large-image-source-zarr 1.30.2__tar.gz → 1.30.2.dev2__tar.gz

{large_image_source_zarr-1.30.2 → large_image_source_zarr-1.30.2.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-zarr
-Version: 1.30.2
+Version: 1.30.2.dev2
 Summary: A OME Zarr tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -19,12 +19,12 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.6
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.30.2
+Requires-Dist: large-image>=1.30.2.dev2
 Requires-Dist: zarr
 Requires-Dist: numcodecs
 Requires-Dist: imagecodecs-numcodecs!=2024.9.22
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.2; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.2.dev2; extra == "girder"
 Provides-Extra: all
 Requires-Dist: large-image-converter; extra == "all"
 

{large_image_source_zarr-1.30.2 → large_image_source_zarr-1.30.2.dev2}/large_image_source_zarr/__init__.py

@@ -98,9 +98,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._largeImagePath = str(self._getLargeImagePath())
         self._zarr = None
         self._editable = False
-        self._frameValues = None
-        self._frameAxes = None
-        self._frameUnits = None
         if not os.path.isfile(self._largeImagePath) and '//:' not in self._largeImagePath:
             raise TileSourceFileNotFoundError(self._largeImagePath) from None
         try:
@@ -155,9 +152,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._imageDescription = None
         self._levels = []
         self._associatedImages = {}
-        self._frameValues = None
-        self._frameAxes = None
-        self._frameUnits = None
 
     def __del__(self):
         if not hasattr(self, '_derivedSource'):
@@ -224,10 +218,10 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             tuple that is used to find the maximum size array, preferring ome
             arrays, then total pixels, then channels.  'is_ome' is a boolean.
             'series' is a list of the found groups and arrays that match the
-            best criteria.  'axes', 'axes_values', 'axes_units', and 'channels'
-            are from the best array. 'associated' is a list of all groups and
-            arrays that might be associated images.  These have to be culled
-            for the actual groups used in the series.
+            best criteria.  'axes' and 'channels' are from the best array.
+            'associated' is a list of all groups and arrays that might be
+            associated images.  These have to be culled for the actual groups
+            used in the series.
         """
         attrs = group.attrs.asdict() if group is not None else {}
         min_version = packaging.version.Version('0.4')
@@ -239,19 +233,9 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             all(packaging.version.Version(m['version']) >= min_version
                 for m in attrs['multiscales'] if 'version' in m))
         channels = None
-        axes_values = None
-        axes_units = None
         if is_ome:
             axes = {axis['name']: idx for idx, axis in enumerate(
                 attrs['multiscales'][0]['axes'])}
-            axes_values = {
-                axis['name']: axis.get('values')
-                for axis in attrs['multiscales'][0]['axes']
-            }
-            axes_units = {
-                axis['name']: axis.get('unit')
-                for axis in attrs['multiscales'][0]['axes']
-            }
             if isinstance(attrs['omero'].get('channels'), list):
                 channels = [channel['label'] for channel in attrs['omero']['channels']]
                 if all(channel.startswith('Channel ') for channel in channels):
@@ -270,8 +254,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             results['series'] = [(group, arr)]
             results['is_ome'] = is_ome
             results['axes'] = axes
-            results['axes_values'] = axes_values
-            results['axes_units'] = axes_units
             results['channels'] = channels
         elif check == results['best']:
             results['series'].append((group, arr))
@@ -351,44 +333,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         except Exception:
             pass
 
-    def _readFrameValues(self, found, baseArray):
-        """
-        Populate frame values and frame units from image metadata.
-        """
-        axes_values = found.get('axes_values')
-        axes_units = found.get('axes_units')
-        if isinstance(axes_values, dict):
-            self._frameAxes = [
-                a for a, i in sorted(self._axes.items(), key=lambda x: x[1])
-                if axes_values.get(a) is not None
-            ]
-            self._frameUnits = {k: axes_units.get(k) for k in self.frameAxes if k in axes_units}
-            frame_values_shape = [baseArray.shape[self._axes[a]] for a in self.frameAxes]
-            frame_values_shape.append(len(frame_values_shape))
-            frame_values = np.empty(frame_values_shape, dtype=object)
-            all_frame_specs = self.getMetadata().get('frames')
-            for axis, values in axes_values.items():
-                if axis in self.frameAxes:
-                    slicing = [slice(None) for i in range(len(frame_values_shape))]
-                    axis_index = self.frameAxes.index(axis)
-                    slicing[-1] = axis_index
-                    if len(values) == frame_values_shape[axis_index]:
-                        # uniform values have same length as axis
-                        for i, value in enumerate(values):
-                            slicing[axis_index] = i
-                            frame_values[tuple(slicing)] = value
-                    elif len(values) == self._framecount:
-                        # non-uniform values have a value for every frame
-                        for i, value in enumerate(values):
-                            if all_frame_specs and len(all_frame_specs) > i:
-                                for k, j in all_frame_specs[i].items():
-                                    if 'Index' in k:
-                                        name = k.replace('Index', '').lower()
-                                        if name:
-                                            slicing[self._frameAxes.index(name)] = j
-                            frame_values[tuple(slicing)] = value
-            self._frameValues = frame_values
-
     def _validateZarr(self):
         """
         Validate that we can read tiles from the zarr parent group in
@@ -403,11 +347,7 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._series = found['series']
         baseGroup, baseArray = self._series[0]
         self._is_ome = found['is_ome']
-        self._axes = {
-            k.lower(): v
-            for k, v in found['axes'].items()
-            if baseArray.shape[v] > 1 or k in found.get('axes_values', {})
-        }
+        self._axes = {k.lower(): v for k, v in found['axes'].items() if baseArray.shape[v] > 1}
         if len(self._series) > 1 and 'xy' in self._axes:
             msg = 'Conflicting xy axis data.'
             raise TileSourceError(msg)
@@ -446,10 +386,8 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         stride = 1
         self._strides = {}
         self._axisCounts = {}
-        for _, k in sorted(
-            (-self._axes.get(k, 'tzc'.index(k) if k in 'tzc' else -1), k)
-            for k in self._axes if k not in 'xys'
-        ):
+        for _, k in sorted((-'tzc'.index(k) if k in 'tzc' else 1, k)
+                           for k in self._axes if k not in 'xys'):
             self._strides[k] = stride
             self._axisCounts[k] = baseArray.shape[self._axes[k]]
             stride *= baseArray.shape[self._axes[k]]
@@ -458,7 +396,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             self._axisCounts['xy'] = len(self._series)
             stride *= len(self._series)
         self._framecount = stride
-        self._readFrameValues(found, baseArray)
 
     def _nonemptyLevelsList(self, frame=0):
         """
@@ -510,16 +447,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 for axis in self._strides:
                     frame['Index' + axis.upper()] = (
                         idx // self._strides[axis]) % self._axisCounts[axis]
-                if self.frameValues is not None and self.frameAxes is not None:
-                    current_frame_slice = tuple(
-                        frame['Index' + axis.upper()] for axis in self.frameAxes
-                    )
-                    current_frame_values = self.frameValues[current_frame_slice]
-                    for i, axis in enumerate(self.frameAxes):
-                        value = current_frame_values[i]
-                        # ensure that values are returned as native python types
-                        native_value = getattr(value, 'tolist', lambda v=value: v)()
-                        frame['Value' + axis.upper()] = native_value
                 frames.append(frame)
             self._addMetadataFrameInformation(result, getattr(self, '_channels', None))
         return result
@@ -669,11 +596,7 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         placement = {
             'x': x,
             'y': y,
-            **{k: v for k, v in kwargs.items() if not k.endswith('_value')},
-        }
-        frame_values = {
-            k.replace('_value', ''): v for k, v in kwargs.items()
-            if k not in placement
+            **kwargs,
         }
         tile, mask, placement, axes = self._validateNewTile(tile, mask, placement, axes)
 
@@ -692,26 +615,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 for i, a in enumerate(axes)
             ])
 
-            if len(frame_values.keys()) > 0:
-                # update self.frameValues
-                self.frameAxes = [
-                    a for a in axes
-                    if a in frame_values or
-                    (self.frameAxes is not None and a in self.frameAxes)
-                ]
-                frames_shape = [new_dims[a] for a in self.frameAxes]
-                frames_shape.append(len(frames_shape))
-                if self.frameValues is None:
-                    self.frameValues = np.empty(frames_shape, dtype=object)
-                elif self.frameValues.shape != frames_shape:
-                    self.frameValues = np.pad(
-                        self.frameValues,
-                        [(0, s - self.frameValues.shape[i]) for i, s in enumerate(frames_shape)],
-                    )
-                current_frame_slice = tuple(placement.get(a) for a in self.frameAxes)
-                for i, k in enumerate(self.frameAxes):
-                    self.frameValues[(*current_frame_slice, i)] = frame_values.get(k)
-
             current_arrays = dict(self._zarr.arrays())
             if store_path == '0':
                 # if writing to base data, invalidate generated levels
@@ -789,48 +692,7 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             )
             self._associatedImages[imageKey] = (group, arr)
 
-    def _getAxisInternalMetadata(self, axis_name):
-        """
-        Get the metadata structure describing an axis in the image.
-        This will be written to the image metadata.
-
-        :param axis_name: a string corresponding to an axis in the image
-        :returns: a dictionary describing the target axis
-        """
-        axis_metadata = {'name': axis_name}
-        if axis_name in ['x', 'y']:
-            axis_metadata['type'] = 'space'
-            axis_metadata['unit'] = 'millimeter'
-        elif axis_name in ['s', 'c']:
-            axis_metadata['type'] = 'channel'
-        if self.frameAxes is not None:
-            axis_index = self.frameAxes.index(axis_name) if axis_name in self.frameAxes else None
-            if axis_index is not None and self.frameValues is not None:
-                all_frame_values = self.frameValues[..., axis_index]
-                split = np.split(
-                    all_frame_values,
-                    all_frame_values.shape[axis_index],
-                    axis=axis_index,
-                )
-                uniform = all(len(np.unique(
-                    # convert all values to strings for mixed type comparison with np.unique
-                    (a[np.not_equal(a, None)]).astype(str),
-                )) == 1 for a in split)
-                if uniform:
-                    values = [a.flat[0] for a in split]
-                else:
-                    values = all_frame_values.flatten().tolist()
-                axis_metadata['values'] = values
-            unit = self.frameUnits.get(axis_name) if self.frameUnits is not None else None
-            if unit is not None:
-                axis_metadata['unit'] = unit
-        return axis_metadata
-
     def _writeInternalMetadata(self):
-        """
-        Write metadata to Zarr attributes.
-        Metadata structure adheres to OME schema from https://ngff.openmicroscopy.org/latest/
-        """
         self._checkEditable()
         with self._threadLock and self._processLock:
             name = str(self._tempdir.name).split('/')[-1]
@@ -855,11 +717,17 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 }
                 datasets.append(dataset_metadata)
             for a in sorted_axes:
-                if a == 't':
+                axis_metadata = {'name': a}
+                if a in ['x', 'y']:
+                    axis_metadata['type'] = 'space'
+                    axis_metadata['unit'] = 'millimeter'
+                elif a in ['s', 'c']:
+                    axis_metadata['type'] = 'channel'
+                elif a == 't':
                     rdefs['defaultT'] = 0
                 elif a == 'z':
                     rdefs['defaultZ'] = 0
-                axes.append(self._getAxisInternalMetadata(a))
+                axes.append(axis_metadata)
             if channel_axis is not None and len(arrays) > 0:
                 base_array = list(arrays.values())[0]
                 base_shape = base_array.shape
@@ -872,21 +740,21 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                         'inverted': False,
                         'label': f'Band {c + 1}',
                     }
-                    # slicing = tuple(
-                    #     slice(None)
-                    #     if k != ('c' if 'c' in self._axes else 's')
-                    #     else c
-                    #     for k, v in self._axes.items()
-                    # )
-                    # channel_data = base_array[slicing]
-                    # channel_min = np.min(channel_data)
-                    # channel_max = np.max(channel_data)
-                    # channel_metadata['window'] = {
-                    #     'end': channel_max,
-                    #     'max': channel_max,
-                    #     'min': channel_min,
-                    #     'start': channel_min,
-                    # }
+                    slicing = tuple(
+                        slice(None)
+                        if k != ('c' if 'c' in self._axes else 's')
+                        else c
+                        for k, v in self._axes.items()
+                    )
+                    channel_data = base_array[slicing]
+                    channel_min = np.min(channel_data)
+                    channel_max = np.max(channel_data)
+                    channel_metadata['window'] = {
+                        'end': channel_max,
+                        'max': channel_max,
+                        'min': channel_min,
+                        'start': channel_min,
+                    }
                     if len(self._channelNames) > c:
                         channel_metadata['label'] = self._channelNames[c]
                     if len(self._channelColors) > c:
@@ -994,47 +862,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._checkEditable()
         self._channelColors = colors
 
-    @property
-    def frameAxes(self):
-        return self._frameAxes
-
-    @frameAxes.setter
-    def frameAxes(self, axes):
-        self._checkEditable()
-        self._frameAxes = axes
-
-    @property
-    def frameUnits(self):
-        return self._frameUnits
-
-    @frameUnits.setter
-    def frameUnits(self, units):
-        self._checkEditable()
-        if self.frameAxes is None:
-            err = 'frameAxes must be set first with a list of frame axis names.'
-            raise ValueError(err)
-        if not isinstance(units, dict) or not all(
-            k in self.frameAxes for k in units.keys()
-        ):
-            err = 'frameUnits must be a dictionary with keys that exist in frameAxes.'
-            raise ValueError(err)
-        self._frameUnits = units
-
-    @property
-    def frameValues(self):
-        return self._frameValues
-
-    @frameValues.setter
-    def frameValues(self, a):
-        self._checkEditable()
-        if self.frameAxes is None:
-            err = 'frameAxes must be set first with a list of frame axis names.'
-            raise ValueError(err)
-        if len(a.shape) != len(self.frameAxes) + 1:
-            err = f'frameValues must have {len(self.frameAxes) + 1} dimensions.'
-            raise ValueError(err)
-        self._frameValues = a
-
     def _generateDownsampledLevels(self, resample_method):
         self._checkEditable()
         current_arrays = dict(self._zarr.arrays())

{large_image_source_zarr-1.30.2 → large_image_source_zarr-1.30.2.dev2}/large_image_source_zarr.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-zarr
-Version: 1.30.2
+Version: 1.30.2.dev2
 Summary: A OME Zarr tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -19,12 +19,12 @@ Classifier: Programming Language :: Python :: 3.13
 Requires-Python: >=3.6
 Description-Content-Type: text/x-rst
 License-File: LICENSE
-Requires-Dist: large-image>=1.30.2
+Requires-Dist: large-image>=1.30.2.dev2
 Requires-Dist: zarr
 Requires-Dist: numcodecs
 Requires-Dist: imagecodecs-numcodecs!=2024.9.22
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.30.2; extra == "girder"
+Requires-Dist: girder-large-image>=1.30.2.dev2; extra == "girder"
 Provides-Extra: all
 Requires-Dist: large-image-converter; extra == "all"
 

{large_image_source_zarr-1.30.2 → large_image_source_zarr-1.30.2.dev2}/large_image_source_zarr.egg-info/requires.txt

@@ -1,4 +1,4 @@
-large-image>=1.30.2
+large-image>=1.30.2.dev2
 zarr
 numcodecs
 imagecodecs-numcodecs!=2024.9.22
@@ -7,4 +7,4 @@ imagecodecs-numcodecs!=2024.9.22
 large-image-converter
 
 [girder]
-girder-large-image>=1.30.2
+girder-large-image>=1.30.2.dev2