large-image-source-multi 1.29.7.dev38__tar.gz → 1.29.8.dev6__tar.gz

{large-image-source-multi-1.29.7.dev38/large_image_source_multi.egg-info → large-image-source-multi-1.29.8.dev6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-multi
-Version: 1.29.7.dev38
+Version: 1.29.8.dev6
 Summary: A tilesource for large_image to composite other tile sources
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -16,14 +16,15 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.6
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: jsonschema
-Requires-Dist: large-image>=1.29.7.dev38
+Requires-Dist: large-image>=1.29.8.dev6
 Requires-Dist: pyyaml
 Provides-Extra: all
 Requires-Dist: scikit-image; extra == "all"
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.29.7.dev38; extra == "girder"
+Requires-Dist: girder-large-image>=1.29.8.dev6; extra == "girder"
 
 A tilesource for large_image to composite other tile sources
 

{large-image-source-multi-1.29.7.dev38 → large-image-source-multi-1.29.8.dev6}/large_image_source_multi/__init__.py

@@ -288,6 +288,18 @@ SourceEntrySchema = {
             'type': 'array',
             'items': {'type': 'integer'},
         },
+        'sampleScale': {
+            'description':
+                'Each pixel sample values is divided by this scale after any '
+                'sampleOffset has been applied',
+            'type': 'number',
+        },
+        'sampleOffset': {
+            'description':
+                'This is added to each pixel sample value before any '
+                'sampleScale is applied',
+            'type': 'number',
+        },
         'style': {'type': 'object'},
         'params': {
             'description':
@@ -806,7 +818,7 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                         self._bands = {}
                     self._bands.update(tsMeta['bands'])
                 lastSource = source
-            self._bandcount = 1 if self._info.get('singleBand') else (
+            self._bandCount = 1 if self._info.get('singleBand') else (
                 len(self._bands) if hasattr(self, '_bands') else (bandCount or None))
             bbox = self._sourceBoundingBox(source, tsMeta['sizeX'], tsMeta['sizeY'])
             computedWidth = max(computedWidth, int(math.ceil(bbox['right'])))
@@ -875,6 +887,20 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         if params is None:
             params = source.get('params', {})
         ts = openFunc(source['path'], **params)
+        if (self._dtype and np.dtype(ts.dtype).kind == 'f' and self._dtype.kind != 'f' and
+                'sampleScale' not in source and 'sampleOffset' not in source):
+            minval = maxval = 0
+            for f in range(ts.frames):
+                ftile = ts.getTile(x=0, y=0, z=0, frame=f, numpyAllowed='always')
+                minval = min(minval, np.amin(ftile))
+                maxval = max(maxval, np.amax(ftile))
+            if minval >= 0 and maxval <= 1:
+                source['sampleScale'] = None
+            elif minval >= 0:
+                source['sampleScale'] = 2 ** math.ceil(math.log2(maxval))
+            else:
+                source['sampleScale'] = 2 ** math.ceil(math.log2(max(-minval, maxval)) + 1)
+                source['sampleOffset'] = source['sampleScale'] / 2
         source['sourceName'] = ts.name
         with self._lastOpenSourceLock:
             self._lastOpenSource = {
@@ -1002,8 +1028,8 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         """
         Determine where the target tile's corners are located on the source.
         Fetch that so that we have at least sqrt(2) more resolution, then use
-        scikit-image warp to transform it.  scikit-image does a better job than
-        scipy.ndimage.affine_transform.
+        scikit-image warp to transform it.  scikit-image does a better and
+        faster job than scipy.ndimage.affine_transform.
 
         :param ts: the source of the image to transform.
         :param transform: a 3x3 affine 2d matrix for transforming the source
@@ -1045,7 +1071,7 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         # we only need every 1/srcscale pixel.
         srcscale = int(2 ** math.log2(max(1, srcscale)))
         # Pad to reduce edge effects at tile boundaries
-        border = int(math.ceil(2 * srcscale))
+        border = int(math.ceil(4 * srcscale))
         region = {
             'left': int(max(0, minx - border) // srcscale) * srcscale,
             'top': int(max(0, miny - border) // srcscale) * srcscale,
@@ -1092,28 +1118,35 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         x, y = int(math.floor(x)), int(math.floor(y))
         # Recompute where the source corners will land
         destcorners = (np.dot(transform, regioncorners.T).T).tolist()
-        destsize = (max(math.ceil(c[0]) for c in destcorners),
-                    max(math.ceil(c[1]) for c in destcorners))
+        destShape = [
+            max(max(math.ceil(c[0]) for c in destcorners), srcImage.shape[1]),
+            max(max(math.ceil(c[1]) for c in destcorners), srcImage.shape[0]),
+        ]
+        if max(0, -x) or max(0, -y):
+            transform[0][2] -= max(0, -x)
+            transform[1][2] -= max(0, -y)
+            destShape[0] -= max(0, -y)
+            destShape[1] -= max(0, -x)
+            x += max(0, -x)
+            y += max(0, -y)
+        destShape = [min(destShape[0], outh - y), min(destShape[1], outw - x)]
+        if destShape[0] <= 0 or destShape[1] <= 0:
+            return None, None, None
         # Add an alpha band if needed
         if srcImage.shape[2] in {1, 3}:
             _, srcImage = _makeSameChannelDepth(np.zeros((1, 1, srcImage.shape[2] + 1)), srcImage)
-        # Add enough space to warp the source image in place
-        srcImage = np.pad(srcImage, (
-            (0, max(0, destsize[1] - srcImage.shape[0])),
-            (0, max(0, destsize[0] - srcImage.shape[1])),
-            (0, 0)), mode='constant')
+        # skimage.transform.warp is faster and has less artifacts than
+        # scipy.ndimage.affine_transform.  It is faster than using cupy's
+        # version of scipy's affine_transform when the source and destination
+        # images are converted from numpy to cupy and back in this method.
         destImage = skimage.transform.warp(
+            # Although using np.float32 could reduce memory use, it doesn't
+            # provide any speed improvement
             srcImage.astype(float),
-            skimage.transform.AffineTransform(np.linalg.inv(
-                transform))).astype(srcImage.dtype)
-        # Trim to target size and location
-        destImage = destImage[max(0, -y):, max(0, -x):, :]
-        x += max(0, -x)
-        y += max(0, -y)
-        if x >= outw or y >= outh:
-            return None, None, None
-        destImage = destImage[:min(destImage.shape[0], outh - y),
-                              :min(destImage.shape[1], outw - x), :]
+            skimage.transform.AffineTransform(np.linalg.inv(transform)),
+            order=3,
+            output_shape=(destShape[0], destShape[1], srcImage.shape[2]),
+        ).astype(srcImage.dtype)
         return destImage, x, y
 
     def _addSourceToTile(self, tile, sourceEntry, corners, scale):
@@ -1190,9 +1223,20 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 ts, transform, corners, scale, sourceEntry.get('frame', 0),
                 source.get('position', {}).get('crop'))
         if sourceTile is not None and all(dim > 0 for dim in sourceTile.shape):
-            sourceTile = sourceTile.astype(
-                ts.dtype if not self._info.get('dtype') else
-                np.dtype(self._info['dtype']))
+            targetDtype = np.dtype(self._info.get('dtype', ts.dtype))
+            changeDtype = sourceTile.dtype != targetDtype
+            if source.get('sampleScale') or source.get('sampleOffset'):
+                sourceTile = sourceTile.astype(float)
+                if source.get('sampleOffset'):
+                    sourceTile[:, :, :-1] += source['sampleOffset']
+                if source.get('sampleScale') and source.get('sampleScale') != 1:
+                    sourceTile[:, :, :-1] /= source['sampleScale']
+            if sourceTile.dtype != targetDtype:
+                if changeDtype:
+                    sourceTile = (
+                        sourceTile.astype(float) * fullAlphaValue(targetDtype) /
+                        fullAlphaValue(sourceTile))
+                sourceTile = sourceTile.astype(targetDtype)
             tile = self._mergeTiles(tile, sourceTile, x, y)
         return tile
 

{large-image-source-multi-1.29.7.dev38 → large-image-source-multi-1.29.8.dev6/large_image_source_multi.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-multi
-Version: 1.29.7.dev38
+Version: 1.29.8.dev6
 Summary: A tilesource for large_image to composite other tile sources
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -16,14 +16,15 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.6
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: jsonschema
-Requires-Dist: large-image>=1.29.7.dev38
+Requires-Dist: large-image>=1.29.8.dev6
 Requires-Dist: pyyaml
 Provides-Extra: all
 Requires-Dist: scikit-image; extra == "all"
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.29.7.dev38; extra == "girder"
+Requires-Dist: girder-large-image>=1.29.8.dev6; extra == "girder"
 
 A tilesource for large_image to composite other tile sources
 

large-image-source-multi-1.29.8.dev6/large_image_source_multi.egg-info/requires.txt

@@ -0,0 +1,9 @@
+jsonschema
+large-image>=1.29.8.dev6
+pyyaml
+
+[all]
+scikit-image
+
+[girder]
+girder-large-image>=1.29.8.dev6

{large-image-source-multi-1.29.7.dev38 → large-image-source-multi-1.29.8.dev6}/setup.py

@@ -37,6 +37,7 @@ setup(
                      'fallback_version': '0.0.0'},
     description=description,
     long_description=long_description,
+    long_description_content_type='text/x-rst',
     license='Apache Software License 2.0',
     author='Kitware, Inc.',
     author_email='kitware@kitware.com',

large-image-source-multi-1.29.7.dev38/large_image_source_multi.egg-info/requires.txt

@@ -1,9 +0,0 @@
-jsonschema
-large-image>=1.29.7.dev38
-pyyaml
-
-[all]
-scikit-image
-
-[girder]
-girder-large-image>=1.29.7.dev38