Merge pull request #88 from TimMonko/new-image-utilities

New image utilities widget

setup.cfg

@@ -47,6 +47,7 @@ install_requires =
     pyclesperanto-prototype
     dask
     napari-workflows
+    natsort
     seaborn
     stackview
     tifffile >= 2023.3.15 # https://github.com/AllenCellModeling/aicsimageio/issues/523 maybe keep for legacy reasons?
@@ -81,8 +82,8 @@ testing =
     pytest-qt  # https://pytest-qt.readthedocs.io/en/latest/
     napari
     pyqt5
-    napari-ndev[all] # just to confirm that bioio dependencies don't conflict with expected readers in tests
-    # napari-bioio @ git+https://github.com/TimMonko/napari-bioio.git@main#egg=napari-bioio
+    bioio-czi >= 1.0.1
+    napari_ndev[extras]
 
 extras =
     napari-pyclesperanto-assistant
@@ -93,7 +94,6 @@ gpl_extras =
     # bioio GPL3 dependencies
     bioio-czi >= 1.0.1
     bioio-lif >= 1
-    # napari-bioio @ git+https://github.com/TimMonko/napari-bioio.git@main#egg=napari-bioio
 
 docs =
     mkdocs

src/napari_ndev/_napari_reader.py

@@ -110,10 +110,9 @@ def napari_reader_function(
         logger.info("Bioio: Expected a single path, got a list of paths.")
         return None
 
-    in_memory = _determine_in_memory(path) if in_memory is None else in_memory
-    logger.info('Bioio: Reading in-memory: %s', in_memory)
-
     img = nImage(path, reader=reader)
+    in_memory = img._determine_in_memory(path) if in_memory is None else in_memory
+    logger.info('Bioio: Reading in-memory: %s', in_memory)
 
     if len(img.scenes) > 1 and not open_first_scene_only:
         _get_scenes(path=path, img=img, in_memory=in_memory)
@@ -126,23 +125,6 @@ def napari_reader_function(
 
     return [(img_data.data, img_meta, layer_type)]
 
-def _determine_in_memory(
-    path: PathLike,
-    max_mem_bytes: int = 4e9,
-    max_mem_percent: int = 0.3
-) -> bool:
-    """Determine whether to read the file in memory."""
-    from bioio_base.io import pathlike_to_fs
-    from psutil import virtual_memory
-
-    fs, path = pathlike_to_fs(path)
-    filesize = fs.size(path)
-    available_mem = virtual_memory().available
-    return (
-        filesize <= max_mem_bytes
-        and filesize / available_mem <= max_mem_percent
-    )
-
 def _widget_is_checked(widget_name: str) -> bool:
     import napari
 
@@ -173,18 +155,18 @@ def _get_scenes(path: PathLike, img: nImage, in_memory: bool) -> None:
 
         # Create a checkbox widget to set "Unpack Channels" or not
         channel_unpack_checkbox = QCheckBox(UNPACK_CHANNELS_TO_LAYERS)
-        channel_unpack_checkbox.setChecked(False)
+        channel_unpack_checkbox.setChecked(True)
 
-        # Create a checkbox widget to set "Mosaic Merge" or not
-        dont_merge_mosaics_checkbox = QCheckBox(DONT_MERGE_MOSAICS)
-        dont_merge_mosaics_checkbox.setChecked(False)
+        # # Create a checkbox widget to set "Mosaic Merge" or not
+        # dont_merge_mosaics_checkbox = QCheckBox(DONT_MERGE_MOSAICS)
+        # dont_merge_mosaics_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_layout.addWidget(dont_merge_mosaics_checkbox)
+        # scene_manager_group_layout.addWidget(dont_merge_mosaics_checkbox)
         scene_manager_group.setLayout(scene_manager_group_layout)
         scene_manager_group.setFixedHeight(100)
 

src/napari_ndev/_tests/test_napari_reader.py

@@ -1,7 +1,7 @@
 from __future__ import annotations
 
 from pathlib import Path
-from typing import TYPE_CHECKING, Any
+from typing import Any
 
 import dask.array as da
 
@@ -11,12 +11,10 @@
 
 from napari_ndev._napari_reader import napari_get_reader
 
-if TYPE_CHECKING:
-    from npe2._pytest_plugin import TestPluginManager
-
 ###############################################################################
 
 RGB_TIFF = "RGB.tiff" # has two scense
+MULTISCENE_CZI = r"0T-4C-0Z-7pos.czi"
 # PNG_FILE = "example.png"
 # GIF_FILE = "example.gif"
 # OME_TIFF = "pipeline-4.ome.tiff"
@@ -49,9 +47,9 @@ def test_reader(
     filename: str,
     in_memory: bool,
     expected_shape: tuple[int, ...],
-    expected_dtype: type,
+    expected_dtype,
     expected_meta: dict[str, Any],
-    npe2pm: TestPluginManager,
+    # npe2pm: TestPluginManager,
 ) -> None:
     # Resolve filename to filepath
     if isinstance(filename, str):
@@ -78,7 +76,54 @@ def test_reader(
         meta.pop('metadata', None)
         assert meta == expected_meta
 
-        # # confirm that this also works via npe2
-        # with npe2pm.tmp_plugin(package='napari-ndev') as plugin:
-        #     [via_npe2] = npe2.read([path], stack=False, plugin_name=plugin.name)
-        #     assert via_npe2[0].shape == data.shape
+
+@pytest.mark.parametrize(
+    ("in_memory", "expected_dtype"),
+    [
+        (True, np.ndarray),
+        (False, da.core.Array),
+    ],
+)
+@pytest.mark.parametrize(
+    ("filename", "expected_shape"),
+    [
+        (RGB_TIFF, (120, 160, 3)),
+        (MULTISCENE_CZI, (32, 32)),
+    ],
+)
+def test_for_multiscene_widget(
+    make_napari_viewer,
+    resources_dir: Path,
+    filename: str,
+    in_memory: bool,
+    expected_dtype,
+    expected_shape: tuple[int, ...],
+) -> None:
+    # Make a viewer
+    viewer = make_napari_viewer()
+    assert len(viewer.layers) == 0
+    assert len(viewer.window._dock_widgets) == 0
+
+    # Resolve filename to filepath
+    if isinstance(filename, str):
+        path = str(resources_dir / filename)
+
+    # Get reader
+    reader = napari_get_reader(path, in_memory)
+
+    if reader is not None:
+        # Call reader on path
+        reader(path)
+
+        if len(viewer.window._dock_widgets) != 0:
+            # Get the second scene
+            viewer.window._dock_widgets[f"{filename} :: Scenes"].widget().setCurrentRow(
+                1
+            )
+            data = viewer.layers[0].data
+            assert isinstance(data, expected_dtype)
+            assert data.shape == expected_shape
+        else:
+            data, _, _ = reader(path)[0]
+            assert isinstance(data, expected_dtype)
+            assert data.shape == expected_shape