Merge pull request #957 from girder/frames-as-axes

Add a framesAsAxes parameter to the multisource.

CHANGELOG.md

@@ -5,6 +5,7 @@
 ### Improvements
 - Reduce rest calls to get settings ([953](../../pull/953))
 - Add an endpoint to delete all annotations in a folder ([954](../../pull/954))
+- Support relabeling axes in the multi source ([957](../../pull/957))
 
 ### Bug Fixes
 - Harden adding images to the item list ([955](../../pull/955))

large_image/tilesource/base.py

@@ -1424,9 +1424,10 @@ def _addMetadataFrameInformation(self, metadata, channels=None):
                 if key in frame and frame[key] + 1 > maxref.get(key, 0):
                     maxref[key] = frame[key] + 1
             frame['Frame'] = idx
-            if idx and any(
+            if idx and (any(
                     frame.get(key) != metadata['frames'][idx - 1].get(key)
-                    for key in refkeys if key != 'IndexC'):
+                    for key in refkeys if key != 'IndexC') or not any(
+                    metadata['frames'][idx].get(key) for key in refkeys)):
                 index += 1
             frame['Index'] = index
         if any(val > 1 for val in maxref.values()):

sources/multi/large_image_source_multi/__init__.py

@@ -198,6 +198,20 @@
             'type': 'integer',
             'exclusiveMinimum': 0,
         },
+        'framesAsAxes': {
+            'description':
+                'An object with keys as axes and values as strides to '
+                'interpret the source frames.  This overrides the internal '
+                'metadata for frames.',
+            'type': 'object',
+            'patternProperties': {
+                '^(c|t|z|xy)$': {
+                    'type': 'integer',
+                    'exclusiveMinimum': 0,
+                }
+            },
+            'additionalProperties': False,
+        },
         'position': {
             'type': 'object',
             'additionalProperties': False,
@@ -531,6 +545,33 @@ def _axisKey(self, source, value, key):
                        (value - len(vals) + source.get(key, 0)))
         return axisKey
 
+    def _adjustFramesAsAxes(self, frames, idx, framesAsAxes):
+        """
+        Given a dictionary of axes and strides, relabel the indices in a frame
+        as if it was based on those strides.
+
+        :param frames: a list of frames from the tile source.
+        :param idx: 0-based index of the frame to adjust.
+        :param framesAsAxes: dictionary of axes and strides to apply.
+        :returns: the adjusted frame record.
+        """
+        axisRange = {}
+        slen = len(frames)
+        check = 1
+        for stride, axis in sorted([[v, k] for k, v in framesAsAxes.items()], reverse=True):
+            axisRange[axis] = slen // stride
+            slen = stride
+            check *= axisRange[axis]
+        if check != len(frames) and not hasattr(self, '_warnedAdjustFramesAsAxes'):
+            self.logger.warning('framesAsAxes strides do not use all frames.')
+            self._warnedAdjustFramesAsAxes = True
+        frame = frames[idx].copy()
+        for axis in ['c', 'z', 't', 'xy']:
+            frame.pop('Index' + axis.upper(), None)
+        for axis, stride in framesAsAxes.items():
+            frame['Index' + axis.upper()] = (idx // stride) % axisRange[axis]
+        return frame
+
     def _addSourceToFrames(self, tsMeta, source, sourceIdx, frameDict):
         """
         Add a source to the all appropriate frames.
@@ -561,6 +602,8 @@ def _addSourceToFrames(self, tsMeta, source, sourceIdx, frameDict):
         for frameIdx, frame in enumerate(frames):
             if 'frames' in source and frameIdx not in source['frames']:
                 continue
+            if source.get('framesAsAxes'):
+                frame = self._adjustFramesAsAxes(frames, frameIdx, source.get('framesAsAxes'))
             fKey = self._axisKey(source, frameIdx, 'frame')
             cIdx = frame.get('IndexC', 0)
             zIdx = frame.get('IndexZ', 0)
@@ -588,8 +631,8 @@ def _addSourceToFrames(self, tsMeta, source, sourceIdx, frameDict):
                 'frame': frameIdx,
                 'kwargs': kwargs,
             })
-            frameDict['axesAllowed'] = frameDict['axesAllowed'] and (
-                len(frames) <= 1 or 'IndexRange' in tsMeta)
+            frameDict['axesAllowed'] = (frameDict['axesAllowed'] and (
+                len(frames) <= 1 or 'IndexRange' in tsMeta)) or aKey != (0, 0, 0, 0)
             frameDict['byAxes'].setdefault(aKey, [])
             frameDict['byAxes'][aKey].append({
                 'sourcenum': sourceIdx,

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -317,8 +317,9 @@ def getMetadata(self):
             for idx in range(self._framecount):
                 frame = {'Frame': idx}
                 for axis, (basis, _pos, count) in self._basis.items():
-                    frame['Index' + (axis.upper() if axis.upper() != 'P' else 'XY')] = (
-                        idx // basis) % count
+                    if axis != 'I':
+                        frame['Index' + (axis.upper() if axis.upper() != 'P' else 'XY')] = (
+                            idx // basis) % count
                 frames.append(frame)
             self._addMetadataFrameInformation(result, getattr(self, '_channels', None))
             if any(v != self._seriesShape[0] for v in self._seriesShape):

test/test_source_multi.py

@@ -156,3 +156,35 @@ def testMultiBand():
     assert len(metadata['bands']) == 6
     image, mimeType = source.getThumbnail(encoding='PNG')
     assert image[:len(utilities.PNGHeader)] == utilities.PNGHeader
+
+
+def testFramesAsAxes():
+    baseSource = {'sources': [{
+        'sourceName': 'test', 'path': '__none__', 'params': {
+            'sizeX': 1000, 'sizeY': 1000, 'frames': 60}}]}
+    source = large_image_source_multi.open(json.dumps(baseSource))
+    tileMetadata = source.getMetadata()
+    assert len(tileMetadata['frames']) == 60
+    assert 'IndexZ' not in tileMetadata['frames'][0]
+
+    asAxesSource1 = {'sources': [{
+        'sourceName': 'test', 'path': '__none__', 'params': {
+            'sizeX': 1000, 'sizeY': 1000, 'frames': 60},
+        'framesAsAxes': {'c': 1, 'z': 5}}]}
+    source = large_image_source_multi.open(json.dumps(asAxesSource1))
+    tileMetadata = source.getMetadata()
+    assert len(tileMetadata['frames']) == 60
+    assert 'IndexZ' in tileMetadata['frames'][0]
+    assert tileMetadata['IndexRange']['IndexC'] == 5
+    assert tileMetadata['IndexRange']['IndexZ'] == 12
+
+    asAxesSource1 = {'sources': [{
+        'sourceName': 'test', 'path': '__none__', 'params': {
+            'sizeX': 1000, 'sizeY': 1000, 'frames': 60},
+        'framesAsAxes': {'c': 1, 'z': 7}}]}
+    source = large_image_source_multi.open(json.dumps(asAxesSource1))
+    tileMetadata = source.getMetadata()
+    assert len(tileMetadata['frames']) == 56
+    assert 'IndexZ' in tileMetadata['frames'][0]
+    assert tileMetadata['IndexRange']['IndexC'] == 7
+    assert tileMetadata['IndexRange']['IndexZ'] == 8