ENH: Add get_roi_image method

Return the NgffImage for the current ROI. Users can select the scale or
specific image data to return. Defaults to the first image loaded at the
currently loaded scale.

Author: bnmajor

itkwidgets/_initialization_params.py

@@ -73,7 +73,7 @@ def parse_input_data(init_data_kwargs):
     return inputs
 
 
-def build_init_data(input_data):
+def build_init_data(input_data, stores):
     result= None
     for input_type in DATA_OPTIONS:
         data = input_data.pop(input_type, None)
@@ -83,12 +83,15 @@ def build_init_data(input_data):
         if render_type is RenderType.IMAGE:
             if input_type == 'label_image':
                 result = _get_viewer_image(data, label=True)
+                stores['LabelImage'] = result
                 render_type = RenderType.LABELIMAGE
             elif input_type == 'fixed_image':
                 result = _get_viewer_image(data)
+                stores['Fixed'] = result
                 render_type = RenderType.FIXEDIMAGE
             else:
                 result = _get_viewer_image(data, label=False)
+                stores['Image'] = result
         elif render_type is RenderType.POINT_SET:
             result = _get_viewer_point_set(data)
         if result is None:

itkwidgets/viewer.py

@@ -5,6 +5,7 @@
 from inspect import isawaitable
 from typing import List, Union, Tuple
 from IPython.display import display, HTML
+from ngff_zarr import from_ngff_zarr, to_ngff_image, NgffImage
 import uuid
 
 from ._type_aliases import Gaussians, Style, Image, PointSet
@@ -136,9 +137,10 @@ def __init__(
         self, ui_collapsed=True, rotate=False, ui="pydata-sphinx", **add_data_kwargs
     ):
         """Create a viewer."""
+        self.stores = {}
         self.name = self.__str__()
         input_data = parse_input_data(add_data_kwargs)
-        data = build_init_data(input_data)
+        data = build_init_data(input_data, self.stores)
         if compare := input_data.get('compare'):
             data['compare'] = compare
         if ENVIRONMENT is not Env.HYPHA:
@@ -213,6 +215,7 @@ def set_image(self, image: Image, name: str = 'Image'):
         render_type = _detect_render_type(image, 'image')
         if render_type is RenderType.IMAGE:
             image = _get_viewer_image(image, label=False)
+            self.stores[name] = image
             if ENVIRONMENT is Env.HYPHA:
                 self.image = image
                 svc_name = f'{self.workspace}/itkwidgets-server:data-set'
@@ -323,6 +326,36 @@ async def get_current_scale(self):
         """
         return await self.viewer_rpc.itk_viewer.getLoadedScale()
 
+    @fetch_value
+    async def get_roi_image(self, scale: int = -1, name: str = 'Image') -> NgffImage:
+        """Get the image for the current ROI.
+
+        :param scale: scale of the primary image to get the slices for the
+        current roi. -1, the default, uses the current scale.
+        :type scale: int
+        :param name: Name of the loaded image data to use. 'Image', the
+        default, selects the first loaded image.
+        :type name:  str
+
+        :return: roi_image
+        :rtype:  NgffImage
+        """
+        roi_slices = await self.get_roi_slice(scale)
+        roi_region = await self.get_roi_region()
+        if store := self.stores.get(name):
+            multiscales = from_ngff_zarr(store)
+            loaded_image = multiscales.images[scale]
+            roi_data = loaded_image.data[roi_slices]
+            return to_ngff_image(
+                roi_data,
+                dims=loaded_image.dims,
+                scale=loaded_image.scale,
+                translation=roi_region[0],
+                name=name,
+                axes_units=loaded_image.axes_units
+            )
+        raise ValueError(f'No image data found for {name}.')
+
     @fetch_value
     async def get_roi_region(self):
         """Get the current region of interest in world / physical space.
@@ -339,7 +372,7 @@ async def get_roi_region(self):
         return [{ 'x': x0, 'y': y0, 'z': z0 }, { 'x': x1, 'y': y1, 'z': z1 }]
 
     @fetch_value
-    async def get_roi_slice(self, scale=-1):
+    async def get_roi_slice(self, scale: int = -1):
         """Get the current region of interest as Python slice objects for the
         current resolution of the primary image. The result is in the order:
 
@@ -395,6 +428,7 @@ def set_label_image(self, label_image: Image):
         render_type = _detect_render_type(label_image, 'image')
         if render_type is RenderType.IMAGE:
             label_image = _get_viewer_image(label_image, label=True)
+            self.stores['LabelImage'] = label_image
             if ENVIRONMENT is Env.HYPHA:
                 self.label_image = label_image
                 svc_name = f"{self.workspace}/itkwidgets-server:data-set"