feature/scene-widget-additions (#27)

* Open QListWidget if len(img.scenes) > 1 * Refactor meta into a function * Initial try at getting LayerData from list * Return [(None,)] and call add_image * Ensure meta["scale"] is used * Add comments * Try Flake8 * Use napari.current_viewer() * Add & use scene indexes * Fix ImgLayer name * Fix lines and return none * Clean-up & comments * change to napari[all] and v4.11 * Fix scale in LIF test * Add pytest-qt to test_req * Test for multi-scene widget * Fix nr of widgets check * Fix flake8 import error? * Fix flake8 imports take 2 (isort) * AICSImageIO~4.1.0 * Don't add a list of widgets!! * Test img layer from widget * Fix (some) linting * Fix linting * Linting—for real this time? * Linting! * Fix typing to use napari.types and TYPE_CHECKING * Add qt support libs to gh workflos * Change napari all to pyqt5 and pyside * Add functionality for clearing layers on scene select * Change to with and run for xvfb runner * Change to napari install all * Fix / update tests to remove n widgets check * Check n number of layers instead of scene shape * Don't test layers * Add scene selector gif * Add scene selection feature and gif to README * Loosen aicsimageio dep pin * Add checkbox for unpack channels and change defaults * Change shape check back to multi-channel * Wrong shape * Update scene selection feature gif * Add scene index to layer names * Set layer name to scene label when not unpking ch * Show scene name in layer Co-authored-by: Peter Sobolewski <[email protected]>
AllenCellModeling · Sep 18, 2021 · ccdc11b · ccdc11b
1 parent 8f298c6
commit ccdc11b
Show file tree

Hide file tree

Showing 9 changed files with 290 additions and 90 deletions.
diff --git a/.github/workflows/build-main.yml b/.github/workflows/build-main.yml
@@ -34,12 +34,17 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[test]
+
+    # Install qt support libs
+    - uses: tlambert03/setup-qt-libs@v1     
+
     - name: Download Test Resources
       run: |
         python scripts/download_test_resources.py
     - name: Test with pytest
-      run: |
-        pytest --cov-report xml --cov=napari_aicsimageio napari_aicsimageio/tests/
+      uses: GabrielBB/xvfb-action@v1
+      with:
+        run: pytest --cov-report xml --cov=napari_aicsimageio napari_aicsimageio/tests/
     - name: Upload codecov
       uses: codecov/codecov-action@v1
 

diff --git a/.github/workflows/test-and-lint.yml b/.github/workflows/test-and-lint.yml
@@ -26,12 +26,17 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         pip install .[test]
+    
+    # Install qt support libs
+    - uses: tlambert03/setup-qt-libs@v1     
+
     - name: Download Test Resources
       run: |
         python scripts/download_test_resources.py
     - name: Test with pytest
-      run: |
-        pytest --cov-report xml --cov=napari_aicsimageio napari_aicsimageio/tests/
+      uses: GabrielBB/xvfb-action@v1
+      with:
+        run: pytest --cov-report xml --cov=napari_aicsimageio napari_aicsimageio/tests/
     - name: Upload codecov
       uses: codecov/codecov-action@v1
 

diff --git a/README.md b/README.md
@@ -8,14 +8,16 @@ AICSImageIO bindings for napari
 ---
 
 ## Features
-* Supports reading metadata and imaging data for:
-    * `CZI`
-    * `OME-TIFF`
-    * `TIFF`
-    * Any formats supported by [aicsimageio](https://github.com/AllenCellModeling/aicsimageio)
-    * Any additional format supported by [imageio](https://github.com/imageio/imageio)
+
+-   Supports reading metadata and imaging data for:
+    -   `CZI`
+    -   `OME-TIFF`
+    -   `TIFF`
+    -   Any formats supported by [aicsimageio](https://github.com/AllenCellModeling/aicsimageio)
+    -   Any additional format supported by [imageio](https://github.com/imageio/imageio)
 
 ## Installation
+
 **Stable Release:** `pip install napari-aicsimageio`<br>
 **Development Head:** `pip install git+https://github.com/AllenCellModeling/napari-aicsimageio.git`
 
@@ -24,9 +26,10 @@ AICSImageIO bindings for napari
 ![screenshot of plugin sorter showing that napari-aicsimageio-in-memory should be placed above napari-aicsimageio-out-of-memory](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/plugin-sorter.png)
 
 There are two variants of this plugin that are added during installation:
-* `aicsimageio-in-memory`, which reads an image fully into memory
-* `aicsimageio-out-of-memory`, which delays reading ZYX chunks until required.
-This allows for incredible large files to be read and displayed.
+
+-   `aicsimageio-in-memory`, which reads an image fully into memory
+-   `aicsimageio-out-of-memory`, which delays reading ZYX chunks until required.
+    This allows for incredible large files to be read and displayed.
 
 ## Examples of Features
 
@@ -41,21 +44,25 @@ napari viewer thanks to `ome-types`.
 
 ![screenshot of an OME-TIFF image view, multi-channel, z-stack, with metadata viewer](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/ome-tiff-with-metadata-viewer.png)
 
-#### Mosaic CZI Reading
+#### Mosaic Reading
 
-When reading CZI images, if the image is a mosaic tiled image, `napari-aicsimageio`
+When reading CZI or LIF images, if the image is a mosaic tiled image, `napari-aicsimageio`
 will return the reconstructed image:
 
-![screenshot of a reconstructed / restitched mosaic tile CZI](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/tiled-czi.png)
+![screenshot of a reconstructed / restitched mosaic tile LIF](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/tiled-lif.png)
+
+#### Multi-Scene Selection
 
-#### Mosaic LIF Reading
+**Experimental**
 
-When reading LIF images, if the image is a mosaic tiled image, `napari-aicsimageio`
-will return the reconstructed image:
+When reading a multi-scene file, a widget will be added to the napari viewer to manage
+scene selection (clearing the viewer each time you change scene or adding the
+scene content to the viewer) and a list of all scenes in the file.
 
-![screenshot of a reconstructed / restitched mosaic tile LIF](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/tiled-lif.png)
+![gif of drag and drop file to scene selection and management](https://raw.githubusercontent.com/AllenCellModeling/napari-aicsimageio/main/images/scene-selection.gif)
 
 ## Development
+
 See [CONTRIBUTING.md](CONTRIBUTING.md) for information related to developing the code.
 
 For additional file format support, contributed directly to

diff --git a/images/scene-selection.gif b/images/scene-selection.gif
diff --git a/napari_aicsimageio/core.py b/napari_aicsimageio/core.py
@@ -2,28 +2,45 @@
 # -*- coding: utf-8 -*-
 
 from functools import partial
-from typing import Any, Callable, Dict, List, Optional, Tuple, Union
+from pathlib import Path
+from typing import TYPE_CHECKING, Any, Dict, List, Optional
 
+import napari
 import xarray as xr
-from aicsimageio import AICSImage, exceptions, types
+from aicsimageio import AICSImage, exceptions
 from aicsimageio.dimensions import DimensionNames
+from qtpy.QtWidgets import (
+    QCheckBox,
+    QGroupBox,
+    QListWidget,
+    QListWidgetItem,
+    QVBoxLayout,
+)
+
+if TYPE_CHECKING:
+    from napari.types import LayerData, PathLike, ReaderFunction
 
 ###############################################################################
 
-LayerData = Union[Tuple[types.ArrayLike, Dict[str, Any], str]]
-PathLike = Union[str, List[str]]
-ReaderFunction = Callable[[PathLike], List[LayerData]]
+AICSIMAGEIO_CHOICES = "AICSImageIO Scene Management"
+CLEAR_LAYERS_ON_SELECT = "Clear All Layers on New Scene Selection"
+UNPACK_CHANNELS_TO_LAYERS = "Unpack Channels as Layers"
+
+SCENE_LABEL_DELIMITER = " :: "
 
 ###############################################################################
 
 
-def _get_full_image_data(img: AICSImage, in_memory: bool) -> Optional[xr.DataArray]:
+def _get_full_image_data(
+    img: AICSImage,
+    in_memory: bool,
+) -> xr.DataArray:
     if DimensionNames.MosaicTile in img.reader.dims.order:
         try:
             if in_memory:
                 return img.reader.mosaic_xarray_data
-            else:
-                return img.reader.mosaic_xarray_dask_data
+
+            return img.reader.mosaic_xarray_dask_data
 
         # Catch reader does not support tile stitching
         except NotImplementedError:
@@ -32,18 +49,139 @@ def _get_full_image_data(img: AICSImage, in_memory: bool) -> Optional[xr.DataArr
                 "not yet supported for this file format reader."
             )
 
+    if in_memory:
+        return img.reader.xarray_data
+
+    return img.reader.xarray_dask_data
+
+
+# Function to get Metadata to provide with data
+def _get_meta(data: xr.DataArray, img: AICSImage) -> Dict[str, Any]:
+    meta: Dict[str, Any] = {}
+    if DimensionNames.Channel in data.dims:
+        # Construct basic metadata
+        channels_with_scene_index = [
+            f"{img.current_scene_index}{SCENE_LABEL_DELIMITER}"
+            f"{img.current_scene}{SCENE_LABEL_DELIMITER}{channel_name}"
+            for channel_name in data.coords[DimensionNames.Channel].data.tolist()
+        ]
+        meta["name"] = channels_with_scene_index
+        meta["channel_axis"] = data.dims.index(DimensionNames.Channel)
+
+    # Not multi-channel, use current scene as image name
     else:
-        if in_memory:
-            return img.reader.xarray_data
-        else:
-            return img.reader.xarray_dask_data
+        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 _widget_is_checked(widget_name: str) -> bool:
+    # Get napari viewer from current process
+    viewer = napari.current_viewer()
+
+    # Get scene management widget
+    scene_manager_choices_widget = viewer.window._dock_widgets[AICSIMAGEIO_CHOICES]
+    for child in scene_manager_choices_widget.widget().children():
+        if isinstance(child, QCheckBox):
+            if child.text() == widget_name:
+                return child.isChecked()
+
+    return False
+
+
+# Function to handle multi-scene files.
+def _get_scenes(path: "PathLike", img: AICSImage, in_memory: bool) -> None:
+    # Get napari viewer from current process
+    viewer = napari.current_viewer()
+
+    # Add a checkbox widget if not present
+    if AICSIMAGEIO_CHOICES not in viewer.window._dock_widgets:
+        # Create a checkbox widget to set "Clear On Scene Select" or not
+        scene_clear_checkbox = QCheckBox(CLEAR_LAYERS_ON_SELECT)
+        scene_clear_checkbox.setChecked(False)
+
+        # Create a checkbox widget to set "Unpack Channels" or not
+        channel_unpack_checkbox = QCheckBox(UNPACK_CHANNELS_TO_LAYERS)
+        channel_unpack_checkbox.setChecked(False)
+
+        # Add all scene management state to a single box
+        scene_manager_group = QGroupBox()
+        scene_manager_group_layout = QVBoxLayout()
+        scene_manager_group_layout.addWidget(scene_clear_checkbox)
+        scene_manager_group_layout.addWidget(channel_unpack_checkbox)
+        scene_manager_group.setLayout(scene_manager_group_layout)
+        scene_manager_group.setFixedHeight(100)
+
+        viewer.window.add_dock_widget(
+            scene_manager_group,
+            area="right",
+            name=AICSIMAGEIO_CHOICES,
+        )
+
+    # Create the list widget and populate with the ids & scenes in the file
+    list_widget = QListWidget()
+    for i, scene in enumerate(img.scenes):
+        list_widget.addItem(f"{i}{SCENE_LABEL_DELIMITER}{scene}")
+
+    # Add this files scenes widget to viewer
+    viewer.window.add_dock_widget(
+        list_widget,
+        area="right",
+        name=f"{Path(path).name}{SCENE_LABEL_DELIMITER}Scenes",
+    )
+
+    # Function to create image layer from a scene selected in the list widget
+    def open_scene(item: QListWidgetItem) -> None:
+        scene_text = item.text()
 
-    return None
+        # Use scene indexes to cover for duplicate names
+        scene_index = int(scene_text.split(SCENE_LABEL_DELIMITER)[0])
 
+        # Update scene on image and get data
+        img.set_scene(scene_index)
+        data = _get_full_image_data(img=img, in_memory=in_memory)
 
-def reader_function(
-    path: PathLike, in_memory: bool, scene_name: Optional[str] = None
-) -> Optional[List[LayerData]]:
+        # Get metadata and add to image
+        meta = _get_meta(data, img)
+
+        # Optionally clear layers
+        if _widget_is_checked(CLEAR_LAYERS_ON_SELECT):
+            viewer.layers.clear()
+
+        # Optionally remove channel axis
+        if not _widget_is_checked(UNPACK_CHANNELS_TO_LAYERS):
+            meta["name"] = scene_text
+            meta.pop("channel_axis", None)
+
+        viewer.add_image(data, **meta)
+
+    list_widget.currentItemChanged.connect(open_scene)
+
+
+def reader_function(path: "PathLike", in_memory: bool) -> Optional[List["LayerData"]]:
     """
     Given a single path return a list of LayerData tuples.
     """
@@ -57,56 +195,27 @@ 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)
+    # 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 experimental. "
+            f"Select a scene from the list widget. There may be dragons!"
+        )
+        # Launch the list widget
+        _get_scenes(path=path, img=img, in_memory=in_memory)
 
-    # Catch None data
-    if data is None:
-        return None
+        # Return an empty LayerData list; ImgLayers 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
-        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}
-
+        data = _get_full_image_data(img, in_memory=in_memory)
+        meta = _get_meta(data, img)
         return [(data.data, meta, "image")]
 
 
-def get_reader(path: PathLike, in_memory: bool) -> Optional[ReaderFunction]:
+def get_reader(path: "PathLike", in_memory: bool) -> Optional["ReaderFunction"]:
     """
     Given a single path or list of paths, return the appropriate aicsimageio reader.
     """
@@ -123,7 +232,7 @@ def get_reader(path: PathLike, in_memory: bool) -> Optional[ReaderFunction]:
 
         # The above line didn't error so we know we have a supported reader
         # Return a partial function with in_memory determined
-        return partial(reader_function, in_memory=in_memory)  # type: ignore
+        return partial(reader_function, in_memory=in_memory)
 
     # No supported reader, return None
     except exceptions.UnsupportedFileFormatError: