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