[med-svn] [Git][med-team/bart][master-contrib] 2522 commits: update commands.txt added in Debian patch
Martin Uecker (@uecker-guest)
gitlab at salsa.debian.org
Sat Sep 26 12:17:55 BST 2026
Martin Uecker pushed to branch master-contrib at Debian Med / bart
Commits:
0e2fe50c by Martin Uecker at 2022-09-25T15:25:10+02:00
update commands.txt added in Debian patch
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ff104939 by Martin Uecker at 2022-09-25T19:24:13+02:00
install get_bart_path.m
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696f1158 by Martin Uecker at 2022-09-25T21:51:59+02:00
relax failing test
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2fe678fa by Christian Holme at 2022-09-26T14:39:32+02:00
skip GPU tests when no GPU available
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7dbdb62b by Christian Holme at 2022-09-26T15:16:10+02:00
.gitlab-ci: Unit Test LTO should run unit tests
and not the integration tests
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b0c2c17f by Christian Holme at 2022-09-26T15:17:31+02:00
gitlab-ci: add LTO integration test
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67c9dd27 by Christian Holme at 2022-09-27T10:11:03+02:00
gitlab-ci: put `if` and command on the same line
This way, the command being run can be seen in the
gitlab runner logs
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cfa6a974 by Christian Holme at 2022-09-27T10:11:30+02:00
gitlab-ci: comment out LTO Integration Test
As it takes too long for now
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7cfc7b20 by Martin Uecker at 2022-10-01T13:03:55+02:00
update standard's version
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9ca87d4d by Martin Uecker at 2022-10-01T13:17:04+02:00
extend devel package
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6932bdb3 by Martin Uecker at 2022-10-01T13:18:48+02:00
mention machine learning
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08bd6c77 by Martin Uecker at 2022-10-01T13:36:06+02:00
properly install files
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809d310b by Martin Uecker at 2022-10-02T17:34:03+02:00
remove unsigned (multind)
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c16bfc83 by Martin Uecker at 2022-10-02T17:34:03+02:00
relax two tests
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9114f1d7 by Martin Uecker at 2022-10-02T17:38:19+02:00
_Bool -> bool
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cf5036a3 by Martin Uecker at 2022-10-02T17:40:19+02:00
flags are unsigned long
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0b430892 by Martin Uecker at 2022-10-02T18:33:27+02:00
unsigned flpmath
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2eba55ce by Martin Uecker at 2022-10-02T18:41:54+02:00
flags are unsigned long (flpmath.h)
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e521f64a by Martin Uecker at 2022-10-02T18:43:49+02:00
_Bool -> bool
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a686f3b0 by Martin Uecker at 2022-10-02T21:48:54+02:00
missing new line
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5428c0ae by Martin Uecker at 2022-10-02T21:48:54+02:00
relax test
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3a84b390 by Martin Uecker at 2022-10-06T15:25:13+02:00
minor
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1d227f55 by Martin Uecker at 2022-10-06T15:25:16+02:00
reporting problems
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9dcaac59 by Martin Uecker at 2022-10-06T15:25:16+02:00
remove old cmake file
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5459c39a by Andreas Tille at 2022-10-07T11:38:41+02:00
Upload to unstable
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efb8777e by Martin Uecker at 2022-10-11T14:28:12+02:00
fix exponent
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1ead7298 by Martin Uecker at 2022-10-11T14:33:32+02:00
rewrite Si
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1720eeee by Christian Holme at 2022-10-11T14:51:58+02:00
tests/rtnlinv: add dimensions tests for rt-ENLIVE
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af4464c3 by Christian Holme at 2022-10-11T14:51:58+02:00
rtnlinv.c: fix ENLIVE dims
Somewhere, the dimension logic was messed up...
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4529e45d by Martin Uecker at 2022-10-11T15:40:12+02:00
updates
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7f5af323 by Martin Uecker at 2022-10-11T15:51:10+02:00
horner schema
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2d4ba14c by Martin Uecker at 2022-10-13T19:08:59+02:00
pow -> powf
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e5f47794 by Martin Uecker at 2022-10-13T19:10:18+02:00
avoid overflowing factorial
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e8aa9da6 by Martin Uecker at 2022-10-13T19:23:22+02:00
copyright
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184e0ce7 by Martin Uecker at 2022-10-13T19:35:55+02:00
backport fixes
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ca40d8dd by Martin Uecker at 2022-10-13T19:36:54+02:00
unit tests on more archs
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1820138f by Martin Uecker at 2022-10-13T20:08:35+02:00
turn off some optimizations for some archs
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e4b40717 by Martin Uecker at 2022-10-13T20:08:35+02:00
update copyright
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494ac798 by Martin Uecker at 2022-10-13T21:01:21+02:00
relax flaky tests
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c5ba90fd by Andreas Tille at 2022-10-14T08:11:40+02:00
Upload to unstable
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62bddb12 by Martin Uecker at 2022-10-14T13:19:19+02:00
fix E-notation
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bf78f16d by Martin Uecker at 2022-10-24T17:15:47+02:00
more tests, remove old port
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4e1df5a1 by Martin Uecker at 2022-10-24T17:15:47+02:00
turn off two tests on i386
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462c49ef by Martin Uecker at 2022-10-24T17:15:58+02:00
update changelog
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0c2a13e6 by Martin Uecker at 2022-10-24T20:16:52+02:00
add geometry library to libbart
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8a18c5bc by Nilesh Patra at 2022-10-25T01:12:53+05:30
Upload to unstable
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97608a7e by Martin Uecker at 2022-10-29T15:28:52+02:00
unsigned flags
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bb37b37c by Martin Uecker at 2022-10-29T15:28:52+02:00
make some small dims signed
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694f25ad by Martin Uecker at 2022-10-29T16:02:05+02:00
remove unsigned from dim
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59c765a6 by Moritz Blumenthal at 2022-10-31T13:13:20+01:00
fix linop_stack
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949c32ce by Moritz Blumenthal at 2022-10-31T13:13:20+01:00
fix memleak
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75a64c2c by Moritz Blumenthal at 2022-10-31T13:13:20+01:00
fix memleak
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3188109b by Moritz Blumenthal at 2022-10-31T13:13:20+01:00
fix nlcmp
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f9a4e962 by Moritz Blumenthal at 2022-10-31T13:13:20+01:00
fix real in t1fun
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ec4d14fb by Moritz Blumenthal at 2022-10-31T13:13:20+01:00
fix UB
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f151f2ae by Moritz Blumenthal at 2022-10-31T13:14:48+01:00
fixup unsigned for flpmath in utest
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f99589ef by Moritz Blumenthal at 2022-10-31T13:15:20+01:00
unsigned int in fft-cuda
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95d46730 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
fix psf for basis with higher dims
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df91b490 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
update lists
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add698ec by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
Add linop is identity
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f411f5aa by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
get list in attach
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e9850311 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
stream selection for gpukernel
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46039c65 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
Prepare gpu init for entering omp regions
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64a18ee1 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
rename zrblock->rblock and zrdiag->rdiag
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04ad6c43 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
add nlops with jacobian for wirtinger calculus
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b0e71e65 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
speedup nlop_zrprecomp
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083c0269 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
Add linop_flip
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46326c01 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
update someops
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0367b820 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
refactor and add activations
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4529ef05 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
add cardioid activation as option to resnet
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fe70cda0 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
add function to compress binary floats
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29885165 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
reduce memory for relu
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7ccd3825 by Moritz Blumenthal at 2022-10-31T13:18:54+01:00
graph optimization remove constant nodes
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21bd1db2 by Moritz Blumenthal at 2022-10-31T13:39:56+01:00
twixread fix for linectr/partctr
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f9f3fc9c by Moritz Blumenthal at 2022-10-31T13:39:56+01:00
option to turn of consistency check
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8fa58b26 by Moritz Blumenthal at 2022-10-31T13:39:56+01:00
add dimensions
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f2aaa8b0 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
meaningful error if not compiled with TensorFlow
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7f7f535a by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
multiple outputs for tf wrapper and detection of inputs and outputs
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d7bc24be by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
reuse tf graph
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023e1f69 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
set tf options (threads/memory/selected gpu)
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b37fead6 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
remove unused code
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bf67f0ea by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
get args from shared graph
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1870e77e by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
allways pass grad_ys (tf2)
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50c99b99 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
support for tensorflow 2 saved model
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ce48c61a by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
fix ifdefs for tensorflow
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4edbe638 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
checkpointing for tensorflow wrapper
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4b299a75 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
fix warnings
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69301151 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
reduce logging for tensorflow
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81a0ed89 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
update tf_wrapper
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4558bfd7 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
tf wrapper restructure and allocate tensors of different types
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effd0200 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
Support for complex tensors in tensorflow wrapper
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4ccf0494 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
add support for tensorflow graphs with jacobian
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dff91b32 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
add utests for tensorflow wrapper
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01058c71 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
update documentation
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8b30558e by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
Initialize with constant array
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2885cc25 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
move residual to interface
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393233ff by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
move bart to channel first dims to networks
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c05a8d63 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
add tensorflow graph to reconet
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ad43b069 by Moritz Blumenthal at 2022-10-31T13:57:36+01:00
fix dependencies
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e4c25fdc by Martin Uecker at 2022-10-31T14:48:52+01:00
coding style
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03c98a03 by Moritz Blumenthal at 2022-10-31T15:33:55+01:00
optimize flattening
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5baa67de by Moritz Blumenthal at 2022-10-31T15:33:55+01:00
join frw and adj
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a553ef05 by Moritz Blumenthal at 2022-10-31T15:33:55+01:00
move rvc in model
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ac174b82 by Moritz Blumenthal at 2022-10-31T15:33:55+01:00
automatic optimization in noir model
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f7faa384 by Moritz Blumenthal at 2022-10-31T15:33:55+01:00
apply mask on image, not coil image
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d371a771 by Moritz Blumenthal at 2022-11-01T15:12:44+01:00
cache nufft for gridding
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3b29e6d7 by Moritz Blumenthal at 2022-11-01T15:20:37+01:00
make lowmem gridding independent
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d75761ff by Moritz Blumenthal at 2022-11-01T15:24:11+01:00
update lowmem code
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0b272fd2 by Moritz Blumenthal at 2022-11-02T14:38:46+01:00
refactor linop_loop (include copy wrapper)
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4e32075b by Moritz Blumenthal at 2022-11-02T14:39:02+01:00
reduce temporary memory
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353e20f7 by Moritz Blumenthal at 2022-11-02T14:39:23+01:00
parallelize gridding over outer dims
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263fd6b4 by Moritz Blumenthal at 2022-11-03T17:38:52+01:00
add function to directly manage pointer by multiplace
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f2a1d183 by Moritz Blumenthal at 2022-11-03T17:40:33+01:00
reduce peak memory in nufft
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34c85e3f by Moritz Blumenthal at 2022-11-03T17:45:52+01:00
turn off caching of psf_nufft by default
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2695b63d by Nick Scholand at 2022-11-04T15:37:06+01:00
Fix coeff split in poly kernel
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5fbc01e1 by Nick Scholand at 2022-11-04T15:40:49+01:00
Simplify sampling
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7d459b6a by Nick Scholand at 2022-11-04T15:40:59+01:00
Make BART geom accessible for component split with test
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c938d542 by Nick Scholand at 2022-11-04T15:43:21+01:00
Combine individual components of BART logo
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e7c3909a by Martin Uecker at 2022-11-06T14:11:35+01:00
fix sign of flags
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67941a77 by Martin Uecker at 2022-11-06T14:11:35+01:00
more sign changes
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7721f65d by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
fix warning
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a69889e0 by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
toeplitz_lowmem: inplace mull with psf if possible
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c4265418 by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
split lowmem code in extra functions
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8bb29d36 by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
make grid.h c++ compatible
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22885212 by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
gpu misc for optimal block/grid size
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d792d998 by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
make device functions static
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83f505b3 by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
optimize fftmod for 2d/3d continous strides
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2f2c01c7 by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
add function to apply linphase
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812a2a8b by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
Add function to apply rolloff correction
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1326cd8d by Moritz Blumenthal at 2022-11-06T14:15:56+01:00
nufft add lowmem option which does not precompute anything
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988ff35f by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
Chaining of nufft normal by linop framework
... this reduces the overhead as not src, dst and tmp are not
allocated at the same time.
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12b5a260 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
Don't copy sens map in linop but use existing map
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d660323c by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
Add operator stack linop output and dup input
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6266e910 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
Option to stack (non-cart) SENSE model
... for a very low memory overhead
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b569300a by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
use fftuc instead of linop (no tmp memory)
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adb99d49 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
lowmem stacking along arbitrary dimensions
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707a4e08 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
add lowmem tests for pics
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32a3e3c6 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
more efficient shuffling on gpu
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651fd7e3 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
gpu gridding
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54a2c6f9 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
add gpu support to adjoint/forward nufft
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aa8f7ab2 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
make nvcc overwritable
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bae0825b by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
gpu use nested lock
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fe1bf974 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
complete reco on GPU
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c3f81320 by Moritz Blumenthal at 2022-11-06T14:15:57+01:00
relax test for gwdg pipeline
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471ae4d2 by Martin Uecker at 2022-11-06T15:02:11+01:00
fix memory leak
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2785e416 by Martin Uecker at 2022-11-06T15:02:23+01:00
fix typo
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6dcd691e by Christian Holme at 2022-11-07T12:06:55+01:00
gridding: error on incompatible dims
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f8124338 by Moritz Blumenthal at 2022-11-07T16:21:53+01:00
turn off gridding on GPU by default
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ed112e5b by Philipp Ehses at 2022-11-09T19:00:55+01:00
bart.py: Print stdout and stderr output from bart call
Previously, it was difficult to get access to bart's error codes and
messages from python, which is especially relevant for interactive
sessions. This patch addresses this issue.
Stdout, stderr, and the error code are stored as function attributes,
so that they can be accessed from outside of bart.py.
Example:
from bart import bart
bart(0, "pics -h")
print("Here's the command output again:")
print(bart.stdout)
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e394ee02 by Philipp Ehses at 2022-11-09T19:00:55+01:00
thread-safety: do not use function attributes within the function
store them for debugging purposes only
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c777c22d by Moritz Blumenthal at 2022-11-11T10:17:03+01:00
fix fftmod on gpu and add tests
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3fcb897f by Christian Holme at 2022-11-11T10:20:20+01:00
fixup: re-add CUDA fft unit test
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11a8a78d by Christian Holme at 2022-11-11T11:21:24+01:00
tests/fft: fix fftmod vs fftshift test
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4ded5814 by Alexander Fyrdahl at 2022-11-15T21:38:25+01:00
fix kwargs
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8c851ae4 by Moritz Blumenthal at 2022-11-24T14:18:56+01:00
Add cpu wrapper for operators
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dfb4fa9e by Moritz Blumenthal at 2022-11-25T11:58:43+01:00
Add gpu support for lowrank (with CPU prox)
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76c4acae by Moritz Blumenthal at 2022-11-29T10:05:10+01:00
Relax lowmem tests
CG piles up "large" errors from small floating point deviations,
hence, we test after 2 iterations with a sharp limit and after
30 iterations with a loose limit
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aae84798 by Moritz Blumenthal at 2022-11-29T10:05:10+01:00
fix c++ compatibility of multiplace.h
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2ab21d21 by Moritz Blumenthal at 2022-11-29T10:05:10+01:00
multiplace_move_F for gpu
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ba378629 by Moritz Blumenthal at 2022-11-29T10:05:10+01:00
refactor initialization of kb_table
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b00a4022 by Moritz Blumenthal at 2022-11-29T10:05:10+01:00
fix scaling of nufft
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538f6a97 by Moritz Blumenthal at 2022-11-29T10:05:10+01:00
tighten test for fixed scaling
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005c1985 by Moritz Blumenthal at 2022-11-29T10:05:10+01:00
optimize linop_fftc
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b09bd4a7 by Moritz Blumenthal at 2022-11-29T10:05:10+01:00
configure fftw wisdom/measure via environment variable
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23ca95c1 by Moritz Blumenthal at 2022-12-01T10:41:35+01:00
optimize fftmod for dims which are multiple of 4
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e8c89d67 by Moritz Blumenthal at 2022-12-01T10:41:35+01:00
make defintion of rolloff consistent
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ef289f40 by Moritz Blumenthal at 2022-12-01T10:41:35+01:00
extend domain of ftkb
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d7a26a6f by Moritz Blumenthal at 2022-12-01T10:41:35+01:00
grid decomposed in normal mode
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f9e6f770 by Moritz Blumenthal at 2022-12-01T10:41:35+01:00
more efficient parallel loop
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626a0cd0 by Moritz Blumenthal at 2022-12-01T10:41:35+01:00
more efficient linphases
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4e7f3f99 by Moritz Blumenthal at 2022-12-01T10:41:35+01:00
compute psf on decomposed grid
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6b8785a8 by Christian Holme at 2022-12-01T10:42:50+01:00
num/ops.c: make gpu-wrapper spam less
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fcb7a5de by Christian Holme at 2022-12-01T10:42:50+01:00
nrmse: add option for scientific notation
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af3cd75b by Christian Holme at 2022-12-01T10:42:50+01:00
rtnlinv: coding style and less debug spam
- - - - -
879ae2db by Christian Holme at 2022-12-01T10:42:50+01:00
nlinv: add option to specifiy non-Cart image size
but unlike rtnlinv, we specify output image size
and not the oversampled size
- - - - -
e9874fd4 by Christian Holme at 2022-12-01T10:42:50+01:00
nufft: use -x for image dimensions
as -d is often used for debug level. But we keep -d around for
compatibility, for now
- - - - -
49354289 by Christian Holme at 2022-12-01T10:42:50+01:00
nufft: document maxiter for inverse nuFFT
- - - - -
f786a48f by Martin Uecker at 2022-12-03T21:25:54+01:00
fix warning
- - - - -
f43b670b by Martin Uecker at 2022-12-08T17:41:28+01:00
coding style
- - - - -
41d2299e by Martin Uecker at 2022-12-08T17:56:25+01:00
coding style
- - - - -
3a3bea8d by Martin Uecker at 2022-12-08T18:08:23+01:00
reduce noise, and tabs
- - - - -
671e6501 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
fix normal of linop_stack_cod for inplace
- - - - -
b2039d96 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
add maxeigen scaling at samplace
- - - - -
fb20cd56 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
Multiple reularizations for primal dual
- - - - -
889c4e29 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
maxeigen scaling in fista/pridu
- - - - -
fc092c63 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
long dims support
- - - - -
731b41aa by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
multiplace for preconditioning
- - - - -
d4f22c17 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
Add script to compute k-space preconditioner
- - - - -
81b07593 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
prox for weighted least squares + gpu support
- - - - -
7d651780 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
add function for preconditioning
- - - - -
632fa98e by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
preconditioning in pics
- - - - -
b0fb68de by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
reduce tmp memory in ops
- - - - -
db485f53 by Moritz Blumenthal at 2022-12-14T10:06:53+01:00
nufft inverse gridding on gpu
- - - - -
9e75c038 by Moritz Blumenthal at 2022-12-15T09:39:04+01:00
reduce peak memory in chambolle pock
- - - - -
226258a1 by Moritz Blumenthal at 2022-12-15T09:39:04+01:00
add subspace to nufft
- - - - -
dcc9c2af by Moritz Blumenthal at 2022-12-15T09:39:04+01:00
add subspace to kspace preconditioner
- - - - -
bd18a37a by Christian Holme at 2023-01-05T15:09:25+01:00
tests: more robust traj rot test
For example on riscv64, it would output a shift of 29.999998
instead of 30.00000, failing the test.
Now we check the nrmse by writing it to a file.
- - - - -
5338ee1a by Moritz Blumenthal at 2023-01-05T15:36:31+01:00
fix old scaling for compatibility mode
- - - - -
cd974af5 by Moritz Blumenthal at 2023-01-05T15:36:48+01:00
fix nufft psf for dims not a multiple of 4
- - - - -
3deb91bf by Christian Holme at 2023-01-05T16:06:12+01:00
pics: add option to specify FISTA
- - - - -
a6e0c6ad by Christian Holme at 2023-01-05T16:18:59+01:00
noncart gpu pics test: use FISTA instead of CG
As this works with a much smaller tolerance
- - - - -
ba80d973 by Moritz Blumenthal at 2023-01-19T11:11:16+01:00
int -> long in gpukrnls
- - - - -
b8e75463 by Martin Uecker at 2023-01-30T23:27:17+01:00
missing spaces
- - - - -
60df0baf by Martin Uecker at 2023-01-30T23:27:17+01:00
VLA macro is only for headers
- - - - -
653f2a7b by Martin Uecker at 2023-01-30T23:31:10+01:00
indent switch correctly
- - - - -
4c01b8f5 by Martin Uecker at 2023-01-31T22:18:57+01:00
spaces...
- - - - -
26190165 by Martin Uecker at 2023-02-01T22:53:03+01:00
unsigned removal
- - - - -
c362c0a9 by Martin Uecker at 2023-02-05T10:11:05+01:00
space
- - - - -
5f7d8a76 by Martin Uecker at 2023-02-05T10:40:12+01:00
remove noir_create{2,3}
- - - - -
42f81936 by Martin Uecker at 2023-02-05T13:24:36+01:00
remove unused headers
- - - - -
aac8a228 by Martin Uecker at 2023-02-07T21:50:53+01:00
remove unsigned from ode
- - - - -
1537e9b8 by Martin Uecker at 2023-02-09T00:35:53+01:00
move perror
- - - - -
039fc790 by Martin Uecker at 2023-02-10T08:49:10+01:00
change default permission for new files
- - - - -
79ddde78 by Martin Uecker at 2023-02-12T20:57:32+01:00
remove unsigned
- - - - -
5947a32f by Martin Uecker at 2023-02-12T20:58:09+01:00
fix mismatching bounds
- - - - -
ae6091de by Martin Uecker at 2023-02-28T20:44:18+01:00
fix linop_transpose_adjoint for non-squared matrices
- - - - -
e84f4ba7 by Christian Holme at 2023-03-01T16:16:20+01:00
pics: merge options to select algorithms
- - - - -
af1c1b42 by Martin Uecker at 2023-03-11T17:52:31+01:00
minor
- - - - -
cc567740 by Martin Uecker at 2023-03-11T17:52:31+01:00
adjoint state
- - - - -
46f30ed1 by Martin Uecker at 2023-03-11T17:52:31+01:00
use nested functions
- - - - -
d459ffe7 by Martin Uecker at 2023-03-11T17:52:31+01:00
quadrature
- - - - -
f862d2fd by Martin Uecker at 2023-03-11T17:52:31+01:00
clang fixes
- - - - -
646de6b0 by Christian Holme at 2023-03-14T13:46:41+01:00
fix minor issues
Resolves #300, resolves #301
- - - - -
93b7c451 by Martin Uecker at 2023-03-14T22:41:41+01:00
coding style / comparison of angles
- - - - -
13b57d54 by Martin Uecker at 2023-03-14T22:41:41+01:00
move sinc into specfun
- - - - -
0f27299a by Martin Uecker at 2023-03-14T22:41:41+01:00
minor
- - - - -
c7bd1708 by Martin Uecker at 2023-03-14T22:41:41+01:00
move matrix ops to numerical libary
- - - - -
17c87496 by Martin Uecker at 2023-03-14T22:41:41+01:00
use quadrature
- - - - -
9cbcea5d by Martin Uecker at 2023-03-14T22:41:41+01:00
simplify
- - - - -
ade93cc5 by Martin Uecker at 2023-03-14T22:41:41+01:00
simplify sinc pulse mathematics
- - - - -
df5b98f9 by Martin Uecker at 2023-03-14T22:41:41+01:00
improve unit test
- - - - -
ff14fb8b by Martin Uecker at 2023-03-14T22:41:41+01:00
turn off contracting of floating point ops
- - - - -
9c6c3213 by Martin Uecker at 2023-03-14T22:41:41+01:00
relax some tests for Macs with M1
- - - - -
e776766b by Martin Uecker at 2023-03-15T08:10:39+01:00
relax one more
- - - - -
f3baa2b4 by Nick Scholand at 2023-03-15T15:49:19+01:00
Option to pass ODE and STM tolerance to sim and moba
- - - - -
68990787 by Nick Scholand at 2023-03-15T15:49:19+01:00
Dynamic rephaser
- - - - -
b96e1bd3 by Nick Scholand at 2023-03-15T15:49:19+01:00
Fix sobolev norm for Bloch moba
- l2 penalty on B1
- regularization towards 0
- - - - -
751cd243 by Nick Scholand at 2023-03-15T15:49:19+01:00
Fix sobolev norm for reparameterized LL model
- Add l2 norm to map
- Fix FFT in initialization
- - - - -
6fae99bb by Nick Scholand at 2023-03-15T15:49:19+01:00
Option to change sobolev norm strength on B1/R1' map
- - - - -
d7a66806 by Nick Scholand at 2023-03-15T15:49:19+01:00
fix r2 scaling
- - - - -
5e63262f by Nick Scholand at 2023-03-15T15:49:19+01:00
comments
- - - - -
a4e4c8a6 by Nick Scholand at 2023-03-15T15:49:19+01:00
Pass B0 map to moba with tests
- - - - -
105a2de5 by Nick Scholand at 2023-03-15T15:49:19+01:00
Make regularization accessible from command line
- - - - -
ade8da90 by Nick Scholand at 2023-03-15T15:49:19+01:00
minor
- - - - -
333f7789 by Nick Scholand at 2023-03-15T15:49:19+01:00
Add partial update to irgnm2
with (1-ratio) contribution of the solution of the previous step
- - - - -
209a4d8b by Nick Scholand at 2023-03-15T15:49:19+01:00
Make l2 flag on parameter maps accessible from CLI
- - - - -
c791e76b by Nick Scholand at 2023-03-15T15:49:19+01:00
Make wavelet strength accessible for moba CL tool
- - - - -
26bff339 by Nick Scholand at 2023-03-15T15:49:19+01:00
Accessible scaling for T1phy + Regularization of R1' around 0
- - - - -
5d367184 by Nick Scholand at 2023-03-15T15:49:19+01:00
Extend accessibility to all models
- - - - -
e3978a1f by Nick Scholand at 2023-03-15T15:49:19+01:00
comment
\
- - - - -
2a5d33ef by Nick Scholand at 2023-03-15T15:49:19+01:00
Input ksp sensitivities to moba
- - - - -
19f5d3e4 by Nick Scholand at 2023-03-15T15:49:19+01:00
Export ksp coils in moba
- - - - -
e4a8aab0 by Nick Scholand at 2023-03-15T15:49:19+01:00
Option to turn off l2 on coils in moba
- - - - -
c69ac177 by Nick Scholand at 2023-03-15T15:49:19+01:00
Option to turn off coil updates in moba
- - - - -
18287d1c by Martin Uecker at 2023-03-15T15:49:19+01:00
coding style
- - - - -
ce15aec0 by Martin Uecker at 2023-03-15T15:49:19+01:00
remove unneeded variable
- - - - -
8fdf64ce by Martin Uecker at 2023-03-15T18:23:26+01:00
move partial update into callback
- - - - -
7a90f1e9 by Martin Uecker at 2023-03-15T18:23:26+01:00
coding style
- - - - -
06d1f2a8 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
make ref/unref of shared pointers threadsafe
- - - - -
88f1d03d by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
Turn off TensorCores in cuDNN 8
- - - - -
f2a2af29 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
Optimizations for cuDNN
- - - - -
a714b056 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
multigpu and streams for cudafft
- - - - -
d962aece by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
threadsafe cuda plan creation
- - - - -
744c1539 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
Add AVL tree (threadsafe)
- - - - -
3e99a311 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
Implement memcache by binary search tree
- - - - -
ed6d3788 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
Add utest for memcache
- - - - -
43c48a7d by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
add functions to manage/sync a pool of cuda streams
- - - - -
aac89ef8 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
reinitialize gpu when entering omp region
- - - - -
d4786869 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
use initialized number of streams in op_loop
- - - - -
6a10b87b by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
updates for managed memory and cuda_get_device num
- - - - -
7b821236 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
merge gpu and copy wraper
- - - - -
a5f32ddd by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
multigpu for multiplace
- - - - -
f2cd0854 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
multigpu for maps operator
- - - - -
389af35b by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
make multiplace threadsafe
- - - - -
f55b3a86 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
pics multigpu now works
- - - - -
e8740fdf by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
add function to assign op to specific gpu
- - - - -
f1656e59 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
add function to assign linop to specific gpu
- - - - -
94294852 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
add function to assign nlop to specific gpu
- - - - -
872009dd by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
add function to assign nn to specific gpu
- - - - -
92cc75fe by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
update checkpointing
- - - - -
80c5bdaa by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
add multigpu to stacking container
- - - - -
d516d47a by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
multigpu with nlop stack container
- - - - -
6a72f007 by Moritz Blumenthal at 2023-03-15T18:23:26+01:00
nn multigpu stack
- - - - -
1d273c30 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
multigpu for reconet
- - - - -
610f5819 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
performance for scalar ops on gpu
- - - - -
251bfb03 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
update blas md_wrapper
- - - - -
e6181626 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
updates for vecops_strided
- - - - -
f39cae01 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
refactor gpumisc
- - - - -
bc144204 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
use gpukrnls_misc in gpu_conv
- - - - -
ab680f4f by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
Add kernels for unfolding
- - - - -
a2d10fd3 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
simplify batchnorm/bias (use optimized strided calls)
- - - - -
017fe813 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
make all blas calls threadsafe by omp lock
- - - - -
a5fe94ac by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
debugging/printing for strided vecops
- - - - -
d179a4ce by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
set threads for nested parallelism
- - - - -
634f7ff6 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
fix GPU_ASSERTS
- - - - -
e308b0b0 by Moritz Blumenthal at 2023-03-15T18:23:27+01:00
kernel for strided copies
- - - - -
83529cc5 by Martin Uecker at 2023-03-15T20:49:54+01:00
relax one test
- - - - -
0622c290 by Martin Uecker at 2023-03-16T16:53:33+01:00
white space, copyright, style
- - - - -
2af3986c by Martin Uecker at 2023-03-16T16:53:33+01:00
simplify rules for header, git tracks it for us
- - - - -
7f84ac10 by Martin Uecker at 2023-03-17T16:06:30+01:00
do not use -ffp-contract=off
- - - - -
0313f4d0 by Martin Uecker at 2023-03-17T16:56:43+01:00
new complex sq kernel
- - - - -
da71aa4d by Nick Scholand at 2023-03-19T15:28:07+01:00
Remove warning and fix nan issue in magnetization preparation
- - - - -
017b8e56 by Nick Scholand at 2023-03-19T18:34:35+01:00
Single regularization for T1phy model in moba
Modified regularization for FA=1 requires test to be initialized closer
to solution.
- - - - -
e3a8b577 by Nick Scholand at 2023-03-19T18:34:35+01:00
Separate function for readout relaxation rate conversion
- - - - -
c5b4fcd2 by Nick Scholand at 2023-03-19T18:34:35+01:00
Replace by macro
- - - - -
a8123d34 by Martin Uecker at 2023-03-19T18:38:11+01:00
move macro
- - - - -
02f368ee by Christian Holme at 2023-03-20T16:28:55+01:00
tests: only compile needed commands
- - - - -
e1e0b525 by Christian Holme at 2023-03-20T16:41:33+01:00
tests/noise: add test for spike noise
- - - - -
0c847a24 by Nick Scholand at 2023-03-27T20:17:19+02:00
Fix special case with ROT test
Special case: TE==TR or TE==TRF together with slice-selection gradient
for ROT simulation
- - - - -
ef982b56 by Moritz Blumenthal at 2023-03-29T20:40:13+02:00
allow inplace for identity
- - - - -
ee7ffb31 by Moritz Blumenthal at 2023-03-29T20:40:53+02:00
use normal operator in irgnm
- - - - -
f6df6e78 by Moritz Blumenthal at 2023-03-29T20:46:20+02:00
don't perform clear in resize if not necessary
- - - - -
a652319b by Moritz Blumenthal at 2023-03-29T20:46:52+02:00
add functions for ops to directly free
- - - - -
e605fd65 by Moritz Blumenthal at 2023-03-29T20:47:23+02:00
optimize operator graph with linop identities
- - - - -
5e22e2d9 by Moritz Blumenthal at 2023-03-29T20:47:58+02:00
optimize nlop_flatten
- - - - -
fa776df4 by Moritz Blumenthal at 2023-03-29T20:48:47+02:00
extend/optimize linops
- - - - -
34749a7c by Moritz Blumenthal at 2023-03-29T20:49:39+02:00
Add function to merge cdiag and fftmod
- - - - -
b99e37d6 by Moritz Blumenthal at 2023-03-29T20:50:18+02:00
add function to construct sobolev operator
- - - - -
95153a58 by Martin Uecker at 2023-03-29T21:00:23+02:00
white space, style
- - - - -
3607e734 by Martin Uecker at 2023-03-29T21:26:35+02:00
options to suppress certain GCC 11 warnings for now
- - - - -
29cc683e by Martin Uecker at 2023-03-31T14:59:27+02:00
update README
- - - - -
5a5c11ed by Moritz Blumenthal at 2023-03-31T21:18:11+02:00
add test for sms nlinv noncart
- - - - -
c630f485 by Martin Uecker at 2023-04-08T13:16:09+02:00
nonnull fixes
- - - - -
f405f63d by Martin Uecker at 2023-04-16T20:10:40+02:00
coding style (Closes: #303, Closes #304)
- - - - -
3664133f by Alexander Fyrdahl at 2023-04-21T22:59:43+02:00
Incorrect grouping of expressions
- - - - -
2b414cdc by Martin Uecker at 2023-04-27T19:06:22+02:00
remove unsigned
- - - - -
fe9a74be by Martin Uecker at 2023-04-30T13:49:07+02:00
use xmalloc
- - - - -
1fb8e924 by Martin Uecker at 2023-04-30T19:09:42+02:00
avoid potential null derefence
- - - - -
4db1ec0d by Martin Uecker at 2023-04-30T19:10:13+02:00
address some analyzer warnings
- - - - -
499c4f21 by Martin Uecker at 2023-04-30T19:10:26+02:00
do not call snprintf with null
- - - - -
4e046ea7 by Martin Uecker at 2023-04-30T20:15:45+02:00
cleanup + analyzer workaround
- - - - -
a88ec880 by Martin Uecker at 2023-04-30T20:25:48+02:00
analyzer built
- - - - -
07d0e919 by Martin Uecker at 2023-05-19T17:39:12+02:00
coding style
- - - - -
894b1f65 by Martin Uecker at 2023-05-19T17:39:12+02:00
remove some more unsigned
- - - - -
31dd0409 by Martin Uecker at 2023-05-19T17:39:12+02:00
another quicksort test
- - - - -
4f508c1c by Nick Scholand at 2023-05-31T18:09:38+02:00
Constrain individual components to 1
Simulation requires components with default amplitude 1
- - - - -
77b04065 by Nick Scholand at 2023-05-31T18:09:38+02:00
Add BRAIN geometry to phantom tool with tests
- - - - -
41029912 by Martin Heide at 2023-05-31T18:09:38+02:00
added 64ch sensitivities
- - - - -
9284be07 by martin.schilling at 2023-05-31T18:09:38+02:00
Add tool for extracting spline control points from SVG files
- - - - -
d7d2234f by Nick Scholand at 2023-05-31T18:09:38+02:00
Add multi cfl passing option for geometry to phantom tool with tests
- - - - -
69b72d86 by Nick Scholand at 2023-05-31T18:09:38+02:00
Change 3D sens interface
- Allows for using less than 8 3D sensitivities
- Introduces struct for future extensions of phantom tool
- Add 3D sens support for polygon based phantoms
- - - - -
2d44a319 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
zero-overhead mode for nuFFT
- - - - -
6bd8f30d by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
optimize toeplitzmult for non-basis case
- - - - -
6ad67ad9 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
Fix race condition in cufft
- - - - -
053032cd by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
rolloff with strides
- - - - -
46ba94c3 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
double precision for precomputed bessel_beta
- - - - -
3084c814 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
double precision bessel function
- - - - -
2a216ce0 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
make width/os config of nufft
- - - - -
0581e208 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
simple chained linop for nufft supporting oversampling other than 2
- - - - -
2bcae977 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
set trajectory of reshaped nufft
- - - - -
ee39238b by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
add functions to move psf kern into nufft
- - - - -
4a7983d4 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
move psf_kern into nufft
- - - - -
e7679c65 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
move psf kern into nufft for decomposed gridding
- - - - -
448cce41 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
remove unused kern functions
- - - - -
3295c484 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
grid with strides
- - - - -
7793d4a7 by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
also loop over singleton ksp_dims
- - - - -
d198fe0c by Moritz Blumenthal at 2023-06-01T16:19:31+02:00
merge dims in grid for efficient subspace gridding
- - - - -
9fc8fcd3 by Moritz BLumenthal at 2023-06-01T16:19:31+02:00
merge apply linphase with fftmod and increase precision
- - - - -
95cf1bbe by Moritz Blumenthal at 2023-06-07T18:36:57+02:00
tool to compute basis function for nufft
- - - - -
19bc5ffb by Christian Holme at 2023-06-13T15:41:05+02:00
gitlab-ci: updates for new debian release
* new versions of clang and libgfortran
* use explicit debian codenames instead of "stable" and "testing"
- - - - -
a9aee034 by Martin Uecker at 2023-06-14T16:45:41+02:00
add error for adjoint + inverse in nufft
- - - - -
099af404 by Martin Uecker at 2023-06-14T16:45:41+02:00
rotation for Cartesian trajectories
- - - - -
fd8b2a4d by Martin Uecker at 2023-06-14T16:45:41+02:00
apply oversampling only to readout for Cartesian trajectories
- - - - -
e7203f43 by Martin Uecker at 2023-06-14T16:45:41+02:00
remove unsed precondition
- - - - -
22b3c07a by Martin Strunz at 2023-06-26T14:53:20+02:00
[misc] rename shadow variables
- - - - -
4d34d264 by Martin Strunz at 2023-07-01T13:11:57+02:00
misc: rename shadow variable
- - - - -
31b3c0b9 by Martin Uecker at 2023-07-01T13:13:16+02:00
fix bounds error
- - - - -
eb71b966 by Martin Uecker at 2023-07-01T13:13:16+02:00
coding style
- - - - -
238fe3ad by Martin Strunz at 2023-07-06T22:35:31+02:00
misc: remove include
- - - - -
ab9ca6d2 by Philip Schaten at 2023-07-07T23:30:25+02:00
add reflectpad
- - - - -
5ee57338 by Philip Schaten at 2023-07-07T23:30:39+02:00
add nlmeans algorithm
- - - - -
ee8f7a4e by Philip Schaten at 2023-07-07T23:30:47+02:00
add nlmeans command
- - - - -
00f38127 by Martin Uecker at 2023-07-07T23:31:45+02:00
remove includes
- - - - -
3ef3cd89 by Martin Uecker at 2023-07-08T16:55:34+02:00
make test conform to the rest
- - - - -
d8c9e045 by Martin Uecker at 2023-07-08T16:55:34+02:00
some spaces
- - - - -
68e200c6 by Martin Uecker at 2023-07-08T16:55:34+02:00
coding style
- - - - -
5f80e7fe by Martin Uecker at 2023-07-08T16:55:34+02:00
format table
- - - - -
ecc25fe5 by Martin Uecker at 2023-07-08T16:55:34+02:00
use correct length
- - - - -
161ca403 by Martin Uecker at 2023-07-08T16:55:34+02:00
includes
- - - - -
8ece26b4 by Martin Uecker at 2023-07-08T16:55:34+02:00
move gauss pdf to flpmath
- - - - -
4fc6b8e3 by Martin Uecker at 2023-07-25T17:27:45+02:00
coding style
- - - - -
cfdccf27 by Martin Uecker at 2023-07-25T17:27:45+02:00
use time dimenion for (undocumented) moving phantom
- - - - -
57b67219 by Martin Uecker at 2023-07-25T17:27:45+02:00
remove unneeded conditional operator in argument to anon/create_cfl
- - - - -
785d7194 by Martin Uecker at 2023-07-25T17:31:37+02:00
fix header for gpu
- - - - -
257121f8 by Moritz Blumenthal at 2023-07-26T17:18:01+02:00
add option to pass diag/fmac tensor without copy
- - - - -
2cbb9a4a by Moritz Blumenthal at 2023-07-26T17:18:01+02:00
implement maps_create by linop_fmac_create
- - - - -
a96b2de9 by Moritz Blumenthal at 2023-07-26T17:18:01+02:00
implement linop_sampling by linop_cdiag
->move to sense/model
- - - - -
bb702f50 by Moritz Blumenthal at 2023-07-26T17:18:01+02:00
add shared-img-dims option to pics
- - - - -
60d12742 by Martin Uecker at 2023-07-26T17:46:23+02:00
remove incorrectly implied nonnull
- - - - -
ad61e16d by Martin Uecker at 2023-07-26T21:41:21+02:00
remove some unsigned
- - - - -
a6d32d93 by Martin Uecker at 2023-07-26T21:41:21+02:00
simplify a bit
- - - - -
6d8d428d by Martin Uecker at 2023-07-26T21:41:21+02:00
make lowmemstack misuse hard errors
- - - - -
8c09b4a9 by Martin Uecker at 2023-07-26T21:41:21+02:00
coding style
- - - - -
526c96ad by Martin Uecker at 2023-07-26T21:41:21+02:00
fix some coding and style errors
- - - - -
e66bc436 by Martin Uecker at 2023-07-26T21:41:21+02:00
remove unsigned
- - - - -
c85c2c6a by Martin Uecker at 2023-07-26T21:41:21+02:00
add assertions to nudft command for unsupported options
- - - - -
eeaf6dc9 by Martin Uecker at 2023-07-28T08:40:42+02:00
remove unneeded header
- - - - -
612d00bf by Martin Uecker at 2023-07-28T11:05:38+02:00
avoid string-op overflow warning
- - - - -
835240c1 by Martin Uecker at 2023-07-28T11:09:31+02:00
transpose
- - - - -
281243d9 by Martin Uecker at 2023-07-28T11:09:44+02:00
noinit adjoint sa
- - - - -
27276fb2 by Martin Uecker at 2023-07-28T11:09:52+02:00
split off interval2
- - - - -
e5af9e7f by Martin Uecker at 2023-07-28T13:46:29+02:00
analyzer false positive
- - - - -
9934e3e5 by Martin Uecker at 2023-07-30T23:45:06+02:00
remove useless casts
- - - - -
1cd0aba5 by Martin Strunz at 2023-07-31T10:13:17+02:00
misc: rename shadow variables
- - - - -
03740d55 by Moritz Blumenthal at 2023-07-31T14:29:55+02:00
variable batch size support in tensorflow
- - - - -
e21baf53 by Moritz Blumenthal at 2023-07-31T14:29:55+02:00
support for placeholdere in dimensions
- - - - -
7db20512 by Moritz Blumenthal at 2023-07-31T14:29:55+02:00
load tensorflow graph without derivatives
- - - - -
0d0a938b by Moritz Blumenthal at 2023-07-31T14:29:55+02:00
support for real tf arguments
- - - - -
2a945224 by Moritz Blumenthal at 2023-07-31T14:29:55+02:00
tf graph function to print nodes
- - - - -
f67a81e6 by Moritz Blumenthal at 2023-07-31T14:29:56+02:00
add tool to debug and apply TensorFlow graph
- - - - -
0238230d by Moritz Blumenthal at 2023-07-31T14:30:16+02:00
add real rand function
- - - - -
a1637196 by Moritz Blumenthal at 2023-07-31T14:30:18+02:00
add gaussian rand to vecops
- - - - -
52ff15e2 by Moritz Blumenthal at 2023-07-31T14:31:16+02:00
add operator p wrapper for nlops
- - - - -
4ac895a2 by Moritz Blumenthal at 2023-07-31T20:09:58+02:00
provide input and output tensors for tf1 graphs
- - - - -
76c3e0e2 by Moritz Blumenthal at 2023-07-31T20:25:06+02:00
fix legacy scaling for basis psf
- - - - -
235f1268 by Martin Uecker at 2023-07-31T20:25:06+02:00
cleanup
- - - - -
ce42ec76 by Christian Tönnes at 2023-08-03T19:45:13+02:00
Added a guide on compiling bart to WebAssembler
- - - - -
a592cd01 by Christian Tönnes at 2023-08-03T20:05:22+02:00
added small web project for testing
- - - - -
bc08641b by Christian Tönnes at 2023-08-03T20:05:49+02:00
added code to test fft & ifft to the test web page
- - - - -
d35f109c by Christian Tönnes at 2023-08-03T20:05:53+02:00
updated instruction to compile bart to WebAssembly
- - - - -
cb4b23bc by Christian Tönnes at 2023-08-03T20:06:01+02:00
added default values for the two new parameters so a normal build still works.
- - - - -
c1c6aa3a by Christian Tönnes at 2023-08-03T20:06:04+02:00
Added PNG option to Makefile
PNG=0 disables libpng and png output.
- - - - -
35461216 by Christian Tönnes at 2023-08-03T20:06:28+02:00
Added FORTRAN option to Makefile.
- - - - -
b7d13338 by Christian Tönnes at 2023-08-03T20:06:31+02:00
new function to list names of all mem files
- - - - -
93b4cd0d by Christian Tönnes at 2023-08-03T20:06:46+02:00
example web project that provides an interface to the bart command line. Only supports memory files.
- - - - -
c2406d3e by Christian Tönnes at 2023-08-03T20:06:57+02:00
script to build webasm files from static bart.o
- - - - -
c5be2458 by Christian Tönnes at 2023-08-03T20:06:59+02:00
removed binary wasm and autogenerated js files
- - - - -
cc71c2a3 by Christian Tönnes at 2023-08-03T20:07:09+02:00
added bsd license headers to my source files
- - - - -
98c6c3ac by Christian Tönnes at 2023-08-03T20:07:11+02:00
small changes to the documentary and renamed build script for the webasm files
- - - - -
711e7395 by Martin Uecker at 2023-08-03T20:57:55+02:00
coding style
- - - - -
8830bdd5 by Christian Holme at 2023-08-04T18:11:16+02:00
add good debug_backtrace
requires libdw and libunwind, installable as
libdw-dev and libunwind-dev
on debian. For static linking,
libbz2-dev liblzma-dev
and additionally required.
For now, prints backtrace on every error, which is not desirable.
- - - - -
ccfd6eb7 by Moritz Blumenthal at 2023-08-04T18:11:16+02:00
assert with backtrace
- - - - -
d614a386 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
fix memleak
- - - - -
c74a6cfe by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
simplify multiplace
- - - - -
d2756c14 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
debug print backtrace in string
- - - - -
1e0378ed by Moritz Blumenthal at 2023-08-04T18:11:16+02:00
deactivated code for saving backtrace in memcache
- - - - -
e07f931a by Moritz Blumenthal at 2023-08-04T18:11:16+02:00
opt for float vector with var length
- - - - -
6d9240bd by Bernhard Rapp at 2023-08-04T18:11:16+02:00
adds VECN
- - - - -
0f387f67 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
make opt parsing threasafe
- - - - -
0fdb4084 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
make save_commandline threadsafe
- - - - -
22df3720 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
make iofiles threadsafe
- - - - -
e3447767 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
Make fftw plan creation threadsafe
- - - - -
6d9dd082 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
add md_unravel
- - - - -
de8eac77 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
prevent reinitialization of gpu
- - - - -
a3a32e05 by Blumenthal, Moritz at 2023-08-04T18:11:16+02:00
Option to turn off device switching for cuda
- - - - -
5dc62521 by Bernhard Rapp at 2023-08-04T18:11:16+02:00
add generic loop interface to bart
- - - - -
18d10371 by Bernhard Rapp at 2023-08-04T18:11:16+02:00
support openmpi for batch processing
- - - - -
238900ee by Bernhard Rapp at 2023-08-04T18:11:16+02:00
bart loop with omp
- - - - -
f6e84ccc by Moritz Blumenthal at 2023-08-04T18:11:16+02:00
loopig for estdelay
- - - - -
934b6d7e by Moritz Blumenthal at 2023-08-04T18:11:16+02:00
use generic looping for pics looping
- - - - -
e1d94c48 by Martin Uecker at 2023-08-04T20:09:01+02:00
new contributors
- - - - -
c954cff8 by Martin Uecker at 2023-08-04T21:53:14+02:00
some style changes
- - - - -
6358d458 by Martin Uecker at 2023-08-04T21:53:14+02:00
changing perrors to errors
- - - - -
d0cf2017 by Martin Uecker at 2023-08-04T21:53:14+02:00
fix command-line help
- - - - -
e66ccf6a by Martin Uecker at 2023-08-06T14:28:56+02:00
analyzer
- - - - -
a61cdc38 by Martin Uecker at 2023-08-08T09:00:27+02:00
remove unsigned
- - - - -
d132a4bf by Martin Uecker at 2023-08-10T17:02:41+02:00
add warning rotation steps
- - - - -
b3e57a32 by Martin Uecker at 2023-08-10T17:02:41+02:00
remove casts and suppress warning
- - - - -
adf11ca3 by Martin Uecker at 2023-08-12T19:58:17+02:00
fix file input
- - - - -
bbffa751 by Martin Uecker at 2023-08-13T21:59:40+02:00
Revert "apply mask on image, not coil image"
This reverts commit f7faa38427ac371d45b0bc89a1e6ec3183d86b36.
- - - - -
dfa0741c by Martin Uecker at 2023-08-14T15:03:32+02:00
fix for warning
- - - - -
e25c0398 by Martin Uecker at 2023-08-18T17:16:18+02:00
tests for twixread
- - - - -
d679ddf4 by Martin Uecker at 2023-08-18T21:12:07+02:00
missing factor in comment
- - - - -
209c6f88 by Martin Uecker at 2023-08-18T21:12:07+02:00
make update of version more robust
- - - - -
5236a036 by Holme, Hans Christian Martin at 2023-08-21T15:57:21+02:00
gitlab-ci: use "make all" for Build_Tensorflow
Also tensorflow should use "make all", to make sure we can actually build all tools
- - - - -
b056f141 by Christian Holme at 2023-08-22T07:43:22+02:00
gitlab-ci: use "tensorflow_dir" to avoid nameclash with the tool
- - - - -
31adc564 by Martin Uecker at 2023-08-22T12:35:48+02:00
rename some local functions
- - - - -
2dd432f4 by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
add IR LL to mobafit
- - - - -
517b48c0 by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
add basis to mobafit
- - - - -
32bbd58c by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
add batched functions to vec_iter_s
- - - - -
65329cbf by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
add batched (blockdiagonal) conjgrad
- - - - -
9e0132d6 by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
batched conjgrad and gpu for mobafit
- - - - -
1c785f83 by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
add md_zsmin2
- - - - -
6175603f by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
bounds, scale and init in mobafit
- - - - -
772ef763 by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
thresh max
- - - - -
4dcbc321 by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
unify cpu and gpu for div
- - - - -
347d70da by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
init gpu in mobafit
- - - - -
89b935ff by Moritz Blumenthal at 2023-08-22T12:35:48+02:00
add tests for mobafit irlll, basis, gpu
- - - - -
59002378 by Moritz Blumenthal at 2023-08-22T12:47:25+02:00
more efficient zscalar and scalar
- - - - -
d42c5487 by Moritz Blumenthal at 2023-08-22T12:47:25+02:00
write dot kernels for gpu
- - - - -
c909b028 by Moritz Blumenthal at 2023-08-22T12:47:25+02:00
fixup calling tf 2 wrapper forward needs grad_y
- - - - -
c88e50a1 by Moritz Blumenthal at 2023-08-22T12:47:25+02:00
use optimized kernels in computation of std
- - - - -
701e9d16 by Moritz Blumenthal at 2023-08-22T12:49:37+02:00
fixup UB check reduce inner
- - - - -
4c37e906 by Martin Uecker at 2023-08-23T08:49:31+02:00
output version when not reproducible
- - - - -
a769c397 by Christian Holme at 2023-08-23T11:28:49+02:00
version: show tensorflow and MPI support
- - - - -
71c8ca91 by Christian Holme at 2023-08-25T09:35:28+02:00
misc.h: add "do { } while (0)" to assert() redefinition
This prevents a misinterpretation. Using `DEBUG_DWARF=1` without this
`do { } while (0)`-wrapper, an `else` following `assert`
might be compiled as belonging to the `if (!expr)` of `assert`.
For example, this happens in `pocsense.c`.
- - - - -
63eb6694 by Christian Holme at 2023-08-30T15:50:16+02:00
gitlab-ci: make wget less verbose
- - - - -
e5145ea6 by Christian Holme at 2023-08-30T15:50:16+02:00
tests/gpu: relax gpu-gridding test
- - - - -
8263e41a by Christian Holme at 2023-08-30T15:50:16+02:00
gitlab-ci: install bc for some tests
some tests in network.mk use this for calculation
- - - - -
a3c9dc31 by Christian Holme at 2023-08-30T15:51:18+02:00
gitlab-ci: updates for test server
- - - - -
eb047635 by Nick Scholand at 2023-08-30T16:20:38+02:00
fix name
- - - - -
1eda98fb by Nick Scholand at 2023-08-30T16:20:38+02:00
Add tool for special function evaluation with tests
- - - - -
96886bcc by Christian Holme at 2023-09-01T10:12:51+02:00
gitlab-ci: test with custom image
which has most dependencies installed
- - - - -
ee13d0f2 by Martin Uecker at 2023-09-01T13:05:41+02:00
linalg functions
- - - - -
d9f84ea9 by Martin Uecker at 2023-09-01T18:03:38+02:00
complex gaussians
- - - - -
16ef03d8 by Christian Holme at 2023-09-02T16:01:09+02:00
tests/pics.mk: fix test prereqs
- - - - -
4fbdfb81 by Christian Holme at 2023-09-02T16:25:00+02:00
sub: check for bart and not sub
as we call bart later, we need to make sure that it exists
- - - - -
3da9011b by Christian Holme at 2023-09-05T14:28:17+02:00
tests: fix some problems
- add some missing prereqs
- fix typo of TESTS_SLOW
- tests/network.mk: add PYTHONPATH to python calls
- tests/network.mk: remove all temporary files
- - - - -
3e71a983 by Christian Holme at 2023-09-05T14:48:19+02:00
gitlab-ci: tensorflow is now part of the docker image
- - - - -
20986c1d by Christian Holme at 2023-09-05T16:28:22+02:00
make clean: also remove gpu utests
- - - - -
48f960f0 by Christian Holme at 2023-09-05T16:28:22+02:00
calc.c: add cppmap header include
required for the MAP macro
- - - - -
bba38668 by Christian Holme at 2023-09-05T16:28:22+02:00
add BART_ prefix to environment variables
but keep support for old TOOLBOX_PATH and DEBUG_LEVEL
- - - - -
612afdbb by Christian Holme at 2023-09-05T16:28:22+02:00
compile commands into subdir
only bart stays in the top level dir, all commands go into the commands/
subdir
- - - - -
b36e0c2f by Christian Holme at 2023-09-05T16:28:22+02:00
move sub into commands/, add test
and document behavior
- - - - -
06dd44e5 by Christian Holme at 2023-09-05T16:28:22+02:00
gitlab-ci: add commands/ to saved artifacts
- - - - -
6482f46d by Christian Holme at 2023-09-11T13:30:49+02:00
for commands: prefer builtin, then check other locations
additionally, we now check the commands/ subdir at the bart exe
location, even if it is not in BART_TOOLBOX_PATH or TOOLBOX_PATH
- - - - -
7e3f5cc6 by Christian Holme at 2023-09-11T13:30:49+02:00
bart.c: restore bart_exit() calls after error()
If we ever change error to no longer call abort(), they will be very
useful
- - - - -
df85a49f by Christian Holme at 2023-09-11T13:30:49+02:00
gitlab-ci: upload GPU, tensorflow, and LTO artifacts
as the maximum artifact size was increased
- - - - -
87a787ff by Christian Holme at 2023-09-11T13:30:49+02:00
gitlab-ci: better format for GPU tests
no ugly multiline scripts
- - - - -
7318b007 by Christian Holme at 2023-09-11T13:30:49+02:00
Makefile: add MAIN_LIST to command targets
- - - - -
2fef74b3 by Christian Holme at 2023-09-11T13:30:49+02:00
utest.h: output name of failed function
- - - - -
aa2f68b0 by Christian Holme at 2023-09-12T13:10:13+02:00
opts: remove old code
that was #ifdef'd out anyway
- - - - -
f210544a by Christian Holme at 2023-09-12T13:10:23+02:00
fix bart opts parsing
We now stop parsing bart options at the first unknown option.
For this, we need to prepent '+' to the optstr passed to ya_getopt,
which needs a new argument to our `options()`, `bool stop_at_nonopt`.
Additionally, `parse_bart_opts()` now prints the correct usage string
(generated from the bart options), and changes argv and argc to remove
the options it parsed.
- - - - -
1f604621 by Christian Holme at 2023-09-13T14:07:15+02:00
version: output environment-variable style if verbose, add clang version
- - - - -
1f9b11a3 by Christian Holme at 2023-09-13T15:36:41+02:00
version: remove clang version
turns out that clang normally claims to be GCC and defines both __GNUC__
and __VERSION__
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410d5fc1 by Christian Holme at 2023-09-13T15:36:41+02:00
Makefile: remove unused BTARGETS variable
probably a leftover from 560cc4c540d92243ad4f353c8f1e6e60ef20245d
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8eb5d057 by Christian Holme at 2023-09-13T15:36:41+02:00
Makefile: error on OMP=0 with CUDA=1
as we do not support that configuration
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5c6a2449 by Christian Holme at 2023-09-13T15:36:41+02:00
Makefile: remove superfluous quotes
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f596c33d by Christian Holme at 2023-09-13T15:37:22+02:00
Makefile: do not add -Wno-vla-parameter for clang
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6ca5b8cb by Christian Holme at 2023-09-13T15:38:20+02:00
misc/opts.c: fix array bounds on options()
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4b05ee20 by Christian Holme at 2023-09-13T16:32:06+02:00
gitlab-ci: enable OMP for clang
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fe63943a by Christian Holme at 2023-09-13T16:32:10+02:00
gitlab-ci: add Clang GPU tests
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2ea8d6bf by Martin Uecker at 2023-09-14T17:15:16+02:00
refactor
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eb2fb27d by Martin Uecker at 2023-09-14T17:15:16+02:00
bloch / pulse tool
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38843b86 by Martin Uecker at 2023-09-14T17:57:35+02:00
bloch mcconnel
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1a0bdebb by Nick Scholand at 2023-09-15T13:35:43+02:00
Add SE model with IR option to signal tool with tests
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9717a4dd by Nick Scholand at 2023-09-15T13:35:55+02:00
Add warning for deprecated TSE model
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11577a6a by Nick Scholand at 2023-09-15T13:37:44+02:00
Set default index in SE model to 1
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4707e6c5 by Martin Heide at 2023-09-18T10:15:19+02:00
added modelfit t1
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a9a6f46f by Martin Heide at 2023-09-18T10:15:39+02:00
added abs(model) to mobafit
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2d6ec2d3 by Martin Heide at 2023-09-18T10:15:42+02:00
add dest for abs(t1fit)
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5f6b0691 by Nick Scholand at 2023-09-19T10:18:17+02:00
Replace deprecated model
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132b1226 by Martin Uecker at 2023-09-19T13:33:54+02:00
white space
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a48af60b by Christian Holme at 2023-09-20T16:27:44+02:00
tests/pics.mk: remove temporary files
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179f36a2 by Philip Schaten at 2023-09-21T17:18:09+02:00
Allow OMP=0 CUDA=1 compilation
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f1192bc2 by Philip Schaten at 2023-09-21T17:18:09+02:00
reduce number of calls to cuda_get_max_threads
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a63cc546 by Philip Schaten at 2023-09-21T17:18:09+02:00
early out in memcache lookup if pointer is not in range
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ccc5b519 by Martin Uecker at 2023-09-22T21:54:04+02:00
add bounds-strict for UBSan
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70c64867 by Christian Holme at 2023-09-25T12:03:22+02:00
toimg: use construct_filename from view
For consitency between toimg and view/cfl2png, it makes more sense to
have this function in bart
Now, if `toimg -D` is used, the filenames output from toimg and
view/cfl2png match
This adds the improvements added in view commit
1e8abf212036251136ac39c75f7b8e9318b2b497
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774527b7 by Christian Holme at 2023-09-25T12:04:27+02:00
toimg: rename loop_flags to im_flags, as they are the image flags
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8af06a2c by Martin Uecker at 2023-09-30T12:15:14+02:00
coding style
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3ce0ff0e by Martin Uecker at 2023-09-30T12:15:14+02:00
fix uint (closes #318)
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31906897 by Martin Uecker at 2023-09-30T12:15:14+02:00
include stdio for FILE (closes: #317)
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8dae4631 by Christian Holme at 2023-09-30T15:12:10+02:00
bart.c: fix option handling
calling bart with a global bart option but without a command
(`bart -l 7`) would fail, as `argv[0]` is `NULL` after advacing argv.
Therefore, we catch that case and print the available commands.
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6eadb63e by Moritz Blumenthal at 2023-10-02T11:40:56+02:00
fixup gpuops bat
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07a3760c by Moritz Blumenthal at 2023-10-02T11:40:57+02:00
fix zero copy case
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de404b79 by Martin Uecker at 2023-10-04T10:07:38+02:00
minor
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e3766eba by Martin Uecker at 2023-10-04T10:07:38+02:00
fix bounds error
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07d0118f by Bernhard Rapp at 2023-10-04T10:09:01+02:00
cleanup mpi, shared filesystems, integration tests
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332e3e17 by Moritz Blumenthal at 2023-10-04T10:09:01+02:00
mmio updates
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aa77268a by Moritz Blumenthal at 2023-10-04T10:09:01+02:00
mpi prevent reinitialization of GPU
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0cd9484c by Bernhard Rapp at 2023-10-04T10:09:01+02:00
adds md_select_strides
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220ac50a by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
Add md_ravel_index
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42db8b7e by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
adds virtual pointer
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d9f22917 by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
Add gpu support to vptr
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16a33ed0 by Bernhard Rapp at 2023-10-04T10:09:01+02:00
extends MPI API
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795e1f06 by Moritz Blumenthal at 2023-10-04T10:09:01+02:00
update debugging for mpi
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01fc6ed0 by Bernhard Rapp at 2023-10-04T10:09:01+02:00
adds MPI to multind
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e2dc5e23 by Bernhard Rapp at 2023-10-04T10:09:01+02:00
adds MPI support to flpmath
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025891a9 by Bernhard Rapp at 2023-10-04T10:09:01+02:00
sameplace for scalar_ops
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131c6195 by Bernhard Rapp at 2023-10-04T10:09:01+02:00
adds MPI to fft
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bb42d2e0 by Bernhard Rapp at 2023-10-04T10:09:01+02:00
adds MPI unit tests
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e1cd76d5 by Bernhard Rapp at 2023-10-04T10:09:01+02:00
adds lin(op) MPI APIs
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cc62e03f by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
add openmpi for gridding
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3ae7e812 by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
update multiplace for vptr
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379261b2 by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
estimate scaling using md functions
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d4e305a4 by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
pics weighting in forward op
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f1e972be by Bernhard Rapp at 2023-10-04T10:09:01+02:00
sameplace for estimate pattern
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7fe6ad30 by Bernhard Rapp at 2023-10-04T10:09:01+02:00
adds MPI to pics
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610a370e by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
move mpi abort to mpi ops
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f1058e2a by Blumenthal, Moritz at 2023-10-04T10:09:01+02:00
only initialize mpi when requested
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86219918 by Martin Uecker at 2023-10-04T10:15:40+02:00
minor warning fixes
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2d626d20 by Moritz Blumenthal at 2023-10-04T22:35:54+02:00
adds averaging losses for nn_stack_multigpu_F
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4c8993aa by Moritz Blumenthal at 2023-10-04T22:35:54+02:00
mpiops add vector reduction
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508d7ae6 by Moritz Blumenthal at 2023-10-04T22:35:54+02:00
replace multigpu stack by openmpi stack
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2ae69139 by Moritz Blumenthal at 2023-10-04T22:35:54+02:00
mpi support for reconet
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41ef2e87 by Moritz Blumenthal at 2023-10-04T22:35:54+02:00
Print warning on initializationn error
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d9619e1d by Moritz Blumenthal at 2023-10-04T22:35:54+02:00
simplify gpuops (multigpu via mpi)
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eed48b37 by Moritz Blumenthal at 2023-10-04T22:35:54+02:00
unify gpu initialization
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ac8a7a96 by Moritz Blumenthal at 2023-10-04T22:35:54+02:00
update doc for mpi
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ed6efe02 by Moritz Blumenthal at 2023-10-05T10:13:21+02:00
fix zdiv_reg on gpu
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22120e7e by Moritz Blumenthal at 2023-10-05T10:13:21+02:00
fixup estdelay
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13548a38 by Blumenthal, Moritz at 2023-10-05T10:13:21+02:00
fix warning
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499d5954 by Moritz Blumenthal at 2023-10-05T10:13:21+02:00
fix tf checkpoint on gpu
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5ce463a6 by Moritz Blumenthal at 2023-10-05T10:13:21+02:00
fix tf1 tests not deleting mapping
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7cd34d7d by Blumenthal, Moritz at 2023-10-05T11:56:45+02:00
fix stream selection
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f7862a95 by Blumenthal, Moritz at 2023-10-05T15:14:57+02:00
fix warning
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7fa17ebd by Martin Juschitz at 2023-10-07T15:43:33+02:00
add bloch_mcconnell_ode
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0b970939 by Martin Juschitz at 2023-10-07T15:43:37+02:00
Add rectangular pulse with test
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88d72a2e by Nick Scholand at 2023-10-07T15:43:37+02:00
Simplify pulse type handling
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de8a9061 by Nick Scholand at 2023-10-07T15:43:37+02:00
Prepare simulation for Bloch-McConnell integration
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d77025e4 by Nick Scholand at 2023-10-07T15:43:37+02:00
Fix STM size and make relaxation2 accessible
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06579736 by Martin Juschitz at 2023-10-07T15:43:37+02:00
Change Th -> m0
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bb614604 by Martin Juschitz at 2023-10-07T15:43:37+02:00
Update k-handling for Bloch-McConnell simulations
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532f4e59 by Martin Juschitz at 2023-10-07T15:43:37+02:00
Add Jacobians of direct sensitivity analysis of Bloch-McConnell with test
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e8b7cd74 by Martin Juschitz at 2023-10-07T15:43:37+02:00
Add direct sensitivity analysis of Bloch-McConnell with test
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c20810de by Martin Juschitz at 2023-10-07T15:43:37+02:00
Add Bloch-McConnell support to simulation backend with tests
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3e62f131 by Martin Juschitz at 2023-10-07T15:43:37+02:00
Add Bloch-McConnell to sim interface
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bd1f796d by Martin Juschitz at 2023-10-07T15:43:37+02:00
Add BMC CEST test
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8f7571ab by Martin Uecker at 2023-10-07T15:43:37+02:00
white space and programming style
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daca5f92 by Martin Heide at 2023-10-10T13:41:58+02:00
added ellipsoid simulation to phantom tool
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47ded36d by Martin Heide at 2023-10-10T14:05:04+02:00
added test for ellipsoid phantom simulation
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7a9578bf by Martin Uecker at 2023-10-12T20:56:16+02:00
coding style
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30cb5a93 by Moritz Blumenthal at 2023-10-13T13:49:04+02:00
sync cuda streams before cuda aware mpi ops
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dd88d078 by Blumenthal, Moritz at 2023-10-17T15:39:00+02:00
copy data back to gpu
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d1141683 by Blumenthal, Moritz at 2023-10-19T13:39:11+02:00
fixup unmap
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ca8226e2 by Martin Uecker at 2023-10-25T21:56:38+02:00
style
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22e4a100 by Martin Uecker at 2023-10-25T21:56:38+02:00
fixes from VLA-enhanced object size pass
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d072aebe by Nick Scholand at 2023-10-25T21:57:37+02:00
Tool to calculate PSF of given trajectory
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a77d2179 by Martin Uecker at 2023-10-25T21:57:37+02:00
rational approximation of golden angles
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e90ff6e4 by Nick Scholand at 2023-10-25T21:57:37+02:00
Unit test and fix for Fibonacci series
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4c3a4020 by Nick Scholand at 2023-10-25T21:57:37+02:00
2 Pi base option for GA
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4ca760ab by Nick Scholand at 2023-10-25T21:57:37+02:00
Separate functions for RAGA sampling, UI checks and tests
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0fb99b29 by Nick Scholand at 2023-10-25T21:57:37+02:00
Add temporal reordering of RAGA sampled data to twixread
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88c30280 by Nick Scholand at 2023-10-25T21:57:37+02:00
Recover GA index from RAGA increment
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9950087d by Nick Scholand at 2023-10-25T21:57:37+02:00
Binning option in twixread for RAGA sampled data
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df2c3422 by Nick Scholand at 2023-10-25T21:57:37+02:00
style
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f9239b66 by Martin Uecker at 2023-10-25T22:29:32+02:00
parameter consistency
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bc5ba1ae by Martin Uecker at 2023-10-25T22:37:36+02:00
do not recover from UBSan error
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d46adcd9 by Jon Tamir at 2023-11-01T21:20:04+01:00
set DEBUG_LEVEL for tests that read from stdout
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63c4e05e by Jon Tamir at 2023-11-01T21:20:27+01:00
relax tolerance for pics test (Mac ARM)
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04870197 by Martin Uecker at 2023-11-02T08:27:22+01:00
remove debug prints
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240b8e7a by Martin Uecker at 2023-11-02T08:27:22+01:00
incorrect static
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2bde1143 by Martin Uecker at 2023-11-02T08:27:22+01:00
unsigned -> int
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3c68f72c by Martin Uecker at 2023-11-02T16:32:28+01:00
cleanup
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fbf58745 by Martin Uecker at 2023-11-02T19:21:34+01:00
update references
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66cbe8b2 by Martin Uecker at 2023-11-04T18:00:42+01:00
check GCC versions, use -std=gnu17
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cf7e9c8c by Martin Uecker at 2023-11-04T20:19:58+01:00
Revert "Fix STM size and make relaxation2 accessible"
This reverts commit d77025e4584f0a8f6d254cd6ed6160d1aff484a1.
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f9b27e0f by Martin Uecker at 2023-11-04T20:19:58+01:00
minor corrections
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16fe4bc0 by Martin Uecker at 2023-11-06T07:39:16+01:00
dependencies
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f335950f by Jon Tamir at 2023-11-10T18:15:06+01:00
Update Mac default gcc version and build instructions
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6c4ce8d5 by Moritz Blumenthal at 2023-11-15T15:55:56+01:00
respect umask in file creation
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fd6ccc1f by Martin Juschitz at 2023-11-19T15:02:13+01:00
Fix potential divide by 0
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8ca18499 by Martin Juschitz at 2023-11-19T15:02:28+01:00
Fix order in simulation call and derivatives
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60183c7c by Martin Juschitz at 2023-11-19T15:02:31+01:00
Fix maps_dim reset
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fcea7c09 by Martin Uecker at 2023-11-19T15:03:15+01:00
whitespace
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77130222 by Martin Uecker at 2023-11-19T21:58:24+01:00
rework pulses
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14cb8b63 by Martin Uecker at 2023-11-19T21:58:24+01:00
set defaults
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589ffaee by Martin Uecker at 2023-11-19T21:58:24+01:00
remove rep_counter
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2f2a5f6f by Martin Uecker at 2023-11-19T21:58:24+01:00
remove spin_counter
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be5cc8e8 by Martin Uecker at 2023-11-19T21:58:24+01:00
remove unused t
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c10e199e by Martin Uecker at 2023-11-19T21:58:24+01:00
remove w1
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f7ae2804 by Martin Uecker at 2023-11-19T21:58:24+01:00
remove global state
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df866cde by Martin Uecker at 2023-11-19T21:58:24+01:00
add vecf_copy
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d1a43631 by Martin Uecker at 2023-11-19T21:58:24+01:00
simplify
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dcbb3452 by Martin Uecker at 2023-11-19T21:58:24+01:00
simplify
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f4c4f1bf by Martin Uecker at 2023-11-19T21:58:24+01:00
simplify
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1363b524 by Martin Uecker at 2023-11-20T10:37:51+01:00
clang workarounds
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cbb6016d by Martin Uecker at 2023-11-24T14:19:14+01:00
early model-based literature
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49bd1328 by Martin Uecker at 2023-11-30T18:10:40+01:00
analyzer fix
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672a840f by Martin Uecker at 2023-12-06T08:30:29+01:00
bump version
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e486669e by Martin Uecker at 2023-12-07T10:21:37+01:00
Merge tag 'v0.9.00'
version 0.9.00
Changes:
- new tools: nlmeans, tensorflow, nufftbase, calc, psf
- calc: access some mathematical functions from the command-line
- nlmean: non-local means filter
- tensorflow: load and apply Tensorflow graph
- nufftbase: compute Fourier transform of basis used in nuFFT
- psf: compute PSF
- nufft: various new options to control behavior
- nufft: basis and weights
- nufft: zero and low memory modes
- nufft: use -x for image dimensions
- sim: Bloch-McConnell simulations
- traj: rotation of Cartesian trajectories
- traj: RAGA trajectories
- reconet: MPI support
- reconet: tensorflow graph support
- reconet: export graph for visualization
- pics: mpi and multi-GPU support
- pics: add shared-img-dims option to pics
- pics: add option to specify FISTA
- pics: preconditioning
- nlinv: add option to specifiy non-Cart image size
- phantom: BRAIN geometry
- phantom: 64ch sensitivities
- phantom: ellipsoid simulation
- phantom: support for generic geometries
- mobafit: add basis to mobafit
- mobafit: add IR and IR LL to mobafit
- mobafit: magnitude fitting
- mobafit: scaling and initial values
- mobafit: minimum and maximum bounds
- mobafit: GPU support
- nrmse: add option for scientific notation
- moba: Export and ksp coils in moba
- moba: Various new options
- estdelay: support for looping
- version: show tensorflow and MPI support
- signal: Spin-Echo signal model
- scripts/shell: kspace_precond.sh: Script to compute k-space preconditioner
- scripts/python: bart_tf.py: Export tensorflow graphs for use with BART
- scripts/python: bart.py: Print stdout and stderr output from bart call
- scripts/python: splines_from_svg.py: extract spline control points from SVG files
- library/geom: Brain geometry
- library/misc: better backtraces
- library/num: md_ravel_index, md_select_strides, md_zsmin2, md_unravel
- library/num: library for complex-valued Gaussians
- library/num: cuda kernels: zdot, zfsq2, zfftmod_3d, zsmin, compress, decompress
- library/num: cuda batch kernels: xpay, axpy, dot_bat
- library/num: cuda kernels: (z)add_unfold, (z)mul(c)_unfold, (z)fmac(c)_unfold
- library/num: md_nlmeans(2), md_nlmeans_distance(2)
- library/num: library for MPI sync, broadcast, reductions
- library/num: double precision bessel function
- library/num: special functions: sinc, sincf, jinc
- library/num: library for virtual pointers
- library/num: time-ordered matrix exponentials: mat_to_exp
- library/num: functions for adjoint sensitivity analysis
- library/num: functions for quadratures: trapezoidal, simpson
- library/num: configure fftw wisdom/measure via environment variable
- library/simu: Bloch McConnell simulations
- library/simu: Spin Echo signal model
- library/linops: linop: flip
- library/nlops: nlops: zphsr and zabs
- library/nn: nlops: ardioid, siglog, igaussian
- library/network: tensorflow networks
- library/noncart: nufft inverse gridding on GPU
- library/noncart: RAGA trajectories
- library/iter: weighted least-squares prox function
- library/iter: batched conjgrad
- library/iter: multiple regularizations for primal-dual
- general: webasm support
- general: BART_ prefix to environment variables
- general: generic loop interface to bart
- general: basic MPI support
- general: OpenMPI and GPU for gridding
- general: zero-overhead mode for nuFFT
- general: performance improvements
- general: many GPU improvements, unified GPU initialization
- built: FORTRAN and PNG options
- built: LTO integration test
- built: OMP=0 CUDA=1 compilation
- built: more unit and integration tests
- many other bug fixes and improvements
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89af9e06 by Martin Uecker at 2023-12-07T10:21:55+01:00
rebase patches (and drop some)
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6fabdd61 by Martin Uecker at 2023-12-07T10:22:06+01:00
udpate copyrights
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d45c5d9b by Martin Uecker at 2023-12-07T10:23:41+01:00
changelog
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850e9e1e by Martin Uecker at 2023-12-07T11:25:17+01:00
fix running testsuite
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ea0569c4 by Martin Uecker at 2023-12-07T12:50:28+01:00
another test fix
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bc45faac by Martin Uecker at 2023-12-07T14:15:15+01:00
fix command-line processing
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82b67b86 by Martin Uecker at 2023-12-07T16:20:16+01:00
add patch to fix tests
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6ca9b25f by Martin Uecker at 2023-12-07T16:39:00+01:00
Revert "fix running testsuite"
This reverts commit 850e9e1e068d9c816adbf26283beea9452733214.
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e9c0d8c5 by Martin Uecker at 2023-12-07T16:39:48+01:00
Revert "another test fix"
This reverts commit ea0569c47d2cee6da3a5d95465c078d258ed5c6c.
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384f8ae5 by Martin Uecker at 2023-12-07T17:02:43+01:00
some tests now also need the bart binary
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9a064b53 by Martin Uecker at 2023-12-07T17:22:45+01:00
and set environment variable for those tests
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502132cf by Martin Uecker at 2023-12-07T17:40:58+01:00
and another enviroment var for tests
- - - - -
5ae4ab49 by Martin Uecker at 2023-12-07T22:03:50+01:00
copy test data
- - - - -
f26d3a1e by Martin Uecker at 2023-12-07T22:24:01+01:00
patch to fix test for Debian
- - - - -
efddf44c by Martin Uecker at 2023-12-07T22:46:35+01:00
fix typo
- - - - -
2385fdc7 by Martin Uecker at 2023-12-07T23:03:46+01:00
another path
- - - - -
530988e8 by Martin Uecker at 2023-12-07T23:26:22+01:00
fix path in test
- - - - -
765a9d16 by Martin Uecker at 2023-12-08T10:57:30+01:00
fix typo
- - - - -
02782af0 by tony mancill at 2023-12-10T21:20:15-08:00
Prepare changelog for upload
- - - - -
ff83203e by Martin Uecker at 2023-12-11T19:11:15+01:00
turn off another unit test for i386
- - - - -
23a318f0 by Martin Uecker at 2023-12-11T19:11:22+01:00
run unit tests on alpha
- - - - -
971a639f by Martin Uecker at 2023-12-11T19:11:26+01:00
update standards version
- - - - -
6013b979 by Martin Uecker at 2023-12-11T19:11:31+01:00
clean up more thoroughly
- - - - -
086124b6 by Martin Uecker at 2023-12-11T19:25:09+01:00
typo + lintian override
- - - - -
3588c960 by Martin Uecker at 2023-12-11T19:28:52+01:00
turn off another related unit test for i386
- - - - -
b5811940 by Martin Uecker at 2023-12-11T19:40:33+01:00
fix email in changelog
- - - - -
8ffb1e86 by Martin Uecker at 2023-12-11T19:46:28+01:00
activate MPI support
- - - - -
b59f2e0e by Martin Uecker at 2023-12-11T20:06:20+01:00
Revert "activate MPI support"
This reverts commit 8ffb1e8675d5c30ddad64389687076f963a29f3a.
- - - - -
1e94a7ce by tony mancill at 2023-12-11T12:07:33-08:00
Prepare changelog for upload
- - - - -
19105e84 by Martin Uecker at 2023-12-12T18:12:20+01:00
more typos
- - - - -
1b228ecc by Martin Uecker at 2023-12-12T18:29:01+01:00
workaround for another two test issues
- - - - -
a9ccbce5 by Martin Uecker at 2023-12-23T14:09:18+01:00
use clang-16 in ci
- - - - -
c6f32ffe by Martin Uecker at 2023-12-23T15:57:08+01:00
C23 features already supported by GCC 11 (remove UNUSED)
- - - - -
a389c627 by Martin Uecker at 2023-12-23T15:57:08+01:00
remove unsigned from splines
- - - - -
b65c6ec7 by Martin Uecker at 2023-12-23T15:57:08+01:00
turn off warnings for C23 in clang
- - - - -
a99bc036 by Martin Uecker at 2023-12-23T16:36:34+01:00
style
- - - - -
76dda25f by Moritz Blumenthal at 2024-01-12T14:51:34+01:00
count in OPT_VECC
- - - - -
e9b56489 by Martin Uecker at 2024-01-19T18:59:14+01:00
fix typos
- - - - -
7f7ec18e by Martin Uecker at 2024-01-20T10:22:34+01:00
update year in license
- - - - -
7cb8c1ff by Blumenthal, Moritz at 2024-01-25T13:21:40+01:00
only link atlas on Red Hat if not OPENBLAS=1
- - - - -
252fdf9f by Martin Uecker at 2024-01-28T21:42:02+01:00
coding style and unused args
- - - - -
e9c04855 by Martin Uecker at 2024-01-28T21:42:02+01:00
coding style
- - - - -
c3f6c01e by Martin Uecker at 2024-01-28T21:42:02+01:00
coding style & spelling
- - - - -
1dfbbd14 by Martin Uecker at 2024-01-28T21:42:02+01:00
use proper for loops
- - - - -
a3c8620c by Martin Uecker at 2024-01-28T21:42:02+01:00
copyright
- - - - -
ceef07e6 by wang53 at 2024-01-28T22:49:40+01:00
Add analytical signal model for IR multi gradient-echo sequences
- - - - -
8eb06a22 by Nick Scholand at 2024-01-28T22:50:32+01:00
Make T1-fat parameter accessible from CLI
- - - - -
2793a15a by Martin Uecker at 2024-01-28T23:04:49+01:00
fix typo
- - - - -
4f15ad19 by Nick Scholand at 2024-01-28T23:23:29+01:00
Variable length vector for moba init and scaling
- - - - -
2e5a816b by Xiaoqing Wang at 2024-01-28T23:25:23+01:00
Add damped update
- - - - -
5a3db3da by Martin Uecker at 2024-01-29T00:25:45+01:00
fix some option descriptions
- - - - -
e0e8de67 by Xiaoqing Wang at 2024-01-29T00:25:45+01:00
signal.c: enable the input of fat fraction
- - - - -
74b632b8 by Xiaoqing Wang at 2024-01-29T00:25:45+01:00
Integrate IR meco signal model in moba framework
- - - - -
c2e49df3 by Christian Holme at 2024-01-30T13:24:44+01:00
phantom: add ellipsoid test using non-Cart tools
- - - - -
28bd94f0 by Christian Holme at 2024-01-30T13:24:44+01:00
phantom: fix non-Cartesian ellipsoid
before, the transformation of center and axes into [-1,1]^3 was done
using the trajectory dimensions, and not the (estimated) image
dimensions, leading to wrong axes and centers of the ellipsoids
- - - - -
c9c72a3b by Christian Holme at 2024-01-31T14:15:21+01:00
phantom: add tests for BRAIN and ellipsoid phantom
using default values
- - - - -
737ac3f5 by Christian Holme at 2024-01-31T14:15:40+01:00
traj: better error message for 3D Cartesian
3D is not implemented for Cartesian trajetories using our non-Cartesian
tools
- - - - -
718931d8 by Christian Holme at 2024-01-31T14:15:40+01:00
phantom: fix 2D non-Cartesian ellipsoid
Because of a wrong dimension test, we used the 3D code for 2D
non-Cartesian Ellipsoid phantoms
- - - - -
17e84163 by Christian Holme at 2024-01-31T15:42:53+01:00
add newline to error messages
- - - - -
a3fef2f6 by Christian Holme at 2024-01-31T15:43:31+01:00
iter6: add error on invalid config
Otherwise we dereference a null pointer in iter6_copy_config_from_opts()
- - - - -
9c8872fd by Christian Holme at 2024-01-31T15:54:07+01:00
tests/sim.mk: add missing lines to tests
- - - - -
97fc4ce3 by Martin Uecker at 2024-02-01T17:24:48+01:00
coding style
- - - - -
99e34e48 by Nick Scholand at 2024-02-02T09:42:38+01:00
Option to avoid short TR approximation in LL signal model
- - - - -
7596c4eb by Nick Scholand at 2024-02-02T09:42:38+01:00
Update error levels
- - - - -
852db233 by CH251834 at 2024-02-02T09:42:38+01:00
test_moba.c: add a derivative test for the IR meco model
- - - - -
dc293f30 by Xiaoqing Wang at 2024-02-02T09:42:38+01:00
moba/recon.c: allow init
- - - - -
ecd326b0 by Xiaoqing Wang at 2024-02-02T09:44:17+01:00
moba.mk: add a test for moba recon of the IR meco signal model
- - - - -
25ae53e3 by Nick Scholand at 2024-02-02T09:44:17+01:00
Update handling of scaling in IR ME model
- - - - -
f193f06b by Nick Scholand at 2024-02-02T09:44:17+01:00
SI unit output for IR ME model
TE input is kept in ms for compatibility with previous meco models
- - - - -
0d515ac3 by Nick Scholand at 2024-02-02T09:44:17+01:00
Make constraint_maps, not_wavelet_maps, and l2_flags accessible from CL for IR ME moba
- - - - -
0114b725 by Nick Scholand at 2024-02-02T09:44:17+01:00
Switch order
The default constraint on maps should be set if variable was not
modified in set_bloch_conf.
- - - - -
7ae99ad9 by Nick Scholand at 2024-02-02T09:44:17+01:00
Set default constrain flag to -1
Flag == 0 allowed as option. Enables removing constraint from all maps
- - - - -
29fc4136 by Nick Scholand at 2024-02-02T09:44:17+01:00
fix assert
- - - - -
d54146c0 by Xiaoqing Wang at 2024-02-02T09:44:17+01:00
moba.mk: fix init for B0
- - - - -
b9018317 by Xiaoqing Wang at 2024-02-02T09:44:17+01:00
moba.mk: add a test for moba recon of the 5-parameter IR meco signal model
- - - - -
16f80af8 by Martin Uecker at 2024-02-02T09:59:14+01:00
change printfs to debug_printfs
- - - - -
b9f2c33b by Martin Uecker at 2024-02-02T13:32:59+01:00
remove ir_mgre enum
- - - - -
1325186c by Christian Holme at 2024-02-02T15:14:48+01:00
gitlab-CI: make builds interruptible by default
- - - - -
3188b1f6 by Martin Uecker at 2024-02-03T10:20:06+01:00
add assertions for unhandled cases
- - - - -
4f487fbd by Christian Holme at 2024-02-06T11:19:50+01:00
tests: nlinv & rtnlinv: use more reasonable sizes
These two tests took almost a minute to run, there is no added benefit
of testing them with large sizes
- - - - -
251bbb24 by Martin Uecker at 2024-02-07T11:46:43+01:00
coding style
- - - - -
0101eb95 by Martin Uecker at 2024-02-07T11:46:43+01:00
use switch statements
- - - - -
e17e2d2a by Martin Uecker at 2024-02-07T11:46:43+01:00
analyzer false positive
- - - - -
553a5edf by Martin Uecker at 2024-02-07T11:46:43+01:00
simplify / fix formula
- - - - -
4ce04f76 by Christian Holme at 2024-02-07T12:11:04+01:00
gitlab-CI: only install clang in clang tests
- - - - -
7eba3550 by Christian Holme at 2024-02-07T12:11:04+01:00
gitlab-CI MPI: replace --allow-run-as-root with environment variables
and fix some indentation in the MPI tests
- - - - -
ef13fe8c by Christian Holme at 2024-02-07T12:11:04+01:00
gitlab-CI MPI: disable vader single_copy mechanism
This leads to errors such as
[runner-...] Read -1, expected <some numer>, errno = 1
in docker, so we disable it. Some more discussion can be found here:
https://github.com/open-mpi/ompi/issues/4948
- - - - -
4dc9cb4c by Christian Holme at 2024-02-07T12:30:12+01:00
gitlab-CI: allow_failre of clang GPU tests
If Build_Clang_GPU fails, the following tests are not skipped, but will
almost certainly fail
So we allow failure in all Clang_GPU tests
- - - - -
8f39d9a3 by Martin Uecker at 2024-02-07T12:56:50+01:00
fix clang build
- - - - -
c8b25d30 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
replace blas dot by kernel dot
- - - - -
f5cc4357 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
update linop_noir_weights_create to specify reference dims
- - - - -
c40c7310 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
Add model2 for nlinv
- - - - -
0a2cecf9 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
Use recon2 in nlinv
- - - - -
1250a298 by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
relax test due to non exact numerics
- - - - -
6d090088 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
Move pattern to top
- - - - -
f1b3a23f by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
perform gridding as preprocessing step
- - - - -
69686986 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
Remove old noncart code
- - - - -
6a7e4241 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
remove strides
- - - - -
e4cd5f31 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
process arbitrary dims
- - - - -
90a3ca14 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
nlinv: nufft, lowrescoils, subspace, realtime
- - - - -
b249664e by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
add tests for nlinv noncart/psf
- - - - -
df2d1d86 by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
fixup reproducibility
- - - - -
cfb35faf by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
allow batch in basis
- - - - -
0ae0b74e by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
add generalized eigenvalue solver
- - - - -
f2cef7d7 by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
add rovir tool
- - - - -
31267095 by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
overcommit memory in load_cfl
- - - - -
21152448 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
update gitignore
- - - - -
655de16e by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
dump static inputs
- - - - -
439a5f2c by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
fixed splitting
- - - - -
c7280938 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
cast linop to nn
- - - - -
d78d2b70 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add linop_reshape with flags
- - - - -
f0ea1685 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
enable trivial im2col for kernel with size 1
- - - - -
7602e1cf by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
refactor linop resize using copy block
- - - - -
c7d33f64 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
refactor linop padding create
- - - - -
c236761f by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add linop for hankelization
- - - - -
1778e5b4 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
linop slicing
- - - - -
364aa1f2 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add linop shift
- - - - -
2d2d6505 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add linop utests
- - - - -
09bad64b by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
stack container for one nlop
- - - - -
617ec4df by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
optimize const for fill with scalar
- - - - -
88a4a495 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add configs for resnet
- - - - -
2905bfc4 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
simple dump
- - - - -
2c14714a by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add functions to stack multiple inputs/outputs
- - - - -
9d87c4a1 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
select mean dims for mse
- - - - -
35b4da89 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
simplify operator graphs
- - - - -
c60c7512 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
unwrap reshape in operator is zero or null
- - - - -
0ca4d0e0 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
no graph optimization wrapper
- - - - -
16102709 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
fix naming of nlop_optimize_graph
- - - - -
20a6e10f by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
nlop loop by checkpointing and stacking
- - - - -
1bd7cf92 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
looping in networks
- - - - -
2f04189c by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
optimize destack for graphs
- - - - -
c77fc9c5 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add nn_optimize_graph
- - - - -
d163ed70 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
inplace for md_select_dims
- - - - -
ada403d2 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
optiomize kern_apply_linphases3D
- - - - -
f55491bd by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
stream support for stack
- - - - -
09f5a1a0 by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
normalized loss
- - - - -
6945135c by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
nmse change batch dim
- - - - -
e638b4b5 by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
fix iter6_configure
- - - - -
0793a961 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add rpath to blas/fftw
- - - - -
57542e38 by Blumenthal, Moritz at 2024-02-07T15:33:47+01:00
update unet
- - - - -
0824d601 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
add nlinvnet
- - - - -
635e56e9 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
simulate signal for physical looklocker
- - - - -
0e658718 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
fix memleak
- - - - -
b5dcaed3 by Moritz Blumenthal at 2024-02-07T15:33:47+01:00
whiten fix non readout dim
- - - - -
2e3e9ed0 by Daniel Mackner at 2024-02-07T15:33:47+01:00
read multi-inversion dataset
- - - - -
05e74efe by Christian Holme at 2024-02-07T16:23:38+01:00
Makefile: remove duplicated ALIBS
Even though it seems to work for now, duplicated libs in ALIBS lead to
multiple definitions of the targets and prereqs for lib/lib*.a
To avoid that, we remove the duplicates introduced in 0824d60140ff
- - - - -
a92a0357 by Martin Uecker at 2024-02-07T17:35:32+01:00
refactor
- - - - -
4583096d by Martin Uecker at 2024-02-07T17:35:32+01:00
better comparison functions
- - - - -
03e20edc by Christian Holme at 2024-02-09T09:46:16+01:00
gitlab-CI: do not run builds as root
instead, we run it as user ibi with sudo
- - - - -
a411faea by Holme, Hans Christian Martin at 2024-02-09T09:46:41+01:00
gitlab-CI: MPI no longer runs as root
so we do not need to confirm that it is OK anymore
- - - - -
42865993 by Nick Scholand at 2024-02-09T13:07:11+01:00
opts.c: Increase max args
- - - - -
18db27f4 by Martin Uecker at 2024-02-09T16:59:40+01:00
add missing dimensions
- - - - -
a695e5bd by Martin Uecker at 2024-02-09T17:00:03+01:00
remove useless casts + copyright
- - - - -
0a7cbda5 by Martin Uecker at 2024-02-09T17:02:46+01:00
bounds mismatch
- - - - -
2042fd84 by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: allclean: remove commands even from top-level dir
When upgrading bart repositories from before the move to `commands/`, it
can happen that, e.g. avg still exists in the top level dir.
However, since we specify dependencies in the tests as just "avg" and
add `commands/` to the vpath, our automatic tests would pick up `avg` in
the top-level dir and therefore not compile it, but then try to call
`commands/avg` which does not exist.
Therefore, we are not also removing any leftover files with the same
names as our commands in the top-level dir
- - - - -
753719e1 by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: change patsubst to addprefix
Makes our intent very clear
- - - - -
50003cf2 by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: single stage Makefile
Our multi-stage build process is hard to understand, so we go back to a
single stage Makefile
- - - - -
a0092fec by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: move cleaning to after filtering of UTARGETS
In a single stage Makefile, we need to have already defined the UTARGETS
(targets for our unit-tests) before we can use it in clean and allclean
- - - - -
a668c327 by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: define paths / load Makefiles early enough
If we only have a single make-stage, we need to load the Makefile.local
and such early enough, so that they can actually change the values they
are supposed to change
But in order to find the relevant Makefiles to inlcude, we need to
define the necessary paths early enough
- - - - -
1468c78d by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: clear out some default variables by hand
In a single-stage Makefile, we cannot us `-rR` to clear out all implicit
rules and variables, as the variables are defined before reading in the
Makefile, so before make gets to our MAKEFLAGS += ...
So we just undefine the variables which we might conceivably overwrite.
We need to take care to only undefine them if they come from their
default values, otherwise syntax such as `CC=clang make` will not work
anymore.
The full list of builtin variables if far too long to include here.
- - - - -
8ea35327 by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: add MAIN_LIST to lib/libbox.a
Otherwise, `make lib/libbox.a` would warn about missing prototypes
- - - - -
ff30a1c5 by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: indentation for readibility
- - - - -
014c059c by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: error on MPI with CC=clang
as we do not support this currently. We would need to set the OMPI_CC
environment variable (and have a compatible MPI implementation),
which we currently do not do
- - - - -
bd2e132c by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile: add .PHONY to phony targets
- - - - -
355c66c8 by Christian Holme at 2024-02-09T17:03:29+01:00
Makefile add alias 'libbart.so' for shared-lib
- - - - -
979f48be by Martin Uecker at 2024-02-09T17:05:00+01:00
remove useless cast
- - - - -
60b6dc63 by Jon Tamir at 2024-02-10T09:52:04+01:00
update instructions for windows
- - - - -
97ddd6af by Martin Uecker at 2024-02-10T09:56:01+01:00
copyright
- - - - -
01adebf3 by Martin Uecker at 2024-02-10T10:17:14+01:00
line break README
- - - - -
a1991849 by Martin Uecker at 2024-02-10T10:22:21+01:00
gcc 11 fix
- - - - -
bb02b070 by Christian Holme at 2024-02-14T14:14:04+01:00
nrmse: respect scientific mode in check for loose tests
- - - - -
071abcdd by Christian Holme at 2024-02-14T14:14:04+01:00
nrmse: automatically switch to scientific output for small errors
Until now, nrmse might show
0.000000
and still fail for a small enough tolerance.
- - - - -
848955c2 by Martin Uecker at 2024-02-18T15:12:07+01:00
atoi
- - - - -
0d069f5d by Moritz Blumenthal at 2024-02-20T14:34:03+01:00
use gpu for pre processing
- - - - -
16534918 by Christian Holme at 2024-02-27T12:59:56+01:00
github-CI: make installation quiet by default
- - - - -
429cda18 by Christian Holme at 2024-02-27T13:01:11+01:00
git-version.sh: add support for shallow clones
In shallow clones, `git describe` cannot help us (as we have no tags to
describe the version). Therefore, we fall back to `git diff` (with
`--quiet`) to check if the working directory is clean.
github actions use a shallow clone by default, so `git-version.sh` used
to incorreclty report `-dirty` there.
- - - - -
2f94c41d by Moritz Blumenthal at 2024-03-07T14:20:42+01:00
apply networks in loop
- - - - -
a4d8a287 by Christian Holme at 2024-03-07T16:01:56+01:00
tests: riscv fixes
- - - - -
f5181009 by Christian Holme at 2024-03-07T16:01:56+01:00
riscv: add -ffp-contract=off to CFLAGS
This fixes an issue in bloch simulation
- - - - -
79bbaa0f by Christian Holme at 2024-03-07T16:01:56+01:00
tests: speed up / mark tests as slow for riscv
- - - - -
ea326965 by Christian Holme at 2024-03-07T16:01:56+01:00
gitlab-CI: rename to UTest and IntTest
The long names don't fit in the gitlab UI...
- - - - -
453b43e1 by Christian Holme at 2024-03-07T16:01:56+01:00
gitlab-CI: add RISC-V jobs + cleanup
- Removed outdated comments
- Commented unneeded apt call, which is slow in docker
- - - - -
dbe29b0b by Christian Holme at 2024-03-07T16:01:56+01:00
gitlab-CI: add testague to RISC-V integration test
- - - - -
4e02b76a by Christian Holme at 2024-03-07T16:01:56+01:00
gitlab-CI, riscv: specify jobs number by make -j
- - - - -
18d913af by Christian Holme at 2024-03-07T21:11:44+01:00
tests/phantom: make --BRAIN tests less large
On good computers, they used take ~30s, on slow ones more than 600s
- - - - -
222fd5a7 by Christian Holme at 2024-03-08T11:12:19+01:00
tests/sim.mk: use common reference for slice profile tests
and make tests/test-sim-slice-profile-density2 faster
- - - - -
ee88b206 by Christian Holme at 2024-03-14T13:34:05+01:00
flpmath: fix comment
- - - - -
7c92712a by Christian Holme at 2024-03-14T14:15:28+01:00
tests/sim: fix tool dependency
- - - - -
727f5d27 by Christian Holme at 2024-03-14T14:43:11+01:00
utest_gpu: make utest MPI-aware
This is not needed for now, but it would be the first stumbling block
when writing an MPI-aware GPU unit test.
- - - - -
d9410a51 by Martin Uecker at 2024-03-17T16:18:11+01:00
pragmas
- - - - -
b5feca77 by Martin Uecker at 2024-03-17T16:18:11+01:00
remove some unneeded casts and MD_ACCESS misuse
- - - - -
55b7b52b by Martin Uecker at 2024-03-17T16:40:03+01:00
cleanup, reduce auto misuse
- - - - -
7468e130 by Moritz Blumenthal at 2024-03-19T15:54:12+01:00
temporal regularization for cols in RT-NLINV-Net
- - - - -
a088cf1f by Christian Holme at 2024-03-21T18:13:40+01:00
nltest: improve derivative test
and improve one of the sites where it is called
- - - - -
80e5c740 by Christian Holme at 2024-03-21T18:13:40+01:00
utests: add option to test derivate at a certain point
This is needed for the IR-MECO model (Multi-Echo Inversion Recovery), as
that model works exceptionally badly with random inputs.
Additionally, we relax some tests here
- - - - -
ab444cf8 by Christian Holme at 2024-03-21T18:13:40+01:00
utests: add script utests_run.sh to run all utests, even if some fail
- - - - -
1baed88c by Christian Holme at 2024-03-21T18:13:40+01:00
DEBUG_DWARF: skip unnecessary functions in backtrace
- - - - -
646d21ba by Christian Holme at 2024-03-21T18:13:40+01:00
utests: add option to abort() in failed backtrace
When the environment variable `BART_UTEST_ABORT` is set to 1, unit tests
will now abort on a failed test (by calling our `error()` function)
- - - - -
0a42fd9c by Christian Holme at 2024-03-21T18:13:40+01:00
utests: rename macros to better reflect their intent
It is not obvious from their names that UT_ASSERT will always return at
that point, while UT_ASSERT2 will only return on failure.
So now they are renamed to
* UT_RETURN_ASSERT, to make it clear that it will always return
* UT_RETURN_ON_FAILURE, to make clear that it will ONLY return
if the test fails
- - - - -
708f48af by Christian Holme at 2024-03-21T18:13:40+01:00
utests: fix tests
mostly two errors, the benign:
* return statements after UT_RETURN_ASSERT, which are dead code
the bad:
* UT_RETURN_ASSERT where UT_RETURN_ON_FAILURE was meant, leading
to skipped tests
- - - - -
d839a322 by Christian Holme at 2024-03-21T18:13:40+01:00
Makefile: DEBUG_DWARF=1 implies DEBUG=1
- - - - -
41e56917 by Christian Holme at 2024-03-21T18:13:40+01:00
Makefile: improve DEBUG_DWARF with clang
clang needs these options to generate backtraces with line numbers
- - - - -
38399a52 by Christian Holme at 2024-03-21T18:13:40+01:00
utests: unitfy utest.c and utest_gpu.c
There really is no good reason to have both, when their contents are so
similar and easily unified
- - - - -
f9518d91 by Christian Holme at 2024-03-21T18:13:40+01:00
gitlab-CI: clang-16 is now part of our docker image
- - - - -
8bae19e8 by Christian Holme at 2024-03-21T18:13:40+01:00
gitlab-CI: make DEBUG_DWARF the new default
- - - - -
66acc713 by Christian Holme at 2024-03-21T18:13:40+01:00
gitlab-CI: libgfortran-dev is now part of the image
- - - - -
c15cc795 by Christian Holme at 2024-03-21T18:13:40+01:00
nlinvnet.c: remove unneeded header
which, incidentially, breaks `make libbart.so` when using GPU
- - - - -
c5126e94 by Christian Holme at 2024-03-21T18:13:40+01:00
gpuops.h: add missing extern
- - - - -
aae2b3a2 by Christian Holme at 2024-03-21T18:13:40+01:00
gitlab-CI: add tests to build shared library libbart.so
- - - - -
5fb912ea by Christian Holme at 2024-03-21T18:13:40+01:00
utests/utest.c: style
- - - - -
fe9ba297 by Christian Holme at 2024-03-21T18:13:40+01:00
gitlab-CI: make utests print backtrace on first error
- - - - -
5dbe4d69 by Jon Tamir at 2024-03-22T12:28:01-05:00
README Mac instructions: install and use gmake for compiling
- - - - -
5fc0c02c by Martin Uecker at 2024-03-23T21:23:57+01:00
improve tests a bit
- - - - -
be7dff02 by Martin Uecker at 2024-03-25T16:27:15+01:00
parametrization of FISTA
- - - - -
90b6e190 by Martin Uecker at 2024-03-25T16:44:43+01:00
analyzer false positive
- - - - -
008f8e7f by Martin Uecker at 2024-03-25T16:54:16+01:00
indentation
- - - - -
edeab3d1 by Martin Uecker at 2024-03-25T17:12:56+01:00
allow use of threshold after final iteration in fista
- - - - -
4c925792 by Martin Uecker at 2024-03-25T18:16:45+01:00
remove this check for clang
- - - - -
e9ecf877 by Philip Schaten at 2024-03-25T19:17:16+01:00
Add some documentation about indentation etc.
- - - - -
143b5fd8 by Philip Schaten at 2024-03-25T19:17:29+01:00
New CLAMP macro
- - - - -
b3f838ab by Martin Uecker at 2024-03-25T22:16:42+01:00
coding style
- - - - -
019b9181 by Martin Uecker at 2024-03-25T22:19:18+01:00
refactor
- - - - -
e513c095 by Martin Uecker at 2024-03-25T22:32:47+01:00
pragmas
- - - - -
426a610b by Martin Uecker at 2024-03-25T22:37:28+01:00
remove unsigned form grid
- - - - -
911c0eb8 by Martin Uecker at 2024-03-25T23:04:26+01:00
don't include unneeded headers
- - - - -
e6e1d1f7 by Martin Uecker at 2024-03-25T23:49:42+01:00
coding style
- - - - -
77f2dccc by Martin Uecker at 2024-03-25T23:51:15+01:00
make analyzer happy
- - - - -
cf816792 by Martin Uecker at 2024-03-26T11:01:40+01:00
add curly braces back to make ptr check work again
- - - - -
40f885cb by Martin Uecker at 2024-03-26T13:45:51+01:00
refactor reading of header
- - - - -
50b3ef99 by Martin Uecker at 2024-03-26T13:46:14+01:00
require cfl header to start with hash
- - - - -
05cee3b4 by Martin Uecker at 2024-03-26T13:54:26+01:00
refactor read_cfl_header
- - - - -
89ab829b by Martin Uecker at 2024-03-26T13:54:26+01:00
refactor
- - - - -
fc52a5ba by Martin Uecker at 2024-03-26T13:54:26+01:00
tabs
- - - - -
2d31ccb6 by Christian Holme at 2024-03-26T15:10:27+01:00
gitlab-CI: add missing AUTOCLEAN=0
- - - - -
6c4ba95e by Christian Holme at 2024-03-26T15:10:27+01:00
gitlab-CI: save version.inc, src/*.o
and only save lib/*.a instead of the lock-files as well
This leads almost eliminates rebuilds in our integration tests
- - - - -
d9dd2acd by Christian Holme at 2024-03-26T15:10:31+01:00
Makefile: fix `make all`
>From at least v0.5.00, `make all` would need to be called
multiple times until it did nothing anymore.
This is the surprisingly simple fix to that issue
- - - - -
93b7fd2a by Martin Uecker at 2024-03-27T16:59:17+01:00
coding style
- - - - -
823bc6a0 by Martin Uecker at 2024-03-27T16:59:17+01:00
change test to sigmoid due to excessive time
- - - - -
f0853ad7 by Martin Uecker at 2024-03-29T16:43:01+01:00
add Wjump-misses-init
- - - - -
1a4345ea by Martin Uecker at 2024-04-02T12:11:12+02:00
fix typo
- - - - -
a96aa79e by Martin Uecker at 2024-04-02T12:27:07+02:00
minor fixes
- - - - -
b83d8c01 by Martin Uecker at 2024-04-02T12:27:08+02:00
remove unsigned
- - - - -
cc3069ab by Christian Holme at 2024-04-05T12:36:42+02:00
tests: add test for BART_COMPAT_VERSION
- - - - -
a24ed810 by Christian Holme at 2024-04-05T12:36:42+02:00
BART_DEBUG_LEVEL: fix bug in strtol conversion
Commit 848955c273f30d05352db92327c8643c33b5431d made it impossible to
disable debug output (for example, by preceding a command with
BART_DEBUG_LEVEL=0), since it ignored that value when returned from
strtol.
- - - - -
85e0f795 by Martin Uecker at 2024-04-09T17:11:21+02:00
style
- - - - -
8f2049c3 by Martin Uecker at 2024-04-10T19:17:31+02:00
remove more unsigned from APIs
- - - - -
7135748a by Martin Uecker at 2024-04-10T19:37:17+02:00
add Wincompatible-pointer-types
- - - - -
bc5c2eb1 by Martin Uecker at 2024-04-10T19:37:25+02:00
more unsigned removal
- - - - -
54032759 by Christian Holme at 2024-04-11T13:27:38+02:00
misc/ya_getopt.{c,h}: update to newest upstream version
More precisely, to commit 6ce431085b81d9bb8639ed2f858c4f4fbc3ab988
from https://github.com/kubo/ya_getopt/
This fixes, for example, mixing of arguments and options, by correctly
sorting all positional arguments to the end of argv.
However, it does not compile without the next commit, which readds
`ya_getopt_reset()`
- - - - -
c07ef8c7 by Christian Holme at 2024-04-11T13:27:38+02:00
misc/ya_getopt.{c,h}: re-add ya_getopt_reset()
Adapted to the newer version of `ya_getopt` that we now use
- - - - -
1c02963e by Christian Holme at 2024-04-11T13:27:38+02:00
tests/opts.mk: add tests for options handling
in particular, add tests for mixing positional arguments and options in
any way
- - - - -
fdd361e6 by Christian Holme at 2024-04-11T14:03:48+02:00
tests/phantom.mk: remove argument error
phantom -b does not take an option. But because our option parsing was
broken, this did not lead to an error up to now...
- - - - -
52f5a359 by Christian Holme at 2024-04-12T14:59:48+02:00
calib/delays.c: fix RING_PAPER output
0 from strcmp means that the strings are equal
- - - - -
327a5a94 by Blumenthal, Moritz at 2024-04-17T13:23:28+02:00
transparent gpu support for model_T2
- - - - -
b67caec2 by Blumenthal, Moritz at 2024-04-17T13:23:28+02:00
transparent gpu support for t1phyfun
- - - - -
64b4f173 by Blumenthal, Moritz at 2024-04-17T13:23:28+02:00
transparent gpu support for bloch model
- - - - -
cda376f5 by Blumenthal, Moritz at 2024-04-17T13:23:28+02:00
transparent gpu support for model_moba
- - - - -
2f94f4ad by Blumenthal, Moritz at 2024-04-17T13:23:28+02:00
transparent gpu support in moba recon
- - - - -
2401348c by Blumenthal, Moritz at 2024-04-17T13:23:28+02:00
remove gpu from moba conf
- - - - -
8bca1f9f by Blumenthal, Moritz at 2024-04-17T13:23:28+02:00
transparent gpu support in moba_meco
- - - - -
e1fd44bc by Blumenthal, Moritz at 2024-04-17T13:23:28+02:00
finalize transparent gpu support in moba
- - - - -
62314ca9 by Martin Uecker at 2024-04-28T10:27:47+02:00
coding style
- - - - -
9b17dfe6 by Martin Uecker at 2024-05-12T11:52:58+02:00
style
- - - - -
9f2216f2 by Martin Uecker at 2024-05-12T11:52:58+02:00
more unsigned removal
- - - - -
869383e7 by Martin Uecker at 2024-05-12T11:52:58+02:00
types, unsigned, ...
- - - - -
8452edd3 by Martin Uecker at 2024-05-12T11:52:58+02:00
more signed conversion work
- - - - -
e9b52135 by Martin Uecker at 2024-05-12T11:52:58+02:00
unsigned removal
- - - - -
af25a469 by Martin Uecker at 2024-05-12T12:03:25+02:00
add OPT_PINT
- - - - -
83b28e89 by Martin Uecker at 2024-05-12T13:11:07+02:00
opt_reg_init, fix initialization
- - - - -
96022e28 by Martin Uecker at 2024-05-12T15:19:06+02:00
remove divergence free wavelets
- - - - -
a0b9f666 by Martin Uecker at 2024-05-12T15:19:19+02:00
unsigned removal
- - - - -
0628f557 by Martin Uecker at 2024-05-13T13:29:53+02:00
show, support for printing real part and index
- - - - -
7709c2d1 by Martin Uecker at 2024-05-13T13:30:49+02:00
invert: option for regularization
- - - - -
0da2740c by Martin Uecker at 2024-05-13T22:44:29+02:00
more unsigned removal
- - - - -
f5b7a111 by Martin Uecker at 2024-05-15T09:47:04+02:00
unsigned and coding style
- - - - -
086cae94 by Martin Uecker at 2024-05-15T20:16:30+02:00
final unsigned removal
- - - - -
584cae58 by Martin Uecker at 2024-05-15T20:30:22+02:00
now add -Wsign-conversion
- - - - -
558b04d0 by Martin Uecker at 2024-05-15T20:39:43+02:00
also remove from test
- - - - -
760b596d by Martin Uecker at 2024-05-15T21:27:10+02:00
fix scanf
- - - - -
150d7c2f by Martin Uecker at 2024-05-16T17:23:23+02:00
left over fixes
- - - - -
57a2c868 by Martin Uecker at 2024-05-17T18:42:12+02:00
fix typo
- - - - -
ce17b7d8 by Nick Scholand at 2024-05-17T16:02:24-04:00
mem.c: Add sys/types.h for ssize_t type definition
- - - - -
2ceb0da4 by Martin Uecker at 2024-05-18T11:30:08+02:00
remove some useless casts
- - - - -
6d83e8dc by Martin Uecker at 2024-05-20T12:56:43+02:00
add version flag
- - - - -
aab5ede0 by Martin Uecker at 2024-05-20T12:56:56+02:00
signed conversions
- - - - -
4c714341 by Nick Scholand at 2024-05-27T22:51:24+02:00
README: Differentiation between brew and backports
Brew install uses <cblas.h> and backports <cblas_openblas.h>
- - - - -
b40a5c1c by Nick Scholand at 2024-05-27T22:51:24+02:00
Makefile: Fix openmp on MacOS
tested on brew installation
- - - - -
1e86b1f9 by Nick Scholand at 2024-05-27T22:51:24+02:00
matexp.c: Complex support for matrix exponentials
- - - - -
a0219f01 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Add Schur decomposition of matrix
- - - - -
97450817 by Nick Scholand at 2024-05-27T22:51:24+02:00
specfun.c: Add approximation of gamma function
- - - - -
c0ce851c by Nick Scholand at 2024-05-27T22:51:24+02:00
specfun.c: Add simplified version of hyp2f1 function
- - - - -
35816960 by Nick Scholand at 2024-05-27T22:51:24+02:00
specfun.c: Add Legendre polynomials
- - - - -
196e01cb by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Complex double eigenvalues exploiting Schur decomposition
- - - - -
d2f1e71e by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Real valued double precision eigenvalues
- - - - -
49a2d165 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Recover real symmetric matrix from band representation
- - - - -
dfa1c18b by Nick Scholand at 2024-05-27T22:51:24+02:00
specfun.c: Evaluate samples and weights for Gauss-Legendre quadrature
- - - - -
f2b1df72 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Solver for equ. with non-unit triangular matrix
- - - - -
a136bb80 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Function to solve complex Sylvester matrix equation
Solves M*X + X*N = scale*C for upper triangular(!) M
- - - - -
bd8f8123 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Matrix square root of triangular matrix
- - - - -
3fcf1e22 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Matrix logarithm of upper triangular matrix
- - - - -
9eb56323 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Add matrix logarithm
- - - - -
ccf1c844 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Add wrapper for complex svd on multi-dim arrays
- - - - -
17279cd4 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Add svd based complex pseudo inverse
- - - - -
5b689380 by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Fix precision warnings
- - - - -
25879a3c by Nick Scholand at 2024-05-27T22:51:24+02:00
linalg.c: Constant inputs
- - - - -
245ca4f5 by Nick Scholand at 2024-05-27T22:51:24+02:00
grog.c: Add tool for GROG calibration and gridding
Includes support for exploiting repeating pattern. See grog.mk for more
details.
- - - - -
707807a2 by Nick Scholand at 2024-05-27T22:51:24+02:00
cosmetic changes
- - - - -
0831be4c by Nick Scholand at 2024-05-27T22:51:24+02:00
traj.c: Option to create RAGA index file
- - - - -
5e4d0be3 by Martin Uecker at 2024-05-27T22:51:24+02:00
fix
- - - - -
9cd5f16b by Martin Uecker at 2024-05-27T22:51:24+02:00
coding style
- - - - -
3107d877 by Martin Uecker at 2024-05-27T23:03:14+02:00
clang fix
- - - - -
c33f40ac by Martin Uecker at 2024-05-28T17:48:24+02:00
more style changes
- - - - -
0967fa79 by Martin Uecker at 2024-05-28T17:52:08+02:00
warning
- - - - -
301ca76d by Martin Uecker at 2024-05-30T14:44:26+02:00
output timing via debug output
- - - - -
86cdc1eb by Martin Uecker at 2024-05-30T15:23:28+02:00
DIMS -> D
- - - - -
d773f14b by Martin Uecker at 2024-05-30T15:29:42+02:00
move to calibration library
- - - - -
5a007619 by Martin Uecker at 2024-05-30T15:35:29+02:00
you can allocate much or on the stack (ulimits)
- - - - -
693a23d7 by Martin Uecker at 2024-05-30T16:49:48+02:00
remove unneeded temporary variable
- - - - -
ca05e6e4 by Martin Uecker at 2024-05-30T16:49:51+02:00
change incorrect comment
- - - - -
3c2691d7 by Martin Uecker at 2024-05-30T18:06:39+02:00
split trajectory computation from gridding
- - - - -
884fb997 by Martin Uecker at 2024-05-30T18:20:06+02:00
add md_(z)round(2) functions
- - - - -
7f0923e7 by Martin Uecker at 2024-05-30T18:20:26+02:00
add round to calc tool (and sort functions)
- - - - -
2242b6d8 by Martin Uecker at 2024-05-30T18:23:37+02:00
add test of trajectory for now
- - - - -
4d08bf0d by Martin Uecker at 2024-05-30T18:53:31+02:00
use round function
- - - - -
3d160b19 by Martin Uecker at 2024-05-30T20:18:48+02:00
simplify
- - - - -
1919fcda by Martin Uecker at 2024-05-30T20:34:30+02:00
simplify
- - - - -
bb57ac4d by Martin Uecker at 2024-05-30T21:07:22+02:00
refactor
- - - - -
a8ed65b6 by Martin Uecker at 2024-05-30T21:27:35+02:00
refactor
- - - - -
f153a258 by Martin Uecker at 2024-05-30T23:51:05+02:00
improve tests
- - - - -
41bb4a2c by Martin Uecker at 2024-05-30T23:51:25+02:00
don't shift by zero
- - - - -
945d542d by Martin Uecker at 2024-05-30T23:51:54+02:00
refactor
- - - - -
45072c50 by Martin Uecker at 2024-05-31T00:00:41+02:00
change interface
- - - - -
58fca7a0 by Martin Uecker at 2024-05-31T00:04:46+02:00
remove pointless pics
- - - - -
545f56b0 by Martin Uecker at 2024-05-31T08:08:40+02:00
reduce tolerance for zmat_exp
- - - - -
b9126a11 by Martin Uecker at 2024-05-31T08:22:31+02:00
use approx. Abelian Lie structure
- - - - -
72225f0e by Blumenthal, Moritz at 2024-06-02T16:33:38+02:00
unused warnings
- - - - -
14fe8982 by Blumenthal, Moritz at 2024-06-02T16:35:27+02:00
signedness warnings
- - - - -
4f5618af by Blumenthal, Moritz at 2024-06-02T16:35:51+02:00
unused warnings
- - - - -
1ff6e485 by Blumenthal, Moritz at 2024-06-03T14:29:00+02:00
improve nested parallelism
- - - - -
fc59c894 by Christian Holme at 2024-06-03T16:17:24+02:00
tests: for CI testing, MPI tests need to be in TESTS_SLOW
- - - - -
4d1aefa8 by Christian Holme at 2024-06-03T16:17:24+02:00
opts: add option for unsigned long long value
this can, for example, be used for seeding the PRNG. For convenience, it
also supports hex (or octal) notation.
- - - - -
d579a34b by Christian Holme at 2024-06-03T16:17:24+02:00
remove direct uses of rand_r, migrate to bart random functions
For now, this is only used directly in dfwavelet, since that code is a
pain to migrate
- - - - -
51f9435d by Christian Holme at 2024-06-03T16:17:24+02:00
use common logic for rng initialization
- - - - -
adadce66 by Jon Tamir at 2024-06-03T16:17:24+02:00
fix bpl1wav admm test
- - - - -
af56f02d by Christian Holme at 2024-06-03T16:17:24+02:00
noise: use md functions
this is much faster, because it can be parallelized. The disadvantage is
higher memory use.
- - - - -
2e8bf8e0 by Christian Holme at 2024-06-03T16:17:25+02:00
utest/test_rand: add tests
This now tests that random numbers using threads are the same as
single-threaded code.
Additionally, it performs a basic Kolmogorov-Smirnov test, and a test
that the rand_range() is in [0, range)
- - - - -
ad468b20 by Christian Holme at 2024-06-03T16:17:25+02:00
utests:test_cuda_flpmath2: rename err_val to err_tol
as it is the tolerance
- - - - -
f7536cf1 by Christian Holme at 2024-06-03T16:17:25+02:00
relax some tests
- - - - -
554e2163 by Christian Holme at 2024-06-03T16:17:25+02:00
wind/rand_r: remove UNUSED and self-include
as we removed it quite a few commits ago
- - - - -
697e84f2 by Christian Holme at 2024-06-03T16:17:25+02:00
stable and improved random number generation with Philox-4x32
We use Philox-4x32 for two reasons:
1) It is fast and easy to implement on the CPU and the GPU
2) With 4 internal counters of 32-bit, we can use it to provide 2 64-bit
counters: This enables us to use one counter for general usage,
incrementing it whenever we access the RNG, and a second counter
for stable generation of arrays of random numbers: by using the
offset into the array as the second counter, we can generate the
same random numbers regardless of number of threads and of GPU
use!
- - - - -
46a34bd4 by Christian Holme at 2024-06-03T16:17:25+02:00
misc/bench.{c.h}: simple function to allow benchmarking
reports Avg, Max and Min to stdout
- - - - -
7ebb7368 by Christian Holme at 2024-06-03T16:17:25+02:00
utests: use bench tool in rand tests
- - - - -
be0fce0f by Christian Holme at 2024-06-03T16:17:25+02:00
tests/nufft: relax test for RISC-V
- - - - -
72c7fa12 by Christian Holme at 2024-06-03T16:17:25+02:00
rand: fix parallel Gaussian rand
- - - - -
1b399178 by Christian Holme at 2024-06-03T16:17:25+02:00
rand.c: pragma style
- - - - -
0bd9a0b3 by Christian Holme at 2024-06-03T16:17:25+02:00
utest: relax tests
- - - - -
e55fb93b by Christian Holme at 2024-06-03T16:17:25+02:00
tests/network.mk: relax test
by increasing the number of epochs
- - - - -
b2287298 by Christian Holme at 2024-06-03T16:17:25+02:00
Makefile: consistent names for rules
also, update_version.sh does not print anything, so no need to eval() it
- - - - -
b614eb03 by Martin Uecker at 2024-06-05T18:55:10+02:00
unsigned
- - - - -
eec1da02 by Christian Holme at 2024-06-06T09:57:27+02:00
misc/bench: avoid unused-parameter warning in non-CUDA builds
- - - - -
c064862b by Christian Holme at 2024-06-06T11:19:40+02:00
Makefile: fix overwriting of CPPFLAGS and CFLAGS
By moving all lines which add something to these flags with += to after
the lines defining our defaults with ?=
- - - - -
ffa79101 by Christian Holme at 2024-06-06T11:19:40+02:00
utests: unused variables and sign-compare
- - - - -
742037cd by Christian Holme at 2024-06-06T11:33:24+02:00
fix useless casts
for -Werror, as it is a warning in newer gcc versions
- - - - -
1a50c599 by Christian Holme at 2024-06-06T14:11:10+02:00
Makefile: DEBUG_WARF=1 implies DEBUG=1 again
- - - - -
1e2dc741 by Christian Holme at 2024-06-06T14:11:10+02:00
Makefile: add option WERROR, to enable -Werror
which simply treats all compilation warnings as error
- - - - -
c4791252 by Christian Holme at 2024-06-06T14:11:10+02:00
gitlab-CI: Try -Werror for selected builds
- - - - -
d5dec140 by Christian Holme at 2024-06-06T14:11:10+02:00
iter/tgv.c: assert necessary precondition
The code breaks for 0 >= N, so we assert that it is not the case
Fixes a warning of stringop-overflow
- - - - -
d7ea9305 by Christian Holme at 2024-06-06T14:11:10+02:00
num: fix some macros
missing close-parens, missing parentheses around macro arguments
- - - - -
f96b4d6e by Christian Holme at 2024-06-06T14:11:10+02:00
utests: fix warnings, clean up code
- - - - -
f3dfea7c by Martin Uecker at 2024-06-11T09:38:29+02:00
opts const
- - - - -
0289bf03 by Martin Uecker at 2024-06-11T09:40:13+02:00
ifdefs for compilation without blas, lapack, fftw
- - - - -
03a0d1af by Moritz Blumenthal at 2024-06-12T13:11:33+02:00
fixup order of evaluation in makefile commandline>Makefiles/Makefile.local>Makefile
- - - - -
6028121d by Martin Uecker at 2024-06-14T13:21:12+02:00
add lockdir config
- - - - -
a12e825e by Martin Uecker at 2024-06-19T12:41:29+02:00
make count an integer
- - - - -
af382dd8 by Martin Uecker at 2024-06-19T18:14:55+02:00
improve command-line description for MESE
- - - - -
59a2d506 by Martin Uecker at 2024-06-20T22:31:49+02:00
unsigned long flags
- - - - -
37674c5d by Martin Uecker at 2024-06-20T22:31:50+02:00
add degree to help
- - - - -
a62f7f67 by Martin Uecker at 2024-06-20T22:31:50+02:00
err_assert uses error
- - - - -
2fa24511 by Martin Uecker at 2024-06-20T22:31:50+02:00
unmap with correct dims
- - - - -
f26260f8 by Christian Holme at 2024-06-24T16:11:39+02:00
tests/pythoncfl: test should be exact
since we are reading and writing complex float data
- - - - -
e35af7ab by Christian Holme at 2024-06-24T16:12:12+02:00
python/cfl.py: add support for .ra-files
- - - - -
2140b73f by Martin Uecker at 2024-06-24T20:06:12+02:00
unsigned long flags
- - - - -
77af73aa by Martin Uecker at 2024-06-24T20:06:12+02:00
missing real
- - - - -
90cb24fa by Martin Uecker at 2024-06-24T20:06:12+02:00
missing float
- - - - -
aa45deab by Martin Uecker at 2024-06-24T20:06:12+02:00
long to int
- - - - -
694883f0 by Martin Uecker at 2024-06-24T20:12:57+02:00
unsigned removal
- - - - -
0636162e by sidharthpunia10500 at 2024-06-29T09:53:51+02:00
pics: use ifftmod on kspace (fixes irregular matrix sizes)
- - - - -
fbe63f63 by Jon Tamir at 2024-06-29T09:54:03+02:00
fix broken macports build with gcc
- - - - -
fada3836 by Philip Schaten at 2024-06-29T14:28:57+02:00
fix makefile issue with webasm, improve webasm docs
- - - - -
a4b4826b by Philip Schaten at 2024-06-29T14:28:57+02:00
workaround for mmapped files
- - - - -
2f073f89 by Philip Schaten at 2024-06-29T14:28:57+02:00
Modularized BART webassembly in a webworker
- - - - -
3c63a87f by Philip Schaten at 2024-06-29T14:28:57+02:00
Python package
- - - - -
f50140e0 by Philip Schaten at 2024-06-29T14:28:57+02:00
call webassembly from python to use from jupyterlite
- - - - -
d6faafa9 by Philip Schaten at 2024-06-29T15:08:20+02:00
fix for wasm/python experiment
- the event loop wrapper didnt work in normal jupyter notebooks.
- thus, refactored the existing bart function into preprocessing and postprocessing (thanks christian)
- no need to 'wrap' an async function anymore! apparently that cant be done in a reliable way. :o
+ the python pkg did not export the bart2 method
- - - - -
56d65e42 by Martin Uecker at 2024-06-29T15:08:20+02:00
initialize variable
- - - - -
cc945de5 by Martin Uecker at 2024-06-29T15:08:20+02:00
remove useless casts
- - - - -
1dadd8b0 by Martin Uecker at 2024-07-01T09:30:50+02:00
analyzer
- - - - -
1d7046be by Blumenthal, Moritz at 2024-07-05T15:13:26+02:00
correctly respect oversampling of coils
- - - - -
00aadb0e by Moritz Blumenthal at 2024-07-05T15:13:26+02:00
allow nlinv without coils
- - - - -
8d638b4a by Blumenthal, Moritz at 2024-07-05T15:27:19+02:00
make cached computation of psf extern
- - - - -
dd1d4ce9 by Philip Schaten at 2024-07-05T15:27:19+02:00
Add an option to BART to wait for debugger.
Simplifies debugging pipelined commands a lot,
because one can attach to a bart cmd in the middle of the pipe.
- - - - -
6b47c313 by Blumenthal, Moritz at 2024-07-05T15:27:53+02:00
optimize strided temul
- - - - -
6364f012 by Blumenthal, Moritz at 2024-07-05T15:27:54+02:00
unfold operations for non-continous strides
- - - - -
4b63cd1d by Martin Uecker at 2024-07-05T15:28:20+02:00
limit header size
- - - - -
942b4d2b by Martin Uecker at 2024-07-05T15:28:36+02:00
introduce xread / xwrite
- - - - -
543578f4 by Martin Uecker at 2024-07-06T15:47:21+02:00
coding style & save one byte
- - - - -
14162944 by Blumenthal, Moritz at 2024-07-06T15:51:34+02:00
remove msgs interfering with streams on stdout + pipe debugging option
- - - - -
371c64bd by Martin Uecker at 2024-07-07T11:54:39+02:00
update lapacke from https://github.com/Reference-LAPACK/lapack
* except lapacke_lsame.c because of some incompatibility
- - - - -
fbc5011d by Philip Schaten at 2024-07-08T12:57:20+02:00
stream protocol implementation + tests;
- - - - -
47b15523 by Moritz Blumenthal at 2024-07-08T12:57:20+02:00
skip post processing in nlinv
- - - - -
5576382c by Blumenthal, Moritz at 2024-07-08T12:57:20+02:00
optimized mode for rt-nlinv
- - - - -
238f321e by Martin Uecker at 2024-07-08T12:57:20+02:00
coding style & copyright
- - - - -
33f3143d by Philip Schaten at 2024-07-08T12:57:20+02:00
mutual exclusion with bart_lock;
this is a wrapper around the locks from the omp runtime - was required to be able to easily switch between mutex implementations.
- - - - -
dbffab57 by Martin Uecker at 2024-07-08T12:58:00+02:00
cond var
- - - - -
1fa89483 by Philip Schaten at 2024-07-09T15:26:11+02:00
fixed msgsize improvments.
- initialize buffers to avoid printing garbage.
- use printable characters for padding.
- remove unused variables.
- expose the msgsize accepted by BART through stream_protocol.h
- - - - -
fa792872 by Christian Holme at 2024-07-09T16:44:26+02:00
gitlab-CI: switch to rootless image
- - - - -
9e06410e by Christian Holme at 2024-07-09T16:57:03+02:00
phantom.c: correctly unmap trajectory
- - - - -
1789348f by Christian Holme at 2024-07-09T16:57:03+02:00
ssa.c: unmap backprojection file
- - - - -
ce01cee0 by Philip Schaten at 2024-07-09T16:57:03+02:00
wasm ci utest
- - - - -
cd721d58 by Christian Holme at 2024-07-09T16:57:03+02:00
Makefile: add node shebang when compiling for WASM
- - - - -
6a11eb92 by Christian Holme at 2024-07-09T16:57:03+02:00
WASM: fix unmapping of .ra files
For .ra files, we called `munmp()` with the wrong size, since we
truncate the pointer (to get the pointer of the mapping without the
header), but did not add that difference to the size.
If we do add that difference, we can call bart tools using node.js
running through wasm with .ra files, which means that we can run our
tests!
- - - - -
1ca2b0a9 by Christian Holme at 2024-07-09T16:57:03+02:00
mmio.c: avoid sign-conversion warning
- - - - -
b1cef4af by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: add EMSCRIPTEN workaround for .ra files
see a4b4826b47 for the previous addition
- - - - -
878356c9 by Christian Holme at 2024-07-09T16:57:03+02:00
gitlab-CI: add integration test for WASM
- - - - -
d3f64b5d by Philip Schaten at 2024-07-09T16:57:03+02:00
cleanup the workaround
- - - - -
b9227ba6 by Philip Schaten at 2024-07-09T16:57:03+02:00
cover all mmaps in mmio.c
- - - - -
cb49e5df by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: consistent naming of file descriptors
- - - - -
1da67866 by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: consistent workaround for EMSCRIPTEN
- - - - -
01873f2a by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio: move EMSCRIPTEN fd-array from header to source file
- - - - -
13453248 by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: allow more fds for EMSCRIPTEN
- - - - -
bd2539f8 by Christian Holme at 2024-07-09T16:57:03+02:00
.gitignore: add *.wasm files and Makefiles/*
- - - - -
32b75a69 by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: move munmap-rounding to separate function
- - - - -
81308b2d by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: improve error messages, consistent fd naming
- - - - -
ec3c2b06 by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: add EMSCRIPTEN workaround for multi cfls
- - - - -
9738eebc by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: fix unmapping of multi-cfls
It used the number of complex float elements in munmap, not the size of
the memory map in bytes.
& code style
- - - - -
f325a7a3 by Christian Holme at 2024-07-09T16:57:03+02:00
misc/mmio.c: unmap_multi_cfl: style
otherwise, the check for `-1 == isze` makes no sense and we do not
detect overflow this early
- - - - -
39d4e308 by Christian Holme at 2024-07-09T16:57:03+02:00
tests/nlinv.mk: relax for WASM
- - - - -
bd7c8269 by Christian Holme at 2024-07-09T16:57:03+02:00
num/fft.c: disable measure for EMSCRIPTEN
apparently, EMSCRIPTEN cannot properly create fftw-measure plans?
- - - - -
12efbde3 by Christian Holme at 2024-07-09T16:57:03+02:00
gitlab-CI: switch wasm to docker image without root
- - - - -
e2ba9777 by Christian Holme at 2024-07-09T16:57:03+02:00
Makefile: move compiler outfile to the end of the commandline
This makes it easier to see which file is being created at that moment
- - - - -
aa78cc84 by Martin Uecker at 2024-07-09T18:27:44+02:00
resize front
- - - - -
e3970d7f by Martin Uecker at 2024-07-10T17:44:22+02:00
use md_unravel_index
- - - - -
980c76c7 by Nick Scholand at 2024-07-10T15:30:16-04:00
bin.c: Fix debug for N < 10
- - - - -
79fd4a72 by Nick Scholand at 2024-07-10T15:30:16-04:00
bin.c: Add zero-fill option
- - - - -
80276643 by Martin Uecker at 2024-07-11T08:56:25+02:00
minor
- - - - -
0f8680e2 by Martin Uecker at 2024-07-11T11:43:03+02:00
improve and rename md_(de)compress -> md_mask_(de)compress
- - - - -
e6ef7118 by Martin Uecker at 2024-07-11T11:43:04+02:00
use md_unravel
- - - - -
96e920c5 by Christian Holme at 2024-07-11T14:34:03+02:00
gitlab-CI: add workaround for non-root docker
Since we are now using a non-root user in Docker, we add this workaround
to that the directories created by gitlab-runner are owned by the user
specified in the Docker file.
see https://gitlab.com/gitlab-org/gitlab-runner/-/issues/1736
- - - - -
976e1e3a by Christian Holme at 2024-07-11T14:44:01+02:00
gitlab-CI: set long timeout for risc-v integration test
When emulating RISC-V using qemu, the integration test can run for a
rather long time. On real hardware, this takes <30 min.
Since we do not want pipeline failures even in the emulated case, we
allow for a very long timeout
- - - - -
1981cd75 by Holme, Hans Christian Martin at 2024-07-11T14:44:01+02:00
gitlab-CI: add workflow to run fewer pipelines
Our CI now only runs in these cases:
1) On the master branch
2) For gitlab merge requests
3) When manually triggered with "Pipelines -> Run Pipeline -> select
branch"
4) When the variable CI_FORCE is 1, which can be achieved by pushing
with: `git push -o ci.variable=CI_FORCE=1`
- - - - -
4c2325c8 by Martin Uecker at 2024-07-12T11:32:04+02:00
fix jump misses init problem and wrong return code
- - - - -
169d8058 by Martin Uecker at 2024-07-12T11:32:04+02:00
optista constants
- - - - -
f9b4467e by Christian Holme at 2024-07-13T11:24:00+02:00
gitlab-CI: add distro build tests
- - - - -
52ce2451 by Christian Holme at 2024-07-15T13:20:37+02:00
README: update instructions for RedHat & co and Fedora 39/40
- - - - -
158448ae by Christian Holme at 2024-07-15T15:08:06+02:00
pkg/rpm: fix Fedora, RedHat... builds
by stripping out the rpath from the bart executable
- - - - -
54e9106b by Martin Uecker at 2024-07-15T16:42:46+02:00
shut up some maybe-unitialized
- - - - -
855b7d31 by Martin Uecker at 2024-07-15T16:42:46+02:00
wrap init with truncated string constant
- - - - -
bac1d482 by Martin Uecker at 2024-07-15T16:51:28+02:00
remove identical condition (thx to: Martin Strunz)
- - - - -
e5ce1976 by Martin Uecker at 2024-07-15T16:51:37+02:00
swap argument names (thx to Martin Strunz)
- - - - -
8abfc2bd by Martin Uecker at 2024-07-15T17:06:00+02:00
make API consistent with use
- - - - -
ff6c8d5b by Blumenthal, Moritz at 2024-07-15T19:59:00+02:00
fix compatibility of nufft for v0.8.00: rolloff with double precision
- - - - -
6817d899 by Blumenthal, Moritz at 2024-07-15T19:59:00+02:00
fix compatibility of nufft for v0.8.00: lower precission modified bessel
- - - - -
e8b552fc by Blumenthal, Moritz at 2024-07-15T19:59:00+02:00
fix compatibility of reconet for v0.8.00: gridding on cpu
- - - - -
5f5ae9e8 by Blumenthal, Moritz at 2024-07-15T19:59:00+02:00
deactivate strided cdotu
- - - - -
328080d6 by Blumenthal, Moritz at 2024-07-16T10:53:12+02:00
fixup reproducibility: don't turn on psf_based_reco by compat
- - - - -
6a9653f3 by Christian Holme at 2024-07-16T13:13:29+02:00
rand: fix backwards-compatibility break in batch_gen
Batch gen used simple modulo to draw samples from a range.
Since this is biased, it was replaced by a non-biased version in
d579a34b2d856
But training of neural nets is quite fragile, and this broke the
reproduciblity of the training of some of our old networks.
- - - - -
8959ac1d by Christian Holme at 2024-07-18T16:30:13+02:00
Makefile: error if we detect GNU Make older than 4.0
- - - - -
d1399db1 by Christian Holme at 2024-07-18T16:32:37+02:00
Makefile: GNU Make 4.4 finally supports parallel builds with ar
How it works:
- Compilation is still in parallel
- ar is called ONCE to update the archive with all new .o files
For us, that means that we now detect GNU Make versions of 4.4 and newer
and use the smarter behavior in that case.
See
https://www.gnu.org/software/make/manual/html_node/Archive-Pitfalls.html
for the documentation of how to use it (basically: redefine the built-in
rules), and
https://savannah.gnu.org/bugs/index.php?func=detailitem&item_id=14927
for a discussion of that feature.
- - - - -
c10aab14 by Christian Holme at 2024-07-19T12:44:49+02:00
Makefile: Correct version check for AR_LOCK_NEEDED
Turns out it is in 4.4.1, which will only be easily checkable once GNU
Make 4.5 releases.
So to not get any nasty surprises, we comment out the entire check for
now, but let people set AR_LOCK_NEEDED=0 by hand if they know that their
version of GNU Make is new enough.
- - - - -
a730cf8b by Martin Uecker at 2024-07-19T13:33:16+02:00
improve unit tests for Gaussian mixtures
- - - - -
3c1d0134 by Martin Uecker at 2024-07-19T13:34:32+02:00
initialize by enumeration constant
- - - - -
ef0fdb24 by Martin Uecker at 2024-07-19T13:35:24+02:00
remove incorrect mode
- - - - -
38f220b8 by Blumenthal, Moritz at 2024-07-19T13:35:33+02:00
gaussian_rand_vec on gpu
- - - - -
24bd36fc by Martin Uecker at 2024-07-19T13:36:10+02:00
add Euler Maruyama
- - - - -
d50c861a by Martin Uecker at 2024-07-19T13:36:29+02:00
pics EM
- - - - -
09a1b6c5 by Martin Uecker at 2024-07-19T13:36:30+02:00
unit test for Euler Maruyama
- - - - -
77f57183 by Martin Uecker at 2024-07-19T13:36:30+02:00
integration tests for Euler Maruyama
- - - - -
76f13716 by Martin Uecker at 2024-07-19T13:36:30+02:00
add comment about scaling in Euler Maruyama
- - - - -
d1a62a63 by Martin Uecker at 2024-07-19T13:36:30+02:00
split up pics tests
- - - - -
a660b547 by Nick Scholand at 2024-07-19T16:52:18+02:00
doc: Add definition files for singularity containers with BART
- - - - -
c344e9e9 by Martin Uecker at 2024-07-19T16:53:59+02:00
updates to readmes
- - - - -
c746940f by Christian Holme at 2024-07-23T16:00:45+02:00
wavelet/wl3-cuda.cu: remove unneeded #includes
fixes a build problem with newer CUDA versions
- - - - -
092f41d8 by Christian Holme at 2024-07-23T16:01:38+02:00
num/rand.c: fix rand_range_state for ranges 0 or 1
In both cases, the only reasonable value to return is 0
- - - - -
59b83dcf by Christian Holme at 2024-07-24T16:11:01+02:00
bart.c: reinitilize PRNG before every call of a builtin
- - - - -
7b64f746 by Christian Holme at 2024-07-24T16:28:46+02:00
num/rand.c: move md_calc_size() out of loop
- - - - -
3e096544 by Christian Holme at 2024-07-24T16:29:03+02:00
add references for our random number generation
- - - - -
bf937560 by Christian Holme at 2024-07-24T16:29:41+02:00
num/rand.c: remove unneeded wrapper
Since we are not using `gaussian_rand_func()` for Philox (for speed
reasons), there is no reason to go through that wrapper.
`gaussian_rand_obsolete()` can simply directly call
`uniform_rand_obsolete()`
- - - - -
f84bcb32 by Christian Holme at 2024-07-24T17:36:02+02:00
bart.c: add missing include
- - - - -
1be200d5 by Christian Holme at 2024-08-01T16:54:33+02:00
gitlab-CI: test AR_LOCK_NEEDED=0 on Arch Linux
- - - - -
576a7d55 by Christian Holme at 2024-08-01T16:54:56+02:00
gitlab-CI: fix indentation of distro tests
- - - - -
efb1de81 by Christian Holme at 2024-08-05T14:29:39+02:00
fix name in paper references
- - - - -
2a772cf7 by Martin Uecker at 2024-08-12T13:56:21+02:00
make compat to version not disturb scripts that parse output
- - - - -
b3be61a2 by Blumenthal, Moritz at 2024-08-16T14:19:00+02:00
fixup init num threads
- - - - -
16691c55 by Blumenthal, Moritz at 2024-08-22T16:21:39+02:00
shared image flags for cartesian pics
- - - - -
b18995ac by Christian Holme at 2024-08-24T11:49:33+02:00
tests/traj.mk: add sequence tests
part of testague for now, as they need files in certain locations
- - - - -
dd15cfc1 by Christian Holme at 2024-08-24T11:49:33+02:00
make traj tests work on gitlab-CI
- - - - -
aef04422 by Christian Holme at 2024-08-24T11:49:33+02:00
traj.c: deprecate golden_partitions
- - - - -
3105afe9 by Martin Uecker at 2024-08-24T12:33:50+02:00
ring: option to ignore phase from b0 eddy currents
- - - - -
4e432813 by Martin Uecker at 2024-08-24T13:19:04+02:00
deprecate golden partition
- - - - -
f721f383 by Martin Uecker at 2024-08-26T15:44:54+02:00
fix help moba
- - - - -
5505709a by Martin Uecker at 2024-08-26T15:44:54+02:00
benchmark ode
- - - - -
f279c20e by Blumenthal, Moritz at 2024-08-28T11:49:05+02:00
separate rand vectors
- - - - -
e1f89c98 by Blumenthal, Moritz at 2024-08-28T11:49:06+02:00
mpi support for random numbers
- - - - -
b9467c02 by Blumenthal, Moritz at 2024-08-28T11:49:06+02:00
add functions to read cfl loop properties
- - - - -
c4dd98a7 by Blumenthal, Moritz at 2024-08-28T11:49:06+02:00
control random numbers in cfl loop via flag
- - - - -
8b7010fa by Blumenthal, Moritz at 2024-08-28T11:49:06+02:00
separate function to access working rand state
- - - - -
09012f67 by Blumenthal, Moritz at 2024-08-28T11:49:06+02:00
let single random numbers respect loop state
- - - - -
990d0a21 by Christian Holme at 2024-08-28T11:49:06+02:00
num/rand.c: style
- - - - -
61ae363c by Christian Holme at 2024-08-28T11:49:06+02:00
num/rand.c: fix WERROR=1 build
- - - - -
7e3c2f12 by Christian Holme at 2024-08-28T11:49:06+02:00
tests: set OMP_NUM_THREADS
so that it actually runs with multiple threads in our gitlab pipeline
- - - - -
ed5f15f6 by Blumenthal, Moritz at 2024-08-28T11:49:06+02:00
warning if rand_state_create is called and different random numbers for cfl loop are requested
- - - - -
19f801f0 by Christian Holme at 2024-08-28T11:49:06+02:00
tests/noise.mk: add loop test for different numbers of threads
- - - - -
61051ebd by Christian Holme at 2024-08-28T11:49:06+02:00
tests/pics.mk: test with both loop and parallel interface
- - - - -
79094d47 by Christian Holme at 2024-08-28T11:49:06+02:00
tests/pics.mk: add test for expected failure with Euler-Maruyama
Since the loop dimension is not the last dimension here, the random
numbers that are generated will be different, leading to large error.
With `! $(ROOTDIR)/bart nrmse -t1.0...` we only pass that test if the
nrmse is larger than 1.0
- - - - -
36f4d320 by Christian Holme at 2024-08-28T11:49:06+02:00
doc: add some info about random numbers and MPI/loop interface
- - - - -
ce281778 by Christian Holme at 2024-08-28T11:49:06+02:00
tests/pics: move eulermaruyama tests to the correct files
Since pics tests are now split into regular, loop and MPI tests
- - - - -
8acc91a5 by Christian Holme at 2024-08-28T11:49:06+02:00
num/rand.c: early return in get_cfl_loop_offset
- - - - -
291d44c7 by Christian Holme at 2024-08-28T11:49:07+02:00
num/rand.c: consolidate logic in single function md_loop_mpi
instead of having the same logic duplicated in each md_*rand function
- - - - -
f553f48d by Christian Holme at 2024-08-28T11:49:07+02:00
loop interface: move cfl_loop_rand_flags from num/rand to misc/mmio
Conceptually, it belong to the loop interface and is only used in rand
- - - - -
b185f553 by Christian Holme at 2024-08-28T11:49:07+02:00
loop interface: warn about possibly different random numbers
- - - - -
c48f0e2c by Christian Holme at 2024-08-28T11:49:07+02:00
loop interface: improve wording of warning
- - - - -
f5824034 by Christian Holme at 2024-08-28T11:49:07+02:00
num/rand: fix obsolete PRNG
In our old rand_r()-based PRNG, we actually do need to modify the global
state, and cannot hide that access behind a funtion
get_worker_state_cfl_loop().
- - - - -
6d0b596e by Blumenthal, Moritz at 2024-08-28T11:49:07+02:00
more precise warning
- - - - -
61a7f6da by Moritz Blumenthal at 2024-08-28T11:49:07+02:00
remove hard coded DIMS=16 from cfl loop
- - - - -
1f87c481 by Christian Holme at 2024-08-28T13:16:51+02:00
fix real problems found by -fanalyzer
- - - - -
8ab9a211 by Christian Holme at 2024-08-28T13:16:51+02:00
add lots of memset(..., 0,...) for -fanalyzer
- - - - -
4575d8d4 by Christian Holme at 2024-08-28T13:16:51+02:00
gitlab-CI: use new gcc-git image for analyzer
- - - - -
c16e3403 by Christian Holme at 2024-08-28T13:16:51+02:00
gitlab-CI: document gcc-git version for analyzer
- - - - -
0fe2607f by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
fixup resize front
- - - - -
773c3bb6 by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
include assert.h in rand.c
- - - - -
c700ec12 by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
let multind.h not undef assert from misc.h
- - - - -
4ef260f8 by Moritz Blumenthal at 2024-08-29T14:06:06+02:00
ncalib tool
- - - - -
e30658a1 by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
show default format for real
- - - - -
e8b7f774 by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
updates for estshift
- - - - -
da835bc0 by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
cleanup cpu/gpu wrapper
- - - - -
89c51f2f by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
rename linop interpolate in nufft_chain
- - - - -
a867167e by Moritz Blumenthal at 2024-08-29T14:06:06+02:00
noise option for twixread
- - - - -
1180e734 by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
support for 3d Cartesian trajectory
- - - - -
75acce1d by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
lapack matrix inverse
- - - - -
ee5890dc by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
sampling of floats
- - - - -
ecfacb96 by Blumenthal, Moritz at 2024-08-29T14:06:06+02:00
more efficient parallel loop
- - - - -
486fa856 by Moritz Blumenthal at 2024-08-30T13:50:30+02:00
add lbfgs
- - - - -
a00931d5 by Moritz Blumenthal at 2024-08-30T13:50:30+02:00
add mutual information metric
- - - - -
bccc0a66 by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
add cross-correlation loss
- - - - -
3cfcc9be by Moritz Blumenthal at 2024-08-30T13:50:30+02:00
bounds in nlops
- - - - -
4e62dee5 by Moritz Blumenthal at 2024-08-30T13:50:30+02:00
early stopping nltest
- - - - -
06d5c5a2 by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
add md_zsmin
- - - - -
5dd4b3d9 by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
more generic l2ball prox
- - - - -
054f9a7b by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
allow more stride combinations in gpu_unfold
- - - - -
4729b227 by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
explicite functions for finite forward/backward/zentral differences
- - - - -
de65b161 by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
define MOTION_DIM
- - - - -
fe8ad453 by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
add linop for convolution with gaussian filter
- - - - -
0a5f4044 by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
convolution on gpu
- - - - -
c7195d85 by Moritz Blumenthal at 2024-08-30T13:50:30+02:00
add motion tools
- - - - -
f0ec5f01 by Blumenthal, Moritz at 2024-08-30T13:50:30+02:00
pattern for kspace precond
- - - - -
d11968c5 by Moritz Blumenthal at 2024-08-30T13:50:30+02:00
ssa with economic svd
- - - - -
56636d18 by Nick Scholand at 2024-08-30T13:50:30+02:00
raga.c: Tool for generating RAGA index files
Used to reorder RAGA sampled datasets into temporal order.
- - - - -
97d69a17 by Moritz Blumenthal at 2024-08-30T13:50:30+02:00
FoV shift with units of pixel
- - - - -
3d84cd8f by Martin Uecker at 2024-09-02T23:04:28+02:00
add alloc_size to xmalloc
- - - - -
b333cdeb by Martin Uecker at 2024-09-03T16:46:15+02:00
fix typo parmeters -> parameters (Closes: #338)
- - - - -
9d019f4d by Martin Uecker at 2024-09-06T08:51:30+02:00
remove unconditional warning in test
- - - - -
7ae7e42a by Martin Uecker at 2024-09-06T08:51:30+02:00
minor
- - - - -
b51d193a by Moritz Blumenthal at 2024-09-07T18:51:05+02:00
error for DFT on gpu (Closes ##322)
- - - - -
a6168825 by Martin Uecker at 2024-09-09T11:19:29+02:00
whitespace
- - - - -
a58fc5b7 by Martin Uecker at 2024-09-09T11:19:29+02:00
use md_zsadd in centered_gradient
- - - - -
1f982c97 by Martin Uecker at 2024-09-09T11:19:29+02:00
minor
- - - - -
b2acb42d by Martin Uecker at 2024-09-09T13:54:32+02:00
_Bool -> bool
- - - - -
ab919731 by Martin Uecker at 2024-09-09T15:16:49+02:00
whitespace
- - - - -
28165a9e by Martin Uecker at 2024-09-10T10:14:11+02:00
coding style
- - - - -
c1116d2d by Martin Uecker at 2024-09-10T10:14:11+02:00
add assertion for GPU
- - - - -
ee4cbb7c by Martin Uecker at 2024-09-10T10:14:11+02:00
benchmark for linear phase
- - - - -
e4a6aa4c by Martin Uecker at 2024-09-10T10:14:11+02:00
reorganize loops
- - - - -
876ed644 by Martin Uecker at 2024-09-10T10:14:11+02:00
gpu nudft
- - - - -
25dcb6ce by Martin Uecker at 2024-09-10T10:14:11+02:00
parallel loop split
- - - - -
b5bed05d by Martin Uecker at 2024-09-10T10:30:25+02:00
clang fix
- - - - -
bf925673 by Christian Holme at 2024-09-10T11:23:39+02:00
bench: fix clang and analyzer
- - - - -
dcd2c47b by Martin Uecker at 2024-09-10T12:45:45+02:00
remove valgrind exceptions
- - - - -
d839f75f by Martin Uecker at 2024-09-10T13:05:57+02:00
coding style
- - - - -
f3c8c132 by Martin Uecker at 2024-09-10T14:04:55+02:00
refactor a bit
- - - - -
2abcc906 by Moritz Blumenthal at 2024-09-10T16:44:48+02:00
fixup fovshift in units of pixels
- - - - -
c83e5445 by Martin Uecker at 2024-09-12T11:31:43+02:00
introduce helper function
- - - - -
dbe0f067 by Martin Uecker at 2024-09-13T09:01:11+02:00
coding style
- - - - -
2a1e3ab5 by Martin Uecker at 2024-09-13T12:18:36+02:00
fix some typos
- - - - -
9286973d by Martin Uecker at 2024-09-13T17:54:01+02:00
clang fix
- - - - -
593a2c54 by Moritz Blumenthal at 2024-09-16T22:05:46+02:00
looping for affinereg
- - - - -
ba88ac9c by Moritz Blumenthal at 2024-09-16T22:06:16+02:00
fovshift pass shift as file
- - - - -
954b6d18 by Moritz Blumenthal at 2024-09-16T22:11:18+02:00
affine_kspace support for higher dimensions
- - - - -
15cbd805 by Blumenthal, Moritz at 2024-09-16T22:34:36+02:00
fovshift more flexible dims
- - - - -
48bcf5b0 by Blumenthal, Moritz at 2024-09-18T09:46:05+02:00
minor
- - - - -
2f6b2722 by Christian Holme at 2024-09-18T11:35:06+02:00
some typos
- - - - -
53787838 by Christian Holme at 2024-09-18T11:35:06+02:00
show: show correct default format
- - - - -
d3dd8735 by Christian Holme at 2024-09-18T11:36:20+02:00
gitlab-CI: switch to new container path
- - - - -
0759d7e2 by Martin Uecker at 2024-09-20T13:38:50+02:00
change scaling and command line for T2 moba to be consistent with mobafit
- - - - -
f1df523c by Martin Uecker at 2024-09-29T11:29:37+02:00
header & copyright
- - - - -
4686ef8a by Martin Uecker at 2024-09-29T11:29:37+02:00
remove outdated emails
- - - - -
2bfd944c by Martin Uecker at 2024-09-29T11:29:37+02:00
white space
- - - - -
3030d9fe by Philip Schaten at 2024-09-29T11:45:46+02:00
simplify streams-protocol.
- - - - -
eff17f67 by Philip Schaten at 2024-09-29T11:45:46+02:00
stream implementation.
- - - - -
ff781943 by Philip Schaten at 2024-09-29T11:45:46+02:00
replace previous synchronization mechanism for FILE_TYPE_PIPE by streams
Co-authored-by: Blumenthal, Moritz <blumenthal at tugraz.at>
- - - - -
96ba6a8a by Philip Schaten at 2024-09-29T11:45:46+02:00
stream-pipeline tests
- - - - -
eda4b06e by Philip Schaten at 2024-09-29T11:45:46+02:00
cleanup all streams on exit; possibility to pass a reference stream;
- bart looping & streams would leave over some open streams otherwise.
- reference stream to specify dimensions for looping.
- - - - -
118a3067 by Moritz Blumenthal at 2024-09-29T11:45:46+02:00
add .fifo filetype, allows piping through fifos
- - - - -
5e6ceeb1 by Blumenthal, Moritz at 2024-09-29T11:45:46+02:00
absolute path for pipe cfls
- - - - -
106b4674 by Philip Schaten at 2024-09-29T11:46:10+02:00
stream support for copy, conway & mandelbrot
- - - - -
50f1981f by Moritz Blumenthal at 2024-09-29T11:46:11+02:00
stream support for nlinv
- - - - -
843b44a8 by Blumenthal, Moritz at 2024-09-29T11:46:11+02:00
stream support for join
- - - - -
6084f1b9 by Moritz Blumenthal at 2024-09-29T11:46:11+02:00
stream support for reshape
- - - - -
33c5a083 by Philip Schaten at 2024-09-29T11:46:11+02:00
bart trx, new tool to (de)serialize streams
- - - - -
f903d5ec by Philip Schaten at 2024-09-29T11:46:11+02:00
bart tee, new tool to multiplex streams
- - - - -
eb7967c7 by Philip Schaten at 2024-09-29T11:46:11+02:00
avoid deadlock for bart tee.
- - - - -
e9cc5516 by Philip Schaten at 2024-09-29T11:46:11+02:00
ccapply realtime geometric coil compression
- - - - -
c70262ea by Philip Schaten at 2024-09-29T11:46:11+02:00
fix wrong unmap_cfl dims in ccapply geometric
- - - - -
a2acc47e by Blumenthal, Moritz at 2024-09-29T11:46:11+02:00
add rtreco script
- - - - -
058b46b6 by Philip Schaten at 2024-09-29T11:46:11+02:00
WASM stream tests. mmap on emscripten.
- - - - -
f00640a1 by Christian Holme at 2024-09-29T11:46:11+02:00
fixes for -Wjump-misses-init
- - - - -
37a82c87 by Philip Schaten at 2024-09-29T11:46:11+02:00
Remove ref-stream option.
- - - - -
57600f38 by Philip Schaten at 2024-09-29T11:46:11+02:00
Fix error when compiled w/o OPENMP, but multiple threads are requested
- - - - -
12b2730d by Philip Schaten at 2024-09-29T11:46:11+02:00
Stream msg size = 24 byte.
Ensure you can transmit at least a petabyte in a raw message (24 - 8).
- - - - -
89c4deb2 by Philip Schaten at 2024-09-29T11:46:11+02:00
set default pattern to 1 in real-time nlinv
- - - - -
848b211a by Martin Uecker at 2024-09-29T12:24:19+02:00
avoid run-time warning
- - - - -
eb332002 by Martin Uecker at 2024-09-29T13:40:15+02:00
style
- - - - -
30343eaa by Martin Uecker at 2024-09-29T13:40:15+02:00
use xmalloc
- - - - -
bd198ff8 by Martin Uecker at 2024-10-02T11:14:16+02:00
add TSE generating function mode
- - - - -
86aff583 by Nick Scholand at 2024-10-03T10:24:53+02:00
Integrate gen.func.-based FSE model into signal tool
- - - - -
06fcd993 by Nick Scholand at 2024-10-04T23:35:15+02:00
Make refocusing FA accessible from epg CLI
- - - - -
d1d623ad by Nick Scholand at 2024-10-04T23:35:15+02:00
Validate stimulated echo with CMPG EPG simulation
- - - - -
d9d19628 by Nick Scholand at 2024-10-04T23:35:15+02:00
Fix mem leak in epg
- - - - -
5554d1ce by Martin Uecker at 2024-10-05T01:22:09+02:00
replace old TSE model with TSE_GEN
- - - - -
d97bb8ab by Juschitz at 2024-10-08T11:20:54+02:00
Prepare init and scaling for BMC
- - - - -
ce70dab0 by Juschitz at 2024-10-08T11:20:54+02:00
Adapt blochfun for Bloch-McConnell
- - - - -
2648e536 by Juschitz at 2024-10-08T11:20:54+02:00
Add simulation based fitting (Bloch + Bloch-McConnell) to mobafit
- - - - -
d95f14f7 by Juschitz at 2024-10-08T11:20:54+02:00
Add mobafit sim tests
- - - - -
639bb1ef by Juschitz at 2024-10-09T18:17:26+02:00
Add CEST sequence to simulation backend
- - - - -
23086064 by Juschitz at 2024-10-09T18:17:26+02:00
Add CEST sequence to sim tool
- - - - -
4a0dccee by Juschitz at 2024-10-09T18:17:26+02:00
CEST fitting for mobafit
- - - - -
f3d8fe57 by Nick Scholand at 2024-10-09T18:17:26+02:00
blochfun.c: long conversion
- - - - -
64f04e60 by Nick Scholand at 2024-10-09T18:17:26+02:00
Increase limit to pass wasm integration test
- - - - -
f6a9d61c by Nick Scholand at 2024-10-09T18:17:26+02:00
blochfun.c: style
- - - - -
17938228 by Nick Scholand at 2024-10-09T18:17:26+02:00
sim.c: style
- - - - -
f161d7dc by Nick Scholand at 2024-10-09T18:17:26+02:00
mobafit.c: style
- - - - -
cd26b4cf by Nick Scholand at 2024-10-09T18:17:26+02:00
Fix initialization
- - - - -
52b962a9 by Martin Uecker at 2024-10-11T17:00:32+02:00
fix tests
- - - - -
71a9c312 by Andreas Tille at 2024-10-12T23:26:37+02:00
Fix FTCBFS: Also export cross tools for make install
- - - - -
7e80df3a by Andreas Tille at 2024-10-12T23:27:02+02:00
Standards-Version: 4.7.0 (routine-update)
- - - - -
8176dd71 by Andreas Tille at 2024-10-12T23:27:05+02:00
No tab in license text (routine-update)
- - - - -
c596da33 by Andreas Tille at 2024-10-12T23:33:21+02:00
routine-update: Ready to upload to unstable
- - - - -
27e4f370 by Blumenthal, Moritz at 2024-10-17T17:03:51+02:00
save memory in T1fun
- - - - -
99860fb9 by Blumenthal, Moritz at 2024-10-17T17:03:51+02:00
correct gridsize in nuFFT
- - - - -
9891600b by Blumenthal, Moritz at 2024-10-17T17:03:51+02:00
sameplace in filter
- - - - -
c8b9aae1 by Blumenthal, Moritz at 2024-10-17T17:03:51+02:00
use tree for cuda_ondevice
- - - - -
15ac5ee1 by Blumenthal, Moritz at 2024-10-17T17:03:51+02:00
unsigned mpi_ops
- - - - -
d7ea79c0 by Blumenthal, Moritz at 2024-10-17T17:03:51+02:00
fix cuda getBlockSize3_internal
- - - - -
5bc9255a by Blumenthal, Moritz at 2024-10-17T17:03:51+02:00
save memory in irgnm
- - - - -
f945653a by Blumenthal, Moritz at 2024-10-17T17:08:00+02:00
remove unused buffer
- - - - -
3505fb7d by Martin Uecker at 2024-10-18T09:22:45+02:00
indentation
- - - - -
dc118688 by Martin Uecker at 2024-10-18T16:15:43+02:00
style
- - - - -
11d81fb8 by Martin Uecker at 2024-10-21T12:59:02+02:00
test for pics: ist vs cg
- - - - -
7cded5c7 by Martin Uecker at 2024-10-22T09:06:16+02:00
use the proper configuration fista by default
- - - - -
07519ff3 by Martin Uecker at 2024-10-25T11:02:49+02:00
for moba switch back to legacy mode
- - - - -
64602cc5 by Martin Uecker at 2024-11-11T16:33:39+01:00
remove incorrect flag for gcc 14
- - - - -
4b326ba2 by Martin Uecker at 2024-11-11T16:33:43+01:00
bit shift fixes
- - - - -
ce03f850 by Martin Uecker at 2024-11-11T16:33:43+01:00
style
- - - - -
8b63b307 by Martin Uecker at 2024-11-11T16:33:43+01:00
unreachable macro
- - - - -
eee06d53 by Martin Uecker at 2024-11-11T16:33:43+01:00
affinereg, style
- - - - -
87a5a8ce by Martin Uecker at 2024-11-12T11:33:26+01:00
test for GCC 12 and use gnu17 language mode
- - - - -
40c99584 by Martin Uecker at 2024-11-12T11:49:26+01:00
fix wasm build
- - - - -
efd30094 by Martin Uecker at 2024-11-13T09:29:13+01:00
fix use of zero as null pointer constant
- - - - -
ee1655f2 by Martin Uecker at 2024-11-13T14:15:41+01:00
fix ubuntu version to 24.04 for github ci
- - - - -
7ea57515 by Christian Holme at 2024-12-01T16:25:18+01:00
fix distro tests
- - - - -
4fd54b3f by Christian Holme at 2024-12-01T16:25:18+01:00
document gcc-12 requirement in README
- - - - -
cbd178c9 by Blumenthal, Moritz at 2024-12-03T15:41:03+01:00
Fix copying into existing array (closes #341)
- - - - -
cb044d79 by Martin Uecker at 2024-12-03T19:04:12+01:00
reference to ROVir
- - - - -
116c32ec by Martin Uecker at 2024-12-03T19:04:12+01:00
style
- - - - -
e93cee65 by Martin Uecker at 2024-12-03T21:12:25+01:00
change error to warning
- - - - -
5d868bf3 by Blumenthal, Moritz at 2024-12-04T14:14:17+01:00
fix cuda kernel limit in unfold
- - - - -
642d2b72 by Blumenthal, Moritz at 2024-12-05T11:40:42+01:00
update multiplace
- - - - -
556b7413 by Blumenthal, Moritz at 2024-12-05T11:40:42+01:00
fix memleak
- - - - -
9642d17a by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
buffer for power iter
- - - - -
84d0765b by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
nlop flatten inputs wrapper
- - - - -
986a5b52 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
compare iovecs
- - - - -
a7e0c719 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
strict checking for operator dimensions in iter2
- - - - -
367fc0e7 by Moritz Blumenthal at 2024-12-05T13:52:51+01:00
split linops in pridu for memory efficience and support for normal eq
- - - - -
c3de1a7f by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
nlinv model keep pattern distributed
- - - - -
ddaeb428 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
rtnlinv test
- - - - -
30e8caf1 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
flatten tgv/ictv supporting variables
- - - - -
a1ca0106 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
export dimensions of supporting variables
- - - - -
4928a095 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
supporting variables for optreg_precond
- - - - -
d91f2d90 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
better dims for tgv
- - - - -
18931398 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
update tgv
- - - - -
d3db1379 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
let fista/pridu respect top level scaling for regularization
- - - - -
66fdd37f by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
nlinv with regularization
- - - - -
99ba21ba by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
regularization for nlinv
- - - - -
c3abf4ba by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
deactivate nlinv legacy early stopping by default
- - - - -
2a930bc2 by Blumenthal, Moritz at 2024-12-05T13:52:51+01:00
updates for ncalib
- - - - -
6a45335f by Blumenthal, Moritz at 2024-12-05T15:01:42+01:00
slightly relax test for wasm
- - - - -
ab1715f1 by Philip Schaten at 2024-12-06T18:47:40+01:00
Replace get_current_dir_name
- - - - -
d482c73b by Daniel Mackner at 2024-12-07T10:58:10+01:00
split definitions from general functions in mri.h
- - - - -
832e7c61 by Martin Uecker at 2024-12-07T10:58:10+01:00
white space
- - - - -
da02b27c by Yaroslav Halchenko at 2024-12-07T11:01:39+01:00
Add github action to codespell master on push and PRs
- - - - -
b7b84a31 by Yaroslav Halchenko at 2024-12-07T11:01:39+01:00
Add rudimentary codespell config
- - - - -
bf23a244 by Yaroslav Halchenko at 2024-12-07T11:01:39+01:00
[DATALAD RUNCMD] run codespell throughout fixing typos automagically (but ignoring overall fail due to ambigous ones)
=== Do not change lines below ===
{
"chain": [],
"cmd": "codespell -w || :",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
- - - - -
dfb09e5e by Yaroslav Halchenko at 2024-12-07T11:01:39+01:00
[DATALAD RUNCMD] Do interactive fixing of some ambigous typos
=== Do not change lines below ===
{
"chain": [],
"cmd": "codespell -w -i 3 -C 2",
"exit": 0,
"extra_inputs": [],
"inputs": [],
"outputs": [],
"pwd": "."
}
^^^ Do not change lines above ^^^
- - - - -
9d9bc902 by Yaroslav Halchenko at 2024-12-07T11:01:39+01:00
Some extra fixes done interactively and ignores
- - - - -
5596517b by Daniel Mackner at 2024-12-07T11:20:01+01:00
double opt
- - - - -
1c9e09af by Christian Holme at 2024-12-07T11:46:50+01:00
multind: add functionalites for iteration over
permuted dimensions
md_copy_order | md_permute_dims_inverse | md_next_order(_unchecked)
- - - - -
aff5ed3a by Martin Uecker at 2024-12-07T13:45:52+01:00
md_permute_flags, refactor md_next_order to md_next_permuted
- - - - -
78028bb5 by Daniel Mackner at 2024-12-07T13:45:52+01:00
traj: mb and turns part of traj_conf
- - - - -
bad3a599 by Daniel Mackner at 2024-12-07T13:45:52+01:00
traj/seq: use indices_from_position in traj-tool
- - - - -
94470d0c by Martin Uecker at 2024-12-07T13:45:52+01:00
remove unused makefile line
- - - - -
4f0c0937 by Blumenthal, Moritz at 2024-12-08T09:54:05+01:00
admm memory: GH_usum
- - - - -
c1c4bfc9 by Blumenthal, Moritz at 2024-12-08T09:54:05+01:00
dynamic rho only possible for !fast plan
- - - - -
80d931a6 by Blumenthal, Moritz at 2024-12-08T09:54:05+01:00
admm memory: s
- - - - -
40072c27 by Blumenthal, Moritz at 2024-12-08T09:54:05+01:00
admm memory: r[j]
- - - - -
c093bab5 by Blumenthal, Moritz at 2024-12-08T09:54:05+01:00
admm memory: rhs
- - - - -
b32a3d44 by Blumenthal, Moritz at 2024-12-09T10:46:40+01:00
syn print loss
- - - - -
61d28a49 by Moritz Blumenthal at 2024-12-09T10:46:40+01:00
dot products by (z)fmac(cD)
- - - - -
de26a782 by Blumenthal, Moritz at 2024-12-09T10:48:55+01:00
optimize const on gpu
- - - - -
44513e72 by Blumenthal, Moritz at 2024-12-09T10:49:12+01:00
make scalar op
- - - - -
a74b2f17 by Moritz Blumenthal at 2024-12-09T10:50:50+01:00
print total freed gpu memory
- - - - -
bc981a57 by Blumenthal, Moritz at 2024-12-09T10:51:32+01:00
Update cuda allocations and streams
- - - - -
14596e76 by Blumenthal, Moritz at 2024-12-09T10:51:51+01:00
md_is_multiplace
- - - - -
306ef4bd by Blumenthal, Moritz at 2024-12-09T10:52:19+01:00
CUDA_KERNEL_ERROR in gpu_conv
- - - - -
ae9ae981 by Blumenthal, Moritz at 2024-12-09T10:52:19+01:00
CUDA_KERNEL_ERROR and gpu limits in gpu_reduce
- - - - -
7ff72bce by Blumenthal, Moritz at 2024-12-09T10:52:19+01:00
CUDA_KERNEL_ERROR in gpukrnls_bat
- - - - -
1a6977a6 by Blumenthal, Moritz at 2024-12-09T10:52:19+01:00
CUDA_KERNEL_ERROR in gpukrnls
- - - - -
e0791126 by Martin Schilling at 2024-12-09T12:46:15+01:00
Added normalization layer
- - - - -
8176f924 by Martin Schilling at 2024-12-09T12:46:15+01:00
Allow more network weights
- - - - -
f910806b by Martin Schilling at 2024-12-09T12:46:15+01:00
Added option for leaky ReLU
- - - - -
a2f9fc01 by Blumenthal, Moritz at 2024-12-09T12:46:15+01:00
softmax without bias
- - - - -
aa19f41d by Martin Schilling at 2024-12-09T12:46:15+01:00
Options for nnU-Net architecture
- - - - -
1ddf0be7 by Martin Schilling at 2024-12-09T12:46:15+01:00
Function to set NaN values to zero
- - - - -
9585d17d by Martin Schilling at 2024-12-09T12:46:15+01:00
Batchnorm with md_zadd
- - - - -
0c346180 by Martin Schilling at 2024-12-09T12:46:15+01:00
nnU-Net down-sampling with old padding
- - - - -
bbdd2f0e by Martin Schilling at 2024-12-09T12:46:15+01:00
Fixed condition
- - - - -
9e0aed20 by Martin Schilling at 2024-12-09T12:46:15+01:00
keep U-Net architecture as short option
- - - - -
ed2e5aa8 by Martin Uecker at 2024-12-09T12:46:15+01:00
fix stringop-overflow error
- - - - -
55312d25 by Martin Uecker at 2024-12-09T12:46:15+01:00
copyright & style
- - - - -
e7159280 by Christian Holme at 2024-12-19T18:31:04+01:00
src/misc,debug: add __attribute__((format(printf,,)) for format-checking
- - - - -
98e590de by Christian Holme at 2024-12-19T18:31:04+01:00
fix format string bugs found by previous commit
- - - - -
03c72d34 by Christian Holme at 2024-12-19T18:31:04+01:00
style
- - - - -
5486954d by Christian Holme at 2024-12-19T18:54:34+01:00
more format string fixes
- - - - -
aaaa1c41 by Nick Scholand at 2024-12-31T19:42:07+01:00
singularity: Update doc and add openMPI and CuDNN
- - - - -
351e837c by Blumenthal, Moritz at 2025-01-15T14:55:36+01:00
fix unmapping in interpolate
- - - - -
79cea832 by Martin Uecker at 2025-01-18T18:23:54+01:00
fix reproducibility of sms-nlinv
- - - - -
738671f0 by Martin Uecker at 2025-01-19T10:53:57+01:00
style
- - - - -
14d3c0c9 by Martin Uecker at 2025-01-19T14:28:47+01:00
minor cleanup
- - - - -
0bce996b by Martin Uecker at 2025-01-19T15:12:32+01:00
signed warnings tf wrapper
- - - - -
9c2db5a7 by Martin Uecker at 2025-01-19T15:13:00+01:00
update tensorflow tests
- - - - -
61741bee by Martin Uecker at 2025-01-19T16:47:53+01:00
integration tests for tensorflow
- - - - -
a9accdbe by Martin Uecker at 2025-01-19T17:08:27+01:00
add backwards compatibility mode
- - - - -
483d3044 by Martin Uecker at 2025-01-20T19:22:03+01:00
pass --break-system-packages when installing tensorflow python package
- - - - -
ec740750 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add pridu conf
- - - - -
fa05aa61 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add adaptive stepsize mechanism to pridu
- - - - -
d78fd37e by Moritz Blumenthal at 2025-01-21T13:47:37+01:00
fix precond + supporting
- - - - -
e58701cc by Ingrid Barth at 2025-01-21T13:47:37+01:00
move tv into separate function
- - - - -
20432fb8 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add gradient scaling to tv and tgv
- - - - -
4785f742 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add parameter alpha to tgv (changes defaults)
- - - - -
3cfad626 by Ingrid Barth at 2025-01-21T13:47:37+01:00
modify symmetrized gradient in tgv to match literature definition (changes defaults)
- - - - -
5a2c7661 by Ingrid Barth at 2025-01-21T13:47:37+01:00
set default soft thresholding flags for tgv (changes defaults)
- - - - -
80d96e27 by Ingrid Barth at 2025-01-21T13:47:37+01:00
modify ictv to match literature definition (changes defaults)
- - - - -
7a02ad06 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add parameter gamma to ictv
- - - - -
f6a89997 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add support for ictgv
- - - - -
c3fd1e99 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add arterial spin labeling with tv regularization
- - - - -
f1856262 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add asl to tgv, ictv and ictgv
- - - - -
6bb19b95 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add asl with l1 regularization
- - - - -
cd544b3a by Ingrid Barth at 2025-01-21T13:47:37+01:00
add hadamard operator for te-asl
- - - - -
af685cfa by Ingrid Barth at 2025-01-21T13:47:37+01:00
add te-asl with l1, tv and tgv regularization
- - - - -
6f2c24fe by Ingrid Barth at 2025-01-21T13:47:37+01:00
add buxton model to signal toolbox
- - - - -
7205f4a4 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add unit test for gradient
- - - - -
2100d3f8 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add denoising toolbox
- - - - -
4fc7d28f by Ingrid Barth at 2025-01-21T13:47:37+01:00
add integration tests for ictv and ictgv
- - - - -
07b9a5a5 by Ingrid Barth at 2025-01-21T13:47:37+01:00
add integration test for asl denoising
- - - - -
246edc66 by Martin Uecker at 2025-01-25T08:36:36+01:00
fix spelling errors
- - - - -
426da276 by Martin Uecker at 2025-01-25T12:38:24+01:00
reduce number of iterations in tv/tgv/ictgv tests
- - - - -
91c2295b by Martin Uecker at 2025-01-25T13:59:48+01:00
rename denoising tool to denoise
- - - - -
84959530 by Martin Uecker at 2025-01-25T13:59:48+01:00
remove unused header
- - - - -
ba96eb67 by Martin Uecker at 2025-01-25T17:10:32+01:00
fix test and remove unneeded dependencies
- - - - -
02f57b6d by Martin Uecker at 2025-01-25T18:17:42+01:00
style changes
- - - - -
b9a2347d by Martin Uecker at 2025-01-25T18:19:47+01:00
remove redundant line
- - - - -
d5d42c9d by Moritz Blumenthal at 2025-03-03T22:17:28+01:00
fix pridu for D=0 case
- - - - -
4414168d by Daniel Mackner at 2025-03-06T14:16:57+01:00
twixread noise scans
- - - - -
fefa6ddb by Daniel Mackner at 2025-03-06T14:16:57+01:00
md_next_permuted: inverse permutation of pos
- - - - -
0f67a62d by Daniel Mackner at 2025-03-06T14:16:57+01:00
hard threshold maximum
- - - - -
c4107e12 by Daniel Mackner at 2025-03-06T14:16:57+01:00
use gpu in rovir script
- - - - -
afd1bf75 by Martin Uecker at 2025-03-08T18:50:15+01:00
institute name
- - - - -
a902642a by Moritz Blumenthal at 2025-03-11T11:06:51+01:00
reduce debugging level of numeric libraries
- - - - -
faccdadd by Blumenthal, Moritz at 2025-03-13T11:53:04+01:00
fixup llr in nlinv
- - - - -
da77cfb4 by Blumenthal, Moritz at 2025-03-14T12:22:25+01:00
fiuxp max norm for mobafit bounds
- - - - -
951cf79d by Martin Uecker at 2025-03-19T16:03:35+01:00
properly implement hiding of options
- - - - -
035cd818 by Christian Holme at 2025-03-19T16:03:35+01:00
move option showing into show_option_p
- - - - -
1d3ba2ad by Christian Holme at 2025-03-19T16:03:35+01:00
opts: support more long-only options
If we use a signed char, we cannot support more than ~30 long-only
options, since there are only ~30 unprintable characters between 0 and
127.
By switchting to an unsigned char, we can support a lot more long-only
options.
This is needed for the new sequence tool
- - - - -
18d02db6 by Martin Uecker at 2025-03-21T09:39:30+01:00
update references
- - - - -
33256f86 by Ingrid Barth at 2025-03-21T09:50:45+01:00
fix secondary tvscales for ictgv
- - - - -
8c962a54 by Martin Uecker at 2025-03-22T10:53:56+01:00
check error or pipe in test
- - - - -
388f8a98 by Martin Uecker at 2025-03-25T08:02:57+01:00
remove INTERFACE macro
- - - - -
42e25e5f by Martin Uecker at 2025-03-26T07:23:43+01:00
remove github action for codespell
- - - - -
55949ff0 by Martin Uecker at 2025-03-28T14:11:49+01:00
use empty initialization
- - - - -
1fc1a5f6 by Martin Uecker at 2025-03-29T13:51:52+01:00
style
- - - - -
6b35b887 by Martin Uecker at 2025-03-29T14:20:49+01:00
style
- - - - -
362f5820 by Martin Uecker at 2025-03-29T14:42:23+01:00
clang fixup
- - - - -
531b623d by Martin Uecker at 2025-03-30T10:14:51+02:00
various minor/style issues, help
- - - - -
09c19b8e by Martin Uecker at 2025-03-31T10:05:53+02:00
add -Wwrite-strings
- - - - -
ee65eaeb by Martin Uecker at 2025-03-31T11:57:54+02:00
put cuda errors into a table
- - - - -
2d27d55b by Martin Uecker at 2025-03-31T12:00:12+02:00
update copyright
- - - - -
bd54d86f by Martin Uecker at 2025-03-31T12:44:41+02:00
remove two useless casts
- - - - -
5bd71031 by Martin Uecker at 2025-03-31T12:45:57+02:00
initialize variable
- - - - -
5acd8cab by Daniel Mackner at 2025-03-31T13:18:21+02:00
twixread: optional read PMU signal
- - - - -
fc826824 by Daniel Mackner at 2025-03-31T14:24:50+02:00
twixread PMU: test
- - - - -
8e6f7883 by Daniel Mackner at 2025-03-31T14:24:50+02:00
twixread whitespaces
- - - - -
1283ca9b by Blumenthal, Moritz at 2025-04-04T12:48:29+02:00
reshaping tfgraph
- - - - -
ff26ec62 by Martin Uecker at 2025-04-06T19:09:58+02:00
void -> complex float
- - - - -
5370acdd by Martin Uecker at 2025-04-06T19:09:58+02:00
const
- - - - -
969925cd by Martin Uecker at 2025-04-07T16:37:59+02:00
move ifdefs to the beginning
- - - - -
59c02363 by Martin Uecker at 2025-04-07T17:01:36+02:00
twixread style and copyright
- - - - -
ddc30d69 by Martin Uecker at 2025-04-07T19:49:54+02:00
remove assertions and add error messages, remove some unneeded headers
- - - - -
193d302c by Moritz Blumenthal at 2025-04-07T22:29:57+02:00
optical flow: keep sigma and tau ratio one and update test
- - - - -
d234347f by Martin Uecker at 2025-04-08T10:04:45+02:00
do not use pipes in tests where this can be avoided
- - - - -
45c379e8 by Martin Uecker at 2025-04-08T10:42:43+02:00
remove unused variable
- - - - -
06517ba8 by Martin Uecker at 2025-04-08T10:45:21+02:00
improve tests
- - - - -
46f04631 by Uhl, Daniel Sebastian at 2025-04-08T12:36:18+02:00
Unitary scaling of nudft WiP (fix testcases)
this breaks some other testcases that still need to be fixed
- - - - -
bc5615f5 by Uhl, Daniel Sebastian at 2025-04-08T12:36:31+02:00
Remove scaling factor in nufft, nudft comparison
- - - - -
d93cc33c by Uhl, Daniel Sebastian at 2025-04-08T12:36:31+02:00
Add factor to account for nudft now being unitary
- - - - -
0d77feee by Uhl, Daniel Sebastian at 2025-04-08T12:36:31+02:00
Remove unused include
- - - - -
5ce86abe by Martin Heide at 2025-04-08T14:45:54+02:00
Add cuda dependency documentation
- - - - -
f809e6fe by Martin Uecker at 2025-04-09T17:20:44+02:00
const correctness and clean up iter/iter6
- - - - -
db0499b8 by Martin Uecker at 2025-04-09T17:29:52+02:00
shut up unused variable warning
- - - - -
e96afe9d by Martin Uecker at 2025-04-09T17:59:47+02:00
add free
- - - - -
d5e48ee3 by Martin Uecker at 2025-04-11T13:59:03+02:00
sound output
- - - - -
13da96df by Martin Uecker at 2025-04-22T09:44:17+02:00
do not plan convolution in conv command
- - - - -
d21d862b by Martin Uecker at 2025-04-22T09:48:36+02:00
group output for risc test
- - - - -
c025b83d by Daniel Mackner at 2025-04-22T15:26:48+02:00
md_unravel with order
- - - - -
0f4336af by Daniel Mackner at 2025-04-24T14:15:48+02:00
finite differences with set to zero
- - - - -
3d6274da by Daniel Mackner at 2025-04-24T14:15:48+02:00
unwrapping
- - - - -
410686f4 by Daniel Mackner at 2025-04-24T14:15:48+02:00
finite differences in filter
- - - - -
74890cea by Daniel Mackner at 2025-04-25T10:08:06+02:00
rename tosnd -> toraw
output type | fix clamp | optional normalize |
optional complex output
- - - - -
8ac25aae by Martin Uecker at 2025-04-25T13:29:04+02:00
refactor
- - - - -
cefb3014 by Martin Uecker at 2025-04-25T13:46:35+02:00
fix dependencies is tests
- - - - -
ddbfbc43 by Martin Uecker at 2025-04-25T13:46:35+02:00
switch condtion
- - - - -
16dd5e43 by Philip Schaten at 2025-04-25T18:12:51+02:00
fix error when reference stream is stdin.
A command like `bart -r - copy - -` fails before this commit,
because `-` is opened already in bart.c, and then does not get the right in/out flags
in the command. Thus, unregister (io_close) after getting flags, dims etc.
- - - - -
b718fb2f by Philip Schaten at 2025-04-25T18:12:51+02:00
stream names: clean up the name mangling
beforehand every stream would get an in_ or out_ prepended,
but it's only neccessary for stdin / stdout.
- - - - -
64af4dd1 by Philip Schaten at 2025-04-25T18:12:51+02:00
stream timestamp logging
- - - - -
e85596fc by Philip Schaten at 2025-04-25T18:12:51+02:00
remove msync except for emscripten
- - - - -
3c39553a by Philip Schaten at 2025-04-25T18:12:51+02:00
remove stream_sync race condition.
previously, stream was serialized in the order in which
threads acquired the lock (i.e. randomly, but still serialized).
Intended behaviour: Work on indices in the order in which they
are received.
- - - - -
17eb6946 by Philip Schaten at 2025-04-25T18:12:51+02:00
stream: add functions to receive new slices in stream order.
- - - - -
387eec44 by Philip Schaten at 2025-04-25T18:12:51+02:00
bart looping: adjustable loop order, explicitly settable flags
- - - - -
57ef0fae by Philip Schaten at 2025-04-25T18:12:51+02:00
fix tee out-of-bounds access
- - - - -
90f1dafc by Philip Schaten at 2025-04-25T18:12:51+02:00
fix copy tool, improve stream_sync_slice.
1) The copy tool has a stream-specific feature, --streams, which allows
creating streams from a fixed data set. This was subtly broken:
If the output was a stream (because "-" was specified as an output
file), but `--streams` was not given, and the input was a stream
but with a larger flag, e.g. 1024, then the copy loop would wrongly
sync the whole output file albeit when only one slice from the input
stream had been copied.
2) fixed problematic behavior of stream_sync_slice, which would sync
an output stream slice if only part of the respective slice was specified.
- - - - -
3d6969a5 by Philip Schaten at 2025-04-25T18:12:56+02:00
streams: out-of-order trx
- - - - -
6d652b1d by Philip Schaten at 2025-04-25T18:12:56+02:00
real-time pattern estimation
- - - - -
4f87287f by Philip Schaten at 2025-04-25T18:12:56+02:00
copy tool: reordering
- - - - -
ec8358e4 by Philip Schaten at 2025-04-25T18:12:56+02:00
Use stream_sync_slice instd of stream_sync in reshape tool.
1) Removes ambiguous stream_sync API.
2) Prerequisite for having out-of-order reshapes.
- - - - -
80af8c22 by Philip Schaten at 2025-04-25T18:12:56+02:00
streams: out-of-order reshape.
Currently, reshape serializes incoming stream due to md_next loop
(and previously also due to the use of stream_sync).
Using stream_receive_pos, the order of the incoming stream is used.
- - - - -
cc697593 by Philip Schaten at 2025-04-25T18:12:56+02:00
bin tool: stream flag for reorder binning
- - - - -
05b7aaf8 by Philip Schaten at 2025-04-25T18:12:56+02:00
fix numthreads in tee
- - - - -
9aa9515e by Philip Schaten at 2025-04-25T18:12:56+02:00
streams: out-of-order bart looping
- - - - -
dc154f60 by Philip Schaten at 2025-04-25T18:12:56+02:00
streams: out-of-order tee
- - - - -
c35709fd by Philip Schaten at 2025-04-25T18:12:56+02:00
rtreco.sh improvements
- TIMELOG option for benchmarking
- RAGA
- detect GPU support.
- sliding window
- cc_none option
- configurable nlmeans options
- less copying
- correctly oriented sliding window
- log timing for median filter
- broke -T timestep option (WIP)
- - - - -
ee5c220b by Philip Schaten at 2025-04-25T18:12:56+02:00
use c11 synchronization.
- - - - -
7e200331 by Philip at 2025-04-25T18:12:56+02:00
append cmdline
- - - - -
cd07ccc0 by Philip at 2025-04-25T18:12:56+02:00
write hdr file to track pipeline cmds
- - - - -
22b5876d by Philip at 2025-04-25T18:12:56+02:00
Don't create fifos.
- - - - -
09febf67 by Philip Schaten at 2025-04-25T18:12:56+02:00
remove redundant options from stream_create
- - - - -
fbf00989 by Philip Schaten at 2025-04-25T18:12:56+02:00
cleanup stream.c:
- pcfl has nothing to do with the actual memory,
thus removed the pointer from that struct.
- remove redundant number of dimensions
- cleaner initialization of stream struct.
- - - - -
2cac7edb by Philip Schaten at 2025-04-25T18:12:56+02:00
read binary streams from anywhere
- - - - -
aae90d48 by Philip Schaten at 2025-04-25T18:12:56+02:00
output binary stream if BART_BINARY_STREAM=1
- - - - -
f8b2badb by Philip Schaten at 2025-04-25T18:12:56+02:00
fix WebASM node.js test..
- - - - -
81b47c2c by Philip Schaten at 2025-04-25T18:12:56+02:00
some cleanup in ismrm:
- split functions (for later use in ismrm stream parsing)
- avoid namespace ISMRMRD
- whitespace
- - - - -
30ab781d by Philip Schaten at 2025-04-25T18:12:56+02:00
fix negativ array index in read.c
- - - - -
abf85592 by Philip Schaten at 2025-04-25T18:12:56+02:00
fix format strings + uninitialized values
- - - - -
87ae949c by Philip Schaten at 2025-04-25T18:12:56+02:00
separate function convert_acquisition (prep for ismrmrd_streams)
- - - - -
eb81bc19 by Philip Schaten at 2025-04-25T18:12:56+02:00
split out ismrm_validate_limits function
- - - - -
a47f4197 by Philip Schaten at 2025-04-25T18:12:56+02:00
add functions to parse ismrmrd streams
- - - - -
7d337df4 by Martin Uecker at 2025-04-26T17:38:30+02:00
rename close_later to wasm_close_later
- - - - -
0e4b4d49 by Martin Uecker at 2025-04-26T17:38:30+02:00
sqrt -> sqrtf
- - - - -
e7cea99a by Martin Uecker at 2025-04-26T17:38:30+02:00
fix copyright
- - - - -
4bd369e4 by Martin Uecker at 2025-04-26T17:47:29+02:00
copyrights
- - - - -
daabfbe4 by Uhl, Daniel Sebastian at 2025-04-27T15:30:26+02:00
implement slow version of field map correction
- - - - -
7319fb94 by Martin Uecker at 2025-04-27T15:30:38+02:00
style & conventions
- - - - -
c83f87a2 by Martin Uecker at 2025-04-27T15:31:21+02:00
output filename when unlinking
- - - - -
87433498 by Martin Uecker at 2025-04-27T15:31:36+02:00
work around riscv issue by turning off new fieldmap tests
- - - - -
c9899f25 by Martin Uecker at 2025-04-27T20:44:32+02:00
const correctness
- - - - -
1d50e3ff by Martin Uecker at 2025-04-27T20:44:32+02:00
ptr_print
- - - - -
e7123f57 by Martin Uecker at 2025-04-27T20:44:32+02:00
container_of_const
- - - - -
0bbd647e by Martin Uecker at 2025-04-27T20:44:32+02:00
remove unneeded functions
- - - - -
395f70fb by Martin Uecker at 2025-04-27T20:44:32+02:00
remove unused function
- - - - -
901cd993 by Martin Uecker at 2025-04-27T20:44:32+02:00
png workaroung
- - - - -
c09c53b5 by Martin Uecker at 2025-04-27T20:44:32+02:00
svthresh
- - - - -
c7a77601 by Martin Uecker at 2025-04-27T20:44:32+02:00
remove test for GCC <= 11
- - - - -
116d6c70 by Martin Uecker at 2025-04-27T20:50:34+02:00
clang workarounds
- - - - -
812c8943 by Martin Uecker at 2025-04-27T21:46:34+02:00
move list of mains into a file to declutter logs
- - - - -
38cad2c6 by Martin Heide at 2025-04-29T11:12:52+02:00
Subopt own description
- - - - -
b9f72aae by Martin Heide at 2025-04-29T11:15:16+02:00
add read/ write stl and cfl conversion
- - - - -
28e6ea50 by Martin Heide at 2025-04-29T11:15:31+02:00
stl tests
- - - - -
ef8dbad8 by Philip at 2025-05-01T22:55:20+02:00
Avoid rebuilding due to changed src/mainlist.inc
- - - - -
b4e61ef6 by Moritz Blumenthal at 2025-05-02T15:56:49+02:00
fixup ictgv
- - - - -
45234d06 by Blumenthal, Moritz at 2025-05-02T16:50:45+02:00
analyzer fixes
- - - - -
9c3b733f by Martin Uecker at 2025-05-04T16:58:30+02:00
style changes
- - - - -
cf83a17c by Martin Uecker at 2025-05-04T16:58:30+02:00
fieldmap test: use correct directory, sim. smaller image, reduce tolerance
- - - - -
d945749a by Martin Uecker at 2025-05-04T16:59:16+02:00
remove MD_INIT_ARRAY macro
- - - - -
b70da1f3 by Martin Uecker at 2025-05-04T17:00:06+02:00
remove RISCV exception for fieldmap test
- - - - -
a05c0001 by Philip Schaten at 2025-05-04T18:21:14+02:00
merge ismrmrds command into ismrmrd
- - - - -
33650aaa by Philip Schaten at 2025-05-04T18:21:14+02:00
ismrmrd improvements
- count conversion attempts
- for debugging
- don't skip invalid indices, but warn and set to 0
- Necessary for FIRE & MiniFLASH on XA50.
- handle interleaved text messages
- - - - -
8e92278e by Philip at 2025-05-04T19:06:44+02:00
Add a test for ISMRMRD reader.
- - - - -
fdcbbd89 by Martin Uecker at 2025-05-06T12:48:14+02:00
output better error messages for command-line options
- - - - -
797c4fd0 by Christian Bardey at 2025-05-08T15:51:26+02:00
ignore new generated file src/mainlist.inc
- - - - -
4f637078 by Martin Heide at 2025-05-21T15:12:02+02:00
fix stl ascii enc read error and test for it
- - - - -
bbcd86d5 by Blumenthal, Moritz at 2025-05-26T18:48:10+02:00
fixup ncalib sos/sms
- - - - -
93ad0d53 by Martin Uecker at 2025-05-27T18:36:42+02:00
fix typo
- - - - -
353af6a2 by Martin Uecker at 2025-05-28T08:41:35+02:00
classify tools
- - - - -
7e5ded78 by Martin Uecker at 2025-05-28T09:17:25+02:00
spaces and imaginary unit
- - - - -
a7445bb7 by Martin Uecker at 2025-05-28T09:17:25+02:00
move some losses into nlops
- - - - -
5521b0b0 by Martin Uecker at 2025-05-28T09:24:43+02:00
more coding style assimilation
- - - - -
bbd7f3af by Martin Uecker at 2025-05-28T10:08:08+02:00
do not overflow buffer
- - - - -
f9849f39 by Martin Uecker at 2025-06-03T14:59:03+02:00
style
- - - - -
6661c47f by Martin Uecker at 2025-06-03T17:43:48+02:00
add preliminary function to synthesize cmdline from argument structs
- - - - -
f8d90b41 by Martin Uecker at 2025-06-03T18:46:00+02:00
switch to clang 19
- - - - -
deb5c12f by Martin Uecker at 2025-06-03T19:02:22+02:00
semicolons
- - - - -
09a2d060 by Martin Uecker at 2025-06-03T19:27:54+02:00
avoid warning
- - - - -
988e9300 by Blumenthal, Moritz at 2025-06-10T13:46:13+02:00
fix: account for terminating \0 in snprintf
- - - - -
512464ce by Blumenthal, Moritz at 2025-06-10T13:48:02+02:00
add isclean to gitignore
- - - - -
43a6086f by Blumenthal, Moritz at 2025-06-10T14:39:29+02:00
fix enlive projection strides (relevant for dims > MAPS_DIM)
- - - - -
87a9e681 by Blumenthal, Moritz at 2025-06-10T16:10:40+02:00
fix enlive projection strides: update test
- - - - -
5e4d74ac by Martin Uecker at 2025-06-16T13:57:33+02:00
typo
- - - - -
3efc51a2 by Martin Uecker at 2025-06-20T15:49:15+02:00
whitespace
- - - - -
aa446a99 by Martin Uecker at 2025-06-20T15:55:52+02:00
remove unneeded headers
- - - - -
e82393d2 by Martin Uecker at 2025-06-21T15:37:45+02:00
computation of trapezoidal gradients
- - - - -
8bd8eb79 by Martin Uecker at 2025-06-21T18:13:37+02:00
error message for psf
- - - - -
4ab9bf95 by Martin Uecker at 2025-06-21T18:13:59+02:00
traj cli consistency
- - - - -
4b59e902 by Martin Uecker at 2025-06-21T18:14:09+02:00
whitespace in traj tests
- - - - -
1da39da8 by Martin Uecker at 2025-06-22T12:11:56+02:00
semicolons
- - - - -
6c176e00 by Martin Uecker at 2025-06-22T12:11:56+02:00
fail hard for GCC < 12
- - - - -
353a0dd3 by Martin Uecker at 2025-06-22T12:27:03+02:00
mention Ubuntu 22.04 issue in README
- - - - -
d691e2e2 by Martin Uecker at 2025-06-24T11:27:09+02:00
check return value for strdup
- - - - -
5a00527f by Martin Uecker at 2025-06-24T11:35:41+02:00
avoid conversion to unsigned
- - - - -
61f161e3 by Martin Uecker at 2025-06-25T13:14:03+02:00
reproducibility of SSA-FARY (partially)
- - - - -
7b2bdc0b by Blumenthal, Moritz at 2025-06-25T13:20:30+02:00
nufft check compatibility of trajectory and kspace
- - - - -
98eadd0f by Blumenthal, Moritz at 2025-06-26T16:31:03+02:00
tool for estimating scaling of data
- - - - -
d48e237f by Blumenthal, Moritz at 2025-06-26T18:49:51+02:00
tool to compress with binary mask
- - - - -
f33431c3 by Martin Uecker at 2025-06-26T21:11:26+02:00
fix bug in nlinvnet
- - - - -
756e2421 by Martin Uecker at 2025-06-26T21:42:40+02:00
fix infinite recursion in phantom tools for -N1
- - - - -
98477841 by Martin Uecker at 2025-06-26T21:42:40+02:00
work around analyzer false warning
- - - - -
8523a4d3 by Martin Uecker at 2025-06-26T21:43:15+02:00
code must be analyzer clean
- - - - -
50ef39b0 by Blumenthal, Moritz at 2025-06-26T23:26:44+02:00
fixup strides for compression
- - - - -
c941fe18 by Martin Uecker at 2025-06-27T07:22:15+02:00
improve robustness of phantom tool
- - - - -
57505e2c by Martin Uecker at 2025-06-27T07:22:15+02:00
remove unused macros
- - - - -
ca8f08aa by Martin Uecker at 2025-06-27T07:22:15+02:00
coding style
- - - - -
ab5968a8 by Martin Uecker at 2025-06-27T09:20:52+02:00
remove default case
- - - - -
662aa983 by Martin Uecker at 2025-06-27T09:55:43+02:00
control no sensitivity case via coil type
- - - - -
d299d46f by Martin Uecker at 2025-06-28T08:22:00+02:00
early out of loop
- - - - -
7e4aa1fa by Martin Uecker at 2025-06-28T08:22:00+02:00
add alloc_size to md_alloc
- - - - -
74e44926 by Martin Uecker at 2025-06-28T09:56:11+02:00
use PINT
- - - - -
4d088969 by Martin Uecker at 2025-06-28T10:12:36+02:00
revise style document
- - - - -
f393e5cc by Martin Uecker at 2025-06-28T11:50:13+02:00
harmonize headers
- - - - -
81faf19f by Martin Uecker at 2025-06-28T12:54:46+02:00
inline a couple of key functions
- - - - -
f08006f9 by Martin Uecker at 2025-06-28T13:15:10+02:00
fix overflow in test
- - - - -
6dcf58ab by Martin Uecker at 2025-06-28T22:52:23+02:00
allow unmap with NULL
- - - - -
03e06c91 by Daniel Mackner at 2025-07-01T15:37:33+02:00
multind: check equal order
- - - - -
0bfa4109 by Daniel Mackner at 2025-07-01T15:37:33+02:00
raga helper fcts
- - - - -
00b19f0f by Daniel Mackner at 2025-07-02T14:02:25+02:00
sms pulse
pulse_t in pulse.h
- - - - -
0cc10788 by Daniel Mackner at 2025-07-02T14:02:25+02:00
move pulse from simu to seq
- - - - -
6de0085e by Daniel Mackner at 2025-07-02T14:02:26+02:00
pulse tool
simulate pulse waveforms
- - - - -
42f73193 by Martin Uecker at 2025-07-02T16:31:37+02:00
revise pulse tool
- - - - -
dcf6f224 by Martin Uecker at 2025-07-02T16:34:21+02:00
add a simple test
- - - - -
67027c35 by Sophie Schauman at 2025-07-05T09:02:40+02:00
Readme updates for MacOS compilation (#353)
* Update README - MacOS compile instructions
* Update README - added dependency
macOS no longer includes libBlocksRuntime in system libraries by default (especially with newer macOS versions or custom compilers).
---------
Co-authored-by: Sophie Schauman <sophie at Sophies-MacBook-Pro.local>
- - - - -
1fb39e23 by Blumenthal, Moritz at 2025-07-07T14:14:50+02:00
add option to twixread to read reference scan
- - - - -
3b7f33ef by Blumenthal, Moritz at 2025-07-07T14:14:54+02:00
twixread don't unfold SIEMENS segment counter
- - - - -
0bfe5f2a by Blumenthal, Moritz at 2025-07-07T23:59:49+02:00
fixup redefinition of MIN/MAX macro for cuda
- - - - -
c06ea5d3 by Blumenthal, Moritz at 2025-07-07T23:59:49+02:00
fix integer overflow in ecalib
- - - - -
ce80319b by Blumenthal, Moritz at 2025-07-07T23:59:49+02:00
twixread option to not include reference lines
- - - - -
3c62daa3 by Daniel Mackner at 2025-07-08T08:58:58+02:00
test raga to ga
- - - - -
dd2d090c by Martin Uecker at 2025-07-08T13:02:08+02:00
add Y and raga_inc to trajectory config
- - - - -
ccfa74e7 by Martin Uecker at 2025-07-08T20:14:49+02:00
refactor raga angle calculation
- - - - -
b5706011 by Martin Uecker at 2025-07-08T20:14:49+02:00
add line break
- - - - -
cf7358fd by Martin Uecker at 2025-07-08T20:14:49+02:00
remove white spaces
- - - - -
41efb6dd by Martin Uecker at 2025-07-08T20:14:49+02:00
make description of options a bit shorter
- - - - -
cfa87e83 by Martin Uecker at 2025-07-08T20:14:49+02:00
minor style fixes
- - - - -
90a99d86 by Martin Uecker at 2025-07-08T21:04:58+02:00
move golden angle calc in function
- - - - -
74328d70 by Martin Uecker at 2025-07-08T21:24:17+02:00
make tests more useful
- - - - -
d72f6e4f by Martin Uecker at 2025-07-08T21:24:41+02:00
refactor
- - - - -
5c1139e9 by Martin Uecker at 2025-07-08T22:31:41+02:00
fix for mems trajectory
- - - - -
66b60b13 by Daniel Mackner at 2025-07-09T10:07:30+02:00
change unravel permuted interface
- - - - -
7d06a8ce by Daniel Mackner at 2025-07-09T10:07:38+02:00
multind: pos to flat index with permutation
- - - - -
e0caf389 by Martin Uecker at 2025-07-09T13:26:15+02:00
remove start_pos_GA
- - - - -
d797a665 by Martin Uecker at 2025-07-09T13:29:31+02:00
introduce traj_read_dir function
- - - - -
b6173603 by Martin Uecker at 2025-07-09T13:48:06+02:00
make dimensions less (?) confusion in trajectory
- - - - -
57f15713 by Martin Uecker at 2025-07-09T14:21:07+02:00
remove option to create raga indices from trajectory tool (use raga)
- - - - -
767b9847 by Martin Uecker at 2025-07-10T14:03:28+02:00
move some tests to slow tests
- - - - -
7bb79bf3 by Blumenthal, Moritz at 2025-07-10T16:39:39+02:00
fix memleak in stacked model_t1
- - - - -
d1bc5574 by Daniel Mackner at 2025-07-10T17:50:53+02:00
raga from atom angle
- - - - -
cdd36631 by Daniel Mackner at 2025-07-10T17:50:53+02:00
RAGA for multislice
aligned across partitions / not-aligned
- - - - -
7244fb02 by Daniel Mackner at 2025-07-10T17:50:53+02:00
raga multislice tests
- - - - -
0c26bf2a by Daniel Mackner at 2025-07-10T17:50:53+02:00
make useful traj tests
minor style
- - - - -
ef4b11d2 by Daniel Mackner at 2025-07-10T17:50:53+02:00
moba traj with spokes insted of turns
-> multislice ga traj to be fixed
(breaks mrirecon/sms-t1-mapping)
- - - - -
21a840f4 by Blumenthal, Moritz at 2025-07-10T18:05:12+02:00
fix memleak in T2_create
- - - - -
bf122c93 by Martin Uecker at 2025-07-10T19:11:00+02:00
add forgotten bloch command
- - - - -
f7f81749 by Martin Uecker at 2025-07-10T21:25:59+02:00
clang fix
- - - - -
decf069a by Daniel Mackner at 2025-07-11T07:12:25+02:00
traj_conf with aligning flags
- - - - -
6806b74c by Daniel Mackner at 2025-07-11T08:39:17+02:00
traj: angle_atom and raga_inc fcts
- - - - -
80136245 by Daniel Mackner at 2025-07-11T09:04:44+02:00
traj: raga from single base_angle, pos and aligned flags
- - - - -
44a03ea1 by Martin Uecker at 2025-07-12T17:08:34+02:00
style
- - - - -
aad837bb by Martin Uecker at 2025-07-12T17:09:42+02:00
add lapack_solve_real
- - - - -
8ded7d31 by Martin Uecker at 2025-07-12T20:40:10+02:00
move stringify
- - - - -
05e9f73f by Martin Uecker at 2025-07-12T20:40:49+02:00
blas
- - - - -
1b183e77 by Martin Uecker at 2025-07-12T20:40:50+02:00
add some functions to linalg
- - - - -
7187efa5 by Martin Uecker at 2025-07-12T20:40:50+02:00
ode: use functions from linalg
- - - - -
31e569f8 by Martin Uecker at 2025-07-12T21:28:49+02:00
add crank nicolson
- - - - -
f1859903 by Martin Heide at 2025-07-14T16:15:24+02:00
add grid tool
- - - - -
941a63df by Martin Heide at 2025-07-14T16:15:30+02:00
test for grid tool
- - - - -
b8978634 by Martin Uecker at 2025-07-14T16:25:44+02:00
style
- - - - -
6e884a41 by Daniel Mackner at 2025-07-17T13:52:11+02:00
seq_events
- - - - -
99367e69 by Daniel Mackner at 2025-07-17T13:52:11+02:00
gradient: rm start from trapezoid, define duration
- - - - -
9feaa36f by Daniel Mackner at 2025-07-17T13:52:11+02:00
sequence: misc functions
- - - - -
8337ca57 by Daniel Mackner at 2025-07-17T13:52:11+02:00
basic sequence functions
- - - - -
4228b194 by Martin Heide at 2025-07-17T15:53:18+02:00
grid compatibility with trajs with time dim
- - - - -
9ff5ec64 by Blumenthal, Moritz at 2025-07-17T17:43:32+02:00
move functions for radial trajectory to noncart
- - - - -
f845cffd by Blumenthal, Moritz at 2025-07-17T17:43:32+02:00
add md_zatan2r
- - - - -
c4f6c49f by Blumenthal, Moritz at 2025-07-17T17:43:32+02:00
refactor radial helper functions
- - - - -
aefc842c by Blumenthal, Moritz at 2025-07-17T17:43:32+02:00
add helper for reading radial trajectory
- - - - -
c8f35f7f by Markus Huemer at 2025-07-17T17:43:32+02:00
inital commit of tool trajcor
- - - - -
7a90428b by Blumenthal, Moritz at 2025-07-17T17:43:32+02:00
specify temporary directory for tests
- - - - -
e1f157ad by Blumenthal, Moritz at 2025-07-17T17:43:32+02:00
trajcor read gradient delays from file and optionally correct transversal
- - - - -
4115d25a by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
cache fft_plans and create fft on the fly
- - - - -
79165ac2 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
cuda fft with multiple, non-contigious batch dimensions
- - - - -
7b573154 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
caching of fft plan no longer required
- - - - -
d0f73e02 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
normal nufft decomposed and no precomputed fftmod/rolloff/linphase
- - - - -
757b5184 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
remove unnecessary caching of nufft
- - - - -
4db326b8 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
refactor compute_psf2_decomposed
- - - - -
284746e3 by Moritz Blumenthal at 2025-07-17T21:05:57+02:00
more efficient gradient
- - - - -
a1d4e9d9 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
compress symmetric/hermitian matrices
- - - - -
359f9d5e by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
support for real valued and upper triag compressed psf in nufft
- - - - -
d5538a85 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
tests for psf and fix nufft header
- - - - -
cad21c63 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
compress psf to sphere
- - - - -
e8fc3af5 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
gridding in shared memory
- - - - -
df391c2d by Moritz Blumenthal at 2025-07-17T21:05:57+02:00
reusable option struct for configuring nufft
- - - - -
3ac6e6e0 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
turn of double print of basis dims
- - - - -
6fb878e8 by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
nufft conf in nufft
- - - - -
9bd8e71f by Blumenthal, Moritz at 2025-07-17T21:05:57+02:00
nufft option in pics
- - - - -
e2e8c679 by Philip Schaten at 2025-07-18T16:41:25+02:00
spaces between options + default print function
- - - - -
bb58bad0 by Jon Tamir at 2025-07-19T13:38:05+02:00
Mac install: coreutils and gcc14
- - - - -
d6a198d7 by Christian Bardey at 2025-07-19T13:38:05+02:00
apply aTrotier's apple patch
- - - - -
f0475d61 by Jon Tamir at 2025-07-19T13:38:05+02:00
streaming: fix format string
header size is int, not long (fixes error on Mac)
- - - - -
43bb2ca3 by Christian Bardey at 2025-07-19T13:38:05+02:00
scripts/affine_kspace: here-doc without process substitution
seems to trip up bash on MacOS
- - - - -
fcbf86c8 by Jon Tamir at 2025-07-19T13:38:05+02:00
tests/mobafit: use more iterations
- - - - -
6b89d0e5 by Jon Tamir at 2025-07-19T13:38:05+02:00
tests/version.mk: relax test
- - - - -
9f66d482 by Jon Tamir at 2025-07-19T13:38:05+02:00
test_optimized_md_zadd2_reduce_inner5: relax test
- - - - -
24e064d3 by Christian Bardey at 2025-07-19T13:38:05+02:00
update linux test
- - - - -
1fe61650 by Christian Bardey at 2025-07-19T13:38:05+02:00
github actions: add MacOS ARM test
- - - - -
88871b04 by Christian Bardey at 2025-07-19T13:38:05+02:00
run testslow
- - - - -
97949805 by Moritz Blumenthal at 2025-07-19T13:38:05+02:00
fix inplace plane detection and plan creation
- - - - -
fb726255 by Daniel Mackner at 2025-07-21T16:49:19+02:00
fix sms pulse integral
- - - - -
98a1be3b by Daniel Mackner at 2025-07-21T22:05:59+02:00
fix hyperbolic secant
- - - - -
bbb4147b by Daniel Mackner at 2025-07-21T22:05:59+02:00
simplify amplitude calculation
- - - - -
bbbc568a by Daniel Mackner at 2025-07-21T22:05:59+02:00
analytical integral hypsec
- - - - -
a797168c by Martin Uecker at 2025-07-23T15:50:09+02:00
harmonize some more types
- - - - -
3db131fe by Daniel Mackner at 2025-07-23T16:00:16+02:00
no lapack
- - - - -
ad226ea3 by Daniel Mackner at 2025-07-24T08:40:47+02:00
rename seq_events/kernel
- - - - -
cf969478 by Tina Holliber at 2025-07-24T13:12:36+02:00
added md_function for score calculation and gmm nlop
- - - - -
f06ffe2d by Moritz Blumenthal at 2025-07-24T13:12:45+02:00
add pytorch wrapper
- - - - -
2d7cd164 by Moritz Blumenthal at 2025-07-24T13:12:45+02:00
tf add signature
- - - - -
1ebf142f by Tina Holliber at 2025-07-24T13:12:48+02:00
Include gradient as prox
- - - - -
ec5527b9 by Tina Holliber at 2025-07-24T13:12:54+02:00
added documentation on libtorch
- - - - -
c1628cb1 by Tina Holliber at 2025-07-24T13:12:59+02:00
add max of array along flag
- - - - -
a77533dd by Tina Holliber at 2025-07-26T17:58:57+02:00
add sample tool with tests
- - - - -
61af679c by Martin Uecker at 2025-07-26T17:58:57+02:00
whitespace fixes
- - - - -
6af777fe by Daniel Mackner at 2025-07-26T17:58:57+02:00
remove unnecessary VLA
- - - - -
cf909093 by Daniel Mackner at 2025-07-26T17:58:57+02:00
basic sequence config
- - - - -
49d93f03 by Daniel Mackner at 2025-07-26T17:58:57+02:00
sequence: more misc functions
- - - - -
4db6dacf by Daniel Mackner at 2025-07-26T17:58:57+02:00
define SEQ_FLAGS and loop order
- - - - -
7ac502ee by Daniel Mackner at 2025-07-26T17:58:57+02:00
spoke angle calculation
Calculate spoke angles for use in radial sequence.
- - - - -
a3cd6bbc by Daniel Mackner at 2025-07-26T17:58:57+02:00
define rf_shape
- - - - -
c8fc93ee by Daniel Mackner at 2025-07-26T17:58:57+02:00
prepare RF pulses and adc for sequence
more generic pulse: do not normalize pulse directly | calc of nominal FA from integral | calc of effective normalized sum
- - - - -
bea08a1e by Daniel Mackner at 2025-07-26T17:58:57+02:00
FLASH kernel
- - - - -
a2e2df19 by Daniel Mackner at 2025-07-26T17:58:57+02:00
prepare rf event for inversion pulse
- - - - -
26a4c09d by Daniel Mackner at 2025-07-26T17:58:57+02:00
end of block for specific mode
move block_end and compute gradients to src/seq
- - - - -
a9b8d7f5 by Daniel Mackner at 2025-07-26T17:58:57+02:00
define sequence interface in src/seq.h
seq_block/continue | sample pulse | calc gradient
include magnetic preparation (inversion pulse)
- - - - -
2ae52f3d by Daniel Mackner at 2025-07-26T17:58:57+02:00
seq tool and test
- - - - -
d2834a3f by Daniel Mackner at 2025-07-26T17:58:57+02:00
seq raga tests
- - - - -
c8681cfc by Daniel Mackner at 2025-07-26T17:58:57+02:00
seq_event: hide some functions
- - - - -
1803e44f by Martin Uecker at 2025-07-26T17:58:57+02:00
whitespace & style
- - - - -
8eb5af1e by Martin Uecker at 2025-07-26T17:58:57+02:00
remove some options, more style changes
- - - - -
0081192f by Blumenthal, Moritz at 2025-07-26T17:58:57+02:00
option to specify number of echos in twixread
- - - - -
e8a9875c by Martin Uecker at 2025-07-26T17:58:57+02:00
don't use reference on riscv
- - - - -
b97560a9 by Martin Uecker at 2025-07-26T17:58:57+02:00
rename pemodes
- - - - -
f142e8c1 by Martin Uecker at 2025-07-26T17:58:57+02:00
pytorch buildable without cuda + test
- - - - -
a57320b4 by Martin Uecker at 2025-07-26T17:58:57+02:00
pytorch buildable without cuda + test
- - - - -
a8608dcc by Tina Holliber at 2025-07-26T17:58:57+02:00
improve flags in sample tool
- - - - -
a42e570e by Martin Uecker at 2025-07-26T17:58:57+02:00
move more tests to slow
- - - - -
bfd9c056 by Martin Heide at 2025-07-28T10:25:53+02:00
default grid tool discretization match phantom tool for x-space
- - - - -
6f2c7ee6 by Martin Heide at 2025-07-28T11:06:56+02:00
check compatibility of grid tool with traj and phantom tools
- - - - -
394bc962 by Philip Schaten at 2025-07-29T00:51:48+02:00
replace environment variable for binary output streams with a bart flag
- - - - -
10d2df32 by Philip Schaten at 2025-07-29T11:01:33+02:00
send debug output to stderr
- debug_printf usage prevents streaming output in some cases (e.g. twixread)
- tools like estdelay already use bart_printf for communicating results
- Thus if output is to be used (and thus should go to stdout instd of stderr)
bart_printf is probably the better function.
- If output is just debug information, it can go to stderr.
- - - - -
db33e707 by Philip Schaten at 2025-07-29T11:01:45+02:00
stream_load_fd
- used for live view with changing scans
- step towards combining multiple cmdlines
- - - - -
31279d11 by Philip Schaten at 2025-07-29T11:01:45+02:00
rtreco.sh: reshape incoming ksp
- - - - -
d9fce2a6 by Philip Schaten at 2025-07-29T11:01:45+02:00
make stream name mangling a static function
- - - - -
e3b7895a by Philip Schaten at 2025-07-29T11:01:45+02:00
Do create fifos from BART
- Previously, fifos were created manually with mkfifo
- Now, fifos are created either by reading or writing BART tool,
if not yet existing.
- I.e. there is a 'race' for creating a fifo, but controlled:
- File system (through open/mkfifo/stat) is used for synchronization
related commit: 22b5876da7d226a4e939dd3edc281c48d7c1da00
- - - - -
39e66453 by Philip Schaten at 2025-07-29T11:01:45+02:00
Revert "write hdr file to track pipeline cmds"
This reverts commit cd07ccc096ee150d6bd43c456ff4f35d8b226554.
- - - - -
b2a553c3 by Philip at 2025-07-29T11:01:45+02:00
free stdin cmdline on exit
- - - - -
e2c150bf by Philip Schaten at 2025-07-29T11:01:45+02:00
split save_command_line in serialize & save; remove analyzer fixme.
- serialize_command_line is later needed for storing the BART tool
graph.
- As of 2025-07-28, analyzer does not to complain anymore.
- - - - -
123afe8f by Philip Schaten at 2025-07-29T11:01:45+02:00
move BART_MAX_DIR_PATH_SIZE to io.h
- - - - -
6fde35da by Philip Schaten at 2025-07-29T11:01:45+02:00
BART_TOOL_GRAPH: Record bart runs to build a graph
- - - - -
aa25333f by Philip at 2025-07-29T11:01:45+02:00
new script: create_toolgraph.py
Reads in files from BART_TOOL_GRAPH directory and creates
a graph representation or script to produce the input
- - - - -
17c9ad10 by Philip Schaten at 2025-07-29T11:01:45+02:00
fix use-after-free in stream_del / stream_stop_log
- - - - -
2b9b44a8 by Philip Schaten at 2025-07-29T11:01:45+02:00
fix memory leak in tee
- - - - -
95c8b0c8 by Philip Schaten at 2025-07-29T11:01:45+02:00
fix streams: Resize shared cfl data file before creating stream.
Fixes inter-process race condition in BART streams, whether
- truncate in the writing process happens before
- mmap in the reading process.
- - - - -
f49777b9 by Philip at 2025-07-29T11:01:45+02:00
tee option to read file instead of stdin
- - - - -
76c41776 by Philip Schaten at 2025-07-29T11:01:45+02:00
rtreco.sh: improved tmpdirs
- more meaningful names
- also remove the my-tmpdir error handling case
- - - - -
3ab54988 by Philip at 2025-07-29T11:01:45+02:00
rtreco.sh: simplify using new tee -i option
- - - - -
71fdad6e by Philip Schaten at 2025-07-29T11:01:45+02:00
rtreco.sh: script works with stdin
Problem: Commands launched to background have /dev/null as stdin.
Thus, added 'main' function to rtreco.sh script and do foreground 'cat'
at end of rtreco.sh to enable reading from stdin
- - - - -
517208fc by Blumenthal, Moritz at 2025-07-31T10:03:22+02:00
sample: remove tmp4 in exp
- - - - -
6a8255c9 by Blumenthal, Moritz at 2025-07-31T10:05:10+02:00
sample: rename tmp4 to AHy
- - - - -
5fa1f09f by Blumenthal, Moritz at 2025-07-31T10:08:03+02:00
sample: remove unused buffers
- - - - -
970146e1 by Blumenthal, Moritz at 2025-07-31T10:12:33+02:00
sample: only create linop_zero once
- - - - -
48d45cf3 by Blumenthal, Moritz at 2025-07-31T10:15:48+02:00
sample: declare nlop_fixed/score_op_p in loop
- - - - -
13abaddf by Blumenthal, Moritz at 2025-07-31T10:18:21+02:00
sample: move declaration/computation of stepsize to corrector step
- - - - -
4bd3b1f3 by Daniel Mackner at 2025-07-31T13:35:01+02:00
seq/events: te as double
- - - - -
98984e82 by Daniel Mackner at 2025-07-31T13:35:01+02:00
remove useless def
- - - - -
25507abc by Daniel Mackner at 2025-07-31T13:35:01+02:00
fix spoiling utest
- - - - -
fe47c8ba by Daniel Mackner at 2025-07-31T13:35:01+02:00
avoid returning empty gradient events
- - - - -
fc482de7 by Daniel Mackner at 2025-07-31T13:35:01+02:00
config: seq_state with start of block, event counter
- - - - -
0556a1dc by Daniel Mackner at 2025-07-31T13:35:01+02:00
rename kernel functions
- - - - -
3c9ba60a by Daniel Mackner at 2025-07-31T13:35:01+02:00
kernel: linearize events
we do not start every block with time=0 but at end of previous block
- - - - -
b619d45b by Daniel Mackner at 2025-07-31T13:35:01+02:00
linearize events in seq tool
- - - - -
bc70deb4 by Daniel Mackner at 2025-07-31T13:35:01+02:00
move pulse interpretation to seq.[c,h]
- - - - -
6466c927 by Daniel Mackner at 2025-07-31T13:35:01+02:00
move set loop dims to helpers
fix set_loop_dim for SMS
- - - - -
677d66f6 by Martin Uecker at 2025-08-04T09:28:59+02:00
compute size in a nicer way
- - - - -
894d57b5 by Martin Uecker at 2025-08-04T09:28:59+02:00
add two assertions
- - - - -
b522502b by Martin Uecker at 2025-08-04T09:28:59+02:00
whitespace
- - - - -
ee6d6757 by Martin Uecker at 2025-08-04T09:28:59+02:00
minor readability improvement
- - - - -
6df5238b by Martin Uecker at 2025-08-04T09:28:59+02:00
initialize to remove warning
- - - - -
73448ff5 by Martin Uecker at 2025-08-04T09:28:59+02:00
raga compatibility
- - - - -
bd7cdd78 by Martin Uecker at 2025-08-04T10:23:41+02:00
add assertion
- - - - -
71ad5b37 by Daniel Mackner at 2025-08-04T11:10:50+02:00
opts.h: double vector 3, N
- - - - -
af22982c by Daniel Mackner at 2025-08-04T11:10:50+02:00
seq tool opts | minor fix
- - - - -
c490ff52 by Blumenthal, Moritz at 2025-08-06T12:28:12+02:00
fix reproducibility of nlinv-net
- - - - -
d6192970 by Blumenthal, Moritz at 2025-08-06T16:49:32+02:00
fix reference pointer freed to early -> always used cpu path
- - - - -
c6659d2c by Blumenthal, Moritz at 2025-08-06T16:49:32+02:00
re-speed up psf computation
- - - - -
9dbd0d1e by Blumenthal, Moritz at 2025-08-06T16:49:32+02:00
add phase normalization to ecalib
- - - - -
e5cf992d by Blumenthal, Moritz at 2025-08-06T16:49:32+02:00
use fixed ac region when phase normalization is requested
- - - - -
b99cfa69 by Blumenthal, Moritz at 2025-08-06T16:49:32+02:00
md_morph operations and labeling
- - - - -
8bae021c by Blumenthal, Moritz at 2025-08-06T17:05:53+02:00
Add tool to detect and sample phase poles
- - - - -
0a433da9 by Blumenthal, Moritz at 2025-08-06T17:07:04+02:00
add phase pole detection to nlinv/ncalib
- - - - -
a35042c0 by Blumenthal, Moritz at 2025-08-06T17:07:32+02:00
phase pole in rtreco script
- - - - -
62615e4f by Daniel Mackner at 2025-08-11T16:33:15+02:00
output of seq-tool adc consistent with traj
- - - - -
aefb1791 by Daniel Mackner at 2025-08-11T16:33:40+02:00
seq-tool: set moment to zero if small
relevant for z-momentum
- - - - -
319d3d63 by Daniel Mackner at 2025-08-11T16:33:40+02:00
seqtool: swap X and Y in adc to be consistent with traj
- - - - -
687b370c by Daniel Mackner at 2025-08-11T16:33:40+02:00
seq-tool: consistent dimensions for gradients/moments
- - - - -
fc7f6f4c by Martin Uecker at 2025-08-18T11:04:08+02:00
undo the rounding
- - - - -
9494477f by Martin Uecker at 2025-08-18T11:39:58+02:00
properly fix inconsistency
- - - - -
9c0418d2 by Martin Uecker at 2025-08-18T11:40:07+02:00
style
- - - - -
aedfa3c9 by Martin Uecker at 2025-08-18T12:00:31+02:00
fix space after while
- - - - -
2bad5822 by Blumenthal, Moritz at 2025-08-18T12:53:22+02:00
use morph functions from num
- - - - -
59eadceb by Daniel Mackner at 2025-08-20T12:02:58+02:00
fix nco frequency in offcenter case
- - - - -
a22ed6b4 by Daniel Mackner at 2025-08-20T12:02:58+02:00
option for spoiling off
- - - - -
2bcf1950 by Daniel Mackner at 2025-08-20T12:57:55+02:00
correct output of phase of adc
- - - - -
904c4cad by Daniel Mackner at 2025-08-20T14:38:56+02:00
move adc to nco shift to idea interpretation
- - - - -
09228f96 by Daniel Mackner at 2025-08-20T14:43:10+02:00
event: add a wait event
- - - - -
c2dc2dd4 by Daniel Mackner at 2025-08-20T14:43:10+02:00
magnetic preparation module
- - - - -
f34a3763 by Daniel Mackner at 2025-08-20T14:43:10+02:00
sample_rf_shapes: use 1us dwell | set fa_prep for inversion
adapt utests to 1us
- - - - -
995d362a by Daniel Mackner at 2025-08-20T14:43:10+02:00
prepare inversion pulse in seq_block
- - - - -
20d6077a by Moritz Blumenthal at 2025-08-26T10:20:16+02:00
add documentation for inversion recovery
- - - - -
71e9a588 by Moritz Blumenthal at 2025-08-27T08:43:08+02:00
fix maybe unitialized warning
- - - - -
7dd53c3c by Moritz Blumenthal at 2025-08-27T08:43:26+02:00
fix maybe unitialized warning
- - - - -
b443d2ae by Blumenthal, Moritz at 2025-09-01T09:46:43+02:00
fix unused warning
- - - - -
1d7a46b3 by Blumenthal, Moritz at 2025-09-01T12:00:57+02:00
only throw error if MPI is used not when compiled with
- - - - -
1b472f2d by Daniel Mackner at 2025-09-01T14:36:13+02:00
fix sms pulse in pulse tool
- - - - -
77cac478 by Daniel Mackner at 2025-09-01T14:36:13+02:00
seq-tool: print debug information for every block
- - - - -
aa1efa38 by Daniel Mackner at 2025-09-01T14:36:13+02:00
seq tool: default behaviour for RAGA
- - - - -
8fe3d024 by Daniel Mackner at 2025-09-01T19:01:20+02:00
initial delay of measurement
to avoid starting an IR experiment from non equilibrium state
- - - - -
4772e0da by Daniel Mackner at 2025-09-01T19:02:20+02:00
pulseq init
- - - - -
3a836536 by Daniel Mackner at 2025-09-01T19:02:20+02:00
vec init
- - - - -
2ed7adff by Daniel Mackner at 2025-09-01T19:02:20+02:00
pulseq free
- - - - -
f9e8c90b by Philip Schaten at 2025-09-01T19:02:20+02:00
fix memory error in VEC_ADD
- - - - -
acb6858a by Daniel Mackner at 2025-09-01T19:02:20+02:00
pulseq make shapes
pulseq test: make shapes
- - - - -
8587421a by Daniel Mackner at 2025-09-01T19:02:20+02:00
refactor compression
- - - - -
4c730a72 by Daniel Mackner at 2025-09-01T19:02:20+02:00
pulseq: pulse shapes to pulseq
- - - - -
25eec9f1 by Daniel Mackner at 2025-09-01T19:02:20+02:00
pulseq: events to pulseq
- - - - -
94126e26 by Daniel Mackner at 2025-09-01T19:02:20+02:00
pulseq: write to file
- - - - -
5082206b by Daniel Mackner at 2025-09-01T19:02:20+02:00
integrate pulseq in seq tool
- - - - -
dc44f4df by Daniel Mackner at 2025-09-01T19:27:19+02:00
avoid error in empty block
- - - - -
9a730353 by Daniel Mackner at 2025-09-02T11:25:55+02:00
write FOV in pulseq header
- - - - -
f2c38260 by Martin Uecker at 2025-09-03T10:58:18+02:00
moving flash timing into a function / structure
- - - - -
b3874ce7 by Blumenthal, Moritz at 2025-09-03T13:13:19+02:00
fixup mpi_allreduce_sumD_gpu
- - - - -
cdc64f4f by Blumenthal, Moritz at 2025-09-03T13:13:19+02:00
extra target for mpi tests
- - - - -
cc5d01c1 by Moritz Blumenthal at 2025-09-03T13:13:19+02:00
whitespace
- - - - -
563741b3 by Blumenthal, Moritz at 2025-09-03T13:13:58+02:00
inplace for select strides
- - - - -
62a0920e by Blumenthal, Moritz at 2025-09-03T13:14:25+02:00
rename _STRINGIFY makro as it is defined in mpi_portable_platform.h
- - - - -
d911ee95 by Christian Bardey at 2025-09-05T13:06:17+02:00
add test and Readme entry for RockyLinux 10
Closes #362
- - - - -
2a4353d2 by Blumenthal, Moritz at 2025-09-08T17:38:56+02:00
allow NULL as reference for CPU
- - - - -
8a9c538b by Blumenthal, Moritz at 2025-09-08T17:39:21+02:00
vptr: remove mpiflags
- - - - -
49260924 by Blumenthal, Moritz at 2025-09-08T17:39:21+02:00
vptr: encapsulate dims in extra struct
- - - - -
16cdd54e by Blumenthal, Moritz at 2025-09-08T17:39:21+02:00
vptr: encapuslate memory blocks in dedicated struct
- - - - -
759b854b by Daniel Mackner at 2025-09-08T22:22:22+02:00
seq-tool: RAGA ordering
- - - - -
26022075 by Daniel Mackner at 2025-09-08T22:22:22+02:00
assert init of rand
- - - - -
523c6d48 by Blumenthal, Moritz at 2025-09-10T18:47:15+02:00
fixup test grid.mk $(TESTS_OUT)/grid_t never made
- - - - -
f96c62bd by Blumenthal, Moritz at 2025-09-10T18:47:15+02:00
fixup stl.mk $(TESTS_OUT)/tetrahedron_cfl never made
- - - - -
c88ed1ea by Moritz Blumenthal at 2025-09-10T18:47:15+02:00
gridding/rolloff correct center for odd dimensions
- - - - -
b28cd941 by Blumenthal, Moritz at 2025-09-10T18:47:15+02:00
add tests for odd dimensions
- - - - -
db7544a3 by Blumenthal, Moritz at 2025-09-10T18:47:15+02:00
nufft with odd dimensions
- - - - -
ee55668f by Blumenthal, Moritz at 2025-09-10T18:47:15+02:00
decomposed computation of psf now works for odd dimensions
- - - - -
854abc1d by Blumenthal, Moritz at 2025-09-10T18:47:15+02:00
update pics lowmem tests
- - - - -
5523cb62 by Martin Uecker at 2025-09-11T07:24:37+02:00
remove some of my author notes and style
- - - - -
09aa877a by Martin Uecker at 2025-09-11T07:24:37+02:00
do not use single letter variables in example
- - - - -
e78f65a2 by Martin Uecker at 2025-09-11T07:24:38+02:00
document coding style a bit more
- - - - -
7f7ac8dc by Martin Uecker at 2025-09-11T07:24:38+02:00
remove semicolon from DEF_TYPEID
- - - - -
9cf76219 by Martin Uecker at 2025-09-11T07:24:38+02:00
improve help a bit
- - - - -
d2896b04 by Martin Uecker at 2025-09-11T14:08:53+02:00
fix format
- - - - -
3d6f19ae by Tina Holliber at 2025-09-12T11:24:01+02:00
add score functions and network as denoiser in sample tool
- - - - -
af984735 by Martin Heide at 2025-09-12T15:15:31+02:00
coil sensivity map simulation
- - - - -
4246d5ee by Martin Heide at 2025-09-12T15:15:31+02:00
coils tests
- - - - -
68ec3806 by Philip Schaten at 2025-09-12T15:15:31+02:00
ensure 64bit unsigned long
- - - - -
5cdd7ed0 by Martin Heide at 2025-09-12T15:15:31+02:00
remove pha_opts
- - - - -
6df5a4b4 by Nick Scholand at 2025-09-12T18:54:50+02:00
noise.c: Add uniform noise option
- - - - -
7b07441b by Blumenthal, Moritz at 2025-09-12T18:54:50+02:00
looping in poisson
- - - - -
969428db by Blumenthal, Moritz at 2025-09-12T18:54:50+02:00
assert init of rand in tools
- - - - -
f2478de6 by Blumenthal, Moritz at 2025-09-12T18:54:50+02:00
simplify and unify reconet mri model
- - - - -
68d35091 by Blumenthal, Moritz at 2025-09-12T18:54:50+02:00
Add option to chain nuFFT/FFT to reconet training operator
- - - - -
8f86fa68 by Blumenthal, Moritz at 2025-09-12T18:54:50+02:00
reconet: option to not precompute adjoint/psf
- - - - -
e46df68b by Blumenthal, Moritz at 2025-09-12T18:54:50+02:00
use nufftconf struct in reconet
- - - - -
4d1b104e by Blumenthal, Moritz at 2025-09-12T18:54:50+02:00
rework test of reconet
- - - - -
fcb66073 by Blumenthal, Moritz at 2025-09-12T18:54:50+02:00
unsigned in cudnn
- - - - -
fa7efed9 by Blumenthal, Moritz at 2025-09-15T14:51:55+02:00
save one copy in compute_psf2_decomposed
- - - - -
ebc8d5e3 by Blumenthal, Moritz at 2025-09-15T15:39:24+02:00
cudnn option to use tensorcores
- - - - -
0b7ace8b by Moritz Blumenthal at 2025-09-15T15:39:24+02:00
uniform rand
- - - - -
977ab90e by Moritz Blumenthal at 2025-09-15T15:39:25+02:00
random numbers in sgd like algorithms
- - - - -
d075b49b by Moritz Blumenthal at 2025-09-15T15:39:25+02:00
sort arguments of nn by name
- - - - -
19dc06b7 by Moritz Blumenthal at 2025-09-15T15:39:25+02:00
fix nn_append_transposed_convcorr_layer
- - - - -
60a40fe7 by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
update normalization
- - - - -
9aee8b82 by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
select derivative with boolean array
- - - - -
12f978ff by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
allow more network weights
- - - - -
25171e52 by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
fix nn_optimize_graph_F
- - - - -
d87ef558 by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
speed up relu inference
- - - - -
bc0d5b4d by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
linop scale with one is identity
- - - - -
c4938272 by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
linop sum summing nothing is identity
- - - - -
50c22757 by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
create nlop from ops
- - - - -
f1236c2d by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
update zaxpbz
- - - - -
beb418d1 by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
md_compare on gpu
- - - - -
046e14a1 by Blumenthal, Moritz at 2025-09-15T15:39:25+02:00
use md_compare in checkpointing
- - - - -
d3c3b9ad by Blumenthal, Moritz at 2025-09-19T16:15:30+02:00
option to use ball as structuring element in morphop
- - - - -
53468d1b by Martin Uecker at 2025-09-19T21:18:04+02:00
whitespace
- - - - -
95e03c11 by Martin Uecker at 2025-09-19T21:41:31+02:00
turn off exec stack warning
- - - - -
77908fcc by Philip Schaten at 2025-09-22T15:59:02+02:00
nlmeans improvements
- - - - -
7f77c69c by Philip Schaten at 2025-09-22T15:59:02+02:00
Increase number of threads for nlmeans in rtreco.sh-script.
- - - - -
ab5b4901 by Daniel Mackner at 2025-09-25T16:24:56+02:00
remove GNU_SOURCE
compatibility when linking to older libraries
- - - - -
6364b928 by Daniel Mackner at 2025-09-25T23:31:45+02:00
pulseq: uint64_t to unsigned long
fixes wasm tests
- - - - -
bb6dba2f by Daniel Mackner at 2025-09-25T23:31:45+02:00
split up flash / seq tests
- - - - -
bbd50b3a by Daniel Mackner at 2025-09-25T23:31:45+02:00
add B0 to config
- - - - -
ea2be757 by Daniel Mackner at 2025-09-25T23:31:45+02:00
fix trajectory scaling from seq tool
- - - - -
0805017b by Daniel Mackner at 2025-09-25T23:31:45+02:00
seq tool: default behaiour raga aligned
- - - - -
44057aae by Martin Uecker at 2025-09-28T11:24:49+02:00
relax fmac2_gemv test
- - - - -
bf25f9ed by Martin Uecker at 2025-09-28T11:25:54+02:00
fix building on MacOS
- - - - -
2d15c6b8 by Martin Uecker at 2025-09-30T13:32:19+02:00
relax fmac2_gemv test
- - - - -
0eb5a8ff by Martin Uecker at 2025-09-30T13:32:20+02:00
properly test for no-warn-execstack
- - - - -
fc05765e by Blumenthal, Moritz at 2025-09-30T18:05:49+02:00
inlcude missing header
- - - - -
9899ac1c by Martin Uecker at 2025-10-01T09:29:33+02:00
wasm build
- - - - -
2cd08f90 by Daniel Mackner at 2025-10-01T10:01:42+02:00
read twix data chronologically
- - - - -
73b6ab4e by Martin Uecker at 2025-10-03T09:32:46+02:00
white space fixes
- - - - -
7de2ee48 by Blumenthal, Moritz at 2025-10-07T08:33:41+02:00
fix offset in phase pole
- - - - -
e6ccccc9 by Daniel Mackner at 2025-10-07T09:45:41+02:00
RAGA-tool: use correct dimension for spokes
- - - - -
0e25e80c by Daniel Mackner at 2025-10-07T09:45:41+02:00
RAGA: extend to multislice/partitions
- - - - -
bdad0cdc by Daniel Mackner at 2025-10-07T09:45:41+02:00
bin: multidimensional reordering
- - - - -
b181be4b by Daniel Mackner at 2025-10-07T09:45:41+02:00
twixread: radial mode multislice/3d
- - - - -
949a9a7c by Daniel Mackner at 2025-10-07T09:45:41+02:00
extend raga to multi-inversion/mutli-shift
- - - - -
2d28614b by Daniel Mackner at 2025-10-07T13:50:46+02:00
arbitrary pulse
added library for oc pulse
- - - - -
b5ae26b6 by Daniel Mackner at 2025-10-07T13:50:46+02:00
gauss pulse
- - - - -
4ce12a3d by Daniel Mackner at 2025-10-07T18:12:51+02:00
add M_PI to angle_e
flips readout direction for every second echo
legacy mode for MEMS
- - - - -
0ec87c81 by Martin Uecker at 2025-10-10T17:04:13+02:00
generalize gaussians
- - - - -
160639e2 by Martin Uecker at 2025-10-10T17:04:13+02:00
compute multiplicative factor for product of Gaussians
- - - - -
c37de748 by Martin Uecker at 2025-10-11T12:07:32+02:00
matrix determinant
- - - - -
c9573504 by Martin Uecker at 2025-10-11T15:10:25+02:00
fix indentation issues
- - - - -
d47a6d8b by Martin Uecker at 2025-10-11T15:10:28+02:00
indentation and split up tests
- - - - -
87d24c49 by Martin Uecker at 2025-10-11T20:16:34+02:00
add mix multiply and tests
- - - - -
d5bf5ce5 by Martin Uecker at 2025-10-11T20:16:34+02:00
don't print unit test as it is redundant
- - - - -
7d3a73b5 by Martin Uecker at 2025-10-11T20:16:34+02:00
histogram tool
- - - - -
c5820740 by Martin Uecker at 2025-10-11T20:16:34+02:00
revise grid tool style and terminology
- - - - -
b85610c4 by Martin Uecker at 2025-10-11T20:16:34+02:00
make it possible again to add new targets in local makefile
- - - - -
88b5a1af by Martin Uecker at 2025-10-11T20:16:34+02:00
add a Gaussian mixture model tool
- - - - -
564f33a8 by Martin Uecker at 2025-10-11T20:16:34+02:00
add sampling test
- - - - -
41d99a63 by Blumenthal, Moritz at 2025-10-12T09:29:20+02:00
fixup nufft upper triag with lowmem toeplitz
- - - - -
fdcf1dbe by Blumenthal, Moritz at 2025-10-12T10:59:18+02:00
fixup vptr_md_fmac_upper_triag2 looping
- - - - -
8501eeb4 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
espirit mode for phase pole
- - - - -
2975ac71 by Moritz Blumenthal at 2025-10-12T13:27:02+02:00
print timing in calone
- - - - -
627ba52a by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
num init in utest to use FFT with threads
- - - - -
68f1323c by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
add linop computing casorati matrix
- - - - -
7a6fbac7 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
[Check reproducibility] Use FFT based computation of casorati matirx in ecalib
- - - - -
83b9993b by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
correct bounds for lapack_econ_svd
- - - - -
874a13a1 by Moritz Blumenthal at 2025-10-12T13:27:02+02:00
lapack econ svd without singular vectors
- - - - -
f1a70759 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
economic ecalib for 3d coils
- - - - -
3ee4f0cf by Moritz Blumenthal at 2025-10-12T13:27:02+02:00
fix link derivative for one input or output
- - - - -
98866cd9 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
update gpu pointwise eigen decomposition
- - - - -
bf4f3d03 by Moritz Blumenthal at 2025-10-12T13:27:02+02:00
timing in bart call
- - - - -
0f79b37f by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
add macros for printing error and tolerance in unit tests
- - - - -
f873396b by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
randomized linear algebra
- - - - -
28768e7e by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
use Nyström approximation in ecalib
- - - - -
f91bfce2 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
calibcu: whitespace
- - - - -
ab15ce8b by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
use shared memory from eigenmapscu_kern as temp buffer for dot
- - - - -
14fc36ce by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
make block size a multiple of two for better coalescend memory access
- - - - -
f89dd5db by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
transpose matrix layout for better coalescend memory access
- - - - -
3e058a4b by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
calibcu directly read upperdiagonal of matrix
- - - - -
802a5f1f by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
do contiguoud copy between cpu and gpu
- - - - -
8a7c63e0 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
precompute fftmod for large batch case
- - - - -
cbb6bc07 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
use debug_printf
- - - - -
e8b4acfe by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
eigenmaps cu independent of blocksize
- - - - -
b24d2eda by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
calibcu: respect rules of __syncthreads()
- - - - -
bfa2b253 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
calibcu: beter use cahed matrix entries
- - - - -
7fe29661 by Blumenthal, Moritz at 2025-10-12T13:27:02+02:00
calibcu: better rules for threadblock selction
- - - - -
0e41db8d by Martin Uecker at 2025-10-13T14:06:03+02:00
whitespace fixes
- - - - -
90d5b31e by Martin Uecker at 2025-10-13T14:06:03+02:00
fix raga single test
- - - - -
5791ddb7 by Moritz Blumenthal at 2025-10-14T13:21:16+02:00
Add md_calc_strides_selected
- - - - -
99b9d1c2 by Moritz Blumenthal at 2025-10-14T13:21:46+02:00
add md_overlap
- - - - -
7fc4eadb by Blumenthal, Moritz at 2025-10-14T13:22:24+02:00
reravel index
- - - - -
cfc942da by Daniel Mackner at 2025-10-14T13:26:17+02:00
print commandline to seq file
- - - - -
beb7d5e2 by Daniel Mackner at 2025-10-14T13:26:17+02:00
style & whitespaces
- - - - -
bff5fb66 by Daniel Mackner at 2025-10-14T13:26:17+02:00
pulseq: re-use existing shapes
- - - - -
d5547ba8 by Daniel Mackner at 2025-10-14T13:26:17+02:00
pulseq: reduce precision for phase shape of rf pulses
- - - - -
93e27626 by Daniel Mackner at 2025-10-14T15:20:00+02:00
fix compression
in case of only two identical values at the end
- - - - -
e0e76786 by Daniel Mackner at 2025-10-14T15:20:00+02:00
fix pulseq interpretation
- - - - -
db5e2266 by Daniel Mackner at 2025-10-14T15:20:00+02:00
pulseq extension for labelset
- - - - -
84d6f5c9 by Daniel Mackner at 2025-10-14T15:20:00+02:00
pulseq multiecho support
- - - - -
7ff8d242 by Daniel Mackner at 2025-10-14T15:20:00+02:00
raga indices from seq tool
- - - - -
31767761 by Daniel Mackner at 2025-10-14T18:28:36+02:00
fix pulse scaling
- - - - -
eded5adf by Daniel Mackner at 2025-10-15T09:42:17+02:00
smaller set_loop_dims function
- - - - -
fc7dc70b by Daniel Mackner at 2025-10-20T13:40:31+02:00
more trajectories: TURN / MEMS
- - - - -
20115281 by Daniel Mackner at 2025-10-20T13:40:35+02:00
seq-tool supporting non-trivial PHS2 DIM
- - - - -
9a2f9dee by Daniel Mackner at 2025-10-20T13:40:35+02:00
define chronologic slice for interleaved SMS
- - - - -
22b7f4e0 by Daniel Mackner at 2025-10-20T13:42:35+02:00
check sequence config
- - - - -
b67811c6 by Daniel Mackner at 2025-10-20T13:42:37+02:00
set fov pos for SMS
slice distance factor in seq tool
- - - - -
bef4c312 by Daniel Mackner at 2025-10-20T13:42:37+02:00
inversion delay time
- - - - -
370acf52 by Daniel Mackner at 2025-10-20T13:42:37+02:00
remove check RAGA total spokes > full frame
fix seq tool for non-full frame
- - - - -
72b4e79c by Martin Uecker at 2025-10-24T20:47:38+02:00
does not need to be info
- - - - -
3a928c1d by Martin Uecker at 2025-10-24T20:47:38+02:00
typo + white space
- - - - -
b1e3f86f by Martin Uecker at 2025-10-25T09:46:52+02:00
better file name for stl tests
- - - - -
219003a1 by Martin Uecker at 2025-10-25T09:46:52+02:00
workaround for stream / nfs issue
- - - - -
f43dbf41 by Philip at 2025-10-26T14:06:32+01:00
cortraj fix
1) BART trajectories have scale FOV size (No. of pixels):
Thus, scale dk before adding to traj.
2) Add test with oversampled (scaled) trajectory.
- - - - -
7a8acf1a by Philip at 2025-10-26T14:10:51+01:00
cortraj minor fixes
- - - - -
a98249b5 by Philip at 2025-10-26T14:11:26+01:00
tighten test tolerance for cortraj
- - - - -
b12a29ff by Blumenthal, Moritz at 2025-10-31T16:02:40+01:00
allow chains with NULL as argument
- - - - -
f40e577a by Moritz Blumenthal at 2025-10-31T16:03:08+01:00
clear with correct dimensions
- - - - -
1ee6083e by Martin Uecker at 2025-11-02T09:13:31+01:00
style
- - - - -
c50737f5 by Martin Uecker at 2025-11-03T11:00:54+01:00
white space
- - - - -
0b5fefe9 by Daniel Mackner at 2025-11-06T07:52:26+01:00
move cumsum to flpmath and remove finite_diff.[c,h]
- - - - -
9976af7e by Daniel Mackner at 2025-11-06T07:52:26+01:00
cumulative sum in filter-tool
- - - - -
e9dd4a0e by Philip Schaten at 2025-11-13T13:02:36+01:00
Streams: Fail if datafile does not exist
The process reading the stream should expect
that the (shared memory) datafile exists already,
because it has been created by the sending process.
- - - - -
978806a2 by Philip at 2025-11-13T13:02:36+01:00
Streams: replace assert by error
- if a given path is not valid, this is not an
program logic error but runtime problem
- - - - -
2fe7500a by Philip at 2025-11-13T13:02:36+01:00
rtreco.sh: improved gradient delay corr. + custom options
- use trajcor to update the existing trajectory with new gradient delays
- increase padding in estdelay default option
- add option `-d` to disable gradient delay correction
- customizable estdelay-options through ESTDELAY_OPTS
- customizable nlinv-options through NLINV_OPTS
- fix bug where rtreco.sh wouldn't work when using median filter
without timelog option
- - - - -
07481de2 by Martin Uecker at 2025-11-15T14:23:05+01:00
copyright and options for nuFFT
- - - - -
7dbe254c by Martin Uecker at 2025-11-17T15:44:38+01:00
last option for IST
- - - - -
028bc546 by Marten Veldmann at 2025-11-17T19:47:52+01:00
print and save both stdout and stderr in real time
- - - - -
066550ad by Martin Uecker at 2025-11-17T19:49:46+01:00
twixread
- - - - -
25189b0f by Blumenthal, Moritz at 2025-11-18T16:08:34+01:00
check compatible dims in compression
- - - - -
008593e4 by Blumenthal, Moritz at 2025-11-18T16:10:10+01:00
fix trajcor for 2d delays
- - - - -
660d8a85 by Blumenthal, Moritz at 2025-11-19T19:38:12+01:00
fixup compression with strides
- - - - -
a7c17325 by Blumenthal, Moritz at 2025-11-20T13:32:21+01:00
kspace precond without pattern
- - - - -
fa581a9d by Moritz Blumenthal at 2025-11-20T14:57:15+01:00
update nlops
- - - - -
86284cdc by Moritz Blumenthal at 2025-11-20T14:57:15+01:00
simple nlops
- - - - -
7c953707 by Tobias Knoll at 2025-11-20T14:57:15+01:00
lorentzian added to mobafit
- - - - -
b69539d0 by Blumenthal, Moritz at 2025-11-20T14:57:15+01:00
add cuda_sadd to gpu iter ops
- - - - -
a1363002 by Blumenthal, Moritz at 2025-11-20T14:57:15+01:00
independent lambda for conjgrad batched
- - - - -
c13bba4e by Blumenthal, Moritz at 2025-11-20T14:57:15+01:00
add batched levenberg marquardt
- - - - -
62489f38 by Blumenthal, Moritz at 2025-11-20T14:57:15+01:00
add lm in mobafit
- - - - -
e5a8ebe2 by Markus Huemer at 2025-11-20T14:57:15+01:00
add test for levenberg-marquardt
- - - - -
7ad61abe by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
fix warnings in cudnn
- - - - -
ccad30de by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
specify percentile for estscaling
- - - - -
f93e17b8 by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
add cudnn library path to runtime search path
- - - - -
db2b8acf by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
allow for formats without leading sign
- - - - -
f27e34d3 by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
add equal to thresholding
- - - - -
f55d62f4 by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
fixup warning for same random numbers
- - - - -
813c2039 by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
fixup gpurand to respect offset
- - - - -
d1502d8d by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
unlinking file is not supported in loop
- - - - -
216dd99b by Blumenthal, Moritz at 2025-11-21T11:22:15+01:00
allow for compression with single one in mask
- - - - -
0d5df6f0 by Martin Uecker at 2025-11-23T21:53:56+01:00
transfer fista_last to IST
- - - - -
117c7586 by Martin Uecker at 2025-11-24T07:03:00+01:00
relax one test for Macs
- - - - -
246046ab by Martin Uecker at 2025-11-28T20:12:23+01:00
remove error codes removed by Nvidia
- - - - -
ccd27d98 by Martin Uecker at 2025-11-29T10:18:31+01:00
update reproducible paper links
- - - - -
df864987 by Martin Uecker at 2025-11-29T10:35:51+01:00
more references
- - - - -
47081ae4 by Daniel Mackner at 2025-12-01T16:51:22+01:00
order of adc samples to moment/time/phase
- - - - -
4af3bb57 by Daniel Mackner at 2025-12-01T16:51:22+01:00
seq-tool change output order
- - - - -
2c07f2c7 by Daniel Mackner at 2025-12-01T16:51:22+01:00
raster times in seq sys
- - - - -
38c33fa9 by Daniel Mackner at 2025-12-01T16:51:22+01:00
round up to raster
- - - - -
2838078f by Daniel Mackner at 2025-12-01T16:51:22+01:00
replace ceil with raster_rf
- - - - -
cf9a8107 by Daniel Mackner at 2025-12-01T16:51:22+01:00
remove round_up_GRT
- - - - -
f25e4eed by Daniel Mackner at 2025-12-01T16:51:22+01:00
remove GRAD_RASTER_TIME
- - - - -
9794b49d by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
linspace/logspace in index tool
- - - - -
e5c3721d by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: better naming of dims
- - - - -
ccc0d4bb by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: correct minimum variance for default init
- - - - -
4b518565 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: correctly initialize weights/variance if not provided
- - - - -
5463d4c6 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
fixup weighting (logsum) in gmm
- - - - -
46bd01e3 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: minimum step size when variance is one
- - - - -
0edb64d2 by Tina Holliber at 2025-12-01T17:51:48+01:00
sample: adjust weigthing in sample tool
- - - - -
5918d3e4 by Tina Holliber at 2025-12-01T17:51:48+01:00
add tests for weighting in 2D
- - - - -
057b2202 by tinhol at 2025-12-01T17:51:48+01:00
fix tests: noise scale to be standard deviation in nlop instead of variance
- - - - -
301f89f7 by Tina Holliber at 2025-12-01T17:51:48+01:00
adjust test
- - - - -
1aefbccf by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: update defaults
- - - - -
d27d2b61 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
define score by complex conjugate gradient
- - - - -
be64f759 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
iter dump with array
- - - - -
866938bd by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
select derivatives with boolean array in iter algorithms
- - - - -
beb4dfa1 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
score functions
- - - - -
a227cb34 by Moritz Blumenthal at 2025-12-01T17:51:48+01:00
cunet
- - - - -
97e96a95 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
function to create operator for joined optimized application
- - - - -
7c58c851 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
cached optimized operator graph
- - - - -
f71e9fdd by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample cunet
- - - - -
df852482 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: add sense model
- - - - -
7040051b by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: add FoV mask
- - - - -
acb5f9fc by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: update statistic to print kspace corner
- - - - -
3de9a458 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: add annealed likelihood option
- - - - -
6fa6bc4b by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
preconditioned em
- - - - -
5f6753b6 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
preconditioned em in sample
- - - - -
0658a1f7 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
sample: initialization for exact likelihood
- - - - -
f3f15433 by Blumenthal, Moritz at 2025-12-01T17:51:48+01:00
turn off scaling of limits with real valued flags
- - - - -
07847688 by Tina Holliber at 2025-12-01T17:51:48+01:00
stricter test limits for sample tool
- - - - -
56364c85 by Blumenthal, Moritz at 2025-12-02T16:48:41+01:00
fixup cunet
- - - - -
2a1b5b39 by Blumenthal, Moritz at 2025-12-02T16:49:12+01:00
remove unused flags
- - - - -
5eef74d3 by Blumenthal, Moritz at 2025-12-03T12:08:40+01:00
fixup expectation with complex score
- - - - -
985b27c2 by Moritz Blumenthal at 2025-12-03T13:43:57+01:00
bart lock independent of omp and trylock
- - - - -
566e7b71 by Blumenthal, Moritz at 2025-12-03T16:07:31+01:00
make batched gpu ops fast for stack of images
- - - - -
bc59b52d by Blumenthal, Moritz at 2025-12-03T16:07:31+01:00
use batched conjgrad in pula
- - - - -
a3069b4c by Blumenthal, Moritz at 2025-12-04T19:10:10+01:00
whitespace and some minor changes
- - - - -
01adc115 by Viktoria Buchegger at 2025-12-04T19:10:10+01:00
Add snlop test
- - - - -
06bd83ac by Daniel Mackner at 2025-12-04T22:11:46+01:00
remove ADC NCO correction
- - - - -
3194d6bd by Daniel Mackner at 2025-12-04T22:11:46+01:00
unified event interpretation for NCO
- - - - -
817bf247 by Daniel Mackner at 2025-12-04T22:11:46+01:00
seq tool: debug prints
- - - - -
8fd661b5 by Daniel Mackner at 2025-12-04T22:11:46+01:00
GYRO to SI units
relax mobafit int test
- - - - -
e211e388 by Daniel Mackner at 2025-12-04T22:11:46+01:00
seq in SI units
gamma
timing (fix ro_shifting)
init delay | inv delay | TI
slice thickness/shifts | FOV | SMS distance
RF duration incl. pulse->sar_dur
TE | TR
pulseq: TR and raster in SI
dwell
relax some seq tests
slice/ro amplitude to SI
remove 360deg scalings due to inconsistent units
- - - - -
b63b6008 by Daniel Mackner at 2025-12-05T10:37:53+01:00
option to set raga full frames
- - - - -
2ebc2eb8 by Daniel Mackner at 2025-12-05T10:43:11+01:00
relative FOV shift in seq tool
- - - - -
06ae008e by Blumenthal, Moritz at 2025-12-05T16:13:54+01:00
whitespace
- - - - -
5337ae0d by Blumenthal, Moritz at 2025-12-05T16:13:54+01:00
fixup multi-gpu training
- - - - -
6b93c2d3 by Martin Uecker at 2025-12-06T15:33:38+01:00
whitespace & coding style
- - - - -
54e3fe5b by Martin Uecker at 2025-12-06T16:41:57+01:00
condense, tighten tests
- - - - -
19120d54 by Martin Uecker at 2025-12-06T16:41:57+01:00
more coding style cleanups
- - - - -
f9235373 by Martin Uecker at 2025-12-06T16:41:57+01:00
coding style
- - - - -
b7881716 by Martin Uecker at 2025-12-06T16:41:57+01:00
simplify size computations
- - - - -
cd89a2df by Martin Uecker at 2025-12-06T16:59:05+01:00
coding style
- - - - -
4886f700 by Martin Uecker at 2025-12-06T17:33:46+01:00
wasm fix
- - - - -
79455539 by Martin Uecker at 2025-12-06T17:49:19+01:00
relax one test
- - - - -
28618b75 by Daniel Mackner at 2025-12-06T18:31:23+01:00
mag preparation to SI
- - - - -
1ab74ef4 by Daniel Mackner at 2025-12-06T18:31:23+01:00
pulseq: sample gradient on correct raster
- - - - -
da8cd379 by Viktoria Buchegger at 2025-12-06T18:44:20+01:00
Check for existing rf and gradient shapes and reuse
- - - - -
79f85236 by Daniel Mackner at 2025-12-06T18:44:20+01:00
pulseq: delay of RF ADC in usec
- - - - -
51fd0338 by Daniel Mackner at 2025-12-06T18:44:20+01:00
ADC: prepare with raster
add some utests for different dwell times,
e.g. start not on rf raster
- - - - -
e6ee49e8 by Daniel Mackner at 2025-12-06T18:44:20+01:00
compute adc samples with correct dwell time
additional integration test on this
- - - - -
99f4cbb3 by Blumenthal, Moritz at 2025-12-08T20:01:28+01:00
document some performance considerations
- - - - -
8a97610d by Martin Uecker at 2025-12-09T11:44:50+01:00
whitespace
- - - - -
3317c908 by Daniel Mackner at 2025-12-10T09:14:05+01:00
fix double options
- - - - -
88bade94 by Daniel Mackner at 2025-12-10T17:46:41+01:00
seq FOV-shift: do not consider os for correct frequency
- - - - -
2a2cc970 by Daniel Mackner at 2025-12-15T14:36:24+01:00
use builtin ffs(l) for windows
- - - - -
8df19742 by Daniel Mackner at 2025-12-15T18:13:32+01:00
no support for threads on windows
- - - - -
408a3399 by Daniel Mackner at 2025-12-15T18:13:41+01:00
mmio windows support
- - - - -
504646a3 by Daniel Mackner at 2025-12-15T18:13:41+01:00
streams: Windows support by MSYS2
- - - - -
0df93778 by Daniel Mackner at 2025-12-15T18:13:41+01:00
streams without fifo
- - - - -
1a957da6 by Daniel Mackner at 2025-12-15T18:13:41+01:00
sum/linalg_rand without lapack
- - - - -
42f47259 by Daniel Mackner at 2025-12-15T18:13:41+01:00
avoid <fcntl.h> for windows
- - - - -
30124ab8 by Philip Schaten at 2025-12-15T18:14:25+01:00
Build static/dynamic library for MRI sequence.
- - - - -
db0c8a4f by Daniel Mackner at 2025-12-15T18:14:25+01:00
build test
- - - - -
c8525373 by Daniel Mackner at 2025-12-15T18:14:25+01:00
src/seq/seq and helpers functions in DLL
- - - - -
e0cb4365 by Daniel Mackner at 2025-12-15T18:14:25+01:00
windows dll: Wine unit tests
- - - - -
bb763035 by Martin Uecker at 2025-12-19T11:29:22+01:00
coding style
- - - - -
6806c3da by Martin Uecker at 2025-12-19T21:29:13+01:00
de-uglify switches again
- - - - -
790f9d93 by Martin Uecker at 2025-12-19T21:29:13+01:00
reorder makefile include
- - - - -
5ed5e570 by Martin Uecker at 2025-12-20T12:34:53+01:00
coding style
- - - - -
9029a185 by Blumenthal, Moritz at 2025-12-20T13:03:46+01:00
remove extensive templating from unfold kernels
- - - - -
3a2ed06b by Martin Uecker at 2025-12-20T16:30:48+01:00
make test for empty shape exact
- - - - -
abb66788 by Martin Uecker at 2025-12-21T12:08:56+01:00
Gaussians: add assertions and fix tests
- - - - -
34adc7fc by Martin Uecker at 2025-12-22T12:59:47+01:00
update code link to codeberg
- - - - -
c08e86b5 by Martin Uecker at 2025-12-22T15:45:40+01:00
white space
- - - - -
a78fa332 by Martin Uecker at 2025-12-30T20:09:58+01:00
update homepage links in README
- - - - -
c04258e0 by Christian Bardey at 2026-01-01T16:32:58+01:00
remove more outdated references to github
- - - - -
1149b5e1 by Martin Uecker at 2026-01-10T15:49:34+01:00
placate analyzer
- - - - -
8255a222 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: refactor vptr_block_loop_flags to decouble block size and mpi flags
- - - - -
e0f85a27 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: remove free_first_only
- - - - -
b4818fd7 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: store vptr location in enum
- - - - -
5e279911 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: vptr_block_loop_flags make strides contiguous
- - - - -
948d2487 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: md_nary_resolve respect contiguous strides
- - - - -
0d59a3b3 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: cache mem in mpi_accessible
- - - - -
4d908a01 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
mpi_copy with contigous stides
- - - - -
05ec01b7 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
add mpi reduction tests
- - - - -
f44f1a3a by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
add vptr_fun
- - - - -
d8f66efb by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
simplify mpi reduction by using temp buffer and let only one rank reduce into this buffer
- - - - -
663b324a by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: get hint
- - - - -
38bc78d3 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
wrap cfls in vptr
- - - - -
78b828ac by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr support in loop
- - - - -
63c877b2 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr support for obsolete rand
- - - - -
641a4c16 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
use vptr_fun in fft
- - - - -
6503a104 by Moritz Blumenthal at 2026-01-10T15:49:34+01:00
use vptr_fun in gridding
- - - - -
915e928d by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
use vptr_fun in wavelet
- - - - -
5320e025 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
use vptr_fun in thresholding
- - - - -
bff5879e by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
use vptr_fun in interpolation
- - - - -
e6ef3bde by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
use vptr_fun for rolloff
- - - - -
1a6c81b8 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
use vptr_fun to apply linphases
- - - - -
687edd24 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
use vptr_fun for mask_compress
- - - - -
528c1176 by Moritz Blumenthal at 2026-01-10T15:49:34+01:00
use vptr_fun for compression with binary mask
- - - - -
8bf06edd by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
check for strided vecops after resolving vptrs
- - - - -
91e3e8e1 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
change vptr_location
- - - - -
8d254514 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: retrospectively set dims
- - - - -
b89ee5a5 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: better error
- - - - -
7ab3bf3d by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
mpi sort error
- - - - -
f163e521 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
operator_set_dims_wrapper
- - - - -
2d6f761c by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
vptr: update operator wrapper for vptr
- - - - -
41c6a1ee by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
estimate scaling on vptr
- - - - -
9b49adfe by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
lazy initialization of vptr
- - - - -
79cd1f51 by Blumenthal, Moritz at 2026-01-10T15:49:34+01:00
mpi aware iter ops
- - - - -
9df93cc9 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vops in iter2/4
- - - - -
70a906e9 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr: alloc_same
- - - - -
45aa00f5 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr support in iter_l1
- - - - -
101fdc0b by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
update mpi tests
- - - - -
5f6816a0 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
refactor pics mpi
- - - - -
cc81227b by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
operator link update ref argument for vptr
- - - - -
c9c5795c by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
split adjoint from lsqr in irgnm2
- - - - -
dec9b3b7 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
move maxeigen iter to iter2 preprocessing
- - - - -
52f3e321 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
map dims to vptr dims
- - - - -
c4a575e8 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
map dims to vptr dims: multind
- - - - -
0c5c475f by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
map dims to vptr dims: flpmath
- - - - -
540a918f by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr: join multiple vptr to virtual range
- - - - -
0aa756d9 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr dims map resolve range
- - - - -
54249938 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr: get len
- - - - -
c488ff88 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
range in mpi_ops
- - - - -
bbd6690d by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr for nlinv
- - - - -
2e0ee8a1 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr: improve debugging
- - - - -
6e050983 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr support in nlop_stack with mpi
- - - - -
7a8bcfbf by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr_debug
- - - - -
23a8a9a5 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
vptr remap only to nonflat dims
- - - - -
02327561 by Christian Scharf at 2026-01-10T15:49:35+01:00
Add MPI support to md_zadd2
- - - - -
2168baa8 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
remove vptr support and optimize vecops_strided
- - - - -
220cca90 by Blumenthal, Moritz at 2026-01-10T15:49:35+01:00
md_gpu_move for vptr
- - - - -
2d1e06ff by Martin Uecker at 2026-01-11T16:06:37+01:00
update copyright
- - - - -
ef280e7e by Martin Uecker at 2026-01-11T16:06:37+01:00
license year
- - - - -
e66b458e by Martin Uecker at 2026-01-11T16:06:37+01:00
fix permissions
- - - - -
51eb2530 by Martin Uecker at 2026-01-11T16:06:37+01:00
space
- - - - -
19fb02a7 by Martin Uecker at 2026-01-11T16:06:37+01:00
remove old mat2cfl tool
- - - - -
f559fbfa by Martin Uecker at 2026-01-11T16:19:36+01:00
coding style
- - - - -
2e18e96a by Martin Uecker at 2026-01-11T19:11:10+01:00
style
- - - - -
79c27170 by Martin Uecker at 2026-01-12T11:21:28+01:00
pulseq, add VEC_LEN
- - - - -
f26358ed by Martin Uecker at 2026-01-12T22:37:33+01:00
pulseq
- - - - -
586bdbba by Martin Uecker at 2026-01-12T22:37:33+01:00
add assertion
- - - - -
f4564017 by Martin Uecker at 2026-01-12T22:42:38+01:00
fix gradims overlapping copy
- - - - -
0a1a248e by Martin Uecker at 2026-01-12T22:42:38+01:00
clear up handling of VLA bound
- - - - -
d47f9e25 by Martin Uecker at 2026-01-12T22:42:38+01:00
add assertion to suppress overflow warning
- - - - -
89a962a4 by Martin Uecker at 2026-01-12T22:42:38+01:00
add assertion and fix typo
- - - - -
d0ae7a31 by Martin Uecker at 2026-01-12T22:42:38+01:00
analyzer options
- - - - -
c4659d38 by Markus Huemer at 2026-01-16T09:50:17+01:00
mobifit: add option for regularization against reference with irgn
- - - - -
603ef6fb by Daniel Mackner at 2026-01-16T09:50:17+01:00
rename nco/pulse interpret
- - - - -
fa6f3d62 by Daniel Mackner at 2026-01-16T09:50:17+01:00
flash: min te/tr
- - - - -
471b791d by Daniel Mackner at 2026-01-16T09:50:17+01:00
helper.h: rename get_slices, set fov
ui info for sms
- - - - -
2da767eb by Martin Uecker at 2026-01-17T19:11:51+01:00
add test for preconditioned maruyama
- - - - -
92113682 by Martin Uecker at 2026-01-17T19:36:39+01:00
rename for clarity
- - - - -
bb2c762b by Martin Uecker at 2026-01-17T19:36:39+01:00
readability
- - - - -
79789f77 by Martin Uecker at 2026-01-17T19:36:39+01:00
make vptr code more readable
- - - - -
828fb5ad by Martin Uecker at 2026-01-17T23:15:31+01:00
move sense_nc_init in its own file
- - - - -
2c2115d9 by Martin Uecker at 2026-01-17T23:15:31+01:00
hadamard encoding before scaling
- - - - -
16eabe16 by Martin Uecker at 2026-01-17T23:15:31+01:00
refactor pics
- - - - -
47c54c09 by Martin Uecker at 2026-01-18T11:06:58+01:00
move pics model in its own file
- - - - -
c2c5508b by Martin Uecker at 2026-01-18T12:06:37+01:00
fix typos
- - - - -
ba0be221 by Martin Uecker at 2026-01-18T13:34:40+01:00
simplify tests
- - - - -
be349db8 by Martin Uecker at 2026-01-18T14:21:40+01:00
move fftmod for sensitivities into sense model
- - - - -
0f16cb65 by Martin Uecker at 2026-01-18T14:25:40+01:00
extend coding style document
- - - - -
786c5c43 by Martin Uecker at 2026-01-18T15:25:55+01:00
add complex Gaussian rand
- - - - -
1bf6021b by Martin Uecker at 2026-01-18T15:38:13+01:00
remove unused variable
- - - - -
d12830f0 by Martin Uecker at 2026-01-18T16:37:42+01:00
simplify pics dimensions
- - - - -
5cbe7bd5 by Martin Uecker at 2026-01-18T16:37:42+01:00
whitespace fix
- - - - -
99f7c144 by Martin Uecker at 2026-01-18T16:37:42+01:00
style
- - - - -
c58245f5 by Martin Uecker at 2026-01-18T16:37:42+01:00
remove maps flags from pics config
- - - - -
4703f930 by Martin Uecker at 2026-01-18T16:49:47+01:00
minor cleanups in pics
- - - - -
39db1950 by Martin Uecker at 2026-01-18T19:06:51+01:00
remove unused code
- - - - -
d716df8a by Martin Uecker at 2026-01-18T19:06:57+01:00
remove const from linop_fmac_create
- - - - -
7e1cd162 by Martin Uecker at 2026-01-18T23:52:55+01:00
sampling tool, remove model from main function
- - - - -
b8af81f9 by Martin Uecker at 2026-01-18T23:52:55+01:00
move file management back into main
- - - - -
cb55e9bc by Martin Uecker at 2026-01-18T23:52:55+01:00
move priors in its own file
- - - - -
e12b9820 by Tina Holliber at 2026-01-19T17:44:10+01:00
input of cunet fits bart standard
- - - - -
683baa8b by Martin Uecker at 2026-01-20T07:56:55+01:00
style
- - - - -
3764be0b by Martin Uecker at 2026-01-20T07:57:20+01:00
update acknowledgements
- - - - -
4f4eda8f by Tina Holliber at 2026-01-20T09:58:46+01:00
change cunet training to new input structure
- - - - -
1c4b96a0 by Martin Uecker at 2026-01-20T17:14:23+01:00
rockylinux path
- - - - -
1c4d592e by Martin Uecker at 2026-01-20T17:14:31+01:00
relax for rockylinux:10
- - - - -
2aafe52c by Martin Uecker at 2026-01-20T18:55:42+01:00
build fixes for cuda 13 (needs testing)
- - - - -
ce4fca2e by Martin Uecker at 2026-01-20T18:55:42+01:00
distro test for trixie with cuda 13
- - - - -
6dde8872 by Moritz Blumenthal at 2026-01-20T21:11:11+01:00
improve error printing
- - - - -
b1bffff9 by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
fix periodic gridding for sorted cuda code
- - - - -
6f30b2f3 by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
fix compare strides in circ_shift
- - - - -
f79c2413 by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
increase threshold due to non-deterministic gridding
- - - - -
be2dfe45 by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
ncalib: default scaling based on bitcount, not on third dimension
- - - - -
259cfa5d by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
fixup "make vptr code more readable"
- - - - -
b9aad569 by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
remove useless cast
- - - - -
3a572dcc by Moritz Blumenthal at 2026-01-20T21:11:11+01:00
make vptr_mem_map_dims more safe for 32bit flags
- - - - -
92f8f587 by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
remove unnecessary gpu path as optimized copy kernel is available
- - - - -
49308304 by Dominik Pruenster at 2026-01-20T21:11:11+01:00
allow batch dimensions in basis
- - - - -
e877076a by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
allow for broadcasting of pattern in pics
- - - - -
c4774553 by Blumenthal, Moritz at 2026-01-20T21:11:11+01:00
fiy python open files in write not append mode
- - - - -
504f7e86 by Martin Heide at 2026-01-21T15:04:39+01:00
rescale stl models to default fov [-0.5, 0.5]
reorder vertices of hex model for correct computation of normal vector
- - - - -
6a263ac4 by Martin Heide at 2026-01-21T15:04:39+01:00
remove unnecessary variable
- - - - -
640d9919 by Martin Heide at 2026-01-21T15:04:39+01:00
phantom_type
- - - - -
b101372f by Martin Heide at 2026-01-21T15:04:39+01:00
simplify sens and sensgrid computation
- - - - -
3a63d1f3 by Martin Heide at 2026-01-21T15:04:39+01:00
use type consts from flpmath.h
- - - - -
f683c73e by Martin Heide at 2026-01-21T15:04:39+01:00
geometry preprocessing of triangles and test
- - - - -
a0fae93a by Martin Heide at 2026-01-21T15:04:39+01:00
stl kspace sampling
- - - - -
e2bdcada by Philip Schaten at 2026-01-21T15:04:39+01:00
Include libstl in dll and libbart.a
Replace getline by fgets
Fixes mingw build.
Fix Makefile
- - - - -
cb4938f1 by Martin Heide at 2026-01-21T15:04:39+01:00
add tests for stl kspace sampling
- - - - -
8fa7d31b by Martin Heide at 2026-01-21T15:04:39+01:00
volume and surface measure option for stl tool
- - - - -
ef3e1f0d by Martin Heide at 2026-01-21T15:04:39+01:00
normal computation
- - - - -
513a780e by Martin Heide at 2026-01-21T15:04:39+01:00
test for surface and volume measures
- - - - -
276c6414 by Martin Uecker at 2026-01-21T20:20:16+01:00
simplify pnp eulermaruyama
- - - - -
271e898d by Martin Uecker at 2026-01-22T12:48:41+01:00
use pics model
- - - - -
0f902df4 by Tina Holliber at 2026-01-22T13:40:05+01:00
fix cunet for single map
- - - - -
f5c82fca by Tina Holliber at 2026-01-22T14:01:25+01:00
fix error notification in sample
- - - - -
69c2561a by Tina Holliber at 2026-01-22T16:04:56+01:00
fix annealed sampling
- - - - -
de9ca479 by Moritz Blumenthal at 2026-01-22T22:57:38+01:00
set winding number to zero, where phase is undefined
- - - - -
644517ac by Martin Uecker at 2026-01-23T13:38:44+01:00
sample tool: test pics model
- - - - -
5424cdcf by Blumenthal, Moritz at 2026-01-23T18:36:47+01:00
fixup COIL_FLAG vs SENS_FLAG
- - - - -
9f4d8983 by Blumenthal, Moritz at 2026-01-23T18:36:47+01:00
deactivate phase pole correction for second map
- - - - -
afdbd294 by Blumenthal, Moritz at 2026-01-23T18:36:47+01:00
phasepole don't use weighting for center of mass
- - - - -
e14e3dc9 by Martin Uecker at 2026-01-23T23:45:46+01:00
whitespace
- - - - -
e213d367 by Martin Uecker at 2026-01-23T23:45:46+01:00
stl test is too slow
- - - - -
b0df7abd by Martin Uecker at 2026-01-23T23:45:46+01:00
remove some variable copies
- - - - -
c4976a9c by Martin Uecker at 2026-01-24T08:46:00+01:00
sigma schedule as nested function
- - - - -
ea773dfa by Martin Uecker at 2026-01-24T08:46:00+01:00
access local variables
- - - - -
32d8ecf9 by Martin Uecker at 2026-01-24T08:46:00+01:00
remove unneeded condition before unmap
- - - - -
ac537a0a by Martin Uecker at 2026-01-24T08:46:00+01:00
sample: add streaming support
- - - - -
b8fa8f33 by Martin Uecker at 2026-01-24T08:46:00+01:00
whitespace
- - - - -
63a609af by Martin Uecker at 2026-01-24T08:46:00+01:00
remove old TOOLBOX_PATH variable
- - - - -
42b9ac2a by Martin Uecker at 2026-01-24T08:46:00+01:00
remove old DEBUG_LEVEL variable
- - - - -
2e9a21ab by Martin Uecker at 2026-01-24T23:00:31+01:00
stream implementation improvements
- - - - -
f341370b by Martin Uecker at 2026-01-24T23:21:22+01:00
do not expose synced array for tests
- - - - -
71cea7e5 by Martin Uecker at 2026-01-25T15:39:59+01:00
coding style / types
- - - - -
659b0b6e by Martin Uecker at 2026-01-25T16:46:03+01:00
move size last as in other bart functions
- - - - -
4b2d2d29 by Martin Uecker at 2026-01-25T18:02:53+01:00
index/offset discrepancy, size types, stream_receive_next
- - - - -
691ef70b by Martin Uecker at 2026-01-25T20:45:51+01:00
remove catch-up logic
- - - - -
43598afd by Moritz Blumenthal at 2026-01-26T12:34:17+01:00
deactivate constant unfolding for non-scalar types (e.g. from vecops strided)
- - - - -
04fcbfb3 by Blumenthal, Moritz at 2026-01-26T12:34:17+01:00
make decomposed computation of psf optional
- - - - -
0c1dd4fe by Blumenthal, Moritz at 2026-01-26T12:34:17+01:00
use optimized cuda kernel for uppertriangular matrix vector multiplication
- - - - -
e180b5b0 by Blumenthal, Moritz at 2026-01-26T12:34:17+01:00
compressed psf for toeplitz_mult_lowmem
- - - - -
5dac00de by Blumenthal, Moritz at 2026-01-26T12:34:17+01:00
general nufft conf in nlinv
- - - - -
22823d22 by Blumenthal, Moritz at 2026-01-26T12:38:44+01:00
optimize unfold kernel
- - - - -
8ee40d84 by Blumenthal, Moritz at 2026-01-26T21:05:28+01:00
add tests and fix posterior sampling for noncart
- - - - -
d11d3392 by Daniel Mackner at 2026-01-27T08:09:53+01:00
events: add ecg-trigger and trigger output type
smaller event struct: wait is empty
- - - - -
2d88b5e8 by Daniel Mackner at 2026-01-27T08:09:53+01:00
event: add adc flags
- - - - -
de2e0794 by Daniel Mackner at 2026-01-27T08:09:53+01:00
config: trigger variables
- - - - -
54d6ea92 by Daniel Mackner at 2026-01-27T08:09:53+01:00
config: fix default order
use default config in utests
- - - - -
2d96ce21 by Daniel Mackner at 2026-01-27T08:09:53+01:00
helpers: RAGA (UI) help
- - - - -
99c041c5 by Daniel Mackner at 2026-01-27T08:09:53+01:00
helpers: minimum TE/TR, measurement time
- - - - -
6c54edc3 by Daniel Mackner at 2026-01-27T08:09:53+01:00
sequence custom UI
- - - - -
b2c2a006 by Daniel Mackner at 2026-01-27T08:09:53+01:00
helpers: ui - custom parameters interface
- - - - -
495d50bd by Daniel Mackner at 2026-01-27T08:09:53+01:00
helpers: standard ui parameters interface
- - - - -
f918199c by Daniel Mackner at 2026-01-27T08:09:53+01:00
helpers: ui - loop_dims interface
- - - - -
d6b80eac by Daniel Mackner at 2026-01-27T08:09:53+01:00
seq tool: WIP / loop dims interface
- - - - -
49c94f78 by Daniel Mackner at 2026-01-27T08:09:53+01:00
commandline for sequence
- - - - -
56e079e9 by Daniel Mackner at 2026-01-27T08:09:53+01:00
add context to seq_state
check sequence config function
avoids deadlocks in UI
avoid ASL for now
add seq_ut
- - - - -
5b555550 by Daniel Mackner at 2026-01-27T08:09:53+01:00
bart_seq: including conf/state/events/shapes
- - - - -
fa95c6f6 by Daniel Mackner at 2026-01-27T08:09:53+01:00
bart_seq @ seq-tool
- - - - -
bb2b7091 by Daniel Mackner at 2026-01-27T08:09:53+01:00
bart_seq @ utests
config: no more dll
- - - - -
681d1eb9 by Daniel Mackner at 2026-01-27T08:09:53+01:00
bart seq prepare
- - - - -
9c101289 by Daniel Mackner at 2026-01-27T08:09:53+01:00
interface struct
- - - - -
8aa86cd9 by Daniel Mackner at 2026-01-27T08:09:53+01:00
print info and radial views
- - - - -
24f076bd by Daniel Mackner at 2026-01-27T08:09:53+01:00
seq header infos
- - - - -
8c6bfbc5 by Daniel Mackner at 2026-01-27T08:09:53+01:00
add some docu on sequence
- - - - -
1c3ee7d7 by Daniel Mackner at 2026-01-27T12:51:08+01:00
raga aligned flags
- - - - -
f9c2bac9 by Daniel Mackner at 2026-01-27T12:56:01+01:00
pulseq fov
- - - - -
9ff55ebe by Daniel Mackner at 2026-01-27T12:58:11+01:00
sequence config: multiple echoes
- - - - -
d0036a4e by Daniel Mackner at 2026-01-27T12:58:11+01:00
timing / ro grad for multiple echoes
available time for multi-echo
necessary rounding of adc time to echo since ADC start on 1us raster
slice rephaser timing check
- - - - -
cb4d3f83 by Daniel Mackner at 2026-01-27T12:58:11+01:00
multiple ADCs / echoes
blips between multi-echo
test_flash: te for multiecho
- - - - -
18baa840 by Daniel Mackner at 2026-01-27T12:58:11+01:00
test momentum for multi-echoes
- - - - -
aded02ae by Daniel Mackner at 2026-01-27T12:58:11+01:00
splitting of blocks for multiple ADCs
ADC end < (block_emd - GRT)
pulseq multi echo ADC label
- - - - -
9c46b1d3 by Daniel Mackner at 2026-01-27T12:58:11+01:00
seq-tool / opts MEMS
- - - - -
9a8d71b6 by Philip Schaten at 2026-01-27T20:21:13+01:00
remove stream_sync and stream_sync_try, replace by stream_sync_slice
- API was used to sync slices up to a given point
- this has 2 problems:
- index ordering is not necessarily linear ascending
- flags from stream are implicitly used; calling program
might end up with smaller then expected slices.
- Replacement has clearer API and handles different orderings
- - - - -
9156370c by Philip Schaten at 2026-01-27T20:21:13+01:00
remove trx
- tool was previously needed to convert from/to binary streams
- every tool now automatically handles binary input streams
- binary output streams can be created using either
- bart tee -b or
- bart --stream-bin-out
- - - - -
709bf1d9 by Philip Schaten at 2026-01-27T20:21:13+01:00
update copyright years
- - - - -
b4d8e80a by Martin Uecker at 2026-01-28T13:12:08+01:00
more precisely describe pics's forward model
- - - - -
b620829c by Martin Uecker at 2026-01-28T13:12:08+01:00
use xaxpy instead of scaling twice
- - - - -
38b286e9 by Martin Uecker at 2026-01-28T17:14:49+01:00
fix dimensions for streaming of samples
- - - - -
ff0832d4 by Markus Huemer at 2026-01-28T17:15:11+01:00
fix typo in signal
- - - - -
d1d84a40 by Viktoria Buchegger at 2026-01-28T17:15:11+01:00
Add mobasig tool
- - - - -
1cec12af by Markus Huemer at 2026-01-28T17:15:11+01:00
use mode_create in mobafit
- - - - -
4899ec5e by Markus Huemer at 2026-01-28T17:15:11+01:00
add IR model
- - - - -
048a1c53 by Markus Huemer at 2026-01-28T17:15:11+01:00
add exp model and simplify
- - - - -
9366e6c0 by Markus Huemer at 2026-01-28T17:15:11+01:00
move mgre to model_create
- - - - -
481a16cf by Markus Huemer at 2026-01-28T17:15:11+01:00
simplify mobafit, move switch
- - - - -
71e8293d by Markus Huemer at 2026-01-28T17:15:11+01:00
fix bug in sim tool for CEST seq
- - - - -
2741292d by Markus Huemer at 2026-01-28T17:15:11+01:00
change mpl test to slow
- - - - -
231fd338 by Markus Huemer at 2026-01-28T18:09:05+01:00
move model creation to modal_moba
- - - - -
3f38b4ec by Martin Uecker at 2026-01-29T09:51:54+01:00
improve warning
- - - - -
7557f5b7 by Martin Uecker at 2026-01-29T10:00:03+01:00
coyright
- - - - -
c3f37b51 by Martin Uecker at 2026-01-29T10:00:03+01:00
typos
- - - - -
3a94c8b0 by Blumenthal, Moritz at 2026-01-29T10:26:52+01:00
ncalib defaults
- - - - -
5354a733 by Blumenthal, Moritz at 2026-01-29T10:27:16+01:00
remove unused old nufft loop code
- - - - -
ba0f386d by Blumenthal, Moritz at 2026-01-29T10:27:16+01:00
mix of create_async_cfl and looping is okay if file is not pipe
- - - - -
faaf2864 by Martin Heide at 2026-01-29T13:01:14+01:00
phantom tool stl usability
- - - - -
181a5bee by Daniel Mackner at 2026-01-29T17:27:45+01:00
minimum te/tr with double
- - - - -
0819e210 by Daniel Mackner at 2026-01-29T17:30:26+01:00
fix minimum te
- - - - -
65de7b5f by Daniel Mackner at 2026-01-29T17:30:26+01:00
seq: unit conversion for rf duration
- - - - -
9b4e8d66 by Daniel Mackner at 2026-01-29T17:30:26+01:00
bart_seq_alloc with (const char) version
- - - - -
9b50c5ef by Daniel Mackner at 2026-01-29T17:30:26+01:00
sequence version check
- - - - -
5df4bc04 by Daniel Mackner at 2026-01-29T17:30:26+01:00
update seq docu
- - - - -
6eeef003 by Daniel Mackner at 2026-01-29T17:30:26+01:00
sequence interface more readable
- - - - -
9821338c by Daniel Mackner at 2026-01-29T17:30:26+01:00
seq tool: minor
- - - - -
56183bde by Daniel Mackner at 2026-01-29T17:30:26+01:00
seq-tool: remove raga_al option
use aligned flags
- - - - -
48623a02 by Daniel Mackner at 2026-01-29T17:30:26+01:00
lock.c: fix linking under linux
- - - - -
13dadd00 by Philip Schaten at 2026-01-29T20:33:15+01:00
update python doc + remove TOOLBOX_PATH variable
- - - - -
14ad8536 by Philip Schaten at 2026-01-29T20:33:15+01:00
streaming docs
- - - - -
10765ff8 by Martin Heide at 2026-01-30T11:33:11+01:00
documentation basics phantom tool
- - - - -
b0c157c0 by Philip Schaten at 2026-01-30T16:13:21+01:00
change rpm versioning to fix copr build
- copr builds from git-urls use shallow clones
- causes unexpected output of `git describe`:
number of commits since latest `v*`-tag is missing
- thus, omit number of commits since latest version tag
in copr-version, just use <date>git<commit>
- increment epoch in .spec-files due to new versioning scheme
- - - - -
9450d04e by Philip Schaten at 2026-01-30T16:13:21+01:00
rpm-packaging: remove rh-07, use openblas
- - - - -
4592be6e by Moritz Blumenthal at 2026-01-30T18:23:49+01:00
warning for pics if coils are not normalized
- - - - -
6dd54fa4 by Martin Uecker at 2026-01-31T10:06:15+01:00
white space
- - - - -
1a97d713 by Martin Uecker at 2026-01-31T10:41:32+01:00
remove reorder
- - - - -
d58409bd by Martin Uecker at 2026-01-31T10:41:32+01:00
refactor and enable streaming for label binning
- - - - -
7d07f453 by Martin Uecker at 2026-02-01T10:36:56+01:00
coding style
- - - - -
e2897f41 by Martin Uecker at 2026-02-01T10:39:40+01:00
coding style
- - - - -
6a532e52 by Blumenthal, Moritz at 2026-02-01T21:35:11+01:00
remove invalid assertion
- - - - -
64c4d274 by Blumenthal, Moritz at 2026-02-02T11:32:36+01:00
nlinvnet make nufft configurable
- - - - -
d6af63d2 by Daniel Mackner at 2026-02-04T13:03:20+01:00
fix typo
- - - - -
4345abb6 by Daniel Mackner at 2026-02-04T13:03:20+01:00
seq-tool: meaningful fov scaling
- - - - -
7e324c99 by Daniel Mackner at 2026-02-04T13:03:20+01:00
seq_print_info function refactor
- - - - -
39502d32 by Daniel Mackner at 2026-02-04T13:03:20+01:00
seq: read config from string
- - - - -
476dac58 by Daniel Mackner at 2026-02-04T13:03:20+01:00
sum of 0th moment without RF pulse reset
change handling in seq tool
tool runtime info
adapt utests
- - - - -
92865597 by Daniel Mackner at 2026-02-04T13:03:20+01:00
compute moments with starting offset
- - - - -
e1cdc150 by Daniel Mackner at 2026-02-04T13:03:20+01:00
compute adc samples for whole adc
- - - - -
94a8d79f by Daniel Mackner at 2026-02-04T13:03:20+01:00
save absolute time for adc
- - - - -
abb51f5c by Daniel Mackner at 2026-02-04T13:03:20+01:00
round up to raster more stable
- - - - -
eec1d6eb by Daniel Mackner at 2026-02-04T13:03:20+01:00
correct momentum, without weird rounding
ro dephaser rework
fix shift
- - - - -
1f210baf by Daniel Mackner at 2026-02-04T13:03:20+01:00
unify adc start time calculation
- - - - -
bc0d90ea by Daniel Mackner at 2026-02-04T13:03:20+01:00
helpers: stanadard ui interface incl. reverse
- - - - -
b061b7b4 by Martin Uecker at 2026-02-04T15:11:15+01:00
remove unneeded ifs for unmap
- - - - -
133ba0eb by Martin Uecker at 2026-02-04T15:24:33+01:00
coding style
- - - - -
88b30eaf by Daniel Mackner at 2026-02-04T23:08:08+01:00
remove get_slices from sequence interface
expose information via seq_interface_conf
- - - - -
ee32c1b3 by Daniel Mackner at 2026-02-04T23:24:17+01:00
seq-tool: warn on not allowed spokes
- - - - -
2622abe5 by Daniel Mackner at 2026-02-05T11:08:21+01:00
print string of error enums
- - - - -
0d77d2b2 by Daniel Mackner at 2026-02-05T11:13:15+01:00
remove pe mode raga_aligned
raga_aligned = raga + aligned_flags=8192
- - - - -
77af87c7 by Daniel Mackner at 2026-02-05T11:34:18+01:00
pulseq: check for even number of adc samples
- - - - -
c786ba64 by Philip Schaten at 2026-02-05T13:19:04+01:00
fixup e2bdcadacc: remove .win.o files from libbart.a
- lib/libbart.a depended on $(stlwinobjs),
ie the files which would compiled by mingw normally
- furthermore, the win-objs were not marked as INTERMEDIATE
and thus not removed, breaking subsequent DLL-builds
- - - - -
a2a24bce by Philip Schaten at 2026-02-05T13:19:04+01:00
libseq_deploy: fix the hash-length to 10 characters
- - - - -
a51f1e65 by Blumenthal, Moritz at 2026-02-05T14:43:44+01:00
print vptr statistics on bart exit
- - - - -
1fb4c23a by Blumenthal, Moritz at 2026-02-05T14:43:44+01:00
add ptr_append_printf
- - - - -
0a206850 by Moritz Blumenthal at 2026-02-05T14:43:44+01:00
add simple and more efficient graph implementation
- - - - -
ebd2e4f9 by Blumenthal, Moritz at 2026-02-05T14:43:44+01:00
prepare virtual pointer for delayed computation
- - - - -
61bca6ac by Blumenthal, Moritz at 2026-02-05T14:43:44+01:00
delayed computation
- - - - -
9faf04bd by Blumenthal, Moritz at 2026-02-05T14:43:44+01:00
make batchsvd vptr and gpu safe
- - - - -
17cdd19b by Blumenthal, Moritz at 2026-02-05T14:43:44+01:00
delayed computation for pics
- - - - -
185c5854 by Blumenthal, Moritz at 2026-02-05T14:43:44+01:00
delayed computation for nlinv
- - - - -
8ece2977 by Martin Uecker at 2026-02-06T09:29:29+01:00
whitespace
- - - - -
99e75a67 by Martin Uecker at 2026-02-06T09:29:29+01:00
overlap and add: fix typo in dimensions (thx to: Martin Strunz)
- - - - -
97dc9258 by Moritz Blumenthal at 2026-02-06T10:18:02+01:00
fix stacking of nn
- - - - -
91b6bc9a by Moritz Blumenthal at 2026-02-06T10:28:37+01:00
helpful warning for using BART_GPU_GLOBAL_MEMORY environment on cuda out of memory
- - - - -
a30a49fa by Martin Uecker at 2026-02-07T23:58:17+01:00
add c++ standard to NVCCFLAGS
- - - - -
678cb4f6 by Martin Uecker at 2026-02-08T08:07:38+01:00
whitespace
- - - - -
42bfdba4 by Martin Uecker at 2026-02-08T08:08:00+01:00
remove unused prototypes
- - - - -
02daa3a9 by Martin Heide at 2026-02-08T08:08:12+01:00
fix phantom kspace sampling (MU: edited)
- - - - -
1e3cf3c6 by Martin Uecker at 2026-02-08T08:08:30+01:00
split stl tests and add FIXME
- - - - -
63d3dbc9 by Martin Uecker at 2026-02-08T08:09:40+01:00
stl code works for three dimensions only
- - - - -
b6376131 by Martin Uecker at 2026-02-08T08:11:15+01:00
use md_calloc
- - - - -
4f528e82 by Martin Uecker at 2026-02-08T08:11:15+01:00
remove print_vec
- - - - -
94758e13 by Martin Uecker at 2026-02-08T08:11:15+01:00
const correctness
- - - - -
f3b58511 by Martin Uecker at 2026-02-08T08:11:15+01:00
remove void pointer and manual indexing
- - - - -
836b0a2d by Martin Uecker at 2026-02-08T08:27:05+01:00
use xmalloc
- - - - -
f9210436 by Martin Uecker at 2026-02-08T08:48:43+01:00
use BART convention for input / output arguments
- - - - -
c7b3fbc2 by Martin Uecker at 2026-02-08T08:49:40+01:00
typos, coding style, and make output required
- - - - -
6820f776 by Martin Uecker at 2026-02-08T08:57:05+01:00
remove stl_read_line
- - - - -
b65a8439 by Martin Uecker at 2026-02-08T15:05:39+01:00
rewrite more succintly
- - - - -
13340ab0 by Martin Uecker at 2026-02-08T15:05:40+01:00
improve header writing
- - - - -
df763ab1 by Martin Uecker at 2026-02-08T15:05:41+01:00
directly write binary stl without buffer
- - - - -
c4c70102 by Martin Uecker at 2026-02-08T15:05:42+01:00
read binary stl without buffer
- - - - -
78487dc2 by Martin Uecker at 2026-02-08T15:05:43+01:00
minor
- - - - -
dbea06c0 by Martin Uecker at 2026-02-08T15:05:44+01:00
remove special string functions
- - - - -
69dcb715 by Martin Uecker at 2026-02-08T15:05:45+01:00
rename vec3d_cp -> vec3d_crossproduct
- - - - -
20d82105 by Martin Uecker at 2026-02-08T15:05:46+01:00
open file just once
- - - - -
8c023cef by Martin Uecker at 2026-02-08T15:05:46+01:00
remove TOL from header
- - - - -
f483b895 by Martin Uecker at 2026-02-08T15:05:47+01:00
move inclusion of header
- - - - -
59da80d0 by Martin Uecker at 2026-02-08T15:05:48+01:00
move file handling out of backend
- - - - -
2628946e by Martin Uecker at 2026-02-08T18:02:51+01:00
add binary/ascii modes
- - - - -
9e29839e by Martin Uecker at 2026-02-08T18:02:51+01:00
simplify cli
- - - - -
0b6566ab by Martin Uecker at 2026-02-08T18:02:51+01:00
static_assert backwards compatibility
- - - - -
ee0909a6 by Martin Uecker at 2026-02-08T18:02:51+01:00
workaround for blocks limitations and emscripten
- - - - -
36879b68 by Martin Uecker at 2026-02-08T18:02:51+01:00
use correct type
- - - - -
47bb256c by Daniel Mackner at 2026-02-09T10:33:53+01:00
consistent random seed initialization
- - - - -
bb8a42e5 by Daniel Mackner at 2026-02-10T09:56:49+01:00
coding style, typo
- - - - -
b9b1025f by Daniel Mackner at 2026-02-10T09:56:57+01:00
set adc_flags
- - - - -
8fa98ced by Daniel Mackner at 2026-02-10T09:56:57+01:00
minor seq_block
- - - - -
8378a5b1 by Daniel Mackner at 2026-02-10T09:56:57+01:00
prepare function
change logic for useful debug info
- - - - -
b291d145 by Daniel Mackner at 2026-02-10T09:56:57+01:00
fix save position for incomplete RAGA frames
- - - - -
01a45d70 by Daniel Mackner at 2026-02-10T09:56:57+01:00
trigger output
scanner notification when acq of frame starts
- - - - -
86c5a778 by Daniel Mackner at 2026-02-10T09:56:57+01:00
useful test on TI
- - - - -
40e4f027 by Daniel Mackner at 2026-02-10T09:56:57+01:00
proper blip timing check
- - - - -
e49cbb7d by Daniel Mackner at 2026-02-10T09:56:57+01:00
delta TE for multiple echoes
- - - - -
3976b15f by Daniel Mackner at 2026-02-10T09:56:57+01:00
echoes looped within spokes
- - - - -
db21667c by Daniel Mackner at 2026-02-10T09:56:57+01:00
RAGA multi-echo
- - - - -
a6780240 by Daniel Mackner at 2026-02-10T09:56:57+01:00
remove unused pemode raga mems
- - - - -
37c2cf3f by Daniel Mackner at 2026-02-10T09:56:57+01:00
seq: more precise interface conf
- - - - -
f1eafd86 by Daniel Mackner at 2026-02-10T09:56:57+01:00
proper name command parameter
- - - - -
22ba90f2 by Daniel Mackner at 2026-02-10T09:56:57+01:00
smaller fixed interface (UI)
- - - - -
3ebda534 by Daniel Mackner at 2026-02-10T09:56:57+01:00
add checkbox for online recon
- - - - -
08b6d91f by Daniel Mackner at 2026-02-10T09:56:57+01:00
Makefile: cleanup wine utests
- - - - -
e391902b by Daniel Mackner at 2026-02-10T10:25:17+01:00
fix config to custom params
- - - - -
f6cdbf58 by Martin Uecker at 2026-02-12T15:57:10+01:00
add test for Fourier transform of polygon
- - - - -
535a34ef by Martin Uecker at 2026-02-12T16:35:12+01:00
move Fouriertransform of tetrahedron in its own function
- - - - -
c5935b0e by Blumenthal, Moritz at 2026-02-12T16:35:54+01:00
sample: fix initialization
- - - - -
886e15a4 by Blumenthal, Moritz at 2026-02-12T16:35:54+01:00
use pULA for intialization of sample
- - - - -
4b01a1f0 by Daniel Mackner at 2026-02-12T17:56:15+01:00
flags for different sequence modes
cleanup interface config
- - - - -
e6d6c684 by Daniel Mackner at 2026-02-12T17:56:15+01:00
asl looping
- - - - -
05c57d4d by Daniel Mackner at 2026-02-12T17:56:15+01:00
seq tool: error message
- - - - -
491f2145 by Martin Uecker at 2026-02-13T22:23:32+01:00
fix dc component for 3D analytical simulation
- - - - -
4a8cf208 by Martin Uecker at 2026-02-13T22:23:32+01:00
replace test
- - - - -
bd733c3e by Philipp Ehses at 2026-02-13T22:54:12+01:00
Improve Python bindings and reduce I/O overhead
- cfl.py: Fix .ra read/write; replace mmap with simple write
to reduce overhead for small files
- bart.py: Write .ra files (single binary file instead of two),
lowering overhead for small files
- general cleanup (remove obsolete from_future imports)
- - - - -
7394cfb9 by Martin Uecker at 2026-02-14T04:12:49+01:00
relax for mac
- - - - -
9d130d72 by Martin Uecker at 2026-02-14T04:28:31+01:00
add assertion for little endian, make error messages unique
- - - - -
9ccaa42b by Martin Uecker at 2026-02-15T13:54:41+01:00
remove outdated comment
- - - - -
13817e62 by Martin Uecker at 2026-02-15T13:54:44+01:00
error exits cleanly
- - - - -
d3ea1e55 by Martin Uecker at 2026-02-15T13:54:44+01:00
surface some errors
- - - - -
66e11277 by Martin Uecker at 2026-02-15T13:54:44+01:00
whitespace
- - - - -
52142246 by Martin Uecker at 2026-02-15T14:32:32+01:00
initialize tmp variable
- - - - -
03e70639 by Martin Uecker at 2026-02-15T14:43:59+01:00
fix gcc 14 warnings
- - - - -
1522f697 by Christian Bardey at 2026-02-15T21:14:57+01:00
stl/misc.c: error messages should end in newline
- - - - -
9b6a032e by Christian Bardey at 2026-02-15T21:33:30+01:00
stl/misc.c: rewind file descriptor for MacOS
Seems like it needs it
- - - - -
da8fa6cb by Martin Uecker at 2026-02-16T05:39:27+01:00
fix checks for stream flags
- - - - -
de933a34 by Martin Uecker at 2026-02-16T05:39:27+01:00
don't have empty error
- - - - -
4360b166 by Martin Uecker at 2026-02-16T11:06:01+01:00
fix test dependencies
- - - - -
f2d4d96a by Martin Uecker at 2026-02-16T11:06:17+01:00
fix typo
- - - - -
4c0236ec by Daniel Mackner at 2026-02-17T09:56:40+01:00
remove equal dims check
- - - - -
f47c8b8d by Philip Schaten at 2026-02-17T09:56:40+01:00
Add string-based custom UI interface
- - - - -
7b1413dc by Philip Schaten at 2026-02-17T09:56:40+01:00
remove constants for UI: _cil and _cid
- - - - -
32f44336 by Daniel Mackner at 2026-02-17T09:56:40+01:00
rename ui enums
- - - - -
a72f7190 by Blumenthal, Moritz at 2026-02-17T09:56:40+01:00
use /tmp or $TMPDIR for streamed cfl files
- - - - -
2e78dbb0 by Martin Uecker at 2026-02-17T09:56:40+01:00
modernize
- - - - -
198263e6 by Martin Uecker at 2026-02-17T09:56:40+01:00
also scale result for lowrank+sparse
- - - - -
64378a09 by Martin Uecker at 2026-02-17T09:56:40+01:00
only remove noise level when it exists
- - - - -
df9a1f6c by Martin Uecker at 2026-02-17T09:56:40+01:00
add low-rank + sparse tests
- - - - -
431a6f25 by Martin Uecker at 2026-02-17T09:56:40+01:00
relax for mac
- - - - -
ee0ea5ef by Martin Uecker at 2026-02-17T09:56:40+01:00
remove RING_PAPER environment variable
- - - - -
a6595f7d by Martin Uecker at 2026-02-17T09:56:40+01:00
document environment variables
- - - - -
82a4b076 by Blumenthal, Moritz at 2026-02-18T09:07:18+01:00
fix compilation with "OPENBLAS=1" and don't change threads.
Fix compilation when <cblas.h> is not from openblas.
Dont change threads for openblas, as it may be relevant for lapack functions
- - - - -
99ab80da by Blumenthal, Moritz at 2026-02-18T09:07:51+01:00
dps sampling
- - - - -
9d7bdf77 by Daniel Mackner at 2026-02-18T09:07:51+01:00
consistent multi-echo trajectories
- - - - -
17a6e3bf by Daniel Mackner at 2026-02-18T09:07:51+01:00
fix linearize events and print total duration in seq tool
- - - - -
0d012015 by Daniel Mackner at 2026-02-18T09:07:51+01:00
add noise scan to measurement time calculation
- - - - -
6bcf5d63 by Daniel Mackner at 2026-02-18T09:07:51+01:00
warn on invalid sequence duration
- - - - -
5ac94e26 by Daniel Mackner at 2026-02-18T09:07:51+01:00
remove loop dims from seq/opts
improved usability in sequence
- - - - -
4f627171 by Daniel Mackner at 2026-02-18T09:07:51+01:00
update sequence docu
- - - - -
37f3c5f0 by Martin Uecker at 2026-02-18T09:07:51+01:00
bump version
- - - - -
170350aa by Martin Uecker at 2026-02-18T18:14:39+01:00
Merge tag 'v1.0.00'
version 1.0.00
Changes:
- doc: Add definition files for singularity containers with BART
- doc: Add documentation of performance options
- doc: Add documentation for singularity container
- doc: Add documentation for environment variables
- affinereg (new): affine registration
- bloch (new): Bloch simulation (work-in-progress)
- coils (new): simulate coil sensitivity maps
- compress (new): compress data using binary mask
- cunet (new): conditional U-Net
- denoise (new): denoising tool
- estmotions (new): non-rigid registration
- estscaling (new): estimate a scaling factor from k-space center
- gmm (new): Gaussian-Mixture models
- grid (new): compute Cartesian grids
- grog (new): GROG calibration and gridding (currently only radials)
- hist (new): compute histograms
- interpolate (new): interpolate and image after transformation
- mobasig (sig): forward calculation of physical signal models
- multicfl (new): combine/split multi-cfl files
- nlinvnet (new): NLINV-Net reconstruction and training
- ncalib (new): sensitivity calibration using NLINV
- phasepole (new): tool to detect phase poles
- pulse (new): compute radio-frequency pulse shapes
- raga (new): tool to compute RAGA indices
- rovir (new): coil compression with region optimization
- sample (new): sample generative score-based models
- seq (new): compute MRI sequences
- stl (new): read/write STL files
- unwrap (new): simply unwrapping tool
- tee (new): copy stdin to file and stdout
- toraw (new): create raw data files
- trajcor (new): retrospectively correct trajectory based on gradient delays
- mat2cfl: removed.
- bin: zero-fill option
- bin: stream support
- calc: new function: round
- ccapply: realtime geometric coil compression
- conway: stream support
- copy: stream support
- copy: support for reordering of dimensions
- epg: make refocusing FA accessible from CLI
- ecalib: use Nyström approximation
- ecalib: economic mode for 3D coils
- fovshift: pass shift as file
- invert: option for regularization
- join: stream support
- mandelbrot: stream support
- moba: IR-MECO reconstruction
- moba: finalize transparent gpu support in moba
- moba: change scaling and command line for T2 moba to be consistent with mobafit
- mobafit: CEST fitting
- mobafit: simulation based fitting (Bloch + Bloch-McConnell)
- nnet: support for nnU-Net for segmenation
- nlinv: basis support, temporal regularization, builtin nufft
- nlinv: stream support
- nufft: fix compatibility to v0.8.00
- pics: use of prox in last iteration of FISTA
- pics: (TE-)ASL reconstruction
- pics: Euler-Maruyama
- reconet: fix compatibility to v0.8.00
- show: support for printing real part and index
- signal: enable the input of fat fraction
- signal: generating function-based FSE model
- signal: buxton model
- signal: option to toggle short TR approximation
- sim: CEST sequence
- traj: option to create RAGA index file
- twixread: optional read PMU signal
- twixread: read noise scans
- rtreco.sh: new script for realtime reconstruction
- library: remove divergence free wavelets
- library (num): stable and improved random number generation with Philox-4x32
- library (num): GPU support for gaussian random numbers
- library (num): rename md_(de)compress -> md_mask_(de)compress
- library (num): new functions: md_(z)round(2) functions, md_zsetnanzero(2)
- library (num): MPI support for md_copy with strides, and md_zadd2
- library (num): new LAPACK wrappers (svd, eigenvalues, solvers)
- library (num): matrix logarithm of upper triangular matrix
- library (num): matrix square root of triangular matrix
- library (num): complex support for matrix exponentials
- library (num): new special functions: Legendre polynomials
- library (num): new special functions: simplified hyp2f1 function
- library (num): new special functions: approximation of gamma function
- library (num): Gauss-Legendre quadrature
- library (num): Crank Nicolson
- library (num): functions for Gaussian mixture models
- library (ismrmd): new functions to parse ismrmrd streams
- library (iter): Euler Mayurama
- library (linop): shift, slice, hankelization, reshape with flags
- library (nn): cast linop to nn
- library (nn): support for leaky ReLU
- library (nn): normalization layer
- library (nn): normalized loss
- library (nlops): checkpointing container
- general: move to codeberg
- general: remove TOOLBOX_PATH and DEBUG_LEVEL (use the new ones with BART_ prefix)
- general: stream protocol implementation + tests
- general: experimental support for delayed computation
- general: Windows DLLs
- - - - -
564aaaae by Martin Uecker at 2026-03-28T17:50:31+01:00
rebase patches
- - - - -
8fda7c07 by Martin Uecker at 2026-03-28T17:50:51+01:00
update changelog
- - - - -
56c8f26a by Martin Uecker at 2026-03-28T17:50:53+01:00
homepage in control
- - - - -
91eceb4e by Martin Uecker at 2026-03-28T18:15:41+01:00
update copyright
- - - - -
03c3ed65 by Martin Uecker at 2026-03-28T18:34:49+01:00
add missing dllspec.h
- - - - -
b6839744 by Martin Uecker at 2026-05-10T09:26:56+02:00
fix commands test
- - - - -
76e0ba73 by Martin Uecker at 2026-05-10T09:26:56+02:00
add rpath patch
- - - - -
646ffecd by Martin Uecker at 2026-05-10T09:26:56+02:00
add patch to remove duplicate entries for commands
- - - - -
30a35d97 by Martin Uecker at 2026-05-10T12:08:11+02:00
turn off all workarounds for now
- - - - -
51f3244f by Martin Uecker at 2026-05-10T12:08:11+02:00
remove feature for local use
- - - - -
410d40b6 by Martin Uecker at 2026-05-10T12:08:11+02:00
add fix required for Debian autopkgtest tests
- - - - -
515390e9 by Martin Uecker at 2026-05-10T12:08:11+02:00
fix debian tests
- - - - -
8f4019e1 by Martin Uecker at 2026-05-10T12:08:11+02:00
do not delete command.txt
- - - - -
9a8bfb05 by Martin Uecker at 2026-05-10T12:08:11+02:00
deterministic archives
- - - - -
7258a093 by Martin Uecker at 2026-05-10T16:41:34+02:00
turn i386 tests off for now
- - - - -
e280bfce by Martin Uecker at 2026-05-10T21:44:30+02:00
turn off parallel builds
- - - - -
40edeeda by Martin Uecker at 2026-05-30T17:04:43+02:00
remove lto
- - - - -
db80d3c3 by Andreas Tille at 2026-06-03T07:37:44+02:00
d/watch: version=5
- - - - -
0ed4502f by Andreas Tille at 2026-06-03T07:38:04+02:00
Standards-Version: 4.7.4 (routine-update)
- - - - -
f797b958 by Andreas Tille at 2026-06-03T07:38:19+02:00
Changes made by cme
- - - - -
1395d0f5 by Andreas Tille at 2026-06-03T07:38:23+02:00
Drop 'Rules-Requires-Root: no' from d/control (routine-update)
- - - - -
6eb6606e by Andreas Tille at 2026-06-03T07:38:30+02:00
debputy lint --auto-fix (routine-update)
- - - - -
c549520e by Andreas Tille at 2026-06-03T08:19:12+02:00
d/copyright: add Files: debian/* paragraph
- - - - -
d506524a by Andreas Tille at 2026-06-03T08:19:23+02:00
add Files: src/misc/ya_getopt* and src/win/mman*
- - - - -
76dbf7c8 by Andreas Tille at 2026-06-03T08:21:49+02:00
add Files: src/lapacke/*
- - - - -
4dd84fd9 by Andreas Tille at 2026-06-03T08:31:25+02:00
Upload to unstable
- - - - -
1fc0410c by Martin Uecker at 2026-06-04T09:29:42+02:00
try AR_LOCK_NEEDED=0
- - - - -
db7d64ce by Martin Uecker at 2026-06-04T09:33:12+02:00
add back exception for hurd
- - - - -
8d8f3e43 by Martin Uecker at 2026-06-04T09:55:47+02:00
drop determinsitic archive patch
- - - - -
8d5232fe by Martin Uecker at 2026-06-04T13:20:19+02:00
remove unused rules
- - - - -
5a21fff0 by Martin Uecker at 2026-06-04T13:21:41+02:00
some archs still needs to turn of expensive optimizations
- - - - -
62ceeef5 by Martin Uecker at 2026-06-04T13:27:43+02:00
update changelog
- - - - -
ac866d4d by Andreas Tille at 2026-06-05T07:41:39+02:00
Upload to unstable
- - - - -
dc673202 by Martin Uecker at 2026-06-12T15:45:07+02:00
try to fix floating point errors on i386
- - - - -
fbbeb4a3 by Martin Uecker at 2026-06-12T16:01:14+02:00
add fix for 32 bit warnings / issues
- - - - -
b889d8cb by Martin Uecker at 2026-09-26T13:02:11+02:00
Merge branch 'master' into master-contrib
- - - - -
1022 changed files:
- + .codespellrc
- .github/workflows/c-cpp.yml → .github/workflows/linux.yml
- + .github/workflows/macos-arm.yml
- .gitignore.main
- .gitlab-ci.yml
- ACKNOWLEDGEMENTS
- LICENSE
- Makefile
- README
- README.md
- ar_lock.sh
- + build_webasm.sh
- + commands/.gitignore
- + commands/sub
- debian/changelog
- debian/control
- debian/copyright
- debian/libbart-dev.install
- debian/patches/0001-remove-empty-directory.patch
- − debian/patches/0002-deactivate-ode-unit-tests.patch
- + debian/patches/0003-cleanup-more-thoroughly.patch
- − debian/patches/0003-relax-failing-unit-test.patch
- + debian/patches/0004-remove-rpath.patch
- − debian/patches/0004-workaround-for-compiler-bug.patch
- debian/patches/0005-do-not-update-doc-commands.txt-automatically.patch
- + debian/patches/0005-remove-commands-listed-twice.patch
- − debian/patches/0006-on-Deban-never-use-git-version.patch
- + debian/patches/0006-remove-exec-command-mechanism.patch
- − debian/patches/0007-add-CXXFLAGS-to-nvcc-to-fix-C-build-issue.patch
- + debian/patches/0007-fix-initialization-for-direct-call-of-tools.patch
- + debian/patches/0008-do-not-delete-command.txt.patch
- − debian/patches/0008-relax-a-failing-test.patch
- + debian/patches/0009-32-bit-issues.patch
- − debian/patches/0009-backport-specfun-fixes.patch
- debian/patches/series
- debian/rules
- debian/tests/commands
- debian/tests/suite
- debian/upstream/metadata
- debian/watch
- doc/bart.1
- doc/building.txt
- + doc/distributed-architectures.txt
- + doc/environment.txt
- + doc/nufft.md
- + doc/performance.txt
- + doc/phantom.txt
- doc/pics.txt
- + doc/pytorch.txt
- + doc/random-numbers.txt
- doc/references.txt
- + doc/sequence.txt
- + doc/singularity/README.md
- + doc/singularity/bart_debian.def
- + doc/singularity/bart_ubuntu.def
- + doc/streaming.md
- doc/style.txt
- + doc/tensorflow.txt
- + doc/webasm.txt
- doxyconfig
- git-version.sh
- matlab/get_bart_path.m
- + pkg/python/LICENSE
- + pkg/python/README.md
- + pkg/python/bart/__init__.py
- + pkg/python/bart/bart.py
- + pkg/python/bart/cfl.py
- + pkg/python/bart/wslsupport.py
- + pkg/python/pyproject.toml
- + pkg/python/version.txt
- pkg/rpm/bart.spec
- pkg/rpm/libbart-devel.spec
- pkg/rpm/octave-bart.spec
- pkg/rpm/rpkg.macros
- python/bart.py
- + python/bart_tf.py
- python/cfl.py
- + python/splines_from_svg.py
- + rules/add_node_shebang.sh
- − rules/update-version.sh
- rules/update_commands.sh
- rules/update-if-changed.sh → rules/update_if_changed.sh
- + rules/update_version.sh
- + scripts/affine_kspace.sh
- + scripts/create_toolgraph.py
- scripts/espirit_econ.sh
- scripts/grasp.sh
- + scripts/kspace_precond.sh
- scripts/life.sh
- scripts/octview.m
- scripts/phantom.sh
- scripts/profile.sh
- scripts/radial_dcf.sh
- + scripts/rovir.sh
- + scripts/rtreco.sh
- + src/affinereg.c
- src/avg.c
- src/bart.c
- src/bench.c
- src/bin.c
- src/bitmask.c
- + src/bloch.c
- src/cabs.c
- + src/calc.c
- src/caldir.c
- src/calib/bin.c
- src/calib/bin.h
- src/calib/calib.c
- src/calib/calib.h
- src/calib/calibcu.cu
- src/calib/calmat.c
- src/calib/calmat.h
- src/calib/cc.c
- src/calib/cc.h
- src/calib/delays.c
- src/calib/delays.h
- src/calib/direct.c
- src/calib/estvar.c
- src/calib/estvar.h
- + src/calib/grog.c
- + src/calib/grog.h
- src/calib/softweight.c
- src/calib/ssa.c
- src/calib/ssa.h
- src/calib/walsh.c
- src/calib/walsh.h
- src/calmat.c
- src/carg.c
- src/casorati.c
- src/cc.c
- src/ccapply.c
- src/cdf97.c
- src/circshift.c
- + src/coils.c
- + src/compress.c
- src/conj.c
- src/conv.c
- src/conway.c
- src/copy.c
- src/cpyphs.c
- src/creal.c
- src/crop.c
- + src/cunet.c
- src/delta.c
- + src/denoise.c
- − src/dfwavelet/dfwavelet.c
- − src/dfwavelet/dfwavelet.h
- − src/dfwavelet/dfwavelet_impl.h
- − src/dfwavelet/dfwavelet_kernels.cu
- − src/dfwavelet/dfwavelet_kernels.h
- − src/dfwavelet/prox_dfwavelet.c
- − src/dfwavelet/prox_dfwavelet.h
- src/ecalib.c
- src/ecaltwo.c
- src/epg.c
- src/estdelay.c
- src/estdims.c
- + src/estmotion.c
- + src/estscaling.c
- src/estshift.c
- src/estvar.c
- src/extract.c
- src/fakeksp.c
- src/fft.c
- src/fftmod.c
- src/fftrot.c
- src/fftshift.c
- src/filter.c
- src/flatten.c
- src/flip.c
- src/fmac.c
- src/fovshift.c
- + src/geom/brain.c
- + src/geom/brain.h
- src/geom/draw.c
- src/geom/polygon.c
- src/geom/polyhedron.c
- src/geom/triangle.c
- + src/gmm.c
- src/grecon/italgo.c
- src/grecon/italgo.h
- src/grecon/losses.c
- src/grecon/losses.h
- + src/grecon/model.c
- + src/grecon/model.h
- src/grecon/network.c
- src/grecon/network.h
- src/grecon/opt_iter6.c
- src/grecon/optreg.c
- src/grecon/optreg.h
- + src/grecon/priors.c
- + src/grecon/priors.h
- + src/grid.c
- + src/grog.c
- + src/hist.c
- src/homodyne.c
- src/ictv.c
- src/index.c
- + src/interpolate.c
- src/invert.c
- src/ismrm/read.c
- src/ismrm/read.h
- src/ismrm/xml_wrapper.cc
- src/ismrm/xml_wrapper.h
- src/ismrmrd.c
- src/iter/admm.c
- src/iter/admm.h
- + src/iter/asl.c
- + src/iter/asl.h
- src/iter/batch_gen.c
- src/iter/batch_gen.h
- src/iter/italgos.c
- src/iter/italgos.h
- src/iter/iter.c
- src/iter/iter.h
- src/iter/iter2.c
- src/iter/iter2.h
- src/iter/iter3.c
- src/iter/iter3.h
- src/iter/iter4.c
- src/iter/iter4.h
- src/iter/iter5.c
- src/iter/iter5.h
- src/iter/iter6.c
- src/iter/iter6.h
- src/iter/iter6_ops.c
- src/iter/iter6_ops.h
- src/iter/iter_dump.c
- src/iter/iter_dump.h
- src/iter/itop.c
- src/iter/itop.h
- src/iter/lad.c
- src/iter/lad.h
- src/iter/lsqr.c
- src/iter/lsqr.h
- src/iter/misc.c
- src/iter/misc.h
- src/iter/monitor.c
- src/iter/monitor.h
- src/iter/monitor_iter6.c
- src/iter/monitor_iter6.h
- src/iter/niht.c
- src/iter/niht.h
- src/iter/proj.c
- src/iter/prox.c
- src/iter/prox.h
- src/iter/prox2.c
- src/iter/prox2.h
- src/iter/tgv.c
- src/iter/tgv.h
- src/iter/thresh.c
- src/iter/thresh.h
- src/iter/vec.c
- src/iter/vec.h
- src/itsense.c
- src/join.c
- src/lapacke/lapacke.h
- src/lapacke/lapacke_cge_nancheck.c
- src/lapacke/lapacke_cge_trans.c
- + src/lapacke/lapacke_cgees.c
- + src/lapacke/lapacke_cgees_work.c
- src/lapacke/lapacke_cgesdd.c
- src/lapacke/lapacke_cgesdd_work.c
- src/lapacke/lapacke_cgesvd.c
- src/lapacke/lapacke_cgesvd_work.c
- src/lapacke/lapacke_che_nancheck.c
- + src/lapacke/lapacke_che_trans.c
- src/lapacke/lapacke_cheev.c
- src/lapacke/lapacke_cheev_work.c
- + src/lapacke/lapacke_chegv.c
- + src/lapacke/lapacke_chegv_work.c
- src/lapacke/lapacke_cpo_nancheck.c
- src/lapacke/lapacke_cpo_trans.c
- src/lapacke/lapacke_cpotrf.c
- src/lapacke/lapacke_cpotrf_work.c
- src/lapacke/lapacke_ctr_nancheck.c
- src/lapacke/lapacke_ctr_trans.c
- + src/lapacke/lapacke_ctrsyl.c
- + src/lapacke/lapacke_ctrsyl_work.c
- src/lapacke/lapacke_ctrtri.c
- src/lapacke/lapacke_ctrtri_work.c
- + src/lapacke/lapacke_ctrtrs.c
- + src/lapacke/lapacke_ctrtrs_work.c
- + src/lapacke/lapacke_nancheck.c
- src/lapacke/lapacke_utils.h
- src/lapacke/lapacke_xerbla.c
- src/lapacke/lapacke_zge_nancheck.c
- src/lapacke/lapacke_zge_trans.c
- + src/lapacke/lapacke_zgees.c
- + src/lapacke/lapacke_zgees_work.c
- src/lapacke/lapacke_zgesdd.c
- src/lapacke/lapacke_zgesdd_work.c
- src/lapacke/lapacke_zhe_nancheck.c
- src/lapacke/lapacke_zhe_trans.c
- src/lapacke/lapacke_zheev.c
- src/lapacke/lapacke_zheev_work.c
- src/lapacke/lapacke_ztr_nancheck.c
- src/lapacke/lapacke_ztr_trans.c
- + src/linops/casorati.c
- + src/linops/casorati.h
- src/linops/decompose_complex.c
- src/linops/decompose_complex.h
- − src/linops/finite_diff.c
- − src/linops/finite_diff.h
- src/linops/fmac.c
- src/linops/fmac.h
- src/linops/grad.c
- src/linops/grad.h
- src/linops/linop.c
- src/linops/linop.h
- src/linops/lintest.c
- src/linops/realval.c
- src/linops/realval.h
- − src/linops/sampling.c
- − src/linops/sampling.h
- src/linops/someops.c
- src/linops/someops.h
- src/linops/sum.c
- src/linops/waveop.c
- src/linops/waveop.h
- src/looklocker.c
- src/lowrank/batchsvd.c
- src/lowrank/batchsvd.h
- src/lowrank/lrthresh.c
- src/lowrank/lrthresh.h
- src/lowrank/svthresh.c
- src/lowrank/svthresh.h
- src/lrmatrix.c
- src/main.h
- src/mandelbrot.c
- − src/mat2cfl.c
- src/measure.c
- src/mip.c
- src/misc/Orchestra.cc
- + src/misc/bench.c
- + src/misc/bench.h
- src/misc/cppwrap.h
- src/misc/debug.c
- src/misc/debug.h
- src/misc/dicom.c
- + src/misc/dllspec.h
- + src/misc/egraph.c
- + src/misc/egraph.h
- src/misc/graph.c
- src/misc/graph.h
- src/misc/io.c
- src/misc/io.h
- src/misc/list.c
- src/misc/list.h
- + src/misc/lock.c
- + src/misc/lock.h
- src/misc/memcfl.c
- src/misc/memcfl.h
- src/misc/misc.c
- src/misc/misc.h
- src/misc/mmio.c
- src/misc/mmio.h
- src/misc/mri.h
- src/misc/mri.c → src/misc/mri2.c
- + src/misc/mri2.h
- src/misc/opts.c
- src/misc/opts.h
- src/misc/pd.c
- src/misc/pd.h
- src/misc/png.c
- src/misc/png.h
- src/misc/resize.c
- src/misc/resize.h
- src/misc/shrdptr.c
- src/misc/shrdptr.h
- + src/misc/stream.c
- + src/misc/stream.h
- + src/misc/stream_protocol.c
- + src/misc/stream_protocol.h
- src/misc/subpixel.c
- src/misc/subpixel.h
- + src/misc/tree.c
- + src/misc/tree.h
- src/misc/types.h
- src/misc/utils.c
- src/misc/utils.h
- src/misc/version.c
- src/misc/version.h
- src/misc/ya_getopt.c
- src/misc/ya_getopt.h
- src/mnist.c
- src/moba.c
- src/moba/T1fun.c
- src/moba/T1fun.h
- src/moba/T1phyfun.c
- src/moba/T1phyfun.h
- src/moba/T2fun.c
- src/moba/T2fun.h
- src/moba/blochfun.c
- src/moba/blochfun.h
- src/moba/exp.c
- + src/moba/ir_meco.c
- + src/moba/ir_meco.h
- src/moba/iter_l1.c
- src/moba/iter_l1.h
- + src/moba/lorentzian.c
- + src/moba/lorentzian.h
- src/moba/meco.c
- src/moba/meco.h
- src/moba/moba.c
- src/moba/moba.h
- src/moba/model_T1.c
- src/moba/model_T2.c
- src/moba/model_T2.h
- src/moba/model_meco.c
- src/moba/model_meco.h
- src/moba/model_moba.c
- src/moba/model_moba.h
- src/moba/optreg.c
- src/moba/optreg.h
- src/moba/recon.c
- src/moba/recon.h
- src/moba/recon_meco.c
- src/moba/recon_meco.h
- src/mobafit.c
- + src/mobasig.c
- src/morphop.c
- + src/motion/affine.c
- + src/motion/affine.h
- + src/motion/displacement.c
- + src/motion/displacement.h
- + src/motion/gpu_interpolate.cu
- + src/motion/gpu_interpolate.h
- + src/motion/interpolate.c
- + src/motion/interpolate.h
- + src/motion/opticalflow.c
- + src/motion/opticalflow.h
- + src/motion/pyramide.c
- + src/motion/pyramide.h
- + src/motion/syn.c
- + src/motion/syn.h
- src/multicfl.c
- + src/ncalib.c
- src/networks/cnn.c
- src/networks/cnn.h
- + src/networks/cunet.c
- + src/networks/cunet.h
- src/networks/losses.c
- src/networks/losses.h
- src/networks/misc.c
- src/networks/misc.h
- + src/networks/nlinvnet.c
- + src/networks/nlinvnet.h
- src/networks/nnet.c
- src/networks/nnet.h
- src/networks/reconet.c
- src/networks/reconet.h
- + src/networks/score.c
- + src/networks/score.h
- + src/networks/tf.c
- + src/networks/tf.h
- src/networks/unet.c
- src/networks/unet.h
- src/nlinv.c
- + src/nlinvnet.c
- + src/nlmeans.c
- src/nlops/cast.c
- src/nlops/chain.c
- src/nlops/chain.h
- src/nlops/checkpointing.c
- src/nlops/checkpointing.h
- src/nlops/const.c
- src/nlops/const.h
- src/nlops/conv.c
- src/nlops/conv.h
- + src/nlops/gmm.c
- + src/nlops/gmm.h
- + src/nlops/losses.c
- + src/nlops/losses.h
- + src/nlops/mi_metric.c
- + src/nlops/mi_metric.h
- src/nlops/mri_ops.c
- src/nlops/mri_ops.h
- src/nlops/nlop.c
- src/nlops/nlop.h
- src/nlops/nlop_jacobian.c
- src/nlops/nlop_jacobian.h
- src/nlops/nltest.c
- src/nlops/nltest.h
- src/nlops/norm_inv.c
- + src/nlops/smath.c
- + src/nlops/smath.h
- + src/nlops/snlop.c
- + src/nlops/snlop.h
- src/nlops/someops.c
- src/nlops/someops.h
- src/nlops/stack.c
- src/nlops/stack.h
- src/nlops/tenmul.c
- src/nlops/zexp.c
- src/nlops/zexp.h
- src/nlops/zhyperbolic.c
- src/nlops/zhyperbolic.h
- + src/nlops/ztrigon.c
- + src/nlops/ztrigon.h
- src/nn/activation.c
- src/nn/activation.h
- src/nn/activation_nn.c
- src/nn/activation_nn.h
- src/nn/batchnorm.c
- src/nn/batchnorm.h
- src/nn/chain.c
- src/nn/chain.h
- src/nn/const.c
- src/nn/const.h
- src/nn/data_list.c
- src/nn/data_list.h
- + src/nn/ext_wrapper.c
- + src/nn/ext_wrapper.h
- src/nn/init.c
- src/nn/init.h
- src/nn/layers.c
- src/nn/layers.h
- src/nn/layers_nn.c
- src/nn/layers_nn.h
- src/nn/losses.c
- src/nn/losses.h
- src/nn/losses_nn.c
- src/nn/losses_nn.h
- src/nn/misc.c
- src/nn/misc.h
- src/nn/nn.c
- src/nn/nn.h
- src/nn/nn_ops.c
- src/nn/nn_ops.h
- + src/nn/pytorch_cpp_wrapper.cc
- + src/nn/pytorch_cpp_wrapper.h
- + src/nn/pytorch_wrapper.c
- + src/nn/pytorch_wrapper.h
- src/nn/rbf.c
- src/nn/rbf.h
- src/nn/tf_wrapper.c
- src/nn/tf_wrapper.h
- src/nn/weights.c
- src/nn/weights.h
- src/nnet.c
- src/noir/misc.c
- src/noir/misc.h
- src/noir/model.c
- src/noir/model.h
- + src/noir/model2.c
- + src/noir/model2.h
- + src/noir/model_net.c
- + src/noir/model_net.h
- + src/noir/pole.c
- + src/noir/pole.h
- src/noir/recon.c
- src/noir/recon.h
- + src/noir/recon2.c
- + src/noir/recon2.h
- src/noir/utils.c
- src/noir/utils.h
- src/noise.c
- + src/noncart/gpu_grid.cu
- + src/noncart/gpu_grid.h
- src/noncart/grid.c
- src/noncart/grid.h
- src/noncart/nudft.c
- src/noncart/nudft.h
- src/noncart/nufft.c
- src/noncart/nufft.h
- + src/noncart/nufft_chain.c
- + src/noncart/nufft_chain.h
- src/noncart/nufft_priv.h
- src/noncart/precond.c
- src/noncart/precond.h
- + src/noncart/radial.c
- + src/noncart/radial.h
- src/noncart/traj.c
- src/noncart/traj.h
- src/normalize.c
- src/nrmse.c
- src/nufft.c
- + src/nufftbase.c
- src/num/blas.c
- src/num/blas.h
- src/num/blas_md_wrapper.c
- src/num/blas_md_wrapper.h
- src/num/blockproc.c
- src/num/blockproc.h
- src/num/casorati.c
- src/num/casorati.h
- src/num/chebfun.c
- + src/num/compress.c
- + src/num/compress.h
- src/num/conv.c
- src/num/conv.h
- src/num/convcorr.c
- src/num/convcorr.h
- src/num/convoaa.c
- src/num/convoaa.h
- src/num/cudnn_wrapper.c
- + src/num/delayed.c
- + src/num/delayed.h
- src/num/fft-cuda.c
- src/num/fft-cuda.h
- src/num/fft.c
- src/num/fft.h
- + src/num/fft_plan.c
- + src/num/fft_plan.h
- src/num/filter.c
- src/num/filter.h
- src/num/flpmath.c
- src/num/flpmath.h
- src/num/fltools.c
- + src/num/gaussians.c
- + src/num/gaussians.h
- src/num/gpu_conv.cu
- src/num/gpu_reduce.cu
- src/num/gpukrnls.cu
- src/num/gpukrnls.h
- + src/num/gpukrnls_bat.cu
- + src/num/gpukrnls_bat.h
- + src/num/gpukrnls_copy.cu
- + src/num/gpukrnls_copy.h
- + src/num/gpukrnls_misc.cu
- + src/num/gpukrnls_misc.h
- + src/num/gpukrnls_triagmat.cu
- + src/num/gpukrnls_triagmat.h
- + src/num/gpukrnls_unfold.cu
- + src/num/gpukrnls_unfold.h
- src/num/gpuops.c
- src/num/gpuops.h
- + src/num/gpurand.cu
- + src/num/gpurand.h
- src/num/init.c
- src/num/init.h
- src/num/iovec.c
- src/num/iovec.h
- src/num/lapack.c
- src/num/lapack.h
- src/num/linalg.c
- src/num/linalg.h
- + src/num/linalg_rand.c
- + src/num/linalg_rand.h
- src/num/loop.c
- src/num/loop.h
- src/num/matexp.c
- src/num/matexp.h
- src/num/md_wrapper.c
- src/num/md_wrapper.h
- src/num/mdfft.c
- src/num/mdfft.h
- src/num/mem.c
- src/num/mem.h
- + src/num/morph.c
- + src/num/morph.h
- + src/num/mpi_ops.c
- + src/num/mpi_ops.h
- src/num/multind.c
- src/num/multind.h
- src/num/multiplace.c
- src/num/multiplace.h
- + src/num/nlmeans.c
- + src/num/nlmeans.h
- src/num/ode.c
- src/num/ode.h
- src/num/ops.c
- src/num/ops.h
- src/num/ops_graph.c
- src/num/ops_graph.h
- src/num/ops_p.c
- src/num/ops_p.h
- src/num/optimize.c
- src/num/optimize.h
- + src/num/philox.inc
- src/num/polynom.c
- src/num/qform.c
- + src/num/quadrature.c
- + src/num/quadrature.h
- src/num/rand.c
- src/num/rand.h
- src/num/reduce_md_wrapper.c
- src/num/reduce_md_wrapper.h
- src/num/shuffle.c
- src/num/shuffle.h
- src/num/simplex.c
- src/num/simplex.h
- src/num/specfun.c
- src/num/specfun.h
- src/num/splines.c
- src/num/splines.h
- + src/num/triagmat.c
- + src/num/triagmat.h
- src/num/vec3.c
- src/num/vecops.c
- src/num/vecops.h
- src/num/vecops_strided.c
- src/num/vecops_strided.h
- + src/num/vptr.c
- + src/num/vptr.h
- + src/num/vptr_fun.c
- + src/num/vptr_fun.h
- + src/num/vptr_iter.c
- + src/num/vptr_iter.h
- src/num/wavelet.c
- src/num/wavelet.h
- src/onehotenc.c
- src/ones.c
- src/pattern.c
- src/phantom.c
- + src/phasepole.c
- src/pics.c
- src/pocsense.c
- src/poisson.c
- src/pol2mask.c
- src/poly.c
- + src/psf.c
- + src/pulse.c
- src/python/pyBART.cpp.in
- + src/raga.c
- src/reconet.c
- src/repmat.c
- src/reshape.c
- src/resize.c
- src/rmfreq.c
- src/rof.c
- src/roistat.c
- + src/rovir.c
- src/rss.c
- src/rtnlinv.c
- src/sake.c
- src/sake/sake.c
- + src/sample.c
- src/saxpy.c
- src/scale.c
- src/sdot.c
- src/sense/model.c
- src/sense/model.h
- + src/sense/modelnc.c
- + src/sense/modelnc.h
- src/sense/optcom.c
- src/sense/optcom.h
- src/sense/pocs.c
- src/sense/pocs.h
- src/sense/recon.c
- src/sense/recon.h
- + src/seq.c
- + src/seq/adc_rf.c
- + src/seq/adc_rf.h
- + src/seq/anglecalc.c
- + src/seq/anglecalc.h
- + src/seq/config.c
- + src/seq/config.h
- + src/seq/custom_ui.c
- + src/seq/custom_ui.h
- + src/seq/event.c
- + src/seq/event.h
- + src/seq/flash.c
- + src/seq/flash.h
- + src/seq/gradient.c
- + src/seq/gradient.h
- + src/seq/helpers.c
- + src/seq/helpers.h
- + src/seq/kernel.c
- + src/seq/kernel.h
- + src/seq/mag_prep.c
- + src/seq/mag_prep.h
- + src/seq/misc.c
- + src/seq/misc.h
- + src/seq/opts.c
- + src/seq/opts.h
- + src/seq/pulse.c
- + src/seq/pulse.h
- + src/seq/pulse_library.c
- + src/seq/pulse_library.h
- + src/seq/pulseq.c
- + src/seq/pulseq.h
- + src/seq/seq.c
- + src/seq/seq.h
- + src/seq/ui_enums.h
- src/show.c
- src/signal.c
- src/sim.c
- src/simu/biot_savart.c
- src/simu/biot_savart.h
- src/simu/bloch.c
- src/simu/bloch.h
- src/simu/coil.c
- src/simu/coil.h
- src/simu/crb.c
- src/simu/crb.h
- src/simu/epg.c
- + src/simu/grid.c
- + src/simu/grid.h
- src/simu/phantom.c
- src/simu/phantom.h
- − src/simu/pulse.c
- − src/simu/pulse.h
- src/simu/sens.c
- src/simu/sens.h
- src/simu/shape.c
- src/simu/shape.h
- src/simu/shepplogan.c
- src/simu/shepplogan.h
- src/simu/signals.c
- src/simu/signals.h
- src/simu/simulation.c
- src/simu/simulation.h
- + src/simu/tsegf.c
- + src/simu/tsegf.h
- src/slice.c
- src/spow.c
- src/sqpics.c
- src/squeeze.c
- src/ssa.c
- src/std.c
- + src/stl.c
- + src/stl/misc.c
- + src/stl/misc.h
- + src/stl/models.c
- + src/stl/models.h
- src/svd.c
- + src/tee.c
- + src/tensorflow.c
- src/tgv.c
- src/threshold.c
- src/toimg.c
- + src/toraw.c
- src/traj.c
- + src/trajcor.c
- src/transpose.c
- src/twixread.c
- + src/unwrap.c
- src/upat.c
- src/var.c
- src/vec.c
- src/version.c
- src/walsh.c
- src/wave.c
- src/wavelet.c
- src/wavelet/wavelet.c
- src/wavelet/wavelet.h
- src/wavelet/wavthresh.c
- src/wavelet/wavthresh.h
- src/wavelet/wl3-cuda.cu
- src/wavepsf.c
- src/whiten.c
- src/win/basename_patch.h
- src/win/fmemopen.c
- src/win/fmemopen.h
- src/win/mman.c
- src/win/open_patch.h
- src/win/rand_r.h
- src/win/vdprintf.h
- src/window.c
- src/wshfl.c
- src/zeros.c
- src/zexp.c
- startup.m
- startup.py
- startup.sh
- − sub
- − tests/CMakeLists.txt
- + tests/asl.mk
- tests/bin.mk
- + tests/calc.mk
- tests/cc.mk
- tests/ccapply.mk
- + tests/coils.mk
- + tests/compress.mk
- tests/copy.mk
- + tests/denoise.mk
- tests/ecalib.mk
- tests/estdelay.mk
- + tests/estscaling.mk
- tests/fft.mk
- + tests/geom/flower.cfl
- + tests/geom/flower.hdr
- + tests/geom/flower2.cfl
- + tests/geom/flower2.hdr
- + tests/gmm.mk
- tests/gpu.mk
- + tests/grid.mk
- + tests/grog.mk
- + tests/ismrmrd.mk
- + tests/ismrmrd_h5tocfl.py
- tests/linsub.mk
- tests/lrmatrix.mk
- tests/measure.mk
- tests/moba.mk
- tests/mobafit.mk
- + tests/mobasig.mk
- + tests/motion.mk
- tests/network.mk
- + tests/network_tf1.py
- + tests/network_tf2.py
- + tests/nlinv-mpi.mk
- tests/nlinv.mk
- + tests/nlmeans.mk
- tests/noise.mk
- tests/nufft.mk
- + tests/opts.mk
- tests/phantom.mk
- + tests/pics-loop.mk
- + tests/pics-mpi.mk
- tests/pics.mk
- + tests/pole.mk
- + tests/psf.mk
- + tests/pulse.mk
- tests/python_bart.mk
- tests/pythoncfl.mk
- + tests/raga.mk
- tests/reshape.mk
- tests/roistat.mk
- tests/rtnlinv.mk
- + tests/sample.mk
- + tests/seq.mk
- tests/signal.mk
- tests/sim.mk
- tests/smallfov.mk
- tests/ssa.mk
- + tests/stl.mk
- + tests/stream.mk
- + tests/sub.mk
- tests/tgv.mk
- tests/traj.mk
- + tests/trajcor.mk
- tests/twixread.mk
- tests/version.mk
- tests/whiten.mk
- + utests/exp_grad.pb
- + utests/exp_grad_jac.pb
- + utests/exp_grad_jac_real.pb
- + utests/test_adc_rf.c
- + utests/test_affine.c
- + utests/test_angle_calc.c
- + utests/test_asl.c
- utests/test_batchsvd.c
- utests/test_biot_savart.c
- + utests/test_casorati.c
- utests/test_convcorr.c
- + utests/test_cuda_affine.c
- utests/test_cuda_convcorr.c
- utests/test_cuda_flpmath.c
- utests/test_cuda_flpmath2.c
- utests/test_cuda_gpukrnls.c
- + utests/test_cuda_memcache_clear.c
- + utests/test_cuda_multind.c
- + utests/test_cuda_rand.c
- + utests/test_cuda_shuffle.c
- utests/test_cudafft.c
- + utests/test_delayed.c
- utests/test_epg.c
- + utests/test_events.c
- + utests/test_fft.c
- + utests/test_fib.c
- + utests/test_flash.c
- utests/test_flpmath.c
- utests/test_flpmath2.c
- + utests/test_gaussians.c
- + utests/test_gradient.c
- + utests/test_graph.c
- + utests/test_grog.c
- utests/test_iter.c
- + utests/test_lapack.c
- utests/test_linalg.c
- + utests/test_linalg_rand.c
- utests/test_linop.c
- + utests/test_matexp.c
- + utests/test_md_gaussians.c
- utests/test_memcfl.c
- utests/test_misc.c
- utests/test_moba.c
- + utests/test_morph.c
- + utests/test_mpi.c
- + utests/test_mpi_fft.c
- + utests/test_mpi_flpmath.c
- + utests/test_mpi_multind.c
- + utests/test_mpi_reduction.c
- utests/test_multind.c
- + utests/test_nlmeans.c
- utests/test_nlop.c
- utests/test_nlop_jacobian.c
- utests/test_nn.c
- utests/test_nn_ops.c
- + utests/test_nn_pytorch.c
- + utests/test_nn_pytorch.pt
- + utests/test_nn_pytorch_cuda.c
- utests/test_nn_tf.c
- + utests/test_ode.c
- utests/test_ode_bloch.c
- utests/test_ode_simu.c
- utests/test_padding.c
- utests/test_pattern.c
- + utests/test_phantom.c
- utests/test_polynom.c
- utests/test_prox.c
- utests/test_prox2.c
- utests/test_pulse.c
- + utests/test_pulseq.c
- + utests/test_rand.c
- + utests/test_score.c
- + utests/test_seq.c
- utests/test_signals.c
- + utests/test_snlop.c
- utests/test_specfun.c
- + utests/test_stl.c
- + utests/test_streams.c
- + utests/test_tree.c
- + utests/test_tsegf.c
- utests/test_types.c
- utests/test_window.c
- utests/utest.c
- utests/utest.h
- − utests/utest_gpu.c
- + utests/utests_run.sh
- − valgrind.supp
- version.txt
- + web/serve.py
- + web/wwwroot/bart_base.js
- + web/wwwroot/bart_worker.js
- + web/wwwroot/cmd.html
- + web/wwwroot/cmd.js
- + web/wwwroot/index.html
- + web/wwwroot/test.js
- + web/wwwroot/worker.html
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View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/153fed083a7f43aaa75aed65f21b3e6f3217ee25...b889d8cbab647b1abbab253cb83cd8b3523ecd06
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