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