Release notes for DIPY version 0.6ΒΆ

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: Seperate 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 refrences 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: Seperate 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: Consisten 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 refrences 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