[med-svn] [bart] branch master updated (8f3b80b -> 0398c92)
Martin Uecker
uecker-guest at moszumanska.debian.org
Sun Nov 26 12:09:13 UTC 2017
This is an automated email from the git hooks/post-receive script.
uecker-guest pushed a change to branch master
in repository bart.
from 8f3b80b update patches
adds edec34e add DOI to README.md
adds 7b064a1 fixes for undefined behaviour
adds 78bd2b3 lsqr: add monitor argument
adds 3a56acf add gpu option to nufft command
adds 646a48a use toeplitz mode by default
adds 29d1bfb optimize redundant clear
adds c785c7f fft: uncentered option (#86)
adds e4df99a png: add more png_write functions (#85)
adds e99689a Parallel batch svd (#89)
adds 33bec26 Hamming and Hann windows (#90)
adds dcb087a Flatten md_parallel_nary (#91)
adds 3655dd8 Makefile: set ARFLAGS if unassigned
adds 6cf0995 window: return 1 for trivial dimensions
adds 0a51c60 deterministic archives
adds 75a4014 mark function as unused
adds ac94575 simplify implementation of window function
adds 89cec08 coding style
adds 3df124e headers and copyright
adds d8faae5 add cs with l1 wavelet test
adds 14b5e06 fix warning
adds df31a67 swapped arguments
adds 3bc6855 wavelet command: allow other dimensions
adds e9b6650 wavelets: preserve untransformed output dims
adds 1dbfe6e wavelet tests
adds b550402 rename wavelet3 to wavelet
adds b8d7edd move src/wavelet3 to src/wavelet
adds 22400a6 check arguments
adds d5ed2b5 fix segfault in threshold
adds aee8546 joint l1-wavelet regularization
adds 083d6f3 additional tests for (joint) l1-wavelet
adds 9e2f2e1 fix output of complex numbers
adds 547e749 noir/model.c use config struct
adds b843e99 noir/model: noncartesian
adds 02f9552 remove unused variable
adds 5125164 minor
adds 944414d noir/recon: defaults + option for non-Cartesian
adds da4fe52 nlinv: change defaults
adds 432c92b nlinv: re-scale option, fix normalize for sensitivities, minor changes
adds 51d746f gpu fix
adds 99c8a33 joint wavelet - relax system test
adds e5ab96c noncart/nufft.c: fix memory leaks (#92)
adds d62b4cc add openmp test for gcc and turn off failing unit tests for clang
adds c4c4025 complete turn off openmp with clang tests due to compiler bugs
adds 03f1a83 NIHT with iter2 interface, first stage (#93)
adds a233394 style
adds 8caa9f6 unit test for hard thresholding, fix off-by-one
adds aa4d53c improve robustness of coo parser
adds 83278f4 mmio: error out if dimensions overflow
adds d15e07f io: reading ra, transform some assertions into errors
adds 70d37ce mmio: convert some aborts to io_errors, and some io_errors to errors to improve error msgs
adds ffae9b7 make error use exit instead of abort
adds 022838f read_cfl: don't hang on broken files
adds 7a62e90 iter/thresh.h: change bool to _Bool
adds 424cc3b add md_zss for sum-of-squares
adds 7e8275d add variance and standard deviation tools
adds 02d85c7 Niht stage2 (#95)
adds d243d94 gpu fix for nonlinear inversion (#96)
adds 980e095 fix wavelet transform for the case where different levels are used for different dimensions (#97)
adds 5a27394 add missing static/extern to DEF_TYPEID
adds 1900873 fix two warnings
adds 9f5abb4 fix out-of-bounds access
adds 499553d raise debug level for wavelet and matmul
adds b837438 lapack: add inverse of triangular, cholesky lower
adds 6c2456e noise whitening
adds 6b70f69 do not use bart command in test
adds a303c62 document WSL for using BART on Windows
adds ea51cca expand and update file structure
adds 6ecda9e move some op data to gpu on first call
adds 95c2baf admm: pass true rho to conjgrad update
adds 2665738 pics: free regularization ops at end of recon
adds f1ca093 lsqr, itop: allow op to be NULL
adds 7bb2bba add basis pursuit formulation to pics
adds fe409d8 pics: add dynamic rho option and adjust ADMM dynamic rho default
adds 4ccc39c sms trajectories (based on work by Sebastian Rosenzweig)
adds b023738 sms for pics (based on work by Sebastian Rosenzweig)
adds be8f35d noir/model.c: make fft flags configurable (based on work by Sebastian Rosenzweig)
adds 001bd6a noir/recon.c: multi-slice recon (based on work by Sebastian Rosenzweig)
adds 9b52158 Adapt scaling for SMS data
adds 50aa965 Add subset of lapacke
adds 21712a4 makefile changes for NOLAPACKE
adds 2fdea31 don't use execinfo/backtrace on cygwin
adds 0b9b6d7 update README
adds 51f9640 detect cygwin on Windows 10
adds 78c24f3 Tiny typo for Cygwin detection on Windows 10 (#103)
adds 9bcf0f9 add two missing LAPACKE files
adds a2d7cb6 add two missing LAPACKE files
adds 4247e3b add test case for compilation with internal lapacke
adds 2876471 pics: option to specify GPU
adds 3379379 prox: change some variable names
adds 57c96c4 vecops: add axpbz (y = ax + bz)
adds a0d4731 italgos: add chambolle_pock primal dual algorithm for solving F(Ax) + G(x)
adds 5879489 pics: add chambolle_pock primal dual algorithm option for basis pursuit case
adds 9c14317 don't pass NULL
adds 49f0364 license update
adds 18768b4 change API of mini_cmdline (fixes the use of -- in some commands)
adds b3505e3 fix memory leak
adds c82491d add missing const
adds f9dd7a5 add vec tool to create vectors from the command line
adds 1e57cef don't include pcaa for newer compilers
adds c17705d Chunk size from environment variable
adds ec64362 improve handling of chunk_size
adds cdd6713 lapacke: header path
adds 1b6d353 change definition of range on extract tool
adds c71f522 add nonlinear operator interface
adds 7f913f4 add iter4 using nonlinear operator interface
adds 67cfffd use nonlinear operator interace in noir
adds 3ce86bb missing copyright notice
adds d4a0fea missing copyright notice
adds 090fc3a add lib to cmake
adds 34571a0 Added NIHT stage 3
adds bb679b7 make option hiding a bit smarter
adds cafb7e4 iter.h: fix bool warning
adds e78d7ae Added python3 bartview and PYTHONPATH instructions to the README
adds 8ed98f0 Updated copyright notice
adds bbb1d2b optimized_nop: make clang happy with D=0 case
adds f4117fe nrmse: error if ref. is zero
adds e520d87 Added wavepsf
adds 8455dca updated copyright notice
adds 562bd54 add troubleshooting section to README
adds df13151 Merge tag 'v0.4.02'
adds b0565ed update patches
adds 2f24c88 update copyright
adds ac36994 change debian standards version to 4.1.1
adds 98f384b change version in changelog
adds fd0eeff change installed files in development package
new 0398c92 add patch for version fix
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.travis.yml | 16 +-
CMakeLists.txt | 2 +-
LICENSE | 5 +-
Makefile | 59 +-
README | 88 +-
README.md | 2 +
build_targets.mk | 8 +-
debian/changelog | 2 +-
debian/control | 2 +-
debian/copyright | 5 +
debian/libbart-dev.install | 6 +-
debian/patches/0001-remove-empty-directory.patch | 4 +-
debian/patches/0002-bump-version.patch | 15 +
.../patches/0002-make-format-security-happy.patch | 21 -
...-remove-typo-in-symbol-and-make-it-static.patch | 21 -
debian/patches/series | 3 +-
python/{bartview.py => bartview3.py} | 16 +-
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 +
209 files changed, 23754 insertions(+), 1214 deletions(-)
create mode 100644 debian/patches/0002-bump-version.patch
delete mode 100644 debian/patches/0002-make-format-security-happy.patch
delete mode 100644 debian/patches/0003-remove-typo-in-symbol-and-make-it-static.patch
copy python/{bartview.py => bartview3.py} (97%)
create mode 100644 rules/lapacke.mk
create mode 100644 rules/nlops.mk
create mode 100644 rules/wavelet.mk
delete mode 100644 rules/wavelet3.mk
delete mode 100644 src/bpsense.c
create mode 100644 src/iter/iter4.c
create mode 100644 src/iter/iter4.h
create mode 100644 src/iter/niht.c
create mode 100644 src/iter/niht.h
create mode 100644 src/lapacke/LICENSE
create mode 100644 src/lapacke/README
create mode 100644 src/lapacke/lapacke.h
create mode 100644 src/lapacke/lapacke_cge_nancheck.c
create mode 100644 src/lapacke/lapacke_cge_trans.c
create mode 100644 src/lapacke/lapacke_cgesdd.c
create mode 100644 src/lapacke/lapacke_cgesdd_work.c
create mode 100644 src/lapacke/lapacke_cgesvd.c
create mode 100644 src/lapacke/lapacke_cgesvd_work.c
create mode 100644 src/lapacke/lapacke_che_nancheck.c
create mode 100644 src/lapacke/lapacke_cheev.c
create mode 100644 src/lapacke/lapacke_cheev_work.c
create mode 100644 src/lapacke/lapacke_cpo_nancheck.c
create mode 100644 src/lapacke/lapacke_cpo_trans.c
create mode 100644 src/lapacke/lapacke_cpotrf.c
create mode 100644 src/lapacke/lapacke_cpotrf_work.c
create mode 100644 src/lapacke/lapacke_ctr_nancheck.c
create mode 100644 src/lapacke/lapacke_ctr_trans.c
create mode 100644 src/lapacke/lapacke_ctrtri.c
create mode 100644 src/lapacke/lapacke_ctrtri_work.c
create mode 100644 src/lapacke/lapacke_lsame.c
create mode 100644 src/lapacke/lapacke_mangling.h
create mode 100644 src/lapacke/lapacke_utils.h
create mode 100644 src/lapacke/lapacke_xerbla.c
create mode 100644 src/lapacke/lapacke_zge_nancheck.c
create mode 100644 src/lapacke/lapacke_zge_trans.c
create mode 100644 src/lapacke/lapacke_zgesdd.c
create mode 100644 src/lapacke/lapacke_zgesdd_work.c
create mode 100644 src/lapacke/lapacke_zhe_nancheck.c
create mode 100644 src/lapacke/lapacke_zhe_trans.c
create mode 100644 src/lapacke/lapacke_zheev.c
create mode 100644 src/lapacke/lapacke_zheev_work.c
create mode 100644 src/lapacke/lapacke_ztr_nancheck.c
create mode 100644 src/lapacke/lapacke_ztr_trans.c
create mode 100644 src/nlops/nlop.c
create mode 100644 src/nlops/nlop.h
create mode 100644 src/noir/nl.c
create mode 100644 src/noir/nl.h
delete mode 100644 src/sense/bprecon.c
create mode 100644 src/std.c
create mode 100644 src/var.c
create mode 100644 src/vec.c
rename src/{wavelet3 => wavelet}/wavelet.c (65%)
rename src/{wavelet3 => wavelet}/wavelet.h (54%)
rename src/{wavelet3 => wavelet}/wavthresh.c (69%)
create mode 100644 src/wavelet/wavthresh.h
rename src/{wavelet3 => wavelet}/wl3-cuda.cu (100%)
rename src/{wavelet3 => wavelet}/wl3-cuda.h (100%)
delete mode 100644 src/wavelet3/wavthresh.h
create mode 100644 src/wavepsf.c
create mode 100644 src/whiten.c
create mode 100644 src/window.c
create mode 100644 tests/wave.mk
create mode 100644 tests/whiten.mk
create mode 100644 utests/test_window.c
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