Add square, cube and threshold to cli #137
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po09i
reviewed
Oct 8, 2020
Added masking cli in entry_points and SCT library
jcohenadad
reviewed
Oct 15, 2020
po09i
reviewed
Oct 15, 2020
po09i
reviewed
Oct 22, 2020
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Just a couple of suggestions to make things more uniform.
- Name of CLI should not have shimmingtoolbox in the name. --> st_mask
- The main could be the same name as the file (mask).
Output: The CLI should save the mask as a nifti array using an option spcifying where to put the output file. The fullpath should be returned.
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LGTM! |
jcohenadad
reviewed
Nov 6, 2020
jcohenadad
reviewed
Nov 6, 2020
jcohenadad
reviewed
Nov 6, 2020
jcohenadad
reviewed
Nov 6, 2020
jidicula
suggested changes
Nov 8, 2020
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Looks good! Just one small change requested so we can keep our docs up-to-date with the library code:
Could you add this CLI to the documentation? An example can be seen here for download_data. If you want to check that it builds correctly with Sphinx, you can cd to docs/ and run make html, then check shimming-toolbox/docs/build/html/6_api_reference/api.html in any web browser. If you're not able to build the docs locally, you can push your .rst changes anyway and check the branch preview on ReadTheDocs:
jcohenadad
reviewed
Nov 27, 2020
jcohenadad
reviewed
Nov 27, 2020
jcohenadad
reviewed
Nov 27, 2020
jcohenadad
reviewed
Nov 27, 2020
jcohenadad
reviewed
Nov 27, 2020
jcohenadad
reviewed
Nov 27, 2020
jcohenadad
reviewed
Nov 27, 2020
jidicula
suggested changes
Dec 1, 2020
po09i
reviewed
Dec 3, 2020
jcohenadad
approved these changes
Dec 3, 2020
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Remaining work to do summarized in this issue. This can be merged. |
po09i
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Get a CLI based working example script
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po09i
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Dec 3, 2020
Get a CLI based working example script
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kousu
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Mar 20, 2021
* First attempt for st_mask w/ some questions * Updated documentation & docstrings * Implementation of CLI allowing to use the following masking techniques: square, cube and threshold * Removal of st_mask.py * Update setup.py Added masking cli in entry_points and SCT library * Changing function name and checking dimensions * Changing function name and checking 2 dimensions * Changing function name * Grouping of 3 masks & addition of functionnalities * Added command mask_shimmingtoolbox * Implementing the test for mask_shimmingtoolbox * Added output nifti file where the mask is stored * Adaptation of input and output file for the test * Modification of entry points * Small comment fixes * Simplified implementation of sizes and cen_dim * Adaptation of tests according to size * Addition of mask in the documentation * addition of the extension sphinx_click.ext * Use of click instead of automodule * Addition of a cli tab in the documentation * Addition of the sphix-click library * Changing the name of the function for mask_cli * Improvement of descriptors and change for box/rect * Adaptation for box and rect masks * Fixed documentation issue * Added mask_cli in the documentation * Change output to file instead of folder * Adaptation of the temporary output of the test Co-authored-by: Alexandre D'Astous <po09i@hotmail.com>
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Create CLI for creating mask
Implementation of st_mask_cube, st_mask_threshold and st_mask_square which allow to apply these masks to the desired files. Each function has its own required input sizes.
Fixes #88
Related to #66