Creating a new workflow.

A workflow is a series of DIPY operations with fixed inputs and outputs that is callable via command line or another interface.

For example, after installing DIPY, you can call anywhere from your command line:

dipy_nlmeans t1.nii.gz t1_denoised.nii.gz

First create your workflow (let’s name this workflow file as my_workflow.py). Usually this is a python file in the <../dipy/workflows> directory.

import shutil

shutil Will be used for sample file manipulation.

from dipy.workflows.workflow import Workflow

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

class AppendTextFlow(Workflow):

    def run(self, input_files, text_to_append='dipy', out_dir='',
            out_file='append.txt'):
        """
        Parameters
        ----------
        input_files : string
            Path to the input files. This path may contain wildcards to
            process multiple inputs at once.

        text_to_append : string, optional
            Text that will be appended to the file. (default 'dipy')

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

        out_file : string, optional
            Name of the result file to be saved. (default 'append.txt')
        """

AppendTextFlow is the name of our workflow. Note that it needs to extend Workflow for everything to work properly. It will append text to a file. 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 run docstring 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 in_file, out_file in io_it:

    shutil.copy(in_file, out_file)

    with open(out_file, 'a') as myfile:

        myfile.write(text_to_append)

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.

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

The code in the loop is the actual workflow processing code. It can be anything. For the example, it just appends text to an input file.

This is it for the workflow! Now to be able to call it easily via command line, you need to add this bit of code. Usually this is in a separate executable file located in bin.

The first line imports the run_flow method from the flow_runner class.

from dipy.workflows.flow_runner import run_flow

The second line imports the AppendTextFlow class from the newly created my_workflow.py file. In this specific case, we comment this import since AppendTextFlow class is not on an external file but in the current file.

# from dipy.workflows.my_workflow import AppendTextFlow

This is the method that will wrap everything that is needed to make a flow command line ready then run it.

if __name__ == "__main__":
    run_flow(AppendTextFlow())

This is the only thing needed to make your workflow available through command line.

Now just call the script you just made with -h to see the argparser help text:

python workflow_creation.py --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.

Now call it for real with a text file:

python workflow_creation.py ./text_file.txt