diff --git a/.mailmap b/.mailmap index 6e88a5e40a..fd2c5a3ec1 100644 --- a/.mailmap +++ b/.mailmap @@ -34,6 +34,7 @@ Shahnawaz Ahmed Your Name smerlet Mauro Zucchelli Mauro Mauro Zucchelli maurozucchelli +Mauro Zucchelli maurozucchelli Andrew Lawrence AndrewLawrence Samuel St-Jean samuelstjean Samuel St-Jean samuelstjean @@ -65,6 +66,7 @@ Alexandre Gauvin Alexandre Gauvin Nil Goyette Eric Peterson etpeterson Rutger Fick Rutger Fick +Rutger Fick Rutger Fick Demian Wassermann Demian Wassermann Sourav Singh Sourav Sven Dorkenwald @@ -75,3 +77,13 @@ Matthieu Dumont unknown Adam Rybinski Bennet Fauber +Aman Arya +Ricci Woo RicciWoo +Francois Rheault +David Hunt David +David Hunt davhunt +Parichit Sharma Parichit Sharma +Chandan Gangwar +Naveen Kumarmarri +Jacob Wasserthal +Shreyas Fadnavis diff --git a/AUTHOR b/AUTHOR index 92832cd1f5..30d0dffcef 100644 --- a/AUTHOR +++ b/AUTHOR @@ -1,33 +1,92 @@ Eleftherios Garyfallidis -Ian Nimmo-Smith +Ariel Rokem Matthew Brett Bago Amirbekian -Stefan Van der Walt -Ariel Rokem -Christopher Nguyen -Yaroslav Halchenko -Emanuele Olivetti -Mauro Zucchelli -Samuel St-Jean -Maxime Descoteaux +Omar Ocegueda +Rafael Neto Henriques +Serge Koudoro +Samuel St-Jean Gabriel Girard +Marc-Alexandre Côté +Rutger Fick +Shahnawaz Ahmed +Ian Nimmo-Smith +Mauro Zucchelli Matthieu Dumont -Kimberly Chan -Erik Ziegler -Emmanuel Caruyer -Matthias Ekman +Stefan van der Walt +Kesshi Jordan +Ranveer Aggarwal +Maxime Descoteaux +Riddhish Bhalodia +Bramsh Qamar +Karandeep +Bishakh Ghosh +Christopher Nguyen +Stephan Meesters +Ricci Woo +Eric Peterson +Manu Tej Sharma +Sourav Singh +Julio Villalon Jean-Christophe Houde -Michael Paquette -Sylvain Merlet -Omar Ocegueda -Marc-Alexandre Cote +Jon Haitz Legarreta Gorroño +Kumar Ashutosh +Shreyas Fadnavis +David Reagan +Parichit Sharma +Guillaume Theaud +Aman Arya +Dimitris Rozakis +Gregory R. Lee +Saber Sheybani +ChantalTax +Nil Goyette +Rohan Prinja +Antonio Ossa Demian Wassermann +Michael Paquette +Tingyi Wanyan +Jiri Borovec +Yaroslav Halchenko +Conor Corbin +Kimberly Chan +ArjitJ <32598699+ArjitJ@users.noreply.github.com> +Enes Albay +Etienne St-Onge +Erik Ziegler +David Qixiang Chen +Francois Rheault +Emanuele Olivetti +David Hunt +Alexandre Gauvin +Pradeep Reddy Raamana +theaverageguy +Julio Villalon endolith +Matthias Ekman +Oscar Esteban +Emmanuel Caruyer +Tom Wright +Jon Haitz Legarreta Gorroño Andrew Lawrence -Gregory R. Lee +Naveen Kumarmarri +Chandan Gangwar +Pradeep Reddy Raamana +Bennet Fauber +Matt Cieslak +Sylvain Merlet +Gonzalo Sanguinetti +Vatsala Swaroop +Vibhatha Abeykoon +Adam Rybinski Maria Luisa Mandelli -Kesshi jordan -Chantal Tax -Qiyuan Tian -Shahnawaz Ahmed -Eric Peterson +Sven Dorkenwald +Qiyuan Tian +Chris Filo Gorgolewski +Bennet Fauber +Daniel Enrico Cahall +Jon Mendoza +Sagun Pai +Javier Guaje +Jacob Wasserthal +Himanshu Mishra \ No newline at end of file diff --git a/Changelog b/Changelog index ef35eb6711..50a3344d1d 100644 --- a/Changelog +++ b/Changelog @@ -24,6 +24,19 @@ Dipy The code found in Dipy was created by the people found in the AUTHOR file. +* 0.15 (Wednesday, 12 December 2018) + +- Updated RecoBundles for automatic anatomical bundle segmentation. +- New Reconstruction Model: qtau-dMRI. +- New command line interfaces (e.g. dipy_slr). +- New continuous integration with AppVeyor CI. +- Nibabel Streamlines API now used almost everywhere for better memory management. +- Compatibility with Python 3.7. +- Many tutorials added or updated (5 New). +- Large documentation update. +- Moved visualization module to a new library: FURY. +- Closed 287 issues and merged 93 pull requests. + * 0.14 (Tuesday, 1 May 2018) - RecoBundles: anatomically relevant segmentation of bundles diff --git a/LICENSE b/LICENSE index b90260ef06..c67326cfdf 100644 --- a/LICENSE +++ b/LICENSE @@ -1,7 +1,7 @@ Unless otherwise specified by LICENSE.txt files in individual directories, or within individual files or functions, all code is: -Copyright (c) 2008-2016, dipy developers +Copyright (c) 2008-2019, dipy developers All rights reserved. Redistribution and use in source and binary forms, with or without diff --git a/dipy/info.py b/dipy/info.py index dd85f5812a..cd6c7c3f91 100644 --- a/dipy/info.py +++ b/dipy/info.py @@ -72,9 +72,7 @@ Please see the LICENSE file in the dipy distribution. DIPY uses other libraries also licensed under the BSD or the -MIT licenses, with the only exception of the SHORE module which -optionally uses the cvxopt library. Cvxopt is licensed -under the GPL license. +MIT licenses. """ # versions for dependencies diff --git a/doc/api_changes.rst b/doc/api_changes.rst index 85e90fe135..42bffd160e 100644 --- a/doc/api_changes.rst +++ b/doc/api_changes.rst @@ -5,6 +5,29 @@ API changes Here we provide information about functions or classes that have been removed, renamed or are deprecated (not recommended) during different release circles. +DIPY 0.15 Changes +----------------- + +**IO** + +``load_tck`` and ``save_tck`` from ``dipy.io.streamline`` has been added. They are highly recommended for managing streamlines. + +**Gradient Table** + +The default value of ``b0_thresold`` has been changed(from 0 to 50). This change can impact your algorithm. +If you want to assure that your code runs in exactly the same manner as before, please initialize your gradient table with the keyword argument ``b0_threshold`` set to 0. + +**Visualization** + +``dipy.viz.fvtk`` module has been removed. Use ``dipy.viz.*`` instead. This implies the following important changes: +- Use ``from dipy.viz import window, actor`` instead of ``from dipy.viz import fvtk`. +- Use ``window.Renderer()`` instead of ``fvtk.ren()``. +- All available actors are in ``dipy.viz.actor`` instead of ``dipy.fvtk.actor``. +- UI elements are available in ``dipy.viz.ui``. + +``dipy.viz`` depends on FURY package. To get more informations about FURY, go to https://fury.gl + + DIPY 0.14 Changes ----------------- diff --git a/doc/conf.py b/doc/conf.py index 67de897743..104e679ef3 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -66,7 +66,7 @@ # General information about the project. project = u'dipy' -copyright = u'2008-2018, %(AUTHOR)s <%(AUTHOR_EMAIL)s>' % rel +copyright = u'2008-2019, %(AUTHOR)s <%(AUTHOR_EMAIL)s>' % rel # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the diff --git a/doc/index.rst b/doc/index.rst index 4de0657c0a..41a56efd0d 100644 --- a/doc/index.rst +++ b/doc/index.rst @@ -13,18 +13,18 @@ visualization, and statistical analysis of MRI data. Highlights ********** -**DIPY 0.14.0** is now available. New features include: - -- RecoBundles: anatomically relevant segmentation of bundles -- New super fast clustering algorithm: QuickBundlesX -- New tracking algorithm: Particle Filtering Tracking. -- New tracking algorithm: Probabilistic Residual Bootstrap Tracking. -- Integration of the Streamlines API for reading, saving and processing tractograms. -- Fiber ORientation Estimated using Continuous Axially Symmetric Tensors (Forecast). -- New command line interfaces. -- Deprecated fvtk (old visualization framework). -- A range of new visualization improvements. +**DIPY 0.15.0** is now available. New features include: + +- Updated RecoBundles for automatic anatomical bundle segmentation. +- New Reconstruction Model: qtau-dMRI. +- New command line interfaces (e.g. dipy_slr). +- New continuous integration with AppVeyor CI. +- Nibabel Streamlines API now used almost everywhere for better memory management. +- Compatibility with Python 3.7. +- Many tutorials added or updated (5 New). - Large documentation update. +- Moved visualization module to a new library: FURY. +- Closed 287 issues and merged 93 pull requests. See :ref:`Older Highlights `. @@ -33,6 +33,7 @@ See :ref:`Older Highlights `. Announcements ************* +- :ref:`DIPY 0.15 ` released December 12, 2018. - :ref:`DIPY 0.14 ` released May 1, 2018. - :ref:`DIPY 0.13 ` released October 24, 2017. - :ref:`DIPY 0.12 ` released June 26, 2017. diff --git a/doc/release0.15.rst b/doc/release0.15.rst new file mode 100644 index 0000000000..8111b2ed5a --- /dev/null +++ b/doc/release0.15.rst @@ -0,0 +1,338 @@ +.. _release0.15: + +==================================== + Release notes for DIPY version 0.15 +==================================== + +GitHub stats for 2018/05/01 - 2018/12/12 (tag: 0.14.0) + +These lists are automatically generated, and may be incomplete or contain duplicates. + +The following 30 authors contributed 676 commits. + +* Ariel Rokem +* Bramsh Qamar +* Chris Filo Gorgolewski +* David Reagan +* Demian Wassermann +* Eleftherios Garyfallidis +* Enes Albay +* Gabriel Girard +* Guillaume Theaud +* Javier Guaje +* Jean-Christophe Houde +* Jiri Borovec +* Jon Haitz Legarreta Gorroño +* Karandeep +* Kesshi Jordan +* Marc-Alexandre Côté +* Matt Cieslak +* Matthew Brett +* Parichit Sharma +* Ricci Woo +* Rutger Fick +* Serge Koudoro +* Shreyas Fadnavis +* Chandan Gangwar +* Daniel Enrico Cahall +* David Hunt +* Francois Rheault +* Jacob Wasserthal + + +We closed a total of 287 issues, 93 pull requests and 194 regular issues; +this is the full list (generated with the script +:file:`tools/github_stats.py`): + +Pull Requests (93): + +* :ghpull:`1684`: [FIX] testing line-based target function +* :ghpull:`1686`: Standardize workflow +* :ghpull:`1685`: [Fix] Typo on examples +* :ghpull:`1663`: Stats, SNR_in_CC workflow +* :ghpull:`1681`: fixed issue with cst orientation in bundle_extraction example +* :ghpull:`1680`: [Fix] workflow variable string +* :ghpull:`1683`: test for new error in IVIM +* :ghpull:`1667`: Changing the default b0_threshold in gtab +* :ghpull:`1677`: [FIX] workflow help msg +* :ghpull:`1678`: Numpy matrix deprecation +* :ghpull:`1676`: [FIX] Example Update +* :ghpull:`1283`: get_data consistence +* :ghpull:`1670`: fixed RecoBundle workflow, SLR reference, and updated fetcher.py +* :ghpull:`1669`: Flow csd sh order +* :ghpull:`1659`: From dipy.viz to FURY +* :ghpull:`1621`: workflows : warn user for strange b0 threshold +* :ghpull:`1657`: DOC: Add spherical harmonics basis documentation. +* :ghpull:`1660`: OPT - moved the tolerance check outside of the for loop +* :ghpull:`1658`: STYLE: Honor 'descoteaux'and 'tournier' SH basis naming. +* :ghpull:`1281`: Representing qtau- signal attenuation using qtau-dMRI functional basis +* :ghpull:`1651`: Add save/load tck +* :ghpull:`1656`: Link to the dipy tag on neurostars +* :ghpull:`1624`: NF: Outlier scoring +* :ghpull:`1655`: [Fix] decrease tolerance on forecast +* :ghpull:`1650`: Increase codecov tolerance +* :ghpull:`1649`: Path Length Map example rebase +* :ghpull:`1556`: RecoBundles and SLR workflows +* :ghpull:`1645`: Fix worflows creation tutorial error +* :ghpull:`1647`: DOC: Fix duplicate link and AppVeyor badge. +* :ghpull:`1644`: Adds an Appveyor badge +* :ghpull:`1643`: Add hash for SCIL b0 file +* :ghpull:`787`: TST: Add an appveyor starter file. +* :ghpull:`1642`: Test that you can use the 724 symmetric sphere in PAM. +* :ghpull:`1641`: changed vertices to float64 in evenly_distributed_sphere_642.npz +* :ghpull:`1564`: Added scroll bar to ListBox2D +* :ghpull:`1636`: Fixed broken link. +* :ghpull:`1584`: Added Examples +* :ghpull:`1554`: Checking if the input file or directory exists when running a workflow +* :ghpull:`1528`: Show spheres with different radii, colors and opacities + add timers + add exit a + resolve issue with imread +* :ghpull:`1526`: Eigenvalue - eigenvector array compatibility check +* :ghpull:`1628`: Adding python 3.7 on travis +* :ghpull:`1623`: NF: Convert between 4D DEC FA and 3D 24 bit representation. +* :ghpull:`1622`: [Fix] viz slice example +* :ghpull:`1626`: RF - removed duplicate tests +* :ghpull:`1619`: [DOC] update VTK version +* :ghpull:`1592`: Added File Menu element to viz.ui +* :ghpull:`1559`: Checkbox and RadioButton elements for viz.ui +* :ghpull:`1583`: Fix the relative SF threshold Issue +* :ghpull:`1602`: Fix random seed in tracking +* :ghpull:`1609`: [DOC] update dependencies file +* :ghpull:`1560`: Removed affine matrices from tracking. +* :ghpull:`1593`: Removed event.abort for release events +* :ghpull:`1597`: Upgrade nibabel minimum version +* :ghpull:`1601`: Fix: Decrease Nosetest warning +* :ghpull:`1515`: RF: Use the new Streamlines API for orienting of streamlines. +* :ghpull:`1590`: Revert 1570 file menu +* :ghpull:`1589`: Fix calculation of highest order for a sh basis set +* :ghpull:`1580`: Allow PRE=1 job to fail +* :ghpull:`1533`: Show message if number of arguments mismatch between the doc string and the run method. +* :ghpull:`1523`: Showing help when no input parameters are given and suppress warnings for cmds +* :ghpull:`1543`: Update the default out_strategy to create the output in the current working directory +* :ghpull:`1574`: Fixed Bug in PR #1547 +* :ghpull:`1561`: add example SDR for binary and fuzzy images +* :ghpull:`1578`: BF - bad condition in maximum dg +* :ghpull:`1570`: Added File Menu element to viz.ui +* :ghpull:`1563`: Replacing major_version in viz.ui +* :ghpull:`1557`: Range slider element for viz.ui +* :ghpull:`1547`: Changed the icon set in Button2D from Dictionary to List of Tuples +* :ghpull:`1555`: Fix bug in actor.label +* :ghpull:`1522`: Image element in dipy.viz.ui +* :ghpull:`1355`: WIP: ENH: UI Listbox +* :ghpull:`1540`: fix potential zero division in demon regist. +* :ghpull:`1548`: Fixed references per request of @garyfallidis. +* :ghpull:`1542`: fix for using cvxpy solver +* :ghpull:`1546`: References to reference +* :ghpull:`1545`: Adding a reference in README.rst +* :ghpull:`1492`: Enh ui components positioning (with code refactoring) +* :ghpull:`1538`: Explanation that is mistakenly rendered as code fixed in example of DKI +* :ghpull:`1536`: DOC: Update Rafael's current institution. +* :ghpull:`1537`: removed unncessary importd from sims example +* :ghpull:`1530`: Wrong default value for parameter 'symmetric' connectivity_matrix function +* :ghpull:`1529`: minor typo fix in quickstart +* :ghpull:`1520`: Updating the documentation for the workflow creation tutorial. +* :ghpull:`1524`: Values from streamlines object +* :ghpull:`1521`: Moved some older highlights and announcements to the old news files. +* :ghpull:`1518`: DOC: updated some developers affiliations. +* :ghpull:`1517`: Dev info update +* :ghpull:`1516`: [DOC] Installation instruction update +* :ghpull:`1514`: Adding pep8speak config file +* :ghpull:`1513`: fix typo in example of quick_start +* :ghpull:`1510`: copyright updated to 2008-2018 +* :ghpull:`1508`: Adds whitespace, to appease the sphinx. +* :ghpull:`1506`: moving to 0.15.0 dev + +Issues (194): + +* :ghissue:`1684`: [FIX] testing line-based target function +* :ghissue:`1679`: Intermittent issue in testing line-based target function +* :ghissue:`1220`: RF: Replaces 1997 definitions of tensor geometric params with 1999 definitions. +* :ghissue:`1686`: Standardize workflow +* :ghissue:`746`: New fetcher returns filenames as dictionary keys in a tuple +* :ghissue:`1685`: [Fix] Typo on examples +* :ghissue:`1663`: Stats, SNR_in_CC workflow +* :ghissue:`1637`: Advice for saving results from MAPMRI +* :ghissue:`1673`: CST Image in bundle extraction is not oriented well +* :ghissue:`1681`: fixed issue with cst orientation in bundle_extraction example +* :ghissue:`1680`: [Fix] workflow variable string +* :ghissue:`1338`: Variable string input does not work with self.get_io_iterator() in workflows +* :ghissue:`1683`: test for new error in IVIM +* :ghissue:`1682`: Add tests for IVIM for new Error +* :ghissue:`634`: BinaryTissueClassifier segfaults on corner case +* :ghissue:`742`: LinAlgError on tracking quickstart, with python 3.4 +* :ghissue:`852`: Problem with spherical harmonics computations on some Anaconda python versions +* :ghissue:`1667`: Changing the default b0_threshold in gtab +* :ghissue:`1500`: Updating streamlines API in streamlinear.py +* :ghissue:`944`: Slicer fix +* :ghissue:`1111`: WIP: A lightweight UI for medical visualizations based on VTK-Python +* :ghissue:`1099`: Needed PRs for merging recobundles into Dipy's master +* :ghissue:`1544`: Plans for viz module +* :ghissue:`641`: Tests raise a deprecation warning +* :ghissue:`643`: Use appveyor for Windows CI? +* :ghissue:`400`: Add travis-ci test without matplotlib installed +* :ghissue:`1677`: [FIX] workflow help msg +* :ghissue:`1674`: Workflows should print out help per default +* :ghissue:`1678`: Numpy matrix deprecation +* :ghissue:`1397`: Running dipy 'Intro to Basic Tracking' code and keep getting error. On Linux Centos +* :ghissue:`1676`: [FIX] Example Update +* :ghissue:`10`: data.get_data() should be consistent across datasets +* :ghissue:`1283`: get_data consistence +* :ghissue:`1670`: fixed RecoBundle workflow, SLR reference, and updated fetcher.py +* :ghissue:`1669`: Flow csd sh order +* :ghissue:`1668`: One issue on handling HCP data -- HCP b vectors raise NaN in the gradient table +* :ghissue:`1662`: Remove the points added oustide of a mask. Fix the related tests. +* :ghissue:`1659`: From dipy.viz to FURY +* :ghissue:`1621`: workflows : warn user for strange b0 threshold +* :ghissue:`1657`: DOC: Add spherical harmonics basis documentation. +* :ghissue:`1296`: Need of a travis bot that runs ana/mini/conda and vtk=7.1.0+ +* :ghissue:`1660`: OPT - moved the tolerance check outside of the for loop +* :ghissue:`1658`: STYLE: Honor 'descoteaux'and 'tournier' SH basis naming. +* :ghissue:`1281`: Representing qtau- signal attenuation using qtau-dMRI functional basis +* :ghissue:`1653`: STYLE: Honor 'descoteaux' SH basis naming. +* :ghissue:`1651`: Add save/load tck +* :ghissue:`1656`: Link to the dipy tag on neurostars +* :ghissue:`1624`: NF: Outlier scoring +* :ghissue:`1655`: [Fix] decrease tolerance on forecast +* :ghissue:`1654`: Test failure in FORECAST +* :ghissue:`1414`: [WIP] Switching tests to pytest and removing nose dependencies +* :ghissue:`1650`: Increase codecov tolerance +* :ghissue:`1093`: WIP: Add functionality to clip streamlines between ROIs in `orient_by_rois` +* :ghissue:`1611`: Preloader element for viz.ui +* :ghissue:`1615`: Color Picker element for viz.ui +* :ghissue:`1631`: Path Length Map example +* :ghissue:`1649`: Path Length Map example rebase +* :ghissue:`1556`: RecoBundles and SLR workflows +* :ghissue:`1645`: Fix worflows creation tutorial error +* :ghissue:`1647`: DOC: Fix duplicate link and AppVeyor badge. +* :ghissue:`1644`: Adds an Appveyor badge +* :ghissue:`1638`: Fetcher downloads data every time it is called +* :ghissue:`1643`: Add hash for SCIL b0 file +* :ghissue:`1600`: NODDIx 2 fibers crossing +* :ghissue:`1618`: viz.ui.FileMenu2D +* :ghissue:`1569`: viz.ui.ListBoxItem2D text overflow +* :ghissue:`1532`: dipy test failed on mac osx sierra with ananoda python. +* :ghissue:`1420`: window.record() resolution limit +* :ghissue:`1396`: Visualization problem with tensors ? +* :ghissue:`1295`: Reorienting peak_slicer and ODF_slicer +* :ghissue:`1232`: With VTK 6.3, streamlines color map bar text disappears when using streamtubes +* :ghissue:`928`: dipy.viz.colormap crash on single fibers +* :ghissue:`923`: change size of colorbar in viz module +* :ghissue:`854`: VTK and Python 3 support in fvtk +* :ghissue:`759`: How to resolve python-vtk6 link issues in Ubuntu +* :ghissue:`647`: fvtk contour function ignores voxsz parameter +* :ghissue:`646`: Dipy visualization with missing (?) affine parameter +* :ghissue:`645`: Dipy visualization (fvtk) crash when saving series of images +* :ghissue:`353`: fvtk.label won't show up if called twice +* :ghissue:`787`: TST: Add an appveyor starter file. +* :ghissue:`1642`: Test that you can use the 724 symmetric sphere in PAM. +* :ghissue:`1641`: changed vertices to float64 in evenly_distributed_sphere_642.npz +* :ghissue:`1203`: Some bots might need a newer version of nibabel +* :ghissue:`1156`: Deterministic tracking workflow +* :ghissue:`642`: WIP - NF parallel framework +* :ghissue:`1135`: WIP : Multiprocessing - implemented a parallel_voxel_fit decorator +* :ghissue:`387`: References do not render correctly in SHORE example +* :ghissue:`442`: Allow length and set_number_of_points to work with generators +* :ghissue:`558`: Allow setting of the zoom on fvtk ren objects +* :ghissue:`1236`: bundle visualisation using nibabel API: wrong colormap +* :ghissue:`1389`: VTK 8: minimal version? +* :ghissue:`1519`: Scipy stopped supporting scipy.misc.imread +* :ghissue:`1596`: Reproducibility in PFT tracking +* :ghissue:`1614`: for GSoC NODDIx_PR +* :ghissue:`1576`: [WIP] Needs Optimization and Cleaning +* :ghissue:`1564`: Added scroll bar to ListBox2D +* :ghissue:`1636`: Fixed broken link. +* :ghissue:`1584`: Added Examples +* :ghissue:`1568`: Multi_io axis out of bounds error +* :ghissue:`1554`: Checking if the input file or directory exists when running a workflow +* :ghissue:`1528`: Show spheres with different radii, colors and opacities + add timers + add exit a + resolve issue with imread +* :ghissue:`1108`: Local PCA Slow Version +* :ghissue:`1526`: Eigenvalue - eigenvector array compatibility check +* :ghissue:`1628`: Adding python 3.7 on travis +* :ghissue:`1623`: NF: Convert between 4D DEC FA and 3D 24 bit representation. +* :ghissue:`1622`: [Fix] viz slice example +* :ghissue:`1629`: [WIP][fix] remove Userwarning message +* :ghissue:`1591`: PRE is failing : module 'cvxpy' has no attribute 'utilities' +* :ghissue:`1626`: RF - removed duplicate tests +* :ghissue:`1582`: SF threshold in PMF is not relative +* :ghissue:`1575`: Website: warning about python versions +* :ghissue:`1619`: [DOC] update VTK version +* :ghissue:`1592`: Added File Menu element to viz.ui +* :ghissue:`1559`: Checkbox and RadioButton elements for viz.ui +* :ghissue:`1583`: Fix the relative SF threshold Issue +* :ghissue:`1602`: Fix random seed in tracking +* :ghissue:`1620`: 3.7 wheels +* :ghissue:`1598`: Apply Transform workflow for transforming a collection of moving images. +* :ghissue:`1595`: Workflow for visualizing the quality of the registered data with DIPY +* :ghissue:`1581`: Image registration Workflow with quality metrices +* :ghissue:`1588`: Dipy.reconst.shm.calculate_max_order only works on specific cases. +* :ghissue:`1608`: Parallelized affine registration +* :ghissue:`1610`: Tortoise - sub +* :ghissue:`1607`: Reminder to add in the docs that users will need to update nibabel to 2.3.0 during the next release +* :ghissue:`1609`: [DOC] update dependencies file +* :ghissue:`1560`: Removed affine matrices from tracking. +* :ghissue:`1593`: Removed event.abort for release events +* :ghissue:`1586`: Slider breaks interaction in viz_advanced example +* :ghissue:`1597`: Upgrade nibabel minimum version +* :ghissue:`1601`: Fix: Decrease Nosetest warning +* :ghissue:`1515`: RF: Use the new Streamlines API for orienting of streamlines. +* :ghissue:`1585`: Add a random seed for reproducibility +* :ghissue:`1594`: Integrating the support for the visualization in Affine registration +* :ghissue:`1590`: Revert 1570 file menu +* :ghissue:`1589`: Fix calculation of highest order for a sh basis set +* :ghissue:`1577`: Revert "Added File Menu element to viz.ui" +* :ghissue:`1571`: WIP: multi-threaded on affine registration +* :ghissue:`1580`: Allow PRE=1 job to fail +* :ghissue:`1533`: Show message if number of arguments mismatch between the doc string and the run method. +* :ghissue:`1523`: Showing help when no input parameters are given and suppress warnings for cmds +* :ghissue:`1579`: Error on PRE=1 (cython / numpy) +* :ghissue:`1543`: Update the default out_strategy to create the output in the current working directory +* :ghissue:`1433`: New version of h5py messing with us? +* :ghissue:`1541`: demon registration, unstable? +* :ghissue:`1574`: Fixed Bug in PR #1547 +* :ghissue:`1573`: Failure in test_ui_listbox_2d +* :ghissue:`1561`: add example SDR for binary and fuzzy images +* :ghissue:`1578`: BF - bad condition in maximum dg +* :ghissue:`1566`: Bad condition in local tracking +* :ghissue:`1570`: Added File Menu element to viz.ui +* :ghissue:`1572`: [WIP] +* :ghissue:`1567`: WIP: NF: multi-threaded on affine registration +* :ghissue:`1563`: Replacing major_version in viz.ui +* :ghissue:`1557`: Range slider element for viz.ui +* :ghissue:`1547`: Changed the icon set in Button2D from Dictionary to List of Tuples +* :ghissue:`1555`: Fix bug in actor.label +* :ghissue:`1551`: Actor.label not working anymore +* :ghissue:`1522`: Image element in dipy.viz.ui +* :ghissue:`1549`: CVXPY installation on >3.5 +* :ghissue:`1355`: WIP: ENH: UI Listbox +* :ghissue:`1562`: Should we retire our Python 3.5 travis builds? +* :ghissue:`1550`: Memory error when running rigid transform +* :ghissue:`1540`: fix potential zero division in demon regist. +* :ghissue:`1548`: Fixed references per request of @garyfallidis. +* :ghissue:`1527`: New version of CVXPY changes API +* :ghissue:`1542`: fix for using cvxpy solver +* :ghissue:`1534`: Changed the icon set in Button2D from Dictionary to List of Tuples +* :ghissue:`1546`: References to reference +* :ghissue:`1545`: Adding a reference in README.rst +* :ghissue:`1492`: Enh ui components positioning (with code refactoring) +* :ghissue:`1538`: Explanation that is mistakenly rendered as code fixed in example of DKI +* :ghissue:`1536`: DOC: Update Rafael's current institution. +* :ghissue:`1487`: Commit for updated check_scratch.py script. +* :ghissue:`1486`: Parichit dipy flows +* :ghissue:`1539`: Changing the default behavior of the workflows to create the output file(s) in the current working directory. +* :ghissue:`1537`: removed unncessary importd from sims example +* :ghissue:`1535`: removed some unnecessary imports from sims example +* :ghissue:`1530`: Wrong default value for parameter 'symmetric' connectivity_matrix function +* :ghissue:`1529`: minor typo fix in quickstart +* :ghissue:`1520`: Updating the documentation for the workflow creation tutorial. +* :ghissue:`1524`: Values from streamlines object +* :ghissue:`1521`: Moved some older highlights and announcements to the old news files. +* :ghissue:`1518`: DOC: updated some developers affiliations. +* :ghissue:`1517`: Dev info update +* :ghissue:`1516`: [DOC] Installation instruction update +* :ghissue:`1514`: Adding pep8speak config file +* :ghissue:`1507`: Mathematical expressions are not rendered correctly in reference page +* :ghissue:`1513`: fix typo in example of quick_start +* :ghissue:`1510`: copyright updated to 2008-2018 +* :ghissue:`1508`: Adds whitespace, to appease the sphinx. +* :ghissue:`1512`: Fix typo in example of quick_start +* :ghissue:`1511`: Fix typo in exaample quick_start +* :ghissue:`1509`: DOC: fix math rendering for some dki functions +* :ghissue:`1506`: moving to 0.15.0 dev diff --git a/doc/stateoftheart.rst b/doc/stateoftheart.rst index 7b8e46e4f8..9d76fbfd21 100644 --- a/doc/stateoftheart.rst +++ b/doc/stateoftheart.rst @@ -28,6 +28,7 @@ For a full list of the features implemented in the most recent release cycle, ch .. toctree:: :maxdepth: 1 + release0.15 release0.14 release0.13 release0.12