[med-svn] [Git][med-team/bart][upstream] 371 commits: Simple MATLAB/Octave Unit Test (#227)

Martin Uecker (@uecker-guest) gitlab at salsa.debian.org
Mon Sep 13 16:55:51 BST 2021



Martin Uecker pushed to branch upstream at Debian Med / bart


Commits:
1512f4dc by Martin Krämer at 2020-07-13T11:26:36+02:00
Simple MATLAB/Octave Unit Test (#227)

* Added simple MATLAB/Octave Unit Test

* Added function header
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af9d4e32 by Martin Krämer at 2020-08-07T19:43:32+02:00
Removed not necessary omp atomics (#230)


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db597b10 by Martin Krämer at 2020-08-10T10:07:31+02:00
Fixed missing linop_free() for local intermediate variable (#232)


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86026f35 by Martin Krämer at 2020-08-10T10:08:03+02:00
Added parallelization to linear phase calculatulation in NUFFT preparation (#233)


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162be159 by Christian Holme at 2020-08-10T18:57:05+02:00
opts: add support for long options

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1f99a871 by Christian Holme at 2020-08-10T18:57:13+02:00
opts: complete long options

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9f0d78f7 by Martin Uecker at 2020-08-10T19:06:42+02:00
minor updates

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b46d2641 by Jon Tamir at 2020-08-10T19:14:14+02:00
add random tube phantom (with -N <num>) (#231)

* add random tube phantom (with -N <num_tubes>)

* phantom: for random tubes, shrink tube size as trials increases

* phantom: for random tubes, warn if >200 tubes are being created

* phantom: random tubes errors out if runtime is too long

* phantom: random tubes -- fix bg in circle check and use circle intersection checks

* simplify to circles only
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7c80e9f2 by Martin Krämer at 2020-08-11T10:25:06+02:00
Changed estimate_im_dims() to always round up (#234)


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9ea47b4a by Martin Krämer at 2020-08-11T13:13:00+02:00
Added support for non squared image sizes to nlinv (#236)

* Added support for non squared image sizes

* Restructured to avoid else clause
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3ef460e2 by Christian Holme at 2020-08-11T13:14:17+02:00
misc/mmio.c: add newlines to error messages

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0bd78907 by Christian Holme at 2020-08-11T13:14:17+02:00
src/mmio.c: whitespace

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5d7e9c02 by Christian Holme at 2020-08-11T13:14:17+02:00
misc: add file_type enum and function

This leads to a bit less duplicated code in the
create_cfl and load_cfl functions.

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b33d3758 by Christian Holme at 2020-08-11T13:14:17+02:00
misc: unlink already opened files

In order to properly support identical input and output in all our
tools, we now remove the input file if it is later opened for writing.

This necessitates that we always create the output files
after all inputs, but this is the logical order anyway.

Since we have a private memory-mapping to the input, we can remove
the file from the filesystem and overwrite it with the output.

Caveat: This might not work on Windows.

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11b0a3c0 by Christian Holme at 2020-08-11T13:14:17+02:00
misc/io: io_unregister removes all IOs of that name

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9af42665 by Christian Holme at 2020-08-11T13:14:17+02:00
join.c: now works with automatically unlinking files

Since we actually do want to append to an input, we cannot
remove it before creating the output.

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0b4a836d by Martin Krämer at 2020-08-11T16:05:44+02:00
Changed to apply oversampling after image size estimation (#237)


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439ef513 by Christian Holme at 2020-08-12T16:38:38+02:00
iter/iter5.c: fix typo

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6d4c51e7 by Xiaoqing Wang at 2020-08-12T16:38:38+02:00
add a zsmax prox operator

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640712ca by Martin Uecker at 2020-08-12T16:38:38+02:00
bump join limit

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d47f3e22 by Martin Uecker at 2020-08-12T16:38:38+02:00
add operator framework (with contribs. by M. Blumenthal)

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67f5577f by Martin Uecker at 2020-08-12T16:38:38+02:00
update vecops

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55f38c6b by Christian Holme at 2020-08-12T20:56:39+02:00
fix bart version

Since git version v2.11, git describe does not always use 7 characters
for its commit hash. This broke bart version parsing, which always
expected 7 characters.

So now git-version.sh forces 7 characters, and additionally the parsing
now accepts up to 40 characters in the commit hash.

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24cf7569 by Christian Holme at 2020-08-12T20:56:39+02:00
add version test

Just to see if bart can parse its own version

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624cf7d7 by Jon Tamir at 2020-08-16T00:11:44-07:00
phantom: for random tubes, use full background and tweak tube size

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e52b2f13 by Xiaoqing Wang at 2020-08-21T11:44:25+02:00
modified the SMS scaling to reproduce results in the SMS moba T1 paper

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72b72baf by Martin Uecker at 2020-08-22T07:32:15+02:00
use md_zexpj in linear_phase

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6194478f by Martin Uecker at 2020-09-06T09:21:26+02:00
fix compatibility with SSA-FARY paper

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4d389014 by Martin Uecker at 2020-09-06T09:21:31+02:00
change debug level for argument linking

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5094eb29 by Martin Uecker at 2020-09-06T09:22:20+02:00
ESPIRiT GPU test

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c520c368 by Christian Holme at 2020-09-06T09:28:31+02:00
nlinv.c: free nufft_op

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e439518c by Martin Uecker at 2020-09-06T10:35:41+02:00
relax utest

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d5115f51 by Martin Uecker at 2020-09-15T11:04:51+02:00
fix admm wrapped in itop (thanks to Zhengguo Tan)

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242b4c31 by Christian Holme at 2020-09-15T13:59:38+02:00
Makefile: make parallelism configurable (edited by M.U.)

use $(MAKE) and add PARALLEL_NJOBS variable

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e7cc414a by Martin Uecker at 2020-09-19T13:54:43+02:00
fix some undefined behaviour

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0f8fd35b by Martin Uecker at 2020-09-19T13:54:43+02:00
code style issues

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67c3b509 by mblum at 2020-10-04T08:56:52+02:00
Merge empty dimensions

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10c2ce9b by mblum at 2020-10-04T09:24:05+02:00
Parallelization cost depending on tensorsize

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b67130ab by mblum at 2020-10-04T09:24:05+02:00
Optimize md_copy2

1.) Reduce the number of cuda_memcpy calls for filling:
Old:
[abc]->[abcxxxxxxxxx]->[abcabcxxxxxx]->[abcabcabcxxx]->[abcabcabcabc]
new:
[abc]->[abcxxxxxxxxx]->[abcabcxxxxxx]->[abcabcabcabc]

2.)
Use cuda_memcpy_strided in more cases by permuting dims wit inputstrides
= 0 to the end

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fb5e598c by mblum at 2020-10-04T09:24:05+02:00
Refactor fill-case of md_copy2

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f4ba6dec by mblum at 2020-10-04T09:24:05+02:00
Don't split dims on gpu

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29e0c0b3 by mblum at 2020-10-04T09:24:05+02:00
Turn off parallelization for h2d and d2h copies

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11b1c115 by Martin Uecker at 2020-10-04T09:24:05+02:00
style

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eba5010c by Martin Uecker at 2020-10-04T10:24:06+02:00
update geometry lib

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3edb1e63 by Martin Uecker at 2020-10-04T10:28:03+02:00
update unit tests for prox operators (thx Xiaoqing Wang)

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40984216 by Martin Uecker at 2020-10-04T10:33:03+02:00
gitlab CI

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0a815ed3 by Martin Uecker at 2020-10-04T17:07:26+02:00
update blas interface

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67a53739 by Christian Holme at 2020-10-04T17:10:03+02:00
version: support dirty no-git version format

If the git command cannot be found or if git describe
fails for any reason, git-version.sh generates a
version string such as
	v0.6.00-dirty
This commit allows the version command to properly parse
such a version string.

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9fa8da71 by Martin Uecker at 2020-10-04T17:10:52+02:00
OMP= in versio

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53fc3f2d by Moritz Blumenthal at 2020-10-05T11:12:17+02:00
Fix memory-leak in nlop_chain

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0502c142 by mblum at 2020-10-05T11:12:22+02:00
Simplify cast to work on operators

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284c7479 by Xiaoqing Wang at 2020-10-05T11:18:44+02:00
moba: add the model-based T2 mapping part

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5fe1c1cf by Xiaoqing Wang at 2020-10-05T11:19:00+02:00
relax the tolerance for moba l2 regularization and fix some dimension issue for moba T1

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b8c2953f by Xiaoqing Wang at 2020-10-05T11:19:11+02:00
moba: add the option to switch off the auto_norm of parameter maps for thresholding

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f6c3f416 by Martin Uecker at 2020-10-05T11:24:21+02:00
fix copyrights

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f03800c9 by Martin Uecker at 2020-10-05T13:59:33+02:00
signal tool

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36d8c6cc by Nick Scholand at 2020-10-05T14:09:41+02:00
Create utest for analytical signals.

IR bSSFP and IR FLASH up to now.

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3eeaa936 by Martin Uecker at 2020-10-05T14:09:41+02:00
add tests for model-based reconstruction (thx Xiaoqing Wang)

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06d46893 by Martin Uecker at 2020-10-05T14:10:31+02:00
use iter4 interface in moba

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a9dd4375 by Nick Scholand at 2020-10-05T14:14:15+02:00
minor

simplify normal fista.

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2637934d by Martin Uecker at 2020-10-05T14:16:56+02:00
rename local function

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a84f371e by Martin Uecker at 2020-10-05T14:18:47+02:00
minor style change

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dbfe26cf by Martin Uecker at 2020-10-05T14:22:36+02:00
minor change

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7e46b948 by Martin Uecker at 2020-10-05T15:05:45+02:00
assertion + comment

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c0d57f1c by Martin Uecker at 2020-10-05T18:47:45+02:00
BLAS accelerated strided operations

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3752655f by Martin Uecker at 2020-10-05T18:48:01+02:00
add noise std test

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9de86314 by mblum at 2020-10-07T21:52:29+02:00
Optimize make_3op_scalar

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f05e5a7d by Martin Uecker at 2020-10-07T22:06:48+02:00
test flpmath stides optimizations

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f5ed3a0f by Martin Uecker at 2020-10-09T07:11:27+02:00
add some more md functions

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cf167328 by Martin Uecker at 2020-10-09T07:21:48+02:00
add optimization for strides

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0dad4934 by Martin Uecker at 2020-10-09T07:44:46+02:00
minor change

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12d21a54 by Martin Uecker at 2020-10-09T07:46:21+02:00
rename utest

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3833681e by Martin Uecker at 2020-10-31T21:32:20+01:00
fix incorrect dims

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60a862be by Martin Uecker at 2020-10-31T21:40:34+01:00
coding style

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5202aac2 by Martin Uecker at 2020-11-01T15:31:07+01:00
stricter array bounds and fixed

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2a4205ba by Christian Holme at 2020-11-05T13:45:32+01:00
nufft_adjoint: split for lower memory consumption

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c2e83c68 by Christian Holme at 2020-11-05T13:45:33+01:00
nufft_adjoint: support noncontiguous ksp access

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cd56ef2c by Christian Holme at 2020-11-05T13:45:33+01:00
add tests for new lowmem option

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51e5e6b1 by Christian Holme at 2020-11-05T13:45:33+01:00
lowmem2 fixes

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f23364a1 by Christian Holme at 2020-11-05T13:45:33+01:00
update debug output

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779ce23b by Christian Holme at 2020-11-05T13:45:33+01:00
lowmem2: sum over extra dimensions in k-space

should further reduce memory consumption

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fa443e83 by Christian Holme at 2020-11-05T14:55:07+01:00
nufft_adjoint: move split calculation to new function

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3197c506 by Christian Holme at 2020-11-05T14:55:07+01:00
nufft: merge lowmem2 into lowmem

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149e2398 by Christian Holme at 2020-11-05T14:55:07+01:00
nufft: remove unused bool lowmem

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c18c3868 by Christian Holme at 2020-11-05T14:55:07+01:00
nlinv: optionally use lowmem for nufft objects

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0df20f7f by Martin Uecker at 2020-11-08T14:16:35+01:00
readability and debug output

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87899149 by Martin Uecker at 2020-11-08T14:16:47+01:00
add low-mem nufft tests

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31b0933e by Moritz Blumenthal at 2020-11-08T15:03:17+01:00
Make op_p chain working on gpu

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7189e800 by Martin Uecker at 2020-11-08T15:07:58+01:00
style and comment

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859f9bc4 by Martin Uecker at 2020-11-08T15:13:24+01:00
correctly null-terminate argument list after parsing arguments

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84181954 by Martin Uecker at 2020-11-08T16:19:25+01:00
implement warmstart for lsqr

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d177cd2f by Zhengguo Tan at 2020-11-08T16:19:25+01:00
add one unit test case for warmstart

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a7cf7e8f by Martin Uecker at 2020-11-08T16:19:26+01:00
simplify test, make more robust, new interface

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8e3e3105 by Martin Uecker at 2020-11-08T16:37:48+01:00
fix lsqr initialization

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6f7065a8 by Martin Uecker at 2020-11-08T17:10:24+01:00
for parallelization, relax test

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86c7367c by Martin Uecker at 2020-11-09T10:49:50+01:00
relax test some more

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2c3eb7d1 by Martin Uecker at 2020-11-09T12:15:59+01:00
update multi-echo signal

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5821fad6 by Martin Uecker at 2020-11-09T14:06:37+01:00
implement continuation for lsqr/itop

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9f2710cd by Martin Uecker at 2020-11-09T14:07:50+01:00
minor whitespace change

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da055d48 by Martin Uecker at 2020-11-09T14:18:50+01:00
refactor config for model-based recons

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020d3411 by Martin Uecker at 2020-11-09T17:19:56+01:00
styles fixes

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c74e81b0 by Martin Uecker at 2020-11-09T20:06:41+01:00
minor floating point tweak for golden-ratio trajectories

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1ad4b763 by Martin Uecker at 2020-11-09T20:06:41+01:00
estdelay: export to file

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9e8fb9a3 by Martin Uecker at 2020-11-09T20:08:51+01:00
multi-echo trajectory & reading of gradient delays from file

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14b94363 by Martin Uecker at 2020-11-09T22:03:26+01:00
model-based recon for multi-echo FLASH

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5b1578f9 by Martin Uecker at 2020-11-09T22:03:26+01:00
integrate meco model into moba tool

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98c36990 by Martin Uecker at 2020-11-09T22:03:26+01:00
meco test

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32b9a671 by Martin Uecker at 2020-11-09T22:03:54+01:00
fixes

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9a594b24 by Martin Uecker at 2020-11-11T12:00:22+01:00
style

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596211ba by Christian Holme at 2020-11-14T12:24:23+01:00
noncart/nufft: properly propagate the lowmem flag

Otherwise, it will not be used in the calculation of the psf, which can
often be the largest nufft performed.

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259a6927 by Christian Holme at 2020-11-14T12:24:23+01:00
noncart/nufft: lower debug level for split adjoint

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772e05a1 by Christian Holme at 2020-11-14T12:24:23+01:00
add test to check if lowmem actually reduces memory

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36a680e9 by Christian Holme at 2020-11-14T12:24:23+01:00
change test to check signficiant mem reduction

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68a01c8a by Christian Holme at 2020-11-14T12:24:23+01:00
change to test to avoid bc

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590fde0e by Martin Uecker at 2020-11-14T12:24:23+01:00
nufft memory usage in no-lowmem branch

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a41604a3 by Martin Uecker at 2020-11-14T12:24:23+01:00
set bash shell for lowmem test

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bf69ba3d by Martin Uecker at 2020-11-14T12:24:23+01:00
do not run moba tests by default

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ba98fc54 by Martin Uecker at 2020-11-14T13:30:05+01:00
Revert "add tests for new lowmem option"

(lowmem tests should not duplicate existing tests but directly
compare lowmem vs no-lowmem)
This reverts commit cd56ef2ce661d2a671f28b0889d96e82550d098d.

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84195c45 by Martin Uecker at 2020-11-14T14:54:37+01:00
avoid out-of-bounds access

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eb254b5a by Martin Uecker at 2020-11-28T12:15:22+01:00
turn-off as it fails for CI

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565db173 by Moritz Blumenthal at 2020-11-28T12:17:52+01:00
Index for nlop der/adj functions

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cc532416 by Moritz Blumenthal at 2020-11-28T12:18:01+01:00
Add operator_ref for bind, attach, loop and copy

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700b340b by Moritz Blumenthal at 2020-11-28T12:26:18+01:00
Fix memory leak and improve operator_apply_parallel_unchecked

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54f2502d by Moritz Blumenthal at 2020-11-28T12:44:53+01:00
Change io_flag bitmask to VLA of booleans

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33b1fe1b by Moritz Blumenthal at 2020-11-28T12:45:12+01:00
Refactor operator reshape

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c73f68d2 by Moritz Blumenthal at 2020-11-28T12:46:27+01:00
Linop_plus by operator_plus

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02c845bd by Moritz Blumenthal at 2020-11-28T12:47:09+01:00
Add operator_p functions

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8a7fc7b6 by Martin Uecker at 2020-11-28T13:02:47+01:00
fix some coding style issues

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38c53d7f by Martin Uecker at 2020-11-28T17:45:47+01:00
relax test

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09b5e5c9 by Jon Tamir at 2020-12-04T17:43:47-06:00
relax test (pass on MacOS)

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19f6b121 by Jon Tamir at 2020-12-04T19:40:46-06:00
change uint to unsigned int (fixes #240)

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2bf63b67 by Jon Tamir at 2020-12-05T21:08:46-06:00
shut up warning

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0f06b3a9 by Jon Tamir at 2020-12-05T21:09:10-06:00
relax test

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d13fc4d6 by Moritz Blumenthal at 2020-12-22T13:15:59+01:00
Reshape linear operators

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52fad1f2 by Xiaoqing Wang at 2020-12-22T13:18:00+01:00
fix the linop reshape

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5b2478aa by Zhengguo Tan at 2020-12-22T13:25:18+01:00
POS regularization: allows for higher dims

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bca22204 by Zhengguo Tan at 2020-12-22T13:25:33+01:00
add an unit test case for POS regularization

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e7f8a725 by Martin Uecker at 2020-12-22T13:26:59+01:00
remove dump_cfl

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1faee6ce by Zhengguo Tan at 2020-12-23T21:31:51+01:00
scale all maps up after recon

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24b30dad by Zhengguo Tan at 2020-12-23T21:32:02+01:00
update regularization options

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73dc4bf2 by Zhengguo Tan at 2020-12-23T21:33:26+01:00
use optreg conf

- to assist processing regularization options for moba

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766900d1 by Zhengguo Tan at 2020-12-23T21:33:44+01:00
allow for multi-echo reconstruction for MGRE

- basically multi-echo parallel imaging using NLINV

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a1818192 by Zhengguo Tan at 2020-12-23T21:36:07+01:00
update moba meco test

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6233602b by Zhengguo Tan at 2020-12-23T21:54:17+01:00
enable cartesian k-space data in moba

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3d74fd47 by Zhengguo Tan at 2020-12-23T21:54:25+01:00
cartesian meco traj

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f5fe2308 by Zhengguo Tan at 2020-12-23T21:54:48+01:00
fix

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6184270a by Martin Uecker at 2020-12-25T09:24:14+01:00
document use of Bessel's correction in md functions

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430351f2 by Martin Uecker at 2020-12-25T09:24:41+01:00
minor

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cb11a429 by Martin Uecker at 2020-12-25T23:41:17+01:00
remove void* argument in loop functions

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9c125a4b by Martin Uecker at 2020-12-25T23:49:07+01:00
white space fixes

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24cf745a by Christian Holme at 2020-12-26T21:47:51+01:00
standardize use_gpu variable name

As far as I can see, all top-level command files now use use_gpu
as their variable name for GPU usage.

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548f6b0e by Martin Uecker at 2020-12-28T13:24:29+01:00
add flags option to linop sum

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1043956c by Martin Uecker at 2020-12-28T13:24:36+01:00
rename linop_sum to linop_avg and add sum

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d901403e by Martin Uecker at 2020-12-28T13:24:45+01:00
make dimension independent

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9ecd499c by Martin Uecker at 2020-12-28T13:24:53+01:00
add const to iter config

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5214f6f9 by Xiaoqing Wang at 2020-12-28T14:56:14+01:00
ops.c:allow the operator_stack along an arbitrary dimension (with Moritz Blumenthal)

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a252ff18 by Martin Uecker at 2020-12-28T14:56:14+01:00
white space fixes

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45b3b200 by Martin Uecker at 2020-12-28T14:56:14+01:00
update unit tests

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b78b3956 by mblum at 2020-12-28T18:37:16+01:00
Express linop_reshape by operator_reshape

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0aa9ea53 by Martin Uecker at 2020-12-29T11:20:27+01:00
redefine SWAP macro

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bb7d99dd by Martin Uecker at 2020-12-29T11:32:23+01:00
coding style

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15893810 by Martin Uecker at 2021-01-03T15:31:11+01:00
add missing md_zslessequal

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e888d51a by Zhengguo Tan at 2021-01-03T17:06:54+01:00
add pixelfit

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14fb3a05 by Zhengguo Tan at 2021-01-03T17:07:07+01:00
relax test

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610809df by Martin Uecker at 2021-01-03T17:07:23+01:00
pixelfit updates

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b95a6cf0 by Martin Uecker at 2021-01-03T17:07:30+01:00
rename pixelfit -> mobafit

- - - - -
7456b1c6 by Martin Uecker at 2021-01-03T17:07:46+01:00
tighten test

- - - - -
950b3a5d by Martin Uecker at 2021-01-03T17:07:55+01:00
add stat tools

- - - - -
b9c642ec by Zhengguo Tan at 2021-01-03T17:22:06+01:00
update fat 1H MR spectrum

- - - - -
4f8f4b20 by Zhengguo Tan at 2021-01-03T17:22:14+01:00
fix and rename

- - - - -
624cd3af by Zhengguo Tan at 2021-01-03T17:22:29+01:00
simulate fat component

- - - - -
b889d1b7 by Zhengguo Tan at 2021-01-03T17:22:33+01:00
update test cases

- - - - -
7f25fa00 by Xiaoqing Wang at 2021-01-03T17:33:40+01:00
fix a memory leak in moba

- - - - -
ce40bb74 by Xiaoqing Wang at 2021-01-03T17:33:51+01:00
unify psf gridding in moba

- - - - -
572bfe94 by Xiaoqing Wang at 2021-01-03T17:33:59+01:00
simplify T1fun and T2fun in moba

- - - - -
21775d2d by Zhengguo Tan at 2021-01-03T23:02:30+01:00
lib order

- - - - -
9dde2ad4 by Martin Uecker at 2021-01-03T23:07:41+01:00
add option for k-space filter

- - - - -
b1ae4161 by Martin Uecker at 2021-01-04T08:51:33+01:00
missing test dependencies

- - - - -
a28c18aa by Martin Uecker at 2021-01-04T15:00:59+01:00
do not use memopt init for GPUs

- - - - -
1bd4ea42 by Christian Holme at 2021-01-15T17:48:46+01:00
add support for BART_COMPAT_VERSION

This allows the use of an environment variable to control
compatibility behavior of BART to old versions (using e.g
BART_COMPAT_VERSION="v0.5.00").

So far, this has only an effect on the golden angle calculation
in the trajectory.

- - - - -
44e18d66 by Martin Uecker at 2021-01-15T21:47:22+01:00
update FFT-based convolutions

- - - - -
cba53c81 by Martin Uecker at 2021-01-15T23:41:51+01:00
Conway's game of life

- - - - -
c2069733 by Christian Holme at 2021-01-16T17:12:48+01:00
fix  use_compat_to_version()

- - - - -
105f41e9 by Siddharth Srinivasan at 2021-01-28T09:26:32+01:00
Bug fix for cartesian moba (#243)


- - - - -
f931b97a by Martin Uecker at 2021-01-28T23:40:46+01:00
add alpha_min0 option for iter4_irgnm2

- - - - -
336a48bf by Martin Uecker at 2021-01-28T23:46:55+01:00
coding style

- - - - -
c37a8551 by Yaël Balbastre at 2021-01-31T09:13:45+01:00
Fix: add target for libismrm.a if ISMRMRD enabled (#244)


- - - - -
7a292fd8 by Nick Scholand at 2021-02-02T21:48:34+01:00
QuantMap::Add binary thresholding for mask creation.

- - - - -
63093297 by Martin Uecker at 2021-02-02T21:57:37+01:00
rewrite hard and binary thresholding to use absolute value

- - - - -
609df9a0 by Martin Uecker at 2021-02-03T20:55:41+01:00
test linearity of adjoint nufft

- - - - -
3385907a by Martin Uecker at 2021-02-07T22:25:25+01:00
coding style

- - - - -
a139b2c0 by Martin Uecker at 2021-02-07T22:35:03+01:00
add warning for dirty git versions

- - - - -
b4f8b67e by Martin Uecker at 2021-02-12T09:11:52+01:00
change cuda default path

- - - - -
06761336 by Martin Uecker at 2021-02-12T09:13:56+01:00
clang fixes

- - - - -
cf15be80 by Martin Uecker at 2021-02-12T09:39:03+01:00
extend ci

- - - - -
bb6703b5 by Monius at 2021-02-12T10:57:36+01:00
add support for IBM POWER9 HPC ppc64le

- - - - -
7d90203b by Martin Uecker at 2021-02-12T10:59:36+01:00
rename HPC to SCALAPACK

- - - - -
535bba9b by Siddharth Srinivasan at 2021-02-12T11:02:28+01:00
wshfl: Add fista option (#245)


- - - - -
5873cb0b by Christian Holme at 2021-02-12T11:20:09+01:00
moba: make coil smoothness configurable

- - - - -
6b23e176 by Christian Holme at 2021-02-12T11:20:09+01:00
misc/opts: add missing OPTL_CLEAR

- - - - -
d35ca140 by Martin Uecker at 2021-02-12T11:20:09+01:00
add command-line option for alpha_min0

- - - - -
762da30b by Xiaoqing Wang at 2021-02-12T11:20:09+01:00
use the signal tool to simulate the IR Look-Locker FLASH Dictionary

- - - - -
49d447da by Zhengguo Tan at 2021-02-12T11:20:09+01:00
enable switch to another fat spectrum

- moba uses '--fat_spec_0' as the switch
- default spectrum is FAT_SPEC_1

- - - - -
e1991487 by Zhengguo Tan at 2021-02-12T11:20:09+01:00
signal: add option for off resonance

- - - - -
85961069 by Martin Uecker at 2021-02-26T20:02:38+01:00
correct typo

- - - - -
d1b0e576 by Martin Uecker at 2021-03-01T15:17:01+01:00
bump version

- - - - -
0973af65 by Philip Schaten at 2021-03-12T07:28:36+01:00
Fix versioning

- correctly sorting main releases
- follow fedora versioning guidelines

- - - - -
9fe5b6e4 by Philip Schaten at 2021-03-12T07:28:36+01:00
bart for centos 7

- - - - -
d1799fab by Martin Uecker at 2021-03-24T11:02:39+01:00
quicksort with nested functions

- - - - -
0585ffe6 by Martin Uecker at 2021-03-24T11:02:39+01:00
minor

- - - - -
2de61b24 by Martin Uecker at 2021-03-25T12:15:23+01:00
clang workarounds

- - - - -
2d067289 by Martin Uecker at 2021-03-25T12:15:50+01:00
relax test for clang

- - - - -
b4057a81 by Martin Uecker at 2021-03-25T15:44:37+01:00
add ubsan option

- - - - -
7825df89 by Martin Uecker at 2021-03-25T21:24:19+01:00
make more variables signed

- - - - -
e5ce9fa7 by Moritz Blumenthal at 2021-04-07T14:08:10+02:00
Update vecops

- - - - -
522bd1d9 by Moritz Blumenthal at 2021-04-07T14:08:50+02:00
Add hyperbolic functions

- - - - -
b1619570 by Moritz Blumenthal at 2021-04-07T14:12:33+02:00
More efficient use of memcache

- - - - -
5c4bd6ff by Moritz Blumenthal at 2021-04-07T14:27:22+02:00
Add name string to types

- - - - -
63f389cf by Martin Uecker at 2021-04-07T14:38:47+02:00
allow additional ones in dims for ra files

- - - - -
be1a35cd by Moritz Blumenthal at 2021-04-07T14:40:06+02:00
Reduce calls of cuda_ondevice

- - - - -
ebd83ff4 by Moritz Blumenthal at 2021-04-07T14:42:28+02:00
reduce memory for linop_fftc

- - - - -
0cd2274e by Martin Uecker at 2021-04-08T20:36:15+02:00
fix compilation errors

- - - - -
1b142f6a by Martin Uecker at 2021-04-08T21:26:36+02:00
POSIX shared memory files

- - - - -
0a80ffe7 by aTrotier at 2021-04-08T21:43:50+02:00
traj test  default vs custom angles

- - - - -
1d7ab0b0 by Moritz Blumenthal at 2021-04-12T09:55:36+02:00
Add test for comparing cpu with gpu

- - - - -
08fbb520 by Martin Uecker at 2021-04-12T10:14:29+02:00
simplify test

- - - - -
5bc24606 by Martin Uecker at 2021-04-12T21:38:30+02:00
support Data flag and stdin

- - - - -
7d0fa021 by Martin Uecker at 2021-04-12T21:38:30+02:00
make reading from pipe robust

- - - - -
8ed4fab7 by Martin Uecker at 2021-04-12T21:38:30+02:00
support writing pipe files & delete read pipe files

- - - - -
c1a47f01 by Martin Uecker at 2021-04-12T21:38:30+02:00
protect against multiple io from pipe

- - - - -
eb0a3a1b by Martin Uecker at 2021-04-12T21:55:26+02:00
remove old mem cfl framework

- - - - -
2b6f82d5 by Martin Uecker at 2021-04-12T23:43:33+02:00
add new memcfl framework

- - - - -
644f71e9 by Martin Uecker at 2021-04-12T23:58:53+02:00
refactor and use mkstemp for temp file

- - - - -
1922723b by Volkert Roeloffs at 2021-04-14T13:37:52+02:00
add initial framework to do Cramér-Rao bound analysis

- - - - -
8053fea2 by Volkert Roeloffs at 2021-04-14T13:37:52+02:00
epg command with utest

- - - - -
eb947323 by Volkert Roeloffs at 2021-04-14T13:37:52+02:00
ADD bSSFP sequence and change M_ini to -M_0 for FLASH

- - - - -
36875671 by Volkert Roeloffs at 2021-04-14T13:37:52+02:00
ADD more details in help strings

- - - - -
78aa1c47 by Martin Uecker at 2021-04-14T13:37:52+02:00
coding style

- - - - -
6d6c0df9 by Martin Uecker at 2021-04-14T13:37:52+02:00
coding style

- - - - -
2b6a234f by Martin Uecker at 2021-04-15T00:05:16+02:00
fix test

- - - - -
95dc57fc by Martin Uecker at 2021-04-15T09:25:06+02:00
C++ compilation fix

- - - - -
ebca599a by Christian Holme at 2021-04-22T11:35:26+02:00
noir/model.c: fix pattern_for_each_coil

fix linop_fmac for a pattern which is different in each coil
and add a test for pattern_for_each_coil using vcc.

- - - - -
d698e01f by Martin Uecker at 2021-04-22T13:17:00+02:00
add unmap_raw

- - - - -
eaa37dda by Martin Uecker at 2021-04-22T13:17:00+02:00
add const

- - - - -
9b542cfc by Martin Uecker at 2021-04-22T13:17:00+02:00
and md_ random functions

- - - - -
23edfa4a by Martin Uecker at 2021-04-22T13:17:00+02:00
nlop reshape function

- - - - -
b533cb36 by Martin Uecker at 2021-04-22T13:17:00+02:00
linear operators and padding operator

- - - - -
2c237371 by Martin Uecker at 2021-04-22T13:17:00+02:00
update copyright year

- - - - -
45f8c5a5 by Martin Uecker at 2021-04-25T16:33:29+02:00
sum: free dimensions and strides

- - - - -
a4ac6608 by Martin Uecker at 2021-04-25T16:33:45+02:00
avoid out-of-bounds read

- - - - -
d744c850 by Martin Uecker at 2021-04-25T16:34:32+02:00
avoid leaks in moba regularizations

- - - - -
22cd040a by Martin Uecker at 2021-04-25T16:34:54+02:00
avoid leak of io_flags

- - - - -
9f339b4c by Martin Uecker at 2021-04-25T16:36:07+02:00
free things in main (for easier debugging)

- - - - -
21a10de8 by Martin Uecker at 2021-04-25T16:36:42+02:00
free things in utests (for easier debugging)

- - - - -
3f76f2f4 by Christian Holme at 2021-04-26T15:52:15+02:00
make cuda lib directory configurable

This is necessary e.g. for Google colab, where CUDA lives in lib64/
instead of lib/

- - - - -
a60dfe4e by Martin Uecker at 2021-04-28T10:10:01+02:00
makefile support for tensorflow

- - - - -
13042d3a by Martin Uecker at 2021-04-28T10:10:01+02:00
add tensorflow build test

- - - - -
899e8dd2 by Martin Uecker at 2021-04-28T10:10:01+02:00
document build

- - - - -
babb3ff7 by Martin Uecker at 2021-05-02T23:22:37+02:00
tensor flow wrapper

- - - - -
3c3eda9d by Christian Holme at 2021-05-03T17:06:07+02:00
epg.c: use logical-or instead of bitwise-or

- - - - -
078434e5 by Tamás Hakkel at 2021-05-05T22:12:38+02:00
add memcfl_register

- - - - -
4f2a7416 by Tamás Hakkel at 2021-05-05T22:12:38+02:00
test added for memcfl_register

- - - - -
a697c3b0 by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.h: remove unused macro OPTL_CFLOAT

This was added by accident in commit 1f99a8718

- - - - -
ca6ff6e6 by Christian Holme at 2021-05-07T12:32:13+02:00
option handling: add option type enum

Instead of having a pointer to the conversion function, we now include
the option type (as an enum specified in misc/opts.h) in the struct
opt_s. This has the following benefits:
	* It will enable a clearer interface description, by e.g.
allowing us to specify which string arguments are filenames and if they
are for input or output
	* It will allow checking if the file arguments are used
correctly

Furthermore, this commit now specifies what is special about
OPT_SPECIAL: From now on, OPT_SPECIAL means that the conversion function
pointer is specified in the struct opt_s, for alle other arguments that
function pointer is NULL.

- - - - -
5602f0cf by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.c: change usage string for vector arguments

We now show the specific way we want to specifiy the arguments in vec2
and vec3.

- - - - -
5c861d66 by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.c: move length check for long options

This check should really be done in the loop, as otherwise we might
write beyond the end of the longopts array

- - - - -
a4be2f19 by Christian Holme at 2021-05-07T12:32:13+02:00
remove mini_cmdline_bool

mini_cmdline_bool just introduces undocumented options, something we
want to avoid for a proper interface description

- - - - -
849e8d8c by Christian Holme at 2021-05-07T12:32:13+02:00
add first version of --interface

- - - - -
cf2e94dc by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.c: check_options for interface and help

- - - - -
3edc7a70 by Christian Holme at 2021-05-07T12:32:13+02:00
slightly improved --interface

- - - - -
04079a45 by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts: allow full range of char

- - - - -
a5b12ca9 by Christian Holme at 2021-05-07T12:32:13+02:00
add new IN, OUT and INOUTFILE options

For now, they just annotate intent. In the future, they can be used to
detect incorrect usage

- - - - -
02b39176 by Christian Holme at 2021-05-07T12:32:13+02:00
check OPT_{IN,OUT}FILE for correct use

and abort with an error when we do things wrong

- - - - -
e8f643d6 by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.c: properly support full range of char for longopts

- - - - -
70845e22 by Christian Holme at 2021-05-07T13:03:22+02:00
misc/opts: properly space help string

and remove the unneeded \t from fftmod

- - - - -
b6c1de19 by Christian Holme at 2021-05-07T13:03:22+02:00
opts: add default argname if argname is empty

- - - - -
9955a26d by Christian Holme at 2021-05-07T13:03:22+02:00
opts: interface update

- - - - -
5857940d by Christian Holme at 2021-05-07T13:03:22+02:00
style

- - - - -
63ad793c by Martin Uecker at 2021-05-08T09:35:36+02:00
prox for arbitrary differentiable loss

- - - - -
dd40a35f by Martin Uecker at 2021-05-08T09:35:47+02:00
refactor prox operators

- - - - -
fa4ab36f by Martin Uecker at 2021-05-08T09:35:48+02:00
refactor complex sort

- - - - -
0a438e4f by Martin Uecker at 2021-05-08T09:35:48+02:00
md_zmaxnorm

- - - - -
f5b9cab7 by Martin Uecker at 2021-05-08T09:35:48+02:00
add option to choose norm

- - - - -
4077ba69 by Martin Uecker at 2021-05-08T09:35:48+02:00
add op_p_conjugate

- - - - -
68b26fbe by Martin Uecker at 2021-05-08T09:35:49+02:00
add zselect

- - - - -
adab2714 by Martin Uecker at 2021-05-08T16:55:41+02:00
not a nested function

- - - - -
ec34c6c6 by Martin Uecker at 2021-05-09T17:38:33+02:00
increase tolerance of nufft batch test

- - - - -
d7382d07 by Christian Holme at 2021-05-11T11:02:42+02:00
update gitlab-ci to make all

- - - - -
3f200b43 by Martin Uecker at 2021-05-11T23:15:25+02:00
split lambda and stepsize

- - - - -
a9d3a873 by Martin Uecker at 2021-05-11T23:15:25+02:00
debug output for auto scaling

- - - - -
8b8d4ed2 by Martin Uecker at 2021-05-11T23:18:54+02:00
tensorflow loss (thx to Guanxiong 'Jason' Luo)

- - - - -
d7b4dcd1 by Martin Uecker at 2021-05-12T09:17:52+02:00
missing library

- - - - -
fcffe716 by Martin Uecker at 2021-05-12T10:49:14+02:00
remove warnings

- - - - -
9d66c09e by Martin Uecker at 2021-05-12T12:40:06+02:00
update references

- - - - -
bef0317e by Tamás Hakkel at 2021-05-17T10:40:41+02:00
Windows support by MSYS2

- - - - -
cbc10b60 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: rename OPT_ARG_TYPE to OPT_TYPE

- - - - -
8ac71e0c by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts.c: fix opt_long

- - - - -
2c85286d by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts.c: make opt_dispatch more general

Making opt_dispatch more general is necessary so that we can reuse it
for handling positional arguments.

- - - - -
0934de86 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts.c: check result of opt_uint

- - - - -
4ef0074d by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: add opt_cfl for parsing complex float

- - - - -
e543ff55 by Christian Holme at 2021-05-18T16:02:09+02:00
tests/test-join: preserve order in join

- - - - -
7da35690 by Christian Holme at 2021-05-18T16:02:09+02:00
add test for vec tool

- - - - -
8af3c9e0 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: check success of parse_cfl

- - - - -
422b1872 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: OPT_INOUTFILE is just a string for now

- - - - -
26adfe08 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: add fist version for positional arguments

- - - - -
2317da92 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/io: only warn for "incorrect" usage

With options, opening an output for reading or an input for writing is
clearly wrong. But with positional arguments, this can be legitimate,
e.g. when overwriting a file: "bart slice 0 0 a.ra a.ra" is a legitimate
use case. So for now, we just warn about it.

- - - - -
3134d286 by Christian Holme at 2021-05-18T16:02:10+02:00
migrate some tools to declared positional arguments

- - - - -
0c45849f by Christian Holme at 2021-05-19T10:03:00+02:00
positional arguemnts: migrate first batch of tools

and remove mini_cmdline, add OPT_ULONG

- - - - -
43d9065b by Christian Holme at 2021-05-19T10:51:28+02:00
migrate more tools, changes for fmac

- - - - -
4d3340e8 by Christian Holme at 2021-05-19T18:06:01+02:00
migrate remaining commands

- - - - -
5e29ca55 by Christian Holme at 2021-05-20T10:01:41+02:00
add positional arguments to --interface

- - - - -
cc4121a8 by Christian Holme at 2021-05-20T10:30:06+02:00
switch from "optional" to "required

so we switch true and false in every single ARG_*() macro

- - - - -
f9074934 by Christian Holme at 2021-05-20T13:53:42+02:00
bugfixes

- - - - -
1d61371b by Christian Holme at 2021-05-20T15:56:01+02:00
properly support inoutfiles

Additionally, it is now an error to open a file for either reading or
writing without first registering its use as an output, input, or inout
file. With declared OPT{IN,OUT}FILE and ARG_{IN,OUT}FILE options, there
should be no need now to open a file without an earlier declaration of
intended use.

- - - - -
478afdae by Christian Holme at 2021-05-20T15:59:58+02:00
misc/io.c: improve error condition

- - - - -
87250e7d by Christian Holme at 2021-05-20T16:17:53+02:00
fix utest test_memcfl

- - - - -
82988d66 by Christian Holme at 2021-05-21T09:47:38+02:00
misc/io: error into warning

on opening files which were not previously reserved as input or output.

- - - - -
a8c0a74f by Christian Holme at 2021-05-21T09:48:44+02:00
misc/opts.c: style

- - - - -
96ce1d67 by Christian Holme at 2021-05-21T10:03:47+02:00
more style

nicer interface, remove remaining usage_str, never end help_str with a
newline

- - - - -
f071aebf by Martin Uecker at 2021-05-21T12:47:45+02:00
minor style changeS

- - - - -
676b41c8 by Martin Uecker at 2021-05-23T11:48:35+02:00
don't create doc/commands.txt by default

- - - - -
f64c7b61 by Martin Uecker at 2021-05-23T18:33:28+02:00
style

- - - - -
8ebb989d by Martin Uecker at 2021-05-23T18:33:28+02:00
avoid pointer arithmetic

- - - - -
e9bb7eb4 by Martin Uecker at 2021-05-23T18:33:28+02:00
string handling

- - - - -
a477a809 by Martin Uecker at 2021-05-26T12:55:23+02:00
typo

- - - - -
49620750 by Zhengguo Tan at 2021-05-26T12:55:23+02:00
mobafit: init output with 0

- - - - -
0d431414 by Philip Schaten at 2021-05-26T12:55:23+02:00
Store meco scaling factor array in CPU memory for compatibility with older GPUs

- - - - -
f09d5d96 by tan4 at 2021-05-27T10:27:21+02:00
bitmask: loop over dims based on count (thanks to Christian Holme)

- - - - -
b80d802a by Philip Schaten at 2021-05-27T10:30:08+02:00
fix bart.spec

- - - - -
3ed31530 by Christian Holme at 2021-05-31T10:25:01+02:00
fix bench and bitmask

- - - - -
f6bd2149 by Christian Holme at 2021-05-31T12:25:31+02:00
moba: fix output of sensitivities

- - - - -
4e2b0c85 by Christian Holme at 2021-05-31T16:08:00+02:00
fix memleaks of ARG_TUPLE

- - - - -
3b5c228d by Christian Holme at 2021-05-31T16:08:25+02:00
poly: do not use argc, and style

- - - - -
be220b0c by Christian Holme at 2021-05-31T16:15:48+02:00
add test for bitmask tool

- - - - -
d4fb3950 by Christian Holme at 2021-05-31T16:17:56+02:00
misc/opts.c: fix string handling

fixes usage string of poly, for example

- - - - -
dd40a4df by Christian Holme at 2021-05-31T17:03:54+02:00
misc/opts.c: fix skipping of optional args, better style

better variable names and more informative (I hope) comments

- - - - -
0bfb0d39 by Moritz Blumenthal at 2021-06-05T14:18:17+02:00
Fix tf_wrapper

- - - - -
02d22826 by Moritz Blumenthal at 2021-06-05T14:18:17+02:00
Test gradients

- - - - -
757401d2 by Moritz Blumenthal at 2021-06-05T14:18:17+02:00
tf wrapper force equal dims for gradient and input

- - - - -
e2fc09a3 by Moritz Blumenthal at 2021-06-05T14:18:17+02:00
Automatically annotate tf graph with gradients

- - - - -
a164650a by Martin Uecker at 2021-06-05T14:25:26+02:00
BART coding style

- - - - -
d24ac66f by Christian Holme at 2021-06-05T14:48:15+02:00
don't install doc/commands.txt by default

since, as of commit 676b41c8 , we don't create it by default anymore

- - - - -
cbf797b3 by Moritz Blumenthal at 2021-06-05T17:50:49+02:00
Add kernels for efficient reduction

- - - - -
647c0c75 by Moritz Blumenthal at 2021-06-05T17:50:49+02:00
Add basic convolution algorithm

- - - - -
954434f1 by Martin Uecker at 2021-06-05T17:50:49+02:00
coding style

- - - - -
9ef9034f by Martin Uecker at 2021-06-05T18:28:41+02:00
missing variable

- - - - -
54bf67c3 by Martin Uecker at 2021-06-05T19:45:15+02:00
no cuda for tensorflow test

- - - - -
29f4d05b by Moritz Blumenthal at 2021-06-05T21:09:28+02:00
Fix linop_plus normal

- - - - -
046a7941 by Moritz Blumenthal at 2021-06-05T21:10:12+02:00
Allow NULL for nlop derivative (fallback to "not implemented")

- - - - -
41ca8e79 by Moritz Blumenthal at 2021-06-05T21:12:30+02:00
Add linops

- - - - -
955187c7 by Moritz Blumenthal at 2021-06-05T21:13:05+02:00
introduce flag to allow non-deterministic functions

- - - - -
52604f9a by Moritz Blumenthal at 2021-06-05T21:17:29+02:00
Make blas in vecops an optional optimization

- - - - -
d3873701 by mblum at 2021-06-05T21:20:58+02:00
Use memcache for cufft workingspace

- - - - -
cfb56bd8 by Moritz Blumenthal at 2021-06-05T21:21:18+02:00
Async cuda calls

- - - - -
dae8f735 by Moritz Blumenthal at 2021-06-05T21:21:34+02:00
reduce tenmul to zmul if possible

- - - - -
a62d72d4 by Moritz Blumenthal at 2021-06-05T21:22:06+02:00
activate zpow on gpu

- - - - -
610f7799 by Moritz Blumenthal at 2021-06-05T21:22:19+02:00
permute for strided_vecops

- - - - -
b9ea29f2 by Moritz Blumenthal at 2021-06-05T21:26:15+02:00
Merge dims again after sorting

- - - - -
cd210f24 by Moritz Blumenthal at 2021-06-05T21:28:47+02:00
Add cudnn support for convolutions

- - - - -
86ac911d by Moritz Blumenthal at 2021-06-05T21:37:23+02:00
rename linop_avg to add real linop_avg

- - - - -
c9a7aa0b by Martin Uecker at 2021-06-07T10:40:08+02:00
silence debug output in test

- - - - -
f0657fe7 by Christian Holme at 2021-06-15T11:15:50+02:00
return 0 instead of exit(0) in some tools

- - - - -
93fbdedb by Christian Holme at 2021-06-15T11:16:34+02:00
nlinv.c: fix memleak

- - - - -
f0e12f8e by Christian Holme at 2021-06-15T11:16:43+02:00
misc/io.c: fix bug in io_unregister

introduced by me in 11b0a3c0

- - - - -
61a3b832 by Martin Uecker at 2021-06-26T16:16:57+02:00
add target for a shared lib on Linux

- - - - -
109536a2 by Christian Holme at 2021-06-29T10:23:41+02:00
improve parsing of int, long and float

atoi, atol and family hide errors by returning 0 when they cannot parse
their string argument. This can lead to bugs when not giving an argument
to e.g. OPT_INT:
	bart nlinv -i -d4
would set the number of iteration (-i) to zero, as it cannot parse -d4
as an integer.

Now, such cases lead to an error.

- - - - -
e0c4de09 by Christian Holme at 2021-06-29T10:35:42+02:00
tests: fix noise -s

noise -s always parsed its argument as an integer, so noise -s1. was
always invalid (but hidden)

- - - - -
04cc35ca by Jon Tamir at 2021-07-09T20:45:31+02:00
fix some errors under MacOS:
1b142f6a (librt)
cbf797b3 (uint)
950b3a5d (test-roistat-mean)

- - - - -
125a8a2c by Jon Tamir at 2021-07-09T14:05:25-05:00
change default Mac gcc version to gcc10

- - - - -
65cb4a3c by Christian Holme at 2021-08-09T16:04:14+02:00
add compat for RING paper

- - - - -
29f303b2 by Christian Holme at 2021-08-16T12:24:25+02:00
update CI for new debian stable

Additionally, start documenting that we only support python 3

- - - - -


30 changed files:

- .gitignore.main
- + .gitlab-ci.yml
- − .travis.yml
- LICENSE
- Makefile
- README
- bart.spec
- doc/building.txt
- doc/references.txt
- git-version.sh
- libbart-devel.spec
- + matlab/test_bart.m
- + msys_setup.sh
- octave-bart.spec
- python/cfl.py
- rpkg.macros
- + scripts/life.sh
- src/avg.c
- src/bart.c
- src/bench.c
- src/bin.c
- src/bitmask.c
- src/cabs.c
- src/caldir.c
- src/calib/bin.c
- src/calib/bin.h
- src/calib/calib.c
- src/calib/calib.h
- src/calib/calmat.c
- src/calib/calmat.h


The diff was not included because it is too large.


View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/e1a4303e29505808dda543e453e54253c95f1284...29f303b26c5a065e095b3977c0b998cfd92fb602

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View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/e1a4303e29505808dda543e453e54253c95f1284...29f303b26c5a065e095b3977c0b998cfd92fb602
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