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 worflows 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 regist.
  • 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 unncessary importd 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 oustide 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 worflows 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 metrices
  • #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 regist.
  • #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 unncessary importd 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