[med-svn] [bart] branch upstream updated (29d1bfb -> 3a4fc5a)
Martin Uecker
uecker-guest at moszumanska.debian.org
Sun Nov 26 12:07:55 UTC 2017
This is an automated email from the git hooks/post-receive script.
uecker-guest pushed a change to branch upstream
in repository bart.
from 29d1bfb optimize redundant clear
new c785c7f fft: uncentered option (#86)
new e4df99a png: add more png_write functions (#85)
new e99689a Parallel batch svd (#89)
new 33bec26 Hamming and Hann windows (#90)
new dcb087a Flatten md_parallel_nary (#91)
new 3655dd8 Makefile: set ARFLAGS if unassigned
new 6cf0995 window: return 1 for trivial dimensions
new 0a51c60 deterministic archives
new 75a4014 mark function as unused
new ac94575 simplify implementation of window function
new 89cec08 coding style
new 3df124e headers and copyright
new d8faae5 add cs with l1 wavelet test
new 14b5e06 fix warning
new df31a67 swapped arguments
new 3bc6855 wavelet command: allow other dimensions
new e9b6650 wavelets: preserve untransformed output dims
new 1dbfe6e wavelet tests
new b550402 rename wavelet3 to wavelet
new b8d7edd move src/wavelet3 to src/wavelet
new 22400a6 check arguments
new d5ed2b5 fix segfault in threshold
new aee8546 joint l1-wavelet regularization
new 083d6f3 additional tests for (joint) l1-wavelet
new 9e2f2e1 fix output of complex numbers
new 547e749 noir/model.c use config struct
new b843e99 noir/model: noncartesian
new 02f9552 remove unused variable
new 5125164 minor
new 944414d noir/recon: defaults + option for non-Cartesian
new da4fe52 nlinv: change defaults
new 432c92b nlinv: re-scale option, fix normalize for sensitivities, minor changes
new 51d746f gpu fix
new 99c8a33 joint wavelet - relax system test
new e5ab96c noncart/nufft.c: fix memory leaks (#92)
new d62b4cc add openmp test for gcc and turn off failing unit tests for clang
new c4c4025 complete turn off openmp with clang tests due to compiler bugs
new 03f1a83 NIHT with iter2 interface, first stage (#93)
new a233394 style
new 8caa9f6 unit test for hard thresholding, fix off-by-one
new aa4d53c improve robustness of coo parser
new 83278f4 mmio: error out if dimensions overflow
new d15e07f io: reading ra, transform some assertions into errors
new 70d37ce mmio: convert some aborts to io_errors, and some io_errors to errors to improve error msgs
new ffae9b7 make error use exit instead of abort
new 022838f read_cfl: don't hang on broken files
new 7a62e90 iter/thresh.h: change bool to _Bool
new 424cc3b add md_zss for sum-of-squares
new 7e8275d add variance and standard deviation tools
new 02d85c7 Niht stage2 (#95)
new d243d94 gpu fix for nonlinear inversion (#96)
new 980e095 fix wavelet transform for the case where different levels are used for different dimensions (#97)
new 5a27394 add missing static/extern to DEF_TYPEID
new 1900873 fix two warnings
new 9f5abb4 fix out-of-bounds access
new 499553d raise debug level for wavelet and matmul
new b837438 lapack: add inverse of triangular, cholesky lower
new 6c2456e noise whitening
new 6b70f69 do not use bart command in test
new a303c62 document WSL for using BART on Windows
new ea51cca expand and update file structure
new 6ecda9e move some op data to gpu on first call
new 95c2baf admm: pass true rho to conjgrad update
new 2665738 pics: free regularization ops at end of recon
new f1ca093 lsqr, itop: allow op to be NULL
new 7bb2bba add basis pursuit formulation to pics
new fe409d8 pics: add dynamic rho option and adjust ADMM dynamic rho default
new 4ccc39c sms trajectories (based on work by Sebastian Rosenzweig)
new b023738 sms for pics (based on work by Sebastian Rosenzweig)
new be8f35d noir/model.c: make fft flags configurable (based on work by Sebastian Rosenzweig)
new 001bd6a noir/recon.c: multi-slice recon (based on work by Sebastian Rosenzweig)
new 9b52158 Adapt scaling for SMS data
new 50aa965 Add subset of lapacke
new 21712a4 makefile changes for NOLAPACKE
new 2fdea31 don't use execinfo/backtrace on cygwin
new 0b9b6d7 update README
new 51f9640 detect cygwin on Windows 10
new 78c24f3 Tiny typo for Cygwin detection on Windows 10 (#103)
new 9bcf0f9 add two missing LAPACKE files
new a2d7cb6 add two missing LAPACKE files
new 4247e3b add test case for compilation with internal lapacke
new 2876471 pics: option to specify GPU
new 3379379 prox: change some variable names
new 57c96c4 vecops: add axpbz (y = ax + bz)
new a0d4731 italgos: add chambolle_pock primal dual algorithm for solving F(Ax) + G(x)
new 5879489 pics: add chambolle_pock primal dual algorithm option for basis pursuit case
new 9c14317 don't pass NULL
new 49f0364 license update
new 18768b4 change API of mini_cmdline (fixes the use of -- in some commands)
new b3505e3 fix memory leak
new c82491d add missing const
new f9dd7a5 add vec tool to create vectors from the command line
new 1e57cef don't include pcaa for newer compilers
new c17705d Chunk size from environment variable
new ec64362 improve handling of chunk_size
new cdd6713 lapacke: header path
new 1b6d353 change definition of range on extract tool
new c71f522 add nonlinear operator interface
new 7f913f4 add iter4 using nonlinear operator interface
new 67cfffd use nonlinear operator interace in noir
new 3ce86bb missing copyright notice
new d4a0fea missing copyright notice
new 090fc3a add lib to cmake
new 34571a0 Added NIHT stage 3
new bb679b7 make option hiding a bit smarter
new cafb7e4 iter.h: fix bool warning
new e78d7ae Added python3 bartview and PYTHONPATH instructions to the README
new 8ed98f0 Updated copyright notice
new bbb1d2b optimized_nop: make clang happy with D=0 case
new f4117fe nrmse: error if ref. is zero
new e520d87 Added wavepsf
new 8455dca updated copyright notice
new 562bd54 add troubleshooting section to README
new 5eb5943 version
new 3a4fc5a fix typo
The 115 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 +-
build_targets.mk | 8 +-
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 | 7 +-
src/iter/italgos.c | 131 +-
src/iter/italgos.h | 11 +-
src/iter/iter.c | 33 +-
src/iter/iter.h | 29 +-
src/iter/iter2.c | 103 +-
src/iter/iter2.h | 8 +-
src/iter/iter4.c | 80 +
src/iter/iter4.h | 23 +
src/iter/itop.c | 27 +-
src/iter/lsqr.c | 43 +-
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 | 16 +-
src/normalize.c | 2 +-
src/nrmse.c | 5 +-
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 | 57 +-
src/num/ops.c | 16 +-
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 | 13 +-
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/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 +
version.txt | 2 +-
196 files changed, 23640 insertions(+), 1075 deletions(-)
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
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bart.git
More information about the debian-med-commit
mailing list