[med-svn] [Git][med-team/bart][upstream] 519 commits: Added a simple example in the end of file (#273)
Martin Uecker (@uecker-guest)
gitlab at salsa.debian.org
Sun Sep 25 10:41:56 BST 2022
Martin Uecker pushed to branch upstream at Debian Med / bart
Commits:
4ffaebeb by Sidharth Kumar at 2021-10-17T01:03:47+02:00
Added a simple example in the end of file (#273)
Added a simple example of bart resize with and without -c flag. Recommended the user to look at the doc/resize.txt file to get more help.
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0d70cdd6 by Martin Uecker at 2021-10-24T23:34:53+02:00
fix compiler version check for dissecting trampolines
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59d89cde by Martin Uecker at 2021-10-24T23:34:53+02:00
add resize.txt to bart.spec
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6068509d by Moritz Blumenthal at 2021-10-26T16:37:15+02:00
Relax tests
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568cc98d by Moritz Blumenthal at 2021-10-26T16:37:43+02:00
fix zpow on gpu
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8ec67706 by Moritz Blumenthal at 2021-10-26T16:38:23+02:00
Refactor test for convcorr
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c51f33d7 by Moritz Blumenthal at 2021-10-26T16:38:55+02:00
Activate gputest for convcorr
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dccb9258 by Moritz Blumenthal at 2021-10-26T16:56:33+02:00
pass non-deterministic flag to nvcc
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87eec682 by Moritz Blumenthal at 2021-10-26T16:58:41+02:00
pass debug flag to nvcc
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2f71325d by Moritz Blumenthal at 2021-10-26T16:59:05+02:00
fix linop stack (P. Schaten)
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b90f2cf3 by Moritz Blumenthal at 2021-10-26T17:01:45+02:00
Use optimizatios from vecops strided
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f48f5d24 by Moritz Blumenthal at 2021-10-26T17:04:31+02:00
linop get normal (P Schaten)
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75dc75d1 by Moritz Blumenthal at 2021-10-26T17:05:16+02:00
Refactor reduction kernels
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f9cb03a6 by Moritz Blumenthal at 2021-10-26T17:05:42+02:00
md_parallel_nary: allow flags exceeding D
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d33961cd by Moritz Blumenthal at 2021-10-26T17:31:33+02:00
add struct holding data at multiple places (gpu + cpu)
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36ebc331 by Moritz Blumenthal at 2021-10-26T17:31:57+02:00
multiplace and lazy initialization for linop_fmac linop_gdiag
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b681b8fc by Martin Uecker at 2021-10-26T19:19:49+02:00
fix multiplace patch
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8e8943c4 by Martin Uecker at 2021-10-26T19:42:24+02:00
refactor multiplace
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92f2b139 by Moritz Blumenthal at 2021-10-26T20:01:29+02:00
Stop gradient by replacing derivative with null-linop
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5fffafda by Moritz Blumenthal at 2021-10-26T20:02:18+02:00
add function to flatten(by reshape) input/output of nlop
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55761b60 by Moritz Blumenthal at 2021-10-26T20:03:37+02:00
Extend nlop framework
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535b1ed5 by Martin Uecker at 2021-10-26T20:05:45+02:00
remove unused headers
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a0d6f4c8 by Martin Uecker at 2021-10-26T20:21:11+02:00
formalities & style
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368d244e by Moritz Blumenthal at 2021-10-26T21:33:57+02:00
make make_z3op_scalar fast
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6277e52b by Moritz Blumenthal at 2021-10-26T21:41:38+02:00
Add function to apply nlop in loop
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8b494d5c by Moritz Blumenthal at 2021-10-26T22:18:04+02:00
Add batch dim
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21fbbb1f by Moritz Blumenthal at 2021-10-26T22:25:34+02:00
Add linop repmat (adjoing sum)
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a72c9d98 by Martin Uecker at 2021-10-26T22:25:34+02:00
formalities
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95df246e by Moritz Blumenthal at 2021-10-26T22:26:49+02:00
add tenmul
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9e3fce01 by Moritz Blumenthal at 2021-10-26T22:42:17+02:00
functions to get highest and lowest selected dim
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ef5294d7 by Moritz Blumenthal at 2021-10-26T22:42:17+02:00
simplify code for fill like copies
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495295db by Martin Uecker at 2021-10-26T22:42:17+02:00
style
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b7162f66 by Moritz Blumenthal at 2021-10-26T22:59:02+02:00
Reduce memory usage
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d7ab615b by Christian Holme at 2021-10-27T10:32:47+02:00
shared-lib: preserve CFLAGS & move to MAKESTAGE=2
We do not want to override the CFLAGS, so just add -fPIC to the normal
initialization of CFLAGS.
Additionally, the target needs to be defined in MAKESTAGE=2,
because the necessary variables are only defined in there.
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a4df6b06 by Martin Uecker at 2021-10-28T21:12:36+02:00
ubsan workaround for zero sized array
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8a5533fa by Moritz Blumenthal at 2021-11-03T09:23:05+01:00
Add support for multi cfl
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6ae13fca by Moritz Blumenthal at 2021-11-03T09:42:26+01:00
Update python cfl + multicfl
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8ec0ebdd by Martin Uecker at 2021-11-03T09:42:26+01:00
copyright update, spelling, style
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970be458 by Moritz Blumenthal at 2021-11-03T11:46:55+01:00
Add generic list
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c0ea904a by Moritz Blumenthal at 2021-11-03T11:49:00+01:00
Add generic graphs
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70776fba by Moritz Blumenthal at 2021-11-04T11:51:04+01:00
Add function to create ptr and printf in it
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a5241548 by Moritz Blumenthal at 2021-11-04T11:51:04+01:00
Add graphs to ops/linops/nlops
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b0a63f22 by Moritz Blumenthal at 2021-11-04T14:20:24+01:00
Managed nlops for save memory of unused derivatives
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89844ddf by Martin Uecker at 2021-11-04T15:03:51+01:00
updates
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d9c36d42 by Moritz Blumenthal at 2021-11-04T15:06:04+01:00
Add nlops based on jacobians
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fe6434da by Moritz Blumenthal at 2021-11-04T15:06:04+01:00
Adapt tenmul to managed interface
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19df772d by Moritz Blumenthal at 2021-11-04T15:06:04+01:00
Add some nlops
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a6b1f1ec by Moritz Blumenthal at 2021-11-04T15:22:11+01:00
checkpointing
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910790fb by Martin Uecker at 2021-11-06T09:06:00+01:00
fix python->python3
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f8b302a8 by Moritz Blumenthal at 2021-11-06T09:06:00+01:00
Add convolution
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f3e7f790 by Moritz Blumenthal at 2021-11-06T09:06:00+01:00
Update iterative algorithms
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e82eb431 by Martin Uecker at 2021-11-06T09:17:17+01:00
style
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b88f5cd7 by Christian Holme at 2021-11-08T14:20:19+01:00
multicfl: fix interface
Now, when combining, the last argument is the multicfl;
and when splitting / separatingg, the first argument is the multicfl.
This is to maintain standard bart usage, with the input coming first
and output last in command-line tools.
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8ba111bb by Christian Holme at 2021-11-08T14:46:33+01:00
tests/multicfl.mk: adapt to interface changes
As the input is now in the beginning, the test needs to be adapted
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2a2cf0bb by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Add projections
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bbd9ab36 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Add nn framework
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14b51ff6 by Martin Uecker at 2021-11-09T14:58:18+01:00
macros for real dims and strides
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c187fc42 by Martin Uecker at 2021-11-09T14:58:18+01:00
ubsan fix
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ab5b187c by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Allow comma separated list for subopts
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6d316276 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Command line opts for iter6
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8046cb22 by Martin Uecker at 2021-11-09T14:58:18+01:00
copyright & indentation
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9428c2c7 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Add function to check if linop is null
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d846cba0 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Optimize operators based on graphs
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67869b34 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Arbitrary number of inputs for operator zadd
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66f710a0 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Make sums with multiple permuted inputs identifyable
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a878e0db by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
nlop_no_der for checkpointing
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d0f21e2d by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Optimize linear operators Ax+Ay ->A(x+y) i
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724e9da8 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Add functions to optimize linops by graph
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a0489d83 by Martin Uecker at 2021-11-09T14:58:18+01:00
fix test
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0f0f1061 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
add utassert only returning when false
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0817d71f by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
add md_is_sameplace
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65c5bd4c by Martin Uecker at 2021-11-09T14:58:18+01:00
fix comment
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864c2446 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
add generic copy wrapper function and return inner operator in list
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8f12c040 by Philipp Ehses at 2021-11-12T08:22:14+01:00
poisson.c: fix calreg position for odd calreg size (#274)
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4f6da5df by Moritz Blumenthal at 2021-11-12T08:28:35+01:00
Multiplace for nufft + later update of traj and psf
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18b818a9 by Martin Uecker at 2021-11-12T08:28:35+01:00
don't initialize
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f842fbcc by Moritz Blumenthal at 2021-11-12T08:28:35+01:00
Add nlops mri
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e54982d8 by Martin Uecker at 2021-11-12T08:28:35+01:00
reduce output
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63f51488 by Moritz Blumenthal at 2021-11-12T08:28:35+01:00
Add nnet and reconet
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a6dd97a9 by Martin Uecker at 2021-11-12T08:28:35+01:00
fix memory leak
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4ff0379f by Martin Uecker at 2021-11-12T08:28:35+01:00
fix ubsan zero array issue
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490ee042 by Martin Uecker at 2021-11-12T08:28:35+01:00
nlinv: fix resource leak
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0e1fdb16 by Martin Uecker at 2021-11-12T08:28:35+01:00
zinv: fix leak
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a9bde381 by Martin Uecker at 2021-11-12T08:28:35+01:00
fix memory leak in test
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3b8a4294 by Martin Uecker at 2021-11-12T08:28:35+01:00
turn off broken tests
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59549982 by Martin Uecker at 2021-11-12T08:28:35+01:00
revise tuple ops and fix some issues
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b57ef427 by Moritz Blumenthal at 2021-11-12T15:19:44+01:00
Add tool to transform onehotencoded data to integer encoded
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e21abdf6 by Moritz Blumenthal at 2021-11-12T15:20:35+01:00
Add attention for unet combine
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53299e1b by Moritz Blumenthal at 2021-11-12T15:20:42+01:00
fix test_nlop for linear optimization
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3abe32d7 by Moritz Blumenthal at 2021-11-12T15:23:42+01:00
copy wrapper at sameplace
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865c8364 by Moritz Blumenthal at 2021-11-12T15:26:30+01:00
improve linop optimization
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5dd970cd by Moritz Blumenthal at 2021-11-12T15:27:13+01:00
fix unsigned int in cudnn wrapper
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555c044c by Moritz Blumenthal at 2021-11-12T15:27:21+01:00
unsigned int gpu conv
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ea6ecc3d by Moritz Blumenthal at 2021-11-12T15:27:32+01:00
test cuda flpmath test for nan
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6793d5b9 by Moritz Blumenthal at 2021-11-12T15:57:55+01:00
fix scaling
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a3f98500 by Moritz Blumenthal at 2021-11-12T16:00:12+01:00
refactor mad loss
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a3babf69 by Moritz Blumenthal at 2021-11-12T16:03:11+01:00
fix mri_ops: allow for shared patterns
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4fcfbb24 by Moritz Blumenthal at 2021-11-12T16:04:31+01:00
fix: "Add nnet and reconet" delete unused options
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c0bdf52e by Martin Uecker at 2021-11-12T16:07:01+01:00
minor
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b3a53546 by Moritz Blumenthal at 2021-11-13T07:24:10+01:00
add mask to loss functions
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5bf58839 by Moritz Blumenthal at 2021-11-13T07:24:20+01:00
update mri ops
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bae11ed9 by Moritz Blumenthal at 2021-11-13T07:24:32+01:00
updates nn
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2b59c312 by Moritz Blumenthal at 2021-11-13T07:24:44+01:00
add list for data passed to training etc ...
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0f768020 by Moritz Blumenthal at 2021-11-13T07:24:57+01:00
refactor reconet dc ops + add mask
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0b16ca02 by Martin Uecker at 2021-11-13T08:12:55+01:00
fix another ubsan issue
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f14ab6fc by Moritz Blumenthal at 2021-11-13T08:24:07+01:00
fix test
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1a97ed62 by Martin Uecker at 2021-11-13T08:24:23+01:00
update BART references
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dc7e8d92 by Martin Uecker at 2021-11-13T09:10:43+01:00
integration with ubsan
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2eba6de1 by Martin Uecker at 2021-11-13T09:10:53+01:00
fixup
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dff5cd25 by Martin Uecker at 2021-11-13T09:10:53+01:00
machine learning references
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86d33b57 by ecat at 2021-11-14T13:20:11+01:00
Added usage notes that may cause issues in pics reconstruction. (#272)
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68758957 by Martin Uecker at 2021-11-14T13:22:10+01:00
move to doc
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84cc4b7d by aTrotier at 2021-11-14T13:28:16+01:00
add 3D uniform traj
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e62c6975 by aTrotier at 2021-11-14T13:28:23+01:00
add 3D uniform half-sphere
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74d22b43 by Martin Uecker at 2021-11-14T14:23:44+01:00
fixes for show command
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af791034 by Martin Uecker at 2021-11-14T15:09:35+01:00
refactor 3D trajectory
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480509c4 by Christian Holme at 2021-11-15T16:09:54+01:00
calib/delays.c: output to stdout for RING paper
Previously, this used files and a specific define during compilation.
Now, we use the environment variable RING_PAPER and output projection
angles and offsets when RING_PAPER=1
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041df1ee by Christian Holme at 2021-11-16T11:29:14+01:00
num/multind: add pointer for clang
For now, this shouldn't change anything. But if we ever support
clang+cuda, it is one thing less to fix
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55e0f8cc by Christian Holme at 2021-11-16T11:56:25+01:00
rtnlinv.c: properly free pattern
by ensuring that it is always allocated by md_alloc
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470ae52e by Moritz Blumenthal at 2021-11-16T14:17:09+01:00
fix overflow
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53e5886a by Moritz Blumenthal at 2021-11-16T14:17:09+01:00
fix basis
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0ce4a4c5 by Moritz Blumenthal at 2021-11-16T14:18:20+01:00
Add function to get nufft_normal op only (toeplitz)
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0227886f by Moritz Blumenthal at 2021-11-16T14:18:20+01:00
use nufft normal op in reconet
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cf69bcc7 by Moritz Blumenthal at 2021-11-16T14:28:33+01:00
optimize coil/psf tenmul on GPU
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578ac9ae by Martin Uecker at 2021-11-16T15:20:03+01:00
merge reorder/label binning
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8f4ee6ef by rosenzweig at 2021-11-17T11:31:18+01:00
bin: Introduce config struct
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c0f025d5 by rosenzweig at 2021-11-17T11:32:14+01:00
bin: Offset option
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ce95a673 by Christian Holme at 2021-11-17T11:32:14+01:00
bin.c: add missing unmap_cfl
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99b781fe by rosenzweig at 2021-11-17T11:32:14+01:00
bin, calib/bin, tests: Amplitude respiratory binning
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2ce3608f by rosenzweig at 2021-11-17T11:32:14+01:00
bin: assertion to avoid mov_avg in amplitude binning
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82a25a6b by Martin Uecker at 2021-11-17T11:48:07+01:00
add geometric median
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006a96c9 by rosenzweig at 2021-11-17T11:48:07+01:00
num/filter: Add moving average
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2abb6f49 by Martin Uecker at 2021-11-17T11:48:07+01:00
rewrite moving average
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30f6563f by rosenzweig at 2021-11-17T11:48:07+01:00
num/filter: median calculation safe for large arrays
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b7ebe767 by rosenzweig at 2021-11-17T11:48:07+01:00
filter: Moving average option
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4df883d2 by Martin Uecker at 2021-11-17T12:05:06+01:00
fix test and coding style
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1f0f7d82 by Christian Holme at 2021-11-17T13:49:52+01:00
tests/bin.mk: clean up after test
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d9fe30bd by schaten at 2021-11-22T18:01:40+01:00
Fix bart.spec - all files matching doc/*.txt are installed as documentation (#275)
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6b6adff8 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
fixes for scaling maxeigen
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03cbda22 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
fix: allow help ('h') in subopts
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b04ca9b4 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
Fix: real from complex strides for double
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325177b8 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
make eval numerically more stable
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64c1d14c by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
fix bufferoverflow
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e1e766f6 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
networks/misc.c: fix memleak
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411dc751 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
nn/nn.c: fix memleak
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101c4725 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
rtnlinv.c: fix memleak
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d260da12 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
fix memleak in opts
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18ad4038 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
calib/bin.c: fix memleak
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4ed5821b by Moritz Blumenthal at 2021-11-22T22:43:29+01:00
add fsanitize=address
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6646e06c by Martin Uecker at 2021-11-23T13:18:16+01:00
minor fix to call to xargs
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8bc8ad7a by Martin Uecker at 2021-12-16T10:16:59+01:00
typo
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2ba88902 by Martin Uecker at 2021-12-16T10:17:05+01:00
add target for slow tests
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509237af by Martin Uecker at 2021-12-16T10:17:09+01:00
run slow tests
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be5b70c8 by Jon Tamir at 2021-12-16T20:19:10+01:00
Create c-cpp.yml (#276)
*
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5f1679dc by Martin Uecker at 2021-12-16T20:19:36+01:00
refactor & unmap trajectory
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a95f1522 by Martin Uecker at 2021-12-16T20:19:36+01:00
fix trajectory scaling in moba
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df7697a2 by Martin Uecker at 2021-12-16T20:19:36+01:00
set default oversampling to 1.
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7d15691f by Martin Uecker at 2021-12-16T21:25:25+01:00
fix help
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f7e84879 by Martin Uecker at 2021-12-16T21:39:02+01:00
fix clang build
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348e1f17 by Moritz Blumenthal at 2021-12-17T12:06:24+01:00
Fix scaling of nlinv
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26417969 by Moritz Blumenthal at 2021-12-17T12:06:33+01:00
fix scaling of psf with basis
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7181e397 by Martin Uecker at 2021-12-18T15:39:04+01:00
set error to zero for tests which should be exact
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012acdf7 by Martin Uecker at 2021-12-18T19:04:51+01:00
tighten some tests
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83c090e9 by Martin Uecker at 2021-12-18T19:04:51+01:00
tell about loose tests
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22d2b4fc by Martin Uecker at 2021-12-18T19:46:20+01:00
use of uninitialized variable
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63a6b28e by Martin Uecker at 2021-12-18T19:46:47+01:00
reduce default optimization
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7aeae14c by Martin Uecker at 2021-12-23T15:39:02+01:00
style & copyright
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12711590 by Christian Holme at 2022-01-04T13:46:55+01:00
allclean now removes saved fftw wisdowm and estvar simulations
since allclean should give you an actually clean repository
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e2e3cc68 by Christian Holme at 2022-01-04T13:47:12+01:00
fftw: use of wisdom now configurable in Makefile
and disabled by default
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d7192dcf by Jon Tamir at 2022-01-14T08:50:07+01:00
fix path finding for bart + WSL in Matlab (#277)
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f82cf94d by Christian Holme at 2022-01-26T12:33:04+01:00
noir/misc: clear correct length for img_output
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92dd921a by Christian Holme at 2022-01-26T12:35:04+01:00
nlinv: fix noncart ENLIVE
Commit 9ea47b4ae66af rewrote part of the image size estimation for
noncartesian nlinv, and overwrote the number of maps in the `dims`
array, breaking noncartesian ENLIVE.
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fc1930ee by Christian Holme at 2022-01-26T13:08:24+01:00
add tests to check ENLIVE maps dimensions
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20ffadae by Jon Tamir at 2022-02-02T16:31:58+01:00
tests: reduce tolerance a little (Mac Intel 12.1 gcc11) (#279)
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33c56b7c by Philipp Ehses at 2022-02-02T16:51:46+01:00
faster write_cfl (#280)
- - - - -
99b39c4b by Martin Uecker at 2022-02-06T12:19:24+01:00
style
- - - - -
ec016f56 by Martin Uecker at 2022-02-06T15:09:03+01:00
coding style, filename handling
- - - - -
350dec93 by Martin Uecker at 2022-02-06T15:09:48+01:00
protect some macros against double evaluation
- - - - -
50936751 by Jon Tamir at 2022-02-07T11:22:34-06:00
matlab test: comment out TOOLBOX_PATH test (not strictly needed)
- - - - -
237f9fec by Martin Uecker at 2022-02-13T12:02:42+01:00
Update README.md
- - - - -
c84712c9 by Martin Uecker at 2022-02-15T10:35:15+01:00
error message for cuda plan
- - - - -
e1adf2a5 by Philip Schaten at 2022-02-16T21:12:42+01:00
Added rpkg.conf and moved anything rpm-related to pkg/rpm
copr-build broke because rpkg-util does not read rpkg.macros by default anymore.
Instead it looks for a file rpkg.conf which points to the file
containing user-defined macros.
https://www.mail-archive.com/devel@lists.fedoraproject.org/msg170768.html
- - - - -
fcd368fd by Philip Schaten at 2022-02-16T21:12:42+01:00
Moved anything rpm-related to pkg/rpm: Fix a path in libbart-devel.spec
- - - - -
1b62b6cd by Martin Uecker at 2022-02-16T22:44:56+01:00
fix some warnings
- - - - -
4c2f2695 by Christian Holme at 2022-02-17T10:48:51+01:00
add strict array bounds to main-functions
- - - - -
a4765911 by Moritz Blumenthal at 2022-02-22T00:04:25+01:00
softsense for varnet
- - - - -
c75b33ee by Moritz Blumenthal at 2022-02-22T00:06:40+01:00
give numeric index to lambda
- - - - -
36100b91 by Moritz Blumenthal at 2022-02-22T00:07:03+01:00
fix normalization for coil images
- - - - -
f5e4f0ce by Moritz Blumenthal at 2022-02-22T00:07:18+01:00
Update ISMRMRD tool
- - - - -
39283237 by Moritz Blumenthal at 2022-02-22T15:56:40+01:00
more iterations for eigenmapscu
- - - - -
568bccef by Moritz Blumenthal at 2022-02-22T15:56:40+01:00
sure_crop on gpu
- - - - -
cf0baa7e by Moritz Blumenthal at 2022-02-23T10:01:49+01:00
only use first map for reconet by default
- - - - -
e35c79cb by Martin Uecker at 2022-03-13T15:21:44+01:00
coding style
- - - - -
53583a05 by Christian Holme at 2022-04-06T11:39:47+02:00
add tests for fakeksp
- - - - -
7d4cd510 by Christian Holme at 2022-04-06T11:39:47+02:00
fakeksp: fix output argument
output should really be an ARG_OUTFILE
Fixes #283
- - - - -
432a7775 by Christian Holme at 2022-04-07T11:13:35+02:00
add tests for pocsense
- - - - -
c5efbab8 by Christian Holme at 2022-04-07T12:00:48+02:00
pocsense: fix infinite loop in linop_wavelet_create
The previous code would lead to in infinite loop in
`wavelet_num_levels`.
This code builds both the flags and minsize correctly.
- - - - -
9daa033b by Christian Holme at 2022-04-07T12:00:48+02:00
pocsense: use more common wavthresh interface
- - - - -
193c849e by Christian Holme at 2022-04-07T12:07:20+02:00
grecon/optreg: remove unnecessary initialization
- - - - -
4cc95c46 by Christian Holme at 2022-04-07T14:13:36+02:00
misc/opts.c: remove unused forward declaration
The function does not exist anymore as of commit
5954998216ff81bd4e06c535179b15f3d79a7099
- - - - -
7992b244 by Martin Uecker at 2022-04-10T12:54:42+02:00
remove dead code
- - - - -
e5a0c6dc by Martin Uecker at 2022-04-10T12:54:42+02:00
join: rename idata -> in_data
- - - - -
71a90847 by Martin Uecker at 2022-04-10T12:54:43+02:00
coding style
- - - - -
21c71e1d by Martin Uecker at 2022-04-10T12:54:43+02:00
improve readability
- - - - -
757e47e0 by Martin Uecker at 2022-04-10T12:54:43+02:00
turn off failing test
- - - - -
6e2fdf08 by Christian Holme at 2022-04-13T16:37:50+02:00
gitlab-ci: correct dependencies for UBSan integration test
- - - - -
863cd9ab by Martin Uecker at 2022-04-15T15:09:04+02:00
new tool: fovshift
- - - - -
1aac884a by Martin Uecker at 2022-04-15T16:13:05+02:00
flag to create oversampled trajectory
- - - - -
2fe3b941 by Martin Uecker at 2022-04-15T17:42:56+02:00
test for trajectory rotation
- - - - -
33eb09dc by Martin Uecker at 2022-04-15T18:21:55+02:00
tests for centered radial trajectory
- - - - -
58095e29 by Martin Uecker at 2022-04-15T21:13:20+02:00
make estdelay more generic regarding un-/centered trajectories
- - - - -
9e361cbe by Martin Uecker at 2022-04-15T21:25:41+02:00
tests for zexp
- - - - -
087ab38f by rosenzweig at 2022-04-15T21:43:18+02:00
tests/filter: Moving average
- - - - -
17bbcb84 by Martin Uecker at 2022-04-15T21:52:50+02:00
radial DCF examples
- - - - -
717bca81 by Martin Uecker at 2022-04-16T17:45:07+02:00
coding style
- - - - -
79647b83 by Martin Uecker at 2022-04-16T21:22:29+02:00
make config constant
- - - - -
e4572759 by Martin Uecker at 2022-04-17T16:31:59+02:00
fix memory leak
- - - - -
c5726533 by Martin Uecker at 2022-04-17T16:38:06+02:00
add missing copyright header
- - - - -
07ed3a63 by Tamás Hakkel at 2022-04-17T17:22:44+02:00
Og flag for debug mode + memcfl_exists
- - - - -
acc83578 by Tamás Hakkel at 2022-04-17T17:24:00+02:00
bugfix
- - - - -
7578c4d3 by Christian Holme at 2022-04-20T11:55:07+02:00
calib/calib.c: use designated initialization for ecalib_defaults
- - - - -
a8302cbd by Christian Holme at 2022-04-20T11:55:07+02:00
ecalib: make number of iterations for orthiter configurable
This reverts 392832378365df541ccb96fb521ad02750152be5
- - - - -
bd4ae41a by Christian Holme at 2022-04-20T14:59:33+02:00
gitlab-ci: add GPU tests running in our system
Using the nvidia cuda docker image
- - - - -
97779c68 by Christian Holme at 2022-04-20T14:59:33+02:00
gitlab-ci: OMP threads to 1, no more tags
tags should come back once we need them or once the gwdg is no longer
relevant
- - - - -
6f1bbac2 by Sebastian Rosenzweig at 2022-04-25T08:04:59+02:00
num/qform: Add bilinear form
- - - - -
f16e5e02 by Martin Uecker at 2022-04-25T08:04:59+02:00
rename gradient_form in quadratic_form
- - - - -
69a67aa4 by Martin Uecker at 2022-04-25T08:04:59+02:00
harmonic fit + tests
- - - - -
fbcde693 by Martin Uecker at 2022-04-25T08:04:59+02:00
move estimate_im_dims to misc/mri.c
- - - - -
075dea69 by Martin Uecker at 2022-04-25T08:04:59+02:00
function to extact angles from radial trajectory
- - - - -
a62a3a6d by Martin Uecker at 2022-04-25T08:04:59+02:00
move some helper functions to misc/mri.c
- - - - -
5be7829d by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
add measure tool
- - - - -
54f9c24e by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
add test ideal for measure tool
- - - - -
451a76c6 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
fixup learned tickhonov init
- - - - -
f2b00d41 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
let linop_sum use md_zsum
- - - - -
6905ef40 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
refactor batch generator
- - - - -
ed6ac838 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
more flexible batch generator configuration in reconet
- - - - -
55467da8 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
move scaling and preprocessing to network data
- - - - -
7dff7588 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
add functions to data list
- - - - -
8ff90ada by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
reconstruction as output name
- - - - -
a7f838cd by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
apply/eval with datalist
- - - - -
17ec0b83 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
move sense initialization to preprocessing
- - - - -
8e3e39a8 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
rename tikhonov->sense
- - - - -
27254cea by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
assert no identical argument names in nn_chain2
- - - - -
c8592bf7 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
update reconet tests
- - - - -
6d7a6762 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
add warmup to learning rate scheduling
- - - - -
2f3bdbd3 by Martin Uecker at 2022-04-28T11:25:16+02:00
add missing workaround for C++
- - - - -
3dc2c17a by Christian Holme at 2022-04-28T12:11:31+02:00
fix measure tests
* Use --mse-mag instead of --mse in the test named mse-mag
* No line continuation before the "touch"
- - - - -
d4db0a1d by Christian Holme at 2022-04-28T12:11:41+02:00
fully reduce default optimization
In line with 63a6b28ea7f5eb85eca8bcccf2ee57bf9658f318, default
optimization is now -O2 without -ffast-math, for CUDA and also for the
automatic tests
- - - - -
9bf00c25 by Christian Holme at 2022-04-28T12:52:33+02:00
gitlab-ci: use UBSAN=1 instead of CFLAGS
and switch Integration_Test_UBSan to debian:testing, as Build_UBSan and
Unit_Test_UBSan also use debian:testing
- - - - -
fe27fa95 by Christian Holme at 2022-04-29T11:31:48+02:00
Makefile: re-add -fsanitize=address
As it was included in the .gitlab-ci.yml, it should also be part of
UBSAN=1
- - - - -
4bc44901 by Martin Uecker at 2022-05-02T21:46:05+02:00
refactor
- - - - -
24a3ca45 by Martin Uecker at 2022-05-02T21:46:05+02:00
merge two functions always used together
- - - - -
9ef31f72 by Martin Uecker at 2022-05-02T21:46:05+02:00
use tenmul instead of clear/fmac
- - - - -
77220b7d by Martin Uecker at 2022-05-02T21:46:05+02:00
copyright + typos
- - - - -
bdfd7d85 by Martin Uecker at 2022-05-02T21:46:05+02:00
allow forward nufft with toeplitz
- - - - -
9d018753 by Martin Uecker at 2022-05-02T21:46:05+02:00
refactor
- - - - -
6d943598 by Martin Uecker at 2022-05-02T21:46:05+02:00
refactor
- - - - -
a77fdf96 by Martin Uecker at 2022-05-02T21:46:05+02:00
copyright, remove unused variable
- - - - -
431c6d45 by Moritz Blumenthal at 2022-05-03T17:26:00+02:00
tenmul for linop_fmac
- - - - -
5145d84b by Moritz Blumenthal at 2022-05-03T17:27:02+02:00
merge fftmod and coils in mriops
- - - - -
2558d8a6 by Moritz Blumenthal at 2022-05-03T17:48:00+02:00
update im2col code
- - - - -
38d6983a by Martin Uecker at 2022-05-03T18:23:38+02:00
minor changes
- - - - -
89cbb85a by Nick Scholand at 2022-05-04T12:16:23+02:00
Add approximation of sine integral with test
Fix date
- - - - -
71210f83 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add windowed sinc functions with utests
- - - - -
f041c80b by Nick Scholand at 2022-05-04T12:16:25+02:00
Add rotation matrices
Defining direction of rotation becomes easier.
- - - - -
49efbb95 by Nick Scholand at 2022-05-04T12:16:25+02:00
Reformulate relaxation and rotation with rotation matrices + utests
- - - - -
d1c6e76b by Nick Scholand at 2022-05-04T12:16:25+02:00
Add rf excitation wrapper for phase and FA + utest
- - - - -
7fb0ebe4 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add excitation with RF phase utest
- - - - -
4bc6c99d by Nick Scholand at 2022-05-04T12:16:25+02:00
Add B1 partial derivative + utests
- - - - -
9b2b45b4 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add ODE based simulation tool with first utests
Utests:
- Test partial derivatives for an IR bSSFP sequence
- Compare simulated IR bSSFP signal with analytical model
- - - - -
9e018e9a by Nick Scholand at 2022-05-04T12:16:25+02:00
Add structural elements for simulation
Increases the flexibility for later extensions.
- - - - -
a3f7fb4c by Nick Scholand at 2022-05-04T12:16:25+02:00
Add ODE simulation offresonance and gradient utests
- - - - -
05f941f5 by Nick Scholand at 2022-05-04T12:16:25+02:00
No inversion
- - - - -
4c9506a2 by Nick Scholand at 2022-05-04T12:16:25+02:00
Avoid case conflict
- - - - -
8eafc33b by Nick Scholand at 2022-05-04T12:16:25+02:00
Add utest linking Bloch simulation and EPG
Idea: Loop through Fourier coefficients by changing the off-resonance of
isochromates.
- - - - -
cde00743 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add hard pulse option with utests
- - - - -
e084b4b8 by Nick Scholand at 2022-05-04T12:16:25+02:00
Remove unused variable
- - - - -
049a636b by Nick Scholand at 2022-05-04T12:16:25+02:00
Fix smooth spoiling for rotation matrix relaxation
- - - - -
b070fe78 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add function for simulation debug output
- - - - -
58c4d3d4 by Nick Scholand at 2022-05-04T12:16:25+02:00
Avoid unnecessary computation
- - - - -
5af80d93 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add simulation interface with tests
Separated in a new tool (sim.c)
- - - - -
ff4db60b by Nick Scholand at 2022-05-04T12:16:25+02:00
Add test for relaxation parameter grid simulation
- - - - -
ba69bc42 by Nick Scholand at 2022-05-04T12:16:25+02:00
Make slice-profile gradient moment accessible from sim interface
- - - - -
8c3fa86a by Nick Scholand at 2022-05-04T12:16:25+02:00
Add NIST phantom (T2 sphere)
- - - - -
bd9ec293 by Nick Scholand at 2022-05-04T12:16:25+02:00
Balance z gradient for bSSFP type sequences
- - - - -
d8db8ea6 by Nick Scholand at 2022-05-04T12:16:25+02:00
Specify pulse type
- - - - -
e74c1e9e by Nick Scholand at 2022-05-04T12:16:25+02:00
style
- - - - -
5065fe6a by Nick Scholand at 2022-05-04T12:16:25+02:00
Add hyperbolic secant inversion pulse with utest
- - - - -
57e3d5a2 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add perfect inversion and inversion spoiler duration
- - - - -
2dd3541a by Nick Scholand at 2022-05-04T12:16:25+02:00
Turn off output
- - - - -
29a9f91f by Nick Scholand at 2022-05-04T12:16:25+02:00
Set hyperbolic secant inversion default
- Tests and utests comparing with analytical models still require
perfect inversion models
- - - - -
9a6d0827 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add simulation type
- - - - -
4ac830cb by Nick Scholand at 2022-05-04T12:16:25+02:00
style
- - - - -
7a255cbe by Nick Scholand at 2022-05-04T12:16:25+02:00
Split Bloch function
- - - - -
76784609 by Nick Scholand at 2022-05-04T12:16:25+02:00
Rename Bloch function
- - - - -
b838ef58 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add matrix exponential estimation
- - - - -
63d9b7f0 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add Bloch system matrices including SAB
- - - - -
161908d4 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add debug output for hyperbolic secant pulse
- - - - -
b12ae3fa by Nick Scholand at 2022-05-04T12:16:25+02:00
Make type for obvious
- - - - -
21f2882f by Nick Scholand at 2022-05-04T12:16:25+02:00
Add functions for STM matrix simulation
- - - - -
dc53b9ac by Nick Scholand at 2022-05-04T12:16:25+02:00
Integrate STM in ODE simulation interface with utests
- - - - -
4fa11246 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add initialization of hyperbolic secant pulses to sim.c
- - - - -
6227bc1a by Nick Scholand at 2022-05-04T12:16:25+02:00
Make simulation types accessible from CLI + tests
- - - - -
77317450 by Nick Scholand at 2022-05-04T12:16:25+02:00
Reorder functions
- - - - -
0aae05c3 by Nick Scholand at 2022-05-04T12:16:25+02:00
style
- - - - -
632aba85 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add slice selection rewinder with utests for ODE and STM
- - - - -
e8b39326 by Nick Scholand at 2022-05-04T12:16:25+02:00
style
- - - - -
df4649b2 by Nick Scholand at 2022-05-04T12:16:25+02:00
Fix terminology
- - - - -
42ccc9fd by Nick Scholand at 2022-05-04T12:16:25+02:00
Add missing header file
- - - - -
5b8f4ff0 by Nick Scholand at 2022-05-04T12:16:25+02:00
True B1
- - - - -
b88e3e6a by Nick Scholand at 2022-05-04T12:16:25+02:00
Fix dimension
- - - - -
d9b325aa by Nick Scholand at 2022-05-04T12:16:25+02:00
Add simulation type debug output
- - - - -
76c9aec1 by Nick Scholand at 2022-05-04T12:16:25+02:00
Reuse temporary arrays
- - - - -
42d8135e by Nick Scholand at 2022-05-04T12:16:25+02:00
Specify struct type
- - - - -
fa09ee08 by Nick Scholand at 2022-05-04T12:16:25+02:00
Style
- - - - -
52c57ff5 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add rectangle geometry to phantom tool
- - - - -
973139ae by Nick Scholand at 2022-05-04T12:16:25+02:00
Add tool for morphological operations with tests
- - - - -
b796b781 by Nick Scholand at 2022-05-04T12:16:25+02:00
Make inversion spoiler duration accessible from CLI
- - - - -
fdc4e57d by Nick Scholand at 2022-05-04T12:16:25+02:00
Rename simulation interface
- - - - -
c320d839 by Nick Scholand at 2022-05-04T12:16:25+02:00
Generalize initialization
- - - - -
a0b73c90 by Nick Scholand at 2022-05-04T12:16:25+02:00
More accurate terminology
- - - - -
b8dd2d92 by Moritz Blumenthal at 2022-05-04T20:54:55+02:00
reconstruct coil images
- - - - -
7e311142 by Martin Uecker at 2022-05-13T14:33:34+02:00
warn about incorrectly scaled trajectories
- - - - -
411f0b88 by Martin Uecker at 2022-05-13T15:53:42+02:00
update directories described in README
- - - - -
900bb5f7 by Martin Uecker at 2022-05-14T19:26:18+02:00
better backwards compatibility for moba
- - - - -
2bf1f14c by Martin Uecker at 2022-05-15T15:37:52+02:00
import/export of PSF in pics
- - - - -
03be2259 by Martin Uecker at 2022-05-15T17:08:39+02:00
ubsan fix
- - - - -
8dd61e15 by Martin Uecker at 2022-05-17T13:44:07+02:00
remove unused variable
- - - - -
d795626e by Martin Uecker at 2022-05-17T13:56:57+02:00
update copyright year
- - - - -
eafe40ab by Martin Uecker at 2022-05-17T15:01:51+02:00
tests for rof / tgv denoising
- - - - -
a1cd998b by Martin Uecker at 2022-05-17T18:38:46+02:00
refactor rof/tgv
- - - - -
5f1a6da4 by Martin Uecker at 2022-05-17T18:49:08+02:00
move tgv code into library
- - - - -
79f98930 by Martin Uecker at 2022-05-17T20:03:31+02:00
implement TGV for pics
- - - - -
564766d6 by Martin Uecker at 2022-05-17T21:17:09+02:00
multiple reglarization parameters + minor changes
- - - - -
873ab951 by Martin Uecker at 2022-05-18T07:13:57+02:00
better test for pics with tgv
- - - - -
f1a66b17 by Martin Uecker at 2022-05-18T07:15:37+02:00
fix copyright
- - - - -
75007b3c by Martin Uecker at 2022-05-18T07:15:37+02:00
minor
- - - - -
4e0caed4 by Martin Uecker at 2022-05-18T07:15:37+02:00
rename variable, remove unused
- - - - -
c9afc50d by Martin Uecker at 2022-05-18T07:15:37+02:00
reduce memory usage
- - - - -
7ccc8008 by Martin Uecker at 2022-05-18T08:51:02+02:00
partially separable function reference
- - - - -
5d48102b by Martin Uecker at 2022-05-21T13:50:42+02:00
fix some warnings
- - - - -
b233b653 by Martin Uecker at 2022-05-21T14:11:48+02:00
rename some set_ to get_ in moba
- - - - -
82f1c1c5 by Martin Uecker at 2022-05-21T14:19:42+02:00
refactor
- - - - -
78e39a91 by Martin Uecker at 2022-05-21T17:26:04+02:00
moba refactoring
- - - - -
834e681e by Martin Uecker at 2022-05-21T23:26:00+02:00
refactoring
- - - - -
e0618861 by Martin Uecker at 2022-05-27T21:37:20+02:00
fix typo in reference
- - - - -
9bfca34f by Martin Uecker at 2022-05-27T21:37:20+02:00
clarfications in mobafit
- - - - -
a8138506 by Martin Uecker at 2022-05-27T21:37:20+02:00
refactor
- - - - -
a5eac34c by Martin Uecker at 2022-05-27T21:37:20+02:00
coding style
- - - - -
afb7d401 by Martin Uecker at 2022-05-27T21:37:20+02:00
generic exponential model
- - - - -
c9e85d2e by Martin Uecker at 2022-05-27T21:37:20+02:00
mobafit: T2
- - - - -
a57a79b0 by Martin Uecker at 2022-05-27T21:37:20+02:00
nlop_attach, for attaching a random data pointer
- - - - -
aa65b9ab by Martin Uecker at 2022-05-27T21:37:20+02:00
remove unneeded headers and outputs
- - - - -
10414893 by Martin Uecker at 2022-05-27T21:37:20+02:00
initial code for using generic exp model in moba
- - - - -
96be7f84 by Martin Uecker at 2022-05-27T21:37:20+02:00
minor
- - - - -
9d319a52 by Martin Uecker at 2022-05-27T21:37:20+02:00
missing test prerequisite
- - - - -
66d1f4cc by Jon Tamir at 2022-06-01T08:31:18+02:00
fix basis pursuit pics when using a sampling pattern (#285)
* re-initialize sense op even if no loop flags
* re-initialize sense op if Cartesian bpsense is active
* test-pics-bpwavl1: check data consistency error
* style
- - - - -
53935168 by Martin Uecker at 2022-06-01T09:39:58+02:00
tgv/ictv + multiple penalties + 3D
- - - - -
ff9de4fe by Jon Tamir at 2022-06-02T22:02:15+02:00
don't change path for main part of bart command (fixes #284)
- - - - -
e782b930 by Jon Tamir at 2022-06-02T22:02:15+02:00
refactor matlab functions and fix failing test
- - - - -
093559fd by Nick Scholand at 2022-06-03T13:38:33+02:00
Add function to pass 4 element vector to CLI
- - - - -
1d82e5e4 by Christian Holme at 2022-06-20T13:16:56+02:00
twixread: updates for VD/VE
- - - - -
d637a5e3 by Christian Holme at 2022-06-20T13:16:56+02:00
twixread: add option for debug_level
- - - - -
50905f7f by Christian Holme at 2022-06-20T13:16:56+02:00
Makefile: add testague for twixread
- - - - -
3efad151 by Christian Holme at 2022-06-23T12:07:16+02:00
tests/twixread: better datasets, better paths
and controlled by an environment variable, so that they are no longer
random paths on our systems
- - - - -
1b8f7541 by Philip Schaten at 2022-06-23T18:28:51+02:00
Fix Fedora Packages
Since Fedora 36, distribution default compiler and linker flags are added implicitly: https://fedoraproject.org/wiki/Changes/SetBuildFlagsBuildCheck#How_To_Test
This includes -Wl,--as-needed ; results in undefined cblas symbols.
- - - - -
1a3e77ef by Christian Holme at 2022-07-01T11:42:17+02:00
twixread: add full adc_flags, more changes for VE
Closes #288
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4743aff7 by Martin Uecker at 2022-07-01T22:22:55+02:00
coding style
- - - - -
7316ac44 by Martin Uecker at 2022-07-01T22:22:55+02:00
update gcc version in the README for Macs
- - - - -
c23ab116 by Nick Scholand at 2022-07-01T22:29:35+02:00
Simplify parameter passing
- - - - -
6be1997c by Martin Uecker at 2022-07-02T10:53:07+02:00
README updates
- - - - -
5f214da9 by Martin Uecker at 2022-08-02T21:45:10+02:00
fix for other wavelet types
- - - - -
43146dda by Martin Uecker at 2022-08-02T21:45:10+02:00
support for different wavelets
- - - - -
e0fe7c0e by Martin Uecker at 2022-08-02T22:26:33+02:00
also update cuda
- - - - -
f0112dd0 by Alexander Fyrdahl at 2022-08-03T22:23:40+02:00
adjoint nufft example used wrong dcf
- - - - -
c56d3080 by Martin Uecker at 2022-08-04T10:18:47+02:00
coding style
- - - - -
2d0a4c2d by Martin Uecker at 2022-08-04T10:21:54+02:00
option to select wavelets in pics
- - - - -
d6ae5521 by Nick Scholand at 2022-08-12T17:43:27+02:00
Add arccos md functions
- - - - -
24d43484 by Nick Scholand at 2022-08-12T19:21:22+02:00
Add rotational matrices simulation option with utest
based on homogeneously discretized sinc shaped rf pulses
- - - - -
af428395 by Nick Scholand at 2022-08-12T19:21:22+02:00
Single hard pulse is special case of rotational matrix based simulation
- - - - -
55204e26 by Martin Uecker at 2022-08-12T19:31:33+02:00
coding style
- - - - -
1ffeb48c by Nick Scholand at 2022-08-12T19:33:22+02:00
Change default pulse duration
- - - - -
ab2904b0 by Nick Scholand at 2022-08-12T19:47:19+02:00
Add option to pass ODE solver tolerance to simulation
- - - - -
46270b18 by Nick Scholand at 2022-08-12T20:28:56+02:00
Add option to remove coeff maps from joint wavelet denoising
- - - - -
badf3b12 by Nick Scholand at 2022-08-12T20:33:09+02:00
More precise description
- - - - -
1008b1dc by Martin Uecker at 2022-08-13T09:44:53+02:00
output number of failing test
- - - - -
959fc981 by Martin Uecker at 2022-08-13T09:45:06+02:00
do not use -fsantize=address in UBSAN=1, introduce ASAN
- - - - -
9d4726ae by Nick Scholand at 2022-08-13T10:33:55+02:00
Copy sim struct
Ensures that the original data is not changed
- - - - -
7cc0864a by Martin Uecker at 2022-08-13T10:34:55+02:00
add blochfun and test
- - - - -
29738920 by Martin Uecker at 2022-08-13T11:20:01+02:00
coding style
- - - - -
e3607c8d by Martin Uecker at 2022-08-13T11:35:00+02:00
coding style
- - - - -
8ad7bd43 by Martin Uecker at 2022-08-13T13:50:18+02:00
Bloch model recon with tests
- - - - -
cb2c99f6 by Martin Uecker at 2022-08-17T11:15:54+02:00
update help str.
- - - - -
97abf8f4 by Martin Uecker at 2022-08-17T11:26:48+02:00
psf test error
- - - - -
8cfd7760 by Nick Scholand at 2022-08-17T13:18:59+02:00
Add reparameterized Look-Locker model (MDB_T1_PHY) with tests
Parameters (M0, R1, FA) are closer to Bloch equations
- - - - -
6a1d3c02 by Martin Uecker at 2022-08-17T15:14:28+02:00
merge functions for sobolev norm weights
- - - - -
3ed1d4c7 by Nick Scholand at 2022-08-17T15:25:15+02:00
Fix R2 map and B1 map tests
- - - - -
b15192f2 by Nick Scholand at 2022-08-17T15:25:15+02:00
Increase strength of Bloch moba IR FLASH tests
Add and set test for flip angle accuracy default
- - - - -
bb07ca8c by Nick Scholand at 2022-08-17T15:32:31+02:00
Reduce debug value for simplified moba debugging
- - - - -
26bb2fed by Martin Uecker at 2022-08-17T15:43:03+02:00
comment
- - - - -
90e93a08 by Nick Scholand at 2022-08-17T16:14:32+02:00
Set constraint maps with flags
allows setting multiple (also non consecutive) dimensions
- - - - -
bdee9153 by Martin Uecker at 2022-08-17T16:14:32+02:00
rewrite positivity constraint
- - - - -
abbeae3c by Nick Scholand at 2022-08-17T16:14:32+02:00
Generalize Bloch moba interface to support IR bSSFP with tests
- - - - -
6f7eb592 by Nick Scholand at 2022-08-17T16:16:01+02:00
minor
- - - - -
61491a52 by Nick Scholand at 2022-08-18T12:00:08+02:00
Add B1 input file option to Bloch model moba with test
- - - - -
34a32cf2 by Christian Holme at 2022-08-18T13:25:50+02:00
ictv.c: typo
- - - - -
0d97a717 by Christian Holme at 2022-08-18T13:25:50+02:00
estdelay.c: warn on unexpected shifts, rename shift1 -> scale
- - - - -
f7e02b2b by Christian Holme at 2022-08-18T13:25:50+02:00
estdelay.c: only add 0.5 for trajs with even number of samples
and add tests for odd number of samples
- - - - -
41dd6bda by Nick Scholand at 2022-08-18T16:06:30+02:00
Add spoke averaging option to simulation interface and integrate option
to moba, sim, and signal with tests
- - - - -
e45e5cdf by Martin Uecker at 2022-08-18T16:06:30+02:00
remove duplicated prepare call
- - - - -
38f32f65 by Martin Uecker at 2022-08-18T16:06:30+02:00
rewrite spoke averaging
- - - - -
13ec7d41 by Martin Uecker at 2022-08-18T16:06:30+02:00
refactor
- - - - -
33bd1afb by Nick Scholand at 2022-08-18T17:11:57+02:00
Add Fourier based slice profile to Bloch moba and sim with tests
(refactored -- MU)
- - - - -
2e5515cd by Nick Scholand at 2022-08-18T17:22:51+02:00
Add option to simulation tool to output partial derivatives
- - - - -
9f4e0e2d by Nick Scholand at 2022-08-18T17:24:03+02:00
Add rotational matrix simulation option to sim CLI with tests
- - - - -
699b47dc by Martin Uecker at 2022-08-18T18:28:18+02:00
bounds fix & minor changes
- - - - -
ab0dd4b3 by Martin Uecker at 2022-08-18T18:32:29+02:00
debug mode for UBSan
- - - - -
67a6e689 by Martin Uecker at 2022-08-18T21:30:53+02:00
relax test some more
- - - - -
19f03ac3 by mavel101 at 2022-08-23T17:22:25+02:00
allow multiple files with the correct option string via keyworded arguments
- - - - -
faac3b9f by Christian Holme at 2022-08-24T13:41:59+02:00
tests/pythoncfl.mk: typo
- - - - -
259cf391 by Christian Holme at 2022-08-24T13:45:48+02:00
tests/python_bart.mk: add tests for python interface
- - - - -
3eb7df53 by Christian Holme at 2022-08-24T13:54:40+02:00
tests/python_bart: fix tolerance
- - - - -
1db46666 by Christian Holme at 2022-08-24T16:09:44+02:00
tests/python_bart: remove superfluous test
this is already tested in tests/pythoncfl.mk
- - - - -
297194d3 by Christian Holme at 2022-08-24T16:21:59+02:00
github action: `make all` instead of `make`
This tests if all commands can be built, and not only if the combined
`bart` command can be built
- - - - -
55b04b44 by Christian Holme at 2022-08-24T16:21:59+02:00
add pythontest to github action
- - - - -
a540f9ed by Nick Scholand at 2022-08-25T20:05:34+02:00
Add rotational matrix simulation option to sim CLI with tests
- - - - -
a6e4f90a by Nick Scholand at 2022-08-25T20:05:34+02:00
Add option to split dimensions to sim tool with tests
- - - - -
d83c13b7 by Nick Scholand at 2022-08-25T20:05:34+02:00
Fix STM simulation for TE equal TRF with test
- - - - -
1816a084 by Nick Scholand at 2022-08-25T20:05:34+02:00
Add output of simulation time
- - - - -
a111af0f by Nick Scholand at 2022-08-25T20:05:34+02:00
Generalize STM matrix creation + utest
- - - - -
8c7e8ba6 by Nick Scholand at 2022-08-25T20:05:34+02:00
Do not estimate STM matrix twice for bSSFP
- - - - -
37bd2332 by Martin Uecker at 2022-08-25T20:05:34+02:00
better array bounds
- - - - -
8cda659a by Nick Scholand at 2022-08-25T20:05:34+02:00
Balance z gradient moment for bSSFP + fix tests and default parameters
- - - - -
1ba1a768 by Nick Scholand at 2022-08-25T20:05:34+02:00
Set all realistic inversion simulations to non slice-selective
- - - - -
33e3d3ff by Martin Uecker at 2022-08-25T20:05:34+02:00
rework fix for timing issue
- - - - -
9a71ae37 by Martin Uecker at 2022-08-25T20:05:34+02:00
tests for LTO builds
- - - - -
3b24afc8 by Nick Scholand at 2022-08-25T20:05:34+02:00
Fix md_zsum hack
Provide correct dimensions
- - - - -
b7e7d9f4 by Nick Scholand at 2022-08-25T20:05:34+02:00
Move special cases of config to separate function
- - - - -
0aa5bbf9 by Nick Scholand at 2022-08-25T20:05:34+02:00
Move postprocessing out of moba's recon
- - - - -
dd84edf8 by Xiaoqing Wang at 2022-08-25T20:05:34+02:00
add the time dim to the moba T1
- - - - -
0934a05b by Xiaoqing Wang at 2022-08-25T20:05:34+02:00
moba T1: add configuration options for ADMM
- - - - -
44644795 by rosenzweig at 2022-08-25T20:05:34+02:00
rmfreq: contrast change option
- - - - -
7999d253 by Martin Uecker at 2022-08-25T20:05:34+02:00
coding style
- - - - -
71eed1c5 by rosenzweig at 2022-08-25T20:05:34+02:00
rmfreq: coilwise contrast
- - - - -
cb8d1723 by wang53 at 2022-08-25T20:05:34+02:00
set the edge filter strength as an input
- - - - -
f2bd9c6e by Moritz Blumenthal at 2022-08-27T12:43:20+02:00
Add simple mnist network for demonstration
- - - - -
f7092ba4 by Christian Holme at 2022-08-31T15:56:22+02:00
misc/opts.c: use correct code path & silence warning
For long-only options using vec2 or vec3, char c is a random,
unprintable letter. Therefore, not a lower-case letter, leading to the
incorrect warning: "the upper-case options for specifying dimensions are
deprecated.".
This fixes that, and uses the new and improved way of reading vec2 and
vec3 arguments.
- - - - -
b65faa9b by Christian Holme at 2022-08-31T15:57:42+02:00
moba/iter_l1.c: fix segfault using some T1 models
- - - - -
85ee9d47 by Christian Holme at 2022-09-01T11:02:13+02:00
moba.c: fix flow reproducibility with MECO_PI model
- - - - -
d1c6a084 by Martin Uecker at 2022-09-05T13:20:13+02:00
rename function
- - - - -
dd8d10e9 by Nick Scholand at 2022-09-05T13:25:23+02:00
Unify and comment rotation systems + fix tests
- Bloch equations and rotation matrices clockwise in right-handed system
- FIXME: Unify with EPGs currently defined in counter clockwise system
- - - - -
d3a4dfc9 by Nick Scholand at 2022-09-05T13:25:23+02:00
Add rotation to TUBE and NIST phantom geometries with tests
- - - - -
ecaf8874 by Nick Scholand at 2022-09-05T13:25:23+02:00
Add diagnostic sonar phantom geometry with tests
- - - - -
41245578 by Nick Scholand at 2022-09-05T13:25:23+02:00
Add a script for creating simulated phantoms + tests
- - - - -
1e67b2ed by Nick Scholand at 2022-09-05T13:25:23+02:00
Update slice profile simulation + fix tests
- Normalize simulation output by spin density
- Remove option for Fourier based slice profile approximation
- Define slice profile simulation with slice-selection gradient strength
and slice thickness
- - - - -
3e8fd94c by Nick Scholand at 2022-09-05T13:25:23+02:00
Allow changing the ODE solver tolerance
- - - - -
dfa21c07 by Nick Scholand at 2022-09-05T13:25:23+02:00
Fix derivative output with tests
- - - - -
946f3197 by wang53 at 2022-09-05T14:19:38+02:00
moba T1: bug fix (thanks to Moritz)
- - - - -
61a047c5 by Martin Uecker at 2022-09-05T20:42:01+02:00
relax test
- - - - -
85a9a517 by Martin Uecker at 2022-09-05T20:47:38+02:00
remove hard-coded scaling from moba
- - - - -
c6ec3e8a by Martin Uecker at 2022-09-05T22:50:51+02:00
parametrize scaling for M0/R1s in T1_fun
- - - - -
01c320f4 by Martin Uecker at 2022-09-05T22:50:51+02:00
remove scaling from looklocker
- - - - -
c2529892 by Martin Uecker at 2022-09-05T23:00:38+02:00
remove hard-coded initialization and scaling from moba
- - - - -
ba80ee61 by Xiaoqing Wang at 2022-09-05T23:00:38+02:00
moba/iter_l1.c: add the ADMM part
- - - - -
e731b123 by Xiaoqing Wang at 2022-09-05T23:00:38+02:00
moba T1: add the optreg for IRLL
- - - - -
09bdf937 by wang53 at 2022-09-06T10:17:10+02:00
moba T1: make the real-constraint compatible with version 0.7.0 (thanks to Christian Holme)
- - - - -
cd394399 by Moritz Blumenthal at 2022-09-06T10:19:07+02:00
transparent allocation for t1fun
- - - - -
d6a6162f by Moritz Blumenthal at 2022-09-06T10:20:10+02:00
fix t1fun (+test)
- - - - -
7560e57f by Moritz Blumenthal at 2022-09-06T10:27:20+02:00
split inversion and adjoint + gpuwrapper if gpu is initialized
- - - - -
2f5c14ac by Moritz Blumenthal at 2022-09-06T10:34:07+02:00
Fix gpuops for large vectors
- - - - -
02a81f2d by Moritz Blumenthal at 2022-09-06T10:44:36+02:00
fix bloch derivative
- - - - -
bb18fe36 by Moritz Blumenthal at 2022-09-06T10:46:35+02:00
transparent gpu allocation
- - - - -
de4e042b by Moritz Blumenthal at 2022-09-06T10:46:43+02:00
simplify copy to gpu
- - - - -
bfc550c2 by Moritz Blumenthal at 2022-09-06T10:46:50+02:00
use pos/dims from compute_mask
- - - - -
c6d76ba3 by Martin Uecker at 2022-09-06T11:21:37+02:00
comment out GPU mode
- - - - -
a0646d55 by Moritz Blumenthal at 2022-09-06T11:48:29+02:00
refactor gpu initialization (with Christian Holme)
- - - - -
07c7d130 by Moritz Blumenthal at 2022-09-06T11:48:37+02:00
refactor cuda errors
- - - - -
77b318d4 by Martin Uecker at 2022-09-06T17:51:49+02:00
fix power iteration issue
- - - - -
a2fd94f7 by Martin Uecker at 2022-09-06T17:51:49+02:00
add alpha to maxeigenval + reduce number of iterations in tests
- - - - -
037e3d8a by Martin Uecker at 2022-09-06T17:51:49+02:00
invert autonorm logic
- - - - -
2c4a4dc2 by Martin Uecker at 2022-09-06T17:51:49+02:00
parameter description
- - - - -
68ea5c4d by Martin Uecker at 2022-09-06T18:05:57+02:00
add GPU test for moba
- - - - -
0c66ebff by Christian Holme at 2022-09-09T09:43:54+02:00
moba: use ! for bool instead of == 0
- - - - -
68e5fcc3 by Christian Holme at 2022-09-09T09:44:05+02:00
moba: compat to old version
- - - - -
4d4a5396 by Christian Holme at 2022-09-09T09:44:05+02:00
moba/iter_l1: keep incorrect eigenvalue calc for compat
- - - - -
910053eb by Martin Uecker at 2022-09-10T11:25:44+02:00
remove script tests
- - - - -
088d4de0 by Martin Uecker at 2022-09-10T14:24:58+02:00
describe more directories
- - - - -
5fe45807 by Martin Uecker at 2022-09-10T14:24:58+02:00
update acknowledgements
- - - - -
923ed7e7 by Martin Uecker at 2022-09-10T14:24:58+02:00
coding style & copyright
- - - - -
006b24e0 by Martin Uecker at 2022-09-10T14:24:58+02:00
fix warning
- - - - -
8a401c45 by Nick Scholand at 2022-09-14T13:23:32+02:00
Divide multi spin simulation output by nominal slice thickness
This change keeps the nlop output similar to the single isochromate
simulation. This ensures a comparable regularization strength for single
and multi isochromate signal models.
- - - - -
e641e74b by Nick Scholand at 2022-09-14T13:23:46+02:00
Capital letters for sequence parameters
- - - - -
0cb1c771 by Moritz Blumenthal at 2022-09-15T10:36:13+02:00
set l2flags for moba l1
- - - - -
1b34f899 by Martin Uecker at 2022-09-16T09:51:43+02:00
reactivate test
- - - - -
6a0dd4d0 by Moritz Blumenthal at 2022-09-16T19:02:29+02:00
multi-gpu option for moba
- - - - -
3b32c90c by wang53 at 2022-09-16T19:04:13+02:00
moba/optreg.c: use a scaling operator for isotropic TV
- - - - -
02947c01 by Martin Uecker at 2022-09-16T20:53:10+02:00
scaling of TV derivatives in moba
- - - - -
6f94ac7a by Martin Uecker at 2022-09-16T20:53:36+02:00
remove pointless variables
- - - - -
894b02dc by Martin Uecker at 2022-09-16T21:20:44+02:00
remove unsigned
- - - - -
4791b2e0 by Moritz Blumenthal at 2022-09-17T14:12:57+02:00
add test dependency
- - - - -
3f65c4e0 by Moritz Blumenthal at 2022-09-17T14:40:44+02:00
sameplace for compute psf
- - - - -
845bfe53 by Moritz Blumenthal at 2022-09-17T14:48:46+02:00
extend linops
- - - - -
774b65aa by Moritz Blumenthal at 2022-09-17T15:12:31+02:00
release memory
- - - - -
4d10f927 by Moritz Blumenthal at 2022-09-18T14:41:30+02:00
provide function to get cuda stream
- - - - -
4ad4700c by Moritz Blumenthal at 2022-09-18T14:44:13+02:00
threadsafe initialization and stream selection for cuDNN wrapper
- - - - -
8e7b8e45 by Moritz Blumenthal at 2022-09-18T14:44:29+02:00
multigpu/streams for cuBLAS
- - - - -
709a235d by Moritz Blumenthal at 2022-09-18T17:29:29+02:00
rename operator_apply_joined_unchecked
- - - - -
f1142310 by Moritz Blumenthal at 2022-09-18T17:29:29+02:00
add function to apply operators in parallel
- - - - -
c732a925 by Moritz Blumenthal at 2022-09-18T17:29:29+02:00
nlop copy wrapper
- - - - -
e51caa36 by Moritz Blumenthal at 2022-09-18T17:29:29+02:00
get nlop/linop data from reshaped nlop/linop
- - - - -
c2703853 by Moritz Blumenthal at 2022-09-18T19:43:58+02:00
add nlop stack container
- - - - -
08928a21 by Moritz Blumenthal at 2022-09-18T19:43:58+02:00
optimize flattening of stacked operator (flatten all stacked operators independently)
- - - - -
365ee11a by Moritz Blumenthal at 2022-09-18T19:43:58+02:00
fix nlop_flatten_F to actually free nlop
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019095c2 by Moritz Blumenthal at 2022-09-18T19:44:20+02:00
add nlop_flatten_F
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916af4c4 by Moritz Blumenthal at 2022-09-18T19:44:20+02:00
stacking for model_T1
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d335fa49 by Moritz Blumenthal at 2022-09-18T19:44:20+02:00
correct fov reduction factor in all models
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3f6ebb12 by Moritz Blumenthal at 2022-09-18T20:30:42+02:00
let utestgpu init gpu
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b6967ac0 by Martin Uecker at 2022-09-23T19:48:59+02:00
coding style
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eacc67b9 by Martin Uecker at 2022-09-24T21:42:23+02:00
bump version
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30 changed files:
- + .github/workflows/c-cpp.yml
- .gitlab-ci.yml
- ACKNOWLEDGEMENTS
- LICENSE
- Makefile
- README
- README.md
- + doc/pics.txt
- doc/references.txt
- + doc/resize.txt
- matlab/bart.m
- + matlab/get_bart_path.m
- matlab/test_bart.m
- matlab/wslPathCorrection.m
- msys_setup.sh
- bart.spec → pkg/rpm/bart.spec
- libbart-dev.install → pkg/rpm/libbart-dev.install
- libbart-devel.spec → pkg/rpm/libbart-devel.spec
- octave-bart.spec → pkg/rpm/octave-bart.spec
- + pkg/rpm/rpkg.conf
- rpkg.macros → pkg/rpm/rpkg.macros
- python/bart.py
- python/cfl.py
- + scripts/phantom.sh
- + scripts/radial_dcf.sh
- src/avg.c
- src/bart.c
- src/bench.c
- src/bin.c
- src/bitmask.c
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/29f303b26c5a065e095b3977c0b998cfd92fb602...eacc67b95cf128487ecc48f0e6541ea4dca08818
--
View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/29f303b26c5a065e095b3977c0b998cfd92fb602...eacc67b95cf128487ecc48f0e6541ea4dca08818
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