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Apply Transform workflow for transforming a collection of moving images. #1598

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parichit commented Jul 25, 2018

This branch contains the 'ApplyTransformFlow' that uses the matrix obtained from the affine registration, to quickly transform a set of moving images (using the affine matrix) to the static image.

This PR must only be merged after PR 1581 and before PR 1595 because it builds on the functionality in PR 1581.

Parichit Sharma and others added some commits Jun 18, 2018

Parichit Sharma
Added the image registration workflow to the align.py and test_align.py
Since the image registration forms the part of alignment so the image registration workflow is added to the align class.

1) Added the ImageRegistrationWorkflow Class to the align.py file.
Parichit Sharma
Added a command line wrapper for the Image Registration workflow.
1) Created the separate command line script for the Image Registration workflow.
Parichit Sharma
Workflow for applying the transform on a set of images.
1)Added the function to load the saved affine matrix that needs to be applied.

2) Added the import for scipy.ndimage in the test_parzenhist.py file.

3) Added the apply_transform workflow to apply the transform.
Parichit Sharma
Created the apply transfomr workflow.
1) Added a function to load the saved affine matrix from the text file.
2) Added the import of ndimage from scipy in the test_parzenhist.py file.
3) Created a new workflow file apply_transform.
Parichit Sharma
1) Added the command line wrapper for the apply_transform workflow and,
2) changed the output_strategy to 'absolute' in the flow runner.
Parichit Sharma
Moved the apply transform code to align.py file.
1) Refactored the apply transform code.
2) Renamed the binary for apply transform workflow.
Future Work:
1) Need to do more manual testing for the apply transform workflow.
2) Need to write test cases for the apply transform workflow.
Parichit Sharma
1) Apply transform code is integrated with the align.py file.
2) Wrote the test cases for the apply transform for automated testing.
3) Did manual testing of the apply transform workflow.
@pep8speaks

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pep8speaks commented Jul 25, 2018

Hello @parichit, Thank you for updating !

Cheers ! There are no PEP8 issues in this Pull Request. 🍻

Comment last updated on July 27, 2018 at 20:09 Hours UTC

Parichit Sharma and others added some commits Jul 25, 2018

Parichit Sharma
Parichit Sharma
1) Updated the test_align.py to contains the latest code from the PR …
…1581.

2) Updated the apply_transform test case to also use assert.
Parichit Sharma
Parichit Sharma Parichit Sharma
Added the image registration workflow to the align.py and test_align.py
Since the image registration forms the part of alignment so the image registration workflow is added to the align class.

1) Added the ImageRegistrationWorkflow Class to the align.py file.
Parichit Sharma Parichit Sharma
Added a command line wrapper for the Image Registration workflow.
1) Created the separate command line script for the Image Registration workflow.
Parichit Sharma Parichit Sharma
Workflow for applying the transform on a set of images.
1)Added the function to load the saved affine matrix that needs to be applied.

2) Added the import for scipy.ndimage in the test_parzenhist.py file.

3) Added the apply_transform workflow to apply the transform.
Parichit Sharma Parichit Sharma
Created the apply transfomr workflow.
1) Added a function to load the saved affine matrix from the text file.
2) Added the import of ndimage from scipy in the test_parzenhist.py file.
3) Created a new workflow file apply_transform.

Parichit Sharma and others added some commits Jun 20, 2018

Parichit Sharma Parichit Sharma
Moved the apply transform code to align.py file.
1) Refactored the apply transform code.
2) Renamed the binary for apply transform workflow.
Future Work:
1) Need to do more manual testing for the apply transform workflow.
2) Need to write test cases for the apply transform workflow.
Parichit Sharma Parichit Sharma
1) Apply transform code is integrated with the align.py file.
2) Wrote the test cases for the apply transform for automated testing.
3) Did manual testing of the apply transform workflow.
Parichit Sharma
1) Updated the test_align.py to contains the latest code from the PR …
…1581.

2) Updated the apply_transform test case to also use assert.
Merge branch 'apply_transform' of https://github.com/parichit/dipy in…
…to apply_transform

Current branch is behind the remote master so merging the changes from the remote master.
@skoudoro

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skoudoro commented Aug 21, 2018

closing in favor of #1605

@skoudoro skoudoro closed this Aug 21, 2018

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