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 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.