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.

Define a Workflow

GUI: Others > Workflows > Define workflow or Ctrl+K → Ctrl+Shift+D

In this dialog, 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.

View & Edit Workflows

GUI: Others > Workflows > View/Edit workflows or Ctrl+K → Ctrl+Shift+E

Here you can see all the workflows defined in the user directory. You can also edit and overwrite them here. The workflows will be updated immediately, without restarting the application.

Run Workflows

API: run_workflow

GUI: Others > Workflows > Run workflow or Ctrl+K → Ctrl+Shift+R

Defined workflows show up in the Others > Workflows menu. You can also open the dialog at Others > Workflows > Run workflow and select the workflow to run. 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.