GitHub stats for 2019/03/11 - 2019/08/05 (tag: 0.16.0) These lists are automatically generated, and may be incomplete or contain duplicates. The following 17 authors contributed 707 commits. Adam Richie-Halford Antoine Theberge Ariel Rokem Clint Greene Eleftherios Garyfallidis Francois Rheault Gabriel Girard Jean-Christophe Houde Jon Haitz Legarreta Gorroño Kevin Sitek Marc-Alexandre Côté Matt Cieslak Rafael Neto Henriques Scott Trinkle Serge Koudoro Shreyas Fadnavis We closed a total of 289 issues, 97 pull requests and 192 regular issues;
this is the full list (generated with the script
Pull Requests (97): PR #1924: Some updates in Horizon fixing some issues for upcoming release PR #1946: Fix empty tractogram loading saving PR #1947: DOC: fixing examples links PR #1942: Remove dipy.io.trackvis PR #1917: A functional implementation of Random matrix local pca. PR #1940: Increase affine consistency in dipy.tracking.streamlines PR #1909: [WIP] - MTMS-CSD Tutorial PR #1931: [BF] IVIM fixes PR #1944: Update DKI, WMTI, fwDTI examples and give more evidence to WMTI and fwDTI models PR #1939: Increase affine consistency in dipy.tracking.utils PR #1943: Increase affine consistency in dipy.tracking.life and dipy.stats.analysis PR #1941: Remove some viz tutorial PR #1926: RF - dipy.tracking.local PR #1935: Remove dipy.external and dipy.fixes packages PR #1903: Skip some tests on big endian architecture (like s390x) PR #1892: Use the correct (row) order of the tensor components PR #1804: BF: added check to avoid infinite loop on consecutive coordinates. PR #1937: Add a warning about future changes that will happen in dipy.stats. PR #1928: Update streamlines formats example PR #1925: FIX: Stateful tractogram examples PR #1927: BF - move import to top level PR #1923: [Fix] removing minmax_norm parameter from peak_direction PR #1894: Default sphere: From symmetric724 to repulsion724 PR #1812: ENH: Statefull tractogram, robust spatial handling and IO PR #1922: Remove deprecated functions from imaffine PR #1885: BF - remove single pts streamline PR #1913: RF - EuDX legacy code/test PR #1915: Doc generation under Windows PR #1630: [Fix] remove Userwarning message PR #1896: New module: dipy.core.interpolation PR #1912: Remove deprecated parameter voxel_size PR #1916: Spherical deconvolution model CANNOT be constructed without specifying a response PR #1918: ENH: Remove unused warning package import PR #1881: DOC - RF tracking examples PR #1911: Add python_requires PR #1914: [Fix] vol_idx missing in snr_in_cc Tutorial PR #1907: DOC: Fix examples documentation generation warnings PR #1908: DOC: Fix typos PR #1887: DOC - updated streamline_tools example with the LocalTracking Framework PR #1905: ENH: Remove deprecated SH bases PR #1849: Adds control for number of iterations in CSD recon PR #1902: Warn users if they don’t have FURY installed PR #1904: DOC: Improve documentation PR #1771: Gibbs removal PR #1899: Fix: Byte ordering error on Python 3.5 PR #1898: Replace SingleTensor by single_tensor PR #1897: DOC: Fix typos PR #1893: Remove scratch folder PR #1891: Move the tests from test_refine_rb to test_bundles. PR #1888: BF - fix eudx tracking for npeaks=1 PR #1879: DOC - explicitly run the streamline generators before saving the trk PR #1884: Clean up: Remove streamlines memory patch PR #1875: ENH: Add binary tissue classifier option for tracking workflow PR #1882: DOC - clarified the state of the tracking process once stopped PR #1880: DOC: Fix typos and improve documentation PR #1878: Clean up: Remove NUMPY_LESS_0.8.x PR #1877: Clean up: Remove all SCIPY_LESS_0.x.x PR #1876: DOC: Fix typos PR #1874: DOC: Fix documentation oversights. PR #1858: NF: MSMT - CSD PR #1843: [NF] new workflow: FetchFlow PR #1866: MAINT: Drop support for Python 3.4 PR #1850: NF: Add is_hemispherical test PR #1855: Pin scipy version for bots that need statsmodels. PR #1835: [Fix] Workflow mask documentation PR #1836: Corrected median_otsu function declaration that was breaking tutorials PR #1792: [NF]: Add seeds to TRK PR #1851: DOC: Add single-module test/coverage instructions PR #1842: [Fix] Remove tput from fetcher PR #1800: Update command line documentation generation PR #1830: Delete six module PR #1821: Fixes 238, by requiring vol_idx input with 4D images. PR #1775: Remove Python 2 dependency. PR #1816: Remove Deprecated function dipy.data.get_data PR #1818: [DOC] fix rank order typo PR #1827: Remove deprecated module dipy.segment.quickbundes PR #1824: Remove deprecated module dipy.reconst.peaks PR #1819: [Fix] Diffeormorphic + CCMetric on small image PR #1823: Remove accent colormap PR #1814: [Fix] add a basic check on dipy_horizon PR #1815: [FIX] median_otsu deprecated parameter PR #1813: [Fix] Add Readme for doc generation PR #1766: NF - add tracking workflow parameters PR #1772: BF: changes min_signal defaults from 1 to 1e-5 PR #1810: [Bug FIx] dipy_fit_csa and dipy_fit_csd workflow PR #1806: Plot both IVIM fits on the same axis PR #1789: VarPro Fit Example IVIM PR #1770: Parallel reconst workflows PR #1796: [Fix] stripping in workflow documentation PR #1795: [Fix] workflows description PR #1768: Add afq to stats PR #1788: Add test for different dtypes PR #1769: Change “is” check for ‘GCV’ PR #1767: BF: self.self PR #1759: Add one more acknowledgement PR #1230: Mean Signal DKI PR #1760: Implements the inverse of decfa Issues (192): #1798: plotting denoised img #1924: Some updates in Horizon fixing some issues for upcoming release #1946: Fix empty tractogram loading saving #1947: DOC: fixing examples links #1942: Remove dipy.io.trackvis #1917: A functional implementation of Random matrix local pca. #1940: Increase affine consistency in dipy.tracking.streamlines #1909: [WIP] - MTMS-CSD Tutorial #1931: [BF] IVIM fixes #1817: Unusual behavior in Dipy IVIM implementation/example #1774: Split up DKI example #1944: Update DKI, WMTI, fwDTI examples and give more evidence to WMTI and fwDTI models #1939: Increase affine consistency in dipy.tracking.utils #1943: Increase affine consistency in dipy.tracking.life and dipy.stats.analysis #1941: Remove some viz tutorial #1926: RF - dipy.tracking.local #1935: Remove dipy.external and dipy.fixes packages #1903: Skip some tests on big endian architecture (like s390x) #1587: Could tests for functionality not supported on big endians just skip? #1890: Tensor I/O in dipy_fit_dti #1892: Use the correct (row) order of the tensor components #1804: BF: added check to avoid infinite loop on consecutive coordinates. #1937: Add a warning about future changes that will happen in dipy.stats. #1933: Remove deprecated voxel_size from seed_from_mask #1928: Update streamlines formats example #985: Getting started example should be commented at each step #1558: Example of creating Trackvis compatible streamlines is needed #1925: FIX: Stateful tractogram examples #1910: BF: IVIM fixes #1927: BF - move import to top level #1923: [Fix] removing minmax_norm parameter from peak_direction #389: minmax_norm in peaks_directions does nothing #1894: Default sphere: From symmetric724 to repulsion724 #590: Change default sphere #1722: Error when using TCK files written by dipy #1832: Tracking workflow header affine issue & fix #1812: ENH: Statefull tractogram, robust spatial handling and IO #1922: Remove deprecated functions from imaffine #1885: BF - remove single pts streamline #1913: RF - EuDX legacy code/test #283: Spherical deconvolution model can be constructed without specifying a response #1915: Doc generation under Windows #1630: [Fix] remove Userwarning message #1896: New module: dipy.core.interpolation #728: Many interpolation functions in different places can they all go to same module? #1912: Remove deprecated parameter voxel_size #1920: How can I get streamlines using fiber orientation by bedpostx of MRtrix3? #1432: DOC/RF - update/standardize tracking examples #1779: Probabilistic Direction Getter gallery example #1916: Spherical deconvolution model CANNOT be constructed without specifying a response #1918: ENH: Remove unused warning package import #1881: DOC - RF tracking examples #1906: Add python_requires=”>=3.5” #1911: Add python_requires #1901: window.record() function shows the coronal view #1914: [Fix] vol_idx missing in snr_in_cc Tutorial #1718: cannot import name window #1747: CI error that sometimes shows up (Python 2.7) #1907: DOC: Fix examples documentation generation warnings #1908: DOC: Fix typos #1887: DOC - updated streamline_tools example with the LocalTracking Framework #1839: [WIP] IVIM fixes #1905: ENH: Remove deprecated SH bases #583: Make a cython style guide #1849: Adds control for number of iterations in CSD recon #1902: Warn users if they don’t have FURY installed #1904: DOC: Improve documentation #1694: Intermittent test failures in test_streamline #1724: Failure on Windows/Python 3.5 #1771: Gibbs removal #1899: Fix: Byte ordering error on Python 3.5 #1898: Replace SingleTensor by single_tensor #844: Refactor behavior of dipy.sims.voxel.single_tensor vs SingleTensor #1752: Intermittent failure on Python 3.4 #1856: Figure out how to get a “used by” button #1897: DOC: Fix typos #1807: tracking fails when npeaks=1 for peaks_from_model with tensor model #1889: segment.bundles package not being tested #1893: Remove scratch folder #1713: Clean up “scratch” #1891: Move the tests from test_refine_rb to test_bundles. #1888: BF - fix eudx tracking for npeaks=1 #668: Add transformation matrix output and input #592: Shouldn’t TRACKPOINT be renamed to NODIRECTION? #1879: DOC - explicitly run the streamline generators before saving the trk #1884: Clean up: Remove streamlines memory patch #1875: ENH: Add binary tissue classifier option for tracking workflow #1811: Add binary tissue classifier option for the tracking workflow #1846: streamlines to array #1831: bvec file dimension prob #1882: DOC - clarified the state of the tracking process once stopped #1880: DOC: Fix typos and improve documentation #1857: point outside data error #1878: Clean up: Remove NUMPY_LESS_0.8.x #1877: Clean up: Remove all SCIPY_LESS_0.x.x #1863: Clean up core.optimize #1876: DOC: Fix typos #1874: DOC: Fix documentation oversights. #1781: [WIP] Random lpca #1858: NF: MSMT - CSD #1843: [NF] new workflow: FetchFlow #1869: get rotation and translation parameters of a rigid transformation #1844: Statsmodels import error #1866: MAINT: Drop support for Python 3.4 #1865: Drop Python 3.4? #1850: NF: Add is_hemispherical test #1860: Dependency Graph: Dependents? #1855: Pin scipy version for bots that need statsmodels. #1168: Nf mtms csd model #1854: Testing the CI. DO NOT MERGE #1835: [Fix] Workflow mask documentation #1764: DTI metrics workflow: mask is optional, but crashes when no mask provided #1836: Corrected median_otsu function declaration that was breaking tutorials #1792: [NF]: Add seeds to TRK #1731: Plan for dropping Python 2 support. #1851: DOC: Add single-module test/coverage instructions #1845: Signal to noise #1842: [Fix] Remove tput from fetcher #1829: When fetching … ‘tput’ is not reco… #1606: Cleaned PR for Visualization Modules to Assess the quality of Registration Qualitatively. #1837: labels #1786: Upcoming DIPY lab meetings #1828: IVIM VarPro implementation throws infeasible ‘x0’ #1833: Affine registration of similar images #1834: Which file to convert from dicom to nifti?! #1800: Update command line documentation generation #1830: Delete six module #1721: using code style #238: Median_otsu b0slices too implicit? #1821: Fixes 238, by requiring vol_idx input with 4D images. #1775: Remove Python 2 dependency. #1816: Remove Deprecated function dipy.data.get_data #1818: [DOC] fix rank order typo #1499: Possible mistake about B matrix in documentation “DIY Stuff about b and q” #1827: Remove deprecated module dipy.segment.quickbundes #1822: .trk file #1824: Remove deprecated module dipy.reconst.peaks #1825: Fury visualizing bug - plane only visible for XY-slice of FODs #1819: [Fix] Diffeormorphic + CCMetric on small image #1048: divide by zero error in DiffeomorphicRegistration of small image volumes #1823: Remove accent colormap #1797: function parameters #1802: crossing fibers & fractional anisotropy #1787: RF - change default tracking algorithm for dipy_track_local to EuDX #1763: Threshold default in QballBaseModel #1814: [Fix] add a basic check on dipy_horizon #1756: Error using dipy_horizon #1815: [FIX] median_otsu deprecated parameter #1761: Deprecation warning when running median_otsu #795: dipy.tracking: Converting an array with ndim > 0 to an index will result in an error #620: Extend the AUTHOR list with more information #1813: [Fix] Add Readme for doc generation #436: Doc won’t build without cvxopt #1758: additional parameters for dipy_track_local workflow #1766: NF - add tracking workflow parameters #1772: BF: changes min_signal defaults from 1 to 1e-5 #1810: [Bug FIx] dipy_fit_csa and dipy_fit_csd workflow #1808: dipy_fit_csd CLI is broken? #1806: Plot both IVIM fits on the same axis #1794: Removed/renamed DetTrackPAMFlow? #1801: segmentation #1803: tools #1809: datasets #1799: steps from nifiti file to tracts #1712: dipy.reconst.peak_direction_getter.PeaksAndMetricsDirectionGetter.initial_direction (dipy/reconst/peak_direction_getter.c:3075) IndexError: point outside data #1789: VarPro Fit Example IVIM #1770: Parallel reconst workflows #1796: [Fix] stripping in workflow documentation #1795: [Fix] workflows description #1768: Add afq to stats #1783: Make trilinear_interpolate4d work with more dtypes. #1784: Generalize trilinear_interpolate4d to other dtypes. #1788: Add test for different dtypes #1790: ValueError: operands could not be broadcast together with remapped shapes [original->remapped]: (13,13)->(13,13) (10000,10)->(10000,newaxis,10) #1782: Conversion from MRTrix SH basis to dipy #1769: Change “is” check for ‘GCV’ #1320: WIP: Bias correction #1245: non_local_means : patch size argument for local mean and variance #1240: WIP: Improve the axonal water fraction estimation. #1237: DOC: Flesh out front page example. #1192: Error handling in SDT #1096: Robust Brain Extraction #832: trilinear_interpolate4d only works on float64 #578: WIP: try out Stefan Behnel’s cython coverage #1780: [WIP]: Randommatrix localpca #1022: Fixes #720 : Auto generate ipython notebooks #1126: Publishing in JOSS : Added paper summary for IVIM #1603: [WIP] - Free water elimination algorithm for single-shell DTI #1767: BF: self.self #1759: Add one more acknowledgement #1230: Mean Signal DKI #1760: Implements the inverse of decfaRelease notes for DIPY version 1.0
tools/github_stats.py):