large-image-source-zarr 1.32.4.dev4__tar.gz → 1.32.4.dev5__tar.gz

{large_image_source_zarr-1.32.4.dev4 → large_image_source_zarr-1.32.4.dev5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: large-image-source-zarr
-Version: 1.32.4.dev4
+Version: 1.32.4.dev5
 Summary: A OME Zarr tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -18,12 +18,12 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.6
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.32.4.dev4
+Requires-Dist: large-image>=1.32.4.dev5
 Requires-Dist: zarr<3
 Requires-Dist: numcodecs<0.16
 Requires-Dist: imagecodecs-numcodecs!=2024.9.22
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.32.4.dev4; extra == "girder"
+Requires-Dist: girder-large-image>=1.32.4.dev5; extra == "girder"
 Provides-Extra: all
 Requires-Dist: large-image-converter; extra == "all"
 Dynamic: author

{large_image_source_zarr-1.32.4.dev4 → large_image_source_zarr-1.32.4.dev5}/large_image_source_zarr/__init__.py

@@ -165,6 +165,8 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._frameValues = None
         self._frameAxes = None
         self._frameUnits = None
+        self._projection = None
+        self._gcps = None
         if not self._created:
             try:
                 self._validateZarr()
@@ -911,31 +913,33 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         with self._threadLock and self._processLock:
             name = str(self._tempdir.name).split('/')[-1]
             arrays = dict(self._zarr.arrays())
-            channel_axis = self._axes.get('c', self._axes.get('s'))
             datasets = []
             axes = []
             channels = []
-            rdefs = {'model': 'color' if len(self._channelColors) else 'greyscale'}
-            sorted_axes = [a[0] for a in sorted(self._axes.items(), key=lambda item: item[1])]
-            for arr_name in arrays:
-                level = int(arr_name)
-                scale = [1.0 for a in sorted_axes]
-                scale[self._axes.get('x')] = (self._mm_x or 0) * (2 ** level)
-                scale[self._axes.get('y')] = (self._mm_y or 0) * (2 ** level)
-                dataset_metadata = {
-                    'path': arr_name,
-                    'coordinateTransformations': [{
-                        'type': 'scale',
-                        'scale': scale,
-                    }],
-                }
-                datasets.append(dataset_metadata)
-            for a in sorted_axes:
-                if a == 't':
-                    rdefs['defaultT'] = 0
-                elif a == 'z':
-                    rdefs['defaultZ'] = 0
-                axes.append(self._getAxisInternalMetadata(a))
+            channel_axis = rdefs = None
+            if hasattr(self, '_axes'):
+                channel_axis = self._axes.get('c', self._axes.get('s'))
+                rdefs = {'model': 'color' if len(self._channelColors) else 'greyscale'}
+                sorted_axes = [a[0] for a in sorted(self._axes.items(), key=lambda item: item[1])]
+                for arr_name in arrays:
+                    level = int(arr_name)
+                    scale = [1.0 for a in sorted_axes]
+                    scale[self._axes.get('x')] = (self._mm_x or 0) * (2 ** level)
+                    scale[self._axes.get('y')] = (self._mm_y or 0) * (2 ** level)
+                    dataset_metadata = {
+                        'path': arr_name,
+                        'coordinateTransformations': [{
+                            'type': 'scale',
+                            'scale': scale,
+                        }],
+                    }
+                    datasets.append(dataset_metadata)
+                for a in sorted_axes:
+                    if a == 't':
+                        rdefs['defaultT'] = 0
+                    elif a == 'z':
+                        rdefs['defaultZ'] = 0
+                    axes.append(self._getAxisInternalMetadata(a))
             if channel_axis is not None and len(arrays) > 0:
                 base_array = list(arrays.values())[0]
                 base_shape = base_array.shape
@@ -1183,6 +1187,76 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._frameValues = a
         self._writeInternalMetadata()
 
+    @property
+    def projection(self):
+        return self._projection
+
+    @projection.setter
+    def projection(self, proj):
+        import pyproj
+
+        self._checkEditable()
+        try:
+            pyproj.CRS.from_string(str(proj))
+        except Exception as e:
+            msg = f'Invalid projection value. Cannot be interpreted by pyproj: {str(e)}'
+            raise TileSourceError(msg)
+        self._projection = proj
+        self._writeInternalMetadata()
+
+    @property
+    def gcps(self):
+        return self._gcps
+
+    @gcps.setter
+    def gcps(self, gcps):
+        self._checkEditable()
+        if isinstance(gcps, str):
+            gcps = list(zip(*[iter(gcps.split())] * 4))
+        if (isinstance(gcps, list) or isinstance(gcps, tuple)):
+            gcps = [
+                [float(v) for v in gcp.split()]
+                if isinstance(gcp, str) else gcp
+                for gcp in gcps
+            ]
+            if any(
+                not isinstance(gcp, list) and not isinstance(gcp, tuple)
+                for gcp in gcps
+            ):
+                msg = 'Each GCP must be specified as a list, tuple, or space-separated string.'
+                raise TileSourceError(msg)
+            if any(len(gcp) != 4 for gcp in gcps):
+                msg = (
+                    'Each GCP must contain four values: '
+                    '[projected_x, projected_y, pixel_x, pixel_y].'
+                )
+                raise TileSourceError(msg)
+            unique_gcps = []
+            dup_gcps = []
+            for gcp in gcps:
+                if not any(
+                    u[0:2] == gcp[0:2] or u[2:4] == gcp[2:4]
+                    for u in unique_gcps
+                ):
+                    unique_gcps.append(gcp)
+                else:
+                    dup_gcps.append(gcp)
+            gcps = unique_gcps
+            if len(dup_gcps):
+                msg = (
+                    f'Removed duplicate GCPs {dup_gcps} from list; shared projected '
+                    'coordinate or pixel coordinate with another GCP.'
+                )
+                warnings.warn(msg, stacklevel=2)
+            if len(gcps) < 2:
+                msg = 'Must specify at least 2 unique GCPs.'
+                raise TileSourceError(msg)
+        else:
+            msg = 'GCPs must be specified as a list, tuple, or space-separated string.'
+            raise TileSourceError(msg)
+        self._gcps = gcps
+        self._writeInternalMetadata()
+
     def _generateDownsampledLevels(self, resample_method):
         self._checkEditable()
         current_arrays = dict(self._zarr.arrays())
@@ -1249,6 +1323,23 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     )
             self._validateZarr()  # refresh self._levels before continuing
 
+    def _applyGeoReferencing(self, path):
+        if self.projection and not self.gcps:
+            msg = (
+                'Projection was specified but GCPs were not specified. '
+                'Cannot write georeferenced file.'
+            )
+            raise TileSourceError(msg)
+        import tifftools
+
+        setlist = []
+        if self.projection is not None:
+            setlist.append(('projection', self.projection))
+        if self.gcps is not None and len(self.gcps):
+            setlist.append(('gcps', self.gcps))
+
+        tifftools.tiff_set(path, setlist=setlist, overwrite=True)
+
     def write(
         self,
         path,
@@ -1355,6 +1446,8 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             params.update(converterParams)
             convert(str(attrs_path), path, overwrite=overwriteAllowed, **params)
 
+            self._applyGeoReferencing(path)
+
 
 def open(*args, **kwargs):
     """

{large_image_source_zarr-1.32.4.dev4 → large_image_source_zarr-1.32.4.dev5}/large_image_source_zarr.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: large-image-source-zarr
-Version: 1.32.4.dev4
+Version: 1.32.4.dev5
 Summary: A OME Zarr tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -18,12 +18,12 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.6
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.32.4.dev4
+Requires-Dist: large-image>=1.32.4.dev5
 Requires-Dist: zarr<3
 Requires-Dist: numcodecs<0.16
 Requires-Dist: imagecodecs-numcodecs!=2024.9.22
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.32.4.dev4; extra == "girder"
+Requires-Dist: girder-large-image>=1.32.4.dev5; extra == "girder"
 Provides-Extra: all
 Requires-Dist: large-image-converter; extra == "all"
 Dynamic: author

{large_image_source_zarr-1.32.4.dev4 → large_image_source_zarr-1.32.4.dev5}/large_image_source_zarr.egg-info/requires.txt

@@ -1,4 +1,4 @@
-large-image>=1.32.4.dev4
+large-image>=1.32.4.dev5
 zarr<3
 numcodecs<0.16
 imagecodecs-numcodecs!=2024.9.22
@@ -7,4 +7,4 @@ imagecodecs-numcodecs!=2024.9.22
 large-image-converter
 
 [girder]
-girder-large-image>=1.32.4.dev4
+girder-large-image>=1.32.4.dev5