large-image-source-zarr 1.29.1.dev6__tar.gz → 1.29.1.dev16__tar.gz

{large-image-source-zarr-1.29.1.dev6 → large-image-source-zarr-1.29.1.dev16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-zarr
-Version: 1.29.1.dev6
+Version: 1.29.1.dev16
 Summary: A OME Zarr tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -17,11 +17,11 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.6
 License-File: LICENSE
-Requires-Dist: large-image>=1.29.1.dev6
+Requires-Dist: large-image>=1.29.1.dev16
 Requires-Dist: zarr
 Requires-Dist: imagecodecs-numcodecs
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.29.1.dev6; extra == "girder"
+Requires-Dist: girder-large-image>=1.29.1.dev16; extra == "girder"
 Provides-Extra: all
 Requires-Dist: large-image-converter; extra == "all"
 

{large-image-source-zarr-1.29.1.dev6 → large-image-source-zarr-1.29.1.dev16}/large_image_source_zarr/__init__.py

@@ -79,6 +79,7 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
     def _initOpen(self, **kwargs):
         self._largeImagePath = str(self._getLargeImagePath())
         self._zarr = None
+        self._editable = False
         if not os.path.isfile(self._largeImagePath) and '//:' not in self._largeImagePath:
             raise TileSourceFileNotFoundError(self._largeImagePath) from None
         try:
@@ -126,7 +127,11 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         self._framecount = 0
         self._mm_x = 0
         self._mm_y = 0
+        self._channelNames = []
+        self._channelColors = []
+        self._imageDescription = None
         self._levels = []
+        self._associatedImages = {}
 
     def __del__(self):
         if not hasattr(self, '_derivedSource'):
@@ -312,6 +317,8 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         Validate that we can read tiles from the zarr parent group in
         self._zarr.  Set up the appropriate class variables.
         """
+        if self._editable:
+            self._writeInternalMetadata()
         found = self._scanZarrGroup(self._zarr)
         if found['best'] is None:
             msg = 'No data array that can be used.'
@@ -324,8 +331,10 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             msg = 'Conflicting xy axis data.'
             raise TileSourceError(msg)
         self._channels = found['channels']
-        self._associatedImages = [
-            (g, a) for g, a in found['associated'] if not any(g is gb for gb, _ in self._series)]
+        self._associatedImages = {
+            g.name.replace('/', ''): (g, a)
+            for g, a in found['associated'] if not any(g is gb for gb, _ in self._series)
+        }
         self.sizeX = baseArray.shape[self._axes['x']]
         self.sizeY = baseArray.shape[self._axes['y']]
         self.tileWidth = (
@@ -429,6 +438,8 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
 
         :returns: a dictionary of data or None.
         """
+        if self._editable:
+            self._writeInternalMetadata()
         result = {}
         result['zarr'] = {
             'base': self._zarr.attrs.asdict(),
@@ -445,7 +456,7 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
 
         :return: the list of image keys.
         """
-        return [f'image_{idx}' for idx in range(len(self._associatedImages))]
+        return list(self._associatedImages.keys())
 
     def _getAssociatedImage(self, imageKey):
         """
@@ -454,15 +465,9 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         :param imageKey: the key of the associated image.
         :return: the image in PIL format or None.
         """
-        if not imageKey.startswith('image_'):
-            return
-        try:
-            idx = int(imageKey[6:])
-        except Exception:
-            return
-        if idx < 0 or idx >= len(self._associatedImages):
+        if imageKey not in self._associatedImages:
             return
-        group, arr = self._associatedImages[idx]
+        group, arr = self._associatedImages[imageKey]
         axes = self._getGeneralAxes(arr)
         trans = [idx for idx in range(len(arr.shape))
                  if idx not in axes.values()] + [axes['y'], axes['x']]
@@ -565,8 +570,6 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
         :param kwargs: start locations for any additional axes.  Note that
             ``level`` is a reserved word and not permitted for an axis name.
         """
-        # TODO: improve band bookkeeping
-
         self._checkEditable()
         store_path = str(kwargs.pop('level', 0))
         placement = {
@@ -629,20 +632,8 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     path=store_path,
                 )
 
-            # If base data changed, update large_image attributes and OME metadata
+            # If base data changed, update large_image attributes
             if store_path == '0':
-                self._zarr.attrs.update({
-                    'multiscales': [{
-                        'version': '0.5-dev',
-                        'axes': [{
-                            'name': a,
-                            'type': 'space' if a in ['x', 'y'] else 'other',
-                        } for a in axes],
-                        'datasets': [{'path': 0}],
-                    }],
-                    'omero': {'version': '0.5-dev'},
-                })
-
                 self._dtype = tile.dtype
                 self._bandCount = new_dims.get(axes[-1])  # last axis is assumed to be bands
                 self.sizeX = new_dims.get('x')
@@ -657,6 +648,113 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                 self.levels = int(max(1, math.ceil(math.log(max(
                     self.sizeX / self.tileWidth, self.sizeY / self.tileHeight)) / math.log(2)) + 1))
 
+    def addAssociatedImage(self, image, imageKey=None):
+        """
+        Add an associated image to this source.
+
+        :param image: a numpy array, PIL Image, or a binary string
+            with an image.  The numpy array can have 2 or 3 dimensions.
+        """
+        data, _ = _imageToNumpy(image)
+        with self._addLock:
+            if imageKey is None:
+                # Each associated image should be in its own group
+                num_existing = len(self.getAssociatedImagesList())
+                imageKey = f'image_{num_existing + 1}'
+            group = self._zarr.require_group(imageKey)
+            arr = zarr.array(
+                data,
+                store=self._zarr_store,
+                path=f'{imageKey}/image',
+            )
+            self._associatedImages[imageKey] = (group, arr)
+
+    def _writeInternalMetadata(self):
+        self._checkEditable()
+        with self._addLock:
+            name = str(self._tempdir.name).split('/')[-1]
+            arrays = dict(self._zarr.arrays())
+            channel_axis = self._axes.get('s') or self._axes.get('c')
+            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 * (2 ** level)
+                scale[self._axes.get('y')] = self._mm_y * (2 ** level)
+                dataset_metadata = {
+                    'path': arr_name,
+                    'coordinateTransformations': [{
+                        'type': 'scale',
+                        'scale': scale,
+                    }],
+                }
+                datasets.append(dataset_metadata)
+            for a in sorted_axes:
+                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(axis_metadata)
+            if channel_axis and len(arrays) > 0:
+                base_array = list(arrays.values())[0]
+                base_shape = base_array.shape
+                for c in range(base_shape[channel_axis]):
+                    channel_metadata = {
+                        'active': True,
+                        'coefficient': 1,
+                        'color': 'FFFFFF',
+                        'family': 'linear',
+                        'inverted': False,
+                        'label': f'Band {c + 1}',
+                    }
+                    channel_data = base_array[..., c]
+                    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:
+                        channel_metadata['color'] = self._channelColors[c]
+                    channels.append(channel_metadata)
+            # Guidelines from https://ngff.openmicroscopy.org/latest/
+            self._zarr.attrs.update({
+                'multiscales': [{
+                    'version': '0.5',
+                    'name': name,
+                    'axes': axes,
+                    'datasets': datasets,
+                    'metadata': {
+                        'description': self._imageDescription or '',
+                        'kwargs': {
+                            'multichannel': (channel_axis is not None),
+                        },
+                    },
+                }],
+                'omero': {
+                    'id': 1,
+                    'version': '0.5',
+                    'name': name,
+                    'channels': channels,
+                    'rdefs': rdefs,
+                },
+                'bioformats2raw.layout': 3,
+            })
+
     @property
     def crop(self):
         """
@@ -682,6 +780,59 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             raise TileSourceError(msg)
         self._crop = (x, y, w, h)
 
+    @property
+    def mm_x(self):
+        return self._mm_x
+
+    @mm_x.setter
+    def mm_x(self, value):
+        self._checkEditable()
+        value = float(value) if value is not None else None
+        if value is not None and value <= 0:
+            msg = 'mm_x must be positive or None'
+            raise TileSourceError(msg)
+        self._mm_x = value
+
+    @property
+    def mm_y(self):
+        return self._mm_y
+
+    @mm_y.setter
+    def mm_y(self, value):
+        self._checkEditable()
+        value = float(value) if value is not None else None
+        if value is not None and value <= 0:
+            msg = 'mm_y must be positive or None'
+            raise TileSourceError(msg)
+        self._mm_y = value
+
+    @property
+    def imageDescription(self):
+        return self._imageDescription
+
+    @imageDescription.setter
+    def imageDescription(self, description):
+        self._checkEditable()
+        self._imageDescription = description
+
+    @property
+    def channelNames(self):
+        return self._channelNames
+
+    @channelNames.setter
+    def channelNames(self, names):
+        self._checkEditable()
+        self._channelNames = names
+
+    @property
+    def channelColors(self):
+        return self._channelColors
+
+    @channelColors.setter
+    def channelColors(self, colors):
+        self._checkEditable()
+        self._channelColors = colors
+
     def _generateDownsampledLevels(self, resample_method):
         self._checkEditable()
         current_arrays = dict(self._zarr.arrays())
@@ -705,6 +856,7 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
             width=4096 + tile_overlap['x'],
             height=4096 + tile_overlap['y'],
         )
+        sorted_axes = [a[0] for a in sorted(self._axes.items(), key=lambda item: item[1])]
         for level in range(1, self.levels):
             scale_factor = 2 ** level
             iterator_output = dict(
@@ -739,7 +891,7 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                         x=x,
                         y=y,
                         **frame_position,
-                        axes=list(self._axes.keys()),
+                        axes=sorted_axes,
                         level=level,
                     )
             self._validateZarr()  # refresh self._levels before continuing
@@ -799,6 +951,8 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                         **frame_position,
                     )
 
+        source._writeInternalMetadata()
+
         if suffix in ['.zarr', '.db', '.sqlite', '.zip']:
             if resample is None:
                 resample = (
@@ -807,6 +961,7 @@ class ZarrFileTileSource(FileTileSource, metaclass=LruCacheMetaclass):
                     else ResampleMethod.NP_NEAREST
                 )
             source._generateDownsampledLevels(resample)
+            source._writeInternalMetadata()  # rewrite with new level datasets
 
             if suffix == '.zarr':
                 shutil.copytree(source._tempdir.name, path)

{large-image-source-zarr-1.29.1.dev6 → large-image-source-zarr-1.29.1.dev16}/large_image_source_zarr.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: large-image-source-zarr
-Version: 1.29.1.dev6
+Version: 1.29.1.dev16
 Summary: A OME Zarr tilesource for large_image.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.
@@ -17,11 +17,11 @@ Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Requires-Python: >=3.6
 License-File: LICENSE
-Requires-Dist: large-image>=1.29.1.dev6
+Requires-Dist: large-image>=1.29.1.dev16
 Requires-Dist: zarr
 Requires-Dist: imagecodecs-numcodecs
 Provides-Extra: girder
-Requires-Dist: girder-large-image>=1.29.1.dev6; extra == "girder"
+Requires-Dist: girder-large-image>=1.29.1.dev16; extra == "girder"
 Provides-Extra: all
 Requires-Dist: large-image-converter; extra == "all"
 

{large-image-source-zarr-1.29.1.dev6 → large-image-source-zarr-1.29.1.dev16}/large_image_source_zarr.egg-info/requires.txt

@@ -1,4 +1,4 @@
-large-image>=1.29.1.dev6
+large-image>=1.29.1.dev16
 zarr
 imagecodecs-numcodecs
 
@@ -6,4 +6,4 @@ imagecodecs-numcodecs
 large-image-converter
 
 [girder]
-girder-large-image>=1.29.1.dev6
+girder-large-image>=1.29.1.dev16