Release notes for Dipy version 0.10

GitHub stats for 2015/03/18 - 2015/11/19 (tag: 0.9.2)

These lists are automatically generated, and may be incomplete or contain duplicates.

The following 20 authors (alphabetically ordered) contributed 1022 commits:

  • Alexandre Gauvin
  • Ariel Rokem
  • Bago Amirbekian
  • David Qixiang Chen
  • Dimitris Rozakis
  • Eleftherios Garyfallidis
  • Gabriel Girard
  • Gonzalo Sanguinetti
  • Jean-Christophe Houde
  • Marc-Alexandre Côté
  • Matthew Brett
  • Mauro Zucchelli
  • Maxime Descoteaux
  • Michael Paquette
  • Omar Ocegueda
  • Oscar Esteban
  • Rafael Neto Henriques
  • Rohan Prinja
  • Samuel St-Jean
  • Stefan van der Walt

We closed a total of 232 issues, 94 pull requests and 138 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (94):

  • PR #769: RF: Remove aniso2iso altogether.
  • PR #772: DOC: Use xvfb when building the docs in a headless machine.
  • PR #754: DOC: Should we add a side-car gitter chat to the website?
  • PR #753: TST: Test DSI with b0s.
  • PR #767: Offscreen is False for test_slicer
  • PR #768: Document dipy.reconst.dti.iter_fit_tensor params
  • PR #766: Add fit_tensor iteration decorator
  • PR #751: Reorient tracks according to ROI
  • PR #765: BF: Typo in data file name.
  • PR #757: Optimize dipy.align.reslice
  • PR #587: Fvtk 2.0 PR1
  • PR #749: Fixed deprecation warning in skimage
  • PR #748: TST: added test for _to_voxel_tolerance.
  • PR #678: BF: added tolerance for negative streamline coordinates checks
  • PR #714: RF: use masks in predictions and cross-validation
  • PR #739: Set number of OpenMP threads during runtime
  • PR #733: Add RTOP, RTAP and RTPP and the relative test
  • PR #743: BF: memleaks with typed memory views in Cython
  • PR #724: @sinkpoint’s power map - refactored
  • PR #741: ENH: it is preferable to use choice rather than randint to not have
  • PR #727: Optimize tensor fitting
  • PR #726: NF - CSD response from a mask
  • PR #729: BF: tensor predict
  • PR #736: Added installation of python-tk package for VTK travis bot
  • PR #735: Added comment on nlmeans example about selecting one volume
  • PR #732: WIP: Test with vtk on Travis
  • PR #731: Np 1.10
  • PR #640: MAPMRI
  • PR #682: Created list of examples for available features and metrics
  • PR #716: Refactor data module
  • PR #699: Added gaussian noise option to estimate_sigma
  • PR #712: DOC: API changes in gh707.
  • PR #713: RF: In case a user just wants to use a single integer.
  • PR #700: TEST: add tests for AffineMap
  • PR #677: DKI PR3 - NF: Adding standard kurtosis statistics on module dki.py
  • PR #721: TST: Verify that output of estimate_sigma is a proper input to nlmeans.
  • PR #572: NF : nlmeans now support arrays of noise std
  • PR #708: Check for bval dimensionality on read.
  • PR #707: BF: Keep up with changes in scipy 0.16
  • PR #709: DOC: Use the identity variable in the resampling transformation.
  • PR #703: Fix syn-3d example
  • PR #705: Fix example in function compress_streamline
  • PR #635: Select streamlines based on logical operations on ROIs
  • PR #702: BF: Use only validated examples when building docs.
  • PR #689: Streamlines compression
  • PR #698: DOC: added NI citation
  • PR #681: RF + DOC: Add MNI template reference. Also import it into the dipy.da…
  • PR #696: Change title of piesno example
  • PR #691: CENIR ‘HCP-like’ multi b-value data
  • PR #661: Test DTI eigenvectors
  • PR #690: BF: nan entries cause segfault
  • PR #667: DOC: Remove Sourceforge related makefile things. Add the gh-pages upl…
  • PR #676: TST: update Travis config to use container infrastructure.
  • PR #533: MRG: some Cython refactorings
  • PR #686: BF: Make buildbot Pyhon26-32 happy
  • PR #683: Fixed initial estimation in piesno
  • PR #654: Affine registration PR 3/3
  • PR #684: BF: Fixed memory leak in QuickBundles.
  • PR #674: NF: Function to sample perpendicular directions relative to a given vector
  • PR #679: BF + NF: Provide dipy version info when running dipy.get_info()
  • PR #680: NF: Fetch and Read the MNI T1 and/or T2 template.
  • PR #664: DKI fitting (DKI PR2)
  • PR #671: DOC: move mailing list links to neuroimaging
  • PR #663: changed samuel st-jean email to the usherbrooke one
  • PR #648: Improve check of collinearity in vec2vec_rotmat
  • PR #582: DKI project: PR#1 Simulations to test DKI
  • PR #660: BF: If scalar-color input has len(shape)<4, need to fill that in.
  • PR #612: BF: Differences in spherical harmonic calculations wrt scipy 0.15
  • PR #651: Added estimate_sigma bias correction + update example
  • PR #659: BF: If n_frames is larger than one use path-numbering.
  • PR #658: FIX: resaved npy file causing load error for py 33
  • PR #657: Fix compilation error caused by inline functions
  • PR #628: Affine registration PR 2/3
  • PR #629: Quickbundles 2.1
  • PR #637: DOC: Fix typo in docstring of Identity class.
  • PR #639: DOC: Render the following line in the code cell.
  • PR #614: Seeds from mask random
  • PR #633: BF - no import of TissueTypes
  • PR #632: fixed typo in dti example
  • PR #627: BF: Add missing opacity property to point actor
  • PR #626: Use LooseVersion to check for scipy versions
  • PR #625: DOC: Include the PIESNO example.
  • PR #624: DOC: Corrected typos in Restore tutorial and docstring.
  • PR #619: DOC: Added missing contributor to developer list
  • PR #618: Update README file
  • PR #616: Raise ValueError when invalid matrix is given
  • PR #576: Piesno example
  • PR #615: bugfix for double word in doc example issue #387
  • PR #610: Added figure with HBM 2015
  • PR #609: Update website documentation
  • PR #607: DOC: Detailed github stats for 0.9
  • PR #606: Removed the word new
  • PR #605: Release mode: updating Changelog and Authors
  • PR #594: DOC + PEP8: Mostly just line-wrapping.

Issues (138):

  • #769: RF: Remove aniso2iso altogether.
  • #772: DOC: Use xvfb when building the docs in a headless machine.
  • #754: DOC: Should we add a side-car gitter chat to the website?
  • #771: Should we remove the deprecated quickbundles module?
  • #753: TST: Test DSI with b0s.
  • #761: reading dconn.nii
  • #723: WIP: Assign streamlines to an existing cluster map via QuickBundles
  • #738: Import tkinter
  • #767: Offscreen is False for test_slicer
  • #752: TST: Install vtk and mesa on Travis to test the fvtk module.
  • #768: Document dipy.reconst.dti.iter_fit_tensor params
  • #763: Tensor Fitting Overflows Memory
  • #766: Add fit_tensor iteration decorator
  • #751: Reorient tracks according to ROI
  • #765: BF: Typo in data file name.
  • #764: 404: Not Found when loading Stanford labels
  • #757: Optimize dipy.align.reslice
  • #587: Fvtk 2.0 PR1
  • #286: WIP - FVTK refactor/cleanup
  • #755: dipy.reconst.tests.test_shm.test_sf_to_sh: TypeError: Cannot cast ufunc add output from dtype(‘float64’) to dtype(‘uint16’) with casting rule ‘same_kind’
  • #749: Fixed deprecation warning in skimage
  • #748: TST: added test for _to_voxel_tolerance.
  • #678: BF: added tolerance for negative streamline coordinates checks
  • #714: RF: use masks in predictions and cross-validation
  • #739: Set number of OpenMP threads during runtime
  • #733: Add RTOP, RTAP and RTPP and the relative test
  • #743: BF: memleaks with typed memory views in Cython
  • #737: Possibly set_number_of_points doesn’t delete memory
  • #672: Power map
  • #724: @sinkpoint’s power map - refactored
  • #741: ENH: it is preferable to use choice rather than randint to not have
  • #730: numpy 1.10 breaks master
  • #727: Optimize tensor fitting
  • #726: NF - CSD response from a mask
  • #729: BF: tensor predict
  • #736: Added installation of python-tk package for VTK travis bot
  • #735: Added comment on nlmeans example about selecting one volume
  • #732: WIP: Test with vtk on Travis
  • #734: WIP: Fvtk 2.0 with travis vtk support
  • #688: dipy.test() fails on centos 6.x / python2.6
  • #731: Np 1.10
  • #725: WIP: TST: Install vtk on travis with conda.
  • #640: MAPMRI
  • #611: OSX test fail ‘we check the default value of lambda ...’
  • #715: In current segment_quickbundles tutorial there is no example for changing number of points
  • #719: Fixes #715
  • #682: Created list of examples for available features and metrics
  • #716: Refactor data module
  • #699: Added gaussian noise option to estimate_sigma
  • #712: DOC: API changes in gh707.
  • #713: RF: In case a user just wants to use a single integer.
  • #700: TEST: add tests for AffineMap
  • #677: DKI PR3 - NF: Adding standard kurtosis statistics on module dki.py
  • #721: TST: Verify that output of estimate_sigma is a proper input to nlmeans.
  • #693: WIP: affine map tests
  • #694: Memory errors / timeouts with affine registration on Windows
  • #572: NF : nlmeans now support arrays of noise std
  • #708: Check for bval dimensionality on read.
  • #697: dipy.io.gradients read_bvals_bvecs does not check bvals length
  • #707: BF: Keep up with changes in scipy 0.16
  • #710: Test dipy.core.tests.test_sphere.test_interp_rbf fails fails on Travis
  • #709: DOC: Use the identity variable in the resampling transformation.
  • #649: ROI seeds not placed at the center of the voxels
  • #656: Build-bot status
  • #701: Changes in syn_registration_3d example
  • #703: Fix syn-3d example
  • #705: Fix example in function compress_streamline
  • #704: Buildbots failure: related to streamline compression?
  • #635: Select streamlines based on logical operations on ROIs
  • #702: BF: Use only validated examples when building docs.
  • #689: Streamlines compression
  • #698: DOC: added NI citation
  • #621: piesno example not rendering correctly on the website
  • #650: profiling hyp1f1
  • #681: RF + DOC: Add MNI template reference. Also import it into the dipy.da…
  • #696: Change title of piesno example
  • #691: CENIR ‘HCP-like’ multi b-value data
  • #661: Test DTI eigenvectors
  • #690: BF: nan entries cause segfault
  • #667: DOC: Remove Sourceforge related makefile things. Add the gh-pages upl…
  • #676: TST: update Travis config to use container infrastructure.
  • #533: MRG: some Cython refactorings
  • #686: BF: Make buildbot Pyhon26-32 happy
  • #622: Fast shm from scipy 0.15.0 does not work on rc version
  • #683: Fixed initial estimation in piesno
  • #233: WIP: Dki
  • #654: Affine registration PR 3/3
  • #684: BF: Fixed memory leak in QuickBundles.
  • #674: NF: Function to sample perpendicular directions relative to a given vector
  • #679: BF + NF: Provide dipy version info when running dipy.get_info()
  • #680: NF: Fetch and Read the MNI T1 and/or T2 template.
  • #664: DKI fitting (DKI PR2)
  • #539: WIP: BF: Catching initial fodf creation of SDT
  • #671: DOC: move mailing list links to neuroimaging
  • #663: changed samuel st-jean email to the usherbrooke one
  • #287: Fvtk sphere origin
  • #648: Improve check of collinearity in vec2vec_rotmat
  • #582: DKI project: PR#1 Simulations to test DKI
  • #660: BF: If scalar-color input has len(shape)<4, need to fill that in.
  • #612: BF: Differences in spherical harmonic calculations wrt scipy 0.15
  • #651: Added estimate_sigma bias correction + update example
  • #659: BF: If n_frames is larger than one use path-numbering.
  • #652: MAINT: work around scipy bug in sph_harm
  • #653: Revisit naming when Matthew is back from Cuba
  • #658: FIX: resaved npy file causing load error for py 33
  • #657: Fix compilation error caused by inline functions
  • #655: Development documentation instructs to remove master
  • #628: Affine registration PR 2/3
  • #629: Quickbundles 2.1
  • #638: tutorial example, code in text format
  • #637: DOC: Fix typo in docstring of Identity class.
  • #639: DOC: Render the following line in the code cell.
  • #614: Seeds from mask random
  • #633: BF - no import of TissueTypes
  • #632: fixed typo in dti example
  • #630: Possible documentation bug (?)
  • #627: BF: Add missing opacity property to point actor
  • #459: streamtubes opacity kwarg
  • #626: Use LooseVersion to check for scipy versions
  • #625: DOC: Include the PIESNO example.
  • #623: DOC: Include the PIESNO example in the documentation.
  • #624: DOC: Corrected typos in Restore tutorial and docstring.
  • #619: DOC: Added missing contributor to developer list
  • #604: Retired ARM buildbot
  • #613: Possible random failure in test_vector_fields.test_reorient_vector_field_2d
  • #618: Update README file
  • #616: Raise ValueError when invalid matrix is given
  • #617: Added build status icon to readme
  • #576: Piesno example
  • #615: bugfix for double word in doc example issue #387
  • #600: Use of nanmean breaks dipy for numpy < 1.8
  • #610: Added figure with HBM 2015
  • #609: Update website documentation
  • #390: WIP: New PIESNO example and small corrections
  • #607: DOC: Detailed github stats for 0.9
  • #606: Removed the word new
  • #605: Release mode: updating Changelog and Authors
  • #594: DOC + PEP8: Mostly just line-wrapping.