[med-svn] [bart] branch upstream updated (856d987 -> f236631)
Martin Uecker
uecker-guest at moszumanska.debian.org
Sat Jan 14 15:41:30 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 856d987 bump version
adds e391ef1 add parallel loop
adds c63c126 add md_parallel_zsample
adds 59a2507 parallelize phantom
adds 647d085 grasp.sh: use show
adds 2e465df move TYPE_CHECK to misc.h and use it in flpmath.c
adds 9334bf9 fixed fftw path for mac in Makefile.
adds 82a2a35 add debug prints to lsqr
adds a3460b8 CUDA compile fix
adds fe0e400 add wavg (weighted average) tool
adds 0124612 add carg
adds 74f2f8e copyright, formatting
adds d3e4ed8 PTR_ALLOC
adds c48fece minor Makefile changes for MacOSX
adds 05be444 make fftwthreads optional
adds d8949f0 add rule to make Doxygen documentation
adds 98b245a minor
adds 6ec4e9a carg/poisson: update help string and style
adds 20181fa use const char array for constant string literals
adds a9b9657 version: output information about dependencies with (-V)
adds c726802 add dims + strides explanation
adds aedbe32 support for ra files (only complex float)
adds 52cc59a fix Matlab error (thanks to Lyu Mengye)
adds 14b1249 Added matlab-like python tool
adds 3ffb032 allow overwriting the compiler on Mac OS X
adds 69d4d4e add build testing
adds bad1b1f add preconditioner operator to lsqr
adds 87cdb8f added preconditioner interface for lsqr, pics and sense_recon added doxygen comments for nufft structure added identity preconditioner for nufft that does nothing
adds c985845 added GTAGS to .gitignore.main
adds 44c8a86 added Strang's preconditioner for nufft
adds 6068255 comment
adds d30aeb7 turn off preconditioner in pics
adds f7cd7d9 added reference to Strang's preconditioner and style change
adds e714df9 Merge pull request #25 from frankong/master
adds 47d2c85 add missing argument to sense_recon_gpu in grecon.c
adds 2d109d4 Merge pull request #26 from grlee77/grecon_fix
adds 3508b2d add sedona ref
adds 560cc4c simplify makefile (remove bbox)
adds a26ca08 add operator/linop_loop
adds 2ad53b0 fix warning
adds b66f708 refactor
adds a5cfa92 3d radial trajectory
adds f1c735a add MD_STRIDES
adds f2932a0 minor
adds fd4e6d3 cuda build test
adds db333fb also test clang-3.5
adds 69eae5e build test osx
adds e266895 Merge pull request #27 from mrirecon/build
adds 96150f1 update comments which (incorrectly) refer to former license
adds 76975e0 refactor optimized ops
adds dfdc827 typo
adds 8cb6a05 minor
adds c99fe82 use MD_STRIDES
adds 116b1ac regularization of imaginary component
adds 5cdeb08 build test for cuda: do not install so many packages
adds ff2427e unhide some help options
adds 20940b8 update ismrmrd support - still very limited
adds 68df330 make ismrmrd a proper bart command
adds c7c7b9f build fix
adds 971f527 Added some error checks to estvar
adds d0271ff Merge pull request #30 from sidward/master
adds 718deec improve fftmod help, add -i option
adds b367e63 add mdfft
adds bd2e9e7 make flags unsigned long + other changes
adds 1715fe9 bpsense:change debug levels
adds d227bff add prox function for l2norm
adds 99b9eb3 prox_l2norm: use mu instead of 1/mu
adds d38ca65 add alternate iter2 interface with support for affine constraints
adds aa47d7e pics: only add l2 if lambda > 0.
adds 18ea7eb adjust debug levels
adds fcf647b extend admm to handle affine constraints
adds 5b641f8 add new tool: sqpics for parallel imaging and compressed sensing using square-root lasso formulation (WIP)
adds 29c43bd use simpler implementation of TYPE_CHECK
adds 2617313 improve help for show
adds 959364f add CONTAINER_OF
adds 508c263 make iter type-safe
adds b48e1ce more type safety in operator interface
adds 8ce586a gpu build fix
adds 604ce6d type safety for linop
adds 555d92d make iter2 type-safe
adds 2fc24b1 type safety for iter3
adds a936f69 fix warnings for gpu case
adds 0e43760 Merge pull request #31 from mrirecon/type-safety
adds f8e73e2 use correct strides in md_zwavg2
adds 54d363e use ARFLAGS
adds 8d4ee2b fix no randshift in lrthresh.c (thanks to Evan G. Levine)
adds 9b7661e pointless comments
adds 1586816 no randshift in threshold.c
adds 6f42dbc use tmp memory to implement in-place circ_shift
adds fb8094c show: allow custom separator
adds 0d7352d use correct strides in md_transpose
adds 7c35cf1 fix debug_print when using debug_logging
adds d72118a homodyne:improve help description
adds 6b8f41e fix warning and minor style changes
adds 074c0b3 Edited weights of softweight
adds 89fe419 Edited gitignore.main to ignore noise simulations
adds ca08729 Editted script 'sub' to call saxpy without throwing an error.
adds 5d7447c Merge pull request #33 from sidward/master
adds aabded9 change scaling of k-space phantom
adds 95c149f nufft: add scale factors
adds 0ef3a54 add tests for fft
adds e2c6956 add test
adds 17a09f5 change variable names
adds 5456973 add phantom.mk
adds 25ec86b nufft tests
adds d9ceece fix inverse
adds 594d474 flip sensitivities to that it matches kspace with iFFT reco
adds 4b01051 test for phantom with coil
adds 1ce2eb7 minor
adds 2e49a94 tests for espirit + pics
adds f3f3898 Merge pull request #34 from mrirecon/tests
adds a7da41e gitignore: remove bbox and add tests
adds a0c42a2 compute_kernels: require svals != NULL
adds 347cc7b add unit test
adds e175771 cleanup
adds e7dcbf9 add more test cases
adds d382e6d - redo testing based on minunit.h - simplify zwavg testing
adds f982626 utests/Makefile: use macros and run tests with command "make run"
adds fbe901c adjust debug levels
adds 074b38f Merge pull request #36 from mrirecon/unit-tests
adds f07c61e unit tests: - add header files to make dependencies and make default as first make goal - add test for md_zfmac2 and consolidate into flpmath file. - autogen gitignore
adds 4e7d93b minor
adds e3b0f80 workaround sanitizer
adds 2c2bfaa add chebfun library
adds a42a2d0 use it for special functions
adds 0465da4 bump version
adds 9485ff1 admm: coding style
adds 709f416 fix const for conjgrad_hist_prealloc
adds 614697a do not use md-functions in admm.c
adds 5a180b6 admm: Aop_data can be zero
adds b55eb38 simplify handling of biases
adds d18e07b write BART version and command line into created files
adds 28b5e81 minor
adds 5edf51d there is no reason data must be non-null
adds fce03ae use array notation in iter2
adds 154033a does not exit
adds 4ec1f39 minor improvements lad/lsqr
adds cb86058 _Bool -> bool, _Complex -> complex in c file
adds 540a1cf make pocs interface more standard
adds 22d67f4 minor
adds 7ce7ad0 use boolean operator
adds be8da6b rewrite blas/lapack interface
adds d60fd05 use openblas on mac os x, fix build testing
adds 0e1f04a rewrite batch_svthresh
adds 9d1f129 move
adds 1cb877c comment
adds 0397161 use union instead of type-punning with pointer cast
adds 215cfab update utests
adds cd4121b Merge pull request #32 from mrirecon/lapack
adds ea4bb61 cleanup nlinv
adds c30300c update README
adds 48535be use config struct for nlinv
adds 1cc6a39 remove useless casts
adds 7768a2d xfree, XFREE, PTR_FREE, PTR_PASS
adds 19f62e6 add debug_backtrace
adds 4abd7f0 use simpler implementation for free checks
adds 776a892 don't use -rdynamic on MacOSX
adds 891015d rewrite test for parallel make
adds f50100b add some missing PTR_PASS
adds 1cc3c4a lowrank: fix call to csyrk
adds 2fc608c update copyright
adds e33252c move regularization options to separate file
adds fa25625 travis: run tests on mac build
adds 0179313 Merge pull request #37 from mrirecon/opt-reg
adds 4202e52 integrate utests into main build system
adds 7dbbf74 add missing file
adds c06cb49 properly generate dependencies
adds cf14772 use our own unit test macros
adds 3867aac coding style
adds 08a88f6 move and rename stuff
adds d37d17c run tests from proper function
adds fa232e4 remove utests/README.md
adds 24ad803 rename data file
adds 6c568c8 a bit simpler to use
adds 7016e2d use linker script to collect unit tests
adds 6deae8e use PTR_FREE
adds 2e7698a utests: be more optimistic
adds 799bc31 utests: be more verbose
adds c4f51a0 use shell script to assemble list of unit tests
adds c153753 test on osx
adds 31cbeea use variable instead of file (makes parallel make work)
adds cdbf667 Merge pull request #38 from mrirecon/utests2
adds 3aeeb27 add some color
adds 99d360f remove some unnecessary includes
adds 8ba25e1 add initial spline code
adds 2a754fe export bernstein
adds 1b16540 missing copyright header
adds 1775d73 add casts to avoid warnings for OpenBLAS
adds c4bfb84 remove unnecessary struct members
adds e6ddf55 ops: fix input and output types
adds d3b49b0 fix type error in nufft
adds 0954a7e missing PTR_PASS
adds 3880365 convert more void* to iter_conf
adds eca407c operators: replace void pointers
adds 68f8ec8 operators from iter2 functios
adds ea57e19 operators for lsqr
adds c807a5a replace README on GitHub with a link to the homepage
adds 28b74a4 fix openblas with macports
adds 0c0ebd7 Merge pull request #39 from frankong/master
adds f25d152 test frank's homebrew install
adds a5b7cce make estimate_pattern_flags function
adds a73f046 pattern: use estimate_pattern_flags
adds 655a66e estimate_pattern now takes flags as input
adds b4be5e4 unit tests for estimate_pattern
adds 88ee403 Merge pull request #41 from mrirecon/pattern-flags
adds 978ac93 travis: add numpy/scipy and remove homebrew test (moved to separate repo)
adds 60d049d add test for python read/writecfl
adds 812b298 add information for contributors
adds af991df use cppwrap instead of redefined __VLA
adds 92f4e31 Update Python wrapper + Python Readme
adds f8d32ab Minor change to citation.
adds 54e09a4 Automated crop threshold
adds f6950cb style changes
adds 9e8a95f Added automate option -a
adds cdf8f20 Removed fmac3 and other stylistic changes.
adds 8da691e Merge pull request #42 from sidward/master
adds 694f2b0 README fixes
adds 56e3f08 fix formatting, improve readability
adds fb30579 simplify md_calc_fmac_dims to md_merge_dims, restore fmac formatting
adds 7c5a563 remove duplicate option
adds 91f5922 move merge_dims to multind.c
adds 68179fc PTR_FREE
adds 8b21783 added a check to avoid divide by zero in soft_weight_singular_vectors
adds cad4e7d TOOLBOX_PATH check in noise estimation (#44)
adds f1ddd3f start to document coding style
adds bfe4571 document use of debugger
adds 321ac2f rename vars.(sh|m) to startup.(sh|m)
adds 242bdf7 move python/matlab scripts into subdirectories
adds eee4314 add memory accounting and cache
adds 2977434 refactor gpuops
adds 9ede8e8 PTR_PASS/PTR_FREE in fft-cuda.c
adds a84e70e guard omp includes
adds 94ba8d3 improve debugging.txt
adds c2ca95e document build system
adds 35f1df2 markdown compatibility
adds e713263 nufft: use OPT macros
adds b816b6b track inputs + outputs
adds 38046e0 PTR_PASS
adds 263c2d7 remove Mac OS X build testing for now
adds 21bcac5 add float vector options
adds e7125f2 OPT macros + copyright
adds 19a5dd2 option formatting fix
adds a7bf8c0 Use single precision floats + remove allocation
adds 0152fd7 Format documentation and remove redundant line
adds 69fe7df Merge pull request #47 from timlod/master
adds f092ea7 add test for join tool
adds 6865c4f simplify md_zwavg
adds e4794e5 cc: reformat options
adds 1cedc3f add num_init() call to standalone tools (#48)
adds 938d6af fix writing of .hdr files
adds ed004f9 Revert "simplify md_zwavg"
adds e242a59 add proper test arrays with 0 entries
adds e338569 rename wavg to avg, add md_zavg, add test for unweighted avg
adds 538caec rename sf to specfun
adds b8804d1 PTR_PASS
adds 6b311e3 replace usr with for macports install
adds 9ff5a49 pics: remove unneeded headers
adds 0d17b10 add auto_scale option to nrmse
adds 395cb7e fix broken test
adds a1cba19 add nrmse scale test
adds 1e56230 covariance_function instead of calmat_svd (estvar) (#52)
adds 49294e1 ENH: Add initial cmake build script (#51)
adds 1290da4 debug_trace
adds 169e355 convert symbols
adds b613140 add tracing to operators
adds 7b6b170 Merge branch 'profile'
adds be6712a Revert "remove Mac OS X build testing for now"
adds d870142 mip: don't do abs by default
adds 9cd88a7 add thomas algorithm
adds 89add9c test for thomas algorithm
adds 4dddd83 update MacOS X instructions (thanks to Jakob Asslaender)
adds 53c401d copyright
adds dccb9c2 renme la.[ch] to linalg.[ch]
adds 9c4b28f add invert tool
adds 60de19b remove extra assert header
adds 19f44df remove deprecated function fftmodk
adds d8a7262 ENH: Add a robust FindOpenBLAS.cmake file
adds 0f97c3e ENH: Add a robust FindLAPACKE.cmake file
adds 929a850 ENH: Add a robust FindATLAS.cmake file
adds 55bc91d ENH: Provide support to build against vendor supplied lapack implementations
adds 945a6b4 SQPE FindAtlas fixes.
adds bca8caf SQME findATLAST
adds 49cdd43 SQME FindOpenBLAS
adds d585228 ENH: Improved lapack, ATLAS, and OpenBLAS support
adds 5869476 ENH: Improve C99 compiler identification
adds dfed1c6 DOC: Provide some documentation for building BART
adds 11b493a move INSTALL.md to doc/cmake_building.txt
adds 459a0ea Merge branch 'AllowVendorSuppliedLAPACK' (closes #53)
adds 7fad141 mip: fix bug with abs option
adds 1470bc7 add optimization for md_axpy, and improve debug info
adds 4136889 move optimize_nop to optimize.[ch]
adds 02c800e change interface to optimize_nop
adds 6c36759 move use_gpu
adds ba969f2 optimization fixes, and improvements
adds 6345058 use generic optimization framework for md_copy/md_clear
adds 2fae325 gpu fix
adds 2799ab8 change debug level for MD time
adds 7c9079a add md_compare
adds 80e517e unit tests for multind
adds b5bac88 utest for md_zmatmul
adds 774d9f1 fix for md_circular_swap
adds 46b5fef utest for md_circular_swap
adds 4894085 use generic optimization framework for md_swap..
adds e36911d GPU system tests
adds 771ee48 add test for weights
adds fecf892 add test for weights on GPU
adds bd48afe README: minor
adds 3a8b80b convoaa: don't use vecops
adds a3c8ce2 remove functions from vecops only needed for vec_iter
adds 7cec7e3 md_free takes const void* ptr
adds 855243a operator inferace to sense recon
adds 58d926d initialize unknown in itop
adds fd9dab9 pics: use sense_recon_create
adds 4d28f82 debug output for toeplitz mode
adds 8d23009 support weights in toeplitz mode
adds d35d104 operators: add ioflags
adds b0e1ded add axpy back to vecops
adds 19e9c8e add (two) shared pointer implementations
adds 12fca9e ops/linops: refactor memory management
adds d238302 UNCONST
adds f80beb5 COMP: Depend on Fortran if LINALG_VENDOR="LAPACKE"
adds c880754 COMP: Add Stage 2 build for bart binaries
adds 0ff121c STYLE: Sanity check that misc/cppmap.h is not needed
adds 33ae164 COMP: Ease syncronization of Makefile & CMake
adds 2fad338 ENH: Added optional matlab dependant functions
adds 1f24aef ENH: Implement ISMRMRD support for reconstructions
adds fb0dc23 ENH: Allow building of tarballs from CMakeLists.txt.
adds ac7ac06 COMP: Add ability to generate doxygen files.
adds 13d233c COMP: Add custom target for building bart.syms file in cmake.
adds b929657 COMP: Add installation rules for bart.
adds 26ba655 ENH: Add ability to automatically generate doc/commands.txt
adds 8f801bd Merge pull request #56 from hjmjohnson/AddSecondStageBuild
adds bbabf55 Function cabs: Complex magnitude of an array (#57)
adds 61d5f51 Updates to SURE + ESPIRiT (#58)
adds 81ced10 DOC: Add some documentation for common failure case
adds ecc862b COMP: Fix linker dependancies
adds bad5670 fix macports openblas library warning
adds 79fa31e admm: minor changes
adds 224049e admm: untangle history
adds 46ee1ea admm: minor changes
adds 2e1ad40 admm: make dynamic rho independent from fast
adds 0db6ae9 relax test criterium
adds 5c3dccf reshape: fix printf
adds 14631ff rename rvc linop_realval
adds c4e4b26 improve linop API consistency (closes #64)
adds 1d1615d no automatic python test
adds 145df11 CAST_UP/CAST_DOWN macros with run-time checking of down-casts
adds c63646b admm: refactor xupdate
adds 4a0d602 merge biases into iter2 interface
adds 5819b80 introduce monitor object
adds 003c76d do not use vops->dot in admm
adds 1ad6cb9 monitor: add history call-back
adds 813338d monitor: make objective value and residuum accessible
adds eb9140f admm: use monitor to record history
adds d2a55d0 add missing extern
adds 243111c nudft
adds ef5ea20 add nudft option to nufft
adds a1f1e24 create default normal operator
adds ed85936 add nudft tests
adds 78e998d twixread: change debug level and show -A in help
adds c41fc6b admm: fix calculation of s norm (broken in 79fa31eb)
adds 27ed3f3 admm: make conjgrad tolerance configurable
adds 95fe8bb missing SET_TYPEID
adds a7e6ba3 gpu reco
adds 627331c make existence of operator_gpu_wrapper independent from USE_CUDA
adds a6ac444 add gpu option to lsqr
adds 4ce20ba new gpu mode
adds d6dbfd0 remove old GPU code path
adds f02e74a lsqr: remove old GPU code path
adds acf2b86 remove use_gpu from operators
adds c13357c debug messages for GPU
adds 1ffa3cd implement lad2_create
adds e38458e use lad2_create in sense_recon_create
adds 54d2530 eliminate grecon and rsense
adds 96502a7 remove sense_recon
adds 700ffc1 minor
adds 1de0021 lazy cufft plans
adds 51a8a88 fftw measure
adds 42d669d lazy cufft 2
adds ca37bdd change gpu initialization
adds e535b49 non-gpu build fix
adds e8d4c5d CAST_UP/CAST_DOWN
adds c4c5b25 warmstart
adds 7ee29a2 ops: copy_wrapper
adds 128cb70 pics: add batch mode
adds 54d75eb pics: test for batch mode
adds 912db9d missing free
adds 829bb0c fix use after free
adds d3aa658 optimize.c: change flags to long
adds 10f0524 references for ADMM
adds 797e6f5 Use low-resolution maps in auto-espirit (#67)
adds 4fbfaa8 Added auto-espirit test in ecalib.mk (#68)
adds 553953a add tool zexpj for complex exponential
adds 6660991 don't re-init cuplan every time (#69)
adds fde9a66 activate nested parallelism
adds 1d240a1 rof: use MAKE_ARRAY
adds 1e25d55 add FT as sparsity transform
adds 0c30913 Linux: add libopenblas-dev to README
adds d69a026 do not use wavelet2
adds 6f0267e test case
adds f587a7e make it possible to change xref in iter3
adds 6c62fad remove mac tests (fail due to timeouts)
adds eb435aa change fftw to use 64-bit interface
adds af6b01d fix warning
adds b53d15b add delta tool
adds a191376 fix warning
adds 2fcc7ae fix use of static
adds b2b764b test clang builds
adds 98f5618 add fmac operator
adds 27be58a add squeeze tool
adds 62989df don't hide some options
adds e288a6f threshold: add hard threshold option
adds 9b60892 add flatten tool
adds d7ed8ad add call to num_init()
adds ec6696b indents
adds 9c56515 fmac tool: if only two args are specified then squash-and-sum <input1>
adds ad2f7b7 show tool: option to use custom number formatting
adds 7725ec2 make custom Makefiles dir and README for explanation (#73)
adds ea576e2 add phase cycling for nufft (#71)
adds c06e2ae add option to specify random seed in poisson (#74)
adds 5862f64 add append mode to join
adds 81e7ed6 add copy command
adds 1547e55 squeeze: remove singletons completely
adds e3e5798 restrict format strings and do not use sprintf
adds bbca3dc turn off nested parallelization
adds f236631 bump version
No new revisions were added by this update.
Summary of changes:
.gitignore.main | 12 +-
.travis.yml | 107 +++++
CMakeLists.txt | 360 ++++++++++++++++
Makefile | 259 +++++++-----
Makefiles/README.md | 52 +++
README | 68 ++-
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/dimensions-and-strides.txt | 42 ++
doc/style.txt | 210 ++++++++++
doxyconfig | 4 +-
makedoc.sh | 3 +-
matlab/bart.m | 4 +-
matlab/readcfl.m | 16 +-
matlab/writecfl.m | 18 +-
python/bart.py | 66 +++
bartview.py => python/bartview.py | 0
rules/box.mk | 11 +-
rules/ismrm.mk | 4 +-
rules/lowrank.mk | 2 +
rules/make_symbol_table.sh | 6 +
rules/misc.mk | 1 +
rules/num.mk | 2 +-
rules/update_commands.sh | 17 +
scripts/bart_completion.sh | 3 +-
scripts/grasp.sh | 8 +-
octview.m => scripts/octview.m | 0
scripts/profile.sh | 70 ++++
src/avg.c | 61 +++
src/bart.c | 5 +-
src/bench.c | 13 +-
src/bitmask.c | 10 +-
src/bpsense.c | 28 +-
src/cabs.c | 44 ++
src/caldir.c | 4 +-
src/calib/calib.c | 254 ++++++++++--
src/calib/calib.h | 2 +
src/calib/calmat.c | 10 +-
src/calib/cc.c | 2 +-
src/calib/direct.c | 2 +-
src/calib/estvar.c | 69 ++-
src/calib/softweight.c | 23 +-
src/calib/softweight.h | 10 +-
src/calib/walsh.c | 3 +-
src/calmat.c | 21 +-
src/{creal.c => carg.c} | 19 +-
src/cc.c | 13 +-
src/cdf97.c | 13 +-
src/circshift.c | 7 +-
src/conj.c | 7 +-
src/conv.c | 6 +-
src/{resize.c => copy.c} | 46 +-
src/cpyphs.c | 8 +-
src/creal.c | 7 +-
src/crop.c | 7 +-
src/delta.c | 55 +++
src/dfwavelet/dfwavelet.c | 2 -
src/dfwavelet/prox_dfwavelet.c | 262 ++++++------
src/ecalib.c | 71 ++--
src/ecaltwo.c | 18 +-
src/estdims.c | 7 +-
src/estvar.c | 19 +-
src/extract.c | 7 +-
src/fakeksp.c | 10 +-
src/fft.c | 15 +-
src/fftmod.c | 28 +-
src/fftshift.c | 7 +-
src/filter.c | 7 +-
src/flatten.c | 53 +++
src/flip.c | 7 +-
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 | 16 +-
src/invert.c | 49 +++
src/ismrm/read.c | 129 ++++++
src/ismrm/read.cc | 205 ---------
src/ismrmrd.c | 6 +-
src/iter/admm.c | 469 ++++++++++++---------
src/iter/admm.h | 66 ++-
src/iter/italgos.c | 352 ++--------------
src/iter/italgos.h | 106 +----
src/iter/iter.c | 88 ++--
src/iter/iter.h | 49 ++-
src/iter/iter2.c | 126 +++---
src/iter/iter2.h | 36 +-
src/iter/iter3.c | 32 +-
src/iter/iter3.h | 21 +-
src/iter/itop.c | 139 +++++++
src/iter/itop.h | 13 +
src/iter/lad.c | 133 ++++--
src/iter/lad.h | 19 +-
src/iter/lsqr.c | 335 ++++++++-------
src/iter/lsqr.h | 78 ++--
src/iter/monitor.c | 100 +++++
src/iter/monitor.h | 37 ++
src/iter/prox.c | 235 ++++++++---
src/iter/prox.h | 3 +-
src/iter/thresh.c | 60 +--
src/iter/thresh.h | 20 +-
src/itsense.c | 6 +-
src/join.c | 57 ++-
src/linops/finite_diff.c | 611 ++++++++++++++-------------
src/linops/finite_diff.h | 53 +--
src/linops/fmac.c | 133 ++++++
src/linops/fmac.h | 7 +
src/linops/grad.c | 59 +--
src/linops/grad.h | 2 +-
src/linops/linop.c | 117 +++---
src/linops/linop.h | 17 +-
src/linops/realval.c | 62 +++
src/linops/realval.h | 7 +
src/linops/rvc.c | 54 ---
src/linops/rvc.h | 7 -
src/linops/sampling.c | 30 +-
src/linops/sampling.h | 2 +-
src/linops/someops.c | 535 +++++++++++++-----------
src/linops/someops.h | 8 +-
src/linops/sum.c | 113 ++---
src/linops/sum.h | 2 +-
src/linops/ufft.c | 108 ++---
src/linops/ufft.h | 2 +-
src/linops/waveop.c | 30 +-
src/linops/waveop.h | 2 +-
src/lowrank/batchsvd.c | 81 ++++
src/lowrank/batchsvd.h | 6 +
src/lowrank/lrthresh.c | 77 ++--
src/lowrank/svthresh.c | 13 +-
src/lrmatrix.c | 50 ++-
src/mip.c | 15 +-
src/misc/cppmap.h | 8 +
src/misc/debug.c | 73 +++-
src/misc/debug.h | 31 +-
src/misc/io.c | 225 +++++++++-
src/misc/io.h | 29 +-
src/misc/misc.c | 49 ++-
src/misc/misc.h | 47 ++-
src/misc/mmio.c | 126 ++++--
src/misc/mmio.h | 18 +-
src/misc/mri.c | 12 +-
src/misc/mri.h | 21 +-
src/misc/opts.c | 26 +-
src/misc/opts.h | 14 +-
src/misc/pd.c | 22 +-
src/misc/pd.h | 15 +-
src/misc/resize.c | 1 -
src/misc/shrdptr.c | 70 ++++
src/misc/shrdptr.h | 39 ++
src/misc/types.h | 40 ++
src/nlinv.c | 70 +---
src/noir/model.c | 5 +-
src/noir/recon.c | 88 +---
src/noir/recon.h | 24 +-
src/noise.c | 19 +-
src/noncart/grid.c | 2 +-
src/noncart/nudft.c | 239 +++++++++++
src/noncart/nudft.h | 33 ++
src/noncart/nufft.c | 430 ++++++++++++++-----
src/noncart/nufft.h | 27 +-
src/normalize.c | 7 +-
src/nrmse.c | 35 +-
src/nufft.c | 61 ++-
src/num/blas.c | 64 +++
src/num/blas.h | 18 +
src/num/blockproc.c | 3 +-
src/num/blockproc.h | 19 +-
src/num/chebfun.c | 234 +++++++++++
src/num/chebfun.h | 13 +
src/num/conv.c | 20 +-
src/num/convoaa.c | 55 +--
src/num/convoaa.h | 4 +-
src/num/fft-cuda.c | 7 +-
src/num/fft.c | 142 +++++--
src/num/fft.h | 25 +-
src/num/filter.h | 19 +-
src/num/flpmath.c | 853 ++++++++++++++++++--------------------
src/num/flpmath.h | 18 +-
src/num/gpuops.c | 206 +--------
src/num/init.c | 19 +-
src/num/iovec.c | 17 +-
src/num/lapack.c | 432 +------------------
src/num/lapack.h | 7 +-
src/num/{la.c => linalg.c} | 32 +-
src/num/{la.h => linalg.h} | 5 +-
src/num/loop.c | 17 +-
src/num/loop.h | 1 +
src/num/mdfft.c | 318 ++++++++++++++
src/num/mdfft.h | 20 +
src/num/mem.c | 255 ++++++++++++
src/num/mem.h | 12 +
src/num/multind.c | 405 +++++++++++-------
src/num/multind.h | 52 +--
src/num/ops.c | 516 +++++++++++++++++------
src/num/ops.h | 54 ++-
src/num/optimize.c | 168 ++++++--
src/num/optimize.h | 20 +-
src/num/simplex.c | 1 -
src/num/{sf.c => specfun.c} | 28 +-
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 | 7 +-
src/pattern.c | 28 +-
src/phantom.c | 7 +-
src/pics.c | 565 ++++++++-----------------
src/pocsense.c | 36 +-
src/poisson.c | 86 ++--
src/repmat.c | 7 +-
src/reshape.c | 9 +-
src/resize.c | 13 +-
src/rof.c | 16 +-
src/rsense.c | 169 --------
src/rss.c | 7 +-
src/sake.c | 4 +-
src/sake/sake.c | 5 +-
src/saxpy.c | 7 +-
src/scale.c | 7 +-
src/sdot.c | 7 +-
src/sense/bprecon.c | 27 +-
src/sense/bprecon.h | 4 +-
src/sense/model.c | 106 +++--
src/sense/model.h | 7 +-
src/sense/optcom.c | 6 +-
src/sense/pocs.c | 41 +-
src/sense/recon.c | 171 ++------
src/sense/recon.h | 44 +-
src/show.c | 53 ++-
src/simu/phantom.c | 12 +-
src/simu/shepplogan.c | 6 +-
src/slice.c | 7 +-
src/spow.c | 7 +-
src/{pics.c => sqpics.c} | 281 +++++--------
src/squeeze.c | 60 +++
src/svd.c | 4 +-
src/threshold.c | 64 ++-
src/toimg.c | 21 +-
src/traj.c | 27 +-
src/transpose.c | 8 +-
src/twixread.c | 38 +-
src/version.c | 46 +-
src/walsh.c | 16 +-
src/wave.c | 30 +-
src/wavelet2/wavelet.c | 155 ++++---
src/wavelet2/wavelet.h | 3 -
src/wavelet2/wavelet_kernels.h | 14 +-
src/wavelet3/wavthresh.c | 34 +-
src/wavelet3/wl3-cuda.h | 16 +-
src/zeros.c | 7 +-
src/{creal.c => zexpj.c} | 20 +-
vars.m => startup.m | 0
startup.py | 8 +
vars.sh => startup.sh | 0
sub | 2 +-
tests/copy.mk | 26 ++
tests/ecalib.mk | 21 +
tests/fft.mk | 31 ++
tests/flatten.mk | 15 +
tests/fmac.mk | 16 +
tests/gpu.mk | 61 +++
tests/join.mk | 24 ++
tests/nrmse.mk | 11 +
tests/nufft.mk | 113 +++++
{lib => tests/out}/.gitignore | 0
tests/phantom.mk | 51 +++
tests/pics.mk | 117 ++++++
tests/pythoncfl.mk | 16 +
tests/pythoncfl.py | 22 +
tests/slice.mk | 15 +
tests/squeeze.mk | 16 +
{lib => tests/tmp}/.gitignore | 0
utests/test_batchsvd.c | 77 ++++
utests/test_flpmath.c | 191 +++++++++
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 +-
296 files changed, 13643 insertions(+), 6732 deletions(-)
create mode 100644 .travis.yml
create mode 100644 CMakeLists.txt
create mode 100644 Makefiles/README.md
mode change 120000 => 100644 README.md
create mode 100644 build_targets.mk
create mode 100644 cmake/FindATLAS.cmake
create mode 100644 cmake/FindFFTW.cmake
create mode 100644 cmake/FindLAPACKE.cmake
create mode 100644 cmake/FindMatlab.cmake
create mode 100644 cmake/FindOpenBLAS.cmake
create mode 100644 doc/building.txt
create mode 100644 doc/cmake_building.txt
create mode 100644 doc/debugging.txt
create mode 100644 doc/dimensions-and-strides.txt
create mode 100644 doc/style.txt
create mode 100644 python/bart.py
rename bartview.py => python/bartview.py (100%)
create mode 100755 rules/make_symbol_table.sh
create mode 100755 rules/update_commands.sh
rename octview.m => scripts/octview.m (100%)
create mode 100644 scripts/profile.sh
create mode 100644 src/avg.c
create mode 100644 src/cabs.c
copy src/{creal.c => carg.c} (60%)
copy src/{resize.c => copy.c} (51%)
create mode 100644 src/delta.c
create mode 100644 src/flatten.c
delete mode 100644 src/grecon/grecon.c
delete mode 100644 src/grecon/grecon.h
create mode 100644 src/grecon/optreg.c
create mode 100644 src/grecon/optreg.h
delete mode 100644 src/grecon/parslices.c
delete mode 100644 src/grecon/parslices.h
create mode 100644 src/invert.c
create mode 100644 src/ismrm/read.c
delete mode 100644 src/ismrm/read.cc
create mode 100644 src/iter/itop.c
create mode 100644 src/iter/itop.h
create mode 100644 src/iter/monitor.c
create mode 100644 src/iter/monitor.h
create mode 100644 src/linops/fmac.c
create mode 100644 src/linops/fmac.h
create mode 100644 src/linops/realval.c
create mode 100644 src/linops/realval.h
delete mode 100644 src/linops/rvc.c
delete mode 100644 src/linops/rvc.h
create mode 100644 src/lowrank/batchsvd.c
create mode 100644 src/lowrank/batchsvd.h
create mode 100644 src/misc/shrdptr.c
create mode 100644 src/misc/shrdptr.h
create mode 100644 src/misc/types.h
create mode 100644 src/noncart/nudft.c
create mode 100644 src/noncart/nudft.h
create mode 100644 src/num/blas.c
create mode 100644 src/num/blas.h
create mode 100644 src/num/chebfun.c
create mode 100644 src/num/chebfun.h
rename src/num/{la.c => linalg.c} (93%)
rename src/num/{la.h => linalg.h} (96%)
create mode 100644 src/num/mdfft.c
create mode 100644 src/num/mdfft.h
create mode 100644 src/num/mem.c
create mode 100644 src/num/mem.h
rename src/num/{sf.c => specfun.c} (74%)
rename src/num/{sf.h => specfun.h} (100%)
create mode 100644 src/num/splines.c
create mode 100644 src/num/splines.h
delete mode 100644 src/rsense.c
copy src/{pics.c => sqpics.c} (74%)
create mode 100644 src/squeeze.c
copy src/{creal.c => zexpj.c} (63%)
rename vars.m => startup.m (100%)
create mode 100644 startup.py
rename vars.sh => startup.sh (100%)
create mode 100644 tests/copy.mk
create mode 100644 tests/ecalib.mk
create mode 100644 tests/fft.mk
create mode 100644 tests/flatten.mk
create mode 100644 tests/fmac.mk
create mode 100644 tests/gpu.mk
create mode 100644 tests/join.mk
create mode 100644 tests/nrmse.mk
create mode 100644 tests/nufft.mk
copy {lib => tests/out}/.gitignore (100%)
create mode 100644 tests/phantom.mk
create mode 100644 tests/pics.mk
create mode 100644 tests/pythoncfl.mk
create mode 100755 tests/pythoncfl.py
create mode 100644 tests/slice.mk
create mode 100644 tests/squeeze.mk
copy {lib => tests/tmp}/.gitignore (100%)
create mode 100644 utests/test_batchsvd.c
create mode 100644 utests/test_flpmath.c
create mode 100644 utests/test_flpmath_data.h
create mode 100644 utests/test_linalg.c
create mode 100644 utests/test_multind.c
create mode 100644 utests/test_pattern.c
create mode 100644 utests/test_splines.c
create mode 100644 utests/utest.c
create mode 100644 utests/utest.h
create mode 100755 utests/utests-collect.sh
create mode 100644 utests/utests.ld
--
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