# 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