[med-svn] [bart] branch master updated (df4e714 -> 17242c5)
Martin Uecker
uecker-guest at moszumanska.debian.org
Fri Jun 30 20:41:22 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 df4e714 hardening=+all
new fdc22db add patch: remove type in symbol
adds 9aee761 threshold: missing break for hard threshold
adds 745f517 wavelet3: change debug level
adds 093e7eb fix segfault in nufft_precond_create
adds b462936 cleanup nufft phase cycle
adds 9341542 add operator_bind2 function
adds bbe201b add operator_p_upcast function
adds d172ec2 add prox_nonneg_create function
adds a7fe4e9 add missing PTR_PASS
adds 1da445c L1 Laplace regularization
adds 0baff2c add MD_SINGLETON macros
adds 336a159 make convolutions more flexible
adds 8c27cb5 missing free
adds 204136b admm: split variables
adds ab1dbce mandelbrot tool
adds 387f5d8 adapt debug putput for CUDA
adds 82b7d7a improve scaling
adds f9e3b9d ecalib: replace assert by error
adds 96d86f2 type safety
adds 3fe3181 fix subopt (#77)
adds b3f8044 ccapply tool to apply coil compression matrix (#75)
adds 91ee4b9 remove wavelet2
adds 3152ce6 fix issue #79 pics over time with weights (#80)
adds 8d22bba completely turn of batch loop if not needed
adds dc4803c pics: support higher dimensions for maps (#81)
adds bcf0f11 document how to save using debugger
adds c694102 cc: explicit option to output compression matrix
adds a964848 more tests for cc/ccapply
adds b5f1c98 version: add compiler version
adds f2f05c4 simple vec3 function
adds 448f838 biot savart law
adds dc83e07 simple coil simulation
adds c378edf rename biots.[ch] -> biot_savart.[ch] and headers
adds 309afa0 update spline code
adds 14b09a9 polynoms
adds 099fa3b utest: nicer output
adds 39b6689 remove obsolete functions
adds 44079fc fix duplicated option
adds 07a7180 add set -e to script
adds dbc5f44 sanity check cli options
adds 8188813 fix duplicated option
adds 86b1d2b type safety
adds 39944c7 fix indentation
adds 9236460 add laplace filter in k-space with scaling parameter
adds a4e2df9 comments for fall through in switch statements
adds 2fc590a est delay command
adds b9796d4 simple quadratic forms
adds d580caa gradient delays
adds 7d0072b gradient delays
adds c115947 tool for estimation of gradient delays from radial data
adds b5992e7 shut up warning
adds 33cb54b correct transverse gradient errors
adds 19873ef remove old code
adds 3a56bba update itsense
adds 52980f1 fix nlinv bug
adds cbe329d add SLICE_FLAG
adds 9541722 add test for NLINV
adds 2d31b70 remove old water/fat code
adds 6e09ec9 minor
adds dc17cdf add assertion to md_circ_shift
adds 7213c9f fix potential memory leak in conjugate gradients (courtesy of Christian Holme)
adds 812e113 introduce defaults for irgnm
adds 876bcbf use defaults in nlinv
adds 5747bbc irgnm: config for cg
adds 819c05b irgnm: nlinv legacy mode (courtesy of Christian Holme)
adds a8cd041 per dimension rand shifts (fixes shifts exceeding size)
adds 8d0f711 logo
adds 2d75464 Computational MRI
adds babaa90 reseach use
adds afc083d casorati tool (#82)
adds 2227401 debug output for chain
adds 846eb24 sense_recon: use linop_(co)domain
adds 4af8a2b function to compute non-trival dims: md_nontriv_dims
adds 982329c use md_notriv_dims
adds a8c5e1a copy parameters in waveop
adds 0bc2efa wavelet tool
adds af0ef6f improve precision of wavelet filter
adds 7503ef0 improve test for pics with weights
adds 655f50f fix weights for non-Cartesian
adds b5d89b3 tests: rename intermediate file
adds 8f38ce8 tests: remove redundancy
adds b546202 tests: remove more redundancy
adds f98dfa2 set std=gnu11 (which we use anyway)
adds 5ac09ea fix warning
adds 42b61eb correct type for linop_get_data
adds d01f094 function md_max_dims
adds 0dfd3b7 function md_matmul_dims
adds 4e14046 add test for linop_matrix
adds b3ea22e fix md_gaussian_rand
adds 93215c6 tests for linear operators
adds 89d939c more unit tests for linop_matrix
adds 8d1c9dd test matrix chain
adds b324885 redesign linop_matrix
adds ad2451e smaller unit tests
adds ef5be99 export simplify_dims
adds 1ce5e25 test case for blas matrix multiply, fix prototype
adds 91ce10d optimize simple matrix multiplication with blas
adds 15d9e41 linop_matrix: refactoring part II
adds aaa0c54 linop_matrix: cuda support
adds f6462d5 optimize transpose case
adds 4c1a7be introduce tenmul as a replacement for matmul
adds 1231ed3 use tenmul
adds 1e256ef use tenmul in benchmark tool
adds 6575046 minor comment fix
adds 0d992a9 fix arguments swapped in blas matrix test
adds 7522622 Fix a few memory leaks, possible stack smashing and an initialization bug in release (#84)
adds bb5db33 refactor
adds 3a46a24 add cmake build to travis
adds 2a9dd2f Enable CUDA compilation when using cmake (#83)
adds c7c7999 turn off failing unit tests on Mac
adds 0574626 relax gpu test for non-Cartesian with weights a bit
adds 7e8a0b9 clean utest object files
adds 3259323 bump version
new cad833e Merge tag 'v0.4.01'
new 8fc3f58 update copyright
new 17242c5 update changelog
The 4 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 | 90 ++
ACKNOWLEDGEMENTS | 2 +
CMakeLists.txt | 48 +-
Makefile | 11 +-
README.md | 10 +-
build_targets.mk | 8 +-
cmake/FindLAPACKE.cmake | 2 +-
debian/changelog | 6 +
debian/copyright | 3 +-
...-remove-typo-in-symbol-and-make-it-static.patch | 21 +
debian/patches/series | 1 +
doc/debugging.txt | 16 +-
git-version.sh | 9 +-
rules/linops.mk | 3 +-
rules/num.mk | 3 +-
rules/simu.mk | 2 +
rules/update_commands.sh | 1 +
rules/wavelet2.mk | 21 -
src/bench.c | 54 +-
src/casorati.c | 77 ++
src/cc.c | 13 +-
src/ccapply.c | 141 +++
src/dfwavelet/prox_dfwavelet.c | 14 +-
src/ecalib.c | 8 +-
src/estdelay.c | 140 +++
src/estshift.c | 59 ++
src/grecon/optreg.c | 413 ++++----
src/grecon/optreg.h | 2 +-
src/iter/admm.c | 179 ++--
src/iter/admm.h | 39 +-
src/iter/italgos.c | 95 +-
src/iter/italgos.h | 98 +-
src/iter/iter.c | 3 +-
src/iter/iter2.c | 54 +-
src/iter/iter2.h | 32 +-
src/iter/iter3.c | 99 +-
src/iter/iter3.h | 17 +-
src/iter/lsqr.c | 8 +-
src/iter/lsqr.h | 4 +-
src/iter/misc.c | 3 +-
src/iter/prox.c | 14 +-
src/iter/prox.h | 1 +
src/itsense.c | 44 +-
src/linops/linop.c | 49 +-
src/linops/linop.h | 10 +-
src/linops/lintest.c | 119 +++
src/linops/lintest.h | 8 +
src/linops/someops.c | 568 ++++++-----
src/linops/someops.h | 3 -
src/linops/waveop.c | 26 +-
src/lrmatrix.c | 1 -
src/mandelbrot.c | 92 ++
src/misc/misc.c | 2 +
src/misc/mri.c | 16 -
src/misc/mri.h | 11 +-
src/misc/opts.c | 26 +-
src/misc/opts.h | 3 +-
src/misc/pd.c | 4 +-
src/misc/subpixel.c | 50 +
src/misc/subpixel.h | 3 +
src/nlinv.c | 31 -
src/noir/model.c | 1 +
src/noir/recon.c | 41 +-
src/noncart/nufft.c | 50 +-
src/num/blas.h | 2 +-
src/num/blockproc.c | 1 +
src/num/conv.c | 19 +-
src/num/filter.c | 12 +-
src/num/filter.h | 1 +
src/num/flpmath.c | 175 +++-
src/num/flpmath.h | 12 +
src/num/linalg.c | 12 +-
src/num/multind.c | 41 +-
src/num/multind.h | 22 +-
src/num/ops.c | 106 +-
src/num/ops.h | 11 +-
src/num/optimize.c | 17 +-
src/num/optimize.h | 4 +-
src/num/polynom.c | 169 ++++
src/num/polynom.h | 16 +
src/num/qform.c | 57 ++
src/num/qform.h | 4 +
src/num/rand.c | 2 +-
src/num/splines.c | 169 +++-
src/num/splines.h | 13 +-
src/num/vec3.c | 69 ++
src/num/vec3.h | 14 +
src/pics.c | 59 +-
src/pocsense.c | 1 -
src/poisson.c | 2 +
src/sense/model.c | 9 +
src/sense/pocs.c | 6 +-
src/sense/recon.c | 9 +-
src/sense/recon.h | 1 -
src/simu/biot_savart.c | 87 ++
src/simu/biot_savart.h | 7 +
src/simu/coil.c | 37 +
src/simu/coil.h | 3 +
src/simu/phantom.c | 12 +-
src/threshold.c | 2 +
src/traj.c | 70 +-
src/version.c | 5 +-
src/wavelet.c | 103 ++
src/wavelet2/wavelet.c | 1030 --------------------
src/wavelet2/wavelet.h | 53 -
src/wavelet2/wavelet_impl.h | 80 --
src/wavelet2/wavelet_kernels.cu | 921 -----------------
src/wavelet2/wavelet_kernels.h | 34 -
src/wavelet3/wavelet.c | 28 +-
src/wavelet3/wavthresh.c | 21 +-
tests/casorati.mk | 19 +
tests/cc.mk | 49 +
tests/ccapply.mk | 78 ++
tests/ecalib.mk | 14 +-
tests/estdelay.mk | 13 +
tests/gpu.mk | 24 +-
tests/nlinv.mk | 13 +
tests/phantom.mk | 21 +-
tests/pics.mk | 61 +-
tests/wavelet.mk | 12 +
utests/test_biot_savart.c | 60 ++
utests/test_blas.c | 79 ++
utests/test_linop_matrix.c | 190 ++++
utests/test_polynom.c | 182 ++++
utests/test_splines.c | 219 ++++-
utests/utest.c | 2 +-
version.txt | 2 +-
127 files changed, 4181 insertions(+), 3367 deletions(-)
create mode 100644 debian/patches/0003-remove-typo-in-symbol-and-make-it-static.patch
delete mode 100644 rules/wavelet2.mk
create mode 100644 src/casorati.c
create mode 100644 src/ccapply.c
create mode 100644 src/estdelay.c
create mode 100644 src/estshift.c
create mode 100644 src/linops/lintest.c
create mode 100644 src/linops/lintest.h
create mode 100644 src/mandelbrot.c
create mode 100644 src/misc/subpixel.c
create mode 100644 src/misc/subpixel.h
create mode 100644 src/num/polynom.c
create mode 100644 src/num/polynom.h
create mode 100644 src/num/qform.c
create mode 100644 src/num/qform.h
create mode 100644 src/num/vec3.c
create mode 100644 src/num/vec3.h
create mode 100644 src/simu/biot_savart.c
create mode 100644 src/simu/biot_savart.h
create mode 100644 src/simu/coil.c
create mode 100644 src/simu/coil.h
create mode 100644 src/wavelet.c
delete mode 100644 src/wavelet2/wavelet.c
delete mode 100644 src/wavelet2/wavelet.h
delete mode 100644 src/wavelet2/wavelet_impl.h
delete mode 100644 src/wavelet2/wavelet_kernels.cu
delete mode 100644 src/wavelet2/wavelet_kernels.h
create mode 100644 tests/casorati.mk
create mode 100644 tests/cc.mk
create mode 100644 tests/ccapply.mk
create mode 100644 tests/estdelay.mk
create mode 100644 tests/nlinv.mk
create mode 100644 tests/wavelet.mk
create mode 100644 utests/test_biot_savart.c
create mode 100644 utests/test_blas.c
create mode 100644 utests/test_linop_matrix.c
create mode 100644 utests/test_polynom.c
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