[med-svn] [Git][med-team/bart][upstream] 169 commits: add parallelization to fftmod
Martin Uecker
gitlab at salsa.debian.org
Tue Nov 20 22:04:06 GMT 2018
Martin Uecker pushed to branch upstream at Debian Med / bart
Commits:
42628438 by Martin Uecker at 2018-04-29T09:29:28Z
add parallelization to fftmod
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d03aaa48 by Martin Uecker at 2018-04-29T09:41:47Z
update operators
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0c87b89a by Martin Uecker at 2018-04-29T09:45:59Z
linop null and plus
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31616e95 by Martin Uecker at 2018-04-29T09:49:50Z
include guards for shrdptr.h
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14819db5 by Martin Uecker at 2018-04-29T09:52:30Z
warnings in ops
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f0acbb12 by Martin Uecker at 2018-04-29T10:22:00Z
update nonlinear operator framework
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573e6038 by Martin Uecker at 2018-04-29T10:34:37Z
add zexp nonlinear operator
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bc8a650f by Martin Uecker at 2018-04-29T10:38:23Z
add md_zexp
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a521ed8f by Martin Uecker at 2018-04-29T10:38:57Z
add tenmul operator
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dc3c19be by Martin Uecker at 2018-04-29T10:40:37Z
run-time type check: improve error message
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d328a05e by Martin Uecker at 2018-04-29T10:43:23Z
add tests for nonlinear operators
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ed1df142 by Martin Uecker at 2018-04-29T13:29:35Z
add safe_isnanf which protects against optimization
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2ae81ea2 by Martin Uecker at 2018-04-29T16:28:06Z
update compiler on travis
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c0fd3d6a by Martin Uecker at 2018-04-29T16:43:25Z
update iovec
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89f2ddec by Martin Uecker at 2018-04-29T16:48:01Z
update flpmath and vecops
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5c6ce3a0 by Martin Uecker at 2018-04-29T16:54:18Z
add test for linop_plus
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2f51dba1 by Sebastian Rosenzweig at 2018-05-27T20:15:12Z
num/flpmath: (Complex) sum along specified dimensions
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973a93d0 by Sebastian Rosenzweig at 2018-05-27T20:15:12Z
num/gpuops: GPU memory usage print function
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b06207de by Sebastian Rosenzweig at 2018-05-27T20:15:12Z
gpuops: Memory print function
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73348761 by Martin Uecker at 2018-05-28T12:25:20Z
gpu fixes
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a8db6f5d by Martin Uecker at 2018-05-28T12:25:20Z
fix md_zlessequal
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62cf0a84 by Christian Holme at 2018-05-31T20:40:06Z
num/ops.c: properly guard OpenMP expressions (#123)
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57e33fdd by Siddharth Iyer at 2018-05-31T20:42:34Z
Added wave-shuffling + fixes to wavepsf (#122)
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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.
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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
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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.
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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].
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cbda5774 by Siddharth Iyer at 2018-06-29T15:14:36Z
Added rounding to reorder related arguements to avoid interger related errors
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b53e1464 by Siddharth Iyer at 2018-06-29T15:14:36Z
Added test for wshfl
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dd798897 by Martin Uecker at 2018-06-29T17:34:55Z
document minimum compiler version
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9a83657c by Martin Uecker at 2018-06-29T17:44:57Z
help for l1-Fourier
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2e8c6f4b by Martin Uecker at 2018-06-29T17:53:07Z
add missing copyright headers
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ea2dbff4 by Martin Uecker at 2018-06-29T19:06:12Z
add test for batch nufft
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2ef396b3 by Martin Uecker at 2018-06-30T15:27:43Z
rename algo enum constants
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15ac5472 by Martin Uecker at 2018-06-30T19:24:01Z
move initialization of italgos in its own function
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a55b9526 by Martin Uecker at 2018-06-30T20:33:10Z
move italgo init into its own file
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9e7fbf31 by Martin Uecker at 2018-07-01T12:08:45Z
memory management
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0d1200c4 by Martin Uecker at 2018-07-01T12:48:16Z
refactor choice of algorithm
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b8f79704 by Martin Uecker at 2018-07-01T13:36:59Z
make basis pursuit possible for noncartesian data
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b7c84844 by Martin Uecker at 2018-07-07T07:02:06Z
fix issue with over-sized trajectories
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186fbd5e by Martin Uecker at 2018-07-07T11:23:16Z
propagate periodic flag to psf
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978a67a0 by Martin Uecker at 2018-07-23T20:37:44Z
fix memory leaks in nonlinear operator chains
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95889313 by Martin Uecker at 2018-07-23T21:50:15Z
fix noreturn issue for c++
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50244f05 by Martin Uecker at 2018-07-23T22:23:40Z
refactor gridding
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abbfd3ef by Martin Uecker at 2018-07-23T22:36:48Z
make clang compatible
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74d5b026 by Nguyen Damien at 2018-07-25T15:17:27Z
Bring unit-testing on CMake up to par with Makefile
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0618e748 by Nguyen Damien at 2018-07-26T08:01:31Z
Remove abort() and replace exit() with return values
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1cba6ca8 by Nguyen Damien at 2018-07-26T12:10:43Z
ecalib: add debug_level argument
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a2330ca3 by Nguyen Damien at 2018-07-26T20:11:22Z
Change getopt to ya_getopt and modify cmdlines fct to return values
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f6634403 by Nguyen Damien at 2018-07-26T20:14:31Z
Prepare debug_printf* functions for external log backends
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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
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30a8971d by Martin Uecker at 2018-07-27T09:34:22Z
minor fixes and style changes
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62dac483 by Martin Uecker at 2018-07-27T10:28:37Z
add missing newlines in error messages
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5a2224a0 by Nguyen Damien at 2018-07-27T10:33:50Z
Add support for in-memory CFL files
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ee06c842 by Martin Uecker at 2018-07-27T12:12:22Z
fix warnings, build, coding style, rewrite list of i/o files
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aa78612c by Nguyen Damien at 2018-07-27T12:43:38Z
Miscellaneous changes to the CMake build systems
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3c71c1fe by Martin Uecker at 2018-07-27T13:25:01Z
fix for next_powerof2 (thanks to Nguyen Damien)
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0ebcd52b by Martin Uecker at 2018-07-30T14:08:33Z
cc: don't warn when correct option is used
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90112eb8 by Martin Uecker at 2018-07-30T14:08:33Z
add FIXME
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a8507500 by Martin Uecker at 2018-07-30T14:08:33Z
add complex-conjugate for matrix
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6f050bc5 by Martin Uecker at 2018-07-30T14:08:33Z
fix bug in phase rotation (now improved results)
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d994489a by Martin Uecker at 2018-07-30T14:08:33Z
reactivate old coil compression test
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0df678d5 by Martin Uecker at 2018-07-30T14:08:33Z
add phase rotation tests
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f9c6bb20 by Martin Uecker at 2018-07-30T16:33:34Z
enhance copy command to do simple copies
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e059a188 by Martin Uecker at 2018-07-30T21:39:28Z
longjmp-based error handling (loosely based on patch by Damien Nguyen)
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58129193 by Martin Uecker at 2018-07-30T21:39:34Z
ismrmrd fix (thanks to Damien Nguyen)
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2da0fa3e by Martin Uecker at 2018-07-30T21:40:10Z
introduce bart_printf
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c1d43557 by Martin Uecker at 2018-07-30T21:40:51Z
add entry point for calling bart commands when used as a library
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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)
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67910d31 by Nguyen Damien at 2018-07-30T22:00:37Z
Fix some runtime issues with clang
Signed-off-by: Nguyen Damien <damien.nguyen at unibas.ch>
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62d30c91 by Martin Uecker at 2018-07-30T22:00:37Z
add comment
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67b4d835 by Nguyen Damien at 2018-07-31T13:21:33Z
Fix ENABLE_LONGJUMP option in CMake + bug in debug_vprintf_trace
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7ee99446 by Christian Holme at 2018-07-31T13:24:38Z
iter/italgos: add alternating minimization
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10b0d6f3 by Christian Holme at 2018-07-31T13:24:38Z
iter/iter4: add iter4_altmin interface
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97e7e36c by Christian Holme at 2018-07-31T13:24:38Z
nlops/tenmul: add GPU support
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9cb7ab7e by Christian Holme at 2018-07-31T13:24:38Z
nlop: properly work with GPU
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7a6cb6ac by Christian Holme at 2018-07-31T13:24:38Z
linop: only free if non-NULL
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5b9f2888 by Christian Holme at 2018-07-31T13:24:38Z
italgos: output number of FISTA iterations
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2a0fee88 by Christian Holme at 2018-07-31T13:24:38Z
italgos.c: output number of CG steps
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62b43445 by Nguyen Damien at 2018-07-31T13:27:53Z
Fix a few issues with pyBART python module
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aa6ec9e4 by Christian Holme at 2018-08-02T14:24:22Z
nlops/nlop.c: properly pass through NULL for normal and norm_inv
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734145e2 by Christian Holme at 2018-08-02T14:24:22Z
linop.c: linop_get_data now performs type check
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761ab125 by Martin Uecker at 2018-08-02T19:10:07Z
add test for null/zero operators
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2dd3382d by Martin Uecker at 2018-08-02T19:10:51Z
linop_null_create and test
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7c10605a by Christian Holme at 2018-08-03T11:57:54Z
linops: optimize linop_plus if one of the arguments is linop_null
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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
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685e77ba by Christian Holme at 2018-08-03T12:01:15Z
noir/model.c: properly free arrays and ops
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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
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ccb9947b by Martin Uecker at 2018-08-07T15:53:47Z
fix bug in septrafo (broke cdf97 wavelets)
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e5e073d2 by Martin Uecker at 2018-08-07T18:09:33Z
add test for cdf97
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e0be139c by Nguyen Damien at 2018-08-08T10:05:15Z
Rename CMake options with prefix BART_
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6e1063e4 by Nguyen Damien at 2018-08-08T10:05:15Z
CMake: add support for NOLAPACKE
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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
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a1344fb5 by Nguyen Damien at 2018-08-08T10:05:15Z
Update Travis CI with some CMake builds
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695949b2 by Nguyen Damien at 2018-08-08T10:05:15Z
CMake: use imported targets + update FindXXX.cmake...
... + add support for the AMD libFlame library
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584e42ac by Martin Uecker at 2018-08-08T10:05:15Z
Update .travis.yml
add back test for parallel make
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53923792 by Nguyen Damien at 2018-08-08T17:38:54Z
CMake: fix automatic detection of BLAS vendor
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3531aabf by Christian Holme at 2018-08-09T10:57:52Z
fix various memory leaks
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b46d8efd by Martin Uecker at 2018-08-09T11:00:29Z
remove unused data structure
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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.
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a57a0bb4 by Siddharth Iyer at 2018-08-10T11:14:57Z
Adding additional options + minor changes to wshfl
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07c17600 by Nguyen Damien at 2018-08-14T17:18:07Z
CMake: add proper exporting of BART + some refactoring
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9d55fca6 by Nguyen Damien at 2018-08-17T09:54:54Z
CMake: update CUDA detection and update FindFFTW.cmake
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5ea0a5ae by Nguyen Damien at 2018-08-17T09:54:54Z
mmiocc: update to C++11 + re-enable debug output
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d1b41fc0 by Martin Uecker at 2018-08-19T06:58:15Z
remove unused header
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6d0c7f2b by Martin Uecker at 2018-08-19T08:13:29Z
style
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0ae18e64 by Martin Uecker at 2018-08-19T08:13:29Z
use auto
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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
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949a5882 by Nguyen Damien at 2018-08-20T12:14:55Z
CMake: properly use version variables from CMake
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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.
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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
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6bcab4fe by Sebastian Rosenzweig at 2018-08-23T15:45:11Z
traj: Option for asymmetric trajectories
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4d2de894 by Sebastian Rosenzweig at 2018-08-23T15:45:11Z
traj: Half circle golden-ratio sampling
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5f8db5ba by Sebastian Rosenzweig at 2018-08-23T15:45:12Z
simu/shepplogan: Fix inconsistency between img-phantom and k-phantom for rectangles
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63551802 by Martin Uecker at 2018-08-23T15:45:12Z
add md_zmul2 benchmark
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0dd6b0e9 by Martin Uecker at 2018-08-23T15:45:12Z
add option to select benchmarks using bitmask
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491175fb by Martin Uecker at 2018-08-26T08:53:11Z
only use cppflags for includes and use iquote
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259b791a by Nguyen Damien at 2018-08-29T06:03:37Z
CMake: fix version.inc + CUDA for users importing BART
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ff52f102 by Nguyen Damien at 2018-08-29T06:03:37Z
CMake: add static analysis tools
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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
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6b1d74eb by Nguyen Damien at 2018-08-29T06:03:37Z
Update CMake buildig guide
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7d1c65e3 by Sebastian Rosenzweig at 2018-09-03T11:44:51Z
add geometric object phantom
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7652f09a by Martin Uecker at 2018-09-03T16:17:46Z
error message for no GPU
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89591882 by Martin Uecker at 2018-09-05T11:50:28Z
fix for optimized strided copy on GPU (thanks to Simon Yeung)
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5cd5307f by Nguyen Damien at 2018-09-06T15:27:32Z
CMake: general fixes and documentation update of FindXXX.cmake files
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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
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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.
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bcdf14cf by Nguyen Damien at 2018-09-08T11:50:33Z
CMake & pyBART: some minor fixes thanks to @jtamir
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a8d5e35f by Nguyen Damien at 2018-09-17T06:03:15Z
pyBART: fix some runtime issues + add better documentation
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757dc7fa by Siddharth Iyer at 2018-09-18T06:02:13Z
Added parallel to kernel_adjoint
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0dcce0fb by Siddharth Iyer at 2018-09-18T06:02:13Z
Initial commit for wshfl with gpu
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c441dfba by Siddharth Iyer at 2018-09-18T06:02:13Z
When using GPU, applied repmat to sampling-temporal kernel for speedup
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e35ccef4 by Siddharth Iyer at 2018-09-18T06:02:13Z
Added GPU support for max eigenvalue
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076acd52 by Siddharth Iyer at 2018-09-18T06:02:13Z
CUDA check before using maximum eigenvalue
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f59a64cc by Siddharth Iyer at 2018-09-18T06:02:13Z
Added openmp flag test in wshfl
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24b81c41 by Siddharth Iyer at 2018-09-18T06:02:13Z
Real value constraint to wshfl
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2cef5441 by Jon Tamir at 2018-09-24T18:54:40Z
wshfl: ifdef code style
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0f516dd6 by Jon Tamir at 2018-09-24T18:55:00Z
wshfl: fix warning without gpu
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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
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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
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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
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f61a747c by Nguyen Damien at 2018-10-06T15:08:14Z
Add integration tests for pyBART
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e550dcff by Nguyen Damien at 2018-10-06T15:08:14Z
pyBART: re-add cleanup_memory() and fix data ordering
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e8c537de by Nguyen Damien at 2018-10-06T15:08:14Z
mmiocc: fix bug when overwriting files
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0f469fb4 by Nguyen Damien at 2018-10-06T15:08:14Z
pyBART: use proper cleanup routines for Python3
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629bc6ca by Jon Tamir at 2018-10-08T07:23:10Z
itsense: fix float size bug and add test
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852a340d by Jon Tamir at 2018-10-13T21:57:28Z
add mkl support (addresses #164)
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078d8012 by Nguyen Damien at 2018-10-18T20:39:44Z
pyBART & mmiocc: fix data ordering for Python arrays
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fa92a4f7 by Sebastian Rosenzweig at 2018-11-05T18:53:15Z
add RING method
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b2b8a492 by Christian Holme at 2018-11-05T18:53:29Z
irgnm: add minimum for alpha as parameter
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cdfc0701 by Martin Uecker at 2018-11-05T18:54:16Z
revert to always using periodic for psf
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94ae49b7 by Martin Uecker at 2018-11-06T12:16:42Z
output for RING paper
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56c6740e by Nguyen Damien at 2018-11-07T11:34:26Z
mmiocc: fix remove function to deallocate memory (#172)
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2c8c1a27 by Martin Uecker at 2018-11-16T15:49:37Z
add smallfov test
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c927ba55 by Martin Uecker at 2018-11-16T16:19:06Z
allow failures
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26b35fd6 by Jon Tamir at 2018-11-19T08:35:00Z
add lz when LINKER=icc
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b6ec275d by Martin Uecker at 2018-11-19T14:25:30Z
smallfov test fixes
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af158b4e by Martin Uecker at 2018-11-19T14:25:30Z
rewrite projection
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da609da4 by Martin Uecker at 2018-11-19T14:25:30Z
introduce option for sms
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326071d6 by Siddharth Iyer at 2018-11-19T14:40:24Z
Save FFTW wisdom when TOOLBOX path is set.
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106832a8 by Siddharth Iyer at 2018-11-19T14:40:24Z
Edit gitignore.main to ignore fftw wisdom
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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
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ce852115 by Siddharth Iyer at 2018-11-19T15:00:22Z
Edit wave to be similar to wshfl
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8bccedfc by Siddharth Iyer at 2018-11-19T15:00:22Z
Edit normalization in wave to be consistent with wshfl
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4794e34e by Siddharth Iyer at 2018-11-19T15:00:22Z
Create-operator timings to wshfl
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a6d1fcb2 by Siddharth Iyer at 2018-11-19T15:00:45Z
Cosmetic changes to wshfl + Operator timing to wave
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52e396aa by Siddharth Iyer at 2018-11-19T15:00:45Z
Removed the debugging step of saving the sampling mask in wave.
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b58d79a4 by Jon Tamir at 2018-11-19T15:06:18Z
add overlapping blocks option for LLR
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e333120b by Martin Uecker at 2018-11-20T21:21:04Z
make using clang easier
- - - - -
15 changed files:
- .gitignore.main
- .travis.yml
- CMakeLists.txt
- 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/d149bc84b65d3c032fd8de198a68600399ed6cc8...e333120bf49178a5ffd1f64c9a8f97f54eaf7dcf
--
View it on GitLab: https://salsa.debian.org/med-team/bart/compare/d149bc84b65d3c032fd8de198a68600399ed6cc8...e333120bf49178a5ffd1f64c9a8f97f54eaf7dcf
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