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 <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bart.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
