[med-svn] [Git][med-team/bart][master] 78 commits: version

Martin Uecker gitlab at salsa.debian.org
Sat Apr 28 19:57:26 BST 2018 

Martin Uecker pushed to branch master at Debian Med / bart


Commits:
5eb5943e by Martin Uecker at 2017-11-24T13:52:09+01:00
version

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3a4fc5a7 by Martin Uecker at 2017-11-24T13:52:23+01:00
fix typo

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68091c24 by Christian Holme at 2017-11-28T21:12:37+01:00
nlinv: add option for debug level

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7353ba36 by Christian Holme at 2017-11-28T21:12:37+01:00
nlinv: describe options

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eed78e1e by Christian Holme at 2017-11-28T21:12:37+01:00
nlinv: make IRGNM reduction factor configurable

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b95fe32c by Christian Holme at 2017-11-28T21:12:37+01:00
nlinv: consistent name for image

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b4cf9343 by Christian Holme at 2017-11-28T21:12:37+01:00
noir/recon.c: rename img to x

since img in that case was actually the image and the coils together.
It now reflects standard usage: x is the variable optimized by the
IRGNM.

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f727271e by Christian Holme at 2017-11-28T21:12:37+01:00
noir/recon: names consistent to header

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928ff3a5 by Christian Holme at 2017-11-28T21:12:37+01:00
nlinv: move initialization to nlinv.c

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f3b492f2 by Martin Uecker at 2017-11-28T21:52:19+01:00
newer gcc on Mac

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072890a9 by Martin Uecker at 2017-11-29T00:13:45+01:00
build fix mac

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bbf37f19 by Martin Uecker at 2017-11-29T20:48:22+01:00
remove macro for type-safe use of const arrays as function arguments on old compilers

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3ffa91f4 by Martin Uecker at 2017-12-03T13:01:28+01:00
remove build test for homebrew

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f69f2b6e by Jon Tamir at 2017-12-03T13:08:36-08:00
ecalib: add option to turn off phase rotation

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62b103a0 by Jon Tamir at 2017-12-04T09:41:14+01:00
homodyne: add option for uncentered ffts (#109)


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fbc2e464 by Martin Uecker at 2017-12-04T21:11:19+01:00
add noreturn to error function

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b015c7b8 by Martin Uecker at 2017-12-05T09:35:26+01:00
minor style changes

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dad94e1b by Martin Uecker at 2017-12-05T09:35:26+01:00
remove unneeded omp.h header

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f504015c by Martin Uecker at 2017-12-05T09:35:26+01:00
remove redundant vecop

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bb8d5fdf by Martin Uecker at 2017-12-05T10:05:35+01:00
hide noreturn from cuda

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1281d1c5 by Christian Holme at 2017-12-05T12:59:44+01:00
nlinv: properly initialize pointer as NULL

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fcfa3a9f by Christian Holme at 2017-12-05T13:00:19+01:00
nlinv: add option to provide initialization

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0a806e87 by Christian Holme at 2017-12-05T13:00:58+01:00
irgnm: improve debug output

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51cb70ee by Christian Holme at 2017-12-05T13:02:10+01:00
irgnm: add callback

The irgnm can now take a callback.

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a274dcf4 by Christian Holme at 2017-12-05T13:02:40+01:00
nlinv: add timing output

nlinv can now calculate how long the reconstruction took

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f909f976 by Christian Holme at 2017-12-07T17:34:41+01:00
nlinv: sensitivity output also when using GPU (#111)

The code now also outputs the sensitivites calculted by nlinv when run
on the GPU. This is possible by excplicitly copying data.
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97634388 by Jon Tamir at 2017-12-07T17:57:22-08:00
use vecop for zabs

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d50f985a by Martin Uecker at 2017-12-08T10:13:07+01:00
fix bug for gpu-mode of cdiag operator

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495613c5 by Martin Uecker at 2017-12-10T12:12:25+01:00
replace free with xfree

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669800c8 by Martin Uecker at 2018-01-21T11:24:23+01:00
update default compiler on Mac OS X (closes #113)

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df893106 by Martin Uecker at 2018-01-21T11:45:21+01:00
change default prefix to /usr/local/

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72ca7ca1 by Martin Uecker at 2018-01-21T11:46:31+01:00
turn off TOOLBOX_PATH overriding by default

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2a08ea1f by Martin Uecker at 2018-01-21T12:19:59+01:00
document clang issues

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2c0b132f by Martin Uecker at 2018-01-21T18:13:44+01:00
uncomment build of stand alone commands for CMake

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e0e7b029 by Martin Uecker at 2018-01-21T18:13:44+01:00
CMake: turn off matlab support by default

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22c87c6a by Martin Uecker at 2018-01-21T18:13:44+01:00
cmake: minimal c version is gnu11

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176055aa by Martin Uecker at 2018-01-24T21:24:39+01:00
fix obvious bug in blockproc

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2c40b79f by Martin Uecker at 2018-01-24T22:24:23+01:00
add missing free

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a0f01dba by Martin Uecker at 2018-01-25T20:59:20+01:00
add script for memory-economic use of espirit

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3c1c2eb7 by Martin Uecker at 2018-01-29T19:59:32+01:00
multind: nested functions

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626cd6fe by Martin Uecker at 2018-01-29T20:00:23+01:00
optimize: nested functions

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74f13399 by Martin Uecker at 2018-01-29T20:00:23+01:00
nested functions: merge fixes

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2dbc8471 by Martin Uecker at 2018-01-29T20:00:23+01:00
make clang compatible

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31c90b28 by Martin Uecker at 2018-01-29T20:00:23+01:00
travis

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47acbcb1 by Martin Uecker at 2018-01-29T20:00:23+01:00
compiler check for cuda

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0c8d2b88 by Martin Uecker at 2018-01-29T20:00:23+01:00
cuda fix

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b3e3c602 by Martin Uecker at 2018-01-29T20:59:14+01:00
add function to detect nontrivial strides

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3af86fca by Martin Uecker at 2018-01-29T21:03:30+01:00
CAST_MAYBE

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b0eff029 by Martin Uecker at 2018-01-29T21:03:30+01:00
fix run-time type check (zero-sized variables may have same address on gcc)

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a2c7270a by Jon Tamir at 2018-02-08T16:22:14+01:00
admm: add parameter selection by residual balancing (#114)


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3b52fa1d by Martin Uecker at 2018-02-08T22:20:36+01:00
implement md_(z)smul using direct calls to vecops

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8467cc38 by Jon Tamir at 2018-02-08T15:31:47-08:00
linops/fmac.c: add gpu tensor

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19948d8f by Martin Uecker at 2018-02-10T22:09:36+01:00
remove some use_gpu flags

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81549d38 by Martin Uecker at 2018-02-10T22:09:36+01:00
remove some more use_gpu flags

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7b8fea4d by Martin Uecker at 2018-02-10T22:09:36+01:00
remove unused undersampled fft operator

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0651f594 by Martin Uecker at 2018-02-10T22:09:36+01:00
remove more use_gpu flags

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90339c8b by Martin Uecker at 2018-02-10T22:09:36+01:00
remove more use_gpu flags

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82f18f35 by Martin Uecker at 2018-02-10T22:13:57+01:00
minor gpu gix

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66294ca1 by Martin Uecker at 2018-02-10T23:28:29+01:00
add benchmark and test for md_fft

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f013618b by Martin Uecker at 2018-02-11T12:02:20+01:00
add benchmarks for fft and fftmod

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cd26f403 by Martin Uecker at 2018-02-11T16:00:32+01:00
error messages for impossible configurations

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c3164588 by Martin Uecker at 2018-02-11T17:41:37+01:00
missing identity operator

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c3889691 by Martin Uecker at 2018-02-20T22:23:31+01:00
add nufft according to conventional definition

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50a4e7af by Christian Holme at 2018-03-16T17:22:31+01:00
nlinv: option for different pattern for each coil

this is needed when usinc virtual-conjugate coils, for example

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e0a3a237 by Christian Holme at 2018-03-16T17:22:31+01:00
nlinv: add ENLIVE support

This commit adds ENLIVE to the exisiting nlinv code.

ENLIVE is a method for allowing multiple sets of images and coil
sensitivity maps in the reconstruction, similar to multiple ESPIRiT
maps.

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b1f62b4a by Christian Holme at 2018-03-16T17:22:31+01:00
nlinv: remove more unused water/fat code

Commit 2d31b70bfbb9d4226950e1a3b34610eaa9f9146e removed most water/fat
code from nlinv. Relics were the sign_dims in model.c and the
CSHIFT_FLAG. This commit removes those, too.

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f967e85f by Christian Holme at 2018-03-16T17:22:31+01:00
nlinv: add (hidden) option to specify coil weighting parameters

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f4d3f32c by Martin Uecker at 2018-03-21T21:02:35+01:00
style changes

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5dc01c5c by Martin Uecker at 2018-03-21T21:24:10+01:00
style

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9d44eecb by Martin Uecker at 2018-04-08T17:28:40+02:00
update references

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0c2a6503 by Martin Uecker at 2018-04-09T11:15:47+02:00
bump version

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458dee0b by Martin Uecker at 2018-04-28T20:46:56+02:00
Merge tag 'v0.4.03'

version 0.4.03

Changes:
	- nlinv: add ENLIVE support (Christian Holme)
	- nlinv: add (hidden) option to specify coil weighting parameters (Christian Holme)
	- nlinv: option for different pattern for each coil (Christian Holme)
	- nlinv: sensitivity output also when using GPU (Christian Holme)
	- nlinv: add timing output (Christian Holme)
	- nlinv: add option for debug level (Christian Holme)
	- nlinv: add option to provide initialization (Christian Holme)
	- nlinv: make IRGNM reduction factor configurable (Christian Holme)
	- nufft: add nufft according to conventional definition
	- ecalib: add option to turn off phase rotation (Jonathan Tamir)
	- homodyne: add option for uncentered ffts (Jonathan Tamir)
	- bench: add benchmarks for fft, fftmod, md_fft
	- library: admm: add parameter selection by residual balancing (Jonathan Tamir)
	- library: add function to detect nontrivial strides
	- library: fix bug for gpu-mode of cdiag operator
	- library: irgnm: add callback (Christian Holme)
	- general: add script for memory-economic use of espirit
	- build: updates and fixes for CMake
	- build: build fixes on Mac OS X
	- many other bug fixes and improvements

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44d46514 by Martin Uecker at 2018-04-28T20:48:04+02:00
remove version patch

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1f025ffe by Martin Uecker at 2018-04-28T20:48:04+02:00
update copyright file

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15786d36 by Martin Uecker at 2018-04-28T20:48:04+02:00
fix install target

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7c583061 by Martin Uecker at 2018-04-28T20:48:04+02:00
update standards version

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36d855dd by Martin Uecker at 2018-04-28T20:48:10+02:00
secure url for copyright format

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24215223 by Martin Uecker at 2018-04-28T20:48:27+02:00
changelog

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30 changed files:

- .travis.yml
- CMakeLists.txt
- LICENSE
- Makefile
- README
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/0001-remove-empty-directory.patch
- − debian/patches/0002-bump-version.patch
- debian/patches/series
- debian/rules
- doc/references.txt
- rules/misc.mk
- rules/num.mk
- + scripts/espirit_econ.sh
- src/bart.c
- src/bench.c
- src/cabs.c
- src/calib/calib.c
- src/calib/estvar.c
- src/dfwavelet/prox_dfwavelet.c
- src/ecalib.c
- src/ecaltwo.c
- src/grecon/optreg.c
- src/homodyne.c
- src/iter/admm.c
- src/iter/admm.h
- src/iter/italgos.c
- src/iter/italgos.h


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View it on GitLab: https://salsa.debian.org/med-team/bart/compare/1e5b75016580fe7fe1544d23ad10f16fda34b2df...24215223daa103a2dbff11a4b9697185f370ceb2

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View it on GitLab: https://salsa.debian.org/med-team/bart/compare/1e5b75016580fe7fe1544d23ad10f16fda34b2df...24215223daa103a2dbff11a4b9697185f370ceb2
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