# 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