Release notes for DIPY version 1.0#

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 tools/github_stats.py):

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 decfa