===================================== Release notes for DIPY version 1.4.1 ===================================== - Patch2Self and its documentation updated. - BUAN and Recobundles documentation updated. - Standardization and improvement of the multiprocessing / multithreading rules. - Community and governance information added. - New surface seeding module for tractography named `mesh`. - Large update of Cython code in respect of the last standard. - Large documentation update. - Closed 61 issues and merged 28 pull requests. 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 :file:`tools/github_stats.py`): Pull Requests (28): * :ghpull:`2367`: [Upcoming] Release 1.4.1 * :ghpull:`2387`: added all examples of CST and updated AFQ file name * :ghpull:`2386`: Adding CST_L back in Bundle Segmentation Tutorial * :ghpull:`2375`: Expanding Bundle Segmentation Tutorial * :ghpull:`2382`: Updated docs for using P2S optimally * :ghpull:`2385`: RF: Standardize the argument name for the number of threads/cores * :ghpull:`2384`: RF - Removed deprecated tracking code * :ghpull:`2351`: Updating Vec2vec_rotmat to deal with numerical issues * :ghpull:`2381`: Adds the NIPY code of conduct to our repo. * :ghpull:`2371`: [Fix] Add "None" options in the CLIs * :ghpull:`2352`: RF: configure num_threads==-1 as the value to use all cores * :ghpull:`2373`: [FIX] warning if not the same number of points * :ghpull:`2372`: Expand patch radius if input is int * :ghpull:`2348`: RF: Use new name for this function. * :ghpull:`2363`: [ENH] Adding cython file(*.pyx) in documentation * :ghpull:`2365`: [DOC]: Change defaults in Patch2Self example * :ghpull:`2349`: [ENH] Allow for other statistics, like median, in afq_profile * :ghpull:`2350`: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays * :ghpull:`2346`: [MNT] Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible * :ghpull:`2347`: Replacing Data in NLMeans Tutorial * :ghpull:`2340`: [FIX] reactivate codecov * :ghpull:`2344`: [FIX] Tractogram Header in RecoBundles Tutorial * :ghpull:`2339`: [FIX] Cleanup deprecated np.float, np.bool, np.int * :ghpull:`1648`: Mesh seeding (surface) * :ghpull:`2337`: BF: Change patch2self defaults. * :ghpull:`2333`: Add __str__ to GradientTable * :ghpull:`2335`: RF: Replaces deprecated basis by its new name. * :ghpull:`2332`: [FIX] fix tests for all new deprecated functions Issues (61): * :ghissue:`2375`: Expanding Bundle Segmentation Tutorial * :ghissue:`1973`: Recobundles documentation * :ghissue:`2382`: Updated docs for using P2S optimally * :ghissue:`2385`: RF: Standardize the argument name for the number of threads/cores * :ghissue:`2377`: RF: standardize the argument name for the number of threads/cores * :ghissue:`2384`: RF - Removed deprecated tracking code * :ghissue:`2351`: Updating Vec2vec_rotmat to deal with numerical issues * :ghissue:`2381`: Adds the NIPY code of conduct to our repo. * :ghissue:`2380`: Community and governance * :ghissue:`2371`: [Fix] Add "None" options in the CLIs * :ghissue:`2300`: NF: Add "None" options in the CLIs * :ghissue:`2352`: RF: configure num_threads==-1 as the value to use all cores * :ghissue:`2373`: [FIX] warning if not the same number of points * :ghissue:`2320`: RecoBundles distances * :ghissue:`2372`: Expand patch radius if input is int * :ghissue:`2341`: Allow use of all threads in the gibbs ringing workflow * :ghissue:`2348`: RF: Use new name for this function. * :ghissue:`2353`: How to create tractogram from a multi-shell data for RecoBundles * :ghissue:`1311`: Adding cython file(*.pyx) in documentation * :ghissue:`2363`: [ENH] Adding cython file(*.pyx) in documentation * :ghissue:`1302`: [DOC] cython (pyx) files are not parsed * :ghissue:`366`: Some doc missing * :ghissue:`2365`: [DOC]: Change defaults in Patch2Self example * :ghissue:`1672`: Dipy Segmentation fault when visualizing * :ghissue:`1444`: Move general registration tools into own package? * :ghissue:`562`: Multiprocessing the tensor reconstruction * :ghissue:`13`: Cordinate maps stuff * :ghissue:`2324`: Dipy for VR/AR * :ghissue:`2345`: Saving and/or importing nonlinear warps * :ghissue:`2349`: [ENH] Allow for other statistics, like median, in afq_profile * :ghissue:`2350`: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays * :ghissue:`423`: Use npy_intp variables instead of int and size_t to iterate over numpy arrays * :ghissue:`837`: Should we enforce float32 in tractography results? * :ghissue:`636`: Get a standard interface for the functions using the noise variance * :ghissue:`861`: open mp defaults to one core, is that a good idea? * :ghissue:`2346`: [MNT] Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible * :ghissue:`1895`: Cython warnings * :ghissue:`545`: Use cnp.PyArray_DATA wherever possible * :ghissue:`2347`: Replacing Data in NLMeans Tutorial * :ghissue:`1847`: Replacing Data in NLMeans Tutorial * :ghissue:`2340`: [FIX] reactivate codecov * :ghissue:`1872`: Did we lose our coverage reporting? * :ghissue:`1646`: Fetcher should not be under coverage * :ghissue:`1635`: Track from mesh * :ghissue:`2344`: [FIX] Tractogram Header in RecoBundles Tutorial * :ghissue:`2309`: Tractogram Header in RecoBundles Tutorial * :ghissue:`2334`: Aphysical signal after running patch2self * :ghissue:`1873`: ERROR while import data * :ghissue:`2343`: Missing Python 3.9 wheels * :ghissue:`1996`: Documentation not being rendered correctly * :ghissue:`2311`: Accuracy of DKI measures * :ghissue:`2274`: DKI metrics' accuracy * :ghissue:`2339`: [FIX] Cleanup deprecated np.float, np.bool, np.int * :ghissue:`1648`: Mesh seeding (surface) * :ghissue:`1675`: WIP: Integer indices * :ghissue:`2316`: TranslationTransform2D Exact X-Y Shift * :ghissue:`2337`: BF: Change patch2self defaults. * :ghissue:`2333`: Add __str__ to GradientTable * :ghissue:`2331`: gtab.info does not print anything * :ghissue:`2335`: RF: Replaces deprecated basis by its new name. * :ghissue:`2332`: [FIX] fix tests for all new deprecated functions