# 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.