Merge pull request #1794 from girder/vips-lower-levels

Improve how we use vips to read lower tile levels

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Change Log
 
+## 1.31.1
+
+### Improvements
+
+- Improve how we use vips to read lower tile levels ([#1794](../../pull/1794))
+
 ## 1.31.0
 
 ### Features

docs/format_examples_datastore.py

@@ -100,7 +100,8 @@
         examples=[
             dict(
                 filename='sample_image.nd2',
-                # originally from 'https://downloads.openmicroscopy.org/images/ND2/aryeh/MeOh_high_fluo_003.nd2',
+                # originally from
+                # 'https://downloads.openmicroscopy.org/images/ND2/aryeh/MeOh_high_fluo_003.nd2',
                 url='https://data.kitware.com/api/v1/file/hashsum/sha512/4e76e490c915b10f646cb516f85a4d36d52aa7eff94715b90222644180e26fef6768493887c05adf182cf0351ba0bce659204041c4698a0f6b08423586788f4d/download',
                 hash='8e23bb594cd18314f9c18e70d736088ae46f8bc696ab7dc047784be416d7a706',
             ),
@@ -127,7 +128,8 @@
         examples=[
             dict(
                 filename='US-MONO2-8-8x-execho.dcm',
-                # originally from 'https://downloads.openmicroscopy.org/images/DICOM/samples/US-MONO2-8-8x-execho.dcm',
+                # originally from
+                # 'https://downloads.openmicroscopy.org/images/DICOM/samples/US-MONO2-8-8x-execho.dcm',
                 url='https://data.kitware.com/api/v1/file/hashsum/sha512/5332044f887d82c7f3693c6ca180f07accf5f00c2b7b1a3a29ef9ae737d5f1975478b5e2d5846c391987b8051416068f57a7062e848323c700412236b35679db/download',
                 hash='7d3f54806d0315c6cfc8b7371649a242b5ef8f31e0d20221971dd8087f2ff1ea',
             ),
@@ -141,7 +143,8 @@
         examples=[
             dict(
                 filename='20191025 Test FRET 585. 423, 426.lif',
-                # originally from 'https://downloads.openmicroscopy.org/images/Leica-LIF/imagesc-30856/20191025%20Test%20FRET%20585.%20423,%20426.lif',
+                # originally from
+                # 'https://downloads.openmicroscopy.org/images/Leica-LIF/imagesc-30856/20191025%20Test%20FRET%20585.%20423,%20426.lif',
                 url='https://data.kitware.com/api/v1/file/hashsum/sha512/d25de002d8a81dfcaf6b062b9f429ca85bb81423bc09d3aa33d9d51e9392cc4ace2b8521475e373ceecaf958effd0fade163e7173c467aab66c957da14482ed7/download',
                 hash='8d4ee62868b9616b832c2eb28e7d62ec050fb032e0bc11ea0a392f5c84390c71',
             ),
@@ -155,7 +158,8 @@
         examples=[
             dict(
                 filename='Animated_PNG_example_bouncing_beach_ball.png',
-                # originally from 'https://upload.wikimedia.org/wikipedia/commons/1/14/Animated_PNG_example_bouncing_beach_ball.png',
+                # originally from
+                # 'https://upload.wikimedia.org/wikipedia/commons/1/14/Animated_PNG_example_bouncing_beach_ball.png',
                 url='https://data.kitware.com/api/v1/file/hashsum/sha512/465ebdc2e81b2576dfc96b34e82db7f968e6d4f32f0fa80ef4bb0e44ed216230e6be1a2e4b11ae301a2905cc582dd24cbd2c360d9567ff7b1dac2c871f6d1e37/download',
                 hash='3b28e2462f1b31d0d15d795e6e58baf397899c3f864be7034bf47939b5bbbc3b',
             ),

sources/vips/large_image_source_vips/__init__.py

@@ -16,7 +16,7 @@
                                    dtypeToGValue)
 from large_image.exceptions import TileSourceError, TileSourceFileNotFoundError
 from large_image.tilesource import FileTileSource
-from large_image.tilesource.utilities import _imageToNumpy, _newFromFileLock
+from large_image.tilesource.utilities import _imageToNumpy, _newFromFileLock, nearPowerOfTwo
 
 logging.getLogger('pyvips').setLevel(logging.ERROR)
 
@@ -98,6 +98,7 @@ def __init__(self, path, **kwargs):  # noqa
         if 'n-pages' in self._image.get_fields():
             pages = self._image.get('n-pages')
         self._frames = [0]
+        self._lowres = {}
         for page in range(1, pages):
             subInputPath = self._largeImagePath + f'[page={page}{self._suffix}]'
             with _newFromFileLock:
@@ -113,21 +114,55 @@ def __init__(self, path, **kwargs):  # noqa
                 self._frames.append(page)
                 continue
             if subImage.width * subImage.height < self.sizeX * self.sizeY:
+                if (nearPowerOfTwo(self.sizeX, subImage.width) and
+                        nearPowerOfTwo(self.sizeY, subImage.height)):
+                    level = int(round(math.log(self.sizeX / subImage.width) / math.log(2)))
+                    self._lowres.setdefault(len(self._frames) - 1, {})[level] = page
                 continue
             self._frames = [page]
+            self._lowres = {}
             self.sizeX = subImage.width
             self.sizeY = subImage.height
             try:
                 self._image.close()
             except Exception:
                 pass
             self._image = subImage
+        self._checkLowerLevels()
         self.levels = int(max(1, math.ceil(math.log(
             float(max(self.sizeX, self.sizeY)) / self.tileWidth) / math.log(2)) + 1))
-        if len(self._frames) > 1:
+        if len(self._frames) > 1 or self._lowres is not None:
             self._recentFrames = cachetools.LRUCache(maxsize=6)
             self._frameLock = threading.RLock()
 
+    def _checkLowerLevels(self):
+        if (len(self._lowres) != len(self._frames) or
+                min(len(v) for v in self._lowres.values()) !=
+                max(len(v) for v in self._lowres.values()) or
+                min(len(v) for v in self._lowres.values()) == 0):
+            self._lowres = None
+            if len(self._frames) == 1 and 'openslide.level-count' in self._image.get_fields():
+                self._lowres = [{}]
+                for oslevel in range(1, int(self._image.get('openslide.level-count'))):
+                    with _newFromFileLock:
+                        try:
+                            subImage = pyvips.Image.new_from_file(
+                                self._largeImagePath, level=oslevel)
+                        except Exception:
+                            continue
+                        if subImage.width * subImage.height < self.sizeX * self.sizeY:
+                            if (nearPowerOfTwo(self.sizeX, subImage.width) and
+                                    nearPowerOfTwo(self.sizeY, subImage.height)):
+                                level = int(round(math.log(
+                                    self.sizeX / subImage.width) / math.log(2)))
+                                self._lowres[0][level] = (self._frames[0], oslevel)
+                if not len(self._lowres[0]):
+                    self._lowres = None
+        else:
+            self._lowres = list(self._lowres.values())
+        if self._lowres is not None:
+            self._populatedLevels = len(self._lowres[0]) + 1
+
     def _initNew(self, **kwargs):
         """
         Initialize the tile class for creating a new image.
@@ -139,6 +174,7 @@ def _initNew(self, **kwargs):
         self.sizeX = self.sizeY = self.levels = 0
         self.tileWidth = self.tileHeight = self._tileSize
         self._frames = [0]
+        self._lowres = None
         self._cacheValue = str(uuid.uuid4())
         self._output = None
         self._editable = True
@@ -194,25 +230,38 @@ def getMetadata(self):
             self._addMetadataFrameInformation(result)
         return result
 
-    def _getFrameImage(self, frame=0):
+    def _getFrameImage(self, frame=0, lowres=None):
         """
         Get the vips image associated with a specific frame.
 
         :param frame: the 0-based frame to get.
+        :param lowres: the lower resolution part of the frame
         :returns: a vips image.
         """
         if self._image is None and self._output:
             self._outputToImage()
         img = self._image
-        if frame > 0:
+        if frame > 0 or lowres:
             with self._frameLock:
-                if frame not in self._recentFrames:
-                    subpath = self._largeImagePath + f'[page={self._frames[frame]}{self._suffix}]'
+                key = (frame, lowres)
+                frameval = self._frames[frame]
+                params = {}
+                if lowres is not None:
+                    if isinstance(self._lowres[frame][lowres], tuple):
+                        frameval = self._lowres[frame][lowres][0]
+                        params = {'level': self._lowres[frame][lowres][1]}
+                    else:
+                        frameval = self._lowres[frame][lowres]
+                if key not in self._recentFrames:
+                    if frameval:
+                        subpath = self._largeImagePath + f'[page={frameval}{self._suffix}]'
+                    else:
+                        subpath = self._largeImagePath
                     with _newFromFileLock:
-                        img = pyvips.Image.new_from_file(subpath)
-                    self._recentFrames[frame] = img
+                        img = pyvips.Image.new_from_file(subpath, **params)
+                    self._recentFrames[key] = img
                 else:
-                    img = self._recentFrames[frame]
+                    img = self._recentFrames[key]
         return img
 
     def getNativeMagnification(self):
@@ -231,8 +280,22 @@ def getNativeMagnification(self):
     def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
         frame = self._getFrame(**kwargs)
         self._xyzInRange(x, y, z, frame, len(self._frames))
-        img = self._getFrameImage(frame)
         x0, y0, x1, y1, step = self._xyzToCorners(x, y, z)
+        lowres = None
+        if self._lowres and step > 1:
+            use = 0
+            for ll in self._lowres[frame].keys():
+                if 2 ** ll <= step:
+                    use = max(use, ll)
+            if use:
+                lowres = use
+                div = 2 ** use
+                x0 //= div
+                y0 //= div
+                x1 //= div
+                y1 //= div
+                step //= div
+        img = self._getFrameImage(frame, lowres)
         tileimg = img.crop(min(x0, img.width), min(y0, img.height),
                            min(x1, img.width) - min(x0, img.width),
                            min(y1, img.height) - min(y0, img.height))