fix: fix rgb MDA (#347)

* fix: fix rgb MDA

* add note and change pyside test ver

* try pyside6

* back to pyside2

* disable pyside2

.github/workflows/ci.yml

@@ -29,9 +29,9 @@ jobs:
           - python-version: "3.11"
             platform: ubuntu-latest
             backend: pyqt5
-          - python-version: "3.10"
-            platform: windows-latest
-            backend: pyside2
+          # - python-version: "3.10"
+          #   platform: windows-latest
+          #   backend: pyside2
 
     steps:
       - uses: actions/checkout@v4

README.md

@@ -17,9 +17,11 @@ You can install `napari-micromanager` via [pip]:
 
     pip install napari-micromanager
 
-You will also need a Qt backend such as PySide2/6, or PyQt5/6.  If you've previously installed napari
-into this environment with `pip install napari[all]`, then you will likely already have it. If not,
-you will also need to install a Qt backend of your choice:
+You will also need a Qt backend such as PySide2/6, or PyQt5/6.  **PyQt is
+preferred and receives more testing**. If you've previously installed napari
+into this environment with `pip install napari[all]`, then you will likely
+already have it. If not, you will also need to install a Qt backend of your
+choice:
 
     pip install pyqt5  # or any of {pyqt5, pyqt6, pyside2, pyside6}
 

src/napari_micromanager/_mda_handler.py

@@ -94,6 +94,8 @@ def _on_mda_started(self, sequence: MDASequence) -> None:
         axis_labels, layers_to_create = _determine_sequence_layers(sequence)
 
         yx_shape = [self._mmc.getImageHeight(), self._mmc.getImageWidth()]
+        if self._mmc.getNumberOfComponents() >= 3:
+            yx_shape = [*yx_shape, 3]
 
         # now create a zarr array in a temporary directory for each layer
         for id_, shape, kwargs in layers_to_create:
@@ -212,17 +214,16 @@ def _create_empty_image_layer(
         """
         # we won't have reached this point if meta is None
         meta = sequence.metadata.get(NMM_METADATA_KEY, {})
+        is_rgb = arr.shape[-1] == 3
+        scale = [1.0] * (arr.ndim - (1 if is_rgb else 0))
 
         # add Z to layer scale
         if (pix_size := self._mmc.getPixelSizeUm()) != 0:
-            scale = [1.0] * (arr.ndim - 2) + [pix_size] * 2
+            scale[-2:] = [pix_size, pix_size]
             if (index := sequence.used_axes.find("z")) > -1:
                 if meta.get("split_channels") and sequence.used_axes.find("c") < index:
                     index -= 1
                 scale[index] = getattr(sequence.z_plan, "step", 1)
-        else:
-            # return to default
-            scale = [1.0, 1.0]
 
         layer_meta["useq_sequence"] = sequence
         layer_meta["uid"] = sequence.uid

tests/test_multid_widget.py

@@ -16,7 +16,7 @@
     from napari_micromanager.main_window import MainWindow
 
 
-def test_main_window_mda(main_window: MainWindow):
+def test_main_window_mda(main_window: MainWindow) -> None:
     assert not main_window.viewer.layers
 
     mda = MDASequence(
@@ -35,6 +35,16 @@ def test_main_window_mda(main_window: MainWindow):
     assert all(key in layer_meta for key in keys)
 
 
+def test_main_window_mda_rgb(main_window: MainWindow) -> None:
+    main_window._mmc.setProperty("Camera", "PixelType", "32bitRGB")
+    main_window._mmc.setProperty("Camera", "Mode", "Color Test Pattern")
+    assert not main_window.viewer.layers
+
+    mda = MDASequence(time_plan={"loops": 4, "interval": 0.01}, channels=["DAPI"])
+    main_window._mmc.mda.run(mda)
+    assert main_window.viewer.layers[-1].data.shape == (4, 1, 512, 512, 3)
+
+
 def test_saving_mda(
     qtbot: QtBot,
     main_window: MainWindow,