feat: remove save logic and use pymmcore-plus writer from MDAWidget

src/napari_micromanager/_gui_objects/_mda_widget.py

@@ -43,13 +43,10 @@ def value(self) -> MDASequence:
         sequence = super().value()
         widget_meta = sequence.metadata.get(MMCORE_WIDGETS_META, {})
         split = self.checkBox_split_channels.isChecked() and len(sequence.channels) > 1
-
         sequence.metadata[SEQUENCE_META_KEY] = SequenceMeta(
             mode="mda",
             split_channels=bool(split),
-            save_dir=widget_meta.get("save_dir", ""),
             file_name=widget_meta.get("save_name", ""),
-            should_save=bool("save_dir" in widget_meta),
         )
         return sequence  # type: ignore[no-any-return]
 
@@ -60,12 +57,6 @@ def setValue(self, value: MDASequence) -> None:
                 nmm_meta = SequenceMeta(**nmm_meta)
             if not isinstance(nmm_meta, SequenceMeta):  # pragma: no cover
                 raise TypeError(f"Expected {SequenceMeta}, got {type(nmm_meta)}")
-
-            # update pymmcore_widgets metadata if SequenceMeta are provided
-            widgets_meta = value.metadata.setdefault(MMCORE_WIDGETS_META, {})
-            widgets_meta.setdefault("save_dir", nmm_meta.save_dir)
-            widgets_meta.setdefault("save_name", nmm_meta.file_name)
-
             # set split_channels checkbox
             self.checkBox_split_channels.setChecked(bool(nmm_meta.split_channels))
         super().setValue(value)

src/napari_micromanager/_mda_handler.py

@@ -11,7 +11,6 @@
 from superqt.utils import create_worker, ensure_main_thread
 
 from ._mda_meta import SEQUENCE_META_KEY, SequenceMeta
-from ._saving import save_sequence
 
 if TYPE_CHECKING:
     from uuid import UUID
@@ -53,6 +52,9 @@ class LayerMeta(TypedDict):
         translate: NotRequired[bool]
 
 
+EXP = "Exp"
+
+
 # NOTE: import from pymmcore-plus when new version will be released:
 # from pymmcore_plus.mda.handlers._util import get_full_sequence_axes
 def get_full_sequence_axes(sequence: MDASequence) -> tuple[str, ...]:
@@ -144,7 +146,7 @@ def _on_mda_started(self, sequence: MDASequence) -> None:
                 dtype=dtype,
                 chunks=tuple([1] * len(shape) + yx_shape),  # VERY IMPORTANT FOR SPEED!
             )
-            fname = meta.file_name if meta.should_save else "Exp"
+            fname = meta.file_name or EXP
             self._create_empty_image_layer(z, f"{fname}_{id_}", sequence, **kwargs)
 
             # store the zarr array and temporary directory for later cleanup
@@ -162,8 +164,6 @@ def _on_mda_started(self, sequence: MDASequence) -> None:
             self._watch_mda,
             _start_thread=True,
             _connect={"yielded": self._update_viewer_dims},
-            # NOTE: once we have a proper writer, we can add here:
-            # "finished": self._process_remaining_frames
         )
 
         # Set the viewer slider on the first layer frame
@@ -237,28 +237,14 @@ def _reset_viewer_dims(self) -> None:
 
     def _on_mda_finished(self, sequence: MDASequence) -> None:
         self._mda_running = False
+        self._process_remaining_frames()
 
-        # NOTE: this will be REMOVED when using proper WRITER (e.g.
-        # https://github.com/pymmcore-plus/pymmcore-MDA-writers or
-        # https://github.com/fdrgsp/pymmcore-MDA-writers/tree/update_writer). See the
-        # comment in _process_remaining_frames for more details.
-        self._process_remaining_frames(sequence)
-
-    def _process_remaining_frames(self, sequence: MDASequence) -> None:
+    def _process_remaining_frames(self) -> None:
         """Process any remaining frames after the MDA has finished."""
-        # NOTE: when switching to a proper wtiter to save files, this method will not
-        # have the sequence argument, it will not be called by `_on_mda_finished` but we
-        # can link it to the self._io_t.finished signal ("finished": self._process_
-        # remaining_frames) and the saving code below will be removed.
         self._reset_viewer_dims()
         while self._deck:
             self._process_frame(*self._deck.pop())
 
-        # to remove when using proper writer
-        if (meta := sequence.metadata.get(SEQUENCE_META_KEY)) is not None:
-            sequence = cast("ActiveMDASequence", sequence)
-            save_sequence(sequence, self.viewer.layers, meta)
-
     def _create_empty_image_layer(
         self,
         arr: zarr.Array,
@@ -344,7 +330,7 @@ def _determine_sequence_layers(
               `[('3670fc63-c570-4920-949f-16601143f2e3', [4, 2, 4], {})]`
     """
     # if we got to this point, sequence.metadata[SEQUENCE_META_KEY] should exist
-    meta = sequence.metadata["napari_mm_sequence_meta"]
+    meta = sequence.metadata[SEQUENCE_META_KEY]  # type: ignore
 
     # these are all the layers we're going to create
     # each item is a tuple of (id, shape, layer_metadata)
@@ -407,7 +393,7 @@ def _id_idx_layer(event: ActiveMDAEvent) -> tuple[str, tuple[int, ...], str]:
     axis_order = list(get_full_sequence_axes(event.sequence))
 
     suffix = ""
-    prefix = meta.file_name if meta.should_save else "Exp"
+    prefix = meta.file_name or EXP
 
     if meta.split_channels and event.channel:
         suffix = f"_{event.channel.config}_{event.index['c']:03d}"

src/napari_micromanager/_mda_meta.py

@@ -21,9 +21,6 @@ class SequenceMeta:
     mode: str = ""
     split_channels: bool = False
     file_name: str = ""
-    save_dir: str = ""
-    should_save: bool = False  # to remove when using pymmcore-plus writers
-    save_pos: bool = False  # to remove when using pymmcore-plus writers
 
     def replace(self, **kwargs: Any) -> SequenceMeta:
         """Return a new SequenceMeta with the given kwargs replaced."""

tests/conftest.py

@@ -44,7 +44,7 @@ def main_window(core: CMMCorePlus, make_napari_viewer):
 
 @pytest.fixture(params=MDAS, ids=MDA_IDS)
 def mda_sequence(request: pytest.FixtureRequest) -> useq.MDASequence:
-    seq_meta = SequenceMeta(mode="mda", file_name="test_mda", should_save=True)
+    seq_meta = SequenceMeta(mode="mda", file_name="test_mda")
     return useq.MDASequence(**request.param, metadata={SEQUENCE_META_KEY: seq_meta})
 
 

tests/test_layer_scale.py

@@ -27,10 +27,14 @@ def test_layer_scale(
 
     sequence = mda_sequence_splits.replace(
         axis_order=axis_order,
-        metadata={SEQUENCE_META_KEY: SequenceMeta(should_save=False)},
     )
     z_step = sequence.z_plan and sequence.z_plan.step
 
+    # the MDASequence 'replace' switchesp the metadata to a dict, here we switch it back
+    meta = sequence.metadata[SEQUENCE_META_KEY]
+    meta = SequenceMeta(**meta)
+    sequence = sequence.replace(metadata={SEQUENCE_META_KEY: meta})
+
     # create zarr layer
     handler._on_mda_started(sequence)
 

tests/test_multid_widget.py

@@ -2,13 +2,10 @@
 
 from typing import TYPE_CHECKING
 
-from napari_micromanager._gui_objects._mda_widget import MultiDWidget
 from napari_micromanager._mda_meta import SEQUENCE_META_KEY, SequenceMeta
-from pymmcore_plus.mda import MDAEngine
 from useq import MDASequence
 
 if TYPE_CHECKING:
-    from pathlib import Path
 
     from napari_micromanager.main_window import MainWindow
     from pytestqt.qtbot import QtBot
@@ -29,63 +26,6 @@ def test_main_window_mda(main_window: MainWindow):
     assert main_window.viewer.layers[-1].data.nchunks_initialized == 32
 
 
-def test_saving_mda(
-    qtbot: QtBot,
-    main_window: MainWindow,
-    mda_sequence_splits: MDASequence,
-    tmp_path: Path,
-) -> None:
-    mda = mda_sequence_splits
-    main_window._show_dock_widget("MDA")
-    mda_widget = main_window._dock_widgets["MDA"].widget()
-    assert isinstance(mda_widget, MultiDWidget)
-
-    # FIXME:
-    # we have a bit of a battle here now for file-saving metadata between
-    # pymmcore_widgets and napari_micromanager's SequenceMetadata
-    # should standardize, possibly by adding to useq-schema
-    # this test uses the pymmcore-widgets metadata for now
-    widget_meta = mda.metadata.setdefault("pymmcore_widgets", {})
-    widget_meta["save_dir"] = str(tmp_path)
-    widget_meta["should_save"] = True
-
-    mda_widget.setValue(mda)
-    assert mda_widget.save_info.isChecked()
-    meta = mda_widget.value().metadata[SEQUENCE_META_KEY]
-    assert meta.save_dir == str(tmp_path)
-    # using `metadata=mda.metadata` here to keep the SequenceMeta object
-    # rather than a serialized dict... this is a hack to get around a broader issue
-    # with the .replace method
-    mda = mda.replace(axis_order=mda_widget.value().axis_order, metadata=mda.metadata)
-    mmc = main_window._mmc
-
-    # re-register twice to fully exercise the logic of the update
-    # functions - the initial connections are made in init
-    # then after that they are fully handled by the _update_mda_engine
-    # callbacks
-    mmc.register_mda_engine(MDAEngine(mmc))
-    mmc.register_mda_engine(MDAEngine(mmc))
-
-    # make the images non-square
-    mmc.setProperty("Camera", "OnCameraCCDYSize", 500)
-    with qtbot.waitSignal(mmc.mda.events.sequenceFinished, timeout=8000):
-        mda_widget.control_btns.run_btn.click()
-
-    data_shape = [x for x in main_window.viewer.layers[-1].data.shape if x > 1]
-    expected_shape = [x for x in (*mda.shape, 500, 512) if x > 1]
-
-    multiC = len(mda.channels) > 1
-    splitC = mda.metadata[SEQUENCE_META_KEY].split_channels
-    if multiC and splitC:
-        expected_shape.pop(mda.used_axes.find("c"))
-        nfiles = len(list((tmp_path / f"{meta.file_name}_000").iterdir()))
-        assert nfiles == 2 if multiC else 1
-    # splitC with one channel is the same as not split
-    else:
-        assert [p.name for p in tmp_path.iterdir()] == [f"{meta.file_name}_000.tif"]
-    assert data_shape == expected_shape
-
-
 def test_script_initiated_mda(main_window: MainWindow, qtbot: QtBot):
     # we should show the mda even if it came from outside
     mmc = main_window._mmc