Release notes for DIPY version 0.8#

GitHub stats for 2013/12/24 - 2014/12/26 (tag: 0.7.0)

The following 19 authors contributed 1176 commits.

  • Andrew Lawrence

  • Ariel Rokem

  • Bago Amirbekian

  • Demian Wassermann

  • Eleftherios Garyfallidis

  • Gabriel Girard

  • Gregory R. Lee

  • Jean-Christophe Houde

  • Kesshi jordan

  • Marc-Alexandre Cote

  • Matthew Brett

  • Matthias Ekman

  • Matthieu Dumont

  • Mauro Zucchelli

  • Maxime Descoteaux

  • Michael Paquette

  • Omar Ocegueda

  • Samuel St-Jean

  • Stefan van der Walt

We closed a total of 388 issues, 155 pull requests and 233 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (155):

  • PR #544: Refactor propspeed - updated

  • PR #543: MRG: update to plot_2d fixes and tests

  • PR #537: NF: add requirements.txt file

  • PR #534: BF: removed ftmp variable

  • PR #536: Update Changelog

  • PR #535: Happy New Year PR!

  • PR #531: BF: extend pip timeout to reduce install failures

  • PR #527: Remove npymath library from cython extensions

  • PR #528: MRG: move conditional compiling to C

  • PR #530: BF: work round ugly MSVC manifest bug

  • PR #529: MRG: a couple of small cleanup fixes

  • PR #526: Readme.rst and info.py update about the license

  • PR #525: Added shore gpl warning in the readme

  • PR #524: Replaced DiPy with DIPY in readme.rst and info.py

  • PR #523: RF: copy includes list for extensions

  • PR #522: DOC: Web-site release notes, and some updates on front page.

  • PR #521: Life bots

  • PR #520: Relaxing precision for win32

  • PR #519: Christmas PR! Correcting typos, linking and language for max odf tracking

  • PR #513: BF + TST: Reinstated eig_from_lo_tri

  • PR #508: Tests for reslicing

  • PR #515: TST: Increasing testing on life.

  • PR #516: TST: Reduce sensitivity on these tests.

  • PR #495: NF - Deterministic Maximum Direction Getter

  • PR #514: Website update

  • PR #510: BF: another fvtk 5 to 6 incompatibility

  • PR #509: DOC: Small fixes in documentation.

  • PR #497: New sphere for ODF reconstruction

  • PR #460: Sparse Fascicle Model

  • PR #499: DOC: Warn about the GPL license of SHORE.

  • PR #491: RF - Make peaks_from_model part of dipy.direction

  • PR #501: TST: Test for both data with and w/0 b0.

  • PR #507: BF - use different sort method to avoid mergsort for older numpy.

  • PR #504: Bug fix float overflow in estimate_sigma

  • PR #494: Fix round

  • PR #503: Fixed compatibility issues between vtk 5 and 6

  • PR #498: DTI min_signal

  • PR #471: Use importlib instead of __import__

  • PR #419: LiFE

  • PR #489: Fix diffeomorphic registration test failures

  • PR #484: Clear tabs from examples for website

  • PR #490: DOC: corrected typos in the tracking PR

  • PR #341: Traco Redesign

  • PR #483: NF: Find the closest vertex on a sphere for an input vector.

  • PR #488: BF: fix travis version setting

  • PR #485: RF: deleted unused files

  • PR #482: Skipping tests for different versions of Scipy for optimize.py

  • PR #480: Enhance SLR to allow for series of registrations

  • PR #479: Report on coverage for old scipy.

  • PR #481: BF - make examples was confusing files with similar names, fixed

  • PR #476: Fix optimize defaults for older scipy versions for L-BFGS-B

  • PR #478: TST: Increase the timeout on the Travis pip install

  • PR #477: MAINT+TST: update minimum nibabel dependency

  • PR #474: RF: switch travis tests to use virtualenvs

  • PR #473: TST: Make Travis provide verbose test outputs.

  • PR #472: ENH: GradientTable now calculates qvalues

  • PR #469: Fix evolution save win32

  • PR #463: DOC: update RESTORE tutorial to use new noise estimation technique

  • PR #466: BF: cannot quote command for Windows

  • PR #465: BF: increased SCIPY version definition flag to 0.12

  • PR #462: BF: fix writing history to file in Python 3

  • PR #433: Added local variance estimation

  • PR #458: DOC: docstring fixes in dipy/align/crosscorr.pyx

  • PR #448: BF: fix link to npy_math function

  • PR #447: BF: supposed fix for the gh-439, but still unable to reproduce OP.

  • PR #443: Fix buildbots errors introduced with the registration module

  • PR #456: MRG: relax threshold for failing test + cleanup

  • PR #454: DOC: fix docstring for compile-time checker

  • PR #453: BF: refactor conditional compiling again

  • PR #446: Streamline-based Linear Registration

  • PR #445: NF: generate config.pxi file with Cython DEF vars

  • PR #440: DOC - add info on how to change default tempdir (multiprocessing).

  • PR #431: Change the writeable flag back to its original state when finished.

  • PR #408: Symmetric diffeomorphic non-linear registration

  • PR #438: Missing a blank line in examples/tracking_quick_start.py

  • PR #405: fixed frozen windows executable issue

  • PR #418: RF: move script running code into own module

  • PR #437: Update Cython download URL

  • PR #435: BF: replaced non-ascii character in dipy.reconst.dti line 956

  • PR #434: DOC: References for the DTI ODF calculation.

  • PR #430: Revert “Support read-only numpy array.”

  • PR #427: Support read-only numpy array.

  • PR #421: Fix nans in gfa

  • PR #422: BF: Use the short version to verify scipy version.

  • PR #415: RF - move around some of the predict stuff

  • PR #420: Rename README.txt to README.rst

  • PR #413: Faster spherical harmonics

  • PR #416: Removed memory_leak unittest in test_strealine.py

  • PR #417: Fix streamlinespeed tests

  • PR #411: Fix memory leak in cython functions length and set_number_of_points

  • PR #409: minor corrections to pipe function

  • PR #396: TST : this is not exactly equal on some platforms.

  • PR #407: BF: fixed problem with NANs in odfdeconv

  • PR #406: Revert “Merge pull request #346 from omarocegueda/syn_registration”

  • PR #402: Fix AE test error in test_peak_directions_thorough

  • PR #403: Added mask shape check in tenfit

  • PR #346: Symmetric diffeomorphic non-linear registration

  • PR #401: BF: fix skiptest invocation for missing mpl

  • PR #340: CSD fit issue

  • PR #397: BF: fix import statement for get_cmap

  • PR #393: RF: update Cython dependency

  • PR #382: Cythonized version of streamlines’ resample() and length() functions.

  • PR #386: DOC: Small fix in the xval example.

  • PR #335: Xval

  • PR #352: Fix utils docs and affine

  • PR #384: odf_sh_sharpening function fix and new test

  • PR #374: MRG: bumpy numpy requirement to 1.5 / compat fixes

  • PR #380: DOC: Update a few Dipy links to link to the correct repo

  • PR #378: Fvtk cleanup

  • PR #379: fixed typos in shm.py

  • PR #339: FVTK small improvement: Arbitrary matplotlib colormaps can be used to color spherical functions

  • PR #373: Fixed discrepancies between doc and code

  • PR #371: RF: don’t use -fopenmp flag if it doesn’t work

  • PR #372: BF: set integer type for crossplatform compilation

  • PR #337: Piesno

  • PR #370: Tone down the front page a bit.

  • PR #364: Add the mode param for border management.

  • PR #368: New banner for website

  • PR #367: MRG: refactor API generation for sharing

  • PR #363: RF: make cvxopt optional for tests

  • PR #362: Changes to fix issue #361: matrix sizing in tracking.utils.connectivity_matrix

  • PR #360: Added missing :math:` sign

  • PR #355: DOC: Updated API change document to add target function change

  • PR #357: Changed the logo to full black as the one that I sent as suggestion for HBM and ISMRM

  • PR #356: Auto-generate API docs

  • PR #349: Added api changes file to track breaks of backwards compatibility

  • PR #348: Website update

  • PR #347: DOC: Updating citations

  • PR #345: TST: Make travis look at test coverage.

  • PR #338: Add positivity constraint on the propagator

  • PR #334: Fix vec2vec

  • PR #324: Constrained optimisation for SHORE to set E(0)=1 when the CVXOPT package is available

  • PR #320: Denoising images using non-local means

  • PR #331: DOC: correct number of seeds in streamline_tools example

  • PR #326: Fix brain extraction example

  • PR #327: add small and big delta

  • PR #323: Shore pdf grid speed improvement

  • PR #319: DOC: Updated the highlights to promote the release and the upcoming paper

  • PR #318: Corrected some rendering problems with the installation instructions

  • PR #317: BF: more problems with path quoting in windows

  • PR #316: MRG: more fixes for windows script tests

  • PR #315: BF: EuDX odf_vertices param has no default value

  • PR #305: DOC: Some more details in installation instructions.

  • PR #314: BF - callable response does not work

  • PR #311: Bf seeds from mask

  • PR #309: MRG: Windows test fixes

  • PR #308: typos + pep stuf

  • PR #303: BF: try and fix nibabel setup requirement

  • PR #304: Update README.txt

  • PR #302: Time for 0.8.0.dev!

  • PR #299: BF: Put back utils.length.

  • PR #301: Updated info.py and copyright year

  • PR #300: Bf fetcher bug on windows

  • PR #298: TST - rework tests so that we do not need to download any data

  • PR #290: DOC: Started generating 0.7 release notes.

Issues (233):

  • #544: Refactor propspeed - updated

  • #540: MRG: refactor propspeed

  • #542: TST: Testing regtools

  • #543: MRG: update to plot_2d fixes and tests

  • #541: BUG: plot_2d_diffeomorphic_map

  • #439: ValueError in RESTORE

  • #538: WIP: TEST: relaxed precision

  • #449: local variable ‘ftmp’ referenced before assignment

  • #537: NF: add requirements.txt file

  • #534: BF: removed ftmp variable

  • #536: Update Changelog

  • #535: Happy New Year PR!

  • #512: reconst.dti.eig_from_lo_tri

  • #467: Optimize failure on Windows

  • #464: Diffeomorphic registration test failures on PPC

  • #531: BF: extend pip timeout to reduce install failures

  • #527: Remove npymath library from cython extensions

  • #528: MRG: move conditional compiling to C

  • #530: BF: work round ugly MSVC manifest bug

  • #529: MRG: a couple of small cleanup fixes

  • #526: Readme.rst and info.py update about the license

  • #525: Added shore gpl warning in the readme

  • #524: Replaced DiPy with DIPY in readme.rst and info.py

  • #523: RF: copy includes list for extensions

  • #522: DOC: Web-site release notes, and some updates on front page.

  • #521: Life bots

  • #520: Relaxing precision for win32

  • #519: Christmas PR! Correcting typos, linking and language for max odf tracking

  • #513: BF + TST: Reinstated eig_from_lo_tri

  • #508: Tests for reslicing

  • #515: TST: Increasing testing on life.

  • #516: TST: Reduce sensitivity on these tests.

  • #495: NF - Deterministic Maximum Direction Getter

  • #514: Website update

  • #510: BF: another fvtk 5 to 6 incompatibility

  • #511: Error estimating tensors on hcp dataset

  • #509: DOC: Small fixes in documentation.

  • #497: New sphere for ODF reconstruction

  • #460: Sparse Fascicle Model

  • #499: DOC: Warn about the GPL license of SHORE.

  • #491: RF - Make peaks_from_model part of dipy.direction

  • #501: TST: Test for both data with and w/0 b0.

  • #507: BF - use different sort method to avoid mergsort for older numpy.

  • #505: stable/wheezy debian – ar.argsort(kind=’mergesort’) causes TypeError: requested sort not available for type (

  • #506: RF: Use integer datatype for unique_rows sorting.

  • #504: Bug fix float overflow in estimate_sigma

  • #399: Multiprocessing runtime error in Windows 64 bit

  • #383: typo in multi tensor fit example

  • #350: typo in SNR example

  • #424: test more python versions with travis

  • #493: BF - older C compilers do not have round in math.h, using dpy_math instead

  • #494: Fix round

  • #503: Fixed compatibility issues between vtk 5 and 6

  • #500: SHORE hyp2F1

  • #502: Fix record vtk6

  • #498: DTI min_signal

  • #496: Revert “BF: supposed fix for the gh-439, but still unable to reproduce O…

  • #492: TST - new DTI test to help develop min_signal handling

  • #471: Use importlib instead of __import__

  • #419: LiFE

  • #489: Fix diffeomorphic registration test failures

  • #484: Clear tabs from examples for website

  • #490: DOC: corrected typos in the tracking PR

  • #341: Traco Redesign

  • #410: Faster spherical harmonics implementation

  • #483: NF: Find the closest vertex on a sphere for an input vector.

  • #487: Travis Problem

  • #488: BF: fix travis version setting

  • #485: RF: deleted unused files

  • #486: cvxopt is gpl licensed

  • #482: Skipping tests for different versions of Scipy for optimize.py

  • #480: Enhance SLR to allow for series of registrations

  • #479: Report on coverage for old scipy.

  • #481: BF - make examples was confusing files with similar names, fixed

  • #428: WIP: refactor travis building

  • #429: WIP: Refactor travising

  • #476: Fix optimize defaults for older scipy versions for L-BFGS-B

  • #478: TST: Increase the timeout on the Travis pip install

  • #477: MAINT+TST: update minimum nibabel dependency

  • #475: Does the optimizer still need tmp_files?

  • #474: RF: switch travis tests to use virtualenvs

  • #473: TST: Make Travis provide verbose test outputs.

  • #470: Enhance SLR with applying series of transformations and fix optimize bug for parameter missing in old scipy versions

  • #472: ENH: GradientTable now calculates qvalues

  • #469: Fix evolution save win32

  • #463: DOC: update RESTORE tutorial to use new noise estimation technique

  • #466: BF: cannot quote command for Windows

  • #461: Buildbot failures with missing ‘nit’ key in dipy.core.optimize

  • #465: BF: increased SCIPY version definition flag to 0.12

  • #462: BF: fix writing history to file in Python 3

  • #433: Added local variance estimation

  • #432: auto estimate the standard deviation globally for nlmeans

  • #451: Warning for DTI normalization

  • #458: DOC: docstring fixes in dipy/align/crosscorr.pyx

  • #448: BF: fix link to npy_math function

  • #447: BF: supposed fix for the gh-439, but still unable to reproduce OP.

  • #443: Fix buildbots errors introduced with the registration module

  • #456: MRG: relax threshold for failing test + cleanup

  • #455: Test failure on master

  • #454: DOC: fix docstring for compile-time checker

  • #450: Find if replacing matrix44 from streamlinear with compose_matrix from dipy.core.geometry is a good idea

  • #453: BF: refactor conditional compiling again

  • #446: Streamline-based Linear Registration

  • #452: Replace raise by auto normalization when creating a gradient table with un-normalized bvecs.

  • #398: assert AE < 2. failure in test_peak_directions_thorough

  • #444: heads up - MKL error in parallel mode

  • #445: NF: generate config.pxi file with Cython DEF vars

  • #440: DOC - add info on how to change default tempdir (multiprocessing).

  • #431: Change the writeable flag back to its original state when finished.

  • #408: Symmetric diffeomorphic non-linear registration

  • #333: Bundle alignment

  • #438: Missing a blank line in examples/tracking_quick_start.py

  • #426: nlmeans_3d breaks with mask=None

  • #405: fixed frozen windows executable issue

  • #418: RF: move script running code into own module

  • #437: Update Cython download URL

  • #435: BF: replaced non-ascii character in dipy.reconst.dti line 956

  • #434: DOC: References for the DTI ODF calculation.

  • #425: NF added class to save streamlines in vtk format

  • #430: Revert “Support read-only numpy array.”

  • #427: Support read-only numpy array.

  • #421: Fix nans in gfa

  • #422: BF: Use the short version to verify scipy version.

  • #415: RF - move around some of the predict stuff

  • #420: Rename README.txt to README.rst

  • #413: Faster spherical harmonics

  • #416: Removed memory_leak unittest in test_strealine.py

  • #417: Fix streamlinespeed tests

  • #411: Fix memory leak in cython functions length and set_number_of_points

  • #412: Use simple multiplication instead exponentiation and pow

  • #409: minor corrections to pipe function

  • #396: TST : this is not exactly equal on some platforms.

  • #407: BF: fixed problem with NANs in odfdeconv

  • #406: Revert “Merge pull request #346 from omarocegueda/syn_registration”

  • #402: Fix AE test error in test_peak_directions_thorough

  • #403: Added mask shape check in tenfit

  • #346: Symmetric diffeomorphic non-linear registration

  • #401: BF: fix skiptest invocation for missing mpl

  • #340: CSD fit issue

  • #397: BF: fix import statement for get_cmap

  • #393: RF: update Cython dependency

  • #391: memory usage: 16GB wasn’t sufficient

  • #382: Cythonized version of streamlines’ resample() and length() functions.

  • #386: DOC: Small fix in the xval example.

  • #385: cross_validation example doesn’t render properly

  • #335: Xval

  • #352: Fix utils docs and affine

  • #384: odf_sh_sharpening function fix and new test

  • #374: MRG: bumpy numpy requirement to 1.5 / compat fixes

  • #381: Bago fix utils docs and affine

  • #380: DOC: Update a few Dipy links to link to the correct repo

  • #378: Fvtk cleanup

  • #379: fixed typos in shm.py

  • #376: BF: Adjust the dimensionality of the peak_values, if provided.

  • #377: Demianw fvtk colormap

  • #339: FVTK small improvement: Arbitrary matplotlib colormaps can be used to color spherical functions

  • #373: Fixed discrepancies between doc and code

  • #371: RF: don’t use -fopenmp flag if it doesn’t work

  • #372: BF: set integer type for crossplatform compilation

  • #337: Piesno

  • #370: Tone down the front page a bit.

  • #364: Add the mode param for border management.

  • #368: New banner for website

  • #367: MRG: refactor API generation for sharing

  • #359: cvxopt dependency

  • #363: RF: make cvxopt optional for tests

  • #361: Matrix size wrong for tracking.utils.connectivity_matrix

  • #362: Changes to fix issue #361: matrix sizing in tracking.utils.connectivity_matrix

  • #360: Added missing ` sign

  • #358: typo in doc

  • #355: DOC: Updated API change document to add target function change

  • #357: Changed the logo to full black as the one that I sent as suggestion for HBM and ISMRM

  • #356: Auto-generate API docs

  • #349: Added api changes file to track breaks of backwards compatibility

  • #348: Website update

  • #347: DOC: Updating citations

  • #345: TST: Make travis look at test coverage.

  • #338: Add positivity constraint on the propagator

  • #334: Fix vec2vec

  • #343: Please Ignore this PR!

  • #324: Constrained optimisation for SHORE to set E(0)=1 when the CVXOPT package is available

  • #277: WIP: PIESNO framework for estimating the underlying std of the gaussian distribution

  • #336: Demianw shore e0 constrained

  • #235: WIP: Cross-validation

  • #329: WIP: Fix vec2vec

  • #320: Denoising images using non-local means

  • #331: DOC: correct number of seeds in streamline_tools example

  • #330: DOC: number of seeds per voxel, inconsistent documentation?

  • #326: Fix brain extraction example

  • #327: add small and big delta

  • #323: Shore pdf grid speed improvement

  • #319: DOC: Updated the highlights to promote the release and the upcoming paper

  • #318: Corrected some rendering problems with the installation instructions

  • #317: BF: more problems with path quoting in windows

  • #316: MRG: more fixes for windows script tests

  • #315: BF: EuDX odf_vertices param has no default value

  • #312: Sphere and default used through the code

  • #305: DOC: Some more details in installation instructions.

  • #314: BF - callable response does not work

  • #16: quickie: ‘from raw data to tractographies’ documentation implies dipy can’t do anything with nonisotropic voxel sizes

  • #311: Bf seeds from mask

  • #307: Streamline_tools example stops working when I change density from 1 to 2

  • #241: Wrong normalization in peaks_from_model

  • #248: Clarify dsi example

  • #220: Add ndindex to peaks_from_model

  • #253: Parallel peaksFromModel timing out on buildbot

  • #256: writing data to /tmp peaks_from_model

  • #278: tenmodel.bvec, not existing anymore?

  • #282: fvtk documentation is incomprehensible

  • #228: buildbot error in mask.py

  • #197: DOC: some docstrings are not rendered correctly

  • #181: OPT: Change dipy.core.sphere_stats.random_uniform_on_sphere

  • #177: Extension test in dipy_fit_tensor seems brittle

  • #171: Fix auto_attrs

  • #31: Plotting in test suite

  • #42: RuntimeWarning in dti.py

  • #43: Problems with edges and faces in create_half_unit_sphere

  • #53: Is ravel_multi_index a new thing?

  • #64: Fix examples that rely on old API and removed data-sets

  • #67: viz.projections.sph_projection is broken

  • #92: dti.fa division by 0 warning in tests

  • #306: Tests fail after windows 32 bit installation and running import dipy; dipy.test()

  • #310: Windows test failure for tracking test_rmi

  • #309: MRG: Windows test fixes

  • #308: typos + pep stuf

  • #303: BF: try and fix nibabel setup requirement

  • #304: Update README.txt

  • #302: Time for 0.8.0.dev!

  • #299: BF: Put back utils.length.

  • #301: Updated info.py and copyright year

  • #300: Bf fetcher bug on windows

  • #298: TST - rework tests so that we do not need to download any data

  • #290: DOC: Started generating 0.7 release notes.