Release notes for Dipy version 0.12

GitHub stats for 2016/02/21 - 2017/06/26 (tag: 0.11.0)

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

The following 48 authors contributed 1491 commits.

  • Alexandre Gauvin
  • Antonio Ossa
  • Ariel Rokem
  • Bago Amirbekian
  • Bishakh Ghosh
  • David Reagan
  • Eleftherios Garyfallidis
  • Etienne St-Onge
  • Gabriel Girard
  • Gregory R. Lee
  • Jean-Christophe Houde
  • Jon Haitz Legarreta
  • Julio Villalon
  • Kesshi Jordan
  • Manu Tej Sharma
  • Marc-Alexandre Côté
  • Matthew Brett
  • Matthieu Dumont
  • Nil Goyette
  • Omar Ocegueda Gonzalez
  • Rafael Neto Henriques
  • Ranveer Aggarwal
  • Riddhish Bhalodia
  • Rutger Fick
  • Samuel St-Jean
  • Serge Koudoro
  • Shahnawaz Ahmed
  • Sourav Singh
  • Stephan Meesters
  • Stonge Etienne
  • Guillaume Theaud
  • Tingyi Wanyan
  • Tom Wright
  • Vibhatha Abeykoon
  • Yaroslav Halchenko
  • Eric Peterson
  • Sven Dorkenwald
  • theaverageguy

We closed a total of 511 issues, 169 pull requests and 342 regular issues; this is the full list (generated with the script tools/github_stats.py):

Pull Requests (169):

  • PR #1273: Release 0.12 doc fix
  • PR #1272: small correction for debugging purpose on nlmeans
  • PR #1269: Odf slicer
  • PR #1271: Viz tut update
  • PR #1268: Following up on #1243.
  • PR #1223: local PCA using SVD
  • PR #1270: Doc cleaning deprecation warning
  • PR #1267: Adding a decorator for skipping test if openmp is not available
  • PR #1090: Documentation for command line interfaces
  • PR #1243: Better fvtk.viz error when no VTK installed
  • PR #1263: Cast Streamline attrs to numpy ints, to avoid buffer mismatch.
  • PR #1254: Automate script installation
  • PR #1261: removing absolute path in tracking module
  • PR #1255: Fix missing documentation content
  • PR #1260: removing absolute path in reconst
  • PR #1241: Csa and csd reconstruction workflow rebased
  • PR #1250: DOC: Fix reconst_dki.py DKI example documentation typos.
  • PR #1244: TEST: Decrease precision of tests for dki micro model prediction
  • PR #1235: New hdf5 file format for saving PeaksAndMetrics objects
  • PR #1231: TST: Reduce precision requirement for test of tortuosity estimation.
  • PR #1233: Feature: Added environment override for dipy_home variable
  • PR #1234: BUG: Fix non-ASCII characters in reconst_dki.py example.
  • PR #1222: A lightweight UI for medical visualizations #5: 2D Circular Slider
  • PR #1228: RF: Use cython imports instead of relying on extern
  • PR #1227: BF: Use np.npy_intp instead of assuming long for ArraySequence attributes
  • PR #1226: DKI Microstructural model
  • PR #1229: RF: allow for scipy pre-release deprecations
  • PR #1225: Add one more multi b-value data-set
  • PR #1219: MRG:Data off dropbox
  • PR #1221: NF: Check multi b-value
  • PR #1212: Follow PEP8 in reconst (part 2)
  • PR #1217: Use integer division in reconst_gqi.py
  • PR #1205: A lightweight UI for medical visualizations #4: 2D Line Slider
  • PR #1166: RF: Use the average sigma in the mask.
  • PR #1216: Use integer division to avoid errors in indexing
  • PR #1214: DOC: add a clarification note to simplify_warp_funcion_3d
  • PR #1208: Follow PEP8 in reconst (part 1)
  • PR #1206: Revert #1204, and add a filter to suppress warnings.
  • PR #1196: MRG: Use dipy’s array comparisons for tests
  • PR #1204: Suppress warnings regarding one-dimensional arrays changes in scipy 0.18
  • PR #1199: A lightweight UI for medical visualizations #3: Changes to Event Handling
  • PR #1202: Use integer division to avoid errors in indexing
  • PR #1198: ENH: avoid log zero
  • PR #1201: Fix out of bounds point not being classified OUTSIDEIMAGE (binary cla…
  • PR #1115: Bayesian Tissue Classification
  • PR #1052: Conda install
  • PR #1183: A lightweight UI for medical visualizations #2: TextBox
  • PR #1186: MRG: use newer wheelhouse for installs
  • PR #1195: Make PeaksAndMetrics pickle-able
  • PR #1194: Use assert_arrays_equal when needed.
  • PR #1193: Deprecate the Accent colormap, in anticipation of changes in MPL 2.0
  • PR #1140: A lightweight UI for medical visualizations #1: Button
  • PR #1171: fix:dev: added numpy.int64 for my triangle array
  • PR #1123: Add the mask workflow
  • PR #1174: NF: added the repulsion 200 sphere.
  • PR #1177: BF: fix interpolation call with Numpy 1.12
  • PR #1162: Return S0 value for DTI fits
  • PR #1147: add this fix for newer version of pytables.
  • PR #1076: ENH: Add support for ArraySequence in length function
  • PR #1050: ENH: expand OpenMP utilities and move from denspeed.pyx to dipy.utils
  • PR #1082: Add documentation uploading script
  • PR #1153: Athena mapmri
  • PR #1159: TST - add tests for various affine matrices for local tracking
  • PR #1157: Replace get_affine with affine and get_header with header.
  • PR #1160: Add Shahnawaz to list of contributors.
  • PR #1158: BF: closing matplotlib plots for each file while running the examples
  • PR #1151: Define fmin() for Visual Studio
  • PR #1149: Change DKI_signal to dki_signal
  • PR #1137: Small fix to insure that fwDTI non-linear procedure does not crash
  • PR #942: NF: Added support to colorize each line points indivdually
  • PR #1141: Do not cover files related to benchmarks.
  • PR #1098: Adding custom interactor for vizualisation
  • PR #1136: Update deprecated function.
  • PR #1113: TST: Test for invariance of model_params to splitting of the data.
  • PR #1134: Rebase of https://github.com/nipy/dipy/pull/993
  • PR #1064: Faster dti odf
  • PR #1114: flexible grid to streamline affine generation and pathlength function
  • PR #1122: Add the reconst_dti workflow
  • PR #1132: Update .travis.yml and README.md
  • PR #1125: Intensity adjustment. Find a better upper bound for interpolating images.
  • PR #1130: Minor corrections for showing surfaces
  • PR #1092: Line-based target()
  • PR #1129: Fix 1127
  • PR #1034: Viz surfaces
  • PR #1060: Fast computation of Cross Correlation metric
  • PR #1124: Small fix in free water DTI model
  • PR #1058: IVIM
  • PR #1110: WIP : Ivim linear fitting
  • PR #1120: Fix 1119
  • PR #1075: Drop26
  • PR #835: NF: Free water tensor model
  • PR #1046: BF - peaks_from_model with nbr_processes <= 0
  • PR #1049: MAINT: minor cython cleanup in align/vector_fields.pyx
  • PR #1087: Base workflow enhancements + tests
  • PR #1112: DOC: Math rendering issue in SFM gallery example.
  • PR #1109: Changed default value of mni template
  • PR #1106: Including MNI Template 2009c in Fetcher
  • PR #1066: Adaptive Denoising
  • PR #1091: Modifications for building docs with python3
  • PR #1105: Import reload function from imp module explicitly for python3
  • PR #1102: MRG: add pytables to travis-ci, Py35 full test run
  • PR #1100: Fix for Python 3 in io.dpy
  • PR #1094: Updates to FBC measures documentation
  • PR #1059: Documentation to discourage misuse of GradientTable
  • PR #1063: Fixes #1061 : Changed all S0 to 1.0
  • PR #1089: BF: fix test error on Python 3
  • PR #1079: Return a generator from orient_by_roi
  • PR #1088: Restored the older implementation of nlmeans
  • PR #1080: DOC: TensorModel.__init__ docstring.
  • PR #828: Fiber to bundle coherence measures
  • PR #1072: DOC: Added a coverage badge to README.rst
  • PR #1025: PEP8: Fix pep8 in segment
  • PR #1077: DOC: update fibernavigator link
  • PR #1069: DOC: Small one – we need this additional line of white space to render.
  • PR #1068: Renamed test_shore for consistency
  • PR #1067: Generate b vectors using disperse_charges
  • PR #1065: improve OMP parallelization with scheduling
  • PR #1062: BF - fix CSD.predict to work with nd inputs.
  • PR #1056: Remove tracking interfaces
  • PR #1028: BF: Predict DKI with a volume of S0
  • PR #1041: NF - Add PMF Threshold to Tractography
  • PR #1039: Doc - fix definition of real_sph_harm functions
  • PR #1019: MRG: fix heavy dependency check; no numpy for setup
  • PR #1018: Fix: denspeed.pyx to give correct output for nlmeans
  • PR #1035: Fix for fetcher files in Windows
  • PR #974: Minor change in tools/github_stats.py
  • PR #1021: Added warning for VTK not installed
  • PR #1024: Documnetation fix for reconst_dsid.py
  • PR #981: Fixes #979 : No figures in DKI example - Add new line after figure
  • PR #958: FIX: PEP8 in testing
  • PR #1005: FIX: Use absolute imports in io
  • PR #951: Contextual Enhancement update: fix SNR issue, fix reference
  • PR #1015: Fix progressbar of fetcher
  • PR #992: FIX: Update the import statements to use absolute import in core
  • PR #1003: FIX: Change the import statements in direction
  • PR #1004: FIX: Use absolute import in pkg_info
  • PR #1006: FIX: Use absolute import in utils and scratch
  • PR #1010: Absolute Imports in Viz
  • PR #929: Fix PEP8 in data
  • PR #941: BW: skimage.filter module name warning
  • PR #976: Fix PEP8 in sims and remove unnecessary imports
  • PR #956: FIX: PEP8 in reconst/test and reconst/benchmarks
  • PR #955: FIX: PEP8 in external
  • PR #952: FIX: PEP8 in tracking and tracking benchmarks/tests
  • PR #982: FIX: relative imports in dipy/align
  • PR #972: Fixes #901 : Added documentation for “step” in dti
  • PR #971: Add progress bar feature to dipy.data.fetcher
  • PR #989: copyright 2008-2016
  • PR #977: Relative import fix in dipy/align
  • PR #957: FIX: PEP8 in denoise
  • PR #959: FIX: PEP8 in utils
  • PR #967: Update index.rst correcting the date of release 0.11
  • PR #954: FIX: PEP8 in direction
  • PR #965: Fix typo
  • PR #948: Fix PEP8 in boots
  • PR #946: FIX: PEP8 for test_sumsqdiff and test_scalespace
  • PR #964: FIX: PEP8 in test_imaffine
  • PR #963: FIX: PEP8 in core
  • PR #947: FIX: PEP8 for test files
  • PR #897: PEP8
  • PR #926: Fix PEP8 in fixes
  • PR #937: BF : Clamping of the value of v in winding function
  • PR #907: DOC: switch to using mathjax for maths
  • PR #932: Fixes #931 : checks if nb_points=0
  • PR #927: Fix PEP8 in io and remove duplicate definition in test_bvectxt.py
  • PR #913: Fix pep8 in workflows
  • PR #935: Setup: go on to version 0.12 development.
  • PR #934: DOC: Update github stats for 0.11 as of today.
  • PR #933: Updating release dates

Issues (342):

  • #1273: Release 0.12 doc fix
  • #1272: small correction for debugging purpose on nlmeans
  • #1269: Odf slicer
  • #1143: Slice through ODF fields
  • #1271: Viz tut update
  • #1246: WIP: Replace widget with ui components in example.
  • #1268: Following up on #1243.
  • #1223: local PCA using SVD
  • #1265: Test failure on OSX in test_nlmeans_4d_3dsigma_and_threads
  • #1270: Doc cleaning deprecation warning
  • #1251: Slice through ODF fields - Rebased
  • #1267: Adding a decorator for skipping test if openmp is not available
  • #1090: Documentation for command line interfaces
  • #1243: Better fvtk.viz error when no VTK installed
  • #1238: Cryptic fvtk.viz error when no VTK installed
  • #1242: DKI microstructure model tests still fail intermittenly
  • #1252: Debug PR only - Odf slicer vtk tests (do not merge)
  • #1263: Cast Streamline attrs to numpy ints, to avoid buffer mismatch.
  • #1257: revamp piesno docstring
  • #978: Use absolute import in align
  • #1179: Automate workflow generation
  • #1253: Automate script installation for workflows
  • #1254: Automate script installation
  • #1261: removing absolute path in tracking module
  • #1001: Use absolute import in tracking
  • #1255: Fix missing documentation content
  • #1260: removing absolute path in reconst
  • #999: Use absolute import in reconst
  • #1258: Fix nlmeans indexing
  • #369: Add TESTs for resample
  • #1155: csa and csd reconstruction workflow
  • #1000: Use absolute import in segment, testing and tests
  • #1070: [Docs] Examples using deprecated function
  • #711: Update api_changes.rst for interp_rbf
  • #321: Median otsu figures in example don’t look good
  • #994: Use absolute import in dipy/core
  • #608: Customize at runtime the number of cores nlmeans is using
  • #865: PEP8 in test_imwarp
  • #591: Allow seed_from_mask to generate random seeds
  • #518: TODO: aniso2iso module will be completely removed in version 0.10.
  • #328: “incompatible” import of peaks_from_model in your recent publication
  • #1241: Csa and csd reconstruction workflow rebased
  • #1250: DOC: Fix reconst_dki.py DKI example documentation typos.
  • #1244: TEST: Decrease precision of tests for dki micro model prediction
  • #1235: New hdf5 file format for saving PeaksAndMetrics objects
  • #1231: TST: Reduce precision requirement for test of tortuosity estimation.
  • #1210: Switching branches in windows and pip install error
  • #1209: Move data files out of dropbox => persistent URL
  • #1233: Feature: Added environment override for dipy_home variable
  • #1234: BUG: Fix non-ASCII characters in reconst_dki.py example.
  • #1222: A lightweight UI for medical visualizations #5: 2D Circular Slider
  • #1185: unable to use fvtk.show after ubuntu 16.10 install
  • #1228: RF: Use cython imports instead of relying on extern
  • #909: Inconsistent output for values_from_volume
  • #1182: CSD vs CSA
  • #1211: dipy.data.read_bundles_2_subjects doesn’t fetch data as expected
  • #1227: BF: Use np.npy_intp instead of assuming long for ArraySequence attributes
  • #1027: (DO NOT MERGE THIS PR) NF: DKI microstructural model
  • #1226: DKI Microstructural model
  • #1229: RF: allow for scipy pre-release deprecations
  • #1225: Add one more multi b-value data-set
  • #1219: MRG:Data off dropbox
  • #1218: [Docs] Error while generating html
  • #1221: NF: Check multi b-value
  • #1212: Follow PEP8 in reconst (part 2)
  • #1217: Use integer division in reconst_gqi.py
  • #1205: A lightweight UI for medical visualizations #4: 2D Line Slider
  • #1166: RF: Use the average sigma in the mask.
  • #1216: Use integer division to avoid errors in indexing
  • #1215: [Docs] Error while building examples: tracking_quick_start.py
  • #1213: dipy.align.vector_fields.simplify_warp_function_3d: Wrong equation in docstring
  • #1214: DOC: add a clarification note to simplify_warp_funcion_3d
  • #1208: Follow PEP8 in reconst (part 1)
  • #1206: Revert #1204, and add a filter to suppress warnings.
  • #1196: MRG: Use dipy’s array comparisons for tests
  • #1191: Test failures for cluster code with current numpy master
  • #1207: Follow PEP8 in reconst
  • #1204: Suppress warnings regarding one-dimensional arrays changes in scipy 0.18
  • #1107: Dipy.align.reslice: either swallow the scipy warning or rework to avoid it
  • #1199: A lightweight UI for medical visualizations #3: Changes to Event Handling
  • #1200: [Docs] Error while generating docs
  • #1202: Use integer division to avoid errors in indexing
  • #1188: Colormap test errors for new matplotlib
  • #1187: Negative integer powers error with numpy 1.12
  • #1170: Importing vtk with dipy
  • #1086: ENH: avoid calling log() on zero-valued elements in anisotropic_power
  • #1198: ENH: avoid log zero
  • #1201: Fix out of bounds point not being classified OUTSIDEIMAGE (binary cla…
  • #1115: Bayesian Tissue Classification
  • #1052: Conda install
  • #1183: A lightweight UI for medical visualizations #2: TextBox
  • #1173: TST: Test on Python 3.6
  • #1186: MRG: use newer wheelhouse for installs
  • #1190: Pickle error for Python 3.6 and test_peaksFromModelParallel
  • #1195: Make PeaksAndMetrics pickle-able
  • #1194: Use assert_arrays_equal when needed.
  • #1193: Deprecate the Accent colormap, in anticipation of changes in MPL 2.0
  • #1189: Np1.12
  • #1140: A lightweight UI for medical visualizations #1: Button
  • #1022: Fixes #720 : Auto generate ipython notebooks
  • #1139: The shebang again! Python: bad interpreter: No such file or directory
  • #1171: fix:dev: added numpy.int64 for my triangle array
  • #1123: Add the mask workflow
  • #1174: NF: added the repulsion 200 sphere.
  • #1176: Dipy.tracking.local.interpolation.nearestneighbor_interpolate raises when used with Numpy 1.12
  • #1177: BF: fix interpolation call with Numpy 1.12
  • #1162: Return S0 value for DTI fits
  • #1142: pytables version and streamlines_format.py example
  • #1147: add this fix for newer version of pytables.
  • #1076: ENH: Add support for ArraySequence in length function
  • #1050: ENH: expand OpenMP utilities and move from denspeed.pyx to dipy.utils
  • #1082: Add documentation uploading script
  • #1153: Athena mapmri
  • #1097: Added to quantize_evecs: multiprocessing and v
  • #1159: TST - add tests for various affine matrices for local tracking
  • #1163: WIP: Combined contour function with slicer to use affine
  • #940: Drop python 2.6
  • #1040: SFM example using deprecated code
  • #1118: pip install dipy failing on my windows
  • #1119: Buildbots failing with workflow merge
  • #1127: Windows buildbot failures after ivim_linear merge
  • #1128: Support for non linear denoise?
  • #1138: A few broken builds
  • #1148: Actual S0 for DTI data
  • #1157: Replace get_affine with affine and get_header with header.
  • #1160: Add Shahnawaz to list of contributors.
  • #740: Improved mapmri implementation with laplacian regularization and new …
  • #1045: Allow affine ‘shear’ tolerance in LocalTracking
  • #1154: [Bug] connectivity matrix image in streamline_tools example
  • #1158: BF: closing matplotlib plots for each file while running the examples
  • #1151: Define fmin() for Visual Studio
  • #1145: DKI_signal should be dki_signal in dipy.sims.voxel
  • #1149: Change DKI_signal to dki_signal
  • #1137: Small fix to insure that fwDTI non-linear procedure does not crash
  • #827: Free Water Elimination DTI
  • #942: NF: Added support to colorize each line points indivdually
  • #1141: Do not cover files related to benchmarks.
  • #1098: Adding custom interactor for vizualisation
  • #1136: Update deprecated function.
  • #1113: TST: Test for invariance of model_params to splitting of the data.
  • #1134: Rebase of https://github.com/nipy/dipy/pull/993
  • #1064: Faster dti odf
  • #1114: flexible grid to streamline affine generation and pathlength function
  • #1122: Add the reconst_dti workflow
  • #1132: Update .travis.yml and README.md
  • #1051: ENH: use parallel processing in the cython code for CCMetric
  • #993: FIX: Use absolute imports in testing,tests and segment files
  • #673: WIP: Workflow for syn registration
  • #859: [WIP] Suppress warnings in tests
  • #983: PEP8 in sims #884
  • #984: PEP8 in reconst #881
  • #1009: Absolute Imports in Tracking
  • #1036: Estimate S0 from data (DTI)
  • #1125: Intensity adjustment. Find a better upper bound for interpolating images.
  • #1130: Minor corrections for showing surfaces
  • #1092: Line-based target()
  • #1129: Fix 1127
  • #1034: Viz surfaces
  • #394: Update documentation for VTK and Anaconda
  • #973: Minor change in tools/github_stats.py
  • #1060: Fast computation of Cross Correlation metric
  • #1124: Small fix in free water DTI model
  • #1058: IVIM
  • #1110: WIP : Ivim linear fitting
  • #1120: Fix 1119
  • #1121: Recons dti workflow
  • #1083: nlmeans problem
  • #1075: Drop26
  • #835: NF: Free water tensor model
  • #1046: BF - peaks_from_model with nbr_processes <= 0
  • #1049: MAINT: minor cython cleanup in align/vector_fields.pyx
  • #1087: Base workflow enhancements + tests
  • #1112: DOC: Math rendering issue in SFM gallery example.
  • #670: Tissue classification using MAP-MRF
  • #332: A sample nipype interface for fit_tensor
  • #1116: failing to build the docs: issue with io.BufferedIOBase
  • #1109: Changed default value of mni template
  • #1106: Including MNI Template 2009c in Fetcher
  • #1066: Adaptive Denoising
  • #351: Dipy.tracking.utils.target affine parameter is misleading
  • #1091: Modifications for building docs with python3
  • #912: Unable to build documentation with Python 3
  • #1105: Import reload function from imp module explicitly for python3
  • #1104: restore_dti.py example does not work in python3
  • #1102: MRG: add pytables to travis-ci, Py35 full test run
  • #1100: Fix for Python 3 in io.dpy
  • #1103: BF: This raises a warning on line 367 otherwise.
  • #1101: Test with optional dependencies (including pytables) on Python 3.
  • #1094: Updates to FBC measures documentation
  • #1059: Documentation to discourage misuse of GradientTable
  • #1061: Inconsistency in specifying S0 values in multi_tensor and single_tensor
  • #1063: Fixes #1061 : Changed all S0 to 1.0
  • #1089: BF: fix test error on Python 3
  • #1079: Return a generator from orient_by_roi
  • #1088: Restored the older implementation of nlmeans
  • #1080: DOC: TensorModel.__init__ docstring.
  • #1085: Enhanced workflows
  • #1081: mean_diffusivity from the reconst.dti module returns incorrect shape
  • #1031: improvements for denoise/denspeed.pyx
  • #828: Fiber to bundle coherence measures
  • #1072: DOC: Added a coverage badge to README.rst
  • #1071: report coverage and add a badge?
  • #1038: BF: Should fix #1037
  • #1078: Fetcher for ivim data, needs md5
  • #953: FIX: PEP8 for segment
  • #1025: PEP8: Fix pep8 in segment
  • #883: PEP8 in segment
  • #1077: DOC: update fibernavigator link
  • #1069: DOC: Small one – we need this additional line of white space to render.
  • #1068: Renamed test_shore for consistency
  • #1067: Generate b vectors using disperse_charges
  • #1011: Discrepancy with output of nlmeans.py
  • #1055: WIP: Ivim implementation
  • #1065: improve OMP parallelization with scheduling
  • #1062: BF - fix CSD.predict to work with nd inputs.
  • #1057: Workaround for https://github.com/nipy/dipy/issues/852
  • #1037: tracking.interfaces imports SlowAdcOpdfModel, but it is not defined
  • #1056: Remove tracking interfaces
  • #813: Windows 64-bit error in segment.featurespeed.extract
  • #1054: Remove tracking interfaces
  • #1028: BF: Predict DKI with a volume of S0
  • #1041: NF - Add PMF Threshold to Tractography
  • #1039: Doc - fix definition of real_sph_harm functions
  • #1019: MRG: fix heavy dependency check; no numpy for setup
  • #1018: Fix: denspeed.pyx to give correct output for nlmeans
  • #1043: DO NOT MERGE: Add a test of local tracking, using data from dipy.data.
  • #899: SNR in contextual enhancement example
  • #991: Documentation footer has 2008-2015 mentioned.
  • #1008: [WIP] NF: Implementation of CHARMED model
  • #1030: Fetcher files not found on Windows
  • #1035: Fix for fetcher files in Windows
  • #1016: viz.fvtk has no attribute ‘ren’
  • #1033: Viz surfaces
  • #1032: Merge pull request #1 from nipy/master
  • #1029: Errors building Cython extensions on Python 3.5
  • #974: Minor change in tools/github_stats.py
  • #1002: Use absolute import in utils and scratch
  • #1014: Progress bar works only for some data
  • #1013: dipy.data.make_fetcher test fails with Python 3
  • #1020: Documentation does not mention Scipy as a dependency for VTK widgets.
  • #1023: display in dsi example is broken
  • #1021: Added warning for VTK not installed
  • #882: PEP8 in reconst tests/benchmarks
  • #888: PEP8 in tracking benchmarks/tests
  • #885: PEP8 in testing
  • #902: fix typo
  • #1024: Documnetation fix for reconst_dsid.py
  • #979: No figures in DKI example
  • #981: Fixes #979 : No figures in DKI example - Add new line after figure
  • #958: FIX: PEP8 in testing
  • #1005: FIX: Use absolute imports in io
  • #997: Use absolute import in io
  • #675: Voxelwise stabilisation
  • #951: Contextual Enhancement update: fix SNR issue, fix reference
  • #1015: Fix progressbar of fetcher
  • #1012: TST: install the dipy.data tests.
  • #992: FIX: Update the import statements to use absolute import in core
  • #1003: FIX: Change the import statements in direction
  • #996: Use absolute import in dipy/direction
  • #1004: FIX: Use absolute import in pkg_info
  • #998: Use absolute import in dipy/pkg_info.py
  • #1006: FIX: Use absolute import in utils and scratch
  • #1010: Absolute Imports in Viz
  • #1007: Use absolute import in viz
  • #929: Fix PEP8 in data
  • #874: PEP8 in data
  • #980: Fix pep8 in reconst
  • #1017: Fixes #1016 : Raises VTK not installed
  • #877: PEP8 in external
  • #887: PEP8 in tracking
  • #941: BW: skimage.filter module name warning
  • #976: Fix PEP8 in sims and remove unnecessary imports
  • #884: PEP8 in sims
  • #956: FIX: PEP8 in reconst/test and reconst/benchmarks
  • #955: FIX: PEP8 in external
  • #952: FIX: PEP8 in tracking and tracking benchmarks/tests
  • #982: FIX: relative imports in dipy/align
  • #972: Fixes #901 : Added documentation for “step” in dti
  • #901: DTI step parameter not documented.
  • #995: Use absolute import in dipy/data/__init__.py
  • #344: Update citation page
  • #971: Add progress bar feature to dipy.data.fetcher
  • #970: Downloading data with dipy.data.fetcher does not show any progress bar
  • #986: “pip3 install dipy” in Installation for python3
  • #990: No figures in DKI example
  • #989: copyright 2008-2016
  • #988: doc/conf.py shows copyright 2008-2015. Should be 2016?
  • #975: Use absolute import in imaffine, imwarp, metrics
  • #517: TODO: Peaks to be removed from dipy.reconst in 0.10
  • #977: Relative import fix in dipy/align
  • #875: PEP8 in denoise
  • #957: FIX: PEP8 in denoise
  • #960: PEP8 in sims #884
  • #961: PEP8 in reconst #880
  • #962: PEP8 in reconst #881
  • #889: PEP8 in utils
  • #959: FIX: PEP8 in utils
  • #866: PEP8 in test_metrics
  • #867: PEP8 in test_parzenhist
  • #868: PEP8 in test_scalespace
  • #869: PEP8 in test_sumsqdiff
  • #870: PEP8 in test_transforms
  • #871: PEP8 in test_vector_fields
  • #864: PEP8 in test_imaffine
  • #967: Update index.rst correcting the date of release 0.11
  • #862: PEP8 in test_crosscorr
  • #873: PEP8 in core
  • #831: ACT tracking example gives weird streamlines
  • #876: PEP8 in direction
  • #954: FIX: PEP8 in direction
  • #965: Fix typo
  • #968: Use relative instead of absolute import
  • #948: Fix PEP8 in boots
  • #872: PEP8 in boots
  • #946: FIX: PEP8 for test_sumsqdiff and test_scalespace
  • #964: FIX: PEP8 in test_imaffine
  • #963: FIX: PEP8 in core
  • #966: fix typo
  • #947: FIX: PEP8 for test files
  • #920: STYLE:PEP8 for test_imaffine
  • #897: PEP8
  • #950: PEP8 fixed in reconst/tests and reconst/benchmarks
  • #949: Fixed Pep8 utils tracking testing denoise
  • #926: Fix PEP8 in fixes
  • #878: PEP8 in fixes
  • #939: Fixed PEP8 in utils, denoise , tracking and testing
  • #945: FIX: PEP8 in test_scalespace
  • #937: BF : Clamping of the value of v in winding function
  • #930: pep8 fix issue #896 - “continuation line over-indented for visual indent”
  • #943: BF: Removed unsused code in slicer
  • #907: DOC: switch to using mathjax for maths
  • #931: dipy/tracking/streamlinespeed set_number_of_points crash when nb_points=0
  • #932: Fixes #931 : checks if nb_points=0
  • #927: Fix PEP8 in io and remove duplicate definition in test_bvectxt.py
  • #924: in dipy/io/tests/test_bvectxt.py function with same name is defined twice
  • #879: PEP8 in io
  • #913: Fix pep8 in workflows
  • #891: PEP8 in workflows
  • #938: PEP8 issues solved in utils, testing and denoise
  • #935: Setup: go on to version 0.12 development.
  • #934: DOC: Update github stats for 0.11 as of today.
  • #933: Updating release dates