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