Release notes for DIPY version 1.4.1#

GitHub stats for 2021/03/14 - 2021/05/05 (tag: 1.4.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 11 authors contributed 153 commits.

  • Ariel Rokem

  • Bramsh Qamar Chandio

  • David Romero-Bascones

  • Eleftherios Garyfallidis

  • Etienne St-Onge

  • Felix Liu

  • Gabriel Girard

  • John Kruper

  • Nasim Anousheh

  • Serge Koudoro

  • Shreyas Fadnavis

We closed a total of 89 issues, 28 pull requests and 61 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (28):

  • PR #2367: [Upcoming] Release 1.4.1

  • PR #2387: added all examples of CST and updated AFQ file name

  • PR #2386: Adding CST_L back in Bundle Segmentation Tutorial

  • PR #2375: Expanding Bundle Segmentation Tutorial

  • PR #2382: Updated docs for using P2S optimally

  • PR #2385: RF: Standardize the argument name for the number of threads/cores

  • PR #2384: RF - Removed deprecated tracking code

  • PR #2351: Updating Vec2vec_rotmat to deal with numerical issues

  • PR #2381: Adds the NIPY code of conduct to our repo.

  • PR #2371: [Fix] Add “None” options in the CLIs

  • PR #2352: RF: configure num_threads==-1 as the value to use all cores

  • PR #2373: [FIX] warning if not the same number of points

  • PR #2372: Expand patch radius if input is int

  • PR #2348: RF: Use new name for this function.

  • PR #2363: [ENH] Adding cython file(*.pyx) in documentation

  • PR #2365: [DOC]: Change defaults in Patch2Self example

  • PR #2349: [ENH] Allow for other statistics, like median, in afq_profile

  • PR #2350: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays

  • PR #2346: [MNT] Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible

  • PR #2347: Replacing Data in NLMeans Tutorial

  • PR #2340: [FIX] reactivate codecov

  • PR #2344: [FIX] Tractogram Header in RecoBundles Tutorial

  • PR #2339: [FIX] Cleanup deprecated np.float, np.bool, np.int

  • PR #1648: Mesh seeding (surface)

  • PR #2337: BF: Change patch2self defaults.

  • PR #2333: Add __str__ to GradientTable

  • PR #2335: RF: Replaces deprecated basis by its new name.

  • PR #2332: [FIX] fix tests for all new deprecated functions

Issues (61):

  • #2375: Expanding Bundle Segmentation Tutorial

  • #1973: Recobundles documentation

  • #2382: Updated docs for using P2S optimally

  • #2385: RF: Standardize the argument name for the number of threads/cores

  • #2377: RF: standardize the argument name for the number of threads/cores

  • #2384: RF - Removed deprecated tracking code

  • #2351: Updating Vec2vec_rotmat to deal with numerical issues

  • #2381: Adds the NIPY code of conduct to our repo.

  • #2380: Community and governance

  • #2371: [Fix] Add “None” options in the CLIs

  • #2300: NF: Add “None” options in the CLIs

  • #2352: RF: configure num_threads==-1 as the value to use all cores

  • #2373: [FIX] warning if not the same number of points

  • #2320: RecoBundles distances

  • #2372: Expand patch radius if input is int

  • #2341: Allow use of all threads in the gibbs ringing workflow

  • #2348: RF: Use new name for this function.

  • #2353: How to create tractogram from a multi-shell data for RecoBundles

  • #1311: Adding cython file(*.pyx) in documentation

  • #2363: [ENH] Adding cython file(*.pyx) in documentation

  • #1302: [DOC] cython (pyx) files are not parsed

  • #366: Some doc missing

  • #2365: [DOC]: Change defaults in Patch2Self example

  • #1672: Dipy Segmentation fault when visualizing

  • #1444: Move general registration tools into own package?

  • #562: Multiprocessing the tensor reconstruction

  • #13: Coordinate maps stuff

  • #2324: Dipy for VR/AR

  • #2345: Saving and/or importing nonlinear warps

  • #2349: [ENH] Allow for other statistics, like median, in afq_profile

  • #2350: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays

  • #423: Use npy_intp variables instead of int and size_t to iterate over numpy arrays

  • #837: Should we enforce float32 in tractography results?

  • #636: Get a standard interface for the functions using the noise variance

  • #861: open mp defaults to one core, is that a good idea?

  • #2346: [MNT] Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible

  • #1895: Cython warnings

  • #545: Use cnp.PyArray_DATA wherever possible

  • #2347: Replacing Data in NLMeans Tutorial

  • #1847: Replacing Data in NLMeans Tutorial

  • #2340: [FIX] reactivate codecov

  • #1872: Did we lose our coverage reporting?

  • #1646: Fetcher should not be under coverage

  • #1635: Track from mesh

  • #2344: [FIX] Tractogram Header in RecoBundles Tutorial

  • #2309: Tractogram Header in RecoBundles Tutorial

  • #2334: Aphysical signal after running patch2self

  • #1873: ERROR while import data

  • #2343: Missing Python 3.9 wheels

  • #1996: Documentation not being rendered correctly

  • #2311: Accuracy of DKI measures

  • #2274: DKI metrics’ accuracy

  • #2339: [FIX] Cleanup deprecated np.float, np.bool, np.int

  • #1648: Mesh seeding (surface)

  • #1675: WIP: Integer indices

  • #2316: TranslationTransform2D Exact X-Y Shift

  • #2337: BF: Change patch2self defaults.

  • #2333: Add __str__ to GradientTable

  • #2331: gtab.info does not print anything

  • #2335: RF: Replaces deprecated basis by its new name.

  • #2332: [FIX] fix tests for all new deprecated functions