Release notes for dipy version 0.8ΒΆ

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 compliers do not have round in math.h, uisng 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 implemenation
  • #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.