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IDProjectCategoryView StatusDate SubmittedLast Update
0003401Slicer4Core: Packagingpublic2013-09-17 05:462014-09-17 22:57
Reporterkikinis Assigned Tojcfr  
PriorityhighSeverityminorReproducibilityhave not tried
Status closedResolutionfixed 
Product Version 
Target VersionSlicer 4.4.0Fixed in VersionSlicer 4.4.0 
Summary0003401: Remove Slicer legacy module from the trunk
Description

See http://www.slicer.org/slicerWiki/index.php/Documentation/Labs/DeprecatedModules

// --------------------------
Jc notes from past discussion:

Module re-organization meeting

  • After loading Dicom, concept of "What 's next", a "task / user case" oriented approach.

  • Goal of this meeting: Look at the topic organized modules menu. We would like the initial presentation to be stripped down.

.

  • Idea: Disable all modules by default expect the "blessed" one.

Todo

  • Wizard + Examples: Hide since there are not modules

  • Legacy:
    ** Make an annoucement + do it

    BRAINS
    DONE Easy Registration -> gone
    DONE     Create Label Maps from prob maps -> "Mistake" - should be disabled

    Simple Region Growing Segmentation -> Legacy

    EMSegment
    -> Extension ?
    -> Should we keep maintaining Slicer3 compat ?

DataProbe -> Associated entry in module menu should be hidden

PET Standard Uptake value computation
-> Consult with Andriy

Set of enabled modules + extensions should be saved from one version to an other.
Check with new version of extension are available

Redesigned Welcome module ?

TagsNo tags attached.

Relationships

related to 0003814 resolvedjcfr Create an extension bundling useful legacy module 
related to 0002398 acknowledgedjcfr Remove the EMSegment module from the Slicer install package and distribute it as an extension 
related to 0003815 closedjcfr Legacy module OtsuThresholdImageFilter is needed by EMSegment 

Activities

jcfr

jcfr

2014-03-07 11:28

administrator   ~0011384

We reviewed the list reported on the wiki during the Slicer hackfest (2014-03-07) and here is a first list of what should be moved out:
AffineRegistration
BSplineDeformableRegistration
LinearRegistration
MultiResolutionAffineRegistration
OtsuThresholdImageFilter
OtsuThresholdSegmentation
RigidRegistration (it's just a simple registration example, BRAINS registration provides all its functionality)
TestGridTransformRegistration
MRIBiasFieldCorrection
MIDASApplications
BatchMakeApplications

Build system should also be updated so that the following tests don't show up as CLIs:
DiffusionTensorTest
jcfr

jcfr

2014-03-07 11:29

administrator   ~0011385

Reminder sent to: fbudin

Hi Francois,

We would like to move from into a dedicated repo the following two modules:

MIDASApplications
BatchMakeApplications

Are they used ? Would that cause any trouble for UNC folks ?

Even better, should we just delete the code ?

Thanks for your feedback,

fbudin

fbudin

2014-03-10 05:34

developer   ~0011398

Hello JC,

I have never used those modules, and as far as I know, nobody uses them in our lab. Thanks for asking though.

Francois
jcfr

jcfr

2014-06-30 05:28

administrator   ~0012111

MIDASApplications and BatchMakeApplications removed in r23396
See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23396
jcfr

jcfr

2014-08-19 06:52

administrator   ~0012400

DiffusionTensorTest
TestGridTransformRegistration
CLIROITest

will not be packaged any-more.

See http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23588
jcfr

jcfr

2014-08-20 13:52

administrator   ~0012407

Last edited: 2014-08-21 18:02

Associated PR: https://github.com/Slicer/Slicer/pull/169

As of r23599 [1], The following modules have been removed:

  • AffineRegistration
  • BSplineDeformableRegistration
  • LinearRegistration
  • RigidRegistration
  • MRIBiasFieldCorrection
  • MultiResolutionAffineRegistration
  • OtsuThresholdImageFilter
  • OtsuThresholdSegmentation

[1] http://viewvc.slicer.org/viewvc.cgi/Slicer4?view=revision&revision=23599

The code (and testing data) associated with each CLI modules has been added to a dedicated GitHub repository:

Note that the Slicer license and a README.md file has been automatically added to each repo to explain that the module has been deprecated and is not maintained.

For example: https://github.com/Slicer/Slicer-OtsuThresholdSegmentation#otsu-threshold-segmentation

For reference, the script that allows to automatically add the README file is https://gist.github.com/jcfr/367bd37e8d5b5c78b0d0

For future references (in case we create an extension bundling some of these modules), the associated wiki pages are:

Note also that these wiki pages have been unreferenced from the main listing. See http://wiki.slicer.org/slicerWiki/index.php?title=Documentation%2FNightly%2FModules&diff=38827&oldid=38346

Issue History

Date Modified Username Field Change
2013-09-17 05:46 jcfr New Issue
2013-09-17 05:46 jcfr Status new => assigned
2013-09-17 05:46 jcfr Assigned To => jcfr
2013-09-17 05:46 jcfr Reporter jcfr => kikinis
2013-09-17 05:46 jcfr Priority normal => low
2013-09-17 05:46 jcfr Target Version => Slicer 4.3.1
2013-10-04 00:52 jcfr Target Version Slicer 4.3.1 => Slicer 4.3.2
2014-03-06 10:15 nicole Target Version Slicer 4.3.2 => Slicer 4.4.0
2014-03-07 10:16 jcfr Priority low => high
2014-03-07 11:28 jcfr Note Added: 0011384
2014-03-07 11:29 jcfr Note Added: 0011385
2014-03-10 05:34 fbudin Note Added: 0011398
2014-05-13 19:53 jcfr Relationship added related to 0002398
2014-06-30 05:28 jcfr Note Added: 0012111
2014-08-19 06:52 jcfr Note Added: 0012400
2014-08-20 13:52 jcfr Note Added: 0012407
2014-08-20 14:17 jcfr Relationship added related to 0003814
2014-08-20 14:18 jcfr Summary Move Slicer legacy module into its own extensions => Remove Slicer legacy module from the trunk
2014-08-20 14:18 jcfr Status assigned => resolved
2014-08-20 14:18 jcfr Fixed in Version => Slicer 4.4.0
2014-08-20 14:18 jcfr Resolution open => fixed
2014-08-21 18:01 jcfr Relationship added related to 0003815
2014-08-21 18:02 jcfr Note Edited: 0012407
2014-09-17 22:57 jcfr Status resolved => closed