Merge pull request #1197 from girder/actual-levels

Report actual populated image levels

CHANGELOG.md

@@ -4,6 +4,7 @@
 
 ### Improvements
 - Better DICOM multi-level detection ([#1196](../../pull/1196))
+- Added an internal field to report populated tile levels in some sources ([#1197](../../pull/1197))
 
 ### Changes
 - Change how extensions and fallback priorities interact ([#1192](../../pull/1192))

girder/girder_large_image/models/image_item.py

@@ -270,6 +270,8 @@ def getInternalMetadata(self, item, **kwargs):
         if tileSource.getICCProfiles(onlyInfo=True):
             result['iccprofiles'] = tileSource.getICCProfiles(onlyInfo=True)
         result['tilesource'] = tileSource.name
+        if hasattr(tileSource, '_populatedLevels'):
+            result['populatedLevels'] = tileSource._populatedLevels
         return result
 
     def getTile(self, item, x, y, z, mayRedirect=False, **kwargs):

sources/bioformats/large_image_source_bioformats/__init__.py

@@ -266,6 +266,8 @@ def __init__(self, path, **kwargs):  # noqa
             self.getTile(0, 0, self.levels - 1)
         except Exception as exc:
             raise TileSourceError('Bioformats cannot read a tile: %r' % exc)
+        self._populatedLevels = len([
+            v for v in self._metadata['frameSeries'][0]['series'] if v is not None])
 
     def __del__(self):
         if getattr(self, '_bioimage', None) is not None:

sources/dicom/large_image_source_dicom/__init__.py

@@ -138,6 +138,7 @@ def __init__(self, path, **kwargs):
         self.tileHeight = min(max(self.tileHeight, self._minTileSize), self._maxTileSize)
         self.levels = int(max(1, math.ceil(math.log(
             max(self.sizeX / self.tileWidth, self.sizeY / self.tileHeight)) / math.log(2)) + 1))
+        self._populatedLevels = len(self._dicom.levels)
 
     def __del__(self):
         if getattr(self, '_dicom', None) is not None:

sources/openjpeg/large_image_source_openjpeg/__init__.py

@@ -128,6 +128,7 @@ def __init__(self, path, **kwargs):
                 self.sizeX, self.sizeY)) / self.tileWidth) / math.log(2))) + 1
             self._minlevel = self.levels - self._openjpeg.codestream.segment[2].num_res - 1
         self._getAssociatedImages()
+        self._populatedLevels = self.levels - self._minlevel
 
     def _getAssociatedImages(self):
         """

sources/openslide/large_image_source_openslide/__init__.py

@@ -160,6 +160,7 @@ def __init__(self, path, **kwargs):  # noqa
                 'svslevel': bestlevel,
                 'scale': scale
             })
+        self._populatedLevels = len({l['svslevel'] for l in self._svslevels})
 
     def _getTileSize(self):
         """

sources/tiff/large_image_source_tiff/__init__.py

@@ -369,6 +369,7 @@ def _checkForInefficientDirectories(self, warn=True):
 
         :param warn: if True and inefficient, emit a warning.
         """
+        self._populatedLevels = len([v for v in self._tiffDirectories if v is not None])
         missing = [v is None for v in self._tiffDirectories]
         maxMissing = max(0 if not v else missing.index(False, idx) - idx
                          for idx, v in enumerate(missing))

sources/tifffile/large_image_source_tifffile/__init__.py

@@ -137,6 +137,7 @@ def __init__(self, path, **kwargs):
             if (key.startswith('is_') and hasattr(self, '_handle_' + key[3:]) and
                     getattr(self._tf, key)):
                 getattr(self, '_handle_' + key[3:])()
+        self._populatedLevels = len(self._baseSeries.levels)
 
     def _biggestSeries(self):
         """