[med-svn] [bart] branch master created (now 93f3b06)
Martin Uecker
uecker-guest at moszumanska.debian.org
Tue Dec 1 16:20:58 UTC 2015
This is an automated email from the git hooks/post-receive script.
uecker-guest pushed a change to branch master
in repository bart.
at 93f3b06 add debian control files
This branch includes the following new commits:
new 0e81e93 root commit
new 713a858 initial commit
new 2ee31ce Changes: - fix xupdate support for admm - fix compilation issues with cuda 6.5 - implement memory caching for cuda - create vec_iter_s for iterative algorithms - prepare operator code for n-ary operators (and re-implement operator_p_s) - clean-up headers and reorganize lsqr - clean-up sense configuration - reorganize code (create linops/iter modules) - extend md_(z)softthresh API - improve md_fill on GPU - change TV operator to store partial derivative in [...]
new d2d1e6f Sync code with internal version
new 9fec031 sync code with internal version
new 8d3a48a add empty lib directory (using the .gitignore trick)
new 5d477a2 sync code with internal version
new 5a85e6b sync code with internal version
new ad38150 sync code with internal version
new dd13f2e add missing make target for sake
new 5db942d add option for static linking to Makefile
new c53dae3 add vars.m
new 6d000db add comment to vars.sh
new 7816f7e add help and error handling to bart.m
new a564b11 update README
new 2d67db1 add svd.c and calmat.c
new eaaa61d rename resize and svd, add md_calloc
new b25ee6c fft: add assert for null plan
new 6462eb6 coding style, copyright years, whitespace fixes
new 0f881d0 add missing initialization
new f2c1e85 add linop inteface for wavelets3 (waveop.[ch])
new 399be78 fix wavelet3 benchmarks
new 906572c set gcc 4.7 as default compiler for MacOS X
new b68c2f8 document possibilities for using bart on windows
new d966568 changes for static linking
new 191a549 add program number
new 316255b add build-essential
new 350ba2f change url to website
new 6091fb3 add windows instructions
new 544e5e8 remove support for CULA
new a506c8d add batch_svthresh
new 9ce96f2 add blockproc
new 5094b93 add lowrank library
new b078868 add very basic lowrank regularization to sense
new 98a3b8e README formatting
new 5fab5a6 add div-free wavelet library
new 96db8c6 README: updates
new 8a23c1e add python image viewer
new 9e30e34 add wavelet (cdf97) tool
new 1c8a7f3 Cygwin Windows support
new 1d58886 minor
new 746a110 Golden angle sampling
new 94f98be remove deprecated function: softthresh
new f43dc77 estimation of max. eigenvalue, minor changes
new d6d1656 add wlsqr2
new e863cb1 add md_check_bounds
new 268a7fa add some more simple linear algebra
new b6696ba rename tv operator
new 1214d98 typos
new d90ba18 bart.m: don't use strjoin for compat. with old matlab
new 26b40ee simulate moving disc
new 65bd9ee python: transpose arrays
new fc60701 python: fix bug in bartview
new ee3f3a0 minor changes
new d82bb8e add divfree reference
new bd47376 make fftmod work for odd sizes
new 7a31230 allow calibration of odd sizes
new baf615c rework nufft, merge nusense back into sense
new 194c476 remove nusense description
new af66aaf for sense, set admm tolerances to zero
new 5647d15 move bitcount function to misc/misc.[ch]
new af2b4d9 add reshape tool
new 206706d fix fft_normal for non-unitay/centered fft
new 33653f9 document version dependency for ismrmrd
new 31683e7 activate phase rotation to principal component by default
new 1c3e6ab rename sense to pics
new 175161b generalize md_minxy/md_maxzy to md_max/md_min
new 79ebecf properly check for non-Cartesian without weights
new b59d79f add sense cmd back to default targets
new b544caa add image export tool: toimg
new 4b80cb3 improve precision of fftmod
new 33e55fe remove some unsupported options
new 4730d68 minor changes
new c1475a3 make headers more C++ friendly
new 991a4b9 updates to installation instructions
new 5c936f4 make headers more C++ friendly
new eddfd7d odd-sized fft
new b167686 fftshift, documentation, fixes, ..
new 9c192bc work around compiler bug in GCC 4.6.3
new 7b2224b minor changes
new 01e155d warning: implicit declaration of function 'basename'
new 8cefb64 fix gcc openmp issue
new c092cbf minor change to help str
new 127e4c6 add pattern input to rsense, allow explicit pattern to vary along channels
new e45992f change md_resize_center for odd differences
new 1e63fc4 fix typo in Matlab interface for windows
new 1550434 extend operator interface
new 89ba4dc add simplex code
new afd67fc generalize calibration matrix construction
new 9fd6e3d update gpu code
new 222b865 add lapack_cholesky
new 06d2d48 add experimental overlap-and-add code
new 2773ed3 change debug level output of admm
new 7c51421 fix memory corruption in admm
new 79ed8c0 add copyright
new 460bf04 allow multiple penalties
new 7ee4edc add wave reconstruction
new 6e489f9 add script for GRASP
new 477c73e add rtnlinv script
new 82a7c10 wavelet3: add missing changes
new 7adc33e fixed grasp script to be more platform independent
new e1d36f2 Merge pull request #2 from davidssmith/grasp
new 45b91b0 fix file permissions
new e6d0043 Merge branch 'master' of github.com:mikgroup/bart
new b099066 exuberant ctags script
new e11350e - autogen .gitignore from .gitignore.main - add show, relnorm, and sub convenience tools - support loading cfl as shared memory - pas cal region directly to estimate_scaling - add DEBUG option to Makefile - use default for common Makefile variables if specified - fftmod of sense maps using cov_dims - add some tools to bart binary - add finite difference operator - add fakeksp tool
new 69df5ca fix case where sense maps don't have higher-order dimensions
new 6bea58d don't free in recon.c, instead free where sense_init is called
new 086e0a5 chmod -x
new a38c1d4 Merge pull request #5 from mikgroup/misc-updates
new 33581fc minor
new fd2912d write sequence of 2D images
new b839b57 write sequence of 2D images (closes #6)
new bfb3040 Merge branch 'master' of github.com:morpheus-med/bart
new 4df80c0 Merge branch 'master' of github.com:mikgroup/bart
new f99502a verbosify load cfl errors and merge
new 41c9b17 chmod -x
new 2557149 write sequence of 2D images (closes #6)
new 5867061 Merge branch 'misc-updates'
new d5de95b make sub executable
new 1d142b0 add global boolean, debug_logging, that prints verbose debug messages if set to true
new 73ff614 use strftime functions
new 9f97e1c add comment about slow datetime
new 28dd313 Merge branch 'master' into logging
new 9c14046 comment out datetime logging since it is very slow
new ee83c3e only get datetime if the debug level is high enough to print
new 29813cb undo accidental comment
new 27453ec use shortcut for false test and call debug_vprintf
new 48b8dd9 typo in comment
new 90614cf minor
new 6c48213 change fista_conf to ist_conf
new 32577fc increase debug level for iterations
new 02742f6 make operator interface independent from flpmath.h
new f60d3af white space
new 1bd2944 minor
new d527db5 linop_chainN
new 92ac028 minor
new ee93a1e use format strings for io_error
new 3dfe7c3 define AR by default
new e8aed51 Merge pull request #7 from mikgroup/logging
new 6560a45 make option switch in mini_cmdline_bool configurable
new c38c431 add nrmse tool
new 7209471 deprecate relnorm program (use nrmse instead)
new 45bff33 be more explicit about no diagnostic use
new ab9ada7 make cfl reader accept future headers
new c74ddb1 clear out implicit rules
new 9a55c7a add tool to print version information
new d01d155 explain version string in help message
new 5a2a390 handle white space
new 6d060ac sort bart commands and verbosify unknown command error
new fececfc revert back to exit(1) for bart exit. (re: 6d060ac)
new 5d202ec fix infinite loop with parallel make
new 1c464c9 scanf %m not supported by Mac OS X
new 0678f51 dicom: write InstanceNumber tag and add some sanity checks. change toimg dicom flag to "-d"
new 900f522 minor
new 51d45a5 ignore mac debug files
new 06fa94c undo minor
new a65a569 delete intermediate files
new 7cf9a15 twixread: fix missing initialization + other improvements
new b4bb067 typo
new 0f07d6b fix fftmod performance regression
new a8f98e1 re-activate parallelization for gram_matrix
new f535fd5 minor
new 13956d2 add some options or radial trajectories
new abc71b4 nmrse: add test option
new a6b635b toimg: simplify and restore filename detection
new a7a543c formatting
new bdacade avoid second dot in filename
new fcfe0c2 added option -C to pics.c to changed maximum cg iter for admm
new a5eb2ef add generalized regularization options (based on Jon's work)
new 468b1cc Merge pull request #9 from mikgroup/gpics2
new 6f24eea l2 penalty by default
new cf4e77b update help
new cb28538 update grasp.sh script
new 6b49844 specify scale factor
new b33bfbb pics: add "-W <image>" for warm start
new c696a4f join: add option to load files based on input format (see -h for usage)
new 146857b join: remove [-p] and show example using seq tool in help
new d4f2583 Merge pull request #10 from mikgroup/join-parfile
new 05848aa update version.txt
new 76f2bc7 add warning for missing step size
new a94706d fixes for linking everything together
new e3acf48 bart with all commands (bbox for fast compilation)
new dd8ca3a ignore priv for .coo
new 430bdff avoid compilation problems
new c90b3e8 add median filter
new 03db89e fix for multiple penalties with gpu
new 27a8a0e update URL
new 633d7c7 add rule to autogenerate doc/commands.txt
new 80f355c phantom: make k-space center consistent with rest of bart
new 3d71a7e if we plan an in-place FFT we need to use it in-place
new d0aabfd homodyne: options to clear unacquired portion and input ref phase
new c77e239 fix bug with gpu less than or equal to kernel
new 3e449e4 add {less,greater} than or equal to prox function and corresponding multind/vecops functions
new c041856 use bart command in matlab wrapper
new 429082f add rule for C++ files
new 80caf78 add code to increase stack limit
new 2a2889f relax cuda fft constraints
new 61a5808 remove -lcuda
new fee801a add real-value prox op
new 79fb1d5 update copyright/contributions
new af32067 add some doxygen comments
new b9631a1 Merge pull request #11 from mrirecon/md-prox-updates
new 5caebb9 Makefile improvements
new 7271b03 fix for 3D CUFFT
new acfbffc missing bracket
new aa277cd free before return statement
new 9cdcb45 actually free before return
new 5d3237d Added noise estimation cmd: estvar
new a3ca3df Made estvar a member of libcalib.
new ab4b0b2 Added a missing free
new 706b862 Minor changes
new 13c5bc9 Minor changes
new ee11f72 Merge pull request #12 from sidward/master
new 721908b Added soft-weighting. Still need to debug
new 3bc2ec4 Soft weighting
new 065d5b9 soft-thresholding implemented.
new 9cedd97 Forcing evecs estimate to not use orthiter fixes soft-weighting map estimate problem
new 863e917 Added abstract reference
new 8858d6e added multi-scale low rank option for pics
new d8bfde3 removed warning about locally low rank in pics
new fd2b14b Added references
new 5f7daa8 added divergence free wavelet thresholding, locally low rank thresholding and wavelet thresholding options to threshold.c
new 13d19cc Merge branch 'master' of https://github.com/frankong/bart
new 05e1a87 Merge pull request #13 from sidward/master
new 543b6b3 Merge pull request #14 from frankong/master
new 89469cf make README markdown friendly and add link for README.md
new 7facb10 README improvements
new 43b5913 add (median) filter tool
new 3e4c26c fix for unitialized singular values for degenerate calibration matrix
new cb56f6f don't set debug_level
new dbe9715 shorten description of -W option, cosmetics
new a8e4026 fix warnings
new 0ab820b add missing const
new 68e2d22 add install target, only build bart by default, remove commands.txt
new a54acf6 add manpage
new 18335fc gitignore bbox
new 4d4ef47 add .gitignore default target in Makefile, add doc/commands.txt to .gitignore
new f2cc7f3 fix install on Mac OS X
new 93f3b06 add debian control files
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