[med-svn] [bart] 03/08: Merge tag 'v0.4.00'
Martin Uecker
uecker-guest at moszumanska.debian.org
Sat Jan 14 16:42:20 UTC 2017
This is an automated email from the git hooks/post-receive script.
uecker-guest pushed a commit to branch master
in repository bart.
commit 0fb42555f6e08957a8b3fa87c61cda95ee88a73c
Merge: 1c5c77d f236631
Author: Martin Uecker <martin.uecker at med.uni-goettingen.de>
Date: Sat Jan 14 14:29:54 2017 +0100
Merge tag 'v0.4.00'
version 0.4.00
Changes:
- new tools: copy, squeeze, flatten, delta, zexpj, invert
- show tool: option to use custom number formatting
- poisson: option to specify random seed in poisson (David Smith)
- threshold: hard threshold option
- join: append mode
- nufft: nudft option
- nufft: randshift for nufft
- pics: batch mode
- pics: FT as sparsity transform
- nrmse: auto_scale option
- fmac tool: if only two args are specified then squash-and-sum <input1>
- remove rsense tool
- support for cmake (Hans Johnson)
- rename vars.(sh|m) to startup.(sh|m)
- more efficient Matlab interface (Tim Loderhose)
- write BART version and command line into created files
- change fftw to use 64-bit interface
- phase out old wavelet2 code
- library: phase cycling for nufft
- library: support weights in toeplitz mode
- library: fmac operator
- library: cabs: complex magnitude
- library: md_compare
- library: thomas algorithm
- library: inital spline code
- many other bug fixes and enhancements
.travis.yml | 51 +++-
CMakeLists.txt | 360 ++++++++++++++++++++++++
Makefile | 148 ++++++----
Makefiles/README.md | 52 ++++
README | 58 +++-
README.md | 24 +-
build_targets.mk | 10 +
cmake/FindATLAS.cmake | 175 ++++++++++++
cmake/FindFFTW.cmake | 65 +++++
cmake/FindLAPACKE.cmake | 190 +++++++++++++
cmake/FindMatlab.cmake | 250 +++++++++++++++++
cmake/FindOpenBLAS.cmake | 170 +++++++++++
doc/building.txt | 207 ++++++++++++++
doc/cmake_building.txt | 53 ++++
doc/debugging.txt | 32 +++
doc/style.txt | 210 ++++++++++++++
matlab/readcfl.m | 16 +-
matlab/writecfl.m | 16 +-
python/bart.py | 6 +-
bartview.py => python/bartview.py | 0
rules/lowrank.mk | 2 +
rules/make_symbol_table.sh | 6 +
rules/misc.mk | 1 +
rules/num.mk | 2 +-
rules/update_commands.sh | 17 ++
octview.m => scripts/octview.m | 0
scripts/profile.sh | 70 +++++
src/{wavg.c => avg.c} | 18 +-
src/bench.c | 9 +-
src/bitmask.c | 6 +-
src/bpsense.c | 18 +-
src/{creal.c => cabs.c} | 28 +-
src/calib/calib.c | 224 +++++++++++++--
src/calib/calib.h | 2 +
src/calib/calmat.c | 6 +-
src/calib/cc.c | 2 +-
src/calib/direct.c | 2 +-
src/calib/estvar.c | 50 ++--
src/calib/softweight.c | 22 +-
src/calib/softweight.h | 10 +-
src/calib/walsh.c | 3 +-
src/calmat.c | 14 +-
src/carg.c | 3 +
src/cc.c | 9 +-
src/cdf97.c | 9 +-
src/circshift.c | 3 +
src/conj.c | 3 +
src/conv.c | 2 +
src/{resize.c => copy.c} | 46 +--
src/cpyphs.c | 4 +-
src/creal.c | 3 +
src/crop.c | 3 +
src/delta.c | 55 ++++
src/dfwavelet/dfwavelet.c | 2 -
src/dfwavelet/prox_dfwavelet.c | 29 +-
src/ecalib.c | 67 +++--
src/ecaltwo.c | 14 +-
src/estdims.c | 3 +
src/estvar.c | 15 +-
src/extract.c | 3 +
src/fakeksp.c | 6 +-
src/fft.c | 11 +-
src/fftmod.c | 3 +
src/fftshift.c | 3 +
src/filter.c | 3 +
src/flatten.c | 53 ++++
src/flip.c | 3 +
src/fmac.c | 43 ++-
src/grecon/grecon.c | 273 ------------------
src/grecon/grecon.h | 58 ----
src/grecon/optreg.c | 364 ++++++++++++++++++++++++
src/grecon/optreg.h | 49 ++++
src/grecon/parslices.c | 188 -------------
src/grecon/parslices.h | 38 ---
src/homodyne.c | 12 +-
src/invert.c | 49 ++++
src/ismrm/read.c | 4 +-
src/iter/admm.c | 464 ++++++++++++++++--------------
src/iter/admm.h | 65 ++---
src/iter/italgos.c | 353 +++--------------------
src/iter/italgos.h | 106 ++-----
src/iter/iter.c | 75 +++--
src/iter/iter.h | 42 ++-
src/iter/iter2.c | 108 ++++---
src/iter/iter2.h | 30 +-
src/iter/iter2_affine.c | 317 ---------------------
src/iter/iter2_affine.h | 45 ---
src/iter/iter3.c | 27 +-
src/iter/iter3.h | 20 +-
src/iter/itop.c | 139 +++++++++
src/iter/itop.h | 13 +
src/iter/lad.c | 131 ++++++---
src/iter/lad.h | 19 +-
src/iter/lsqr.c | 287 +++++++++----------
src/iter/lsqr.h | 68 ++---
src/iter/monitor.c | 100 +++++++
src/iter/monitor.h | 37 +++
src/iter/prox.c | 103 ++++---
src/iter/prox.h | 2 +-
src/iter/thresh.c | 37 ++-
src/iter/thresh.h | 20 +-
src/itsense.c | 2 +-
src/join.c | 53 +++-
src/linops/finite_diff.c | 62 ++--
src/linops/finite_diff.h | 53 ++--
src/linops/fmac.c | 133 +++++++++
src/linops/fmac.h | 7 +
src/linops/grad.c | 41 +--
src/linops/grad.h | 2 +-
src/linops/linop.c | 88 +++---
src/linops/linop.h | 4 +-
src/linops/{rvc.c => realval.c} | 18 +-
src/linops/realval.h | 7 +
src/linops/rvc.h | 7 -
src/linops/sampling.c | 16 +-
src/linops/sampling.h | 2 +-
src/linops/someops.c | 289 +++++++++----------
src/linops/someops.h | 8 +-
src/linops/sum.c | 27 +-
src/linops/sum.h | 2 +-
src/linops/ufft.c | 27 +-
src/linops/ufft.h | 2 +-
src/linops/waveop.c | 19 +-
src/linops/waveop.h | 2 +-
src/lowrank/batchsvd.c | 81 ++++++
src/lowrank/batchsvd.h | 6 +
src/lowrank/lrthresh.c | 21 +-
src/lowrank/svthresh.c | 5 +-
src/lrmatrix.c | 33 ++-
src/mip.c | 11 +-
src/misc/cppmap.h | 8 +
src/misc/debug.c | 73 ++++-
src/misc/debug.h | 31 +-
src/misc/io.c | 117 +++++++-
src/misc/io.h | 14 +-
src/misc/misc.c | 22 +-
src/misc/misc.h | 40 ++-
src/misc/mmio.c | 6 +-
src/misc/mmio.h | 16 +-
src/misc/mri.c | 12 +-
src/misc/mri.h | 21 +-
src/misc/opts.c | 12 +
src/misc/opts.h | 10 +-
src/misc/resize.c | 1 -
src/misc/shrdptr.c | 70 +++++
src/misc/shrdptr.h | 39 +++
src/misc/types.h | 40 +++
src/nlinv.c | 23 +-
src/noir/model.c | 2 +-
src/noir/recon.c | 88 ++----
src/noir/recon.h | 24 +-
src/noise.c | 15 +-
src/noncart/grid.c | 2 +-
src/noncart/nudft.c | 239 ++++++++++++++++
src/noncart/nudft.h | 33 +++
src/noncart/nufft.c | 198 ++++++++++---
src/noncart/nufft.h | 4 +-
src/normalize.c | 3 +
src/nrmse.c | 31 +-
src/nufft.c | 56 ++--
src/num/blas.c | 64 +++++
src/num/blas.h | 18 ++
src/num/blockproc.h | 19 +-
src/num/convoaa.c | 27 +-
src/num/convoaa.h | 4 +-
src/num/fft-cuda.c | 5 +-
src/num/fft.c | 129 +++++++--
src/num/fft.h | 25 +-
src/num/filter.h | 19 +-
src/num/flpmath.c | 235 ++++++----------
src/num/flpmath.h | 18 +-
src/num/gpuops.c | 206 ++------------
src/num/init.c | 11 +-
src/num/iovec.c | 6 +-
src/num/lapack.c | 438 ++---------------------------
src/num/lapack.h | 7 +-
src/num/{la.c => linalg.c} | 32 ++-
src/num/{la.h => linalg.h} | 5 +-
src/num/mem.c | 255 +++++++++++++++++
src/num/mem.h | 12 +
src/num/multind.c | 148 ++++++----
src/num/multind.h | 28 +-
src/num/ops.c | 296 ++++++++++++++-----
src/num/ops.h | 28 +-
src/num/optimize.c | 168 +++++++++--
src/num/optimize.h | 20 +-
src/num/simplex.c | 1 -
src/num/{sf.c => specfun.c} | 2 +-
src/num/{sf.h => specfun.h} | 0
src/num/splines.c | 249 ++++++++++++++++
src/num/splines.h | 17 ++
src/num/vecops.c | 23 +-
src/num/vecops.h | 16 +-
src/ones.c | 3 +
src/pattern.c | 24 +-
src/phantom.c | 3 +
src/pics.c | 577 +++++++++++---------------------------
src/pocsense.c | 32 ++-
src/poisson.c | 10 +-
src/repmat.c | 3 +
src/reshape.c | 5 +-
src/resize.c | 9 +-
src/rof.c | 12 +-
src/rsense.c | 169 -----------
src/rss.c | 3 +
src/sake/sake.c | 5 +-
src/saxpy.c | 3 +
src/scale.c | 3 +
src/sdot.c | 3 +
src/sense/bprecon.c | 20 +-
src/sense/model.c | 87 ++++--
src/sense/model.h | 7 +-
src/sense/optcom.c | 6 +-
src/sense/pocs.c | 25 +-
src/sense/recon.c | 182 +++---------
src/sense/recon.h | 43 +--
src/show.c | 39 ++-
src/slice.c | 3 +
src/spow.c | 3 +
src/sqpics.c | 46 ++-
src/squeeze.c | 60 ++++
src/threshold.c | 45 ++-
src/toimg.c | 3 +
src/traj.c | 3 +
src/transpose.c | 4 +-
src/twixread.c | 34 +--
src/version.c | 6 +-
src/walsh.c | 12 +-
src/wave.c | 24 +-
src/wavelet2/wavelet.c | 32 ++-
src/wavelet2/wavelet_kernels.h | 14 +-
src/wavelet3/wavthresh.c | 12 +-
src/wavelet3/wl3-cuda.h | 16 +-
src/zeros.c | 3 +
src/{creal.c => zexpj.c} | 18 +-
vars.m => startup.m | 0
startup.py | 8 +
vars.sh => startup.sh | 0
tests/copy.mk | 26 ++
tests/ecalib.mk | 20 +-
tests/fft.mk | 17 +-
tests/flatten.mk | 15 +
tests/fmac.mk | 16 ++
tests/gpu.mk | 61 ++++
tests/join.mk | 24 ++
tests/nrmse.mk | 11 +
tests/nufft.mk | 111 ++++++--
tests/phantom.mk | 40 +--
tests/pics.mk | 119 ++++++--
tests/pythoncfl.mk | 16 ++
tests/pythoncfl.py | 22 ++
tests/slice.mk | 15 +
tests/squeeze.mk | 16 ++
utests/.gitignore.main | 1 -
utests/Makefile | 71 -----
utests/README.md | 4 -
utests/build_run_utests.sh | 11 -
utests/minunit.h | 21 --
utests/test_batchsvd.c | 77 +++++
utests/test_flpmath.c | 192 ++++++++-----
utests/test_flpmath.h | 353 -----------------------
utests/test_flpmath_data.h | 479 +++++++++++++++++++++++++++++++
utests/test_linalg.c | 44 +++
utests/test_multind.c | 131 +++++++++
utests/test_pattern.c | 80 ++++++
utests/test_splines.c | 99 +++++++
utests/utest.c | 60 ++++
utests/utest.h | 38 +++
utests/utests-collect.sh | 7 +
utests/utests.ld | 13 +
version.txt | 2 +-
271 files changed, 9589 insertions(+), 5697 deletions(-)
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