# 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