
@@ -164,6 +164,9 @@ def getGirderTileSourceName(item, file=None, *args, **kwargs):  # noqa
     properties = {}
     if localPath:
         properties['_geospatial_source'] = tilesource.isGeospatial(localPath)
+    ignored_names = config.getConfig('all_sources_ignored_names')
+    ignoreName = (ignored_names and re.search(
+        ignored_names, baseName, flags=re.IGNORECASE))
     sourceList = []
     for sourceName in availableSources:
         if not getattr(availableSources[sourceName], 'girderSource', False):
@@ -183,7 +186,7 @@ def getGirderTileSourceName(item, file=None, *args, **kwargs):  # noqa
             if ext in sourceExtensions:
                 priority = min(priority, sourceExtensions[ext])
                 fallback = False
-        if priority >= SourcePriority.MANUAL:
+        if priority >= SourcePriority.MANUAL or (ignoreName and fallback):
             continue
         propertiesClash = any(
             getattr(availableSources[sourceName], k, False) != v

diff --git a/sources/bioformats/large_image_source_bioformats/__init__.py b/sources/bioformats/large_image_source_bioformats/__init__.py
@@ -183,6 +183,7 @@ class BioformatsFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     extensions = {
         None: SourcePriority.FALLBACK,
         'czi': SourcePriority.PREFERRED,
+        'ets': SourcePriority.LOW,  # part of vsi
         'lif': SourcePriority.MEDIUM,
         'vsi': SourcePriority.PREFERRED,
     }

diff --git a/sources/openslide/large_image_source_openslide/__init__.py b/sources/openslide/large_image_source_openslide/__init__.py
@@ -48,6 +48,7 @@ class OpenslideFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         None: SourcePriority.MEDIUM,
         'bif': SourcePriority.LOW,  # Ventana
         'dcm': SourcePriority.LOW,  # DICOM
+        'ini': SourcePriority.LOW,  # Part of mrxs
         'mrxs': SourcePriority.PREFERRED,  # MIRAX
         'ndpi': SourcePriority.PREFERRED,  # Hamamatsu
         'scn': SourcePriority.LOW,  # Leica