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
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
run docstring is very important, you need to document every
parameter as they will be used with inspection to build the command line
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
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
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
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
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
Example source code
You can download
the full source code of this example. This same script is also included in the dipy source distribution under the