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