==================================== Release notes for DIPY version 1.2 ==================================== GitHub stats for 2020/01/10 - 2020/09/08 (tag: 1.1.1) These lists are automatically generated, and may be incomplete or contain duplicates. The following 27 authors contributed 491 commits. * Ariel Rokem * Aryansh Omray * Bramsh Qamar * Charles Poirier * Derek Pisner * Eleftherios Garyfallidis * Fabio Nery * Francois Rheault * Gabriel Girard * Gregory Lee * Jean-Christophe Houde * Jirka Borovec * Jon Haitz Legarreta Gorroño * Leevi Kerkela * Leon Weninger * Martijn Nagtegaal * Rafael Neto Henriques * Sarath Chandra * Serge Koudoro * Shrishti Hore * Shubham Shaswat * Takis Panagopoulos * Tashrif Billah * Kunal Mehta * svabhishek29 * Areesha Tariq * Philippe Karan We closed a total of 256 issues, 94 pull requests and 163 regular issues; Pull Requests (94): * :ghpull:`2191`: Multi-shell multi-tissue constrained spherical deconvolution * :ghpull:`2212`: [FIX] renamed Direct Streamline Normalization tutorial title * :ghpull:`2207`: [FIX] Horizon shader warning * :ghpull:`2208`: Removing Python 3.5 from Travis and Azure due to its end of life (2020-09-13) * :ghpull:`2157`: BF: Fix variable may be used uninitialized warning * :ghpull:`2205`: Add optional installs for different settings. * :ghpull:`2204`: from Renderer to scene * :ghpull:`2183`: _streamlines_in_mask bounds check * :ghpull:`2203`: End of line period in sft * :ghpull:`2142`: ENH: function to calculate size/shape parameters of b-tensors and vice-versa * :ghpull:`2195`: [ENH] Validate streamlines pre-LiFE * :ghpull:`2161`: Fix a memory overlap bug in multi_median (and median_otsu) * :ghpull:`2163`: BF: Fix Cython label defined but not used warning * :ghpull:`2174`: Improve performance of tissue classification * :ghpull:`2168`: add fig_kwargs * :ghpull:`2178`: Add full SH basis * :ghpull:`2193`: BUAN_flow.rst to buan_flow.rst * :ghpull:`2196`: [Fix] update save_vtk_streamlines and load_vtk_streamlines * :ghpull:`2188`: [Fix] update mapmri due to cvxpy 1.1 * :ghpull:`2176`: [DOC] Update SH basis documentation * :ghpull:`2173`: Install ssl certificate for azure pipeline windows * :ghpull:`2171`: Gitter url update: from nipy/dipy to dipy/dipy * :ghpull:`2154`: Bundle segmentation CLI tutorial * :ghpull:`2162`: BF: Fix string literal comparison warning * :ghpull:`2156`: BF: Fix Cython signed vs. unsigned integer comparison warning * :ghpull:`2160`: TST: Change assert_equal(statement, True) to assert_(statement). * :ghpull:`2158`: BF: Fix Cython floating point absolute value warning * :ghpull:`2155`: [Fix] sfm RuntimeWarning * :ghpull:`2147`: BF: Fix Cython function override warning * :ghpull:`2148`: BF: Fix `distutils` Python version requirement option warning * :ghpull:`2150`: [Fix] some warning on clustering test * :ghpull:`2149`: [Fix] some warning on stats module * :ghpull:`2145`: Rename dipy_track command line * :ghpull:`2152`: changed buan_flow.rst to BUAN_flow.rst * :ghpull:`2146`: Cluster threshold parameter in dipy_buan_shapes workflow * :ghpull:`2134`: Slicing, adding function of StatefulTractogram * :ghpull:`2001`: Basic processing documentation for CLI. * :ghpull:`2135`: [Fix] shm.py RuntimeWarning * :ghpull:`2141`: [FIX] doc generation issue * :ghpull:`2136`: [Fix] laplacian_regularization on MAPMRI + cleanup warning * :ghpull:`2140`: BF: Fix NumPy warning when creating arrays from ragged sequences * :ghpull:`2139`: BF: Use equality check instead of identity check * :ghpull:`2108`: [Horizon] Update clipping range on slicer * :ghpull:`2121`: BF: ensure `btens` attribute of `GradientTable` is initialised * :ghpull:`2129`: BF: Fix sequence stacking warning in LiFE tracking * :ghpull:`2133`: BF: Fix NumPy warning when creating arrays from ragged sequences * :ghpull:`2125`: ENH: function to calculate anisotropy of b-tensors * :ghpull:`2124`: BUAN framework documentation * :ghpull:`2033`: RF - Direction getters naming * :ghpull:`2111`: Added an epsilon to bounding_box check * :ghpull:`2086`: WIP Issue 1996 * :ghpull:`2091`: Modified the model for multiple hidden layers * :ghpull:`2057`: DOC: Add DIPY dataset list to documentation. * :ghpull:`2103`: Documentation typos, grammar corrections & imports * :ghpull:`2088`: BUAN paper code and CLIs * :ghpull:`2120`: rename var sp to sph * :ghpull:`2113`: BF: refer to cigar_tensor * :ghpull:`2116`: fixed code tags and minor changes * :ghpull:`2100`: Fixed typos, grammatical errors and time import * :ghpull:`2101`: Minor typos and imports * :ghpull:`2095`: Fixed typos in dipy.align * :ghpull:`2099`: Minor Typos and imports in the beginning * :ghpull:`2102`: Modules imported in the beginning * :ghpull:`2055`: Multidimensional gradient table * :ghpull:`2097`: Replace manual sform values with get_best_affine * :ghpull:`2104`: Fixed minor typos * :ghpull:`2065`: Some typos and grammatical errors * :ghpull:`2090`: Small fix reorient_bvecs * :ghpull:`2067`: Some spelling and grammatical mistakes * :ghpull:`2093`: Placed all imports in the beginning * :ghpull:`2077`: Fixed minor typos in tutorials * :ghpull:`2071`: Some change backs * :ghpull:`2084`: Kunakl07 patch 7 * :ghpull:`2085`: Kunakl07 patch 8 * :ghpull:`2068`: Some spelling and grammatical errors * :ghpull:`2069`: some typos * :ghpull:`2063`: Gibbs tutorial patch * :ghpull:`2045`: [Fix] workflow variable string * :ghpull:`2060`: Replace old function with cython version * :ghpull:`2058`: DOC: Fix `Sphinx` link in `CONTRIBUTING.md` * :ghpull:`2059`: DOC: Add `Azure Pipelines` to CI tools in `CONTRIBUTING.md` * :ghpull:`2056`: MAINT: Up Numpy version to 1.12. * :ghpull:`2053`: Correct TYPO on the note about n_points in _gibbs_removal_2d() * :ghpull:`2043`: [NF] Add a Deprecation system * :ghpull:`2047`: [fix] Doc generation issue * :ghpull:`2044`: [FIX] check seeds dtype * :ghpull:`2041`: BF: SFM prediction with mask * :ghpull:`2039`: Remove __future__ * :ghpull:`2042`: Add tests to rng module * :ghpull:`2040`: RF: Swallow a couple of warnings that are safe to ignore. * :ghpull:`2038`: [DOC] Update repo path * :ghpull:`2037`: DOC: fix typo in FW DTI tutorial * :ghpull:`2028`: Adapted for patch_radius with radii differing xyz direction. * :ghpull:`2035`: DOC: Update DKI documentation according to the new get data functions Issues (164): * :ghissue:`2114`: Tutorial title in Streamline-based registration section is misleading * :ghissue:`2207`: [FIX] Horizon shader warning * :ghissue:`2208`: Removing Python 3.5 from Travis and Azure due to its end of life (2020-09-13) * :ghissue:`1793`: ENH: Improving Command Line and WF Docs * :ghissue:`2007`: Reference for `load_trk` in recobundles example * :ghissue:`2061`: Is dipy.viz supported in Colab or Kaggle Notebooks? * :ghissue:`2070`: Python has stopped working during import * :ghissue:`2107`: PNG images saved by window.record in the tutorial example are always black * :ghissue:`2153`: lowercase .rst file names * :ghissue:`2138`: Basic introduction to CLI needs better dataset to showcase capabilities * :ghissue:`2194`: LiFE model won't fit ? * :ghissue:`2157`: BF: Fix variable may be used uninitialized warning * :ghissue:`2177`: VIZ: streamline actor failing on Windows + macOS due to the new VTK9 * :ghissue:`2205`: Add optional installs for different settings. * :ghissue:`2204`: from Renderer to scene * :ghissue:`2183`: _streamlines_in_mask bounds check * :ghissue:`2182`: `target_line_based` might read out of bounds * :ghissue:`2203`: End of line period in sft * :ghissue:`2200`: BF: Fix `'tp_print' is deprecated` Cython warning * :ghissue:`2142`: ENH: function to calculate size/shape parameters of b-tensors and vice-versa * :ghissue:`2199`: BUG: Fix NumPy and Cython deprecation and initialization warnings * :ghissue:`2195`: [ENH] Validate streamlines pre-LiFE * :ghissue:`2161`: Fix a memory overlap bug in multi_median (and median_otsu) * :ghissue:`2163`: BF: Fix Cython label defined but not used warning * :ghissue:`2174`: Improve performance of tissue classification * :ghissue:`2168`: add fig_kwargs * :ghissue:`2178`: Add full SH basis * :ghissue:`2193`: BUAN_flow.rst to buan_flow.rst * :ghissue:`2196`: [Fix] update save_vtk_streamlines and load_vtk_streamlines * :ghissue:`2175`: Save streamlines as vtk polydata to a supported format file updated t… * :ghissue:`2188`: [Fix] update mapmri due to cvxpy 1.1 * :ghissue:`2190`: Reconstruction with Multi-Shell Multi-Tissue CSD * :ghissue:`2051`: BF: Non-negative Least Squares for IVIM * :ghissue:`2176`: [DOC] Update SH basis documentation * :ghissue:`2173`: Install ssl certificate for azure pipeline windows * :ghissue:`2172`: fetch_gold_standard_io fetcher failed regularly * :ghissue:`2169`: saving tracts in obj format * :ghissue:`2170`: Output of utils.density_map() using tck file is different than MRTrix * :ghissue:`2171`: Gitter url update: from nipy/dipy to dipy/dipy * :ghissue:`2144`: Move gitter to dipy/dipy? * :ghissue:`2154`: Bundle segmentation CLI tutorial * :ghissue:`2162`: BF: Fix string literal comparison warning * :ghissue:`2156`: BF: Fix Cython signed vs. unsigned integer comparison warning * :ghissue:`2160`: TST: Change assert_equal(statement, True) to assert_(statement). * :ghissue:`2158`: BF: Fix Cython floating point absolute value warning * :ghissue:`2155`: [Fix] sfm RuntimeWarning * :ghissue:`2159`: BF: Fix Cython different sign integer comparison warning * :ghissue:`2147`: BF: Fix Cython function override warning * :ghissue:`2148`: BF: Fix `distutils` Python version requirement option warning * :ghissue:`2151`: [DOC] Fixed minor typos, grammar errors and moved imports up in all examples * :ghissue:`2130`: Checking empty Cluster objects generates NumPy warning * :ghissue:`2131`: Elementwise comparison failure warning in multi_voxel test * :ghissue:`2150`: [Fix] some warning on clustering test * :ghissue:`2149`: [Fix] some warning on stats module * :ghissue:`2145`: Rename dipy_track command line * :ghissue:`2152`: changed buan_flow.rst to BUAN_flow.rst * :ghissue:`2146`: Cluster threshold parameter in dipy_buan_shapes workflow * :ghissue:`2128`: Registration Module failing with pre-matrix on Travis with future Numpy/Scipy release * :ghissue:`2134`: Slicing, adding function of StatefulTractogram * :ghissue:`2001`: Basic processing documentation for CLI. * :ghissue:`2135`: [Fix] shm.py RuntimeWarning * :ghissue:`2141`: [FIX] doc generation issue * :ghissue:`2136`: [Fix] laplacian_regularization on MAPMRI + cleanup warning * :ghissue:`1765`: Refactor dipy/stats/analysis.py * :ghissue:`2122`: [WIP] Add build template * :ghissue:`2140`: BF: Fix NumPy warning when creating arrays from ragged sequences * :ghissue:`2139`: BF: Use equality check instead of identity check * :ghissue:`2127`: DOC : Minor grammar fixes and moved imports up with respective comments * :ghissue:`2108`: [Horizon] Update clipping range on slicer * :ghissue:`2121`: BF: ensure `btens` attribute of `GradientTable` is initialised * :ghissue:`2129`: BF: Fix sequence stacking warning in LiFE tracking * :ghissue:`2133`: BF: Fix NumPy warning when creating arrays from ragged sequences * :ghissue:`2125`: ENH: function to calculate anisotropy of b-tensors * :ghissue:`2124`: BUAN framework documentation * :ghissue:`2126`: dipy / fury fails to install on Ubuntu 18 with pip3 * :ghissue:`2033`: RF - Direction getters naming * :ghissue:`2111`: Added an epsilon to bounding_box check * :ghissue:`2112`: [WIP] BUndle ANalytics (BUAN) pipeline documentation * :ghissue:`2086`: WIP Issue 1996 * :ghissue:`2091`: Modified the model for multiple hidden layers * :ghissue:`2096`: Deep Code * :ghissue:`2057`: DOC: Add DIPY dataset list to documentation. * :ghissue:`2103`: Documentation typos, grammar corrections & imports * :ghissue:`2088`: BUAN paper code and CLIs * :ghissue:`2120`: rename var sp to sph * :ghissue:`2118`: Local namespace of Scipy is same as a variable name * :ghissue:`1861`: WIP: Refactoring the stats module * :ghissue:`2113`: BF: refer to cigar_tensor * :ghissue:`2116`: fixed code tags and minor changes * :ghissue:`2024`: DIPY open lab meetings, Winter 2020 * :ghissue:`2100`: Fixed typos, grammatical errors and time import * :ghissue:`2101`: Minor typos and imports * :ghissue:`2094`: Detailed Beginner Friendly Tutorials * :ghissue:`2095`: Fixed typos in dipy.align * :ghissue:`2099`: Minor Typos and imports in the beginning * :ghissue:`2102`: Modules imported in the beginning * :ghissue:`2055`: Multidimensional gradient table * :ghissue:`2097`: Replace manual sform values with get_best_affine * :ghissue:`2105`: Tutorial Symmetric Regn 3D patch 3 * :ghissue:`2104`: Fixed minor typos * :ghissue:`2078`: Applying affine transform to streamlines in a SFT object * :ghissue:`2065`: Some typos and grammatical errors * :ghissue:`1305`: Questions/policies about writing .rst/web doc files * :ghissue:`2090`: Small fix reorient_bvecs * :ghissue:`2067`: Some spelling and grammatical mistakes * :ghissue:`2093`: Placed all imports in the beginning * :ghissue:`2077`: Fixed minor typos in tutorials * :ghissue:`2089`: Transforming bvecs after registration * :ghissue:`2071`: Some change backs * :ghissue:`2084`: Kunakl07 patch 7 * :ghissue:`2085`: Kunakl07 patch 8 * :ghissue:`2072`: Some typos and grammatical errors in faq.rst * :ghissue:`2073`: Some minor grammatical fixes old_highlights.txt * :ghissue:`2074`: Small typos * :ghissue:`2075`: Some grammatical changes in maintainer_workflow.rst * :ghissue:`2076`: Some grammatical changes in maintainer_workflow.rst * :ghissue:`2079`: Some minor typos in gimbal_lock.rst * :ghissue:`2080`: Some minor grammatical errors fixes * :ghissue:`2081`: Some typos and grammatical corrections in Changelog * :ghissue:`2082`: Grammatical fixes in readme.rst * :ghissue:`2083`: Fixes in regtools.py * :ghissue:`2066`: Fixed some typos * :ghissue:`2068`: Some spelling and grammatical errors * :ghissue:`2069`: some typos * :ghissue:`2063`: Gibbs tutorial patch * :ghissue:`2045`: [Fix] workflow variable string * :ghissue:`2060`: Replace old function with cython version * :ghissue:`2058`: DOC: Fix `Sphinx` link in `CONTRIBUTING.md` * :ghissue:`2059`: DOC: Add `Azure Pipelines` to CI tools in `CONTRIBUTING.md` * :ghissue:`1363`: MDF not working properly * :ghissue:`2056`: MAINT: Up Numpy version to 1.12. * :ghissue:`1871`: apply transformation to all volumes in a series of DWI (4D) * :ghissue:`2052`: dipy.tracking.utils.density_map order of arguments changed by mistake * :ghissue:`1785`: Could we use gifti for streamlines? * :ghissue:`1728`: Bug in shm_coeff computation? * :ghissue:`1699`: Details in aparc-reduced.nii.gz * :ghissue:`1671`: Question about shm_coeff * :ghissue:`1552`: dti.py - quantize_evecs - error * :ghissue:`1373`: How to convert from converted isotropic to original resolution (anisotropic) * :ghissue:`1364`: SNR estimation troubleshooting * :ghissue:`1152`: nan gfa and odf values when mask includes voxels with 0 dwi signal * :ghissue:`1047`: Gradient flipped in the x-direction - FSL bvecs handling * :ghissue:`2019`: Apply deformation map to render "registered" image * :ghissue:`2049`: KFA calculation * :ghissue:`2048`: Group analysis * :ghissue:`2053`: Correct TYPO on the note about n_points in _gibbs_removal_2d() * :ghissue:`2043`: [NF] Add a Deprecation system * :ghissue:`218`: Callable response broken in csd module * :ghissue:`2047`: [fix] Doc generation issue * :ghissue:`313`: csdeconv response as callable * :ghissue:`1848`: Add Dipy to MRI-Hub (ISMRM Reproducible Research Study Group) * :ghissue:`2044`: [FIX] check seeds dtype * :ghissue:`2034`: Using the tutorial on Euler method on my data * :ghissue:`2041`: BF: SFM prediction with mask * :ghissue:`1724`: Failure on Windows/Python 3.5 * :ghissue:`1938`: Auto-clearing the AppVeyor queue backlog * :ghissue:`2039`: Remove __future__ * :ghissue:`2042`: Add tests to rng module * :ghissue:`1864`: Add tests to dipy.core.rng * :ghissue:`2040`: RF: Swallow a couple of warnings that are safe to ignore. * :ghissue:`2038`: [DOC] Update repo path * :ghissue:`2037`: DOC: fix typo in FW DTI tutorial * :ghissue:`2028`: Adapted for patch_radius with radii differing xyz direction. * :ghissue:`2035`: DOC: Update DKI documentation according to the new get data functions