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 #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
#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