Release notes for DIPY version 0.14#

GitHub stats for 2017/10/24 - 2018/05/01 (tag: 0.13.0)

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

The following 24 authors contributed 645 commits.

  • Ariel Rokem

  • Bago Amirbekian

  • Bennet Fauber

  • Conor Corbin

  • David Reagan

  • Eleftherios Garyfallidis

  • Gabriel Girard

  • Jean-Christophe Houde

  • Jiri Borovec

  • Jon Haitz Legarreta Gorroño

  • Jon Mendoza

  • Karandeep Singh Juneja

  • Kesshi Jordan

  • Kumar Ashutosh

  • Marc-Alexandre Côté

  • Matthew Brett

  • Nil Goyette

  • Pradeep Reddy Raamana

  • Ricci Woo

  • Serge Koudoro

  • Shreyas Fadnavis

  • Aman Arya

  • Mauro Zucchelli

We closed a total of 215 issues, 70 pull requests and 145 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (70):

  • PR #1504: Fix test_whole_brain_slr precision

  • PR #1503: fix plotting issue on Mapmri example

  • PR #1424: ENH: Use the CFIN dataset rather than the CENIR dataset.

  • PR #1502: [DOC] Fix doc generation

  • PR #1498: BF: fix bug in example of segment_quickbundles.py

  • PR #1431: NF - Bootstrap Direction Getter (cythonized)

  • PR #1443: RecoBundles - recognition of bundles

  • PR #1398: Deform streamlines

  • PR #1447: DOC: Link Coding Style Guide ref in CONTRIBUTING to the website.

  • PR #1423: DOC: Fix reconst_mapmri example markup.

  • PR #1493: Fix surface rendering bugs in VTK8

  • PR #1497: BF: fix bug in example of fiber_to_bundle_coherence.py

  • PR #1496: BF: fix bug in example of streamline_tools.py

  • PR #1495: BF: fix bug in example of sfm_reconst.py

  • PR #1494: BF: fix bug in example of reconst_csd.py

  • PR #1474: DOC: Fix typo on website & examples

  • PR #1471: Code Cleaning

  • PR #1457: Fix for “Sliders in examples don’t react properly to clicks”

  • PR #1491: Fix documentation typos

  • PR #1468: DOC: correct error when doing ‘make html’

  • PR #1484: DOC: Use the correct punctuation marks for et al..

  • PR #1475: Refactor demon registration - _iterate

  • PR #1482: DOC: Fix typo in test_mapmri.py file.

  • PR #1460: Fix for “DiskSlider does not rotate actor in opposite direction”

  • PR #1452: actor.slicer.copy() copies opacity set via actor.slicer.opacity()

  • PR #1466: DOC: Limit the DIPY logo height in README for better rendering.

  • PR #1464: DOC: Use the correct DIPY logo as the banner in README.

  • PR #1465: Fixed the Progit book link in doc

  • PR #1451: DOC: Add the DIPY banner to the README file.

  • PR #1379: New streamlines API integration on dipy examples

  • PR #1445: repr and get methods for AffineMap, w/ precise exceptions

  • PR #1450: [Fix] Manage multiple space delimiter

  • PR #1425: DOC: Add different GitHub badges to the README.rst file.

  • PR #1446: DOC: Fix bad hyperlink format to CONTRIBUTING.md from README.rst.

  • PR #1437: DOC: Fix missing reference to QuickBundles paper.

  • PR #1440: Raise Error when MDFmetric is used in QB or QBX

  • PR #1428: Mapmri workflow rebased

  • PR #1385: Enh textblock

  • PR #1422: [MRG] Improves delimiter in read_bvals_bvecs

  • PR #1434: QuickBundlesX

  • PR #1430: BF - replaced non-ascii character in workflows/reconst.py

  • PR #1421: DOC: Fix reStructuredText formatting issues in coding style guideline.

  • PR #1416: Updated links

  • PR #1413: BF::Fix inspect.getargspec deprecation warning in Python 3

  • PR #1393: Adds a DKI workflow.

  • PR #1294: Suppress a warning in geometry.

  • PR #1419: Suppress rcond warning

  • PR #1358: Det track workflow rebased (merge)

  • PR #1384: NF - Particle Filtering Tractography (merge)

  • PR #1411: Added eddy_rotated_bvecs extension

  • PR #1407: [MRG] Default colormap changed in examples

  • PR #1408: Updated color map in reconst_csa.py and reconst_forecast.py

  • PR #1406: [MRG] assert_true which checks for equality replaced with assert_equal

  • PR #1347: Replacing fvtk by the new viz API

  • PR #1322: Forecast

  • PR #1326: BUG: Fix factorial import module in test_mapmri.py.

  • PR #1400: BF: fixes #1399, removing an un-needed singleton dimension.

  • PR #1391: Re-entering conflict-free typos from deleted PR 1331

  • PR #1386: Possible fix for the inline compilation problem

  • PR #1165: Make vtk contour take an affine

  • PR #1300: RF: Remove patch for older numpy ravel_multi_index.

  • PR #1381: DOC - re-orientation of figures in the DKI example

  • PR #1375: Fix piesno type

  • PR #1342: Cythonize DirectionGetter and whatnot

  • PR #1378: Fix: numpy legacy print again…

  • PR #1377: FIX: update printing format for numpy 1.14

  • PR #1374: FIX: Viz test correction

  • PR #1368: DOC: Update developers’ affiliations.

  • PR #1370: TST - add tracking tests for PeaksAndMetricsDirectionGetter

  • PR #1369: MRG: add procedure for building, uploading wheels

Issues (145):

  • #1504: Fix test_whole_brain_slr precision

  • #1418: Adding parallel_voxel_fit decorator

  • #1503: fix plotting issue on Mapmri example

  • #1291: Existing MAPMRI tutorial does not render correctly and MAPL looks hidden in the existing tutorial.

  • #1424: ENH: Use the CFIN dataset rather than the CENIR dataset.

  • #1502: [DOC] Fix doc generation

  • #1498: BF: fix bug in example of segment_quickbundles.py

  • #1431: NF - Bootstrap Direction Getter (cythonized)

  • #1443: RecoBundles - recognition of bundles

  • #644: Dipy visualization: it does not seem possible to position tensor ellipsoid slice in fvtk

  • #1398: Deform streamlines

  • #1447: DOC: Link Coding Style Guide ref in CONTRIBUTING to the website.

  • #1423: DOC: Fix reconst_mapmri example markup.

  • #1493: Fix surface rendering bugs in VTK8

  • #1490: Streamtube visualization problem with vtk 8.1

  • #1469: Errors in generating documents (.rst) of examples

  • #1497: BF: fix bug in example of fiber_to_bundle_coherence.py

  • #1496: BF: fix bug in example of streamline_tools.py

  • #1495: BF: fix bug in example of sfm_reconst.py

  • #1494: BF: fix bug in example of reconst_csd.py

  • #1474: DOC: Fix typo on website & examples

  • #1485: BF: Fix bug in example of segment_quickbundles.py

  • #1483: BF: Fix bug in example of fiber_to_bundle_coherence.py

  • #1480: BF: Fix bug in example of streamline_tool.py

  • #1479: BF: Fix bug in example of sfm_reconst.py

  • #1477: BF: Fix bug in example of reconst_csd.py

  • #1448: Enh ui components positioning

  • #1471: Code Cleaning

  • #1481: BF: Fix bug of no attribute ‘GlobalImmediateModeRenderingOn’ in actor.py

  • #1454: Sliders in examples don’t react properly to clicks

  • #1457: Fix for “Sliders in examples don’t react properly to clicks”

  • #1491: Fix documentation typos

  • #1468: DOC: correct error when doing ‘make html’

  • #1467: Error on “from dipy.core.gradients import gradient_table”

  • #1488: Unexpected behavior in the DIPY workflow script

  • #1484: DOC: Use the correct punctuation marks for et al..

  • #1475: Refactor demon registration - _iterate

  • #1482: DOC: Fix typo in test_mapmri.py file.

  • #1478: DOC: Add comment about package CVXPY in example of reconst_mapmri.py

  • #1476: BF: Fix bug in example of reconst_csd.py

  • #1470: simplify SDR iterate

  • #1458: DiskSlider does not rotate actor in opposite direction

  • #1460: Fix for “DiskSlider does not rotate actor in opposite direction”

  • #1452: actor.slicer.copy() copies opacity set via actor.slicer.opacity()

  • #1438: actor.slicer.copy() doesn’t copy opacity if set via actor.slicer.opacity()

  • #1473: Uploading Windows wheels

  • #1466: DOC: Limit the DIPY logo height in README for better rendering.

  • #1472: Invalid dims failure in 32-bit Python on Windows

  • #1464: DOC: Use the correct DIPY logo as the banner in README.

  • #1462: Logo/banner on README not the correct one!

  • #1461: Broken link in Documentation: Git Resources

  • #1465: Fixed the Progit book link in doc

  • #1463: Fixed the Progit book link in the docs

  • #1455: Using pyautogui to adapt to users’ monitor size in viz examples

  • #1459: Fix for “DiskSlider does not rotate actor in opposite direction”

  • #1456: Fix for “Sliders in examples don’t react properly to clicks”

  • #1453: changed window.record() to a large value

  • #1451: DOC: Add the DIPY banner to the README file.

  • #1379: New streamlines API integration on dipy examples

  • #1339: Deprecate dipy.io.trackvis?

  • #1445: repr and get methods for AffineMap, w/ precise exceptions

  • #1441: Cleaning UI and improving positioning of Panel2D

  • #1450: [Fix] Manage multiple space delimiter

  • #1449: read_bvals_bvecs crash with bvec rotated eddy

  • #1425: DOC: Add different GitHub badges to the README.rst file.

  • #1446: DOC: Fix bad hyperlink format to CONTRIBUTING.md from README.rst.

  • #1437: DOC: Fix missing reference to QuickBundles paper.

  • #1371: Quickbundles tutorials miss reference

  • #1362: Make more use of TextBlock2D constructor

  • #1440: Raise Error when MDFmetric is used in QB or QBX

  • #1395: Mapmri workflow

  • #1428: Mapmri workflow rebased

  • #1385: Enh textblock

  • #1436: Fixed delimiter issue #1417

  • #1422: [MRG] Improves delimiter in read_bvals_bvecs

  • #1417: Improve delimiter on read_bvals_bvecs()

  • #1435: compilation failed with the new cython version (0.28)

  • #1439: BF: Avoid using memview in struct (Cython 0.28)

  • #1434: QuickBundlesX

  • #1184: Bootstrap direction getter

  • #1380: WIP: QuickBundlesX

  • #1429: BUG - SyntaxError (Non-ASCII character ‘xe2’ in file dipy/workflows/reconst.py on line 596

  • #1430: BF - replaced non-ascii character in workflows/reconst.py

  • #1421: DOC: Fix reStructuredText formatting issues in coding style guideline.

  • #1390: coding_style_guideline.rst does not render correctly

  • #1427: Add delimiter to read_bvals_bvecs()

  • #1426: Add delimiter parameter to numpy.loadtxt

  • #1416: Updated links

  • #987: Practical FAQs don’t have hyperlinks to modules/libraries.

  • #1327: Fix inspect.getargspec deprecation warning in Python 3

  • #1413: BF::Fix inspect.getargspec deprecation warning in Python 3

  • #1393: Adds a DKI workflow.

  • #1294: Suppress a warning in geometry.

  • #1181: peaks warning while CSD reconstructing

  • #1419: Suppress rcond warning

  • #1150: Line-based version of streamline_mapping

  • #1358: Det track workflow rebased (merge)

  • #1384: NF - Particle Filtering Tractography (merge)

  • #1409: create documentation in multiple languages

  • #1415: NF: check compiler flags before compiling

  • #1117: .eddy_rotated_bvecs file throws error from io.gradients read_bvals_bvecs function

  • #1411: Added eddy_rotated_bvecs extension

  • #1412: BF:Fix inspect.getargspec deprecation warning in Python 3

  • #791: Possible divide by zero in reconst.sfm.py

  • #1410: BF: Added .eddy_rotated_bvecs extension support

  • #1407: [MRG] Default colormap changed in examples

  • #1403: Avoid promoting jet color map in examples

  • #1408: Updated color map in reconst_csa.py and reconst_forecast.py

  • #1406: [MRG] assert_true which checks for equality replaced with assert_equal

  • #1387: Assert equality, instead of asserting that a == b is true

  • #1405: Error using CSD model on data

  • #1347: Replacing fvtk by the new viz API

  • #1402: [Question] rint() or round()

  • #1321: mapfit_laplacian_aniso (high non-Gaussianity, NG values in CSF)

  • #1161: fvtk volume doesn’t handle affine (crashes notebook)

  • #1394: Deprecation warning in newer versions of scipy, because scipy.misc is going away

  • #1382: is there any defined function that reads locally stored data or is all downloaded? I refer to nii or nifti files

  • #1322: Forecast

  • #1326: BUG: Fix factorial import module in test_mapmri.py.

  • #1399: New test errors on Python 3 Travis bots

  • #1400: BF: fixes #1399, removing an un-needed singleton dimension.

  • #1350: WIP: Add mapmri flow

  • #1392: Gitter chat box not visible on chrome?

  • #1391: Re-entering conflict-free typos from deleted PR 1331

  • #1331: Update gradients_spheres.py

  • #1388: Mapmri workflow

  • #1386: Possible fix for the inline compilation problem

  • #1165: Make vtk contour take an affine

  • #1340: NF - Particle Filtering Tractography

  • #1383: Mmriflow

  • #1299: test_rmi on 32 bit: invalid dims: array size defined by dims is larger than the maximum possible size.

  • #1300: RF: Remove patch for older numpy ravel_multi_index.

  • #1381: DOC - re-orientation of figures in the DKI example

  • #1301: Brains need re-orientation in plotting in DKI example

  • #1375: Fix piesno type

  • #1342: Cythonize DirectionGetter and whatnot

  • #1378: Fix: numpy legacy print again…

  • #1376: New test failures with pre-release numpy

  • #1377: FIX: update printing format for numpy 1.14

  • #1343: ActiveAx model fitting using MIX framework

  • #1374: FIX: Viz test correction

  • #1282: Tests fail on viz module

  • #1368: DOC: Update developers’ affiliations.

  • #1370: TST - add tracking tests for PeaksAndMetricsDirectionGetter

  • #1369: MRG: add procedure for building, uploading wheels