# Release notes for DIPY version 0.15

GitHub stats for 2018/05/01 - 2018/12/12 (tag: 0.14.0)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 30 authors contributed 676 commits.

- Ariel Rokem

- Bramsh Qamar

- Chris Filo Gorgolewski

- David Reagan

- Demian Wassermann

- Eleftherios Garyfallidis

- Enes Albay

- Gabriel Girard

- Guillaume Theaud

- Javier Guaje

- Jean-Christophe Houde

- Jiri Borovec

- Jon Haitz Legarreta Gorroño

- Karandeep

- Kesshi Jordan

- Marc-Alexandre Côté

- Matt Cieslak

- Matthew Brett

- Parichit Sharma

- Ricci Woo

- Rutger Fick

- Serge Koudoro

- Shreyas Fadnavis

- Chandan Gangwar

- Daniel Enrico Cahall

- David Hunt

- Francois Rheault

- Jakob Wasserthal

We closed a total of 287 issues, 93 pull requests and 194 regular issues; this is the full list (generated with the script `tools/github_stats.py`):

Pull Requests (93):

- PR #1684: [FIX] testing line-based target function

- PR #1686: Standardize workflow

- PR #1685: [Fix] Typo on examples

- PR #1663: Stats, SNR_in_CC workflow

- PR #1681: fixed issue with cst orientation in bundle_extraction example

- PR #1680: [Fix] workflow variable string

- PR #1683: test for new error in IVIM

- PR #1667: Changing the default b0_threshold in gtab

- PR #1677: [FIX] workflow help msg

- PR #1678: Numpy matrix deprecation

- PR #1676: [FIX] Example Update

- PR #1283: get_data consistence

- PR #1670: fixed RecoBundle workflow, SLR reference, and updated fetcher.py

- PR #1669: Flow csd sh order

- PR #1659: From dipy.viz to FURY

- PR #1621: workflows : warn user for strange b0 threshold

- PR #1657: DOC: Add spherical harmonics basis documentation.

- PR #1660: OPT - moved the tolerance check outside of the for loop

- PR #1658: STYLE: Honor ‘descoteaux’and ‘tournier’ SH basis naming.

- PR #1281: Representing qtau- signal attenuation using qtau-dMRI functional basis

- PR #1651: Add save/load tck

- PR #1656: Link to the dipy tag on neurostars

- PR #1624: NF: Outlier scoring

- PR #1655: [Fix] decrease tolerance on forecast

- PR #1650: Increase codecov tolerance

- PR #1649: Path Length Map example rebase

- PR #1556: RecoBundles and SLR workflows

- PR #1645: Fix workflows creation tutorial error

- PR #1647: DOC: Fix duplicate link and AppVeyor badge.

- PR #1644: Adds an Appveyor badge

- PR #1643: Add hash for SCIL b0 file

- PR #787: TST: Add an appveyor starter file.

- PR #1642: Test that you can use the 724 symmetric sphere in PAM.

- PR #1641: changed vertices to float64 in evenly_distributed_sphere_642.npz

- PR #1564: Added scroll bar to ListBox2D

- PR #1636: Fixed broken link.

- PR #1584: Added Examples

- PR #1554: Checking if the input file or directory exists when running a workflow

- PR #1528: Show spheres with different radii, colors and opacities + add timers + add exit a + resolve issue with imread

- PR #1526: Eigenvalue - eigenvector array compatibility check

- PR #1628: Adding python 3.7 on travis

- PR #1623: NF: Convert between 4D DEC FA and 3D 24 bit representation.

- PR #1622: [Fix] viz slice example

- PR #1626: RF - removed duplicate tests

- PR #1619: [DOC] update VTK version

- PR #1592: Added File Menu element to viz.ui

- PR #1559: Checkbox and RadioButton elements for viz.ui

- PR #1583: Fix the relative SF threshold Issue

- PR #1602: Fix random seed in tracking

- PR #1609: [DOC] update dependencies file

- PR #1560: Removed affine matrices from tracking.

- PR #1593: Removed event.abort for release events

- PR #1597: Upgrade nibabel minimum version

- PR #1601: Fix: Decrease Nosetest warning

- PR #1515: RF: Use the new Streamlines API for orienting of streamlines.

- PR #1590: Revert 1570 file menu

- PR #1589: Fix calculation of highest order for a sh basis set

- PR #1580: Allow PRE=1 job to fail

- PR #1533: Show message if number of arguments mismatch between the doc string and the run method.

- PR #1523: Showing help when no input parameters are given and suppress warnings for cmds

- PR #1543: Update the default out_strategy to create the output in the current working directory

- PR #1574: Fixed Bug in PR #1547

- PR #1561: add example SDR for binary and fuzzy images

- PR #1578: BF - bad condition in maximum dg

- PR #1570: Added File Menu element to viz.ui

- PR #1563: Replacing major_version in viz.ui

- PR #1557: Range slider element for viz.ui

- PR #1547: Changed the icon set in Button2D from Dictionary to List of Tuples

- PR #1555: Fix bug in actor.label

- PR #1522: Image element in dipy.viz.ui

- PR #1355: WIP: ENH: UI Listbox

- PR #1540: fix potential zero division in demon register.

- PR #1548: Fixed references per request of @garyfallidis.

- PR #1542: fix for using cvxpy solver

- PR #1546: References to reference

- PR #1545: Adding a reference in README.rst

- PR #1492: Enh ui components positioning (with code refactoring)

- PR #1538: Explanation that is mistakenly rendered as code fixed in example of DKI

- PR #1536: DOC: Update Rafael’s current institution.

- PR #1537: removed unnecessary imported from sims example

- PR #1530: Wrong default value for parameter ‘symmetric’ connectivity_matrix function

- PR #1529: minor typo fix in quickstart

- PR #1520: Updating the documentation for the workflow creation tutorial.

- PR #1524: Values from streamlines object

- PR #1521: Moved some older highlights and announcements to the old news files.

- PR #1518: DOC: updated some developers affiliations.

- PR #1517: Dev info update

- PR #1516: [DOC] Installation instruction update

- PR #1514: Adding pep8speak config file

- PR #1513: fix typo in example of quick_start

- PR #1510: copyright updated to 2008-2018

- PR #1508: Adds whitespace, to appease the sphinx.

- PR #1506: moving to 0.15.0 dev

Issues (194):

- #1684: [FIX] testing line-based target function

- #1679: Intermittent issue in testing line-based target function

- #1220: RF: Replaces 1997 definitions of tensor geometric params with 1999 definitions.

- #1686: Standardize workflow

- #746: New fetcher returns filenames as dictionary keys in a tuple

- #1685: [Fix] Typo on examples

- #1663: Stats, SNR_in_CC workflow

- #1637: Advice for saving results from MAPMRI

- #1673: CST Image in bundle extraction is not oriented well

- #1681: fixed issue with cst orientation in bundle_extraction example

- #1680: [Fix] workflow variable string

- #1338: Variable string input does not work with self.get_io_iterator() in workflows

- #1683: test for new error in IVIM

- #1682: Add tests for IVIM for new Error

- #634: BinaryTissueClassifier segfaults on corner case

- #742: LinAlgError on tracking quickstart, with python 3.4

- #852: Problem with spherical harmonics computations on some Anaconda python versions

- #1667: Changing the default b0_threshold in gtab

- #1500: Updating streamlines API in streamlinear.py

- #944: Slicer fix

- #1111: WIP: A lightweight UI for medical visualizations based on VTK-Python

- #1099: Needed PRs for merging recobundles into Dipy’s master

- #1544: Plans for viz module

- #641: Tests raise a deprecation warning

- #643: Use appveyor for Windows CI?

- #400: Add travis-ci test without matplotlib installed

- #1677: [FIX] workflow help msg

- #1674: Workflows should print out help per default

- #1678: Numpy matrix deprecation

- #1397: Running dipy ‘Intro to Basic Tracking’ code and keep getting error. On Linux Centos

- #1676: [FIX] Example Update

- #10: data.get_data() should be consistent across datasets

- #1283: get_data consistence

- #1670: fixed RecoBundle workflow, SLR reference, and updated fetcher.py

- #1669: Flow csd sh order

- #1668: One issue on handling HCP data – HCP b vectors raise NaN in the gradient table

- #1662: Remove the points added outside of a mask. Fix the related tests.

- #1659: From dipy.viz to FURY

- #1621: workflows : warn user for strange b0 threshold

- #1657: DOC: Add spherical harmonics basis documentation.

- #1296: Need of a travis bot that runs ana/mini/conda and vtk=7.1.0+

- #1660: OPT - moved the tolerance check outside of the for loop

- #1658: STYLE: Honor ‘descoteaux’and ‘tournier’ SH basis naming.

- #1281: Representing qtau- signal attenuation using qtau-dMRI functional basis

- #1653: STYLE: Honor ‘descoteaux’ SH basis naming.

- #1651: Add save/load tck

- #1656: Link to the dipy tag on neurostars

- #1624: NF: Outlier scoring

- #1655: [Fix] decrease tolerance on forecast

- #1654: Test failure in FORECAST

- #1414: [WIP] Switching tests to pytest and removing nose dependencies

- #1650: Increase codecov tolerance

- #1093: WIP: Add functionality to clip streamlines between ROIs in orient_by_rois

- #1611: Preloader element for viz.ui

- #1615: Color Picker element for viz.ui

- #1631: Path Length Map example

- #1649: Path Length Map example rebase

- #1556: RecoBundles and SLR workflows

- #1645: Fix workflows creation tutorial error

- #1647: DOC: Fix duplicate link and AppVeyor badge.

- #1644: Adds an Appveyor badge

- #1638: Fetcher downloads data every time it is called

- #1643: Add hash for SCIL b0 file

- #1600: NODDIx 2 fibers crossing

- #1618: viz.ui.FileMenu2D

- #1569: viz.ui.ListBoxItem2D text overflow

- #1532: dipy test failed on mac osx sierra with ananoda python.

- #1420: window.record() resolution limit

- #1396: Visualization problem with tensors ?

- #1295: Reorienting peak_slicer and ODF_slicer

- #1232: With VTK 6.3, streamlines color map bar text disappears when using streamtubes

- #928: dipy.viz.colormap crash on single fibers

- #923: change size of colorbar in viz module

- #854: VTK and Python 3 support in fvtk

- #759: How to resolve python-vtk6 link issues in Ubuntu

- #647: fvtk contour function ignores voxsz parameter

- #646: Dipy visualization with missing (?) affine parameter

- #645: Dipy visualization (fvtk) crash when saving series of images

- #353: fvtk.label won’t show up if called twice

- #787: TST: Add an appveyor starter file.

- #1642: Test that you can use the 724 symmetric sphere in PAM.

- #1641: changed vertices to float64 in evenly_distributed_sphere_642.npz

- #1203: Some bots might need a newer version of nibabel

- #1156: Deterministic tracking workflow

- #642: WIP - NF parallel framework

- #1135: WIP : Multiprocessing - implemented a parallel_voxel_fit decorator

- #387: References do not render correctly in SHORE example

- #442: Allow length and set_number_of_points to work with generators

- #558: Allow setting of the zoom on fvtk ren objects

- #1236: bundle visualisation using nibabel API: wrong colormap

- #1389: VTK 8: minimal version?

- #1519: Scipy stopped supporting scipy.misc.imread

- #1596: Reproducibility in PFT tracking

- #1614: for GSoC NODDIx_PR

- #1576: [WIP] Needs Optimization and Cleaning

- #1564: Added scroll bar to ListBox2D

- #1636: Fixed broken link.

- #1584: Added Examples

- #1568: Multi_io axis out of bounds error

- #1554: Checking if the input file or directory exists when running a workflow

- #1528: Show spheres with different radii, colors and opacities + add timers + add exit a + resolve issue with imread

- #1108: Local PCA Slow Version

- #1526: Eigenvalue - eigenvector array compatibility check

- #1628: Adding python 3.7 on travis

- #1623: NF: Convert between 4D DEC FA and 3D 24 bit representation.

- #1622: [Fix] viz slice example

- #1629: [WIP][fix] remove Userwarning message

- #1591: PRE is failing : module ‘cvxpy’ has no attribute ‘utilities’

- #1626: RF - removed duplicate tests

- #1582: SF threshold in PMF is not relative

- #1575: Website: warning about python versions

- #1619: [DOC] update VTK version

- #1592: Added File Menu element to viz.ui

- #1559: Checkbox and RadioButton elements for viz.ui

- #1583: Fix the relative SF threshold Issue

- #1602: Fix random seed in tracking

- #1620: 3.7 wheels

- #1598: Apply Transform workflow for transforming a collection of moving images.

- #1595: Workflow for visualizing the quality of the registered data with DIPY

- #1581: Image registration Workflow with quality metrics

- #1588: Dipy.reconst.shm.calculate_max_order only works on specific cases.

- #1608: Parallelized affine registration

- #1610: Tortoise - sub

- #1607: Reminder to add in the docs that users will need to update nibabel to 2.3.0 during the next release

- #1609: [DOC] update dependencies file

- #1560: Removed affine matrices from tracking.

- #1593: Removed event.abort for release events

- #1586: Slider breaks interaction in viz_advanced example

- #1597: Upgrade nibabel minimum version

- #1601: Fix: Decrease Nosetest warning

- #1515: RF: Use the new Streamlines API for orienting of streamlines.

- #1585: Add a random seed for reproducibility

- #1594: Integrating the support for the visualization in Affine registration

- #1590: Revert 1570 file menu

- #1589: Fix calculation of highest order for a sh basis set

- #1577: Revert “Added File Menu element to viz.ui”

- #1571: WIP: multi-threaded on affine registration

- #1580: Allow PRE=1 job to fail

- #1533: Show message if number of arguments mismatch between the doc string and the run method.

- #1523: Showing help when no input parameters are given and suppress warnings for cmds

- #1579: Error on PRE=1 (cython / numpy)

- #1543: Update the default out_strategy to create the output in the current working directory

- #1433: New version of h5py messing with us?

- #1541: demon registration, unstable?

- #1574: Fixed Bug in PR #1547

- #1573: Failure in test_ui_listbox_2d

- #1561: add example SDR for binary and fuzzy images

- #1578: BF - bad condition in maximum dg

- #1566: Bad condition in local tracking

- #1570: Added File Menu element to viz.ui

- #1572: [WIP]

- #1567: WIP: NF: multi-threaded on affine registration

- #1563: Replacing major_version in viz.ui

- #1557: Range slider element for viz.ui

- #1547: Changed the icon set in Button2D from Dictionary to List of Tuples

- #1555: Fix bug in actor.label

- #1551: Actor.label not working anymore

- #1522: Image element in dipy.viz.ui

- #1549: CVXPY installation on >3.5

- #1355: WIP: ENH: UI Listbox

- #1562: Should we retire our Python 3.5 travis builds?

- #1550: Memory error when running rigid transform

- #1540: fix potential zero division in demon register.

- #1548: Fixed references per request of @garyfallidis.

- #1527: New version of CVXPY changes API

- #1542: fix for using cvxpy solver

- #1534: Changed the icon set in Button2D from Dictionary to List of Tuples

- #1546: References to reference

- #1545: Adding a reference in README.rst

- #1492: Enh ui components positioning (with code refactoring)

- #1538: Explanation that is mistakenly rendered as code fixed in example of DKI

- #1536: DOC: Update Rafael’s current institution.

- #1487: Commit for updated check_scratch.py script.

- #1486: Parichit dipy flows

- #1539: Changing the default behavior of the workflows to create the output file(s) in the current working directory.

- #1537: removed unnecessary imported from sims example

- #1535: removed some unnecessary imports from sims example

- #1530: Wrong default value for parameter ‘symmetric’ connectivity_matrix function

- #1529: minor typo fix in quickstart

- #1520: Updating the documentation for the workflow creation tutorial.

- #1524: Values from streamlines object

- #1521: Moved some older highlights and announcements to the old news files.

- #1518: DOC: updated some developers affiliations.

- #1517: Dev info update

- #1516: [DOC] Installation instruction update

- #1514: Adding pep8speak config file

- #1507: Mathematical expressions are not rendered correctly in reference page

- #1513: fix typo in example of quick_start

- #1510: copyright updated to 2008-2018

- #1508: Adds whitespace, to appease the sphinx.

- #1512: Fix typo in example of quick_start

- #1511: Fix typo in exaample quick_start

- #1509: DOC: fix math rendering for some dki functions

- #1506: moving to 0.15.0 dev