# Release notes for DIPY version 1.3

GitHub stats for 2020/09/09 - 2020/11/02 (tag: 1.2.0)

The following 14 authors contributed 284 commits.

- Areesha Tariq

- Ariel Rokem

- Basile Pinsard

- Bramsh Qamar

- Charles Poirier

- Eleftherios Garyfallidis

- Eric Larson

- Gregory Lee

- Jaewon Chung

- Jon Haitz Legarreta Gorroño

- Philippe Karan

- Rafael Neto Henriques

- Serge Koudoro

- Siddharth Kapoor

We closed a total of 134 issues, 49 pull requests and 85 regular issues; this is the full list (generated with the script `tools/github_stats.py`):

Pull Requests (49):

- PR #2181: BUAN bundle highlight option in horizon

- PR #2223: [NF] new linear transforms for Rigid+IsoScaling and Rigid+Scaling

- PR #2238: [FIX] fix cython error from pre matrix

- PR #2265: Gibbs denoising: fft only along the axis of interest

- PR #2206: NF: Update definitions of SH bases and documentation

- PR #2266: STYLE: minor refactoring in TissueClassifierHMRF

- PR #2255: Modifying dti.design_matrix to take gtab.btens into account

- PR #2271: Increase Azure pipeline timeout

- PR #2263: [FIX] update multiple models due to cvxpy 1.1 (part2)

- PR #2259: [Fix] Allow read_bvals_bvecs to have 1 or 2 dwi volumes only

- PR #2264: BF: Fix dipy_align_syn default value assumptions

- PR #2268: BUG: Fix literal

- PR #2267: BUG: Fix string literal

- PR #2262: [FIX] update tests to respect numpy NEP 34

- PR #2244: DOC : Denoising CLI

- PR #2119: RecoBundles updated to read and save .trk files from Old API

- PR #2260: [Fix] Better error handling in Diffeomorphic map get_map

- PR #2258: [FIX] update Azure OSX CI + remove Azure Linux CI’s

- PR #2257: [Fix] warning if not the same number of points

- PR #2261: [DOC]:Removed tracking evaluation section

- PR #1919: [DOC] Add an overview of reconstruction models

- PR #2256: update BUAN citations

- PR #2253: Improve FFT efficiency in gibbs_removal

- PR #2240: [ENH] Deprecate interp parameter name in AffineMap

- PR #2198: Make single and multi tensor simulations compatible with btensors

- PR #2025: Adds an align.api module, which provides simplified API to registration functions

- PR #2197: Estimate smt2 metrics from mean signal kurtosis

- PR #2227: RF: Replaces our own custom progressbar with a tqdm progressbar.

- PR #2250: [ENH] Add parallelization to gibbs denoising

- PR #2252: BUG: Set tau factor to parameter value in local PCA

- PR #2248: [DOC] fetching dataset

- PR #2249: [fix] fix value_range in HORIZON

- PR #2247: BF: In LiFE, set nan signals to 0.

- PR #2246: [DOC] Replace simple backticks with double backticks

- PR #2239: [ENH] Add inplace kwarg to gibbs_removal

- PR #2242: maintenance of bundle_shape_similarity function

- PR #2241: STYLE: Exclude package information file from PEP8 checks

- PR #2235: DOC: Add tips to the documentation build section

- PR #2234: DOC: Improve some of the links in the info.py file

- PR #2233: Clarifying msmt response function docstrings

- PR #2231: DOC: Fix HTML tag in dataset list documentation table

- PR #2221: Robustify solve_qp for possible SolverError in one odd voxel

- PR #2226: STYLE: Conform to reStructuredText syntax in examples sections

- PR #2225: [CI] Replace Rackspace by https://anaconda.org/scipy-wheels-nightly

- PR #2224: Replace pytest.xfail by npt.assert_raises

- PR #2220: [DOC] move Denoising on its own section

- PR #2218: DOC : inconsistent save_seeds documentation

- PR #2217: Fixing numpy version rcond issue in numpy.linalg.lstsq

- PR #2211: [FIX] used numerical indices for references

Issues (85):

- #2181: BUAN bundle highlight option in horizon

- #2272: DOC : Registration CLI

- #2223: [NF] new linear transforms for Rigid+IsoScaling and Rigid+Scaling

- #2180: [NF] add new linear transforms for Rigid+IsoScaling and Rigid+Scaling

- #2238: [FIX] fix cython error from pre matrix

- #2265: Gibbs denoising: fft only along the axis of interest

- #2206: NF: Update definitions of SH bases and documentation

- #392: mrtrix 0.3 default basis is different from mrtrix 0.2

- #2266: STYLE: minor refactoring in TissueClassifierHMRF

- #2255: Modifying dti.design_matrix to take gtab.btens into account

- #2271: Increase Azure pipeline timeout

- #2054: Discrepancy between dipy.gibbs.gibbs_removal and reisert/unring/

- #2263: [FIX] update multiple models due to cvxpy 1.1 (part2)

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

- #2259: [Fix] Allow read_bvals_bvecs to have 1 or 2 dwi volumes only

- #2046: read_bvals_bvecs can’t read a single volume dwi

- #2264: BF: Fix dipy_align_syn default value assumptions

- #2268: BUG: Fix literal

- #2267: BUG: Fix string literal

- #2262: [FIX] update tests to respect numpy NEP 34

- #2132: Generating ndarrays with different shapes generates NumPy warning at testing

- #1266: test_mapmri_isotropic_static_scale_factor failure on OSX buildbot

- #1264: FBC measures test failure on PPC

- #2244: DOC : Denoising CLI

- #2119: RecoBundles updated to read and save .trk files from Old API

- #2117: RecoBundles workflow still using old API

- #2260: [Fix] Better error handling in Diffeomorphic map get_map

- #2202: Add error handling in Diffeomorphic map get_map

- #2258: [FIX] update Azure OSX CI + remove Azure Linux CI’s

- #2257: [Fix] warning if not the same number of points

- #342: Missing a warning if not the same number of points

- #2261: [DOC]:Removed tracking evaluation section

- #2115: Independent section on Fiber tracking evaluation not necessary

- #1744: [WIP] [NF] Free Water Elimination for single-shell DTI (updated version)

- #1919: [DOC] Add an overview of reconstruction models

- #1489: Documentation: how to know which models support multi-shell?

- #2256: update BUAN citations

- #2253: Improve FFT efficiency in gibbs_removal

- #2240: [ENH] Deprecate interp parameter name in AffineMap

- #2192: Bringing AffineMap and DiffeomorphicMap a little closer together

- #2198: Make single and multi tensor simulations compatible with btensors

- #2025: Adds an align.api module, which provides simplified API to registration functions

- #2201: Gradient table message error

- #2232: This should be len(np.unique(gtab.bvals)) - 1 or somesuch

- #2197: Estimate smt2 metrics from mean signal kurtosis

- #2227: RF: Replaces our own custom progressbar with a tqdm progressbar.

- #2219: Replace fetcher progress bar with tqdm

- #2250: [ENH] Add parallelization to gibbs denoising

- #2236: Parallelize gibbs_removal

- #2254: Trackvis header saved with Dipy (nibabel) is not read by Matlab or other tools

- #2252: BUG: Set tau factor to parameter value in local PCA

- #2251: localpca tau_factor is hard coded to 2.3

- #2248: [DOC] fetching dataset

- #2249: [fix] fix value_range in HORIZON

- #2243: Unable to visualize data through dipy_horizon

- #2247: BF: In LiFE, set nan signals to 0.

- #2246: [DOC] Replace simple backticks with double backticks

- #2239: [ENH] Add inplace kwarg to gibbs_removal

- #2237: gibbs_removal overwrites input data when inputting 3-d or 4-d data.

- #2245: DOC: Fix Sphinx verbatim syntax in coding style guide

- #2242: maintenance of bundle_shape_similarity function

- #2241: STYLE: Exclude package information file from PEP8 checks

- #2235: DOC: Add tips to the documentation build section

- #2234: DOC: Improve some of the links in the info.py file

- #2222: How can I track different streamlines in DIPY?

- #2233: Clarifying msmt response function docstrings

- #2231: DOC: Fix HTML tag in dataset list documentation table

- #2230: TST: Assert the shape of the output based on the docstring.

- #2228: Best practices for saving a tissue classifier object?

- #2221: Robustify solve_qp for possible SolverError in one odd voxel

- #2109: DIPY lab meetings, Spring 2020

- #2226: STYLE: Conform to reStructuredText syntax in examples sections

- #2225: [CI] Replace Rackspace by https://anaconda.org/scipy-wheels-nightly

- #2214: Rackspace does not exist anymore -> Update PRE-matrix on Travis and Azure required

- #2224: Replace pytest.xfail by npt.assert_raises

- #2220: [DOC] move Denoising on its own section

- #2218: DOC : inconsistent save_seeds documentation

- #2217: Fixing numpy version rcond issue in numpy.linalg.lstsq

- #2216: test_multi_shell_fiber_response failed with Numpy 1.13.3

- #2211: [FIX] used numerical indices for references

- #2185: Inconsistency in stating references in dti.py

- #2215: problem with fetching stanford data

- #1762: Font on instructions is small on mac

- #1354: strange tracks

- #325: streamline extraction from eudx is failing - but perhaps eudx is failing