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; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (94):

  • PR #2191: Multi-shell multi-tissue constrained spherical deconvolution

  • PR #2212: [FIX] renamed Direct Streamline Normalization tutorial title

  • PR #2207: [FIX] Horizon shader warning

  • PR #2208: Removing Python 3.5 from Travis and Azure due to its end of life (2020-09-13)

  • PR #2157: BF: Fix variable may be used uninitialized warning

  • PR #2205: Add optional installs for different settings.

  • PR #2204: from Renderer to scene

  • PR #2183: _streamlines_in_mask bounds check

  • PR #2203: End of line period in sft

  • PR #2142: ENH: function to calculate size/shape parameters of b-tensors and vice-versa

  • PR #2195: [ENH] Validate streamlines pre-LiFE

  • PR #2161: Fix a memory overlap bug in multi_median (and median_otsu)

  • PR #2163: BF: Fix Cython label defined but not used warning

  • PR #2174: Improve performance of tissue classification

  • PR #2168: add fig_kwargs

  • PR #2178: Add full SH basis

  • PR #2193: BUAN_flow.rst to buan_flow.rst

  • PR #2196: [Fix] update save_vtk_streamlines and load_vtk_streamlines

  • PR #2188: [Fix] update mapmri due to cvxpy 1.1

  • PR #2176: [DOC] Update SH basis documentation

  • PR #2173: Install ssl certificate for azure pipeline windows

  • PR #2171: Gitter url update: from nipy/dipy to dipy/dipy

  • PR #2154: Bundle segmentation CLI tutorial

  • PR #2162: BF: Fix string literal comparison warning

  • PR #2156: BF: Fix Cython signed vs. unsigned integer comparison warning

  • PR #2160: TST: Change assert_equal(statement, True) to assert_(statement).

  • PR #2158: BF: Fix Cython floating point absolute value warning

  • PR #2155: [Fix] sfm RuntimeWarning

  • PR #2147: BF: Fix Cython function override warning

  • PR #2148: BF: Fix distutils Python version requirement option warning

  • PR #2150: [Fix] some warning on clustering test

  • PR #2149: [Fix] some warning on stats module

  • PR #2145: Rename dipy_track command line

  • PR #2152: changed buan_flow.rst to BUAN_flow.rst

  • PR #2146: Cluster threshold parameter in dipy_buan_shapes workflow

  • PR #2134: Slicing, adding function of StatefulTractogram

  • PR #2001: Basic processing documentation for CLI.

  • PR #2135: [Fix] shm.py RuntimeWarning

  • PR #2141: [FIX] doc generation issue

  • PR #2136: [Fix] laplacian_regularization on MAPMRI + cleanup warning

  • PR #2140: BF: Fix NumPy warning when creating arrays from ragged sequences

  • PR #2139: BF: Use equality check instead of identity check

  • PR #2108: [Horizon] Update clipping range on slicer

  • PR #2121: BF: ensure btens attribute of GradientTable is initialised

  • PR #2129: BF: Fix sequence stacking warning in LiFE tracking

  • PR #2133: BF: Fix NumPy warning when creating arrays from ragged sequences

  • PR #2125: ENH: function to calculate anisotropy of b-tensors

  • PR #2124: BUAN framework documentation

  • PR #2033: RF - Direction getters naming

  • PR #2111: Added an epsilon to bounding_box check

  • PR #2086: WIP Issue 1996

  • PR #2091: Modified the model for multiple hidden layers

  • PR #2057: DOC: Add DIPY dataset list to documentation.

  • PR #2103: Documentation typos, grammar corrections & imports

  • PR #2088: BUAN paper code and CLIs

  • PR #2120: rename var sp to sph

  • PR #2113: BF: refer to cigar_tensor

  • PR #2116: fixed code tags and minor changes

  • PR #2100: Fixed typos, grammatical errors and time import

  • PR #2101: Minor typos and imports

  • PR #2095: Fixed typos in dipy.align

  • PR #2099: Minor Typos and imports in the beginning

  • PR #2102: Modules imported in the beginning

  • PR #2055: Multidimensional gradient table

  • PR #2097: Replace manual sform values with get_best_affine

  • PR #2104: Fixed minor typos

  • PR #2065: Some typos and grammatical errors

  • PR #2090: Small fix reorient_bvecs

  • PR #2067: Some spelling and grammatical mistakes

  • PR #2093: Placed all imports in the beginning

  • PR #2077: Fixed minor typos in tutorials

  • PR #2071: Some change backs

  • PR #2084: Kunakl07 patch 7

  • PR #2085: Kunakl07 patch 8

  • PR #2068: Some spelling and grammatical errors

  • PR #2069: some typos

  • PR #2063: Gibbs tutorial patch

  • PR #2045: [Fix] workflow variable string

  • PR #2060: Replace old function with cython version

  • PR #2058: DOC: Fix Sphinx link in CONTRIBUTING.md

  • PR #2059: DOC: Add Azure Pipelines to CI tools in CONTRIBUTING.md

  • PR #2056: MAINT: Up Numpy version to 1.12.

  • PR #2053: Correct TYPO on the note about n_points in _gibbs_removal_2d()

  • PR #2043: [NF] Add a Deprecation system

  • PR #2047: [fix] Doc generation issue

  • PR #2044: [FIX] check seeds dtype

  • PR #2041: BF: SFM prediction with mask

  • PR #2039: Remove __future__

  • PR #2042: Add tests to rng module

  • PR #2040: RF: Swallow a couple of warnings that are safe to ignore.

  • PR #2038: [DOC] Update repo path

  • PR #2037: DOC: fix typo in FW DTI tutorial

  • PR #2028: Adapted for patch_radius with radii differing xyz direction.

  • PR #2035: DOC: Update DKI documentation according to the new get data functions

Issues (164):

  • #2114: Tutorial title in Streamline-based registration section is misleading

  • #2207: [FIX] Horizon shader warning

  • #2208: Removing Python 3.5 from Travis and Azure due to its end of life (2020-09-13)

  • #1793: ENH: Improving Command Line and WF Docs

  • #2007: Reference for load_trk in recobundles example

  • #2061: Is dipy.viz supported in Colab or Kaggle Notebooks?

  • #2070: Python has stopped working during import

  • #2107: PNG images saved by window.record in the tutorial example are always black

  • #2153: lowercase .rst file names

  • #2138: Basic introduction to CLI needs better dataset to showcase capabilities

  • #2194: LiFE model won’t fit ?

  • #2157: BF: Fix variable may be used uninitialized warning

  • #2177: VIZ: streamline actor failing on Windows + macOS due to the new VTK9

  • #2205: Add optional installs for different settings.

  • #2204: from Renderer to scene

  • #2183: _streamlines_in_mask bounds check

  • #2182: target_line_based might read out of bounds

  • #2203: End of line period in sft

  • #2200: BF: Fix ‘tp_print’ is deprecated Cython warning

  • #2142: ENH: function to calculate size/shape parameters of b-tensors and vice-versa

  • #2199: BUG: Fix NumPy and Cython deprecation and initialization warnings

  • #2195: [ENH] Validate streamlines pre-LiFE

  • #2161: Fix a memory overlap bug in multi_median (and median_otsu)

  • #2163: BF: Fix Cython label defined but not used warning

  • #2174: Improve performance of tissue classification

  • #2168: add fig_kwargs

  • #2178: Add full SH basis

  • #2193: BUAN_flow.rst to buan_flow.rst

  • #2196: [Fix] update save_vtk_streamlines and load_vtk_streamlines

  • #2175: Save streamlines as vtk polydata to a supported format file updated t…

  • #2188: [Fix] update mapmri due to cvxpy 1.1

  • #2190: Reconstruction with Multi-Shell Multi-Tissue CSD

  • #2051: BF: Non-negative Least Squares for IVIM

  • #2176: [DOC] Update SH basis documentation

  • #2173: Install ssl certificate for azure pipeline windows

  • #2172: fetch_gold_standard_io fetcher failed regularly

  • #2169: saving tracts in obj format

  • #2170: Output of utils.density_map() using tck file is different than MRTrix

  • #2171: Gitter url update: from nipy/dipy to dipy/dipy

  • #2144: Move gitter to dipy/dipy?

  • #2154: Bundle segmentation CLI tutorial

  • #2162: BF: Fix string literal comparison warning

  • #2156: BF: Fix Cython signed vs. unsigned integer comparison warning

  • #2160: TST: Change assert_equal(statement, True) to assert_(statement).

  • #2158: BF: Fix Cython floating point absolute value warning

  • #2155: [Fix] sfm RuntimeWarning

  • #2159: BF: Fix Cython different sign integer comparison warning

  • #2147: BF: Fix Cython function override warning

  • #2148: BF: Fix distutils Python version requirement option warning

  • #2151: [DOC] Fixed minor typos, grammar errors and moved imports up in all examples

  • #2130: Checking empty Cluster objects generates NumPy warning

  • #2131: Elementwise comparison failure warning in multi_voxel test

  • #2150: [Fix] some warning on clustering test

  • #2149: [Fix] some warning on stats module

  • #2145: Rename dipy_track command line

  • #2152: changed buan_flow.rst to BUAN_flow.rst

  • #2146: Cluster threshold parameter in dipy_buan_shapes workflow

  • #2128: Registration Module failing with pre-matrix on Travis with future Numpy/Scipy release

  • #2134: Slicing, adding function of StatefulTractogram

  • #2001: Basic processing documentation for CLI.

  • #2135: [Fix] shm.py RuntimeWarning

  • #2141: [FIX] doc generation issue

  • #2136: [Fix] laplacian_regularization on MAPMRI + cleanup warning

  • #1765: Refactor dipy/stats/analysis.py

  • #2122: [WIP] Add build template

  • #2140: BF: Fix NumPy warning when creating arrays from ragged sequences

  • #2139: BF: Use equality check instead of identity check

  • #2127: DOC : Minor grammar fixes and moved imports up with respective comments

  • #2108: [Horizon] Update clipping range on slicer

  • #2121: BF: ensure btens attribute of GradientTable is initialised

  • #2129: BF: Fix sequence stacking warning in LiFE tracking

  • #2133: BF: Fix NumPy warning when creating arrays from ragged sequences

  • #2125: ENH: function to calculate anisotropy of b-tensors

  • #2124: BUAN framework documentation

  • #2126: dipy / fury fails to install on Ubuntu 18 with pip3

  • #2033: RF - Direction getters naming

  • #2111: Added an epsilon to bounding_box check

  • #2112: [WIP] BUndle ANalytics (BUAN) pipeline documentation

  • #2086: WIP Issue 1996

  • #2091: Modified the model for multiple hidden layers

  • #2096: Deep Code

  • #2057: DOC: Add DIPY dataset list to documentation.

  • #2103: Documentation typos, grammar corrections & imports

  • #2088: BUAN paper code and CLIs

  • #2120: rename var sp to sph

  • #2118: Local namespace of Scipy is same as a variable name

  • #1861: WIP: Refactoring the stats module

  • #2113: BF: refer to cigar_tensor

  • #2116: fixed code tags and minor changes

  • #2024: DIPY open lab meetings, Winter 2020

  • #2100: Fixed typos, grammatical errors and time import

  • #2101: Minor typos and imports

  • #2094: Detailed Beginner Friendly Tutorials

  • #2095: Fixed typos in dipy.align

  • #2099: Minor Typos and imports in the beginning

  • #2102: Modules imported in the beginning

  • #2055: Multidimensional gradient table

  • #2097: Replace manual sform values with get_best_affine

  • #2105: Tutorial Symmetric Regn 3D patch 3

  • #2104: Fixed minor typos

  • #2078: Applying affine transform to streamlines in a SFT object

  • #2065: Some typos and grammatical errors

  • #1305: Questions/policies about writing .rst/web doc files

  • #2090: Small fix reorient_bvecs

  • #2067: Some spelling and grammatical mistakes

  • #2093: Placed all imports in the beginning

  • #2077: Fixed minor typos in tutorials

  • #2089: Transforming bvecs after registration

  • #2071: Some change backs

  • #2084: Kunakl07 patch 7

  • #2085: Kunakl07 patch 8

  • #2072: Some typos and grammatical errors in faq.rst

  • #2073: Some minor grammatical fixes old_highlights.txt

  • #2074: Small typos

  • #2075: Some grammatical changes in maintainer_workflow.rst

  • #2076: Some grammatical changes in maintainer_workflow.rst

  • #2079: Some minor typos in gimbal_lock.rst

  • #2080: Some minor grammatical errors fixes

  • #2081: Some typos and grammatical corrections in Changelog

  • #2082: Grammatical fixes in readme.rst

  • #2083: Fixes in regtools.py

  • #2066: Fixed some typos

  • #2068: Some spelling and grammatical errors

  • #2069: some typos

  • #2063: Gibbs tutorial patch

  • #2045: [Fix] workflow variable string

  • #2060: Replace old function with cython version

  • #2058: DOC: Fix Sphinx link in CONTRIBUTING.md

  • #2059: DOC: Add Azure Pipelines to CI tools in CONTRIBUTING.md

  • #1363: MDF not working properly

  • #2056: MAINT: Up Numpy version to 1.12.

  • #1871: apply transformation to all volumes in a series of DWI (4D)

  • #2052: dipy.tracking.utils.density_map order of arguments changed by mistake

  • #1785: Could we use gifti for streamlines?

  • #1728: Bug in shm_coeff computation?

  • #1699: Details in aparc-reduced.nii.gz

  • #1671: Question about shm_coeff

  • #1552: dti.py - quantize_evecs - error

  • #1373: How to convert from converted isotropic to original resolution (anisotropic)

  • #1364: SNR estimation troubleshooting

  • #1152: nan gfa and odf values when mask includes voxels with 0 dwi signal

  • #1047: Gradient flipped in the x-direction - FSL bvecs handling

  • #2019: Apply deformation map to render “registered” image

  • #2049: KFA calculation

  • #2048: Group analysis

  • #2053: Correct TYPO on the note about n_points in _gibbs_removal_2d()

  • #2043: [NF] Add a Deprecation system

  • #218: Callable response broken in csd module

  • #2047: [fix] Doc generation issue

  • #313: csdeconv response as callable

  • #1848: Add Dipy to MRI-Hub (ISMRM Reproducible Research Study Group)

  • #2044: [FIX] check seeds dtype

  • #2034: Using the tutorial on Euler method on my data

  • #2041: BF: SFM prediction with mask

  • #1724: Failure on Windows/Python 3.5

  • #1938: Auto-clearing the AppVeyor queue backlog

  • #2039: Remove __future__

  • #2042: Add tests to rng module

  • #1864: Add tests to dipy.core.rng

  • #2040: RF: Swallow a couple of warnings that are safe to ignore.

  • #2038: [DOC] Update repo path

  • #2037: DOC: fix typo in FW DTI tutorial

  • #2028: Adapted for patch_radius with radii differing xyz direction.

  • #2035: DOC: Update DKI documentation according to the new get data functions