Task Generation #2
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
…, the current pydra version, and be useable by BRAINSTools (in particular, BRAINSConstellationDetector) The following changes were made to the script: - Removed exists as an input_spec field - Removed hash_files as an input_spec field - Removed variable placeholders from argstr (for example --inputVolume %s -> --inputVolume) - Removed the spaces around the executable parameter (note, this may affect using the launcher in the future, but I have not been using a launcher." - Removed generating __init__ files which cause relative imports to fail
…RAINSToolsResample.
…ut file name to be specified, but the filename does not already have to exist.
…ut_field outputVolume rather than inputVolume.
…tead of MultipleInputFile.
…g issues with pydra ShellCommandTasks.
…pe File, not MultiInputFile/MultiOutputFile.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Co-authored-by: Michal Brzus [email protected]
Co-authored-by: Benjamin Gorman [email protected]
Description
This PR is a continuation of the work that was started during ohbm brainhack 2020.
This PR allows pydra tasks to be generated from Slicer Execution Model xml files.
The generated pydra tasks are python 3.7 compatible.
The xml files included cover the BRAINSia/BRAINSTools image processing set of tools. The tasks generated by this script allowed me to create a pydra workflow with BRAINSResample and BRAINSConstellationDetector using the output volumes of BRAINSResample as the input volumes of BRAINSConstellationDetector (workflow not included in this repo).
Note: This work is a continuation from Pull Request #1 but was done in a new pull request because PR#1 came from unknown repository to which I do not have access.