Custom Workflows

Once you decided how to process your data, you may want to automate the workflow and repetitively apply the same operations to many images. Of course, everything is Python, so you can copy & paste the macro script to somewhere.

In cylindra, we provide a more elegant way to do this. You can define your own workflows, browse and edit them in the GUI, and run them manually or programmatically.

Open the Workflow Editor

GUI: Others > Workflows > Open workflow edit

cylindra has a dedicated workflow editor. You can create a new workflow, edit existing ones, run, and delete them in this editor.

Write Your Workflows

In the workflow editor, you can define a workflow by writing a Python script. The script will be saved in the user directory as a file of the given "file name". Since cylindra is aware of all the files in the user directory, you don't have to keep them by yourself.

A simple example

The main function defined in the workflow will be called when the workflow is run. The first argument is always ui, the GUI object.

Following workflow is a simple example that measure the local properties of all the splines and summarize the results in a histogram.

from cylindra.widgets import CylindraMainWidget
import matplotlib.pyplot as plt

def main(ui: "CylindraMainWidget"):
    # fit and measure
    ui.fit_splines(splines="all")
    ui.measure_radius(splines="all", bin_size=2)
    ui.local_cft_analysis(splines="all", bin_size=2)

    # plot histograms of lattice spacings
    for spl in ui.splines:
        plt.hist(spl.props.get_loc("spacing"))
    plt.show()

This workflow can be called at any time → Run Workflows.

Workflow with input parameters

The main function accepts more input arguments. The function signature will be automatically interpreted by magicgui and converted into a dialog.

Following workflow is a completely redundant function as it does no more than the open_image method, but it shows how to define a workflow with input parameters.

from pathlib import Path
from cylindra.widgets import CylindraMainWidget

def main(
    ui: "CylindraMainWidget",
    path: Path,
    tilt_range: tuple[float, float] = (-60, 60),
):
    ui.open_image(path, tilt_range=tilt_range)

The resulting dialog will be like this.

The path argument, which is annotated with Path type, will be converted into a file input box. The tilt_range argument, which is annotated with tuple[float, float] type, will be converted into two float input boxes.

Run Workflows

API: run_workflow

Defined workflows show up in the bottom of the Others > Workflows menu. You can also open the workflow editor, choose a workflow and click the "Run" button. If the workflow does not have any input arguments, it will be run immediately. If it has, a new dialog will be opened to ask for the input arguments.

Note

The defined workflows can also be found in the command palette (Ctrl+P) labeled as the file name.