Merge pull request #1373 from girder/generalize-level-skipping

General handling of skipped levels

CHANGELOG.md

@@ -8,7 +8,12 @@
 - Configurable item list grid view ([#1363](../../pull/1363))
 - Allow labels in item list view ([#1366](../../pull/1366))
 - Improve cache key guard ([#1368](../../pull/1368))
-- Improve handling dicom files in the working directory ([#1370](../../pull/137068))
+- Improve handling dicom files in the working directory ([#1370](../../pull/1370))
+- General handling of skipped levels ([#1373](../../pull/1373))
+
+### Changes
+- Update WsiDicomWebClient init call ([#1371](../../pull/1371))
+- Rename DICOMweb AssetstoreImportView ([#1372](../../pull/1372))
 
 ### Bug Fixes
 - Default to "None" for the DICOM assetstore limit ([#1359](../../pull/1359))

large_image/tilesource/base.py

@@ -57,6 +57,14 @@ class TileSource(IPyLeafletMixin):
 
     geospatial = False
 
+    # When getting tiles for otherwise empty levels (missing powers of two), we
+    # composite the tile from higher resolution levels.  This can use excessive
+    # memory if there are too many missing levels.  For instance, if there are
+    # six missing levels and the tile size is 1024 square RGBA, then 16 Gb are
+    # needed for the composited tile at a minimum.  By setting
+    # _maxSkippedLevels, such large gaps are composited in stages.
+    _maxSkippedLevels = 3
+
     def __init__(self, encoding='JPEG', jpegQuality=95, jpegSubsampling=0,
                  tiffCompression='raw', edge=False, style=None, noCache=None,
                  *args, **kwargs):
@@ -1924,6 +1932,54 @@ def _xyzToCorners(self, x, y, z):
         y1 = min((y + 1) * step * self.tileHeight, self.sizeY)
         return x0, y0, x1, y1, step
 
+    def _nonemptyLevelsList(self, frame=0):
+        """
+        Return a list of one value per level where the value is None if the
+        level does not exist in the file and any other value if it does.
+
+        :param frame: the frame number.
+        :returns: a list of levels length.
+        """
+        return [True] * self.levels
+
+    def _getTileFromEmptyLevel(self, x, y, z, **kwargs):
+        """
+        Given the x, y, z tile location in an unpopulated level, get tiles from
+        higher resolution levels to make the lower-res tile.
+
+        :param x: location of tile within original level.
+        :param y: location of tile within original level.
+        :param z: original level.
+        :returns: tile in PIL format.
+        """
+        basez = z
+        scale = 1
+        dirlist = self._nonemptyLevelsList(kwargs.get('frame'))
+        while dirlist[z] is None:
+            scale *= 2
+            z += 1
+        while z - basez > self._maxSkippedLevels:
+            z -= self._maxSkippedLevels
+            scale = int(scale / 2 ** self._maxSkippedLevels)
+        tile = PIL.Image.new('RGBA', (
+            min(self.sizeX, self.tileWidth * scale), min(self.sizeY, self.tileHeight * scale)))
+        maxX = 2.0 ** (z + 1 - self.levels) * self.sizeX / self.tileWidth
+        maxY = 2.0 ** (z + 1 - self.levels) * self.sizeY / self.tileHeight
+        for newX in range(scale):
+            for newY in range(scale):
+                if ((newX or newY) and ((x * scale + newX) >= maxX or
+                                        (y * scale + newY) >= maxY)):
+                    continue
+                subtile = self.getTile(
+                    x * scale + newX, y * scale + newY, z,
+                    pilImageAllowed=True, numpyAllowed=False,
+                    sparseFallback=True, edge=False, frame=kwargs.get('frame'))
+                subtile = _imageToPIL(subtile)
+                tile.paste(subtile, (newX * self.tileWidth,
+                                     newY * self.tileHeight))
+        return tile.resize((self.tileWidth, self.tileHeight),
+                           getattr(PIL.Image, 'Resampling', PIL.Image).LANCZOS)
+
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
                 sparseFallback=False, frame=None):
@@ -1993,10 +2049,16 @@ def getPreferredLevel(self, level):
         :param level: desired level
         :returns level: a level with actual data that is no lower resolution.
         """
-        metadata = self.getMetadata()
-        if metadata['levels'] is None:
+        if self.levels is None:
             return level
-        return max(0, min(level, metadata['levels'] - 1))
+        level = max(0, min(level, self.levels - 1))
+        baselevel = level
+        levelList = self._nonemptyLevelsList()
+        while levelList[level] is None and level < self.levels - 1:
+            level += 1
+        while level - baselevel >= self._maxSkippedLevels:
+            level -= self._maxSkippedLevels
+        return level
 
     def convertRegionScale(
             self, sourceRegion, sourceScale=None, targetScale=None,

sources/bioformats/large_image_source_bioformats/__init__.py

@@ -480,6 +480,19 @@ def _computeMagnification(self):
                 self._magnification['magnification'] = float(metadata[key])
                 break
 
+    def _nonemptyLevelsList(self, frame=0):
+        """
+        Return a list of one value per level where the value is None if the
+        level does not exist in the file and any other value if it does.
+
+        :param frame: the frame number.
+        :returns: a list of levels length.
+        """
+        nonempty = [True if v is not None else None
+                    for v in self._metadata['frameSeries'][0]['series']][:self.levels]
+        nonempty += [None] * (self.levels - len(nonempty))
+        return nonempty[::-1]
+
     def getNativeMagnification(self):
         """
         Get the magnification at a particular level.
@@ -537,35 +550,6 @@ def getInternalMetadata(self, **kwargs):
         """
         return self._metadata
 
-    def _getTileFromEmptyLevel(self, x, y, z, **kwargs):
-        """
-        Composite tiles from missing levels from larger levels in pieces to
-        avoid using too much memory.
-        """
-        fac = int(2 ** self._maxSkippedLevels)
-        z += self._maxSkippedLevels
-        scale = 2 ** (self.levels - 1 - z)
-        result = None
-        for tx in range(fac - 1, -1, -1):
-            if x * fac + tx >= int(math.ceil(self.sizeX / self.tileWidth / scale)):
-                continue
-            for ty in range(fac - 1, -1, -1):
-                if y * fac + ty >= int(math.ceil(self.sizeY / self.tileHeight / scale)):
-                    continue
-                tile = self.getTile(
-                    x * fac + tx, y * fac + ty, z, pilImageAllowed=False,
-                    numpyAllowed=True, **kwargs)
-                if result is None:
-                    result = np.zeros((
-                        ty * fac + tile.shape[0],
-                        tx * fac + tile.shape[1],
-                        tile.shape[2]), dtype=tile.dtype)
-                result[
-                    ty * fac:ty * fac + tile.shape[0],
-                    tx * fac:tx * fac + tile.shape[1],
-                    ::] = tile
-        return result[::scale, ::scale, ::]
-
     @methodcache()
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         self._xyzInRange(x, y, z)
@@ -601,6 +585,7 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
 
         if scale >= 2 ** self._maxSkippedLevels:
             tile = self._getTileFromEmptyLevel(x, y, z, **kwargs)
+            tile = large_image.tilesource.base._imageToNumpy(tile)[0]
             format = TILE_FORMAT_NUMPY
         else:
             with self._tileLock:

sources/dicom/large_image_source_dicom/__init__.py

@@ -157,6 +157,8 @@ def __init__(self, path, **kwargs):
         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)
+        # We need to detect which levels are functionally present if we want to
+        # return a sensible _nonemptyLevelsList
 
     def _open_wsi_dicom(self, path):
         if isinstance(path, dict):

sources/openjpeg/large_image_source_openjpeg/__init__.py

@@ -33,6 +33,7 @@
 from large_image.constants import TILE_FORMAT_NUMPY, SourcePriority
 from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError
 from large_image.tilesource import FileTileSource, etreeToDict
+from large_image.tilesource.utilities import _imageToNumpy
 
 try:
     __version__ = _importlib_version(__name__)
@@ -158,6 +159,17 @@ def _getAssociatedImages(self):
                     if getattr(subbox, 'icc_profile', None):
                         self._iccprofiles = [subbox.icc_profile]
 
+    def _nonemptyLevelsList(self, frame=0):
+        """
+        Return a list of one value per level where the value is None if the
+        level does not exist in the file and any other value if it does.
+
+        :param frame: the frame number.
+        :returns: a list of levels length.
+        """
+        return [True if self.levels - 1 - idx < self._populatedLevels else None
+                for idx in range(self.levels)]
+
     def getNativeMagnification(self):
         """
         Get the magnification at a particular level.
@@ -243,26 +255,30 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         self._xyzInRange(x, y, z)
         x0, y0, x1, y1, step = self._xyzToCorners(x, y, z)
         scale = None
-        if z < self._minlevel:
-            scale = int(2 ** (self._minlevel - z))
-            step = int(2 ** (self.levels - 1 - self._minlevel))
-        # possibly open the file multiple times so multiple threads can access
-        # it concurrently.
-        while True:
+        if self._minlevel - z > self._maxSkippedLevels:
+            tile = self._getTileFromEmptyLevel(x, y, z, **kwargs)
+            tile = _imageToNumpy(tile)[0]
+        else:
+            if z < self._minlevel:
+                scale = int(2 ** (self._minlevel - z))
+                step = int(2 ** (self.levels - 1 - self._minlevel))
+            # possibly open the file multiple times so multiple threads can access
+            # it concurrently.
+            while True:
+                try:
+                    # A timeout prevents uninterupptable waits on some platforms
+                    openjpegHandle = self._openjpegHandles.get(timeout=1.0)
+                    break
+                except queue.Empty:
+                    continue
+            if openjpegHandle is None:
+                openjpegHandle = glymur.Jp2k(self._largeImagePath)
             try:
-                # A timeout prevents uninterupptable waits on some platforms
-                openjpegHandle = self._openjpegHandles.get(timeout=1.0)
-                break
-            except queue.Empty:
-                continue
-        if openjpegHandle is None:
-            openjpegHandle = glymur.Jp2k(self._largeImagePath)
-        try:
-            tile = openjpegHandle[y0:y1:step, x0:x1:step]
-        finally:
-            self._openjpegHandles.put(openjpegHandle)
-        if scale:
-            tile = tile[::scale, ::scale]
+                tile = openjpegHandle[y0:y1:step, x0:x1:step]
+            finally:
+                self._openjpegHandles.put(openjpegHandle)
+            if scale:
+                tile = tile[::scale, ::scale]
         return self._outputTile(tile, TILE_FORMAT_NUMPY, x, y, z,
                                 pilImageAllowed, numpyAllowed, **kwargs)
 

sources/openslide/large_image_source_openslide/__init__.py

@@ -225,6 +225,16 @@ def _getAvailableLevels(self, path):
                   nearPowerOfTwo(levels[0]['height'], entry['height'])]
         return levels
 
+    def _nonemptyLevelsList(self, frame=0):
+        """
+        Return a list of one value per level where the value is None if the
+        level does not exist in the file and any other value if it does.
+
+        :param frame: the frame number.
+        :returns: a list of levels length.
+        """
+        return [True if l['scale'] == 1 else None for l in self._svslevels]
+
     def getNativeMagnification(self):
         """
         Get the magnification at a particular level.
@@ -284,18 +294,21 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         # We ask to read an area that will cover the tile at the z level.  The
         # scale we computed in the __init__ process for this svs level tells
         # how much larger a region we need to read.
-        try:
-            tile = self._openslide.read_region(
-                (offsetx, offsety), svslevel['svslevel'],
-                (self.tileWidth * svslevel['scale'],
-                 self.tileHeight * svslevel['scale']))
-        except openslide.lowlevel.OpenSlideError as exc:
-            raise TileSourceError(
-                'Failed to get OpenSlide region (%r).' % exc)
-        # Always scale to the svs level 0 tile size.
-        if svslevel['scale'] != 1:
-            tile = tile.resize((self.tileWidth, self.tileHeight),
-                               getattr(PIL.Image, 'Resampling', PIL.Image).LANCZOS)
+        if svslevel['scale'] > 2 ** self._maxSkippedLevels:
+            tile = self._getTileFromEmptyLevel(x, y, z, **kwargs)
+        else:
+            try:
+                tile = self._openslide.read_region(
+                    (offsetx, offsety), svslevel['svslevel'],
+                    (self.tileWidth * svslevel['scale'],
+                     self.tileHeight * svslevel['scale']))
+            except openslide.lowlevel.OpenSlideError as exc:
+                raise TileSourceError(
+                    'Failed to get OpenSlide region (%r).' % exc)
+            # Always scale to the svs level 0 tile size.
+            if svslevel['scale'] != 1:
+                tile = tile.resize((self.tileWidth, self.tileHeight),
+                                   getattr(PIL.Image, 'Resampling', PIL.Image).LANCZOS)
         return self._outputTile(tile, TILE_FORMAT_PIL, x, y, z, pilImageAllowed,
                                 numpyAllowed, **kwargs)
 

sources/tiff/large_image_source_tiff/__init__.py

@@ -72,14 +72,6 @@ class TiffFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         'image/x-ptif': SourcePriority.PREFERRED,
     }
 
-    # When getting tiles for otherwise empty directories (missing powers of
-    # two), we composite the tile from higher resolution levels.  This can use
-    # excessive memory if there are too many missing levels.  For instance, if
-    # there are six missing levels and the tile size is 1024 square RGBA, then
-    # 16 Gb are needed for the composited tile at a minimum.  By setting
-    # _maxSkippedLevels, such large gaps are composited in stages.
-    _maxSkippedLevels = 3
-
     _maxAssociatedImageSize = 8192
 
     def __init__(self, path, **kwargs):  # noqa
@@ -643,7 +635,7 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
             if dir is None:
                 try:
                     if not kwargs.get('inSparseFallback'):
-                        tile = self.getTileFromEmptyDirectory(x, y, z, **kwargs)
+                        tile = self._getTileFromEmptyLevel(x, y, z, **kwargs)
                     else:
                         raise IOTiffError('Missing z level %d' % z)
                 except Exception:
@@ -713,64 +705,19 @@ def getTileIOTiffError(self, x, y, z, pilImageAllowed=False,
                                     numpyAllowed, applyStyle=False, **kwargs)
         raise TileSourceError('Internal I/O failure: %s' % exception.args[0])
 
-    def getTileFromEmptyDirectory(self, x, y, z, **kwargs):
+    def _nonemptyLevelsList(self, frame=0):
         """
-        Given the x, y, z tile location in an unpopulated level, get tiles from
-        higher resolution levels to make the lower-res tile.
+        Return a list of one value per level where the value is None if the
+        level does not exist in the file and any other value if it does.
 
-        :param x: location of tile within original level.
-        :param y: location of tile within original level.
-        :param z: original level.
-        :returns: tile in PIL format.
+        :param frame: the frame number.
+        :returns: a list of levels length.
         """
-        basez = z
-        scale = 1
         dirlist = self._tiffDirectories
-        frame = self._getFrame(**kwargs)
+        frame = int(frame or 0)
         if frame > 0 and hasattr(self, '_frames'):
             dirlist = self._frames[frame]['dirs']
-        while dirlist[z] is None:
-            scale *= 2
-            z += 1
-        while z - basez > self._maxSkippedLevels:
-            z -= self._maxSkippedLevels
-            scale = int(scale / 2 ** self._maxSkippedLevels)
-        tile = PIL.Image.new('RGBA', (
-            min(self.sizeX, self.tileWidth * scale), min(self.sizeY, self.tileHeight * scale)))
-        maxX = 2.0 ** (z + 1 - self.levels) * self.sizeX / self.tileWidth
-        maxY = 2.0 ** (z + 1 - self.levels) * self.sizeY / self.tileHeight
-        for newX in range(scale):
-            for newY in range(scale):
-                if ((newX or newY) and ((x * scale + newX) >= maxX or
-                                        (y * scale + newY) >= maxY)):
-                    continue
-                subtile = self.getTile(
-                    x * scale + newX, y * scale + newY, z,
-                    pilImageAllowed=True, numpyAllowed=False,
-                    sparseFallback=True, edge=False, frame=frame)
-                if not isinstance(subtile, PIL.Image.Image):
-                    subtile = PIL.Image.open(io.BytesIO(subtile))
-                tile.paste(subtile, (newX * self.tileWidth,
-                                     newY * self.tileHeight))
-        return tile.resize((self.tileWidth, self.tileHeight),
-                           getattr(PIL.Image, 'Resampling', PIL.Image).LANCZOS)
-
-    def getPreferredLevel(self, level):
-        """
-        Given a desired level (0 is minimum resolution, self.levels - 1 is max
-        resolution), return the level that contains actual data that is no
-        lower resolution.
-
-        :param level: desired level
-        :returns level: a level with actual data that is no lower resolution.
-        """
-        level = max(0, min(level, self.levels - 1))
-        baselevel = level
-        while self._tiffDirectories[level] is None and level < self.levels - 1:
-            level += 1
-        while level - baselevel >= self._maxSkippedLevels:
-            level -= self._maxSkippedLevels
-        return level
+        return dirlist
 
     def getAssociatedImagesList(self):
         """