# 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.