Martin Uecker pushed to branch patch-queue/master at Debian Med / bart
Commits: 5eb5943e by Martin Uecker at 2017-11-24T12:52:09Z version - - - - - 3a4fc5a7 by Martin Uecker at 2017-11-24T12:52:23Z fix typo - - - - - 0398c922 by Martin Uecker at 2017-11-26T11:58:38Z add patch for version fix - - - - - cd648f4d by Martin Uecker at 2017-11-26T18:30:51Z autopkgtest - - - - - 189acba6 by Martin Uecker at 2017-11-26T18:33:32Z update changelog - - - - - ada4fe5f by Andreas Tille at 2017-11-27T07:32:33Z Sponsored upload to unstable - - - - - d8c19c06 by Martin Uecker at 2017-11-27T22:57:22Z turn off some tests on some architectures - - - - - 931ca19a by Martin Uecker at 2017-11-28T19:04:12Z fix misleading changelog - - - - - 68091c24 by Christian Holme at 2017-11-28T20:12:37Z nlinv: add option for debug level - - - - - 7353ba36 by Christian Holme at 2017-11-28T20:12:37Z nlinv: describe options - - - - - eed78e1e by Christian Holme at 2017-11-28T20:12:37Z nlinv: make IRGNM reduction factor configurable - - - - - b95fe32c by Christian Holme at 2017-11-28T20:12:37Z nlinv: consistent name for image - - - - - b4cf9343 by Christian Holme at 2017-11-28T20:12:37Z noir/recon.c: rename img to x since img in that case was actually the image and the coils together. It now reflects standard usage: x is the variable optimized by the IRGNM. - - - - - f727271e by Christian Holme at 2017-11-28T20:12:37Z noir/recon: names consistent to header - - - - - 928ff3a5 by Christian Holme at 2017-11-28T20:12:37Z nlinv: move initialization to nlinv.c - - - - - f3b492f2 by Martin Uecker at 2017-11-28T20:52:19Z newer gcc on Mac - - - - - 1e5b7501 by Andreas Tille at 2017-11-28T21:20:59Z Upload to unstable - - - - - 072890a9 by Martin Uecker at 2017-11-28T23:13:45Z build fix mac - - - - - bbf37f19 by Martin Uecker at 2017-11-29T19:48:22Z remove macro for type-safe use of const arrays as function arguments on old compilers - - - - - 3ffa91f4 by Martin Uecker at 2017-12-03T12:01:28Z remove build test for homebrew - - - - - f69f2b6e by Jon Tamir at 2017-12-03T21:08:36Z ecalib: add option to turn off phase rotation - - - - - 62b103a0 by Jon Tamir at 2017-12-04T08:41:14Z homodyne: add option for uncentered ffts (#109) - - - - - fbc2e464 by Martin Uecker at 2017-12-04T20:11:19Z add noreturn to error function - - - - - b015c7b8 by Martin Uecker at 2017-12-05T08:35:26Z minor style changes - - - - - dad94e1b by Martin Uecker at 2017-12-05T08:35:26Z remove unneeded omp.h header - - - - - f504015c by Martin Uecker at 2017-12-05T08:35:26Z remove redundant vecop - - - - - bb8d5fdf by Martin Uecker at 2017-12-05T09:05:35Z hide noreturn from cuda - - - - - 1281d1c5 by Christian Holme at 2017-12-05T11:59:44Z nlinv: properly initialize pointer as NULL - - - - - fcfa3a9f by Christian Holme at 2017-12-05T12:00:19Z nlinv: add option to provide initialization - - - - - 0a806e87 by Christian Holme at 2017-12-05T12:00:58Z irgnm: improve debug output - - - - - 51cb70ee by Christian Holme at 2017-12-05T12:02:10Z irgnm: add callback The irgnm can now take a callback. - - - - - a274dcf4 by Christian Holme at 2017-12-05T12:02:40Z nlinv: add timing output nlinv can now calculate how long the reconstruction took - - - - - f909f976 by Christian Holme at 2017-12-07T16:34:41Z nlinv: sensitivity output also when using GPU (#111) The code now also outputs the sensitivites calculted by nlinv when run on the GPU. This is possible by excplicitly copying data. - - - - - 97634388 by Jon Tamir at 2017-12-08T01:57:22Z use vecop for zabs - - - - - d50f985a by Martin Uecker at 2017-12-08T09:13:07Z fix bug for gpu-mode of cdiag operator - - - - - 495613c5 by Martin Uecker at 2017-12-10T11:12:25Z replace free with xfree - - - - - 669800c8 by Martin Uecker at 2018-01-21T10:24:23Z update default compiler on Mac OS X (closes #113) - - - - - df893106 by Martin Uecker at 2018-01-21T10:45:21Z change default prefix to /usr/local/ - - - - - 72ca7ca1 by Martin Uecker at 2018-01-21T10:46:31Z turn off TOOLBOX_PATH overriding by default - - - - - 2a08ea1f by Martin Uecker at 2018-01-21T11:19:59Z document clang issues - - - - - 2c0b132f by Martin Uecker at 2018-01-21T17:13:44Z uncomment build of stand alone commands for CMake - - - - - e0e7b029 by Martin Uecker at 2018-01-21T17:13:44Z CMake: turn off matlab support by default - - - - - 22c87c6a by Martin Uecker at 2018-01-21T17:13:44Z cmake: minimal c version is gnu11 - - - - - 176055aa by Martin Uecker at 2018-01-24T20:24:39Z fix obvious bug in blockproc - - - - - 2c40b79f by Martin Uecker at 2018-01-24T21:24:23Z add missing free - - - - - a0f01dba by Martin Uecker at 2018-01-25T19:59:20Z add script for memory-economic use of espirit - - - - - 3c1c2eb7 by Martin Uecker at 2018-01-29T18:59:32Z multind: nested functions - - - - - 626cd6fe by Martin Uecker at 2018-01-29T19:00:23Z optimize: nested functions - - - - - 74f13399 by Martin Uecker at 2018-01-29T19:00:23Z nested functions: merge fixes - - - - - 2dbc8471 by Martin Uecker at 2018-01-29T19:00:23Z make clang compatible - - - - - 31c90b28 by Martin Uecker at 2018-01-29T19:00:23Z travis - - - - - 47acbcb1 by Martin Uecker at 2018-01-29T19:00:23Z compiler check for cuda - - - - - 0c8d2b88 by Martin Uecker at 2018-01-29T19:00:23Z cuda fix - - - - - b3e3c602 by Martin Uecker at 2018-01-29T19:59:14Z add function to detect nontrivial strides - - - - - 3af86fca by Martin Uecker at 2018-01-29T20:03:30Z CAST_MAYBE - - - - - b0eff029 by Martin Uecker at 2018-01-29T20:03:30Z fix run-time type check (zero-sized variables may have same address on gcc) - - - - - a2c7270a by Jon Tamir at 2018-02-08T15:22:14Z admm: add parameter selection by residual balancing (#114) - - - - - 3b52fa1d by Martin Uecker at 2018-02-08T21:20:36Z implement md_(z)smul using direct calls to vecops - - - - - 8467cc38 by Jon Tamir at 2018-02-08T23:31:47Z linops/fmac.c: add gpu tensor - - - - - 19948d8f by Martin Uecker at 2018-02-10T21:09:36Z remove some use_gpu flags - - - - - 81549d38 by Martin Uecker at 2018-02-10T21:09:36Z remove some more use_gpu flags - - - - - 7b8fea4d by Martin Uecker at 2018-02-10T21:09:36Z remove unused undersampled fft operator - - - - - 0651f594 by Martin Uecker at 2018-02-10T21:09:36Z remove more use_gpu flags - - - - - 90339c8b by Martin Uecker at 2018-02-10T21:09:36Z remove more use_gpu flags - - - - - 82f18f35 by Martin Uecker at 2018-02-10T21:13:57Z minor gpu gix - - - - - 66294ca1 by Martin Uecker at 2018-02-10T22:28:29Z add benchmark and test for md_fft - - - - - f013618b by Martin Uecker at 2018-02-11T11:02:20Z add benchmarks for fft and fftmod - - - - - cd26f403 by Martin Uecker at 2018-02-11T15:00:32Z error messages for impossible configurations - - - - - c3164588 by Martin Uecker at 2018-02-11T16:41:37Z missing identity operator - - - - - c3889691 by Martin Uecker at 2018-02-20T21:23:31Z add nufft according to conventional definition - - - - - 50a4e7af by Christian Holme at 2018-03-16T16:22:31Z nlinv: option for different pattern for each coil this is needed when usinc virtual-conjugate coils, for example - - - - - e0a3a237 by Christian Holme at 2018-03-16T16:22:31Z nlinv: add ENLIVE support This commit adds ENLIVE to the exisiting nlinv code. ENLIVE is a method for allowing multiple sets of images and coil sensitivity maps in the reconstruction, similar to multiple ESPIRiT maps. - - - - - b1f62b4a by Christian Holme at 2018-03-16T16:22:31Z nlinv: remove more unused water/fat code Commit 2d31b70bfbb9d4226950e1a3b34610eaa9f9146e removed most water/fat code from nlinv. Relics were the sign_dims in model.c and the CSHIFT_FLAG. This commit removes those, too. - - - - - f967e85f by Christian Holme at 2018-03-16T16:22:31Z nlinv: add (hidden) option to specify coil weighting parameters - - - - - f4d3f32c by Martin Uecker at 2018-03-21T20:02:35Z style changes - - - - - 5dc01c5c by Martin Uecker at 2018-03-21T20:24:10Z style - - - - - 9d44eecb by Martin Uecker at 2018-04-08T15:28:40Z update references - - - - - 0c2a6503 by Martin Uecker at 2018-04-09T09:15:47Z bump version - - - - - 714b5be2 by Jon Tamir at 2018-04-10T07:21:45Z optreg: add non-negative constraint - - - - - 7bd88449 by Jon Tamir at 2018-04-10T10:02:52Z use long for tenmul_dims - - - - - 75957eeb by Jon Tamir at 2018-04-10T18:48:45Z vecops: add smax for scalar max - - - - - d149bc84 by Nguyen Damien at 2018-04-19T13:02:23Z Update mat2cfl for new Matlab interleaved complex API Signed-off-by: Nguyen Damien <[email protected]> - - - - - 458dee0b by Martin Uecker at 2018-04-28T18:46:56Z Merge tag 'v0.4.03' version 0.4.03 Changes: - nlinv: add ENLIVE support (Christian Holme) - nlinv: add (hidden) option to specify coil weighting parameters (Christian Holme) - nlinv: option for different pattern for each coil (Christian Holme) - nlinv: sensitivity output also when using GPU (Christian Holme) - nlinv: add timing output (Christian Holme) - nlinv: add option for debug level (Christian Holme) - nlinv: add option to provide initialization (Christian Holme) - nlinv: make IRGNM reduction factor configurable (Christian Holme) - nufft: add nufft according to conventional definition - ecalib: add option to turn off phase rotation (Jonathan Tamir) - homodyne: add option for uncentered ffts (Jonathan Tamir) - bench: add benchmarks for fft, fftmod, md_fft - library: admm: add parameter selection by residual balancing (Jonathan Tamir) - library: add function to detect nontrivial strides - library: fix bug for gpu-mode of cdiag operator - library: irgnm: add callback (Christian Holme) - general: add script for memory-economic use of espirit - build: updates and fixes for CMake - build: build fixes on Mac OS X - many other bug fixes and improvements - - - - - 44d46514 by Martin Uecker at 2018-04-28T18:48:04Z remove version patch - - - - - 1f025ffe by Martin Uecker at 2018-04-28T18:48:04Z update copyright file - - - - - 15786d36 by Martin Uecker at 2018-04-28T18:48:04Z fix install target - - - - - 7c583061 by Martin Uecker at 2018-04-28T18:48:04Z update standards version - - - - - 36d855dd by Martin Uecker at 2018-04-28T18:48:10Z secure url for copyright format - - - - - 24215223 by Martin Uecker at 2018-04-28T18:48:27Z changelog - - - - - 0a4b3707 by Martin Uecker at 2018-04-28T19:32:54Z really fix install - - - - - 303ae9a2 by Martin Uecker at 2018-04-28T19:47:19Z points vcs to salsa - - - - - e5c8d43c by Andreas Tille at 2018-04-28T20:02:15Z Vcs-Browser has no .git extension - - - - - c52eb1a3 by Andreas Tille at 2018-04-28T20:03:05Z debhelper 11 - - - - - 7c3098a5 by Andreas Tille at 2018-04-28T20:07:57Z Upload to unstable - - - - - 42628438 by Martin Uecker at 2018-04-29T09:29:28Z add parallelization to fftmod - - - - - d03aaa48 by Martin Uecker at 2018-04-29T09:41:47Z update operators - - - - - 0c87b89a by Martin Uecker at 2018-04-29T09:45:59Z linop null and plus - - - - - 31616e95 by Martin Uecker at 2018-04-29T09:49:50Z include guards for shrdptr.h - - - - - 14819db5 by Martin Uecker at 2018-04-29T09:52:30Z warnings in ops - - - - - f0acbb12 by Martin Uecker at 2018-04-29T10:22:00Z update nonlinear operator framework - - - - - 573e6038 by Martin Uecker at 2018-04-29T10:34:37Z add zexp nonlinear operator - - - - - bc8a650f by Martin Uecker at 2018-04-29T10:38:23Z add md_zexp - - - - - a521ed8f by Martin Uecker at 2018-04-29T10:38:57Z add tenmul operator - - - - - dc3c19be by Martin Uecker at 2018-04-29T10:40:37Z run-time type check: improve error message - - - - - d328a05e by Martin Uecker at 2018-04-29T10:43:23Z add tests for nonlinear operators - - - - - ed1df142 by Martin Uecker at 2018-04-29T13:29:35Z add safe_isnanf which protects against optimization - - - - - 2ae81ea2 by Martin Uecker at 2018-04-29T16:28:06Z update compiler on travis - - - - - c0fd3d6a by Martin Uecker at 2018-04-29T16:43:25Z update iovec - - - - - 89f2ddec by Martin Uecker at 2018-04-29T16:48:01Z update flpmath and vecops - - - - - 5c6ce3a0 by Martin Uecker at 2018-04-29T16:54:18Z add test for linop_plus - - - - - 1fe524c0 by Martin Uecker at 2018-05-03T19:51:08Z add missing file to libbart-dev to fix bart-view - - - - - 3482b461 by Andreas Tille at 2018-05-04T17:05:46Z Upload to unstable - - - - - 2f51dba1 by Sebastian Rosenzweig at 2018-05-27T20:15:12Z num/flpmath: (Complex) sum along specified dimensions - - - - - 973a93d0 by Sebastian Rosenzweig at 2018-05-27T20:15:12Z num/gpuops: GPU memory usage print function - - - - - b06207de by Sebastian Rosenzweig at 2018-05-27T20:15:12Z gpuops: Memory print function - - - - - 73348761 by Martin Uecker at 2018-05-28T12:25:20Z gpu fixes - - - - - a8db6f5d by Martin Uecker at 2018-05-28T12:25:20Z fix md_zlessequal - - - - - 62cf0a84 by Christian Holme at 2018-05-31T20:40:06Z num/ops.c: properly guard OpenMP expressions (#123) - - - - - 57e33fdd by Siddharth Iyer at 2018-05-31T20:42:34Z Added wave-shuffling + fixes to wavepsf (#122) - - - - - 0c6a3011 by Siddharth Iyer at 2018-06-01T05:42:06Z Add hogwild opt + wavelet randshift set to true - Added hogwild option to command line interface. - Set wavelet->randshift to true after talking to Frank. - Minor cosmetic changes. - - - - - 028ff76d by Jon Tamir at 2018-06-15T06:36:29Z toimg: add windowing and option to re-scale images to full dynamic range (#125) * toimg: add windowing and option to re-scale images to full dynamic range - - - - - d3da0832 by Siddharth Iyer at 2018-06-29T15:14:36Z wshfl updates - Applies fftmod onto data table to avoid using fftc in linops. - Reconstruction now uses iter2 to be consistent with pics. - Formatting changes. - Remove the GPU option. - - - - - 5331cb53 by Siddharth Iyer at 2018-06-29T15:14:36Z Added command poly Convenience command like zeroes and ones to generate arrays with simple patterns like [0, 1, 2, ... L-1]. - - - - - cbda5774 by Siddharth Iyer at 2018-06-29T15:14:36Z Added rounding to reorder related arguements to avoid interger related errors - - - - - b53e1464 by Siddharth Iyer at 2018-06-29T15:14:36Z Added test for wshfl - - - - - dd798897 by Martin Uecker at 2018-06-29T17:34:55Z document minimum compiler version - - - - - 9a83657c by Martin Uecker at 2018-06-29T17:44:57Z help for l1-Fourier - - - - - 2e8c6f4b by Martin Uecker at 2018-06-29T17:53:07Z add missing copyright headers - - - - - ea2dbff4 by Martin Uecker at 2018-06-29T19:06:12Z add test for batch nufft - - - - - 2ef396b3 by Martin Uecker at 2018-06-30T15:27:43Z rename algo enum constants - - - - - 15ac5472 by Martin Uecker at 2018-06-30T19:24:01Z move initialization of italgos in its own function - - - - - a55b9526 by Martin Uecker at 2018-06-30T20:33:10Z move italgo init into its own file - - - - - 9e7fbf31 by Martin Uecker at 2018-07-01T12:08:45Z memory management - - - - - 0d1200c4 by Martin Uecker at 2018-07-01T12:48:16Z refactor choice of algorithm - - - - - b8f79704 by Martin Uecker at 2018-07-01T13:36:59Z make basis pursuit possible for noncartesian data - - - - - b7c84844 by Martin Uecker at 2018-07-07T07:02:06Z fix issue with over-sized trajectories - - - - - 186fbd5e by Martin Uecker at 2018-07-07T11:23:16Z propagate periodic flag to psf - - - - - 978a67a0 by Martin Uecker at 2018-07-23T20:37:44Z fix memory leaks in nonlinear operator chains - - - - - 95889313 by Martin Uecker at 2018-07-23T21:50:15Z fix noreturn issue for c++ - - - - - 50244f05 by Martin Uecker at 2018-07-23T22:23:40Z refactor gridding - - - - - abbfd3ef by Martin Uecker at 2018-07-23T22:36:48Z make clang compatible - - - - - 74d5b026 by Nguyen Damien at 2018-07-25T15:17:27Z Bring unit-testing on CMake up to par with Makefile - - - - - 0618e748 by Nguyen Damien at 2018-07-26T08:01:31Z Remove abort() and replace exit() with return values - - - - - 1cba6ca8 by Nguyen Damien at 2018-07-26T12:10:43Z ecalib: add debug_level argument - - - - - a2330ca3 by Nguyen Damien at 2018-07-26T20:11:22Z Change getopt to ya_getopt and modify cmdlines fct to return values - - - - - f6634403 by Nguyen Damien at 2018-07-26T20:14:31Z Prepare debug_printf* functions for external log backends - - - - - bfddec7f by Nguyen Damien at 2018-07-26T20:17:56Z Add support for external logging backends For now supported backends are - Siemens - GE (still experimental) - Gadgetron NB: Compilation for the Siemens backend requires the file src/misc/UTrace.cc that can be found on the Siemens IDEA board at the URL below: https://www.mr-idea.com/communities/idea/Lists/Customer/UTrace.cc - - - - - 30a8971d by Martin Uecker at 2018-07-27T09:34:22Z minor fixes and style changes - - - - - 62dac483 by Martin Uecker at 2018-07-27T10:28:37Z add missing newlines in error messages - - - - - 5a2224a0 by Nguyen Damien at 2018-07-27T10:33:50Z Add support for in-memory CFL files - - - - - ee06c842 by Martin Uecker at 2018-07-27T12:12:22Z fix warnings, build, coding style, rewrite list of i/o files - - - - - aa78612c by Nguyen Damien at 2018-07-27T12:43:38Z Miscellaneous changes to the CMake build systems - - - - - 3c71c1fe by Martin Uecker at 2018-07-27T13:25:01Z fix for next_powerof2 (thanks to Nguyen Damien) - - - - - 0ebcd52b by Martin Uecker at 2018-07-30T14:08:33Z cc: don't warn when correct option is used - - - - - 90112eb8 by Martin Uecker at 2018-07-30T14:08:33Z add FIXME - - - - - a8507500 by Martin Uecker at 2018-07-30T14:08:33Z add complex-conjugate for matrix - - - - - 6f050bc5 by Martin Uecker at 2018-07-30T14:08:33Z fix bug in phase rotation (now improved results) - - - - - d994489a by Martin Uecker at 2018-07-30T14:08:33Z reactivate old coil compression test - - - - - 0df678d5 by Martin Uecker at 2018-07-30T14:08:33Z add phase rotation tests - - - - - f9c6bb20 by Martin Uecker at 2018-07-30T16:33:34Z enhance copy command to do simple copies - - - - - e059a188 by Martin Uecker at 2018-07-30T21:39:28Z longjmp-based error handling (loosely based on patch by Damien Nguyen) - - - - - 58129193 by Martin Uecker at 2018-07-30T21:39:34Z ismrmrd fix (thanks to Damien Nguyen) - - - - - 2da0fa3e by Martin Uecker at 2018-07-30T21:40:10Z introduce bart_printf - - - - - c1d43557 by Martin Uecker at 2018-07-30T21:40:51Z add entry point for calling bart commands when used as a library - - - - - 49a1da32 by Nguyen Damien at 2018-07-30T22:00:37Z Add pyBART Python module and bartmain library - bartmain (CMake only for now) is a library containing all BART commands in a single library - pyBART is a "native" Python module based on BART (slightly edited - Martin Uecker) - - - - - 67910d31 by Nguyen Damien at 2018-07-30T22:00:37Z Fix some runtime issues with clang Signed-off-by: Nguyen Damien <[email protected]> - - - - - 62d30c91 by Martin Uecker at 2018-07-30T22:00:37Z add comment - - - - - 67b4d835 by Nguyen Damien at 2018-07-31T13:21:33Z Fix ENABLE_LONGJUMP option in CMake + bug in debug_vprintf_trace - - - - - 7ee99446 by Christian Holme at 2018-07-31T13:24:38Z iter/italgos: add alternating minimization - - - - - 10b0d6f3 by Christian Holme at 2018-07-31T13:24:38Z iter/iter4: add iter4_altmin interface - - - - - 97e7e36c by Christian Holme at 2018-07-31T13:24:38Z nlops/tenmul: add GPU support - - - - - 9cb7ab7e by Christian Holme at 2018-07-31T13:24:38Z nlop: properly work with GPU - - - - - 7a6cb6ac by Christian Holme at 2018-07-31T13:24:38Z linop: only free if non-NULL - - - - - 5b9f2888 by Christian Holme at 2018-07-31T13:24:38Z italgos: output number of FISTA iterations - - - - - 2a0fee88 by Christian Holme at 2018-07-31T13:24:38Z italgos.c: output number of CG steps - - - - - 62b43445 by Nguyen Damien at 2018-07-31T13:27:53Z Fix a few issues with pyBART python module - - - - - aa6ec9e4 by Christian Holme at 2018-08-02T14:24:22Z nlops/nlop.c: properly pass through NULL for normal and norm_inv - - - - - 734145e2 by Christian Holme at 2018-08-02T14:24:22Z linop.c: linop_get_data now performs type check - - - - - 761ab125 by Martin Uecker at 2018-08-02T19:10:07Z add test for null/zero operators - - - - - 2dd3382d by Martin Uecker at 2018-08-02T19:10:51Z linop_null_create and test - - - - - 7c10605a by Christian Holme at 2018-08-03T11:57:54Z linops: optimize linop_plus if one of the arguments is linop_null - - - - - ac4cfaaa by Christian Holme at 2018-08-03T12:01:15Z nlinv: update to new non-linear operator interface This code was originally written by Martin Uecker - - - - - 685e77ba by Christian Holme at 2018-08-03T12:01:15Z noir/model.c: properly free arrays and ops - - - - - 7931f538 by Christian Holme at 2018-08-03T12:01:15Z iter3.c: simplify we already have iter_op_s's, no need to create extra functions to call them - - - - - ccb9947b by Martin Uecker at 2018-08-07T15:53:47Z fix bug in septrafo (broke cdf97 wavelets) - - - - - e5e073d2 by Martin Uecker at 2018-08-07T18:09:33Z add test for cdf97 - - - - - e0be139c by Nguyen Damien at 2018-08-08T10:05:15Z Rename CMake options with prefix BART_ - - - - - 6e1063e4 by Nguyen Damien at 2018-08-08T10:05:15Z CMake: add support for NOLAPACKE - - - - - 9672046d by Nguyen Damien at 2018-08-08T10:05:15Z CMake: only use C++ if needed + add clang flags + fix python3... ... + use CMAKE_POSITION_INDEPENDENT_CODE variable - - - - - a1344fb5 by Nguyen Damien at 2018-08-08T10:05:15Z Update Travis CI with some CMake builds - - - - - 695949b2 by Nguyen Damien at 2018-08-08T10:05:15Z CMake: use imported targets + update FindXXX.cmake... ... + add support for the AMD libFlame library - - - - - 584e42ac by Martin Uecker at 2018-08-08T10:05:15Z Update .travis.yml add back test for parallel make - - - - - 53923792 by Nguyen Damien at 2018-08-08T17:38:54Z CMake: fix automatic detection of BLAS vendor - - - - - 3531aabf by Christian Holme at 2018-08-09T10:57:52Z fix various memory leaks - - - - - b46d8efd by Martin Uecker at 2018-08-09T11:00:29Z remove unused data structure - - - - - 7cca41ac by Nguyen Damien at 2018-08-10T11:14:21Z Fix compilation with Gadgetron + fix issues with external logging... ... + fix one last issue with FindlibFlame.cmake. - - - - - a57a0bb4 by Siddharth Iyer at 2018-08-10T11:14:57Z Adding additional options + minor changes to wshfl - - - - - 07c17600 by Nguyen Damien at 2018-08-14T17:18:07Z CMake: add proper exporting of BART + some refactoring - - - - - 9d55fca6 by Nguyen Damien at 2018-08-17T09:54:54Z CMake: update CUDA detection and update FindFFTW.cmake - - - - - 5ea0a5ae by Nguyen Damien at 2018-08-17T09:54:54Z mmiocc: update to C++11 + re-enable debug output - - - - - d1b41fc0 by Martin Uecker at 2018-08-19T06:58:15Z remove unused header - - - - - 6d0c7f2b by Martin Uecker at 2018-08-19T08:13:29Z style - - - - - 0ae18e64 by Martin Uecker at 2018-08-19T08:13:29Z use auto - - - - - 94d848f8 by Nguyen Damien at 2018-08-20T12:14:55Z CMake: cleaning up and small fixes CMake build tested with all major versions of CMake from 2.8.12 up to 3.12.1 - - - - - 949a5882 by Nguyen Damien at 2018-08-20T12:14:55Z CMake: properly use version variables from CMake - - - - - 5309329e by Nguyen Damien at 2018-08-20T12:14:55Z CMake/CPack: introduce CPack to easily package BART With the help of CPack, packaging BART as ZIP, self-extracting TGZ archives, DEB or RPM packages on Linux or even as installers under Windows should be much easier. - - - - - 5d596732 by Nguyen Damien at 2018-08-20T12:14:55Z CMake: add integration tests contained in tests/*.mk files Building the target `integration` will run all integration tests, while building `ingtegration_XXX` where `XXX` is the basename of one of the test rule files (ie. XXX.mk), will run only those particular tests. Not all integration tests have been added to the CMake build due to some limitations of the current approach. The ones currently missing are: - estdelay - join - - - - - 6bcab4fe by Sebastian Rosenzweig at 2018-08-23T15:45:11Z traj: Option for asymmetric trajectories - - - - - 4d2de894 by Sebastian Rosenzweig at 2018-08-23T15:45:11Z traj: Half circle golden-ratio sampling - - - - - 5f8db5ba by Sebastian Rosenzweig at 2018-08-23T15:45:12Z simu/shepplogan: Fix inconsistency between img-phantom and k-phantom for rectangles - - - - - 63551802 by Martin Uecker at 2018-08-23T15:45:12Z add md_zmul2 benchmark - - - - - 0dd6b0e9 by Martin Uecker at 2018-08-23T15:45:12Z add option to select benchmarks using bitmask - - - - - 491175fb by Martin Uecker at 2018-08-26T08:53:11Z only use cppflags for includes and use iquote - - - - - 259b791a by Nguyen Damien at 2018-08-29T06:03:37Z CMake: fix version.inc + CUDA for users importing BART - - - - - ff52f102 by Nguyen Damien at 2018-08-29T06:03:37Z CMake: add static analysis tools - - - - - 7b4a056d by Nguyen Damien at 2018-08-29T06:03:37Z CMake: fix compilation flags + add modern OpenMP target - Make compilation of main functions more similar to the Makefile build - Prefer generator-expressions for compiler flags for recent CMake versions - - - - - 6b1d74eb by Nguyen Damien at 2018-08-29T06:03:37Z Update CMake buildig guide - - - - - 7d1c65e3 by Sebastian Rosenzweig at 2018-09-03T11:44:51Z add geometric object phantom - - - - - 7652f09a by Martin Uecker at 2018-09-03T16:17:46Z error message for no GPU - - - - - 89591882 by Martin Uecker at 2018-09-05T11:50:28Z fix for optimized strided copy on GPU (thanks to Simon Yeung) - - - - - 5cd5307f by Nguyen Damien at 2018-09-06T15:27:32Z CMake: general fixes and documentation update of FindXXX.cmake files - - - - - 0498bfa8 by Nguyen Damien at 2018-09-06T15:27:32Z CMake: backport FindPython from CMake 3.12 to all other version Also fixed a linking bug for pyBART - - - - - fc0d7b8d by Nguyen Damien at 2018-09-06T15:27:32Z Update CMake building guide Following a question from J. Tamir, added more precisions on how to compile with CMake when using libraries in non-standard locations. - - - - - bcdf14cf by Nguyen Damien at 2018-09-08T11:50:33Z CMake & pyBART: some minor fixes thanks to @jtamir - - - - - a8d5e35f by Nguyen Damien at 2018-09-17T06:03:15Z pyBART: fix some runtime issues + add better documentation - - - - - 757dc7fa by Siddharth Iyer at 2018-09-18T06:02:13Z Added parallel to kernel_adjoint - - - - - 0dcce0fb by Siddharth Iyer at 2018-09-18T06:02:13Z Initial commit for wshfl with gpu - - - - - c441dfba by Siddharth Iyer at 2018-09-18T06:02:13Z When using GPU, applied repmat to sampling-temporal kernel for speedup - - - - - e35ccef4 by Siddharth Iyer at 2018-09-18T06:02:13Z Added GPU support for max eigenvalue - - - - - 076acd52 by Siddharth Iyer at 2018-09-18T06:02:13Z CUDA check before using maximum eigenvalue - - - - - f59a64cc by Siddharth Iyer at 2018-09-18T06:02:13Z Added openmp flag test in wshfl - - - - - 24b81c41 by Siddharth Iyer at 2018-09-18T06:02:13Z Real value constraint to wshfl - - - - - 2cef5441 by Jon Tamir at 2018-09-24T18:54:40Z wshfl: ifdef code style - - - - - 0f516dd6 by Jon Tamir at 2018-09-24T18:55:00Z wshfl: fix warning without gpu - - - - - 6ccbc653 by Nguyen Damien at 2018-10-06T15:08:14Z pyBART: general fixes / mmiocc: add missing line returns pyBART fixes: - fix array ordering of returned values - properly unload memory from on-disk CFL files - add get/set functions for the debugging level - update documentation - - - - - be03a330 by Nguyen Damien at 2018-10-06T15:08:14Z CMake: fix Python executable for tests + other fixes Fixes include: - Using C++14 since BART requires GCC >= 5.0 - Removing debug postfix for pyBART - - - - - 00ccf201 by Nguyen Damien at 2018-10-06T15:08:14Z pyBART & mmmiocc: general fixes and introduce pybind11 - pyBART now relies on pybind11 for easier handling of the Python API and is now written in C++ - Overall, pyBART should better manage the memory it receives as input, as well as the ones it outputs. - Failure to load a memory CFL file is now properly treated as an error in mmio.c - - - - - f61a747c by Nguyen Damien at 2018-10-06T15:08:14Z Add integration tests for pyBART - - - - - e550dcff by Nguyen Damien at 2018-10-06T15:08:14Z pyBART: re-add cleanup_memory() and fix data ordering - - - - - e8c537de by Nguyen Damien at 2018-10-06T15:08:14Z mmiocc: fix bug when overwriting files - - - - - 0f469fb4 by Nguyen Damien at 2018-10-06T15:08:14Z pyBART: use proper cleanup routines for Python3 - - - - - 629bc6ca by Jon Tamir at 2018-10-08T07:23:10Z itsense: fix float size bug and add test - - - - - 852a340d by Jon Tamir at 2018-10-13T21:57:28Z add mkl support (addresses #164) - - - - - 078d8012 by Nguyen Damien at 2018-10-18T20:39:44Z pyBART & mmiocc: fix data ordering for Python arrays - - - - - fa92a4f7 by Sebastian Rosenzweig at 2018-11-05T18:53:15Z add RING method - - - - - b2b8a492 by Christian Holme at 2018-11-05T18:53:29Z irgnm: add minimum for alpha as parameter - - - - - cdfc0701 by Martin Uecker at 2018-11-05T18:54:16Z revert to always using periodic for psf - - - - - 94ae49b7 by Martin Uecker at 2018-11-06T12:16:42Z output for RING paper - - - - - 56c6740e by Nguyen Damien at 2018-11-07T11:34:26Z mmiocc: fix remove function to deallocate memory (#172) - - - - - 2c8c1a27 by Martin Uecker at 2018-11-16T15:49:37Z add smallfov test - - - - - c927ba55 by Martin Uecker at 2018-11-16T16:19:06Z allow failures - - - - - 26b35fd6 by Jon Tamir at 2018-11-19T08:35:00Z add lz when LINKER=icc - - - - - b6ec275d by Martin Uecker at 2018-11-19T14:25:30Z smallfov test fixes - - - - - af158b4e by Martin Uecker at 2018-11-19T14:25:30Z rewrite projection - - - - - da609da4 by Martin Uecker at 2018-11-19T14:25:30Z introduce option for sms - - - - - 326071d6 by Siddharth Iyer at 2018-11-19T14:40:24Z Save FFTW wisdom when TOOLBOX path is set. - - - - - 106832a8 by Siddharth Iyer at 2018-11-19T14:40:24Z Edit gitignore.main to ignore fftw wisdom - - - - - 7dd3a1a2 by Siddharth Iyer at 2018-11-19T15:00:22Z Initial guess option to wave-shuffling + Modify wshfl forward to output table with centered FFT - - - - - ce852115 by Siddharth Iyer at 2018-11-19T15:00:22Z Edit wave to be similar to wshfl - - - - - 8bccedfc by Siddharth Iyer at 2018-11-19T15:00:22Z Edit normalization in wave to be consistent with wshfl - - - - - 4794e34e by Siddharth Iyer at 2018-11-19T15:00:22Z Create-operator timings to wshfl - - - - - a6d1fcb2 by Siddharth Iyer at 2018-11-19T15:00:45Z Cosmetic changes to wshfl + Operator timing to wave - - - - - 52e396aa by Siddharth Iyer at 2018-11-19T15:00:45Z Removed the debugging step of saving the sampling mask in wave. - - - - - b58d79a4 by Jon Tamir at 2018-11-19T15:06:18Z add overlapping blocks option for LLR - - - - - e333120b by Martin Uecker at 2018-11-20T21:21:04Z make using clang easier - - - - - 70329a5a by Martin Uecker at 2018-11-20T21:46:17Z add mvec for static linking - - - - - 5c57e9cf by Martin Uecker at 2018-11-20T22:19:26Z fix operator_p_(co)domain (thanks to Christian Holme) - - - - - 65131eeb by Martin Uecker at 2018-11-20T22:33:15Z license year - - - - - 57d51b86 by Martin Uecker at 2018-11-21T12:41:58Z add runga-kutta ode solver - - - - - 323811e8 by Martin Uecker at 2018-11-21T12:45:20Z bloch equations - - - - - 98f0d032 by Martin Uecker at 2018-11-21T12:45:34Z add ode unit test - - - - - 2eb8fa11 by Martin Uecker at 2018-11-21T12:47:19Z explanation for bitmasks - - - - - 6130d746 by Martin Uecker at 2018-11-24T11:43:36Z fix leaks in unit tests - - - - - fc7a16ce by Martin Uecker at 2018-11-24T13:04:59Z add missing frees - - - - - 1d8bf952 by soumickOVGU at 2018-12-01T07:09:04Z Helper Function for BART with WSL - - - - - f045ad2a by soumickOVGU at 2018-12-01T07:09:22Z Helper Function for BART with WSL - - - - - 3c39bfe1 by soumickOVGU at 2018-12-01T07:09:39Z Added WSL BART Calls Can now work with BART inside WSL - - - - - 249d8904 by soumickOVGU at 2018-12-01T07:09:55Z Added WSL BART Calls Can now work with BART inside WSL - - - - - 512e7e04 by Martin Uecker at 2018-12-02T21:25:46Z fix chambolle-pock scaling - - - - - 5ef3533a by Martin Uecker at 2018-12-02T21:25:46Z coding style - - - - - dcfe39bb by Martin Uecker at 2018-12-05T08:12:34Z replace zexpj with zexp - - - - - 59a407ca by Martin Uecker at 2018-12-05T08:12:59Z index command - - - - - 58ff16c8 by Martin Uecker at 2018-12-05T08:12:59Z change warnings for random shifts - - - - - bbdec08c by Martin Uecker at 2018-12-05T20:06:14Z nufft unit tests - - - - - 4dc9f95e by Martin Uecker at 2018-12-05T20:13:02Z relax assertion for non-used dims - - - - - 25242e03 by Martin Uecker at 2018-12-08T20:09:11Z update nufft - - - - - 3d91bd4b by Martin Uecker at 2018-12-08T20:39:17Z nufft basis unit tests - - - - - 8a9b8865 by Martin Uecker at 2018-12-09T09:17:38Z deactivate cmake integration tests - - - - - 830e1ab9 by Martin Uecker at 2018-12-09T09:48:08Z update acknowledgements - - - - - f6be8893 by Martin Uecker at 2018-12-09T10:55:17Z update references - - - - - 053eba80 by Martin Uecker at 2018-12-09T11:06:56Z update pics command (basis) - - - - - 69c7f7c5 by Martin Uecker at 2018-12-09T11:07:49Z add linear constraint tests (t2 shuffling, etc.) - - - - - 5527f073 by Martin Uecker at 2018-12-09T11:08:03Z test for estshift - - - - - cf3bef95 by Martin Uecker at 2018-12-09T11:09:39Z update README - - - - - b301ca87 by Martin Uecker at 2018-12-09T20:32:46Z bump version - - - - - 5ac18f2c by Martin Uecker at 2018-12-10T13:19:57Z Merge tag 'v0.4.04' version 0.4.04 Changes: - new tools: index poly wshfl zexp - index: generate indices - poly: generate polynomial patterns (Siddharth Iyer) - wshfl: wave-shuffling (Siddharth Iyer) - zexp: replace zexpj with zexp for complex exponentials - pics: support for temporal basis - pics: overlapping blocks option for LLR (Jon Tamir) - pics: make basis pursuit possible for noncartesian data - pics: non-negative constraint (Jon Tamir) - nlinv: introduce option for sms - ecalib: fix bug in phase rotation - ecalib: add debug_level argument - estdelay: RING method (Sebastian Rosenzweig) - traj: Half circle golden-ratio sampling (Sebastian Rosenzweig) - traj: Option for asymmetric trajectories (Sebastian Rosenzweig) - bench: add option to select benchmarks using bitmask - phantom: add geometric object phantom (Sebastian Rosenzweig) - phantom: fix inconsistency between img-phantom and k-phantom for rectangles (Sebastian Rosenzweig) - copy: enhance copy command to do simple copies - toimg: windowing and option to re-scale images to full dynamic range (Jon Tamir) - generic: many new integration and unit tests - generic: improved WSL support (Soumick Chatterjee) - generic: add mkl support (Jon Tamir) - generic: bart as a library (Damien Nguyen) - generic: CMake improvements (Damien Nguyen) - generic: Save FFTW wisdom when TOOLBOX path is set (Siddharth Iyer) - generic: fixes for memory leaks - library: optimized strided copy on GPU (Simon Yeung) - library: parallelization to fftmod - library: nufft: efficient use with temporal basis - library: nufft: fix issue with over-sized trajectories - library: add runga-kutta ode solver - library: iter/italgos: alternating minimization (Christian Holme) - library: irgnm: add minimum for alpha as parameter (Christian Holme) - library: step size support in chambolle-pock - library: add tenmul operator - library: add md_zexp - library: add zexp nonlinear operator - library: add linop_null and linop_plus - library: add md_zsum: (Complex) sum along specified dimensions (Sebastian Rosenzweig) - library: fix bug in septrafo (broke cdf97 wavelets) - many other bug fixes and improvements - - - - - 8900be9b by Martin Uecker at 2018-12-10T13:24:32Z makefile change for compatibility with debian - - - - - c93e7c29 by Martin Uecker at 2018-12-10T13:24:32Z remove empty directory - - - - - 2d8657e4 by Martin Uecker at 2018-12-10T13:44:21Z relax unit test - - - - - 17 changed files: - .gitignore.main - .travis.yml - ACKNOWLEDGEMENTS - CMakeLists.txt - LICENSE - Makefile - README - build_targets.mk - + cmake/BARTConfig.cmake.in - + cmake/BARTFindBLASlib.cmake - cmake/FindATLAS.cmake - + cmake/FindBOpenMP.cmake - + cmake/FindBPython.cmake - + cmake/FindCUDAlibs.cmake - cmake/FindFFTW.cmake - cmake/FindLAPACKE.cmake - cmake/FindOpenBLAS.cmake The diff was not included because it is too large. View it on GitLab: https://salsa.debian.org/med-team/bart/compare/77783d5f8b5236352a1ca5740214a6dc8eef5fde...2d8657e4e45aee6c9fed28447582a3023b4e05d8 -- View it on GitLab: https://salsa.debian.org/med-team/bart/compare/77783d5f8b5236352a1ca5740214a6dc8eef5fde...2d8657e4e45aee6c9fed28447582a3023b4e05d8 You're receiving this email because of your account on salsa.debian.org.
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