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RecoBundles and SLR workflows #1556

Merged
merged 106 commits into from Oct 11, 2018
Merged

RecoBundles and SLR workflows #1556

merged 106 commits into from Oct 11, 2018

Commits on May 8, 2018

  1. NF: Started new workflow for SLR

    @Garyfallidis
    Garyfallidis committed May 8, 2018
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  2. Mapmri not read/write

    @Garyfallidis
    Garyfallidis committed May 8, 2018
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Commits on May 9, 2018

  1. NF: add horizon minimalistic visualization tool

    @Garyfallidis
    Garyfallidis committed May 9, 2018
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  2. NF: adding RecoBundles workflow

    @BramshQamar
    BramshQamar committed May 9, 2018
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  3. Merge pull request dipy#54 from BramshQamar/rb_workflows 

    NF: adding RecoBundles workflow
    @Garyfallidis
    Garyfallidis committed May 9, 2018
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Commits on May 10, 2018

  1. Refactoring horizon still in progress

    @Garyfallidis
    Garyfallidis committed May 10, 2018
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  2. Added some width to the streamlines

    @Garyfallidis
    Garyfallidis committed May 10, 2018
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Commits on May 11, 2018

  1. RF: recobunldes flow needed some tweaking, now better, still some pol… 

    …ishing is needed
    @Garyfallidis
    Garyfallidis committed May 11, 2018
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  2. NF: allow tractograms with random colors

    @Garyfallidis
    Garyfallidis committed May 11, 2018
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  3. Local SLR was not invoked not sure why

    @Garyfallidis
    Garyfallidis committed May 11, 2018
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Commits on May 14, 2018

  1. added new workflow apply_labels

    @BramshQamar
    BramshQamar committed May 14, 2018
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  2. More work is needed for picking

    @Garyfallidis
    Garyfallidis committed May 14, 2018
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Commits on May 15, 2018

  1. added new workflow slr for bundles

    @BramshQamar
    BramshQamar committed May 15, 2018
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  2. added changes

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    BramshQamar committed May 15, 2018
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  3. added changes

    @BramshQamar
    BramshQamar committed May 15, 2018
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Commits on May 16, 2018

  1. updated slr workflow

    @BramshQamar
    BramshQamar committed May 16, 2018
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  2. updated recognize workflow

    @BramshQamar
    BramshQamar committed May 16, 2018
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  3. NF: slr_with_qb changed to slr_with_qbx

    @Garyfallidis
    Garyfallidis committed May 16, 2018
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  4. NF: SLR workflow now uses QBX

    @Garyfallidis
    Garyfallidis committed May 16, 2018
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  5. updated

    @BramshQamar
    BramshQamar committed May 16, 2018
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  6. changes in slr workflow

    @BramshQamar
    BramshQamar committed May 16, 2018
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  7. Picking objects - so much simpler than ever

    @Garyfallidis
    Garyfallidis committed May 16, 2018
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Commits on May 17, 2018

  1. Basic horizon seems working needs more refactoring

    @Garyfallidis
    Garyfallidis committed May 17, 2018
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  2. fixed slr workflow

    @BramshQamar
    BramshQamar committed May 17, 2018
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Commits on May 18, 2018

  1. Merge pull request dipy#55 from BramshQamar/rb_workflows 

    Slr and apply_labels workflows
    @Garyfallidis
    Garyfallidis committed May 18, 2018
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  2. NF: qbx default for SLR workflow

    @Garyfallidis
    Garyfallidis committed May 18, 2018
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  3. Updates in RecoBundles Flow

    @Garyfallidis
    Garyfallidis committed May 18, 2018
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  4. Increased logging output

    @Garyfallidis
    Garyfallidis committed May 18, 2018
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  5. RF: rename dipy_recognize to dipy_recobundles

    @Garyfallidis
    Garyfallidis committed May 18, 2018
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  6. WIP with labels

    @Garyfallidis
    Garyfallidis committed May 18, 2018
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  7. BF: labelsbundles script runs

    @Garyfallidis
    Garyfallidis committed May 18, 2018
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  8. Updated labelsbunles

    @Garyfallidis
    Garyfallidis committed May 18, 2018
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  9. changes in slr

    @BramshQamar
    BramshQamar committed May 18, 2018
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  10. Merge branch 'rb_workflows' into rb_workflows

    @BramshQamar
    BramshQamar committed May 18, 2018
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  11. Merge pull request dipy#57 from BramshQamar/rb_workflows 

    changes in slr
    @Garyfallidis
    Garyfallidis committed May 18, 2018
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Commits on May 19, 2018

  1. Correct output for labelsbundles

    @Garyfallidis
    Garyfallidis committed May 19, 2018
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Commits on May 21, 2018

  1. New horizon works again with one volume and tractograms together

    @Garyfallidis
    Garyfallidis committed May 21, 2018
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  2. RF: removed old horizon

    @Garyfallidis
    Garyfallidis committed May 21, 2018
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  3. RF: transform_streamlines uses the Streamlines API

    @Garyfallidis
    Garyfallidis committed May 21, 2018
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  4. Pressing a for selecting all seems working

    @Garyfallidis
    Garyfallidis committed May 21, 2018
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  5. Needs more cleanup but getting there

    @Garyfallidis
    Garyfallidis committed May 21, 2018
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Commits on May 22, 2018

  1. Changed picking memory to dictionary

    @Garyfallidis
    Garyfallidis committed May 22, 2018
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  2. Working on saving bundles...

    @Garyfallidis
    Garyfallidis committed May 22, 2018
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  3. NF: first successful effort of saving bundles directly from horizon

    @Garyfallidis
    Garyfallidis committed May 22, 2018
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  4. Changed key from h to c for showing hiding the centroids

    @Garyfallidis
    Garyfallidis committed May 22, 2018
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Commits on May 25, 2018

  1. added metric in recobundles

    @BramshQamar
    BramshQamar committed May 25, 2018
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Commits on Jun 4, 2018

  1. updates in recobundles

    @BramshQamar
    BramshQamar committed Jun 4, 2018
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Commits on Jun 7, 2018

  1. changes

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    BramshQamar committed Jun 7, 2018
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  2. changes

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  3. changes

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Commits on Jun 8, 2018

  1. changes

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    BramshQamar committed Jun 8, 2018
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  2. changes

    @BramshQamar
    BramshQamar committed Jun 8, 2018
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  3. changes

    @BramshQamar
    BramshQamar committed Jun 8, 2018
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  4. changes

    @BramshQamar
    BramshQamar committed Jun 8, 2018
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  5. changes

    @BramshQamar
    BramshQamar committed Jun 8, 2018
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  6. Delete viz parts

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Commits on Jun 11, 2018

  1. cleaned some code comments

    @BramshQamar
    BramshQamar committed Jun 11, 2018
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Commits on Aug 2, 2018

  1. fixed the issue with bounds for second local slr in recobundle refine… 

    … workflow
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    BramshQamar committed Aug 2, 2018
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  2. Merge branch 'master' into rb_slr_workflows

    @Garyfallidis
    Garyfallidis committed Aug 2, 2018
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Commits on Aug 5, 2018

  1. Added documentation in refine, and valuate_results methods in bundle.… 

    …py. Cleaned comments and fixed PIP8 errors
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    BramshQamar committed Aug 5, 2018
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Commits on Aug 9, 2018

  1. fixed test_rb.py file

    @BramshQamar
    BramshQamar committed Aug 9, 2018
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Commits on Aug 10, 2018

  1. fixed test_whole_brain_slr.py file

    @BramshQamar
    BramshQamar committed Aug 10, 2018
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  2. added fetcher for atlas and bundles of hcp842 data

    @BramshQamar
    BramshQamar committed Aug 10, 2018
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Commits on Aug 17, 2018

  1. TEST:Fixed minimum threshold issue

    @Garyfallidis
    Garyfallidis committed Aug 17, 2018
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  2. BF: return empty arrays when there are no neighbors

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    Garyfallidis committed Aug 17, 2018
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  3. Merge pull request #1 from Garyfallidis/rb_slr_workflows 

    Rb slr workflows - test fixes
    @BramshQamar
    BramshQamar committed Aug 17, 2018
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Commits on Aug 20, 2018

  1. sm

    @BramshQamar
    BramshQamar committed Aug 20, 2018
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  2. fixed return value in recobundle

    @BramshQamar
    BramshQamar committed Aug 20, 2018
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  3. fixed test_whole_brain_slr errors

    @BramshQamar
    BramshQamar committed Aug 20, 2018
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  4. added test for refine recobundles function

    @BramshQamar
    BramshQamar committed Aug 20, 2018
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Commits on Aug 23, 2018

  1. fixed errors in test whole brain slr

    @BramshQamar
    BramshQamar committed Aug 23, 2018
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  2. fixed tests

    @BramshQamar
    BramshQamar committed Aug 23, 2018
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  3. BF: transform_streamlines was working only inplace

    @Garyfallidis
    Garyfallidis committed Aug 23, 2018
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  4. Updated test_whole_brain_slr needs work

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    Garyfallidis committed Aug 23, 2018
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  5. Merge pull request #2 from Garyfallidis/rb_slr_workflows 

    Fix for transform_streamlines
    @BramshQamar
    BramshQamar committed Aug 23, 2018
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  6. fixed tests

    @BramshQamar
    BramshQamar committed Aug 23, 2018
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  7. new changes in transform bundle

    @BramshQamar
    BramshQamar committed Aug 23, 2018
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  8. fixed errors in test_refine_rb.py

    @BramshQamar
    BramshQamar committed Aug 23, 2018
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  9. ENH: Select_random_set_of_streamlines works now with Streamlines objects

    @Garyfallidis
    Garyfallidis committed Aug 23, 2018
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  10. Updated SLR test

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    Garyfallidis committed Aug 23, 2018
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  11. fixed test_whole_brain_slr

    @BramshQamar
    BramshQamar committed Aug 23, 2018
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Commits on Aug 24, 2018

  1. fixed precision error in test_whole_brain_slr

    @BramshQamar
    BramshQamar committed Aug 24, 2018
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  2. fixed precision error in test_whole_brain_slr

    @BramshQamar
    BramshQamar committed Aug 24, 2018
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  3. fixed precision error in test_whole_brain_slr and errors in test_rb.py

    @BramshQamar
    BramshQamar committed Aug 24, 2018
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  4. Adding RandomStates everywhere

    @Garyfallidis
    Garyfallidis committed Aug 24, 2018
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  5. Merge pull request #3 from Garyfallidis/rb_slr_workflows 

    Adding RandomStates everywhere
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    BramshQamar committed Aug 24, 2018
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Commits on Aug 27, 2018

  1. fixed valid_examples.txt file

    @BramshQamar
    BramshQamar committed Aug 27, 2018
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  2. merged test_rb.py and test_refine_rb.py into one test, and added fetc… 

    …her for target HCP tractogram
    @BramshQamar
    BramshQamar committed Aug 27, 2018
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Commits on Aug 28, 2018

  1. added tutorial for bundle extraction using RecoBundles

    @BramshQamar
    BramshQamar committed Aug 28, 2018
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  2. added tutorial for bundle extraction using RecoBundles

    @BramshQamar
    BramshQamar committed Aug 28, 2018
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Commits on Sep 5, 2018

  1. fixed issue with use of pjoin in fetcher.py

    @BramshQamar
    BramshQamar committed Sep 5, 2018
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Commits on Sep 6, 2018

  1. fixed precision errors in test_dki.py

    @BramshQamar
    BramshQamar committed Sep 6, 2018
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Commits on Sep 7, 2018

  1. fixed test_rb_refine.py

    @BramshQamar
    BramshQamar committed Sep 7, 2018
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  2. Merge branch 'master' into rb_slr_workflows

    @BramshQamar
    BramshQamar committed Sep 7, 2018
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Commits on Sep 21, 2018

  1. added tests for recobundle workflow, label bundle workflow and slr wo… 

    …rkflow
    @BramshQamar
    BramshQamar committed Sep 21, 2018
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  2. added tests for workflows

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    BramshQamar committed Sep 21, 2018
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Commits on Sep 24, 2018

  1. fixed test_align

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    BramshQamar committed Sep 24, 2018
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  2. fixed test_align

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    BramshQamar committed Sep 24, 2018
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Commits on Sep 28, 2018

  1. deleted the commented parts from PR

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    BramshQamar committed Sep 28, 2018
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  2. deleted the commented parts from PR

    @BramshQamar
    BramshQamar committed Sep 28, 2018
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Commits on Oct 8, 2018

  1. fixed issues serge pointed in his review

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    BramshQamar committed Oct 8, 2018
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  2. fixed issues a pathlib library error

    @BramshQamar
    BramshQamar committed Oct 8, 2018
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Commits on Oct 9, 2018

  1. fixed issues with no neigbhor streamlines in refine function

    @BramshQamar
    BramshQamar committed Oct 9, 2018
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  2. fixed issues with no neigbhor streamlines in refine function

    @BramshQamar
    BramshQamar committed Oct 9, 2018
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Commits on Oct 11, 2018

  1. renamed read function to get in fetcher.py

    @BramshQamar
    BramshQamar committed Oct 11, 2018
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  2. renamed read function to get in fetcher.py

    @BramshQamar
    BramshQamar committed Oct 11, 2018
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