Creating a new combined workflow

A CombinedWorkflow is a series of DIPY workflows organized together in a way that the output of a workflow serves as input for the next one.

First create your CombinedWorkflow class. Your CombinedWorkflow class file is usually located in the dipy/workflows directory.

import os

from dipy.workflows.combined_workflow import CombinedWorkflow

CombinedWorkflow is the base class that will be extended to create our combined workflow.

from dipy.workflows.denoise import NLMeansFlow
from dipy.workflows.segment import MedianOtsuFlow

MedianOtsuFlow and NLMeansFlow will be combined to create our processing section.

class DenoiseAndSegment(CombinedWorkflow):
    """
    ``DenoiseAndSegment`` is the name of our combined workflow. Note that
    it needs to extend CombinedWorkflow for everything to work properly.
    """

    def _get_sub_flows(self):
        return [NLMeansFlow, MedianOtsuFlow]

        """
        It is mandatory to implement this method if you want to make all the
        sub workflows parameters available in commandline.
        """

    def run(
        self,
        input_files,
        out_dir="",
        out_denoised="processed.nii.gz",
        out_mask="brain_mask.nii.gz",
        out_masked="dwi_masked.nii.gz",
    ):
        """
        Parameters
        ----------
        input_files : string
            Path to the input files. This path may contain wildcards to
            process multiple inputs at once.

        out_dir : string, optional
            Where the resulting file will be saved. (default '')

        out_denoised : string, optional
            Name of the denoised file to be saved.

        out_mask : string, optional
            Name of the Otsu mask file to be saved.

        out_masked : string, optional
            Name of the Otsu masked file to be saved.
        """

        """
        Just like a normal workflow, it is mandatory to have out_dir as a
        parameter. It is also mandatory to put 'out_' in front of every
        parameter that is going to be an output. Lastly, all out_ params needs
        to be at the end of the params list.

        The class docstring part is very important, you need to document
        every parameter as they will be used with inspection to build the
        command line argument parser.
        """

        io_it = self.get_io_iterator()

        for fnames in io_it:
            in_fname = fnames[0]
            _out_denoised = os.path.basename(fnames[1])
            _out_mask = os.path.basename(fnames[2])
            _out_masked = os.path.basename(fnames[3])

            nl_flow = NLMeansFlow()
            self.run_sub_flow(
                nl_flow, in_fname, out_dir=out_dir, out_denoised=_out_denoised
            )
            denoised = nl_flow.last_generated_outputs["out_denoised"]

            me_flow = MedianOtsuFlow()
            self.run_sub_flow(
                me_flow,
                denoised,
                out_dir=out_dir,
                out_mask=_out_mask,
                out_masked=_out_masked,
            )

Use self.get_io_iterator() in every workflow you create. This creates an IOIterator object that create output file names and directory structure based on the inputs and some other advanced output strategy parameters.

Iterating on the IOIterator object you created previously you conveniently get all input and output paths for every input file found when globbin the input parameters.

In the IOIterator loop you can see how we create a new NLMeans workflow then run it using self.run_sub_flow. Running it this way will pass any workflow specific parameter that was retrieved from the command line and will append the ones you specify as optional parameters (out_dir in this case).

Lastly, the outputs paths are retrieved using workflow.last_generated_outputs. This allows to use denoise as the input for the MedianOtsuFlow.

This is it for the combined workflow class! Now to be able to call it easily via command line, you need to add this workflow in 2 different files:

• <dipy_root>/pyproject.toml: open this file and add the following line to the [project.scripts] section: dipy_denoise_segment = "dipy.workflows.cli:run"

• <dipy_root>/dipy/workflows/cli.py: open this file and add the workflow information to the cli_flows dictionary. The key is the name of the command line command and the value is a tuple with the module name and the workflow class name. In this case it would be: "dipy_denoise_segment": ("dipy.workflows.my_combined_workflow", "DenoiseAndSegment")

That`s it! Now you can call your workflow from anywhere with the command line. Let’s just call the script you just made with -h to see the argparser help text:

dipy_denoise_segment --help

You should see all your parameters available along with some extra common ones like logging file and force overwrite. Also all the documentation you wrote about each parameter is there.