# 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