large-image-source-multi 1.27.5.dev6__py3-none-any.whl → 1.30.7.dev10__py3-none-any.whl

large_image_source_multi/__init__.py

@@ -10,7 +10,6 @@ from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 from pathlib import Path
 
-import jsonschema
 import numpy as np
 import yaml
 
@@ -27,6 +26,26 @@ except PackageNotFoundError:
     # package is not installed
     pass
 
+jsonschema = None
+_validator = None
+
+
+def _lazyImport():
+    """
+    Import the jsonschema module.  This is done when needed rather than in the
+    module initialization because it is slow.
+    """
+    global jsonschema, _validator
+
+    if jsonschema is None:
+        try:
+            import jsonschema
+
+            _validator = jsonschema.Draft6Validator(MultiSourceSchema)
+        except ImportError:
+            msg = 'jsonschema module not found.'
+            raise TileSourceError(msg)
+
 
 SourceEntrySchema = {
     'type': 'object',
@@ -269,10 +288,24 @@ SourceEntrySchema = {
             'type': 'array',
             'items': {'type': 'integer'},
         },
-        'style': {'type': 'object'},
-        'params': {
+        'sampleScale': {
             'description':
-                'Additional parameters to pass to the base tile source',
+                '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': {
+            'description': 'A style specification to pass to the base tile source',
+            'type': 'object',
+        },
+        'params': {
+            'description': 'Additional parameters to pass to the base tile source',
             'type': 'object',
         },
     },
@@ -333,6 +366,10 @@ MultiSourceSchema = {
                 'layout and size, assume all sources are so similar',
             'type': 'boolean',
         },
+        'dtype': {
+            'description': 'If present, a numpy dtype name to use for the data.',
+            'type': 'string',
+        },
         'singleBand': {
             'description':
                 'If true, output only the first band of compositied results',
@@ -376,6 +413,7 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         None: SourcePriority.FALLBACK,
         'application/json': SourcePriority.PREFERRED,
         'application/yaml': SourcePriority.PREFERRED,
+        'text/yaml': SourcePriority.PREFERRED,
     }
 
     _minTileSize = 64
@@ -383,9 +421,7 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     _defaultTileSize = 256
     _maxOpenHandles = 6
 
-    _validator = jsonschema.Draft6Validator(MultiSourceSchema)
-
-    def __init__(self, path, **kwargs):
+    def __init__(self, path, **kwargs):  # noqa
         """
         Initialize the tile class.  See the base class for other available
         parameters.
@@ -394,11 +430,22 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         """
         super().__init__(path, **kwargs)
 
+        _lazyImport()
+        self._validator = _validator
         self._largeImagePath = self._getLargeImagePath()
         self._lastOpenSourceLock = threading.RLock()
         # 'c' must be first as channels are special because they can have names
         self._axesList = ['c', 'z', 't', 'xy']
-        if not os.path.isfile(self._largeImagePath):
+        if isinstance(path, dict) and 'sources' in path:
+            self._info = path.copy()
+            self._basePath = '.'
+            self._largeImagePath = '.'
+            try:
+                self._validator.validate(self._info)
+            except jsonschema.ValidationError:
+                msg = 'File cannot be validated via multi-source reader.'
+                raise TileSourceError(msg)
+        elif not os.path.isfile(self._largeImagePath):
             try:
                 possibleYaml = self._largeImagePath.split('multi://', 1)[-1]
                 self._info = yaml.safe_load(possibleYaml)
@@ -410,7 +457,8 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             try:
                 with builtins.open(self._largeImagePath) as fptr:
                     start = fptr.read(1024).strip()
-                    if start[:1] not in ('{', '#', '-') and (start[:1] < 'a' or start[:1] > 'z'):
+                    if (start[:1] not in ('{', '#', '-') and
+                            (start[:1] < 'a' or start[:1] > 'z')) or 'FeatureCollection' in start:
                         msg = 'File cannot be opened via multi-source reader.'
                         raise TileSourceError(msg)
                     fptr.seek(0)
@@ -661,9 +709,15 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             aKey = tuple(self._axisKey(source, frame.get(f'Index{axis.upper()}') or 0, axis)
                          for axis in self._axesList)
             channel = channels[cIdx] if cIdx < len(channels) else None
+            # We add the channel name to our channel list if the individual
+            # source lists the channel name or a set of channels OR the source
+            # appends channels to an existing set.
             if channel and channel not in self._channels and (
-                    'channel' in source or 'channels' in source):
+                    'channel' in source or 'channels' in source or
+                    len(self._channels) == aKey[0]):
                 self._channels.append(channel)
+            # Adjust the channel number if the source named the channel; do not
+            # do so in other cases
             if (channel and channel in self._channels and
                     'c' not in source and 'cValues' not in source):
                 aKey = tuple([self._channels.index(channel)] + list(aKey[1:]))
@@ -759,7 +813,11 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 self.tileWidth = self.tileWidth or ts.tileWidth
                 self.tileHeight = self.tileHeight or ts.tileHeight
                 if not hasattr(self, '_firstdtype'):
-                    self._firstdtype = ts.dtype
+                    self._firstdtype = (
+                        ts.dtype if not self._info.get('dtype') else
+                        np.dtype(self._info['dtype']))
+                    if self._info.get('dtype'):
+                        self._dtype = np.dtype(self._info['dtype'])
                 if not numChecked:
                     tsMag = ts.getNativeMagnification()
                     for key in self._nativeMagnification:
@@ -773,7 +831,7 @@ 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'])))
@@ -828,7 +886,8 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         with self._lastOpenSourceLock:
             if (hasattr(self, '_lastOpenSource') and
                     self._lastOpenSource['source'] == source and
-                    self._lastOpenSource['params'] == params):
+                    (self._lastOpenSource['params'] == params or (
+                        params == {} and self._lastOpenSource['params'] is None))):
                 return self._lastOpenSource['ts']
         if not len(large_image.tilesource.AvailableTileSources):
             large_image.tilesource.loadTileSources()
@@ -841,6 +900,22 @@ 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 == 'check' or np.dtype(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 = {
                 'source': source,
@@ -860,7 +935,7 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             None if the associated image doesn't exist.
         """
         if imageKey not in self._associatedImages:
-            return
+            return None
         source = self._sources[self._associatedImages[imageKey]['sourcenum']]
         ts = self._openSource(source)
         return ts.getAssociatedImage(self._associatedImages[imageKey]['key'], *args, **kwargs)
@@ -894,7 +969,7 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         """
         Return additional known metadata about the tile source.  Data returned
         from this method is not guaranteed to be in any particular format or
-        have specific values.
+        have specific values.  Also, only the first 100 sources are used.
 
         :returns: a dictionary of data or None.
         """
@@ -903,7 +978,7 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             'sources': copy.deepcopy(self._sources),
             'sourceFiles': [],
         }
-        for path in self._sourcePaths.values():
+        for path in list(self._sourcePaths.values())[:100]:
             source = self._sources[min(path['sourcenum'])]
             ts = self._openSource(source)
             result['sourceFiles'].append({
@@ -937,38 +1012,39 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 (tile.shape[0] + y - base.shape[0], base.shape[1], base.shape[2]),
                 dtype=base.dtype)
             if base.shape[2] in {2, 4}:
-                vfill[:, :, -1] = fullAlphaValue(self.dtype)
+                vfill[:, :, -1] = fullAlphaValue(base.dtype)
             base = np.vstack((base, vfill))
         if base.shape[1] < tile.shape[1] + x:
             hfill = np.zeros(
                 (base.shape[0], tile.shape[1] + x - base.shape[1], base.shape[2]),
                 dtype=base.dtype)
             if base.shape[2] in {2, 4}:
-                hfill[:, :, -1] = fullAlphaValue(self.dtype)
+                hfill[:, :, -1] = fullAlphaValue(base.dtype)
             base = np.hstack((base, hfill))
         if base.flags.writeable is False:
             base = base.copy()
         if base.shape[2] in {2, 4}:
             baseA = base[y:y + tile.shape[0], x:x + tile.shape[1], -1].astype(
-                float) / fullAlphaValue(self.dtype)
-            tileA = tile[:, :, -1].astype(float) / fullAlphaValue(self.dtype)
+                float) / fullAlphaValue(base.dtype)
+            tileA = tile[:, :, -1].astype(float) / fullAlphaValue(tile.dtype)
             outA = tileA + baseA * (1 - tileA)
             base[y:y + tile.shape[0], x:x + tile.shape[1], :-1] = (
-                np.where(tileA[..., np.newaxis], tile[:, :, :-1], 0) +
+                np.where(tileA[..., np.newaxis], tile[:, :, :-1] * tileA[..., np.newaxis], 0) +
                 base[y:y + tile.shape[0], x:x + tile.shape[1], :-1] * baseA[..., np.newaxis] *
                 (1 - tileA[..., np.newaxis])
             ) / np.where(outA[..., np.newaxis], outA[..., np.newaxis], 1)
-            base[y:y + tile.shape[0], x:x + tile.shape[1], -1] = outA * fullAlphaValue(self.dtype)
+            base[y:y + tile.shape[0], x:x + tile.shape[1], -1] = outA * fullAlphaValue(base.dtype)
         else:
             base[y:y + tile.shape[0], x:x + tile.shape[1], :] = tile
         return base
 
-    def _getTransformedTile(self, ts, transform, corners, scale, frame, crop=None):
+    def _getTransformedTile(self, ts, transform, corners, scale, frame,
+                            crop=None, firstMerge=False):
         """
         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
@@ -980,6 +1056,9 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         :param crop: an optional dictionary to crop the source image in full
             resolution, untransformed coordinates.  This may contain left, top,
             right, and bottom values in pixels.
+        :param firstMerge: if False and using an alpha channel, transform
+            with nearest neighbor rather than a higher order function to
+            avoid transparency effects.
         :returns: a numpy array tile or None, x, y coordinates within the
             target tile for the placement of the numpy tile array.
         """
@@ -1010,7 +1089,7 @@ 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,
@@ -1057,28 +1136,38 @@ 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))
-        # Add an alpha band if needed
+        destShape = [
+            max(max(math.ceil(c[1]) for c in destcorners), srcImage.shape[0]),
+            max(max(math.ceil(c[0]) for c in destcorners), srcImage.shape[1]),
+        ]
+        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.  This has to be done before the
+        # transform if it isn't the first tile, since the unused transformed
+        # areas need to have a zero alpha value
         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')
+        useNearest = srcImage.shape[2] in {2, 4} and not firstMerge
+        # 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=0 if useNearest else 3,
+            output_shape=(destShape[0], destShape[1], srcImage.shape[2]),
+        ).astype(srcImage.dtype)
         return destImage, x, y
 
     def _addSourceToTile(self, tile, sourceEntry, corners, scale):
@@ -1098,12 +1187,12 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         :returns: a numpy array of the tile.
         """
         source = self._sources[sourceEntry['sourcenum']]
-        ts = self._openSource(source, sourceEntry['kwargs'])
         # If tile is outside of bounding box, skip it
         bbox = source['bbox']
         if (corners[2][0] <= bbox['left'] or corners[0][0] >= bbox['right'] or
                 corners[2][1] <= bbox['top'] or corners[0][1] >= bbox['bottom']):
             return tile
+        ts = self._openSource(source, sourceEntry['kwargs'])
         transform = bbox.get('transform')
         x = y = 0
         # If there is no transform or the diagonals are positive and there is
@@ -1153,8 +1242,23 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         else:
             sourceTile, x, y = self._getTransformedTile(
                 ts, transform, corners, scale, sourceEntry.get('frame', 0),
-                source.get('position', {}).get('crop'))
+                source.get('position', {}).get('crop'),
+                firstMerge=tile is None)
         if sourceTile is not None and all(dim > 0 for dim in sourceTile.shape):
+            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-1.27.5.dev6.dist-info → large_image_source_multi-1.30.7.dev10.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.2
 Name: large-image-source-multi
-Version: 1.27.5.dev6
+Version: 1.30.7.dev10
 Summary: A tilesource for large_image to composite other tile sources
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -15,15 +15,29 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
-Requires-Python: >=3.6
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: jsonschema
-Requires-Dist: large-image >=1.27.5.dev6
+Requires-Dist: large-image>=1.30.7.dev10
 Requires-Dist: pyyaml
 Provides-Extra: all
-Requires-Dist: scikit-image ; extra == 'all'
+Requires-Dist: scikit-image; extra == "all"
 Provides-Extra: girder
-Requires-Dist: girder-large-image >=1.27.5.dev6 ; extra == 'girder'
+Requires-Dist: girder-large-image>=1.30.7.dev10; extra == "girder"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: provides-extra
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 A tilesource for large_image to composite other tile sources
 

large_image_source_multi-1.30.7.dev10.dist-info/RECORD

@@ -0,0 +1,8 @@
+large_image_source_multi/__init__.py,sha256=rUPaj9H32i9v89rCPsjmIfCIEi_N-ZOE9jTiRMrllDc,59131
+large_image_source_multi/girder_source.py,sha256=YOp9hFCv-fzEhOIGAPdRewmyHM1jNu6WLr5Vt6cFtIA,1356
+large_image_source_multi-1.30.7.dev10.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+large_image_source_multi-1.30.7.dev10.dist-info/METADATA,sha256=ovk964Jj7KL1Fyqg1kACs_qKr1W0DGP8sOgJ_lx-ZHM,1482
+large_image_source_multi-1.30.7.dev10.dist-info/WHEEL,sha256=In9FTNxeP60KnTkGw7wk6mJPYd_dQSjEZmXdBdMCI-8,91
+large_image_source_multi-1.30.7.dev10.dist-info/entry_points.txt,sha256=1ufcPRbofaLVrGNESx1R9QhdUovr4jTzte185wHqpcU,172
+large_image_source_multi-1.30.7.dev10.dist-info/top_level.txt,sha256=v6W6Hkx77lY-DGQ8XqRgbdxYSJRLFv90dCrIJe15d2A,25
+large_image_source_multi-1.30.7.dev10.dist-info/RECORD,,

{large_image_source_multi-1.27.5.dev6.dist-info → large_image_source_multi-1.30.7.dev10.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (75.8.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

large_image_source_multi-1.27.5.dev6.dist-info/RECORD

@@ -1,8 +0,0 @@
-large_image_source_multi/__init__.py,sha256=E4xscgnBb1l0EsUQtaj5LoWpiiBhMqjm5MStHneiaio,54069
-large_image_source_multi/girder_source.py,sha256=YOp9hFCv-fzEhOIGAPdRewmyHM1jNu6WLr5Vt6cFtIA,1356
-large_image_source_multi-1.27.5.dev6.dist-info/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-large_image_source_multi-1.27.5.dev6.dist-info/METADATA,sha256=cB51hajqTzKi4NdqeSwiOfJawQsmi3YjNpIp1TamqP8,1139
-large_image_source_multi-1.27.5.dev6.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-large_image_source_multi-1.27.5.dev6.dist-info/entry_points.txt,sha256=1ufcPRbofaLVrGNESx1R9QhdUovr4jTzte185wHqpcU,172
-large_image_source_multi-1.27.5.dev6.dist-info/top_level.txt,sha256=v6W6Hkx77lY-DGQ8XqRgbdxYSJRLFv90dCrIJe15d2A,25
-large_image_source_multi-1.27.5.dev6.dist-info/RECORD,,