[med-svn] [bart] 01/08: Merge tag 'v0.4.02'
Martin Uecker
uecker-guest at moszumanska.debian.org
Sun Nov 26 12:08:57 UTC 2017
This is an automated email from the git hooks/post-receive script.
uecker-guest pushed a commit to branch patch-queue/master
in repository bart.
commit df13151a2195c33a9fcf227467876d28d4e1ff73
Merge: 8f3b80b 562bd54
Author: Martin Uecker <martin.uecker at med.uni-goettingen.de>
Date: Sun Nov 26 11:46:35 2017 +0100
Merge tag 'v0.4.02'
version 0.4.02
Changes:
- new tools: std var vec wavepsf whiten
- std: compute standard deviation (Jonathan Tamir)
- var: compute variance (Jonathan Tamir)
- vec: create vectors from the command line
- wavepsf: create PSF for wave acquisition (Siddharth Iyer)
- whiten: compute/apply whitening matrix (Jonathan Tamir)
- pics: basis pursuit formulation (Jonathan Tamir)
- nlinv: support for simultaneous multi-slice (Sebastian Rosenzweig)
- nlinv: various enhancements and fixes (Christian Holme)
- pics: support for simultaneous multi-slice (Sebastian Rosenzweig)
- traj: radial simultaneous multi-slice trajectories (Sebastian Rosenzweig)
- fft: uncentered option (Jonathan Tamir)
- nufft: use Toepliz-mode by default
- nufft: add GPU option
- python 3 version for bartview (Siddharth Iyer)
- fix compilation for Cygwin on Windows (Johannes Töger)
- include relevant parts of LAPACKE in BART
- library: add NIHT algorithm (Sofia Dimoudi)
- library: add Chambolle-Pock primal dual algorithm for F(Ax) + G(x) (Jonathan Tamir)
- library: add md_zss function for sum-of-squares (Jonathan Tamir)
- library: improved parallelization (Michael Anderson)
- library: joint l1-wavelet regularization
- library: rename wavelet3 to wavelet
- library: Hamming and Hann windows (Jonathan Tamir)
- library: png write functions (Christian Holme)
- library: initial interface for nonlinear operators
- many other bug fixes and improvements
.travis.yml | 16 +-
CMakeLists.txt | 2 +-
LICENSE | 5 +-
Makefile | 59 +-
README | 88 +-
README.md | 2 +
build_targets.mk | 8 +-
python/bartview3.py | 362 +
rules/lapacke.mk | 9 +
rules/nlops.mk | 12 +
rules/num.mk | 2 +-
rules/wavelet.mk | 14 +
rules/wavelet3.mk | 21 -
src/bart.c | 2 +-
src/bench.c | 4 +-
src/bpsense.c | 255 -
src/cabs.c | 2 +-
src/caldir.c | 2 +-
src/carg.c | 2 +-
src/circshift.c | 2 +-
src/conj.c | 2 +-
src/cpyphs.c | 2 +-
src/creal.c | 2 +-
src/crop.c | 2 +-
src/delta.c | 2 +-
src/dfwavelet/prox_dfwavelet.c | 6 +-
src/estdelay.c | 8 +-
src/estdims.c | 2 +-
src/estshift.c | 9 +-
src/extract.c | 10 +-
src/fft.c | 4 +-
src/fftshift.c | 2 +-
src/flatten.c | 2 +-
src/flip.c | 2 +-
src/grecon/optreg.c | 122 +-
src/grecon/optreg.h | 14 +-
src/invert.c | 2 +-
src/iter/admm.c | 15 +-
src/iter/italgos.c | 131 +-
src/iter/italgos.h | 11 +-
src/iter/iter.c | 33 +-
src/iter/iter.h | 29 +-
src/iter/iter2.c | 109 +-
src/iter/iter2.h | 8 +-
src/iter/iter4.c | 80 +
src/iter/iter4.h | 23 +
src/iter/itop.c | 35 +-
src/iter/itop.h | 4 +-
src/iter/lsqr.c | 111 +-
src/iter/lsqr.h | 8 +-
src/iter/monitor.c | 2 +-
src/iter/niht.c | 249 +
src/iter/niht.h | 50 +
src/iter/prox.c | 79 +-
src/iter/thresh.c | 57 +-
src/iter/thresh.h | 3 +
src/iter/vec.h | 2 +
src/itsense.c | 4 +-
src/lapacke/LICENSE | 26 +
src/lapacke/README | 7 +
src/lapacke/lapacke.h | 16445 ++++++++++++++++++++++++++++++++
src/lapacke/lapacke_cge_nancheck.c | 62 +
src/lapacke/lapacke_cge_trans.c | 65 +
src/lapacke/lapacke_cgesdd.c | 106 +
src/lapacke/lapacke_cgesdd_work.c | 158 +
src/lapacke/lapacke_cgesvd.c | 94 +
src/lapacke/lapacke_cgesvd_work.c | 149 +
src/lapacke/lapacke_che_nancheck.c | 43 +
src/lapacke/lapacke_cheev.c | 86 +
src/lapacke/lapacke_cheev_work.c | 93 +
src/lapacke/lapacke_cpo_nancheck.c | 43 +
src/lapacke/lapacke_cpo_trans.c | 45 +
src/lapacke/lapacke_cpotrf.c | 50 +
src/lapacke/lapacke_cpotrf_work.c | 82 +
src/lapacke/lapacke_ctr_nancheck.c | 85 +
src/lapacke/lapacke_ctr_trans.c | 85 +
src/lapacke/lapacke_ctrtri.c | 50 +
src/lapacke/lapacke_ctrtri_work.c | 84 +
src/lapacke/lapacke_lsame.c | 41 +
src/lapacke/lapacke_mangling.h | 17 +
src/lapacke/lapacke_utils.h | 579 ++
src/lapacke/lapacke_xerbla.c | 46 +
src/lapacke/lapacke_zge_nancheck.c | 62 +
src/lapacke/lapacke_zge_trans.c | 65 +
src/lapacke/lapacke_zgesdd.c | 106 +
src/lapacke/lapacke_zgesdd_work.c | 158 +
src/lapacke/lapacke_zhe_nancheck.c | 43 +
src/lapacke/lapacke_zhe_trans.c | 45 +
src/lapacke/lapacke_zheev.c | 86 +
src/lapacke/lapacke_zheev_work.c | 93 +
src/lapacke/lapacke_ztr_nancheck.c | 85 +
src/lapacke/lapacke_ztr_trans.c | 85 +
src/linops/finite_diff.c | 4 +-
src/linops/fmac.c | 2 +-
src/linops/grad.c | 2 +-
src/linops/linop.c | 2 +-
src/linops/linop.h | 2 +-
src/linops/lintest.c | 2 +-
src/linops/realval.c | 2 +-
src/linops/sampling.c | 56 +-
src/linops/someops.c | 14 +-
src/linops/sum.c | 2 +-
src/linops/ufft.c | 2 +-
src/linops/waveop.c | 84 +-
src/linops/waveop.h | 2 +-
src/lowrank/batchsvd.c | 4 +
src/lowrank/lrthresh.c | 2 +-
src/lrmatrix.c | 2 +-
src/misc/debug.c | 7 +
src/misc/io.c | 41 +-
src/misc/misc.c | 121 +-
src/misc/misc.h | 10 +-
src/misc/mmio.c | 138 +-
src/misc/opts.c | 4 +-
src/misc/pcaa.h | 5 +
src/misc/pd.c | 6 +-
src/misc/png.c | 46 +-
src/misc/png.h | 3 +
src/nlinv.c | 49 +-
src/nlops/nlop.c | 168 +
src/nlops/nlop.h | 44 +
src/noir/model.c | 79 +-
src/noir/model.h | 12 +-
src/noir/nl.c | 74 +
src/noir/nl.h | 22 +
src/noir/recon.c | 70 +-
src/noir/recon.h | 1 +
src/noncart/nufft.c | 31 +-
src/normalize.c | 2 +-
src/nrmse.c | 5 +-
src/nufft.c | 16 +-
src/num/blas.h | 11 +-
src/num/fft.c | 2 +-
src/num/filter.c | 148 +-
src/num/filter.h | 14 +-
src/num/flpmath.c | 285 +-
src/num/flpmath.h | 14 +
src/num/gpukrnls.cu | 20 +-
src/num/gpukrnls.h | 3 +-
src/num/gpuops.c | 7 +-
src/num/init.c | 18 +
src/num/lapack.c | 38 +-
src/num/lapack.h | 7 +-
src/num/multind.c | 68 +-
src/num/ops.c | 23 +-
src/num/optimize.c | 27 +-
src/num/specfun.c | 4 +-
src/num/vecops.c | 109 +-
src/num/vecops.h | 6 +-
src/ones.c | 2 +-
src/pics.c | 145 +-
src/pocsense.c | 2 +-
src/repmat.c | 2 +-
src/rof.c | 2 +-
src/rss.c | 2 +-
src/saxpy.c | 2 +-
src/scale.c | 2 +-
src/sense/bprecon.c | 247 -
src/sense/model.c | 2 +-
src/sense/pocs.c | 2 +-
src/sense/recon.c | 18 +-
src/sense/recon.h | 1 +
src/show.c | 2 +-
src/slice.c | 2 +-
src/spow.c | 2 +-
src/sqpics.c | 7 +-
src/squeeze.c | 2 +-
src/std.c | 59 +
src/threshold.c | 14 +-
src/toimg.c | 2 +-
src/traj.c | 95 +-
src/transpose.c | 2 +-
src/var.c | 59 +
src/vec.c | 46 +
src/wave.c | 4 +-
src/wavelet.c | 9 +-
src/{wavelet3 => wavelet}/wavelet.c | 268 +-
src/{wavelet3 => wavelet}/wavelet.h | 17 +-
src/{wavelet3 => wavelet}/wavthresh.c | 29 +-
src/wavelet/wavthresh.h | 7 +
src/{wavelet3 => wavelet}/wl3-cuda.cu | 0
src/{wavelet3 => wavelet}/wl3-cuda.h | 0
src/wavelet3/wavthresh.h | 7 -
src/wavepsf.c | 146 +
src/whiten.c | 179 +
src/window.c | 55 +
src/zeros.c | 2 +-
src/zexpj.c | 2 +-
tests/casorati.mk | 2 +-
tests/ccapply.mk | 6 +-
tests/fft.mk | 12 +-
tests/nlinv.mk | 4 +-
tests/nufft.mk | 18 +-
tests/pics.mk | 56 +
tests/wave.mk | 14 +
tests/wavelet.mk | 78 +-
tests/whiten.mk | 24 +
utests/test_biot_savart.c | 2 +-
utests/test_flpmath.c | 67 +
utests/test_window.c | 90 +
200 files changed, 24080 insertions(+), 1155 deletions(-)
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