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pymmcore-widgets PyPI version

MDAWidget

MDAWidgetMDAWidget

Screenshot generated from the example below.

Example

examples/mda_widget.py
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"""MDAWidget is a widget for creating and running a useq.MDASequence.

It is fully connected to the CMMCorePlus object, and has a "run" button.
"""

from contextlib import suppress

import useq
from pymmcore_plus import CMMCorePlus
from qtpy.QtWidgets import QApplication

from pymmcore_widgets import MDAWidget

with suppress(ImportError):
    from rich import print

app = QApplication([])

CMMCorePlus.instance().loadSystemConfiguration()

wdg = MDAWidget()
# start from a sequence (or build one in the GUI)
wdg.setValue(
    useq.MDASequence(
        channels=["DAPI", "FITC"],
        time_plan=useq.TIntervalLoops(interval=0.5, loops=11),
    )
)
wdg.valueChanged.connect(lambda: print(wdg.value()))
wdg.show()
app.exec()

API

Bases: MDASequenceWidget

Main MDA Widget connected to a pymmcore_plus.CMMCorePlus instance.

It provides a GUI to construct and run a useq.MDASequence. Unlike useq_widgets.MDASequenceWidget, this widget is connected to a pymmcore_plus.CMMCorePlus instance, enabling awareness and control of the current state of the microscope.

Parameters:

Name Type Description Default
parent QWidget | None

Optional parent widget, by default None.

 None
mmcore CMMCorePlus | None

Optional CMMCorePlus micromanager core. By default, None. If not specified, the widget will use the active (or create a new) CMMCorePlus.instance.

 None
Referenced by: Returned by:

valueChanged 

valueChanged = Signal()

Emitted (with no arguments) when the sequence changes; read it with value().

time_plan property 

time_plan: TimePlanWidget

channels property 

channels: CoreConnectedChannelTable

z_plan property 

z_plan: CoreConnectedZPlanWidget

stage_positions property 

stage_positions: CoreConnectedPositionTable

grid_plan property 

grid_plan: CoreConnectedGridPlanWidget

save 

save(file: str | Path | None = None) -> None

Save the current useq.MDASequence to a file.

load 

load(file: str | Path | None = None) -> None

Load a useq.MDASequence from a file.

value 

value() -> MDASequence

Return the current state of the widget as a useq.MDASequence.

Some fields are filled in from the current state of the core. For example, if there are no stage positions, the current stage position is used.

setValue 

setValue(value: MDASequence) -> None

Set the state of the widget from a useq.MDASequence.

get_next_available_path 

get_next_available_path(requested_path: Path) -> Path

Get the next available path.

This method is called immediately before running an MDA to ensure that the file being saved does not overwrite an existing file. It is also called at the end of the experiment to update the save widget with the next available path.

It may be overridden to provide custom behavior, but it should always return a Path object to a non-existing file or folder.

The default behavior adds/increments a 3-digit counter at the end of the path (before the extension) if the path already exists.

Parameters:

Name Type Description Default
requested_path Path

The path we are requesting for use.

 required

prepare_mda 

prepare_mda() -> bool | str | Path | None

Prepare the MDA sequence experiment.

Returns:

Type Description
bool

False if MDA to be cancelled due to autofocus issue.
str | Path

Preparation successful, save path to be used for saving and saving active
None

Preparation successful, saving deactivated
Referenced by:

execute_mda 

execute_mda(
    output: Path
    | str
    | SupportsFrameReady
    | Sequence[Path | str | SupportsFrameReady]
    | None,
) -> None

Execute the MDA experiment corresponding to the current value.

Referenced by:

run_mda 

run_mda() -> None

Run the current sequence (what the "Run" button does).

Calls prepare_mda, then execute_mda unless preparation was cancelled.