Release notes for DIPY version 0.6#

GitHub stats for 2011/02/12 - 2013/03/20

The following 13 authors contributed 972 commits.

Ariel Rokem
Bago Amirbekian
Eleftherios Garyfallidis
Emanuele Olivetti
Ian Nimmo-Smith
Maria Luisa Mandelli
Matthew Brett
Maxime Descoteaux
Michael Paquette
Samuel St-Jean
Stefan van der Walt
Yaroslav Halchenko
endolith

We closed a total of 225 issues, 100 pull requests and 125 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (100):

PR #146: BF - allow Bootstrap Wrapper to work with markov tracking
PR #143: Garyfallidis tutorials 0.6
PR #145: Mdesco dti metrics
PR #141: Peak extraction isbi
PR #142: RF - always use theta and phi in that order, (not “phi, theta”)
PR #140: Sf2sh second try at correcting suggestions
PR #139: Spherical function to spherical harmonics and back
PR #138: Coding style fix for dsi_deconv
PR #137: BF - check shapes before allclose
PR #136: BF: add top-level benchmarking command
PR #135: Refactor local maxima
PR #134: BF - fix shm tests to accept antipodal directions as the same
PR #133: Corrected test for Deconvolution after the discrete direction finder was removed
PR #124: Remove direction finder
PR #77: Rework tracking
PR #132: A new fvtk function for visualizing fields of odfs
PR #131: Add missing files
PR #130: Implementation of DSI deconvolution from E.J. Canales-Rodriguez
PR #128: Colorfa
PR #129: RF - minor cleanup of pdf_odf code
PR #127: Adding multi-tensor simulation
PR #126: Improve local maxima
PR #122: Removed calculation of gfa and other functions from inside the odf(sphere) of DSI and GQI
PR #103: Major update of the website, with a few examples and with some additional minor RFs
PR #121: NF: Allow the smoothing parameter to come through to rbf interpolation.
PR #120: Fast squash fix
PR #116: RF: common dtype for squash without result_type
PR #117: Fix directions on TensorFit and add getitem
PR #119: RF: raise errors for Python version dependencies
PR #118: Separate fa
PR #111: RF - clean up _squash in multi_voxel and related code
PR #112: RF: fix vec_val_vect logic, generalize for shape
PR #114: BF: fix face and edge byte order for sphere load
PR #109: Faster einsum
PR #110: TST: This is only almost equal on XP, for some reason.
PR #108: TST + STY: Use and assert_equal so that we get more information upon failure
PR #107: RF: A.dot(B) => np.dot(A, B) for numpy < 1.5
PR #102: BF - Allow ndindex to work with older numpy than 1.6.
PR #106: RF: allow optional scipy.spatial.Delaunay
PR #105: Skip doctest decorator
PR #104: RF: remove deprecated old parametric testing
PR #101: WIP: Fix isnan windows
PR #100: Small stuff
PR #94: Multivoxel dsi and gqi are back!
PR #96: ENH: Implement masking for the new TensorModel implementation.
PR #95: NF fetch publicly available datasets
PR #26: Noise
PR #84: Non linear peak finding
PR #82: DTI new api
PR #91: Shm new api
PR #88: NF - wrapper function for multi voxel models
PR #86: DOC: Fixed some typos, etc in the FAQ
PR #90: A simpler ndindex using generators.
PR #87: RF - Provide shape as argument to ndindex.
PR #85: Add fast ndindex.
PR #81: RF - fixup peaks_from_model to take use remove_similar_vertices and
PR #79: BF: Fixed projection plots.
PR #80: RF - remove some old functions tools
PR #71: ENH: Make the internals of the io module visible on tab completion in ip…
PR #76: Yay, more gradient stuff
PR #75: Rename L2norm to vector_norm
PR #74: Gradient rf
PR #73: RF/BF - removed duplicate vector_norm/L2norm
PR #72: Mr bago model api
PR #68: DSI seems working again - Have a look
PR #65: RF: Make the docstring and call consistent with scipy.interpolate.Rbf.
PR #61: RF - Refactor direction finding.
PR #60: NF - Add key-value cache for use in models.
PR #63: TST - Disable reconstruction methods that break the test suite.
PR #62: BF - Fix missing import in peak finding tests.
PR #37: cleanup references in the code to E1381S6_edcor* (these were removed from…
PR #55: Ravel multi index
PR #58: TST - skip doctest when matplotlib is not available
PR #59: optional_traits is not needed anymore
PR #56: TST: Following change to API in dipy.segment.quickbundles.
PR #52: Matplotlib optional
PR #50: NF - added subdivide method to sphere
PR #51: Fix tracking utils
PR #48: BF - Brought back _filter peaks and associated test.
PR #47: RF - Removed reduce_antipodal from sphere.
PR #41: NF - Add radial basis function interpolation on the sphere.
PR #39: GradientTable
PR #40: BF - Fix axis specification in sph_project.
PR #28: Odf+shm api update
PR #36: Nf hemisphere preview
PR #34: RF - replace _filter_peaks with unique_vertices
PR #35: BF - Fix imports from dipy.core.sphere.
PR #21: Viz 2d
PR #32: NF - Sphere class.
PR #30: RF: Don’t import all this every time.
PR #24: TST: Fixing tests in reconst module.
PR #27: DOC - Add reference to white matter diffusion values.
PR #25: NF - Add prolate white matter as defaults for multi-tensor signal sim.
PR #22: Updating my fork with the nipy master
PR #20: RF - create OptionalImportError for traits imports
PR #19: DOC: add comments and example to commit codes
PR #18: DOC: update gitwash from source
PR #17: Optional traits
PR #14: DOC - fix frontpage example
PR #12: BF(?): cart2sphere and sphere2cart are now invertible.
PR #11: BF explicit type declaration and initialization for longest_track_len[AB] – for cython 0.15 compatibility

Issues (125):

#99: RF - Separate direction finder from model fit.
#143: Garyfallidis tutorials 0.6
#144: DTI metrics
#145: Mdesco dti metrics
#123: Web content and examples for 0.6
#141: Peak extraction isbi
#142: RF - always use theta and phi in that order, (not “phi, theta”)
#140: Sf2sh second try at correcting suggestions
#139: Spherical function to spherical harmonics and back
#23: qball not properly import-able
#29: Don’t import everything when you import dipy
#138: Coding style fix for dsi_deconv
#137: BF - check shapes before allclose
#136: BF: add top-level benchmarking command
#135: Refactor local maxima
#134: BF - fix shm tests to accept antipodal directions as the same
#133: Corrected test for Deconvolution after the discrete direction finder was removed
#124: Remove direction finder
#77: Rework tracking
#132: A new fvtk function for visualizing fields of odfs
#125: BF: Remove ‘mayavi’ directory, to avoid triggering mayavi import warning…
#131: Add missing files
#130: Implementation of DSI deconvolution from E.J. Canales-Rodriguez
#128: Colorfa
#129: RF - minor cleanup of pdf_odf code
#127: Adding multi-tensor simulation
#126: Improve local maxima
#97: BF - separate out storing of fit values in gqi
#122: Removed calculation of gfa and other functions from inside the odf(sphere) of DSI and GQI
#103: Major update of the website, with a few examples and with some additional minor RFs
#121: NF: Allow the smoothing parameter to come through to rbf interpolation.
#120: Fast squash fix
#116: RF: common dtype for squash without result_type
#117: Fix directions on TensorFit and add getitem
#119: RF: raise errors for Python version dependencies
#118: Separate fa
#113: RF - use min_diffusivity relative to 1 / max(bval)
#111: RF - clean up _squash in multi_voxel and related code
#112: RF: fix vec_val_vect logic, generalize for shape
#114: BF: fix face and edge byte order for sphere load
#109: Faster einsum
#110: TST: This is only almost equal on XP, for some reason.
#98: This is an update of PR #94 mostly typos and coding style
#108: TST + STY: Use and assert_equal so that we get more information upon failure
#107: RF: A.dot(B) => np.dot(A, B) for numpy < 1.5
#102: BF - Allow ndindex to work with older numpy than 1.6.
#106: RF: allow optional scipy.spatial.Delaunay
#105: Skip doctest decorator
#104: RF: remove deprecated old parametric testing
#101: WIP: Fix isnan windows
#100: Small stuff
#94: Multivoxel dsi and gqi are back!
#96: ENH: Implement masking for the new TensorModel implementation.
#95: NF fetch publicly available datasets
#26: Noise
#84: Non linear peak finding
#82: DTI new api
#91: Shm new api
#88: NF - wrapper function for multi voxel models
#86: DOC: Fixed some typos, etc in the FAQ
#89: Consistent ndindex behaviour
#90: A simpler ndindex using generators.
#87: RF - Provide shape as argument to ndindex.
#85: Add fast ndindex.
#81: RF - fixup peaks_from_model to take use remove_similar_vertices and
#83: Non linear peak finding
#78: This PR replaces PR 70
#79: BF: Fixed projection plots.
#80: RF - remove some old functions tools
#70: New api dti
#71: ENH: Make the internals of the io module visible on tab completion in ip…
#76: Yay, more gradient stuff
#69: New api and tracking refacotor
#75: Rename L2norm to vector_norm
#74: Gradient rf
#73: RF/BF - removed duplicate vector_norm/L2norm
#72: Mr bago model api
#66: DOCS - docs for model api
#49: Reworking tracking code.
#68: DSI seems working again - Have a look
#65: RF: Make the docstring and call consistent with scipy.interpolate.Rbf.
#61: RF - Refactor direction finding.
#60: NF - Add key-value cache for use in models.
#63: TST - Disable reconstruction methods that break the test suite.
#62: BF - Fix missing import in peak finding tests.
#37: cleanup references in the code to E1381S6_edcor* (these were removed from…
#55: Ravel multi index
#46: BF: Trying to fix test failures.
#57: TST: Reverted back to optional definition of the function to make TB hap…
#58: TST - skip doctest when matplotlib is not available
#59: optional_traits is not needed anymore
#56: TST: Following change to API in dipy.segment.quickbundles.
#52: Matplotlib optional
#50: NF - added subdivide method to sphere
#51: Fix tracking utils
#48: BF - Brought back _filter peaks and associated test.
#47: RF - Removed reduce_antipodal from sphere.
#41: NF - Add radial basis function interpolation on the sphere.
#33: Gradients Table class
#39: GradientTable
#45: BF - Fix sphere creation in triangle_subdivide.
#38: Subdivide octahedron
#40: BF - Fix axis specification in sph_project.
#28: Odf+shm api update
#36: Nf hemisphere preview
#34: RF - replace _filter_peaks with unique_vertices
#35: BF - Fix imports from dipy.core.sphere.
#21: Viz 2d
#32: NF - Sphere class.
#30: RF: Don’t import all this every time.
#24: TST: Fixing tests in reconst module.
#27: DOC - Add reference to white matter diffusion values.
#25: NF - Add prolate white matter as defaults for multi-tensor signal sim.
#22: Updating my fork with the nipy master
#20: RF - create OptionalImportError for traits imports
#8: X error BadRequest with fvtk.show
#19: DOC: add comments and example to commit codes
#18: DOC: update gitwash from source
#17: Optional traits
#15: Octahedron in dipy.core.triangle_subdivide has wrong faces
#14: DOC - fix frontpage example
#12: BF(?): cart2sphere and sphere2cart are now invertible.
#11: BF explicit type declaration and initialization for longest_track_len[AB] – for cython 0.15 compatibility
#5: Add DSI reconstruction in Dipy
#9: Bug in dipy.tracking.metrics.downsampling when we downsample a track to more than 20 points