large-image-source-multi 1.30.1.dev16__tar.gz → 1.33.6.dev6__tar.gz

{large_image_source_multi-1.30.1.dev16/large_image_source_multi.egg-info → large_image_source_multi-1.33.6.dev6}/PKG-INFO

@@ -1,31 +1,42 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: large-image-source-multi
-Version: 1.30.1.dev16
+Version: 1.33.6.dev6
 Summary: A tilesource for large_image to composite other tile sources
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
 Author-email: kitware@kitware.com
-License: Apache Software License 2.0
+License: Apache-2.0
 Keywords: large_image,tile source
 Classifier: Development Status :: 5 - Production/Stable
-Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: jsonschema
-Requires-Dist: large-image>=1.30.1.dev16
+Requires-Dist: large-image>=1.33.6.dev6
 Requires-Dist: pyyaml
 Provides-Extra: all
 Requires-Dist: scikit-image; extra == "all"
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.1.dev16; extra == "girder"
+Requires-Dist: girder-large-image>=1.33.6.dev6; extra == "girder"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+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-1.30.1.dev16 → large_image_source_multi-1.33.6.dev6}/README.rst

@@ -1,25 +1,23 @@
 Large Image
 ===========
 
-|build-status| |codecov-io| |license-badge| |doi-badge| |pypi-badge|
+.. image:: https://img.shields.io/circleci/build/github/girder/large_image.svg
+  :target: https://circleci.com/gh/girder/large_image
+  :alt: Build Status
 
-.. |build-status| image:: https://img.shields.io/circleci/build/github/girder/large_image.svg
-    :target: https://circleci.com/gh/girder/large_image
-    :alt: Build Status
+.. image:: https://img.shields.io/badge/license-Apache%202-blue.svg
+  :target: https://raw.githubusercontent.com/girder/large_image/master/LICENSE
+  :alt: License
 
-.. |license-badge| image:: https://img.shields.io/badge/license-Apache%202-blue.svg
-    :target: https://raw.githubusercontent.com/girder/large_image/master/LICENSE
-    :alt: License
+.. image:: https://img.shields.io/codecov/c/github/girder/large_image.svg
+  :target: https://codecov.io/github/girder/large_image?branch=master
+  :alt: codecov.io
 
-.. |codecov-io| image:: https://img.shields.io/codecov/c/github/girder/large_image.svg
-   :target: https://codecov.io/github/girder/large_image?branch=master
-   :alt: codecov.io
+.. image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4562625-blue.svg
+  :target: https://doi.org/10.5281/zenodo.4562625
 
-.. |doi-badge| image:: https://img.shields.io/badge/DOI-10.5281%2Fzenodo.4723355-blue.svg
-   :target: https://zenodo.org/badge/latestdoi/45569214
-
-.. |pypi-badge| image:: https://img.shields.io/pypi/v/large-image.svg?logo=python&logoColor=white
-   :target: https://pypi.org/project/large-image/
+.. image:: https://img.shields.io/pypi/v/large-image.svg?logo=python&logoColor=white
+  :target: https://pypi.org/project/large-image/
 
 *Python modules to work with large, multiresolution images.*
 
@@ -156,13 +154,15 @@ There is also cache management to balance memory use and speed of response in Gi
 
 Most tile sources can be used with Girder Large Image.  You can specify an extras_require of ``girder`` to install the following packages:
 
-  - ``girder-large-image``: Large Image as a Girder 3.x plugin.
-    You can install ``large-image[tasks]`` to install a Girder Worker task that can convert otherwise unreadable images to pyramidal tiff files.
+- ``girder-large-image``: Large Image as a Girder 3.x plugin.
+
+  You can install ``large-image[tasks]`` to install a Girder Worker task that can convert otherwise unreadable images to pyramidal tiff files.
+
+- ``girder-large-image-annotation``: Adds models to the Girder database for supporting annotating large images.  These annotations can be rendered on images. Annotations can include polygons, points, image overlays, and other types. Each annotation can have a label and metadata.
 
-  - ``girder-large-image-annotation``: Adds models to the Girder database for supporting annotating large images.  These annotations can be rendered on images. Annotations can include polygons, points, image overlays, and other types. Each annotation can have a label and metadata.
+- ``large-image-tasks``: A utility for running the converter via Girder Worker.
 
-  - ``large-image-tasks``: A utility for running the converter via Girder Worker.
-    You can specify an extras_require of ``girder`` to include modules needed to work with the Girder remote worker or ``worker`` to include modules needed on the remote side of the Girder remote worker.  If neither is specified, some conversion tasks can be run using Girder local jobs.
+  You can specify an extras_require of ``girder`` to include modules needed to work with the Girder remote worker or ``worker`` to include modules needed on the remote side of the Girder remote worker.  If neither is specified, some conversion tasks can be run using Girder local jobs.
 
 
 

{large_image_source_multi-1.30.1.dev16 → large_image_source_multi-1.33.6.dev6}/large_image_source_multi/__init__.py

@@ -6,6 +6,7 @@ import math
 import os
 import re
 import threading
+import warnings
 from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as _importlib_version
 from pathlib import Path
@@ -28,6 +29,7 @@ except PackageNotFoundError:
 
 jsonschema = None
 _validator = None
+skimage_transform = None
 
 
 def _lazyImport():
@@ -47,6 +49,20 @@ def _lazyImport():
             raise TileSourceError(msg)
 
 
+def _lazyImportSkimageTransform():
+    """
+    Import the skimage.transform module. This is only needed when a TPS warp is used.
+    """
+    global skimage_transform
+
+    if skimage_transform is None:
+        try:
+            import skimage.transform as skimage_transform
+        except ImportError:
+            msg = 'scikit-image transform module not found.'
+            raise TileSourceError(msg)
+
+
 SourceEntrySchema = {
     'type': 'object',
     'additionalProperties': True,
@@ -270,6 +286,54 @@ SourceEntrySchema = {
                     # TODO: Add polygon option
                     # TODO: Add postTransform option
                 },
+                'warp': {
+                    'description':
+                        'An object describing a series of landmarks which have both '
+                        'a source location and a destination location. These sets of points '
+                        'define a warp (thin plate spline or affine transform) that will '
+                        'be applied to the source image.',
+                    'type': 'object',
+                    'properties': {
+                        'src': {
+                            'description':
+                                'The set of source locations for landmarks defining a warp. '
+                                'This can be described by a list of [x, y] points or a mapping of '
+                                'unique marker IDs to [x, y] points.',
+                            'type': ['array', 'object'],
+                            'items': {
+                                'type': 'array',
+                                'items': {'type': 'number'},
+                                'minItems': 2,
+                                'maxItems': 2,
+                            },
+                            'additionalProperties': {
+                                'type': 'array',
+                                'items': {'type': 'number'},
+                                'minItems': 2,
+                                'maxItems': 2,
+                            },
+                        },
+                        'dst': {
+                            'description':
+                                'The set of destination locations for landmarks defining a warp. '
+                                'This can be described by a list of [x, y] points or a mapping of '
+                                'unique marker IDs to [x, y] points.',
+                            'type': ['array', 'object'],
+                            'items': {
+                                'type': 'array',
+                                'items': {'type': 'number'},
+                                'minItems': 2,
+                                'maxItems': 2,
+                            },
+                            'additionalProperties': {
+                                'type': 'array',
+                                'items': {'type': 'number'},
+                                'minItems': 2,
+                                'maxItems': 2,
+                            },
+                        },
+                    },
+                },
                 'scale': {
                     'description':
                         'Values less than 1 will downsample the source.  '
@@ -300,10 +364,12 @@ SourceEntrySchema = {
                 'sampleScale is applied',
             'type': 'number',
         },
-        'style': {'type': 'object'},
+        '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',
+            'description': 'Additional parameters to pass to the base tile source',
             'type': 'object',
         },
     },
@@ -440,9 +506,12 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             self._largeImagePath = '.'
             try:
                 self._validator.validate(self._info)
-            except jsonschema.ValidationError:
-                msg = 'File cannot be validated via multi-source reader.'
-                raise TileSourceError(msg)
+            except jsonschema.ValidationError as exp:
+                from large_image.exceptions import _improveJsonschemaValidationError
+
+                _improveJsonschemaValidationError(exp)
+                msg = f'File cannot be validated via multi-source reader {str(exp)}.'
+                raise TileSourceError(msg) from None
         elif not os.path.isfile(self._largeImagePath):
             try:
                 possibleYaml = self._largeImagePath.split('multi://', 1)[-1]
@@ -455,7 +524,8 @@ 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)
@@ -470,9 +540,12 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 raise TileSourceError(msg)
             try:
                 self._validator.validate(self._info)
-            except jsonschema.ValidationError:
-                msg = 'File cannot be validated via multi-source reader.'
-                raise TileSourceError(msg)
+            except jsonschema.ValidationError as exp:
+                from large_image.exceptions import _improveJsonschemaValidationError
+
+                _improveJsonschemaValidationError(exp)
+                msg = f'File cannot be validated via multi-source reader {str(exp)}.'
+                raise TileSourceError(msg) from None
             self._basePath = Path(self._largeImagePath).parent
         self._basePath /= Path(self._info.get('basePath', '.'))
         for axis in self._info.get('axes', []):
@@ -571,6 +644,62 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 source['path'] = source['path'].resolve(False)
         return sources
 
+    def _getWarp(self, warp, m):
+        """
+        Preprocess a warp specification and transformation matrix prior to applying the warp.
+
+        :param warp: A dictionary with a warp specification,
+            adhering to the schema for ``MultiSource.SourceEntry.position.warp``.
+        :param m: An ndarray representing a transformation matrix,
+            that may be modified according to the warp specification.
+        """
+        ret = None
+        warp_src = warp.get('src')
+        warp_dst = warp.get('dst')
+        if isinstance(warp_src, dict) and isinstance(warp_dst, dict):
+            src_key_set = set(warp_src.keys())
+            dst_key_set = set(warp_dst.keys())
+            keys = list(src_key_set & dst_key_set)
+            warp_src = [warp_src[key] for key in keys]
+            warp_dst = [warp_dst[key] for key in keys]
+            unused = (src_key_set | dst_key_set) - set(keys)
+            if len(unused):
+                msg = (
+                    'The following keys did not have a value in both src and dst, '
+                    f'so they were dropped: {unused}.'
+                )
+                warnings.warn(msg, stacklevel=2)
+        elif isinstance(warp_src, list) and isinstance(warp_dst, list):
+            pass
+        else:
+            msg = 'warp src and warp dst must either be both dicts or both lists.'
+            raise TileSourceError(msg)
+        if len(warp_src) != len(warp_dst):
+            msg = 'warp src and warp dst must have the same number of points.'
+            raise TileSourceError(msg)
+        if len(warp_src) < 1:
+            msg = 'warp src and warp dst must have at least one point.'
+            raise TileSourceError(msg)
+
+        warp_src = np.array(warp_src or []).astype(float)
+        warp_dst = np.array(warp_dst or []).astype(float)
+        warp_src = warp_src[:min(warp_src.shape[0], warp_dst.shape[0]), :]
+        warp_dst = warp_dst[:warp_src.shape[0], :]
+        if warp_src.shape[0] < 1:
+            pass
+        elif warp_src.shape[0] == 1:
+            m[0][2] += warp_dst[0][0] - warp_src[0][0]
+            m[1][2] += warp_dst[0][1] - warp_src[0][1]
+        elif warp_src.shape[0] <= 3:
+            transformer = skimage_transform.AffineTransform()
+            transformer.estimate(warp_src, warp_dst)
+            m = np.dot(transformer.params, m)
+        else:
+            warp_dst = np.dot(m, np.hstack([warp_dst, np.ones((len(warp_dst), 1))]).T).T[:, :2]
+            ret = {'src': warp_src, 'dst': warp_dst}
+            m = np.identity(3)
+        return ret, m
+
     def _sourceBoundingBox(self, source, width, height):
         """
         Given a source with a possible transform and an image width and height,
@@ -588,6 +717,8 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         bbox = {'left': 0, 'top': 0, 'right': width, 'bottom': height}
         if not pos:
             return bbox
+        if 'warp' in pos:
+            _lazyImportSkimageTransform()
         x0, y0, x1, y1 = 0, 0, width, height
         if 'crop' in pos:
             x0 = min(max(pos['crop'].get('left', x0), 0), width)
@@ -603,6 +734,8 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         m[1][0] = pos.get('s21', 0) * pos.get('scale', 1)
         m[1][1] = pos.get('s22', 1) * pos.get('scale', 1)
         m[1][2] = pos.get('y', 0)
+        if 'warp' in pos and skimage_transform is not None:
+            bbox['warp'], m = self._getWarp(pos.get('warp'), m)
         if not np.array_equal(m, np.identity(3)):
             bbox['transform'] = m
             try:
@@ -610,11 +743,23 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             except np.linalg.LinAlgError:
                 msg = 'The position for a source is not invertable (%r)'
                 raise TileSourceError(msg, pos)
-        transcorners = np.dot(m, corners.T)
+        warp = bbox.get('warp')
+        if warp is None:
+            transcorners = np.dot(m, corners.T)
+        elif skimage_transform is not None:
+            transformer = skimage_transform.ThinPlateSplineTransform()
+            transformer.estimate(warp.get('src'), warp.get('dst'))
+            # We might want to adjust the number of points based on some
+            # criteria such as source image size or number of warp points
+            corners = self._perimeterPoints(x0, y0, x1, y1, 8)
+            transcorners = transformer(corners).T
         bbox['left'] = min(transcorners[0])
         bbox['top'] = min(transcorners[1])
         bbox['right'] = max(transcorners[0])
         bbox['bottom'] = max(transcorners[1])
+        # TODO: Maybe inflate this a bit for warp because of edge effects?
+        # That is, it can warp outside of the specified box because we don't
+        # have infinite perimeter sampling
         return bbox
 
     def _axisKey(self, source, value, key):
@@ -897,7 +1042,8 @@ 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
+        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):
@@ -931,7 +1077,7 @@ 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)
@@ -1034,7 +1180,34 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             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 _perimeterPoints(self, x0, y0, x1, y1, sample):
+        return np.vstack([
+            np.column_stack([np.linspace(x0, x1, sample, endpoint=False), np.full(sample, y0)]),
+            np.column_stack([np.full(sample, x1), np.linspace(y0, y1, sample, endpoint=False)]),
+            np.column_stack([np.linspace(x1, x0, sample, endpoint=False), np.full(sample, y1)]),
+            np.column_stack([np.full(sample, x0), np.linspace(y1, y0, sample, endpoint=False)]),
+        ])
+
+    def _smallestSpacingRatio(self, srcpts, destpts):
+        """
+        Find the smallest ratio of the distance between two adjacent source
+        perimeter points (srccorners) and two destination perimeter points
+
+        :param srcpts: an ndarray of points that correspond with the
+            destination points.
+        :param dstpts: an ndarray of corresponding points.
+        :returns: the minimum ratio of the distance between a source section
+            and a destination section.
+        """
+        srcdist = np.linalg.norm(srcpts - np.roll(srcpts, 1, axis=0), axis=1)
+        destdist = np.linalg.norm(destpts - np.roll(destpts, 1, axis=0), axis=1)
+        if np.all(destdist == 0):
+            return 1
+        minratio = np.min(srcdist[destdist != 0] / destdist[destdist != 0])
+        return minratio or 1
+
+    def _getTransformedTile(self, ts, transform, corners, scale, frame,  # noqa
+                            warp=None, 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
@@ -1048,36 +1221,66 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             corner 0 must be the upper left, 2 must be the lower right.
         :param scale: scaling factor from full res to the target resolution.
         :param frame: frame number of the source image.
+        :param warp: an optional dictionary to specify a thin plate spline
+            transformation to apply to the source image. This dictionary must
+            contain keys 'src' and 'dst', each with a list of [x, y] points.
+            The length of the 'src' list of points must equal the length of the
+            'dst' list of points (both must have at least 3 points).
         :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.
         """
-        try:
-            import skimage.transform
-        except ImportError:
-            msg = 'scikit-image is required for affine transforms.'
-            raise TileSourceError(msg)
         # From full res source to full res destination
         transform = transform.copy() if transform is not None else np.identity(3)
+        warp_src = warp_dst = None
+        _lazyImportSkimageTransform()
+        if warp is not None:
+            warp_src = warp['src'].copy()
+            warp_dst = warp['dst'].copy()
         # Scale dest corners to actual size; adjust transform for the same
         corners = np.array(corners)
         corners[:, :2] //= scale
-        transform[:2, :] /= scale
         # Offset so our target is the actual destination array we use
-        transform[0][2] -= corners[0][0]
-        transform[1][2] -= corners[0][1]
+        if warp is None:
+            transform[:2, :] /= scale
+            transform[0][2] -= corners[0][0]
+            transform[1][2] -= corners[0][1]
+        else:
+            warp_dst /= scale
+            warp_dst[:, 0] -= corners[0][0]
+            warp_dst[:, 1] -= corners[0][1]
         corners[:, :2] -= corners[0, :2]
         outw, outh = corners[2][0], corners[2][1]
         if not outh or not outw:
             return None, 0, 0
-        srccorners = np.dot(np.linalg.inv(transform), np.array(corners).T).T.tolist()
+        if warp is None:
+            dstcorners = corners
+            srccorners = np.dot(np.linalg.inv(transform), np.array(corners).T).T.tolist()
+        else:
+            transformer = skimage_transform.ThinPlateSplineTransform()
+            transformer.estimate(warp_dst, warp_src)
+            # Is there any way to be smarter about the sampling?
+            dstcorners = self._perimeterPoints(0, 0, outw, outh, 8)
+            srccorners = transformer(dstcorners)
         minx = min(c[0] for c in srccorners)
         maxx = max(c[0] for c in srccorners)
         miny = min(c[1] for c in srccorners)
         maxy = max(c[1] for c in srccorners)
-        srcscale = max((maxx - minx) / outw, (maxy - miny) / outh)
+        if warp is None:
+            srcscale = max((maxx - minx) / outw, (maxy - miny) / outh)
+        else:
+            # Use the half spacing for better interpolation.  If the warped
+            # image were uniform, this could be a factor of sqrt(2), since the
+            # image could be rotated and we might need to interpolate from
+            # that; using a bigger factor can ensure we have enough pixels for
+            # warps that are no more than another factor of sqrt(2) in
+            # variation from the sampled perimeter.
+            srcscale = self._smallestSpacingRatio(srccorners, dstcorners) / 2
         # we only need every 1/srcscale pixel.
         srcscale = int(2 ** math.log2(max(1, srcscale)))
         # Pad to reduce edge effects at tile boundaries
@@ -1109,52 +1312,69 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             [region['right'] // srcscale, region['top'] // srcscale, 1],
             [region['right'] // srcscale, region['bottom'] // srcscale, 1],
             [region['left'] // srcscale, region['bottom'] // srcscale, 1]], dtype=float)
-        # adjust our transform if we took a low res version of the source
-        transform[:2, :2] *= srcscale
-        # Find where the source corners land on the destination.
-        preshiftcorners = (np.dot(transform, regioncorners.T).T).tolist()
-        regioncorners[:, :2] -= regioncorners[0, :2]
-        destcorners = (np.dot(transform, regioncorners.T).T).tolist()
-        offsetx, offsety = None, None
-        for idx in range(4):
-            if offsetx is None or destcorners[idx][0] < offsetx:
-                x = preshiftcorners[idx][0]
-                offsetx = destcorners[idx][0] - (x - math.floor(x))
-            if offsety is None or destcorners[idx][1] < offsety:
-                y = preshiftcorners[idx][1]
-                offsety = destcorners[idx][1] - (y - math.floor(y))
-        transform[0][2] -= offsetx
-        transform[1][2] -= offsety
-        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()
-        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
+        if warp is None:
+            # adjust our transform if we took a low res version of the source
+            transform[:2, :2] *= srcscale
+        else:
+            warp_src /= srcscale
+            warp_src -= regioncorners[0, :2]
+        if warp is None:
+            # Find where the source corners land on the destination.
+            preshiftcorners = (np.dot(transform, regioncorners.T).T).tolist()
+            regioncorners[:, :2] -= regioncorners[0, :2]
+            destcorners = (np.dot(transform, regioncorners.T).T).tolist()
+            offsetx, offsety = None, None
+            for idx in range(4):
+                if offsetx is None or destcorners[idx][0] < offsetx:
+                    x = preshiftcorners[idx][0]
+                    offsetx = destcorners[idx][0] - (x - math.floor(x))
+                if offsety is None or destcorners[idx][1] < offsety:
+                    y = preshiftcorners[idx][1]
+                    offsety = destcorners[idx][1] - (y - math.floor(y))
+            transform[0][2] -= offsetx
+            transform[1][2] -= offsety
+            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()
+            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
+        else:
+            x = y = 0
+            destShape = [outh, outw]
+        # 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)
+        useNearest = srcImage.shape[2] in {2, 4} and not firstMerge
+
+        if warp is None:
+            transformer = skimage_transform.AffineTransform(np.linalg.inv(transform))
+        else:
+            transformer = skimage_transform.ThinPlateSplineTransform()
+            transformer.estimate(warp_dst, warp_src)
         # 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(
+        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)),
-            order=3,
+            transformer,
+            order=0 if useNearest else 3,
             output_shape=(destShape[0], destShape[1], srcImage.shape[2]),
         ).astype(srcImage.dtype)
         return destImage, x, y
@@ -1183,13 +1403,14 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             return tile
         ts = self._openSource(source, sourceEntry['kwargs'])
         transform = bbox.get('transform')
+        warp = bbox.get('warp')
         x = y = 0
         # If there is no transform or the diagonals are positive and there is
         # no sheer and integer pixel alignment, use getRegion with an
         # appropriate size
         scaleX = transform[0][0] if transform is not None else 1
         scaleY = transform[1][1] if transform is not None else 1
-        if ((transform is None or (
+        if (warp is None and (transform is None or (
                 transform[0][0] > 0 and transform[0][1] == 0 and
                 transform[1][0] == 0 and transform[1][1] > 0 and
                 transform[0][2] % scaleX == 0 and transform[1][2] % scaleY == 0)) and
@@ -1230,8 +1451,9 @@ class MultiFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 resample=None, format=TILE_FORMAT_NUMPY)
         else:
             sourceTile, x, y = self._getTransformedTile(
-                ts, transform, corners, scale, sourceEntry.get('frame', 0),
-                source.get('position', {}).get('crop'))
+                ts, transform, corners, scale, sourceEntry.get('frame', 0), warp,
+                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

{large_image_source_multi-1.30.1.dev16 → large_image_source_multi-1.33.6.dev6/large_image_source_multi.egg-info}/PKG-INFO

@@ -1,31 +1,42 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: large-image-source-multi
-Version: 1.30.1.dev16
+Version: 1.33.6.dev6
 Summary: A tilesource for large_image to composite other tile sources
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
 Author-email: kitware@kitware.com
-License: Apache Software License 2.0
+License: Apache-2.0
 Keywords: large_image,tile source
 Classifier: Development Status :: 5 - Production/Stable
-Classifier: License :: OSI Approved :: Apache Software License
 Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.6
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: jsonschema
-Requires-Dist: large-image>=1.30.1.dev16
+Requires-Dist: large-image>=1.33.6.dev6
 Requires-Dist: pyyaml
 Provides-Extra: all
 Requires-Dist: scikit-image; extra == "all"
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.1.dev16; extra == "girder"
+Requires-Dist: girder-large-image>=1.33.6.dev6; extra == "girder"
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+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-1.33.6.dev6/large_image_source_multi.egg-info/requires.txt

@@ -0,0 +1,9 @@
+jsonschema
+large-image>=1.33.6.dev6
+pyyaml
+
+[all]
+scikit-image
+
+[girder]
+girder-large-image>=1.33.6.dev6

{large_image_source_multi-1.30.1.dev16 → large_image_source_multi-1.33.6.dev6}/pyproject.toml

@@ -1,3 +1,7 @@
 [build-system]
 requires = ["setuptools", "setuptools-scm"]
 build-backend = "setuptools.build_meta"
+
+[tool.setuptools_scm]
+fallback_version = "0.0.0"
+root = "../.."

{large_image_source_multi-1.30.1.dev16 → large_image_source_multi-1.33.6.dev6}/setup.py

@@ -6,52 +6,32 @@ description = 'A tilesource for large_image to composite other tile sources'
 long_description = description + '\n\nSee the large-image package for more details.'
 
 
-def prerelease_local_scheme(version):
-    """
-    Return local scheme version unless building on master in CircleCI.
-
-    This function returns the local scheme version number
-    (e.g. 0.0.0.dev<N>+g<HASH>) unless building on CircleCI for a
-    pre-release in which case it ignores the hash and produces a
-    PEP440 compliant pre-release version number (e.g. 0.0.0.dev<N>).
-    """
-    from setuptools_scm.version import get_local_node_and_date
-
-    if os.getenv('CIRCLE_BRANCH') in ('master', ):
-        return ''
-    else:
-        return get_local_node_and_date(version)
-
-
 try:
     from setuptools_scm import get_version
 
-    version = get_version(root='../..', local_scheme=prerelease_local_scheme)
+    version = get_version(root='../..')
     limit_version = f'>={version}' if '+' not in version and not os.getenv('TOX_ENV_NAME') else ''
 except (ImportError, LookupError):
     limit_version = ''
 
 setup(
     name='large-image-source-multi',
-    use_scm_version={'root': '../..', 'local_scheme': prerelease_local_scheme,
-                     'fallback_version': '0.0.0'},
     description=description,
     long_description=long_description,
     long_description_content_type='text/x-rst',
-    license='Apache Software License 2.0',
+    license='Apache-2.0',
     author='Kitware, Inc.',
     author_email='kitware@kitware.com',
     classifiers=[
         'Development Status :: 5 - Production/Stable',
-        'License :: OSI Approved :: Apache Software License',
         'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.8',
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
     ],
+    python_requires='>=3.9',
     install_requires=[
         'jsonschema',
         f'large-image{limit_version}',
@@ -66,7 +46,6 @@ setup(
     keywords='large_image, tile source',
     packages=find_packages(exclude=['test', 'test.*']),
     url='https://github.com/girder/large_image',
-    python_requires='>=3.6',
     entry_points={
         'large_image.source': [
             'multi = large_image_source_multi:MultiFileTileSource',

large_image_source_multi-1.30.1.dev16/large_image_source_multi.egg-info/requires.txt

@@ -1,9 +0,0 @@
-jsonschema
-large-image>=1.30.1.dev16
-pyyaml
-
-[all]
-scikit-image
-
-[girder]
-girder-large-image>=1.30.1.dev16