feature/add-scene-selection-widget

napari_aicsimageio/core.py

@@ -7,13 +7,35 @@
 import xarray as xr
 from aicsimageio import AICSImage, exceptions, types
 from aicsimageio.dimensions import DimensionNames
+from qtpy.QtWidgets import QListWidget
+from qtpy.QtCore import Qt
+from napari import Viewer
 
 ###############################################################################
 
 LayerData = Union[Tuple[types.ArrayLike, Dict[str, Any], str]]
 PathLike = Union[str, List[str]]
 ReaderFunction = Callable[[PathLike], List[LayerData]]
 
+###############################################################################
+# _get_viewer() function from https://github.com/napari/napari/issues/2202
+# To provide access to the napari viewer to make the dock widget
+# Copyright (c) 2021 Jonas Windhager
+# Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+# The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+def _get_viewer() -> Optional[Viewer]:
+    import inspect
+
+    frame = inspect.currentframe().f_back
+    while frame:
+        instance = frame.f_locals.get("self")
+        if instance is not None and isinstance(instance, Viewer):
+            return instance
+        frame = frame.f_back
+    return None
+
+
 ###############################################################################
 
 
@@ -41,6 +63,77 @@ def _get_full_image_data(img: AICSImage, in_memory: bool) -> Optional[xr.DataArr
     return None
 
 
+# Function to handle multi-scene files.
+def _get_scenes(img: AICSImage, in_memory: bool) -> Optional[xr.DataArray]:
+    # Create the list widget and populate with the scenes in the file
+    list_widget = QListWidget()
+    for scene in img.scenes:
+        list_widget.addItem(scene)
+    viewer = _get_viewer()
+    viewer.window.add_dock_widget([list_widget], area="right", name="Scene Selector")
+
+    # Function to create image layer from a scene selected in the list widget
+    def open_scene(item):
+        scene = item.text()
+        img.set_scene(scene)
+        if DimensionNames.MosaicTile in img.reader.dims.order:
+            try:
+                if in_memory:
+                    data = img.reader.mosaic_xarray_data
+                else:
+                    data = img.reader.mosaic_xarray_dask_data
+
+            # Catch reader does not support tile stitching
+            except NotImplementedError:
+                print(
+                    "AICSImageIO: Mosaic tile stitching "
+                    "not yet supported for this file format reader."
+                )
+        else:
+            if in_memory:
+                data = img.reader.xarray_data
+            else:
+                data = img.reader.xarray_dask_data
+        meta = _get_meta(data, img)
+        viewer.add_image(data, name=scene, metadata=meta, scale=meta["scale"])
+
+    list_widget.currentItemChanged.connect(open_scene)
+    return None
+
+
+# Function to get Metadata to provide with data
+def _get_meta(data, img):
+    meta = {}
+    if DimensionNames.Channel in data.dims:
+        # Construct basic metadata
+        meta["name"] = data.coords[DimensionNames.Channel].data.tolist()
+        meta["channel_axis"] = data.dims.index(DimensionNames.Channel)
+    # Not multi-channel, use current scene as image name
+    else:
+        meta["name"] = img.reader.current_scene
+    # Handle samples / RGB
+    if DimensionNames.Samples in img.reader.dims.order:
+        meta["rgb"] = True
+    # Handle scales
+    scale: List[float] = []
+    for dim in img.reader.dims.order:
+        if dim in [
+            DimensionNames.SpatialX,
+            DimensionNames.SpatialY,
+            DimensionNames.SpatialZ,
+        ]:
+            scale_val = getattr(img.physical_pixel_sizes, dim)
+            if scale_val is not None:
+                scale.append(scale_val)
+    # Apply scales
+    if len(scale) > 0:
+        meta["scale"] = tuple(scale)
+    # Apply all other metadata
+    meta["metadata"] = {"ome_types": img.metadata}
+
+    return meta
+
+
 def reader_function(
     path: PathLike, in_memory: bool, scene_name: Optional[str] = None
 ) -> Optional[List[LayerData]]:
@@ -57,53 +150,27 @@ def reader_function(
 
     # Open file and get data
     img = AICSImage(path)
-    print(
-        f"AICSImageIO: Image contains {len(img.scenes)} scenes. "
-        f"napari-aicsimageio currently only supports loading first scene, "
-        f"will load scene: '{img.current_scene}'."
-    )
-
-    data = _get_full_image_data(img, in_memory=in_memory)
 
-    # Catch None data
-    if data is None:
-        return None
+    # Check for multiple scenes
+    if len(img.scenes) > 1:
+        print(
+            f"AICSImageIO: Image contains {len(img.scenes)} scenes. "
+            f"Supporting more than the first scene is a work in progress. "
+            f"Select a scene from the list widget. There may be dragons!"
+        )
+        # Launch the list widget
+        _get_scenes(img, in_memory=in_memory)
+        # Return an empty LayerData list, because Layers will be handled via the widget. HT Jonas Windhager
+        return [(None,)]
     else:
-        # Metadata to provide with data
-        meta = {}
-        if DimensionNames.Channel in data.dims:
-            # Construct basic metadata
-            meta["name"] = data.coords[DimensionNames.Channel].data.tolist()
-            meta["channel_axis"] = data.dims.index(DimensionNames.Channel)
-
-        # Not multi-channel, use current scene as image name
+        data = _get_full_image_data(img, in_memory=in_memory)
+
+        # Catch None data
+        if data is None:
+            return None
         else:
-            meta["name"] = img.reader.current_scene
-
-        # Handle samples / RGB
-        if DimensionNames.Samples in img.reader.dims.order:
-            meta["rgb"] = True
-
-        # Handle scales
-        scale: List[float] = []
-        for dim in img.reader.dims.order:
-            if dim in [
-                DimensionNames.SpatialX,
-                DimensionNames.SpatialY,
-                DimensionNames.SpatialZ,
-            ]:
-                scale_val = getattr(img.physical_pixel_sizes, dim)
-                if scale_val is not None:
-                    scale.append(scale_val)
-
-        # Apply scales
-        if len(scale) > 0:
-            meta["scale"] = tuple(scale)
-
-        # Apply all other metadata
-        meta["metadata"] = {"ome_types": img.metadata}
-
-        return [(data.data, meta, "image")]
+            meta = _get_meta(data, img)
+            return [(data.data, meta, "image")]
 
 
 def get_reader(path: PathLike, in_memory: bool) -> Optional[ReaderFunction]: