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