[med-svn] [Git][med-team/bart][master] 140 commits: doc/ add more papers
Martin Uecker
gitlab at salsa.debian.org
Sat Jul 11 15:13:53 BST 2020
Martin Uecker pushed to branch master at Debian Med / bart
Commits:
07647711 by Martin Uecker at 2019-09-09T15:53:53+02:00
doc/ add more papers
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b62ca497 by Melvin Robinson at 2019-10-22T07:16:09+02:00
Fix for MKL
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2796062c by Pim Borman at 2019-10-30T17:37:49+01:00
fixed bug in sms-nlinv golden-angle partition trajectory (#208)
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472524e5 by aTrotier at 2019-11-07T15:46:20+01:00
Fix custom_angle with rewrite of traj tool (#209)
Fix custom_angle with new traj tool
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75d27c00 by Christian Holme at 2019-11-07T22:19:13+01:00
misc: add debug function to print bitmasks (#211)
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afc700e1 by Christian Holme at 2019-11-07T22:21:05+01:00
cuda fft: fix behavior and add unit test (#210)
This commit fixes an unfortunate bug with the
CUDA fft interface, cuFFT:
if a transform is along several, non-adjacent dimensions
in such a way that it skips some dimensions, the cuFFT
will fail. Unfortunately, not always with an error,
sometimes it will silently generate a plan which does
not work correclty.
Therefore, we now detect whether the flags are non-adjacent
and genrate chained transforms in those cases.
Additionally, this commit adds a unit test which checks such cases.
This fixes the bug in SMS-NLINV on the GPU reported by Pim Borman.
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4d430446 by Martin Uecker at 2019-11-10T19:05:07+01:00
application paper
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2b0a1871 by Martin Uecker at 2019-11-10T19:12:25+01:00
missing error check
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fdc1228a by Martin Uecker at 2019-11-10T19:55:56+01:00
refactor cuda fft
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85610737 by giladddd at 2019-11-13T21:53:02+01:00
Use cuCrealf instead of cuCabsf for cuda_zexpj - supports negative numbers correctly (#212)
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52ffa948 by Siddharth Iyer at 2019-11-15T19:29:03+01:00
Add rescaling back into wave-shuffling (#213)
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cf0ba3f8 by Martin Uecker at 2019-11-17T14:05:24+01:00
split gradient delay estimation off into a backend
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31ff0529 by William A. Romero R at 2019-11-21T18:10:04+01:00
Replace deprecated argument 'axisbg'. (#214)
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07f191b3 by Christian Holme at 2019-11-29T18:36:12+01:00
noncart/traj.c: revert undocumented change
This change was introduced in the traj.c rewrite, but it breaks
exisiting code.
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4772b917 by Sebastian Rosenzweig at 2019-11-29T18:38:18+01:00
Fix numerical stability issue for golden angle
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b197fe35 by Christian Holme at 2019-11-29T18:38:22+01:00
typos in style.txt
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7b93ec24 by Martin Uecker at 2019-12-21T12:14:18+01:00
refactor internal md_zvarstd2
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b6c1f10f by Martin Uecker at 2019-12-21T12:34:43+01:00
refactor md_zstd, md_zvar etc. and add md_zss2
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5102cb3e by Martin Uecker at 2019-12-21T13:10:28+01:00
md_zcovar function
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e8ce95aa by Martin Uecker at 2019-12-21T18:47:21+01:00
test for noncartesian pics with sms
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67712d5b by Martin Uecker at 2019-12-21T18:47:21+01:00
add assert in nufft
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98a68ee6 by Martin Uecker at 2019-12-21T18:47:21+01:00
refactor sms support in pics
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ef1de9d2 by Martin Uecker at 2019-12-21T19:03:58+01:00
cosmetic changes
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265dafc5 by Martin Uecker at 2019-12-21T19:42:06+01:00
fix invalid free
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2c5a1c3e by Martin Uecker at 2019-12-21T19:46:05+01:00
linop_plus_FF
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6e91186d by Martin Uecker at 2019-12-21T19:46:50+01:00
simplify tgv command
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17211cc2 by Martin Uecker at 2020-01-03T19:44:51+01:00
return NULL instead of type failures for nlop_get_data/linop_from_nlop
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ada6c23e by xwang at 2020-01-03T19:45:51+01:00
chain.c: add nlop_dup (remove duplicated inputs for nlop)(by Martin)
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1600236a by Martin Uecker at 2020-01-03T19:47:19+01:00
fix memory leak
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5672c30e by Martin Uecker at 2020-01-03T19:47:19+01:00
fix memory leak in nlop_permuts_inputs
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2f9b1f86 by Martin Uecker at 2020-01-03T20:06:15+01:00
update ring code
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dddb6f86 by Martin Uecker at 2020-01-03T20:11:46+01:00
do complete builds for some test configuations
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79928b28 by Martin Uecker at 2020-01-03T20:21:30+01:00
use generic rule (function) for building libs
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0c1b0e5a by Martin Uecker at 2020-01-03T20:22:29+01:00
missing lapacke lib
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c248235f by Martin Uecker at 2020-01-03T20:22:41+01:00
make c++ case work
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71985d98 by Martin Uecker at 2020-01-03T20:28:37+01:00
update unit tests
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1f68e2f2 by Martin Uecker at 2020-01-03T20:44:22+01:00
relax some unit tests for clang
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efa2666a by Martin Uecker at 2020-01-03T22:38:15+01:00
missing __VLA
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f9175e43 by Martin Uecker at 2020-01-16T19:58:45+01:00
make: fix handling of intermediate files
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930e1c9e by Martin Uecker at 2020-01-21T22:58:08+01:00
document possibility to run individual tests on their own
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35f982e7 by Martin Uecker at 2020-01-21T22:58:59+01:00
minor
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58a2367d by Martin Uecker at 2020-01-21T22:58:59+01:00
nlinv with const. sensitivities along some dimensions
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20b319d1 by Martin Uecker at 2020-01-21T22:58:59+01:00
additional testing
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d41b27ac by Martin Uecker at 2020-01-21T22:59:12+01:00
use sms config flag
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1870ceed by Martin Uecker at 2020-01-21T23:13:35+01:00
better ring test
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e211b950 by Martin Uecker at 2020-01-21T23:13:35+01:00
use global defaults for ring
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2d52147b by Martin Uecker at 2020-01-21T23:21:25+01:00
relax test
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783236d0 by mblum at 2020-01-28T00:03:17+01:00
Typo
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2853b959 by Martin Uecker at 2020-01-28T00:03:17+01:00
new benchmarks (zfill, zsmul)
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eb676c29 by Martin Uecker at 2020-01-31T22:52:23+01:00
compilation on Red Hat/CentOS
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9ae7c0d9 by Martin Uecker at 2020-01-31T22:54:41+01:00
document required libraries for CentOS 7
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2d692bac by Martin Uecker at 2020-02-05T19:56:51+01:00
add tubes phantom (courtesy of Nick Scholand)
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10fb39bb by Martin Uecker at 2020-02-05T19:56:51+01:00
new optimization for tensor/scalar operations
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98943bd2 by Martin Uecker at 2020-02-06T13:36:54+01:00
fix assertion
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9159cbfe by Martin Uecker at 2020-02-12T22:00:22+01:00
make no measure the default
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1d9a2251 by Martin Uecker at 2020-02-12T22:07:36+01:00
fix for cuda fft corner case
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9aa6c831 by Christian Holme at 2020-02-12T22:10:16+01:00
num/ops.c: replace assert(0) with proper error()
gpuwrp_fun had an assert(0) if not both CUDA and OpenMP were found.
Using CMake with CUDA, which by default does not use OpenMP but does
define NDEBUG this would lead to unwanted behavior: Since NDEBUG was
defined, assert(0) would not trigger an error. Still, the function would
do nothing useful, leading to all-zero results.
This commit leads to an error message and an abort in that case.
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ab872c58 by Martin Uecker at 2020-02-14T20:19:53+01:00
add support for version check
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2ad3e105 by Martin Uecker at 2020-02-16T19:47:06+01:00
remove cmake files
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ea17820a by Martin Uecker at 2020-02-16T19:47:06+01:00
remove build_targets.mk
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9d1fd72f by Martin Uecker at 2020-02-16T19:47:06+01:00
remove CMake continuous integration
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495718d8 by Martin Uecker at 2020-02-16T19:47:06+01:00
remove CMake documentation
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f7ac0905 by Moritz Blumenthal at 2020-02-17T09:59:53+01:00
Extend linop_null to have different an amount of input dims than output dims
This is needed to have different number of dims in non-linear operators
as the linop_null operator is needed for the derivatives of the
combine_nlop
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ba462953 by Moritz Blumenthal at 2020-02-17T10:30:06+01:00
Simplify chaining with null_op (refactored, M.U.)
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39db9762 by Moritz Blumenthal at 2020-02-17T10:34:55+01:00
Get nlop dom via operator, not via derivative (refactored, M.U.)
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52a66014 by Moritz Blumenthal at 2020-02-17T10:35:08+01:00
Extend nlop_combine to have different number od dimensions
Bug Fix in chain2
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c81ef622 by Martin Uecker at 2020-03-03T22:39:09+01:00
fix bug when using multiple maps with basis
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ecbc2c65 by Martin Uecker at 2020-03-06T19:35:22+01:00
fix for vec_iter_s
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88f43e3a by Martin Uecker at 2020-03-25T18:22:57+01:00
nufft not removing oversampling
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aafd9eed by Martin Uecker at 2020-03-28T22:10:36+01:00
fix bug
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0f8b6b05 by Max Litster at 2020-04-02T19:58:15+02:00
allow users to specify precision in format strings (#215)
* specify precision in show format strings
* requires user to input sign, changed default fmt to match
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b5d69752 by Sebastian Rosenzweig at 2020-04-10T10:30:59+02:00
num/linalg: Moore Penrose 'right inverse'
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e5e9fbb0 by Martin Uecker at 2020-04-10T10:36:55+02:00
update multind (md_pad and md_check_equal_dims)
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ecd4559c by Sebastian Rosenzweig at 2020-04-10T10:40:59+02:00
noncart/nufft: Estimate fast square image dims
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76ebbc7d by rosenzweig at 2020-04-10T10:42:40+02:00
phantom: Time dimension
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44f8539c by rosenzweig at 2020-04-10T10:42:40+02:00
tests/pics: add missing module
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ee19d14a by rosenzweig at 2020-04-10T10:52:31+02:00
rmfreq tool
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9087e226 by rosenzweig at 2020-04-10T14:15:40+02:00
ssa tool
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959f932e by rosenzweig at 2020-04-10T14:15:40+02:00
ssa: tests
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6039088c by Martin Uecker at 2020-04-10T14:15:40+02:00
split up
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27020ba3 by Martin Uecker at 2020-04-10T14:15:41+02:00
refactor
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73a21356 by Jon Tamir at 2020-04-19T09:01:01+02:00
pics: allow data in COEFF_DIM if basis is not used (#217)
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8428a797 by Martin Uecker at 2020-04-25T18:13:38+02:00
md_reshape
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b46d3944 by Martin Uecker at 2020-04-25T18:13:38+02:00
generalize reshape
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5fcfe86f by Martin Uecker at 2020-04-25T18:13:38+02:00
bin tool
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4994a48a by Martin Uecker at 2020-04-25T19:21:29+02:00
code for creating special SoS trajectory used in SSA-FARY paper
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13ba90f2 by Martin Uecker at 2020-04-26T09:32:58+02:00
remove old debug code
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ce6e6e1f by Martin Uecker at 2020-04-26T09:33:04+02:00
fix check
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6d925e50 by Martin Uecker at 2020-04-26T15:26:59+02:00
BART logo
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eba6bd91 by Martin Uecker at 2020-04-26T18:52:30+02:00
bart phantom
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64e9efe1 by Jon Tamir at 2020-04-26T16:31:24-07:00
gitignore
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ecda288f by spam-depository at 2020-05-02T22:05:30+02:00
Fix for MKL (#218)
Allow to use MKL version of LAPACK
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2a7004e6 by Martin Uecker at 2020-05-09T08:37:53+02:00
upat
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9f9afd12 by Martin Uecker at 2020-05-09T08:48:04+02:00
drawing routines required for view
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73708254 by Martin Uecker at 2020-05-10T15:21:18+02:00
rtnlinv
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d3dd3b3c by Martin Uecker at 2020-05-11T13:46:43+02:00
update md_ functions
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94a73c8a by Martin Uecker at 2020-05-11T15:27:42+02:00
changes for SMS T1 model-based reconstruction
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acfbe011 by Martin Uecker at 2020-05-11T20:46:41+02:00
missing library
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fe5a7656 by Martin Uecker at 2020-05-16T20:06:10+02:00
fix dicom padding
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1f236ee5 by Martin Uecker at 2020-05-21T13:06:31+02:00
traj: fix Cartesian undersampling
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79650d19 by Martin Uecker at 2020-05-23T19:00:08+02:00
relax tests for new GCC
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637b1184 by Martin Uecker at 2020-05-26T07:23:19+02:00
linop_copy_wrapper, and loop refcount fix
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c3302947 by Martin Uecker at 2020-05-26T07:23:19+02:00
minor changes
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c182c0b5 by Martin Uecker at 2020-05-26T07:23:19+02:00
nufft: option for looping
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959ef283 by Martin Uecker at 2020-05-31T14:02:58+02:00
support non-Cartesian trajectories in nlinv tool
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8b759e4b by Zhengguo Tan at 2020-06-01T10:00:23+02:00
add partial-Fourier trajectory
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752b9351 by martinkraemer84 at gmail.com at 2020-06-05T12:40:14+02:00
Renamed WSLPathCorrection to lower case for consistency
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92732113 by martinkraemer84 at gmail.com at 2020-06-05T12:40:14+02:00
Better documentation when using the help command
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4456a04d by martinkraemer84 at gmail.com at 2020-06-05T12:40:14+02:00
Changed LD_LIBRARY_PATH (linux) and DYLD_LIBRARY_PATH (mac) to be cleared only temporarily and to be restored at the end of the bart call
Added separation of varargin inputs into character inputs and data inputs. Character inputs are then appended to the given bart command. This enables calling of only "bart" or "bart traj -h" commands from within matlab, e.g. when no data input is given
Renamed loop variables ("i" should not be used as it represents the complex number)
Better function description when using the help command
Added section comments and cleaned up formatting warnings
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ef6c522c by martinkraemer84 at gmail.com at 2020-06-05T12:40:14+02:00
Fixed typo and changed all(cmd==0) to isempty(cmd)
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a82d5b7c by martinkraemer84 at gmail.com at 2020-06-05T12:40:14+02:00
Added usage of bart_path to wsl
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c0623be6 by Siddharth Iyer at 2020-06-15T14:06:00+02:00
Added option to create projection k-space in wshfl
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d2a41d21 by Siddharth Iyer at 2020-06-15T14:06:00+02:00
Move wshfl to ADMM with generalized regularazation options
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c3cf9a47 by Philip Schaten at 2020-06-15T14:06:21+02:00
Build RPMS for bart in copr
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6c5d8ec4 by Philip Schaten at 2020-06-15T14:06:21+02:00
libbart-devel; fix bart version command; install man page
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52b2ca31 by Philip Schaten at 2020-06-15T14:06:21+02:00
octave-bart package
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bef61f9a by Martin Uecker at 2020-06-15T14:22:03+02:00
Makefile: forward pythontest target to 2nd stage
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f525fef2 by Christian Holme at 2020-06-18T15:02:30+02:00
README: install devtoolset after centos-release-scl
For me, I received "No package devtoolset-8 available." when
trying to install devtoolset-8 before centos-release-scl.
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95b8145d by Christian Holme at 2020-06-30T18:35:02+02:00
rtnlinv: fix scaling and tests
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2ac528e9 by Nick Scholand at 2020-06-30T18:48:35+02:00
Add rings to tube phantom
- Add struct for ellipsis geometry including background boolean
- Make rings the default for TUBE phantom
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9ece077a by Martin Uecker at 2020-06-30T18:58:43+02:00
support for using valgrind on unit tests
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53dbf683 by Martin Uecker at 2020-06-30T19:05:37+02:00
test for bart logo phantom
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0a38b3b1 by Martin Uecker at 2020-06-30T19:16:19+02:00
update test_iter
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4335f677 by Martin Uecker at 2020-06-30T19:23:10+02:00
fix operator stacking for non-singleton dimensions
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4bbefe25 by Xiaoqing Wang at 2020-06-30T19:24:27+02:00
add a utest for operator_p_stack along the last second dimension
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9417d79c by Martin Uecker at 2020-06-30T19:42:19+02:00
nlinv tests
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6aa22f85 by Moritz Blumenthal at 2020-06-30T19:43:10+02:00
FIX ifftc for odd dimensions
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0e39a1c4 by Christian Holme at 2020-07-02T13:51:34+02:00
{rt,}nlinv: hide some options
we actually need to remove their argument name as well,
otherwise option hiding does not work.
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b54a8587 by Melvin Robinson at 2020-07-03T13:55:02+02:00
Address deprecated time.clock()
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c822a528 by Martin Uecker at 2020-07-03T14:18:12+02:00
update copyright
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e3144db5 by Martin Uecker at 2020-07-03T17:22:48+02:00
references
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478ec7ae by Martin Uecker at 2020-07-07T09:47:56+02:00
upd. acknowledgments
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e1a4303e by Martin Uecker at 2020-07-07T09:47:56+02:00
bump version
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e00400d9 by Martin Uecker at 2020-07-09T14:07:02+02:00
Merge tag 'v0.6.00'
version 0.6.00
Changes:
- new tools: bin ssa upat rmfreq
- bin: tool for binning of dynamic data (Sebastian Rosenzweig)
- ssa: Singular Spectrum Analysis (SSA) and SSA-FARY method (Sebastian Rosenzweig)
- rmfreq: remove angle-dependent frequency in radial acquisitions (Sebastian Rosenzweig)
- upat: generate Cartesian undersampling patterns
- phantom: tubes and BART logo phantoms
- reshape: perform more general reshapes
- show: control precision (Max Litster)
- nufft: option to output over-sampled grid
- version: check for minimum BART version
- traj: problems introduced in 0.5.00 fixed (208, 209, ...)
- traj: support for asymetric echos
- pics: allow data in COEFF_DIM if basis is not used
- nlinv: add direct support for non-Cartesian trajectories
- wshfl: various improvements (Siddharth Iyer)
- tests: bin, estdelay, ssa, nlinv, pics, nufft, phantom, reshape, upat
- generic: removed CMake build system
- generic: simplify building of libraries
- generic: support running valgrind on unit tests
- generic: better support and packages for Fedora and CentOS (Philip Schaten)
- library: new functions: md_reshape, md_pad, md_check_equal_dims, md_zcovar,
md_zdiv_reg, md_exp, md_log, md_zsin, md_zcos, md_zatanr, md_zss2,
md_zsmin, md_real, md_imag
- library: new line drawing functions required by view
- library: new functions: mat_pinv_left, mat_pinv_right
- library: new debug function to print bitmasks
- library: fix GPU fft to work with more complicated dimensions (Christian Holme)
- many other bug fixes and improvements
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6fdcb229 by Martin Uecker at 2020-07-09T16:44:05+02:00
update patches
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4755a69f by Martin Uecker at 2020-07-11T15:14:22+02:00
update copyright
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067ae608 by Martin Uecker at 2020-07-11T15:28:02+02:00
standard version 4.5.0
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fec74f31 by Martin Uecker at 2020-07-11T15:28:55+02:00
debian/control: rules does not require root
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6c60fecb by Martin Uecker at 2020-07-11T15:41:43+02:00
add upstream metadata file
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58ee511e by Martin Uecker at 2020-07-11T15:51:34+02:00
update changelog
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21 changed files:
- .gitignore.main
- .travis.yml
- ACKNOWLEDGEMENTS
- − CMakeLists.txt
- LICENSE
- Makefile
- Makefiles/README.md
- README
- README.md
- + bart.spec
- − build_targets.mk
- − cmake/BARTConfig.cmake.in
- − cmake/BARTFindBLASlib.cmake
- − cmake/FindATLAS.cmake
- − cmake/FindBOpenMP.cmake
- − cmake/FindBPython.cmake
- − cmake/FindCUDAlibs.cmake
- − cmake/FindFFTW.cmake
- − cmake/FindLAPACKE.cmake
- − cmake/FindMatlab.cmake
- − cmake/FindOpenBLAS.cmake
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/418fa54f3a550a8f5ba29bce721ea364c2fd24d7...58ee511e05bdbd66dc8930750ff5ade6e82ad356
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View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/418fa54f3a550a8f5ba29bce721ea364c2fd24d7...58ee511e05bdbd66dc8930750ff5ade6e82ad356
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