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**DIPY 1.9.0** is now available. New features include: - Numpy 2.0.0 support. - DeepN4 novel DL-based N4 Bias Correction method added. - Multiple Workflows added. - Large update of DIPY Horizon features. - Pytest for Cython files(*.pyx) added. - Large documentation update. - Support of Python 3.8 removed. - Closed 142 issues and merged 60 pull requests. ==================================== Release notes for DIPY version 1.9 ==================================== GitHub stats for 2023/12/14 - 2024/03/07 (tag: 1.8.0) These lists are automatically generated, and may be incomplete or contain duplicates. The following 17 authors contributed 175 commits. * Ariel Rokem * Atharva Shah * Ebrahim Ebrahim * Eleftherios Garyfallidis * Gabriel Girard * John Shen * Jon Haitz Legarreta Gorroño * Jong Sung Park * Maharshi Gor * Matthew Feickert * Philippe Karan * Praitayini Kanakaraj * Sam Coveney * Sandro * Serge Koudoro * dependabot[bot] * Étienne Mollier We closed a total of 139 issues, 60 pull requests and 81 regular issues; this is the full list (generated with the script :file:`tools/github_stats.py`): Pull Requests (60): * :ghpull:`3095`: [UPCOMING] Release preparation for 1.9.0 * :ghpull:`3086`: [RF] Fix spherical harmonic terminology swap * :ghpull:`3105`: [doc] improve some tutorials rendering * :ghpull:`3109`: [BF] convert_tractogram fix * :ghpull:`3108`: enabled trx support with correct header * :ghpull:`3107`: enabled trx support for viz * :ghpull:`3033`: [RF] fix dki mask for nlls * :ghpull:`3104`: Dkimaskfix * :ghpull:`3106`: volume slices visibility fixed * :ghpull:`3102`: Bugfix for peaks slices and synchronization. * :ghpull:`3078`: return S0 from dki fit * :ghpull:`3101`: [BF] Uniformize cython version * :ghpull:`3097`: Feature/surface * :ghpull:`3048`: [TEST] Adds support of cython for pytest * :ghpull:`3053`: [NF] Add workflow to convert tensors in different formats * :ghpull:`3073`: [NF] Add DSI workflow * :ghpull:`3099`: [DOC] fix some typo [ci skip] * :ghpull:`3098`: Removing tensorflow addon from DL models * :ghpull:`2973`: Tab names for slice tabs as file names. * :ghpull:`3081`: NF: Adding N4 bias correction deep learning model * :ghpull:`3092`: Feature: volume synchronizing * :ghpull:`3059`: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors * :ghpull:`3090`: RF - changed memory view to double* trilinear_interpolation_4d * :ghpull:`3080`: Adding SH basis legacy option support to peaks_from_model * :ghpull:`3087`: backward compatibility fixed * :ghpull:`3088`: [TEST] Pin pytest * :ghpull:`3084`: fixed 4d slice issue * :ghpull:`3083`: Np.unique check removed. * :ghpull:`3082`: Add Fedora installation instructions [ci skip] * :ghpull:`3076`: [CI] Update scientific-python/upload-nightly-action to 0.5.0 * :ghpull:`3070`: [DOC] Fix installation link in README [ci skip] * :ghpull:`3069`: [DOC] Fix DTI Tutorial [ci skip] * :ghpull:`3063`: [RF] remove cpdef in PmfGen * :ghpull:`3054`: [DOC] Fix some links [ci skip] * :ghpull:`3060`: Bump codecov/codecov-action from 3 to 4 * :ghpull:`3061`: [OPT] Enable openmp for macOS wheel and CI's * :ghpull:`3049`: [MTN] code cleaning: remove some dependencies version checking * :ghpull:`3050`: [RF] Move ``dipy.boots.resampling`` to ``dipy.stats.resampling`` * :ghpull:`3051`: [RF] Remove dipy.io.bvectxt module * :ghpull:`3052`: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b3845d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874 * :ghpull:`3045`: [DOC] fix `multi_shell_fiber_response` docstring array dims [ci skip] * :ghpull:`3041`: [NF] Add convert tractograms flow * :ghpull:`3040`: [BW] Remove some python2 reference * :ghpull:`3039`: [TEST] Add setup_module and teardown_module * :ghpull:`3038`: [NF] Update `dipy_info`: allow tractogram files format * :ghpull:`3043`: d/d/t/test_data.py: endian independent dtype. * :ghpull:`3042`: pyproject.toml: no cython at run time. * :ghpull:`3027`: [NF] Add Concatenate tracks workflows * :ghpull:`3008`: NF: add SH basis conversion between dipy and mrtrix3 * :ghpull:`3025`: [TEST] Manage http errors for stateful tractograms * :ghpull:`3031`: Bugfix: Horizon image's dtype validation * :ghpull:`3021`: [MTN] Remove 3.8 Ci's * :ghpull:`3026`: [RF] Fix cython 3 warnings * :ghpull:`3022`: [DOC] Fix logo size and link [ci skip] * :ghpull:`3013`: Added Fibonacci spiral and test for it * :ghpull:`3019`: DOC: Fix link to toolchain roadmap page in `README` * :ghpull:`3012`: DOC: Document observance for Scientific Python min supported versions * :ghpull:`3018`: Bump actions/download-artifact from 3 to 4 * :ghpull:`3017`: Bump actions/upload-artifact from 3 to 4 * :ghpull:`3014`: Update release1.8.rst Issues (81): * :ghissue:`2970`: spherical harmonic degree/order terminology swapped * :ghissue:`3105`: [doc] improve some tutorials rendering * :ghissue:`3109`: [BF] convert_tractogram fix * :ghissue:`3108`: enabled trx support with correct header * :ghissue:`3107`: enabled trx support for viz * :ghissue:`2994`: DKI masking * :ghissue:`3033`: [RF] fix dki mask for nlls * :ghissue:`3104`: Dkimaskfix * :ghissue:`3106`: volume slices visibility fixed * :ghissue:`3102`: Bugfix for peaks slices and synchronization. * :ghissue:`2281`: Black Output for pam5 file with dipy_horizon * :ghissue:`3078`: return S0 from dki fit * :ghissue:`3101`: [BF] Uniformize cython version * :ghissue:`3097`: Feature/surface * :ghissue:`2719`: pytest and cdef functions * :ghissue:`3048`: [TEST] Adds support of cython for pytest * :ghissue:`3053`: [NF] Add workflow to convert tensors in different formats * :ghissue:`3073`: [NF] Add DSI workflow * :ghissue:`3099`: [DOC] fix some typo [ci skip] * :ghissue:`3098`: Removing tensorflow addon from DL models * :ghissue:`2973`: Tab names for slice tabs as file names. * :ghissue:`3081`: NF: Adding N4 bias correction deep learning model * :ghissue:`3092`: Feature: volume synchronizing * :ghissue:`3093`: Can I use a different sort of dataset and also what if I don't have a bval , I use . mat images format PATCH2Self * :ghissue:`3059`: Generalize special casing while loading bvecs, to include the case of transposed 2,3 vectors * :ghissue:`3090`: RF - changed memory view to double* trilinear_interpolation_4d * :ghissue:`3080`: Adding SH basis legacy option support to peaks_from_model * :ghissue:`3085`: Viz Tests failing * :ghissue:`3087`: backward compatibility fixed * :ghissue:`3088`: [TEST] Pin pytest * :ghissue:`3074`: Horizon for large datasets - concerns regarding np.unique * :ghissue:`3075`: Horizon - 4D data support - slicing on the 4-th dim * :ghissue:`3084`: fixed 4d slice issue * :ghissue:`3083`: Np.unique check removed. * :ghissue:`3082`: Add Fedora installation instructions [ci skip] * :ghissue:`3065`: Add s390x test workflow * :ghissue:`3076`: [CI] Update scientific-python/upload-nightly-action to 0.5.0 * :ghissue:`3070`: [DOC] Fix installation link in README [ci skip] * :ghissue:`3069`: [DOC] Fix DTI Tutorial [ci skip] * :ghissue:`3066`: Dipy website incorrect image * :ghissue:`3063`: [RF] remove cpdef in PmfGen * :ghissue:`3054`: [DOC] Fix some links [ci skip] * :ghissue:`3060`: Bump codecov/codecov-action from 3 to 4 * :ghissue:`3061`: [OPT] Enable openmp for macOS wheel and CI's * :ghissue:`3057`: Using the atlas HCP1065 in DIPY * :ghissue:`3055`: [RF] replace Bunch by Enum * :ghissue:`3049`: [MTN] code cleaning: remove some dependencies version checking * :ghissue:`3050`: [RF] Move ``dipy.boots.resampling`` to ``dipy.stats.resampling`` * :ghissue:`3051`: [RF] Remove dipy.io.bvectxt module * :ghissue:`3052`: Bump scientific-python/upload-nightly-action from 3eb3a42b50671237cace9be2d18a3e4b38 8000 45d3c4 to 66bc1b6beedff9619cdff8f3361a06802c8f5874 * :ghissue:`2789`: Horizon image's dtype validation * :ghissue:`3047`: "Editable" installation broken * :ghissue:`3045`: [DOC] fix `multi_shell_fiber_response` docstring array dims [ci skip] * :ghissue:`3041`: [NF] Add convert tractograms flow * :ghissue:`3040`: [BW] Remove some python2 reference * :ghissue:`3039`: [TEST] Add setup_module and teardown_module * :ghissue:`3038`: [NF] Update `dipy_info`: allow tractogram files format * :ghissue:`3043`: d/d/t/test_data.py: endian independent dtype. * :ghissue:`3042`: pyproject.toml: no cython at run time. * :ghissue:`3027`: [NF] Add Concatenate tracks workflows * :ghissue:`3035`: If I want to use 6D array in "actor.odf_slicer", how can i do? * :ghissue:`2993`: Add conversion utility between DIPY and MRtrix3 spherical harmonic basis * :ghissue:`3008`: NF: add SH basis conversion between dipy and mrtrix3 * :ghissue:`3025`: [TEST] Manage http errors for stateful tractograms * :ghissue:`3031`: Bugfix: Horizon image's dtype validation * :ghissue:`3032`: Consider moving your nightly wheel away from the scipy-wheel-nightly (old location) to scientific-python-nightly-wheels * :ghissue:`3021`: [MTN] Remove 3.8 Ci's * :ghissue:`3003`: DIPY installation raises Cython warnings * :ghissue:`3026`: [RF] Fix cython 3 warnings * :ghissue:`2852`: Different behavior regarding color channels of horizon * :ghissue:`2378`: A novice's request for advice on loading very large tractograms (.tck) * :ghissue:`2064`: How to register MR to CT of the same person? * :ghissue:`2601`: read_bvals_bvecs can't read double volume dwi * :ghissue:`3022`: [DOC] Fix logo size and link [ci skip] * :ghissue:`3013`: Added Fibonacci spiral and test for it * :ghissue:`3020`: load_nifti import doesn't work if using submodule directly * :ghissue:`3019`: DOC: Fix link to toolchain roadmap page in `README` * :ghissue:`3012`: DOC: Document observance for Scientific Python min supported versions * :ghissue:`3018`: Bump actions/download-artifact from 3 to 4 * :ghissue:`3017`: Bump actions/upload-artifact from 3 to 4 * :ghissue:`3014`: Update release1.8.rst * :ghissue:`1525`: Clang-omp moved to boneyard on brew
**DIPY 1.8.0** is now available. New features include: - Python 3.12.0 support. - Cython 3.0.0 compatibility. - Migrated to Meson build system. Setuptools is no more. - EVAC+ novel DL-based brain extraction method added. - Parallel Transport Tractography (PTT) 10X faster. - Many Horizon updates. Fast overlays of many images. - New Correlation Tensor Imaging (CTI) method added. - Improved warnings for optional dependencies. - Large documentation update. New theme/design integration. - Closed 197 issues and merged 130 pull requests.
==================================== Release notes for DIPY version 1.7 ==================================== **DIPY 1.7.0** is now available. New features include: - NF: BundleWarp - Streamline-based nonlinear registration method for bundles added. - NF: DKI+ - Diffusion Kurtosis modeling with advanced constraints added. - NF: Synb0 - Synthetic b0 creation added using deep learning added. - NF: New Parallel Transport Tractography (PTT) added. - NF: Fast Streamline Search algorithm added. - NF: New denoising methods based on 1D CNN added. - Handle Asymmetric Spherical Functions. - Large update of DIPY Horizon features. - Multiple Workflows updated - Large codebase cleaning. - Large documentation update. Integration of Sphinx-Gallery. - Closed 53 issues and merged 34 pull requests. GitHub stats for 2023/01/16 - 2023/04/23 (tag: 1.6.0) These lists are automatically generated, and may be incomplete or contain duplicates. The following 21 authors contributed 496 commits. * Ariel Rokem * Bramsh Qamar * Charles Poirier * Dogu Baran Aydogan * Eleftherios Garyfallidis * Etienne St-Onge * Francois Rheault * Gabriel Girard * Javier Guaje * Jong Sung Park * Martino Pilia * Mitesh Gulecha * Rahul Ubale * Sam Coveney * Serge Koudoro * Shilpi * Tom Dela Haije * Yaroslav Halchenko * karp2601 * lb-97 * ujjwal-shekhar We closed a total of 87 issues, 34 pull requests and 53 regular issues; this is the full list (generated with the script :file:`tools/github_stats.py`): Pull Requests (34): * :ghpull:`2765`: Sphinx-gallery integration * :ghpull:`2788`: Remove NoseTester * :ghpull:`2768`: BundleWarp, streamline-based nonlinear registration of white matter tracts * :ghpull:`2749`: adding a new getitem method * :ghpull:`2744`: Horizon Tabs * :ghpull:`2785`: EVAC+ workflow * :ghpull:`2540`: Updates the default value of rm_small_clusters variable in slr_with_qbx function * :ghpull:`2609`: NF: DKI+ constraints * :ghpull:`2596`: NF - Parallel Transport Tractography (PTT) * :ghpull:`2740`: Integration of Denoising Method for DWI with 1D CNN * :ghpull:`2773`: Including EVAC+ and util function * :ghpull:`2783`: Fix test_roi_images * :ghpull:`2782`: [MTN] Fix CI codecov upload * :ghpull:`2780`: Added option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff * :ghpull:`2778`: BF: QBX and merge clusters should return streamlines * :ghpull:`2767`: NF - add utility functions to fast_numpy * :ghpull:`2626`: Adding Synb0 * :ghpull:`2763`: Update dki.py * :ghpull:`2751`: [ENH] Asymmetric peak_directions * :ghpull:`2762`: Remove Python 3.7 from CI * :ghpull:`2753`: Update adaptive_soft_matching.py * :ghpull:`2722`: fixed pca for features > samples, and fixed pca_noise_estimate * :ghpull:`2741`: Fixing solve_qp error * :ghpull:`2739`: codespell: config, workflow, typos fixed * :ghpull:`2590`: Fast Streamline Search algorithm implementation * :ghpull:`2733`: Update SynRegistrationFlow for dipy#2648 * :ghpull:`2723`: TRX integration, requires new attributes for SFT * :ghpull:`2727`: Fix EXTRAS_REQUIRE * :ghpull:`2725`: DOC - Update RUMBA-SD data requirement * :ghpull:`2716`: NF - Added cython utility functions * :ghpull:`2717`: fixed bug for non-linear fitting with masks * :ghpull:`2628`: resolve some CI's script typo * :ghpull:`2713`: Empty vtk support * :ghpull:`2625`: [Upcoming] Release 1.6.0 Issues (53): * :ghissue:`2537`: Importing an example in another example - doc * :ghissue:`1778`: jupyter notebooks from examples * :ghissue:`720`: Auto-convert the examples into IPython notebooks * :ghissue:`1990`: [WIP] Sphinx-Gallery integration * :ghissue:`2765`: Sphinx-gallery integration * :ghissue:`2788`: Remove NoseTester * :ghissue:`2768`: BundleWarp, streamline-based nonlinear registration of white matter tracts * :ghissue:`1073`: Add a method to slice gtab using bvals (Eg : gtab[bvals>200]) * :ghissue:`2749`: adding a new getitem method * :ghissue:`2744`: Horizon Tabs * :ghissue:`2785`: EVAC+ workflow * :ghissue:`2530`: slr_with_qbx breaks when bundle has only one streamline * :ghissue:`2540`: Updates the default value of rm_small_clusters variable in slr_with_qbx function * :ghissue:`2609`: NF: DKI+ constraints * :ghissue:`2596`: NF - Parallel Transport Tractography (PTT) * :ghissue:`2756`: Remove unused inplace param from gibbs_removal() * :ghissue:`2754`: [Question] dipy/denoise/gibbs.py * :ghissue:`2740`: Integration of Denoising Method for DWI with 1D CNN * :ghissue:`2773`: Including EVAC+ and util function * :ghissue:`2783`: Fix test_roi_images * :ghissue:`2782`: [MTN] Fix CI codecov upload * :ghissue:`2775`: NF - Add option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff(.) * :ghissue:`2780`: Added option to set Legacy=False in PmfGenDirectionGetter.from_shcoeff * :ghissue:`2778`: BF: QBX and merge clusters should return streamlines * :ghissue:`2767`: NF - add utility functions to fast_numpy * :ghissue:`2626`: Adding Synb0 * :ghissue:`2770`: BF - update viz.py * :ghissue:`2763`: Update dki.py * :ghissue:`2751`: [ENH] Asymmetric peak_directions * :ghissue:`2762`: Remove Python 3.7 from CI * :ghissue:`2753`: Update adaptive_soft_matching.py * :ghissue:`2722`: fixed pca for features > samples, and fixed pca_noise_estimate * :ghissue:`2750`: Adding tests for gradient.py. * :ghissue:`2741`: Fixing solve_qp error * :ghissue:`2745`: Dipy Segmentation Core Dumped - Windows.Record * :ghissue:`2742`: ValueError: slice step cannot be zero * :ghissue:`2739`: codespell: config, workflow, typos fixed * :ghissue:`2590`: Fast Streamline Search algorithm implementation * :ghissue:`2733`: Update SynRegistrationFlow for dipy#2648 * :ghissue:`2723`: TRX integration, requires new attributes for SFT * :ghissue:`2729`: Numpy Version Incompatibility, AttributeError in dipy.align * :ghissue:`2726`: Setup broken on Python 3.10.9 setuptools 67.2.0 * :ghissue:`2727`: Fix EXTRAS_REQUIRE * :ghissue:`2725`: DOC - Update RUMBA-SD data requirement * :ghissue:`2707`: Fixdenoise * :ghissue:`2575`: [WIP] Define curvature and stepsize as default parameter instead of max_angle for tractography * :ghissue:`2414`: AffineMap.transform with option: interpolation='nearest' returns: "TypeError: No matching signature found" * :ghissue:`2716`: NF - Added cython utility functions * :ghissue:`2717`: fixed bug for non-linear fitting with masks * :ghissue:`2628`: resolve some CI's script typo * :ghissue:`2713`: Empty vtk support * :ghissue:`2599`: Support empty ArraySequence in transform_streamlines * :ghissue:`2625`: [Upcoming] Release 1.6.0
==================================== Release notes for DIPY version 1.6 ==================================== - NF: Unbiased groupwise linear bundle registration added. - NF: MAP+ constraints added. - Generalized PCA to less than 3 spatial dims. - Add positivity constraints to QTI. - Ability to apply Symmetric Diffeomorphic Registration to points/streamlines. - New Human Connectome Project (HCP) data fetcher added. - New Healthy Brain Network (HBN) data fetcher added. - Multiple Workflows updated (DTIFlow, LPCAFlow, MPPCA) and added (RUMBAFlow). - Ability to handle VTP files. - Large codebase cleaning. - Large documentation update. - Closed 75 issues and merged 41 pull requests. GitHub stats for 2022/03/11 - 2023/01/12 (tag: 1.5.0) These lists are automatically generated, and may be incomplete or contain duplicates. The following 15 authors contributed 242 commits. * Ariel Rokem * David Romero-Bascones * Deneb Boito * Eleftherios Garyfallidis * Emmanuelle Renauld * Eric Larson * Francois Rheault * Jacob Roberts * Jon Haitz Legarreta Gorroño * Malinda Dilhara * Omar Ocegueda * Sam Coveney * Serge Koudoro * Shreyas Fadnavis * Tom Dela Haije We closed a total of 116 issues, 41 pull requests and 75 regular issues; this is the full list (generated with the script :file:`tools/github_stats.py`): Pull Requests (41): * :ghpull:`2710`: small fixes for tutorials * :ghpull:`2711`: [FIX] use tempfile module instead of nibabel for TemporaryDirectory * :ghpull:`2702`: One more small fix to the hcp fetcher. * :ghpull:`2704`: MAINT: Fixes for 3.11 and sdist * :ghpull:`2701`: FIX: Don't print a progbar for downloading unless you need to. * :ghpull:`2700`: [FIX] incompatible type in numpy array * :ghpull:`2694`: NF: Add RUMBA-SD reconstruction workflow * :ghpull:`2697`: NF: Adds a fetcher for HCP data. * :ghpull:`2692`: RF: Improve multi-shell RUMBA test WM response parameterization * :ghpull:`2693`: TEST: Fix `Node.js` warnings linked to GitHub actions * :ghpull:`2687`: DOC: Fix typos in SH theory documentation page * :ghpull:`2690`: STYLE: Remove unnecessary b-val print in CSD reconstruction flow * :ghpull:`2688`: DOC: Document Dirac delta generation method missing member * :ghpull:`2683`: DOC: Adds missing documentation for a kwarg. * :ghpull:`2668`: ENH: Make the DTI fit CLI metric saving message accurate * :ghpull:`2674`: Improve doc (tensor values' order) * :ghpull:`2670`: ENH: Allow non-default parameters to `Patch2Self` CLI * :ghpull:`2672`: DOC: Miscellaneous docstring fixes * :ghpull:`2669`: DOC: Remove inaccurate `patch2self` docstring default values * :ghpull:`2664`: DOC: Fix DTI fit CLI docstring * :ghpull:`2553`: NF: Unbiased groupwise linear bundle registration * :ghpull:`2369`: Transform points with DiffeormorphicMap * :ghpull:`2631`: [FIX] Allow patch size parameter to be an int on denoise Workflow * :ghpull:`2630`: [DOC] Remove search index * :ghpull:`2629`: [FIX ] Handle save VTP * :ghpull:`2618`: Use np.linalg.multi_dot instead of multiple np.dot routines * :ghpull:`2606`: STYLE: Fix miscellaneous Python warnings * :ghpull:`2600`: Pin Ray * :ghpull:`2531`: NF: MAP+ constraints * :ghpull:`2589`: Switch from using nibabel InTemporaryDirectory to standard library tmpfile module * :ghpull:`2577`: Add positivity constraints to QTI * :ghpull:`2595`: Temporary skip Cython 0.29.29 * :ghpull:`2591`: STYLE: Avoid array-like mutable default argument values * :ghpull:`2592`: STYLE: Fix miscellaneous Python warnings * :ghpull:`2579`: Generalized PCA to less than 3 spatial dims * :ghpull:`2584`: transform_streamlines changes dtype to float64 * :ghpull:`2566`: [FIX] Update tests for the deprecated `dipy.io.bvectxt` module * :ghpull:`2581`: Fix logger in SFT * :ghpull:`2580`: DOC: Fix typos and grammar * :ghpull:`2576`: DOC: Documentation fixes * :ghpull:`2568`: DOC: Fix the docstring of `write_mapping` Issues (75): * :ghissue:`2710`: small fixes for tutorials * :ghissue:`2711`: [FIX] use tempfile module instead of nibabel for TemporaryDirectory * :ghissue:`2709`: DiffeomorphicMap object on github not the same as recent release * :ghissue:`2708`: Provide the dataset of this code * :ghissue:`2699`: WIP: Single shell/noreg redux * :ghissue:`2702`: One more small fix to the hcp fetcher. * :ghissue:`2704`: MAINT: Fixes for 3.11 and sdist * :ghissue:`2701`: FIX: Don't print a progbar for downloading unless you need to. * :ghissue:`2700`: [FIX] incompatible type in numpy array * :ghissue:`2694`: NF: Add RUMBA-SD reconstruction workflow * :ghissue:`2696`: Port HCP fetcher from pyAFQ into here * :ghissue:`2697`: NF: Adds a fetcher for HCP data. * :ghissue:`2692`: RF: Improve multi-shell RUMBA test WM response parameterization * :ghissue:`2693`: TEST: Fix `Node.js` warnings linked to GitHub actions * :ghissue:`1418`: Adding parallel_voxel_fit decorator * :ghissue:`2687`: DOC: Fix typos in SH theory documentation page * :ghissue:`2690`: STYLE: Remove unnecessary b-val print in CSD reconstruction flow * :ghissue:`2688`: DOC: Document Dirac delta generation method missing member * :ghissue:`2683`: DOC: Adds missing documentation for a kwarg. * :ghissue:`2679`: Problems with a .nii.gz file when loading and floating * :ghissue:`2676`: Does ```convert_sh_to_legacy``` work as intended ? * :ghissue:`2668`: ENH: Make the DTI fit CLI metric saving message accurate * :ghissue:`2674`: Improve doc (tensor values' order) * :ghissue:`2670`: ENH: Allow non-default parameters to `Patch2Self` CLI * :ghissue:`2673`: ENH: Doc: DTI format * :ghissue:`2667`: Defaults for Patch2Self * :ghissue:`2672`: DOC: Miscellaneous docstring fixes * :ghissue:`2669`: DOC: Remove inaccurate `patch2self` docstring default values * :ghissue:`2662`: Update cmd_line dipy_fit_dti * :ghissue:`2664`: DOC: Fix DTI fit CLI docstring * :ghissue:`2658`: Any chance of arm64 wheels for Mac / Python 3.10? * :ghissue:`2659`: Angle var * :ghissue:`2649`: IVIM VarPro fitting running error * :ghissue:`2553`: NF: Unbiased groupwise linear bundle registration * :ghissue:`2424`: Transforming individual points with SDR * :ghissue:`2327`: Diffeomorphic transformation of coordinates * :ghissue:`2313`: deform_streamlines for wholebrain tractogram doesn't function properly * :ghissue:`936`: WIP: coordinate mapping with DiffeomorphicMap * :ghissue:`2369`: Transform points with DiffeormorphicMap * :ghissue:`2616`: dti TensorModel fitting issue * :ghissue:`2627`: Free-Water Analysis Gradient Table Error * :ghissue:`2635`: get_flexi_tvis_affine(tvis_hdr, nii_aff) * :ghissue:`2634`: Fix small difference between pdfs dense 2d/3d * :ghissue:`2559`: CLI denoise patch_size error * :ghissue:`2631`: [F 10000 IX] Allow patch size parameter to be an int on denoise Workflow * :ghissue:`2564`: Search, index, module links not working in the doc * :ghissue:`2630`: [DOC] Remove search index * :ghissue:`2572`: Saving vtp file error * :ghissue:`2629`: [FIX ] Handle save VTP * :ghissue:`2622`: Error with Illustrating Electrostatic Repulsion * :ghissue:`2618`: Use np.linalg.multi_dot instead of multiple np.dot routines * :ghissue:`2617`: DKI model fit shape broadcast error * :ghissue:`2606`: STYLE: Fix miscellaneous Python warnings * :ghissue:`2602`: Dear experts, how can I set different number of fiber tracks before generating streamlines? * :ghissue:`2603`: Dear experts, how to save dti_peaks? * :ghissue:`2600`: Pin Ray * :ghissue:`2531`: NF: MAP+ constraints * :ghissue:`2587`: Thread safety concerns with reliance on `nibabel.tmpdirs.InTemporaryDirectory` * :ghissue:`2589`: Switch from using nibabel InTemporaryDirectory to standard library tmpfile module * :ghissue:`2577`: Add positivity constraints to QTI * :ghissue:`2450`: [NF] New tracking Algorithm: Parallel Transport Tractography (PTT) * :ghissue:`2594`: DIPY compilation fails with the last release of cython (0.29.29) * :ghissue:`2595`: Temporary skip Cython 0.29.29 * :ghissue:`2591`: STYLE: Avoid array-like mutable default argument values * :ghissue:`2592`: STYLE: Fix miscellaneous Python warnings * :ghissue:`2579`: Generalized PCA to less than 3 spatial dims * :ghissue:`2584`: transform_streamlines changes dtype to float64 * :ghissue:`2566`: [FIX] Update tests for the deprecated `dipy.io.bvectxt` module * :ghissue:`2581`: Fix logger in SFT * :ghissue:`2580`: DOC: Fix typos and grammar * :ghissue:`2576`: DOC: Documentation fixes * :ghissue:`2573`: Cannot Import "Feature" From "dipy.segment.metric" * :ghissue:`2568`: DOC: Fix the docstring of `write_mapping` * :ghissue:`2567`: This should be a `1` * :ghissue:`2565`: compress_streamlines() not available anymore
=================================== Release notes for DIPY version 1.5 =================================== GitHub stats for 2021/05/06 - 2022/03/10 (tag: 1.4.1) These lists are automatically generated, and may be incomplete or contain duplicates. The following 22 authors contributed 573 commits. * Ariel Rokem * Dan Bullock * David Romero-Bascones * Derek Pisner * Eleftherios Garyfallidis * Eric Larson * Francis Jerome * Francois Rheault * Gabriel Girard * Giulia Bertò * Javier Guaje * Jon Haitz Legarreta Gorroño * Joshua Newton * Kenji Marshall * Leevi Kerkela * Leon Weninger * Lucas Da Costa * Nasim Anousheh * Rafael Neto Henriques * Sam Coveney * Serge Koudoro * Shreyas Fadnavis We closed a total of 200 issues, 72 pull requests and 128 regular issues; this is the full list (generated with the script :file:`tools/github_stats.py`): Pull Requests (72): * :ghpull:`2561`: [FIX] Motion correction tutorial * :ghpull:`2520`: Resdnn inference * :ghpull:`2558`: BUG: Fix errant warning about starting_affine * :ghpull:`2557`: MAINT: Fix version * :ghpull:`2556`: [FIX] Update `dipy.segment` tutorials * :ghpull:`2554`: Support .vtp files * :ghpull:`2555`: Limit `peaks_from_model` number of processes in examples * :ghpull:`2539`: Adds utilities for embarassingly parallel loops. * :ghpull:`2545`: Stateful Tractogram DPS and DPP keys ordering * :ghpull:`2548`: Add timeout + concurrency to GHA * :ghpull:`2549`: [ENH] Clarify reconst_sh tutorial * :ghpull:`2550`: [ENH] Add sigma to DTI/DKI RESTORE workflow * :ghpull:`2551`: [MNT] Update mininal dependencies version * :ghpull:`2536`: Random colors fix in horizon * :ghpull:`2533`: [FIX] Docstring cleaning: wrong underline length... * :ghpull:`2342`: NF: q-space trajectory imaging * :ghpull:`2512`: Masking for affine registration * :ghpull:`2526`: TEST: Filter legacy SH bases warnings in tests * :ghpull:`2534`: TEST: Remove unnecessary `main` method definition in tests * :ghpull:`2532`: STYLE: Remove unused import statements * :ghpull:`2529`: STYLE: Remove unused import statements * :ghpull:`2528`: TEST: Remove legacy `nose`-related dead testing code * :ghpull:`2527`: TEST: Fix intermittent RUMBA test check failure * :ghpull:`2493`: Fury dependency resolution * :ghpull:`2522`: ENH: Miscellaneous cleanup * :ghpull:`2521`: DOC: Use GitHub actions status badge in README * :ghpull:`2420`: Documentation corrections * :ghpull:`2482`: ENH: Improve SH bases warning messages * :ghpull:`2423`: NF: rumba reconst * :ghpull:`2518`: Migrations from Azure Pipeline to Github Actions * :ghpull:`2515`: Default to False output for null streamlines in streamline_near_roi * :ghpull:`2513`: [MNT] Drop distutils * :ghpull:`2506`: Horizon FURY update * :ghpull:`2510`: Optimize sfm (reboot) * :ghpull:`2487`: ENH: Better error message * :ghpull:`2442`: [NF] Add Motion correction workflow * :ghpull:`2470`: Add utilities functions: radius curvature <--> maximum deviation angle * :ghpull:`2485`: DOC: Small updates. * :ghpull:`2481`: ENH: Import ABCs from `collections.abc` * :ghpull:`2480`: STYLE: Make `sklearn` import warning messages consistent * :ghpull:`2478`: ENH: Deal appropriately with user warnings * :ghpull:`2479`: STYLE: Improve style in misc files * :ghpull:`2475`: ENH: Fix `complex` type `NumPy` alias deprecation warnings * :ghpull:`2476`: ENH: Fix `dipy.io.bvectxt` deprecation warning * :ghpull:`2472`: ENH: Return unique invalid streamline removal indices * :ghpull:`2471`: DOC: Fix coding style guideline link * :ghpull:`2468`: [MNT] Use windows-latest on azure pipeline * :ghpull:`2467`: [ENH] Add fit_method option in DTI and DKI CLI * :ghpull:`2466`: deprecate dipy.io.bvectxt module * :ghpull:`2453`: make it compatible when number of volume is 2 * :ghpull:`2413`: Azure pipeline: from ubuntu 1604 to 2004 * :ghpull:`2447`: reduce_rois: Force input array type to bool to avoid bitwise or errors * :ghpull:`2444`: [DOC] : Added citation for IVIM dataset * :ghpull:`2434`: MAINT: Update import from ndimage * :ghpull:`2435`: BUG: Backward compat support for pipeline * :ghpull:`2436`: MAINT: Bump tolerance * :ghpull:`2438`: BUG: Fix misplaced comma in `warn()` call from `patch2self.py` * :ghpull:`2374`: ROIs visualizer * :ghpull:`2390`: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling * :ghpull:`2417`: OPT: Initialize `Shape` struct * :ghpull:`2419`: Fixes the default option in the command line for Patch2Self 'ridge' -> 'ols' * :ghpull:`2406`: Manage Approx_polygon_track with repeated points * :ghpull:`2411`: [FIX] `c_compress_streamline` discard identical points * :ghpull:`2416`: OPT: Prefer using a typed index to get the PMF value * :ghpull:`2415`: Implementation multi_voxel_fit progress bar * :ghpull:`2410`: [ENH] Improve Shore Tests * :ghpull:`2409`: NF - Sample PMF for an input position and direction * :ghpull:`2405`: Small correction on KFA * :ghpull:`2407`: from random to deterministic test for deform_streamlines * :ghpull:`2392`: Add decomposition * :ghpull:`2389`: [Fix] bundles_distances_mdf asymmetric values * :ghpull:`2368`: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline. Issues (128): * :ghissue:`2561`: [FIX] Motion correction tutorial * :ghissue:`2123`: WIP: Residual Deep NN * :ghissue:`2520`: Resdnn inference * :ghissue:`2558`: BUG: Fix errant warning about starting_affine * :ghissue:`2557`: MAINT: Fix version * :ghissue:`2489`: MAINT: Get Python 3.10 binaries up on scipy-wheels-nightly * :ghissue:`2556`: [FIX] Update `dipy.segment` tutorials * :ghissue:`2554`: Support .vtp files * :ghissue:`2525`: Support Opening `.vtp` files * :ghissue:`2555`: Limit `peaks_from_model` number of processes in examples * :ghissue:`2539`: Adds utilities for embarassingly parallel loops. * :ghissue:`2509`: Easy robustness for streamline_near_roi and near_roi for empty streamlines? * :ghissue:`2543`: StatefulTractogram.are_compatible compare data_per_point keys as list instead of set * :ghissue:`2545`: Stateful Tractogram DPS and DPP keys ordering * :ghissue:`2548`: Add timeout + concurrency to GHA * :ghissue:`2549`: [ENH] Clarify reconst_sh tutorial * :ghissue:`2546`: Confusing import in 'reconst_sh` * :ghissue:`2550`: [ENH] Add sigma to DTI/DKI RESTORE workflow * :ghissue:`2542`: DTI workflow should allow user-defined fitting method * :ghissue:`2551`: [MNT] Update mininal dependencies version * :ghissue:`2477`: Numpy min dependency update * :ghissue:`2541`: Issue with coverage and pytests for numpy.min() * :ghissue:`2507`: kernel died when use dipy.viz * :ghissue:`2536`: Random colors fix in horizon * :ghissue:`2533`: [FIX] Docstring cleaning: wrong underline length... * :ghissue:`2422`: WIP-Adding math in SLR tutorial * :ghissue:`2342`: NF: q-space trajectory imaging * :ghissue:`2512`: Masking for affine registration * :ghissue:`1969`: imaffine mask support * :ghissue:`2526`: TEST: Filter legacy SH bases warnings in tests * :ghissue:`2456`: Horizon tests failing * :ghissue:`2534`: TEST: Remove unnecessary `main` method definition in tests * :ghissue:`2532`: STYLE: Remove unused import statements * :ghissue:`2524`: Add concurrency + timeout to Github Actions (GHA) * :ghissue:`2529`: STYLE: Remove unused import statements * :ghissue:`2528`: TEST: Remove legacy `nose`-related dead testing code * :ghissue:`2527`: TEST: Fix intermittent RUMBA test check failure * :ghissue:`2493`: Fury dependency resolution * :ghissue:`2522`: ENH: Miscellaneous cleanup * :ghissue:`2521`: DOC: Use GitHub actions status badge in README * :ghissue:`2420`: Documentation corrections * :ghissue:`2482`: ENH: Improve SH bases warning messages * :ghissue:`2449`: Nonsense deprecation warning * :ghissue:`2423`: NF: rumba reconst * :ghissue:`2179`: NF: Complete masking implementation in affine registration with MI * :ghissue:`2518`: Migrations from Azure Pipeline to Github Actions * :ghissue:`2492`: Move to GitHub actions / reusable actions * :ghissue:`2515`: Default to False output for null streamlines in streamline_near_roi * :ghissue:`2497`: Remove python 3.6 from Azure pipelines * :ghissue:`2495`: Remove Distutils (deprecated) * :ghissue:`2513`: [MNT] Drop distutils * :ghissue:`2506`: Horizon FURY update * :ghissue:`2305`: [WIP] Brain Tumor Image Segmentation Code * :ghissue:`2499`: Problem generating Connectivity Matrix: "Slice step cannot be zero" * :ghissue:`2510`: Optimize sfm (reboot) * :ghissue:`2488`: Minimize memory footprint whereever possible, add joblib support for … * :ghissue:`2504`: Why are there many small dots on the fwdwi image? * :ghissue:`2502`: Can i read specific b-values from my own multishell data? * :ghissue:`2500`: MAP issue * :ghissue:`2490`: [BUG] MRI-CT alignment failure * :ghissue:`2487`: ENH: Better error message * :ghissue:`2402`: Dipy 1.4.1 breaks nipype.interfaces.dipy.dipy_to_nipype_interface * :ghissue:`2486`: Wrong doc in interpolation * :ghissue:`2442`: [NF] Add Motion correction workflow * :ghissue:`2470`: Add utilities functions: radius curvature <--> maximum deviation angle * :ghissue:`2485`: DOC: Small updates. * :ghissue:`2484`: [ENH] Add grid search to `AffineRegistration.optimize` * :ghissue:`2483`: [DOC] Stable/Latest Documentation Structure * :ghissue:`2481`: ENH: Import ABCs from `collections.abc` * :ghissue:`2480`: STYLE: Make `sklearn` import warning messages consistent * :ghissue:`2478`: ENH: Deal appropriately with user warnings * :ghissue:`2479`: STYLE: Improve style in misc files * :ghissue:`2475`: ENH: Fix `complex` type `NumPy` alias deprecation warnings * :ghissue:`2476`: ENH: Fix `dipy.io.bvectxt` deprecation warning * :ghissue:`2472`: ENH: Return unique invalid streamline removal indices * :ghissue:`2471`: DOC: Fix coding style guideline link * :ghissue:`2468`: [MNT] Use windows-latest on azure pipeline * :ghissue:`2467`: [ENH] Add fit_method option in DTI and DKI CLI * :ghissue:`2463`: DTI RESTORE on the CLI * :ghissue:`2466`: deprecate dipy.io.bvectxt module * :ghissue:`2460`: Deprecate and Remove dipy.io.bvectxt * :ghissue:`2429`: random_colors flag in dipy_horizon does not work as before * :ghissue:`2461`: Patch2Self: Less than 10 3D Volumes Bug * :ghissue:`2464`: Typo on the homepage * :ghissue:`2453`: make it compatible when number of volume is 2 * :ghissue:`2457`: Choosing sigma_diff and radius parameters for SyN registration * :ghissue:`2413`: Azure pipeline: from ubuntu 1604 to 2004 * :ghissue:`2454`: Can I show fiber with vtk? * :ghissue:`2446`: Use of bitwise or with non-bool inputs results in ufunc 'bitwise_or' error * :ghissue:`2447`: reduce_rois: Force input array type to bool to avoid bitwise or errors * :ghissue:`2444`: [DOC] : Added citation for IVIM dataset * :ghissue:`2443`: Citation for IVIM dataset not present in docs * :ghissue:`2434`: MAINT: Update import from ndimage * :ghissue:`2441`: Horizon error - disk position outside the slider line * :ghissue:`2435`: BUG: Backward compat support for pipeline * :ghissue:`2436`: MAINT: Bump tolerance * :ghissue:`2438`: BUG: Fix misplaced comma in `warn()` call from `patch2self.py` * :ghissue:`2430`: dipy.align.reslice * :ghissue:`2431`: dipy.align.reslice interpolation order for downsampling * :ghissue:`2432`: How to apply MI metric in dipy？ * :ghissue:`2374`: ROIs visualizer * :ghissue:`2390`: NF: extend the align workflow with Rigid+IsoScaling and Rigid+Scaling * :ghissue:`2417`: OPT: Initialize `Shape` struct * :ghissue:`2419`: Fixes the default option in the command line for Patch2Self 'ridge' -> 'ols' * :ghissue:`2406`: Manage Approx_polygon_track with repeated points * :ghissue:`2314`: Approx_polygon_track with repeated points gives an error * :ghissue:`2411`: [FIX] `c_compress_streamline` discard identical points * :ghissue:`1805`: `c_compress_streamline` keeps identical points when it shouldn't * :ghissue:`2418`: kernel failure when importing mask from dipy.segment * :ghissue:`2416`: OPT: Prefer using a typed index to get the PMF value * :ghissue:`2415`: Implementation multi_voxel_fit progress bar * :ghissue:`2410`: [ENH] Improve Shore Tests * :ghissue:`365`: Code review items for `dipy.reconst.shore` * :ghissue:`2409`: NF - Sample PMF for an input position and direction * :ghissue:`2404`: Change affine in StatefulTractogram * :ghissue:`2405`: Small correction on KFA * :ghissue:`2407`: from random to deterministic test for deform_streamlines * :ghissue:`2392`: Add decomposition * :ghissue:`717`: Download each shell of the CENIR data separately? * :ghissue:`2209`: _pytest.pathlib.ImportPathMismatchError: * :ghissue:`1934`: Random lpca denoise * :ghissue:`2312`: DIPY open group meetings, Spring 2021 * :ghissue:`2383`: error in mcsd model fitting (DCPError) * :ghissue:`2391`: error performing cross-validation on diffusion HCP data * :ghissue:`2393`: Add a function to read streamline from the result generated by the command "probtrackx2" in FMRIB's Diffusion Toolbox * :ghissue:`2389`: [Fix] bundles_distances_mdf asymmetric values * :ghissue:`2310`: `bundles_distances_mdf` asymmetric values * :ghissue:`2368`: RF - Moved tracking.localtrack._local_tracker to DirectionGetter.generate_streamline.
===================================== Release notes for DIPY version 1.4.1 ===================================== - Patch2Self and its documentation updated. - BUAN and Recobundles documentation updated. - Standardization and improvement of the multiprocessing / multithreading rules. - Community and governance information added. - New surface seeding module for tractography named `mesh`. - Large update of Cython code in respect of the last standard. - Large documentation update. - Closed 61 issues and merged 28 pull requests. GitHub stats for 2021/03/14 - 2021/05/05 (tag: 1.4.0) These lists are automatically generated, and may be incomplete or contain duplicates. The following 11 authors contributed 153 commits. * Ariel Rokem * Bramsh Qamar Chandio * David Romero-Bascones * Eleftherios Garyfallidis * Etienne St-Onge * Felix Liu * Gabriel Girard * John Kruper * Nasim Anousheh * Serge Koudoro * Shreyas Fadnavis We closed a total of 89 issues, 28 pull requests and 61 regular issues; this is the full list (generated with the script :file:`tools/github_stats.py`): Pull Requests (28): * :ghpull:`2367`: [Upcoming] Release 1.4.1 * :ghpull:`2387`: added all examples of CST and updated AFQ file name * :ghpull:`2386`: Adding CST_L back in Bundle Segmentation Tutorial * :ghpull:`2375`: Expanding Bundle Segmentation Tutorial * :ghpull:`2382`: Updated docs for using P2S optimally * :ghpull:`2385`: RF: Standardize the argument name for the number of threads/cores * :ghpull:`2384`: RF - Removed deprecated tracking code * :ghpull:`2351`: Updating Vec2vec_rotmat to deal with numerical issues * :ghpull:`2381`: Adds the NIPY code of conduct to our repo. * :ghpull:`2371`: [Fix] Add "None" options in the CLIs * :ghpull:`2352`: RF: configure num_threads==-1 as the value to use all cores * :ghpull:`2373`: [FIX] warning if not the same number of points * :ghpull:`2372`: Expand patch radius if input is int * :ghpull:`2348`: RF: Use new name for this function. * :ghpull:`2363`: [ENH] Adding cython file(*.pyx) in documentation * :ghpull:`2365`: [DOC]: Change defaults in Patch2Self example * :ghpull:`2349`: [ENH] Allow for other statistics, like median, in afq_profile * :ghpull:`2350`: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays * :ghpull:`2346`: [MNT] Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible * :ghpull:`2347`: Replacing Data in NLMeans Tutorial * :ghpull:`2340`: [FIX] reactivate codecov * :ghpull:`2344`: [FIX] Tractogram Header in RecoBundles Tutorial * :ghpull:`2339`: [FIX] Cleanup deprecated np.float, np.bool, np.int * :ghpull:`1648`: Mesh seeding (surface) * :ghpull:`2337`: BF: Change patch2self defaults. * :ghpull:`2333`: Add __str__ to GradientTable * :ghpull:`2335`: RF: Replaces deprecated basis by its new name. * :ghpull:`2332`: [FIX] fix tests for all new deprecated functions Issues (61): * :ghissue:`2375`: Expanding Bundle Segmentation Tutorial * :ghissue:`1973`: Recobundles documentation * :ghissue:`2382`: Updated docs for using P2S optimally * :ghissue:`2385`: RF: Standardize the argument name for the number of threads/cores * :ghissue:`2377`: RF: standardize the argument name for the number of threads/cores * :ghissue:`2384`: RF - Removed deprecated tracking code * :ghissue:`2351`: Updating Vec2vec_rotmat to deal with numerical issues * :ghissue:`2381`: Adds the NIPY code of conduct to our repo. * :ghissue:`2380`: Community and governance * :ghissue:`2371`: [Fix] Add "None" options in the CLIs * :ghissue:`2300`: NF: Add "None" options in the CLIs * :ghissue:`2352`: RF: configure num_threads==-1 as the value to use all cores * :ghissue:`2373`: [FIX] warning if not the same number of points * :ghissue:`2320`: RecoBundles distances * :ghissue:`2372`: Expand patch radius if input is int * :ghissue:`2341`: Allow use of all threads in the gibbs ringing workflow * :ghissue:`2348`: RF: Use new name for this function. * :ghissue:`2353`: How to create tractogram from a multi-shell data for RecoBundles * :ghissue:`1311`: Adding cython file(*.pyx) in documentation * :ghissue:`2363`: [ENH] Adding cython file(*.pyx) in documentation * :ghissue:`1302`: [DOC] cython (pyx) files are not parsed * :ghissue:`366`: Some doc missing * :ghissue:`2365`: [DOC]: Change defaults in Patch2Self example * :ghissue:`1672`: Dipy Segmentation fault when visualizing * :ghissue:`1444`: Move general registration tools into own package? * :ghissue:`562`: Multiprocessing the tensor reconstruction * :ghissue:`13`: Cordinate maps stuff * :ghissue:`2324`: Dipy for VR/AR * :ghissue:`2345`: Saving and/or importing nonlinear warps * :ghissue:`2349`: [ENH] Allow for other statistics, like median, in afq_profile * :ghissue:`2350`: [FIX] Use npy_intp variables instead of int and size_t to iterate over numpy arrays * :ghissue:`423`: Use npy_intp variables instead of int and size_t to iterate over numpy arrays * :ghissue:`837`: Should we enforce float32 in tractography results? * :ghissue:`636`: Get a standard interface for the functions using the noise variance * :ghissue:`861`: open mp defaults to one core, is that a good idea? * :ghissue:`2346`: [MNT] Update and fix Cython warnings and use cnp.PyArray_DATA wherever possible * :ghissue:`1895`: Cython warnings * :ghissue:`545`: Use cnp.PyArray_DATA wherever possible * :ghissue:`2347`: Replacing Data in NLMeans Tutorial * :ghissue:`1847`: Replacing Data in NLMeans Tutorial * :ghissue:`2340`: [FIX] reactivate codecov * :ghissue:`1872`: Did we lose our coverage reporting? * :ghissue:`1646`: Fetcher should not be under coverage * :ghissue:`1635`: Track from mesh * :ghissue:`2344`: [FIX] Tractogram Header in RecoBundles Tutorial * :ghissue:`2309`: Tractogram Header in RecoBundles Tutorial * :ghissue:`2334`: Aphysical signal after running patch2self * :ghissue:`1873`: ERROR while import data * :ghissue:`2343`: Missing Python 3.9 wheels * :ghissue:`1996`: Documentation not being rendered correctly * :ghissue:`2311`: Accuracy of DKI measures * :ghissue:`2274`: DKI metrics' accuracy * :ghissue:`2339`: [FIX] Cleanup deprecated np.float, np.bool, np.int * :ghissue:`1648`: Mesh seeding (surface) * :ghissue:`1675`: WIP: Integer indices * :ghissue:`2316`: TranslationTransform2D Exact X-Y Shift * :ghissue:`2337`: BF: Change patch2self defaults. * :ghissue:`2333`: Add __str__ to GradientTable * :ghissue:`2331`: gtab.info does not print anything * :ghissue:`2335`: RF: Replaces deprecated basis by its new name. * :ghissue:`2332`: [FIX] fix tests for all new deprecated functions
.. _release1.4: ==================================== Release notes for DIPY version 1.4 ==================================== GitHub stats for 2020/11/05 - 2021/03/13 (tag: 1.3.0) These lists are automatically generated, and may be incomplete or contain duplicates. The following 8 authors contributed 119 commits. * Areesha Tariq * Ariel Rokem * Bramsh Qamar * Eleftherios Garyfallidis * Jon Haitz Legarreta Gorroño * Philippe Karan * Serge Koudoro * Shreyas Fadnavis We closed a total of 47 issues, 19 pull requests and 28 regular issues; this is the full list (generated with the script :file:`tools/github_stats.py`): Pull Requests (19): * :ghpull:`2318`: [MAINT] Fixed Handling Negative Values for P2S * :ghpull:`2317`: Allowing response_from_mask_msmt to take btens into account * :ghpull:`2315`: Add weekly build to azure + update linux matrix * :ghpull:`2307`: BUAN Documentation Typo * :ghpull:`2278`: BUAN and RB Documentation update * :ghpull:`2275`: [DOC]: Reconstruction CLI * :ghpull:`2277`: [DOC] Registration CLI * :ghpull:`2289`: Patch2Self: Denoising Diffusion MRI with Self-supervised Learning * :ghpull:`2292`: [DOC]: Add Tracking CLI Documentation * :ghpull:`2296`: [DOC] Fix the 'None' value in num_threads attribute * :ghpull:`2294`: [DOC]: Remove default values from docstrings * :ghpull:`2291`: Adds for the dipy.align._public module * :ghpull:`2295`: [DOC]: Fix inconsistent function parameters * :ghpull:`2280`: DOC: Improve the denoising workflow documentation * :ghpull:`2287`: [DOC] Remove default values from doctstrings for reconstruction methods * :ghpull:`2286`: [DOC] fix inconsistent citation style * :ghpull:`2284`: [DOC] Fix incorrect default output directory in doctsrings * :ghpull:`2283`: [DOC] Fix incorrect default output directory in doctsrings * :ghpull:`2282`: [DOC] fix minor typo Issues (28): * :ghissue:`2210`: Really release the memory used by arclength variable. * :ghissue:`722`: Adding optional (GPL) dependencies to have new features * :ghissue:`2328`: Website is down * :ghissue:`2323`: Brain mask as a required argument to CLI * :ghissue:`2318`: [MAINT] Fixed Handling Negative Values for P2S * :ghissue:`2317`: Allowing response_from_mask_msmt to take btens into account * :ghissue:`2315`: Add weekly build to azure + update linux matrix * :ghissue:`2229`: DIPY open group meetings, Fall 2020 * :ghissue:`2307`: BUAN Documentation Typo * :ghissue:`2098`: Q-Space Interpolation Methods * :ghissue:`2278`: BUAN and RB Documentation update * :ghissue:`2275`: [DOC]: Reconstruction CLI * :ghissue:`2277`: [DOC] Registration CLI * :ghissue:`2303`: DKI ODF * :ghissue:`685`: (WIP) DKI PR5 - NF: DKI-ODF estimation * :ghissue:`2289`: Patch2Self: Denoising Diffusion MRI with Self-supervised Learning * :ghissue:`2292`: [DOC]: Add Tracking CLI Documentation * :ghissue:`2296`: [DOC] Fix the 'None' value in num_threads attribute * :ghissue:`2294`: [DOC]: Remove default values from docstrings * :ghissue:`2291`: Adds for the dipy.align._public module * :ghissue:`2295`: [DOC]: Fix inconsistent function parameters * :ghissue:`2280`: DOC: Improve the denoising workflow documentation * :ghissue:`2287`: [DOC] Remove default values from doctstrings for reconstruction methods * :ghissue:`2286`: [DOC] fix inconsistent citation style * :ghissue:`2284`: [DOC] Fix incorrect default output directory in doctsrings * :ghissue:`2283`: [DOC] Fix incorrect default output directory in doctsrings * :ghissue:`2282`: [DOC] fix minor typo * :ghissue:`2279`: Visibility of Workflow Tutorials on DIPY website
==================================== Release notes for DIPY version 1.3 ==================================== GitHub stats for 2020/09/09 - 2020/11/02 (tag: 1.2.0) Highlight: --------- - Gibbs Ringing correction 10X faster. - Spherical harmonics basis definitions updated. - Added SMT2 metrics from mean signal diffusion kurtosis. - New interface functions added to the registration module. - New linear transform added to the registration module. - New tutorials for DIPY command line interfaces. - Fixed compatibility issues with different dependencies. - Tqdm (multiplatform progress bar for data downloading) dependency added. - Large documentation update. - Bundle section highlight from BUAN added in Horizon. - Closed 134 issues and merged 49 pull requests. The following 14 authors contributed 284 commits. * Areesha Tariq * Ariel Rokem * Basile Pinsard * Bramsh Qamar * Charles Poirier * Eleftherios Garyfallidis * Eric Larson * Gregory Lee * Jaewon Chung * Jon Haitz Legarreta Gorroño * Philippe Karan * Rafael Neto Henriques * Serge Koudoro * Siddharth Kapoor We closed a total of 134 issues, 49 pull requests and 85 regular issues; this is the full list (generated with the script :file:`tools/github_stats.py`): Pull Requests (49): * :ghpull:`2181`: BUAN bundle highlight option in horizon * :ghpull:`2223`: [NF] new linear transforms for Rigid+IsoScaling and Rigid+Scaling * :ghpull:`2238`: [FIX] fix cython error from pre matrix * :ghpull:`2265`: Gibbs denoising: fft only along the axis of interest * :ghpull:`2206`: NF: Update definitions of SH bases and documentation * :ghpull:`2266`: STYLE: minor refactoring in TissueClassifierHMRF * :ghpull:`2255`: Modifying dti.design_matrix to take gtab.btens into account * :ghpull:`2271`: Increase Azure pipeline timeout * :ghpull:`2263`: [FIX] update multiple models due to cvxpy 1.1 (part2) * :ghpull:`2259`: [Fix] Allow read_bvals_bvecs to have 1 or 2 dwi volumes only * :ghpull:`2264`: BF: Fix `dipy_align_syn` default value assumptions * :ghpull:`2268`: BUG: Fix literal * :ghpull:`2267`: BUG: Fix string literal * :ghpull:`2262`: [FIX] update tests to respect numpy NEP 34 * :ghpull:`2244`: DOC : Denoising CLI * :ghpull:`2119`: RecoBundles updated to read and save .trk files from Old API * :ghpull:`2260`: [Fix] Better error handling in Diffeomorphic map `get_map` * :ghpull:`2258`: [FIX] update Azure OSX CI + remove Azure Linux CI's * :ghpull:`2257`: [Fix] warning if not the same number of points * :ghpull:`2261`: [DOC]:Removed tracking evaluation section * :ghpull:`1919`: [DOC] Add an overview of reconstruction models * :ghpull:`2256`: update BUAN citations * :ghpull:`2253`: Improve FFT efficiency in gibbs_removal * :ghpull:`2240`: [ENH] Deprecate interp parameter name in AffineMap * :ghpull:`2198`: Make single and multi tensor simulations compatible with btensors * :ghpull:`2025`: Adds an align.api module, which provides simplified API to registration functions * :ghpull:`2197`: Estimate smt2 metrics from mean signal kurtosis * :ghpull:`2227`: RF: Replaces our own custom progressbar with a tqdm progressbar. * :ghpull:`2250`: [ENH] Add parallelization to gibbs denoising * :ghpull:`2252`: BUG: Set tau factor to parameter value in local PCA * :ghpull:`2248`: [DOC] fetching dataset * :ghpull:`2249`: [fix] fix value_range in HORIZON * :ghpull:`2247`: BF: In LiFE, set nan signals to 0. * :ghpull:`2246`: [DOC] Replace simple backticks with double backticks * :ghpull:`2239`: [ENH] Add inplace kwarg to gibbs_removal * :ghpull:`2242`: maintenance of bundle_shape_similarity function * :ghpull:`2241`: STYLE: Exclude package information file from PEP8 checks * :ghpull:`2235`: DOC: Add tips to the documentation build section * :ghpull:`2234`: DOC: Improve some of the links in the `info.py` file * :ghpull:`2233`: Clarifying msmt response function docstrings * :ghpull:`2231`: DOC: Fix HTML tag in dataset list documentation table * :ghpull:`2221`: Robustify solve_qp for possible SolverError in one odd voxel * :ghpull:`2226`: STYLE: Conform to `reStructuredText` syntax in examples sections * :ghpull:`2225`: [CI] Replace Rackspace by https://anaconda.org/scipy-wheels-nightly * :ghpull:`2224`: Replace pytest.xfail by npt.assert_raises * :ghpull:`2220`: [DOC] move Denoising on its own section * :ghpull:`2218`: DOC : inconsistent save_seeds documentation * :ghpull:`2217`: Fixing numpy version rcond issue in numpy.linalg.lstsq * :ghpull:`2211`: [FIX] used numerical indices for references Issues (85): * :ghissue:`2181`: BUAN bundle highlight option in horizon * :ghissue:`2272`: DOC : Registration CLI * :ghissue:`2223`: [NF] new linear transforms for Rigid+IsoScaling and Rigid+Scaling * :ghissue:`2180`: [NF] add new linear transforms for Rigid+IsoScaling and Rigid+Scaling * :ghissue:`2238`: [FIX] fix cython error from pre matrix * :ghissue:`2265`: Gibbs denoising: fft only along the axis of interest * :ghissue:`2206`: NF: Update definitions of SH bases and documentation * :ghissue:`392`: mrtrix 0.3 default basis is different from mrtrix 0.2 * :ghissue:`2266`: STYLE: minor refactoring in TissueClassifierHMRF * :ghissue:`2255`: Modifying dti.design_matrix to take gtab.btens into account * :ghissue:`2271`: Increase Azure pipeline timeout * :ghissue:`2054`: Discrepancy between dipy.gibbs.gibbs_removal and reisert/unring/ * :ghissue:`2263`: [FIX] update multiple models due to cvxpy 1.1 (part2) * :ghissue:`2190`: Reconstruction with Multi-Shell Multi-Tissue CSD * :ghissue:`2259`: [Fix] Allow read_bvals_bvecs to have 1 or 2 dwi volumes only * :ghissue:`2046`: read_bvals_bvecs can't read a single volume dwi * :ghissue:`2264`: BF: Fix `dipy_align_syn` default value assumptions * :ghissue:`2268`: BUG: Fix literal * :ghissue:`2267`: BUG: Fix string literal * :ghissue:`2262`: [FIX] update tests to respect numpy NEP 34 * :ghissue:`2132`: Generating ndarrays with different shapes generates NumPy warning at testing * :ghissue:`1266`: test_mapmri_isotropic_static_scale_factor failure on OSX buildbot * :ghissue:`1264`: FBC measures test failure on PPC * :ghissue:`2244`: DOC : Denoising CLI * :ghissue:`2119`: RecoBundles updated to read and save .trk files from Old API * :ghissue:`2117`: RecoBundles workflow still using old API * :ghissue:`2260`: [Fix] Better error handling in Diffeomorphic map `get_map` * :ghissue:`2202`: Add error handling in Diffeomorphic map `get_map` * :ghissue:`2258`: [FIX] update Azure OSX CI + remove Azure Linux CI's * :ghissue:`2257`: [Fix] warning if not the same number of points * :ghissue:`342`: Missing a warning if not the same number of points * :ghissue:`2261`: [DOC]:Removed tracking evaluation section * :ghissue:`2115`: Independent section on Fiber tracking evaluation not necessary * :ghissue:`1744`: [WIP] [NF] Free Water Elimination for single-shell DTI (updated version) * :ghissue:`1919`: [DOC] Add an overview of reconstruction models * :ghissue:`1489`: Documentation: how to know which models support multi-shell? * :ghissue:`2256`: update BUAN citations * :ghissue:`2253`: Improve FFT efficiency in gibbs_removal * :ghissue:`2240`: [ENH] Deprecate interp parameter name in AffineMap * :ghissue:`2192`: Bringing AffineMap and DiffeomorphicMap a little closer together * :ghissue:`2198`: Make single and multi tensor simulations compatible with btensors * :ghissue:`2025`: Adds an align.api module, which provides simplified API to registration functions * :ghissue:`2201`: Gradient table message error * :ghissue:`2232`: This should be len(np.unique(gtab.bvals)) - 1 or somesuch * :ghissue:`2197`: Estimate smt2 metrics from mean signal kurtosis * :ghissue:`2227`: RF: Replaces our own custom progressbar with a tqdm progressbar. * :ghissue:`2219`: Replace fetcher progress bar with tqdm * :ghissue:`2250`: [ENH] Add parallelization to gibbs denoising * :ghissue:`2236`: Parallelize gibbs_removal * :ghissue:`2254`: Trackvis header saved with Dipy (nibabel) is not read by Matlab or other tools * :ghissue:`2252`: BUG: Set tau factor to parameter value in local PCA * :ghissue:`2251`: localpca tau_factor is hard coded to 2.3 * :ghissue:`2248`: [DOC] fetching dataset * :ghissue:`2249`: [fix] fix value_range in HORIZON * :ghissue:`2243`: Unable to visualize data through dipy_horizon * :ghissue:`2247`: BF: In LiFE, set nan signals to 0. * :ghissue:`2246`: [DOC] Replace simple backticks with double backticks * :ghissue:`2239`: [ENH] Add inplace kwarg to gibbs_removal * :ghissue:`2237`: gibbs_removal overwrites input data when inputting 3-d or 4-d data. * :ghissue:`2245`: DOC: Fix Sphinx verbatim syntax in coding style guide * :ghissue:`2242`: maintenance of bundle_shape_similarity function * :ghissue:`2241`: STYLE: Exclude package information file from PEP8 checks * :ghissue:`2235`: DOC: Add tips to the documentation build section * :ghissue:`2234`: DOC: Improve some of the links in the `info.py` file * :ghissue:`2222`: How can I track different streamlines in DIPY? * :ghissue:`2233`: Clarifying msmt response function docstrings * :ghissue:`2231`: DOC: Fix HTML tag in dataset list documentation table * :ghissue:`2230`: TST: Assert the shape of the output based on the docstring. * :ghissue:`2228`: Best practices for saving a tissue classifier object? * :ghissue:`2221`: Robustify solve_qp for possible SolverError in one odd voxel * :ghissue:`2109`: DIPY lab meetings, Spring 2020 * :ghissue:`2226`: STYLE: Conform to `reStructuredText` syntax in examples sections * :ghissue:`2225`: [CI] Replace Rackspace by https://anaconda.org/scipy-wheels-nightly * :ghissue:`2214`: Rackspace does not exist anymore -> Update PRE-matrix on Travis and Azure required * :ghissue:`2224`: Replace pytest.xfail by npt.assert_raises * :ghissue:`2220`: [DOC] move Denoising on its own section * :ghissue:`2218`: DOC : inconsistent save_seeds documentation * :ghissue:`2217`: Fixing numpy version rcond issue in numpy.linalg.lstsq * :ghissue:`2216`: test_multi_shell_fiber_response failed with Numpy 1.13.3 * :ghissue:`2211`: [FIX] used numerical indices for references * :ghissue:`2185`: Inconsistency in stating references in dti.py * :ghissue:`2215`: problem with fetching stanford data * :ghissue:`1762`: Font on instructions is small on mac * :ghissue:`1354`: strange tracks * :ghissue:`325`: streamline extraction from eudx is failing - but perhaps eudx is failing
==================================== Release notes for DIPY version 1.2 ==================================== GitHub stats for 2020/01/10 - 2020/09/08 (tag: 1.1.1) These lists are automatically generated, and may be incomplete or contain duplicates. The following 27 authors contributed 491 commits. * Ariel Rokem * Aryansh Omray * Bramsh Qamar * Charles Poirier * Derek Pisner * Eleftherios Garyfallidis * Fabio Nery * Francois Rheault * Gabriel Girard * Gregory Lee * Jean-Christophe Houde * Jirka Borovec * Jon Haitz Legarreta Gorroño * Leevi Kerkela * Leon Weninger * Martijn Nagtegaal * Rafael Neto Henriques * Sarath Chandra * Serge Koudoro * Shrishti Hore * Shubham Shaswat * Takis Panagopoulos * Tashrif Billah * Kunal Mehta * svabhishek29 * Areesha Tariq * Philippe Karan We closed a total of 256 issues, 94 pull requests and 163 regular issues; Pull Requests (94): * :ghpull:`2191`: Multi-shell multi-tissue constrained spherical deconvolution * :ghpull:`2212`: [FIX] renamed Direct Streamline Normalization tutorial title * :ghpull:`2207`: [FIX] Horizon shader warning * :ghpull:`2208`: Removing Python 3.5 from Travis and Azure due to its end of life (2020-09-13) * :ghpull:`2157`: BF: Fix variable may be used uninitialized warning * :ghpull:`2205`: Add optional installs for different settings. * :ghpull:`2204`: from Renderer to scene * :ghpull:`2183`: _streamlines_in_mask bounds check * :ghpull:`2203`: End of line period in sft * :ghpull:`2142`: ENH: function to calculate size/shape parameters of b-tensors and vice-versa * :ghpull:`2195`: [ENH] Validate streamlines pre-LiFE * :ghpull:`2161`: Fix a memory overlap bug in multi_median (and median_otsu) * :ghpull:`2163`: BF: Fix Cython label defined but not used warning * :ghpull:`2174`: Improve performance of tissue classification * :ghpull:`2168`: add fig_kwargs * :ghpull:`2178`: Add full SH basis * :ghpull:`2193`: BUAN_flow.rst to buan_flow.rst * :ghpull:`2196`: [Fix] update save_vtk_streamlines and load_vtk_streamlines * :ghpull:`2188`: [Fix] update mapmri due to cvxpy 1.1 * :ghpull:`2176`: [DOC] Update SH basis documentation * :ghpull:`2173`: Install ssl certificate for azure pipeline windows * :ghpull:`2171`: Gitter url update: from nipy/dipy to dipy/dipy * :ghpull:`2154`: Bundle segmentation CLI tutorial * :ghpull:`2162`: BF: Fix string literal comparison warning * :ghpull:`2156`: BF: Fix Cython signed vs. unsigned integer comparison warning * :ghpull:`2160`: TST: Change assert_equal(statement, True) to assert_(statement). * :ghpull:`2158`: BF: Fix Cython floating point absolute value warning * :ghpull:`2155`: [Fix] sfm RuntimeWarning * :ghpull:`2147`: BF: Fix Cython function override warning * :ghpull:`2148`: BF: Fix `distutils` Python version requirement option warning * :ghpull:`2150`: [Fix] some warning on clusteri 8738 ng test * :ghpull:`2149`: [Fix] some warning on stats module * :ghpull:`2145`: Rename dipy_track command line * :ghpull:`2152`: changed buan_flow.rst to BUAN_flow.rst * :ghpull:`2146`: Cluster threshold parameter in dipy_buan_shapes workflow * :ghpull:`2134`: Slicing, adding function of StatefulTractogram * :ghpull:`2001`: Basic processing documentation for CLI. * :ghpull:`2135`: [Fix] shm.py RuntimeWarning * :ghpull:`2141`: [FIX] doc generation issue * :ghpull:`2136`: [Fix] laplacian_regularization on MAPMRI + cleanup warning * :ghpull:`2140`: BF: Fix NumPy warning when creating arrays from ragged sequences * :ghpull:`2139`: BF: Use equality check instead of identity check * :ghpull:`2108`: [Horizon] Update clipping range on slicer * :ghpull:`2121`: BF: ensure `btens` attribute of `GradientTable` is initialised * :ghpull:`2129`: BF: Fix sequence stacking warning in LiFE tracking * :ghpull:`2133`: BF: Fix NumPy warning when creating arrays from ragged sequences * :ghpull:`2125`: ENH: function to calculate anisotropy of b-tensors * :ghpull:`2124`: BUAN framework documentation * :ghpull:`2033`: RF - Direction getters naming * :ghpull:`2111`: Added an epsilon to bounding_box check * :ghpull:`2086`: WIP Issue 1996 * :ghpull:`2091`: Modified the model for multiple hidden layers * :ghpull:`2057`: DOC: Add DIPY dataset list to documentation. * :ghpull:`2103`: Documentation typos, grammar corrections & imports * :ghpull:`2088`: BUAN paper code and CLIs * :ghpull:`2120`: rename var sp to sph * :ghpull:`2113`: BF: refer to cigar_tensor * :ghpull:`2116`: fixed code tags and minor changes * :ghpull:`2100`: Fixed typos, grammatical errors and time import * :ghpull:`2101`: Minor typos and imports * :ghpull:`2095`: Fixed typos in dipy.align * :ghpull:`2099`: Minor Typos and imports in the beginning * :ghpull:`2102`: Modules imported in the beginning * :ghpull:`2055`: Multidimensional gradient table * :ghpull:`2097`: Replace manual sform values with get_best_affine * :ghpull:`2104`: Fixed minor typos * :ghpull:`2065`: Some typos and grammatical errors * :ghpull:`2090`: Small fix reorient_bvecs * :ghpull:`2067`: Some spelling and grammatical mistakes * :ghpull:`2093`: Placed all imports in the beginning * :ghpull:`2077`: Fixed minor typos in tutorials * :ghpull:`2071`: Some change backs * :ghpull:`2084`: Kunakl07 patch 7 * :ghpull:`2085`: Kunakl07 patch 8 * :ghpull:`2068`: Some spelling and grammatical errors * :ghpull:`2069`: some typos * :ghpull:`2063`: Gibbs tutorial patch * :ghpull:`2045`: [Fix] workflow variable string * :ghpull:`2060`: Replace old function with cython version * :ghpull:`2058`: DOC: Fix `Sphinx` link in `CONTRIBUTING.md` * :ghpull:`2059`: DOC: Add `Azure Pipelines` to CI tools in `CONTRIBUTING.md` * :ghpull:`2056`: MAINT: Up Numpy version to 1.12. * :ghpull:`2053`: Correct TYPO on the note about n_points in _gibbs_removal_2d() * :ghpull:`2043`: [NF] Add a Deprecation system * :ghpull:`2047`: [fix] Doc generation issue * :ghpull:`2044`: [FIX] check seeds dtype * :ghpull:`2041`: BF: SFM prediction with mask * :ghpull:`2039`: Remove __future__ * :ghpull:`2042`: Add tests to rng module * :ghpull:`2040`: RF: Swallow a couple of warnings that are safe to ignore. * :ghpull:`2038`: [DOC] Update repo path * :ghpull:`2037`: DOC: fix typo in FW DTI tutorial * :ghpull:`2028`: Adapted for patch_radius with radii differing xyz direction. * :ghpull:`2035`: DOC: Update DKI documentation according to the new get data functions Issues (164): * :ghissue:`2114`: Tutorial title in Streamline-based registration section is misleading * :ghissue:`2207`: [FIX] Horizon shader warning * :ghissue:`2208`: Removing Python 3.5 from Travis and Azure due to its end of life (2020-09-13) * :ghissue:`1793`: ENH: Improving Command Line and WF Docs * :ghissue:`2007`: Reference for `load_trk` in recobundles example * :ghissue:`2061`: Is dipy.viz supported in Colab or Kaggle Notebooks? * :ghissue:`2070`: Python has stopped working during import * :ghissue:`2107`: PNG images saved by window.record in the tutorial example are always black * :ghissue:`2153`: lowercase .rst file names * :ghissue:`2138`: Basic introduction to CLI needs better dataset to showcase capabilities * :ghissue:`2194`: LiFE model won't fit ? * :ghissue:`2157`: BF: Fix variable may be used uninitialized warning * :ghissue:`2177`: VIZ: streamline actor failing on Windows + macOS due to the new VTK9 * :ghissue:`2205`: Add optional installs for different settings. * :ghissue:`2204`: from Renderer to scene * :ghissue:`2183`: _streamlines_in_mask bounds check * :ghissue:`2182`: `target_line_based` might read out of bounds * :ghissue:`2203`: End of line period in sft * :ghissue:`2200`: BF: Fix `'tp_print' is deprecated` Cython warning * :ghissue:`2142`: ENH: function to calculate size/shape parameters of b-tensors and vice-versa * :ghissue:`2199`: BUG: Fix NumPy and Cython deprecation and initialization warnings * :ghissue:`2195`: [ENH] Validate streamlines pre-LiFE * :ghissue:`2161`: Fix a memory overlap bug in multi_median (and median_otsu) * :ghissue:`2163`: BF: Fix Cython label defined but not used warning * :ghissue:`2174`: Improve performance of tissue classification * :ghissue:`2168`: add fig_kwargs * :ghissue:`2178`: Add full SH basis * :ghissue:`2193`: BUAN_flow.rst to buan_flow.rst * :ghissue:`2196`: [Fix] update save_vtk_streamlines and load_vtk_streamlines * :ghissue:`2175`: Save streamlines as vtk polydata to a supported format file updated t… * :ghissue:`2188`: [Fix] update mapmri due to cvxpy 1.1 * :ghissue:`2190`: Reconstruction with Multi-Shell Multi-Tissue CSD * :ghissue:`2051`: BF: Non-negative Least Squares for IVIM * :ghissue:`2176`: [DOC] Update SH basis documentation * :ghissue:`2173`: Install ssl certificate for azure pipeline windows * :ghissue:`2172`: fetch_gold_standard_io fetcher failed regularly * :ghissue:`2169`: saving tracts in obj format * :ghissue:`2170`: Output of utils.density_map() using tck file is different than MRTrix * :ghissue:`2171`: Gitter url update: from nipy/dipy to dipy/dipy * :ghissue:`2144`: Move gitter to dipy/dipy? * :ghissue:`2154`: Bundle segmentation CLI tutorial * :ghissue:`2162`: BF: Fix string literal comparison warning * :ghissue:`2156`: BF: Fix Cython signed vs. unsigned integer comparison warning * :ghissue:`2160`: TST: Change assert_equal(statement, True) to assert_(statement). * :ghissue:`2158`: BF: Fix Cython floating point absolute value warning * :ghissue:`2155`: [Fix] sfm RuntimeWarning * :ghissue:`2159`: BF: Fix Cython different sign integer comparison warning * :ghissue:`2147`: BF: Fix Cython function override warning * :ghissue:`2148`: BF: Fix `distutils` Python version requirement option warning * :ghissue:`2151`: [DOC] Fixed minor typos, grammar errors and moved imports up in all examples * :ghissue:`2130`: Checking empty Cluster objects generates NumPy warning * :ghissue:`2131`: Elementwise comparison failure warning in multi_voxel test * :ghissue:`2150`: [Fix] some warning on clustering test * :ghissue:`2149`: [Fix] some warning on stats module * :ghissue:`2145`: Rename dipy_track command line * :ghissue:`2152`: changed buan_flow.rst to BUAN_flow.rst * :ghissue:`2146`: Cluster threshold parameter in dipy_buan_shapes workflow * :ghissue:`2128`: Registration Module failing with pre-matrix on Travis with future Numpy/Scipy release * :ghissue:`2134`: Slicing, adding function of StatefulTractogram * :ghissue:`2001`: Basic processing documentation for CLI. * :ghissue:`2135`: [Fix] shm.py RuntimeWarning * :ghissue:`2141`: [FIX] doc generation issue * :ghissue:`2136`: [Fix] laplacian_regularization on MAPMRI + cleanup warning * :ghissue:`1765`: Refactor dipy/stats/analysis.py * :ghissue:`2122`: [WIP] Add build template * :ghissue:`2140`: BF: Fix NumPy warning when creating arrays from ragged sequences * :ghissue:`2139`: BF: Use equality check instead of identity check * :ghissue:`2127`: DOC : Minor grammar fixes and moved imports up with respective comments * :ghissue:`2108`: [Horizon] Update clipping range on slicer * :ghissue:`2121`: BF: ensure `btens` attribute of `GradientTable` is initialised * :ghissue:`2129`: BF: Fix sequence stacking warning in LiFE tracking * :ghissue:`2133`: BF: Fix NumPy warning when creating arrays from ragged sequences * :ghissue:`2125`: ENH: function to calculate anisotropy of b-tensors * :ghissue:`2124`: BUAN framework documentation * :ghissue:`2126`: dipy / fury fails to install on Ubuntu 18 with pip3 * :ghissue:`2033`: RF - Direction getters naming * :ghissue:`2111`: Added an epsilon to bounding_box check * :ghissue:`2112`: [WIP] BUndle ANalytics (BUAN) pipeline documentation * :ghissue:`2086`: WIP Issue 1996 * :ghissue:`2091`: Modified the model for multiple hidden layers * :ghissue:`2096`: Deep Code * :ghissue:`2057`: DOC: Add DIPY dataset list to documentation. * :ghissue:`2103`: Documentation typos, grammar corrections & imports * :ghissue:`2088`: BUAN paper code and CLIs * :ghissue:`2120`: rename var sp to sph * :ghissue:`2118`: Local namespace of Scipy is same as a variable name * :ghissue:`1861`: WIP: Refactoring the stats module * :ghissue:`2113`: BF: refer to cigar_tensor * :ghissue:`2116`: fixed code tags and minor changes * :ghissue:`2024`: DIPY open lab meetings, Winter 2020 * :ghissue:`2100`: Fixed typos, grammatical errors and time import * :ghissue:`2101`: Minor typos and imports * :ghissue:`2094`: Detailed Beginner Friendly Tutorials * :ghissue:`2095`: Fixed typos in dipy.align * :ghissue:`2099`: Minor Typos and imports in the beginning * :ghissue:`2102`: Modules imported in the beginning * :ghissue:`2055`: Multidimensional gradient table * :ghissue:`2097`: Replace manual sform values with get_best_affine * :ghissue:`2105`: Tutorial Symmetric Regn 3D patch 3 * :ghissue:`2104`: Fixed minor typos * :ghissue:`2078`: Applying affine transform to streamlines in a SFT object * :ghissue:`2065`: Some typos and grammatical errors * :ghissue:`1305`: Questions/policies about writing .rst/web doc files * :ghissue:`2090`: Small fix reorient_bvecs * :ghissue:`2067`: Some spelling and grammatical mistakes * :ghissue:`2093`: Placed all imports in the beginning * :ghissue:`2077`: Fixed minor typos in tutorials * :ghissue:`2089`: Transforming bvecs after registration * :ghissue:`2071`: Some change backs * :ghissue:`2084`: Kunakl07 patch 7 * :ghissue:`2085`: Kunakl07 patch 8 * :ghissue:`2072`: Some typos and grammatical errors in faq.rst * :ghissue:`2073`: Some minor grammatical fixes old_highlights.txt * :ghissue:`2074`: Small typos * :ghissue:`2075`: Some grammatical changes in maintainer_workflow.rst * :ghissue:`2076`: Some grammatical changes in maintainer_workflow.rst * :ghissue:`2079`: Some minor typos in gimbal_lock.rst * :ghissue:`2080`: Some minor grammatical errors fixes * :ghissue:`2081`: Some typos and grammatical corrections in Changelog * :ghissue:`2082`: Grammatical fixes in readme.rst * :ghissue:`2083`: Fixes in regtools.py * :ghissue:`2066`: Fixed some typos * :ghissue:`2068`: Some spelling and grammatical errors * :ghissue:`2069`: some typos * :ghissue:`2063`: Gibbs tutorial patch * :ghissue:`2045`: [Fix] workflow variable string * :ghissue:`2060`: Replace old function with cython version * :ghissue:`2058`: DOC: Fix `Sphinx` link in `CONTRIBUTING.md` * :ghissue:`2059`: DOC: Add `Azure Pipelines` to CI tools in `CONTRIBUTING.md` * :ghissue:`1363`: MDF not working properly * :ghissue:`2056`: MAINT: Up Numpy version to 1.12. * :ghissue:`1871`: apply transformation to all volumes in a series of DWI (4D) * :ghissue:`2052`: dipy.tracking.utils.density_map order of arguments changed by mistake * :ghissue:`1785`: Could we use gifti for streamlines? * :ghissue:`1728`: Bug in shm_coeff computation? * :ghissue:`1699`: Details in aparc-reduced.nii.gz * :ghissue:`1671`: Question about shm_coeff * :ghissue:`1552`: dti.py - quantize_evecs - error * :ghissue:`1373`: How to convert from converted isotropic to original resolution (anisotropic) * :ghissue:`1364`: SNR estimation troubleshooting * :ghissue:`1152`: nan gfa and odf values when mask includes voxels with 0 dwi signal * :ghissue:`1047`: Gradient flipped in the x-direction - FSL bvecs handling * :ghissue:`2019`: Apply deformation map to render "registered" image * :ghissue:`2049`: KFA calculation * :ghissue:`2048`: Group analysis * :ghissue:`2053`: Correct TYPO on the note about n_points in _gibbs_removal_2d() * :ghissue:`2043`: [NF] Add a Deprecation system * :ghissue:`218`: Callable response broken in csd module * :ghissue:`2047`: [fix] Doc generation issue * :ghissue:`313`: csdeconv response as callable * :ghissue:`1848`: Add Dipy to MRI-Hub (ISMRM Reproducible Research Study Group) * :ghissue:`2044`: [FIX] check seeds dtype * :ghissue:`2034`: Using the tutorial on Euler method on my data * :ghissue:`2041`: BF: SFM prediction with mask * :ghissue:`1724`: Failure on Windows/Python 3.5 * :ghissue:`1938`: Auto-clearing the AppVeyor queue backlog * :ghissue:`2039`: Remove __future__ * :ghissue:`2042`: Add tests to rng module * :ghissue:`1864`: Add tests to dipy.core.rng * :ghissue:`2040`: RF: Swallow a couple of warnings that are safe to ignore. * :ghissue:`2038`: [DOC] Update repo path * :ghissue:`2037`: DOC: fix typo in FW DTI tutorial * :ghissue:`2028`: Adapted for patch_radius with radii differing xyz direction. * :ghissue:`2035`: DOC: Update DKI documentation according to the new get data functions
DIPY 1.1.1 ---------- - New module for deep learning DIPY.NN (uses TensorFlow 2.0). - Improved DKI performance and increased utilities. - Non-linear and RESTORE fits from DTI compatible now with DKI. - Numerical solutions for estimating axial, radial and mean kurtosis. - Added Kurtosis Fractional Anisotropy by Glenn et al. 2015. - Added Mean Kurtosis Tensor by Hansen et al. 2013. - Nibabel minimum version is 3.0.0. - Azure CI added and Appveyor CI removed. - New command line interfaces for LPCA, MPPCA and Gibbs Unringing. - New MTMS CSD tutorial added. - Horizon refactored and updated to support StatefulTractograms. - Speeded up all cython modules by using a smarter configuration setting. - All tutorials updated to API changes and 2 new tutorials added. - Large documentation update. - Closed 126 issues and merged 50 pull requests.
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