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.