Used the absolute path to create the temporary label file in propseg #1487

peristeri · 2017-10-11T20:57:44Z

Description of the Change

The filename for the temporary label file did not match with the one used when cleaning up.

Applicable Issues

Implements or Fixes #1483

jcohenadad · 2017-10-13T15:24:00Z

tested-- still failing. Should we reinstall sct?
EDITED: yes, SCT needs to be reinstalled with pip install. @peristeri: please ALWAYS mention at the beginning of the PR if SCT needs to be reinstalled, and how to do it. Something like this:

For testing this PR, go to SCT folder and run:

source python/bin/activate
pip install -e .

jcohenadad · 2017-10-13T15:31:09Z

Tested the viewer. There is no crash, however the functionality is broken. Example here:
https://www.dropbox.com/s/ekeqwlfsgj7ihxt/20171013_bugViewer.m4v?dl=0

@peristeri: This is HIGH priority. If you cannot fix it today, please come back to the previous version of the viewer we had prior to introducing the QT version.

peristeri · 2017-10-13T15:35:56Z

the behavior is as expected. It allows maximum 3 points. If that's not the case, I could remove the limit.

…

On Oct 13, 2017 11:31 AM, "Julien Cohen-Adad" ***@***.***> wrote: Tested the viewer. There is no crash, however the functionality is broken. Example here: https://www.dropbox.com/s/ekeqwlfsgj7ihxt/20171013_bugViewer.m4v?dl=0 @peristeri <https:/peristeri>: This is *HIGH* priority. If you cannot fix it today, please come back to the previous version of the viewer we had prior to introducing the QT version. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1487 (comment)>, or mute the thread <https:/notifications/unsubscribe-auth/AAzRaA9f4STstml4CJIxI4Q6uTMpkAcSks5sr4I-gaJpZM4P2HZo> .

jcohenadad · 2017-10-13T15:38:46Z

@peristeri: this not correct. -init-mask asks for three points while -init-centerline asks for any number of points along the centerline.

peristeri · 2017-10-13T16:41:20Z

OK. I'll fix that soon.

…

On Oct 13, 2017 11:38 AM, "Julien Cohen-Adad" ***@***.***> wrote: @peristeri <https:/peristeri>: this not correct. -init-mask asks for three points while -init-centerline asks for any number of points along the centerline. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1487 (comment)>, or mute the thread <https:/notifications/unsubscribe-auth/AAzRaJEt9zo6BCf4hz-LSS_1kBd8n3fVks5sr4QHgaJpZM4P2HZo> .

benjamindeleener

Hi George, I tested the viewer. The centerline functionality works now. I saw a couple of things that should still be changed:

The title on the right panel should be only "Select the center of the spinal cord" without the number at the beginning.
When we reach the bottom of the image, the latest point is not displayed and there is no indication that the end has been reached.
The first and last slices are not available in the automatic situation.

- Made sure that the GUI saved the points to file - Set the initial auto point to 0 - When reaching the last valid point in auto mode, stay at that slice.

jcohenadad · 2017-10-13T21:54:11Z

tested 5bcbd70:

init-mask: previous behaviour was that the first slice would be located in the middle slice (currently top slice)

jcohenadad · 2017-10-14T10:52:50Z

@peristeri: your latest commit 1e37757 does not fix the issue i raised here: #1487 (comment).
i'll take care of it.

jcohenadad

we can merge, but minor fixes will need to be addressed:
#1494

i moved your requests in issue #1494 because we need to merge this PR ASAP

…x into jca_issue1452 * 'jca_issue1452' of github.com:neuropoly/spinalcordtoolbox: Used the absolute path to create the temporary label file in propseg (#1487)

* master: (43 commits) BUG: put back default value for labels (made batch_processing crash) BUG: replaced run(mkdir) with python’s makedirs raise in sct.run in bad order. Also added specific sct errors (#1503) Major refactoring of testing framework (#1453) More improvements to the viewer (#1496) DEV: add a line in the output excel that compute the percentage of a given tract occupied by lesionS: vol_lesionS_in_PAM50_04 / vol_PAM50_04_tot BUG: fix errors in create_atlas.m (#1499) Used the absolute path to create the temporary label file in propseg (#1487) Option to install SCT in development mode (#1491) Refactored WM atlas creation pipeline and improved documentation (#1492) Updated bibliographic URL on ReadMe (#1489) Fix a regression bug. Added key bindings to the undo, save and help actions. (#1480) OPT: propseg: fixed issue 1484 (#1485) Fixed global dependency in sct_process_segmentation call (#1481) Introduced the zoom functionality to the anatomical canvas (#1477) Poq issue 1409 log (#1411) The minimal QT dialog (#1379) Update README.md download_data: forgot to add pmj_models in the -d flag ...

* jca-release: (44 commits) updated CHANGES for 3.1 BUG: put back default value for labels (made batch_processing crash) BUG: replaced run(mkdir) with python’s makedirs raise in sct.run in bad order. Also added specific sct errors (#1503) Major refactoring of testing framework (#1453) More improvements to the viewer (#1496) DEV: add a line in the output excel that compute the percentage of a given tract occupied by lesionS: vol_lesionS_in_PAM50_04 / vol_PAM50_04_tot BUG: fix errors in create_atlas.m (#1499) Used the absolute path to create the temporary label file in propseg (#1487) Option to install SCT in development mode (#1491) Refactored WM atlas creation pipeline and improved documentation (#1492) Updated bibliographic URL on ReadMe (#1489) Fix a regression bug. Added key bindings to the undo, save and help actions. (#1480) OPT: propseg: fixed issue 1484 (#1485) Fixed global dependency in sct_process_segmentation call (#1481) Introduced the zoom functionality to the anatomical canvas (#1477) Poq issue 1409 log (#1411) The minimal QT dialog (#1379) Update README.md ... # Conflicts: # dev/straightening/sct_straighten_spinalcord_LargeFOVOutput.py

* jca-release: (44 commits) updated CHANGES for 3.1 BUG: put back default value for labels (made batch_processing crash) BUG: replaced run(mkdir) with python’s makedirs raise in sct.run in bad order. Also added specific sct errors (#1503) Major refactoring of testing framework (#1453) More improvements to the viewer (#1496) DEV: add a line in the output excel that compute the percentage of a given tract occupied by lesionS: vol_lesionS_in_PAM50_04 / vol_PAM50_04_tot BUG: fix errors in create_atlas.m (#1499) Used the absolute path to create the temporary label file in propseg (#1487) Option to install SCT in development mode (#1491) Refactored WM atlas creation pipeline and improved documentation (#1492) Updated bibliographic URL on ReadMe (#1489) Fix a regression bug. Added key bindings to the undo, save and help actions. (#1480) OPT: propseg: fixed issue 1484 (#1485) Fixed global dependency in sct_process_segmentation call (#1481) Introduced the zoom functionality to the anatomical canvas (#1477) Poq issue 1409 log (#1411) The minimal QT dialog (#1379) Update README.md ... # Conflicts: # dev/straightening/sct_straighten_spinalcord_LargeFOVOutput.py Former-commit-id: 45518c6

Used the absolute path to create the temporary label file in propseg

dee11b8

peristeri added bug category: fixes an error in the code card:TO_REVIEW priority:HIGH labels Oct 11, 2017

peristeri added this to the Release v3.0.9 milestone Oct 11, 2017

peristeri requested review from jcohenadad and benjamindeleener October 11, 2017 20:58

Merge branch 'master' into qt-propseg

6317bd1

Set limit of 3 points only for -init-mask parameter in sct_propseg

47a4188

benjamindeleener previously requested changes Oct 13, 2017

View reviewed changes

peristeri and others added 2 commits October 13, 2017 14:12

Small modifications

25d38b9

- Made sure that the GUI saved the points to file - Set the initial auto point to 0 - When reaching the last valid point in auto mode, stay at that slice.

Merge branch 'master' into qt-propseg

5bcbd70

jcohenadad and others added 3 commits October 13, 2017 20:58

Merge branch 'master' into qt-propseg

0ec5c54

Merge branch 'master' into qt-propseg

1eb9c73

Adjusted the starting slice and added some safe guards.

1e37757

jcohenadad added 6 commits October 14, 2017 06:55

OPT: propseg: with init-mask mode, start default slice at middle of FOV

0675de9

OPT: propseg: fixed typo

efc8b15

DOC: gui/centerline: fixed usage

135da9e

DOC: gui/centerline: fixed typo

f4be115

DOC: gui/base: fixed wrong message

7f877e6

Merge branch 'master' into qt-propseg

0f2ff0a

jcohenadad approved these changes Oct 14, 2017

View reviewed changes

jcohenadad merged commit deb96b9 into master Oct 14, 2017

jcohenadad deleted the qt-propseg branch October 14, 2017 15:24

peristeri removed the card:TO_REVIEW label Mar 27, 2018

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Used the absolute path to create the temporary label file in propseg #1487

Used the absolute path to create the temporary label file in propseg #1487

peristeri commented Oct 11, 2017

jcohenadad commented Oct 13, 2017 •

edited

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Used the absolute path to create the temporary label file in propseg #1487

Used the absolute path to create the temporary label file in propseg #1487

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peristeri commented Oct 11, 2017

Description of the Change

Applicable Issues

jcohenadad commented Oct 13, 2017 • edited Loading

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jcohenadad commented Oct 13, 2017 •

edited

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