girder-large-image 1.35.7.dev4__tar.gz → 1.35.7.dev8__tar.gz

{girder_large_image-1.35.7.dev4 → girder_large_image-1.35.7.dev8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: girder-large-image
-Version: 1.35.7.dev4
+Version: 1.35.7.dev8
 Summary: A Girder plugin to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -20,9 +20,9 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: girder<5,>=3.1.18
 Requires-Dist: girder-jobs<5,>=3.0.3
-Requires-Dist: large_image>=1.35.7.dev4
+Requires-Dist: large_image>=1.35.7.dev8
 Provides-Extra: tasks
-Requires-Dist: large-image-tasks[girder]>=1.35.7.dev4; extra == "tasks"
+Requires-Dist: large-image-tasks[girder]>=1.35.7.dev8; extra == "tasks"
 Requires-Dist: girder-worker[girder]<5,>=0.6.0; extra == "tasks"
 Dynamic: author
 Dynamic: author-email

{girder_large_image-1.35.7.dev4 → girder_large_image-1.35.7.dev8}/girder_large_image/__init__.py

@@ -207,6 +207,45 @@ def checkForMergeDicom(item):
     Item().remove(item)
 
 
+def checkForFlatLargeImage(item, imagePattern):
+    """
+    Check if an item that contains a companion file of a folder/image style
+    image is adjacent to the image file itself ("flat" layout).  The image
+    file can be another file in the same item or the sole file of another item
+    in the same folder.  If found, try to make it a large image.
+
+    :param item: the item containing the companion file.
+    :param imagePattern: a regex that matches the name of the image file.
+    :returns: True if a large image was created.
+    """
+    # A failed createImageItem can leave a partial largeImage record on the
+    # in-memory item, so always use a fresh copy
+    item = Item().load(item['_id'], force=True)
+    if not item.get('largeImage'):
+        for imageFile in File().find({'itemId': item['_id']}):
+            if not re.search(imagePattern, imageFile['name']):
+                continue
+            try:
+                ImageItem().createImageItem(item, imageFile, createJob=False)
+                return True
+            except Exception:
+                item = Item().load(item['_id'], force=True)
+    for imageItem in Item().find({
+            'folderId': item['folderId'], '_id': {'$ne': item['_id']},
+            'name': {'$regex': imagePattern}}):
+        if imageItem.get('largeImage'):
+            continue
+        files = list(Item().childFiles(item=imageItem, limit=2))
+        if len(files) != 1:
+            continue
+        try:
+            ImageItem().createImageItem(imageItem, files[0], createJob=False)
+            return True
+        except Exception:
+            pass
+    return False
+
+
 def checkForLargeImageFiles(event):  # noqa
     file = event.info
     if 'file.save' in event.name and 's3FinalizeRequest' in file:
@@ -245,6 +284,11 @@ def checkForLargeImageFiles(event):  # noqa
             'up': 1,
             'folder': r'^(.*)$',
             'image': '\\1.mrxs',
+            # Some openslide builds can read "flat" mirax files where the
+            # companion files are adjacent to the .mrxs file rather than in a
+            # subfolder.  The companion files can be sibling items in the same
+            # folder or sibling files in the same item.
+            'flat': r'\.mrxs$',
         },
         'vsi': {
             'match': r'^.*\.ets$',
@@ -255,6 +299,12 @@ def checkForLargeImageFiles(event):  # noqa
     }
     for check in imageFolderRecords.values():
         if re.match(check['match'], file['name']):
+            if check.get('flat'):
+                try:
+                    if checkForFlatLargeImage(item, check['flat']):
+                        return
+                except Exception:
+                    pass
             try:
                 folderId = item['folderId']
                 folder = None

{girder_large_image-1.35.7.dev4 → girder_large_image-1.35.7.dev8}/girder_large_image.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: girder-large-image
-Version: 1.35.7.dev4
+Version: 1.35.7.dev8
 Summary: A Girder plugin to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -20,9 +20,9 @@ Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: girder<5,>=3.1.18
 Requires-Dist: girder-jobs<5,>=3.0.3
-Requires-Dist: large_image>=1.35.7.dev4
+Requires-Dist: large_image>=1.35.7.dev8
 Provides-Extra: tasks
-Requires-Dist: large-image-tasks[girder]>=1.35.7.dev4; extra == "tasks"
+Requires-Dist: large-image-tasks[girder]>=1.35.7.dev8; extra == "tasks"
 Requires-Dist: girder-worker[girder]<5,>=0.6.0; extra == "tasks"
 Dynamic: author
 Dynamic: author-email

{girder_large_image-1.35.7.dev4 → girder_large_image-1.35.7.dev8}/girder_large_image.egg-info/requires.txt

@@ -1,7 +1,7 @@
 girder<5,>=3.1.18
 girder-jobs<5,>=3.0.3
-large_image>=1.35.7.dev4
+large_image>=1.35.7.dev8
 
 [tasks]
-large-image-tasks[girder]>=1.35.7.dev4
+large-image-tasks[girder]>=1.35.7.dev8
 girder-worker[girder]<5,>=0.6.0

{girder_large_image-1.35.7.dev4 → girder_large_image-1.35.7.dev8}/test_girder/test_tiles_rest.py

@@ -1142,6 +1142,62 @@ def testTilesAutoSetOption(server, admin, fsAssetstore):
     assert utilities.respStatus(resp) == 200
 
 
+@pytest.mark.usefixtures('unbindLargeImage')
+@pytest.mark.plugin('large_image')
+def testTilesAutoSetMiraxCompanionFiles(server, admin, fsAssetstore, tmp_path):
+    # Mirax images are a small .mrxs file plus companion files, normally in a
+    # subfolder named after the image.  Some openslide builds can also read a
+    # "flat" layout where the companion files are adjacent to the .mrxs file.
+    # Adding the .mrxs file by itself can't make a large image, but adding the
+    # companion files afterwards should.  Files are imported rather than
+    # uploaded so that openslide can find the companion files on disk.
+    import zipfile
+
+    from girder.models.folder import Folder
+    from girder.utility import assetstore_utilities
+
+    name = 'Mirax2-Fluorescence-1'
+    with zipfile.ZipFile(utilities.datastore.fetch(name + '.mrxs.zip')) as archive:
+        archive.extractall(tmp_path / 'src')
+    srcMrxs = tmp_path / 'src' / (name + '.mrxs')
+    srcCompanions = tmp_path / 'src' / name
+    adapter = assetstore_utilities.getAssetstoreAdapter(fsAssetstore)
+    public = utilities.namedFolder(admin)
+
+    for layout in ('nested', 'flat', 'item'):
+        dest = tmp_path / layout
+        dest.mkdir()
+        shutil.copy(srcMrxs, dest)
+        folder = Folder().createFolder(public, layout, creator=admin)
+        item = Item().createItem(name + '.mrxs', admin, folder)
+        mrxsFile = adapter.importFile(item, str(dest / (name + '.mrxs')), admin)
+        # Without the companion files, this isn't a large image
+        assert 'largeImage' not in Item().load(item['_id'], force=True)
+        if layout == 'nested':
+            companionDir = dest / name
+            companionFolder = Folder().createFolder(folder, name, creator=admin)
+        else:
+            companionDir = dest
+            companionFolder = folder
+        shutil.copytree(srcCompanions, companionDir, dirs_exist_ok=True)
+        # Slidedat.ini is what triggers rechecking the .mrxs file, so add it
+        # last
+        paths = sorted(path for path in companionDir.iterdir() if path.suffix == '.dat')
+        paths.append(companionDir / 'Slidedat.ini')
+        for path in paths:
+            if layout == 'item':
+                companionItem = item
+            else:
+                companionItem = Item().createItem(path.name, admin, companionFolder)
+            adapter.importFile(companionItem, str(path), admin)
+        item = Item().load(item['_id'], force=True)
+        assert item.get('largeImage', {}).get('fileId') == mrxsFile['_id'], layout
+        resp = server.request(path='/item/%s/tiles' % item['_id'], user=admin)
+        assert utilities.respStatus(resp) == 200
+        assert resp.json['sizeX'] == 10487
+        assert resp.json['sizeY'] == 13350
+
+
 @pytest.mark.usefixtures('unbindLargeImage')
 @pytest.mark.plugin('large_image')
 def testTilesAssociatedImages(server, admin, fsAssetstore):