[med-svn] [bart] annotated tag v0.4.00 created (now 97890b6)
Martin Uecker
uecker-guest at moszumanska.debian.org
Sat Jan 14 15:23:02 UTC 2017
This is an automated email from the git hooks/post-receive script.
uecker-guest pushed a change to annotated tag v0.4.00
in repository bart.
at 97890b6 (tag)
tagging f236631b70a32454a0604a738282f27bc5ffe849 (commit)
replaces v0.3.01
tagged by Martin Uecker
on Wed Dec 21 22:49:49 2016 +0100
- Log -----------------------------------------------------------------
version 0.4.00
Changes:
- new tools: copy, squeeze, flatten, delta, zexpj, invert
- show tool: option to use custom number formatting
- poisson: option to specify random seed in poisson (David Smith)
- threshold: hard threshold option
- join: append mode
- nufft: nudft option
- nufft: randshift for nufft
- pics: batch mode
- pics: FT as sparsity transform
- nrmse: auto_scale option
- fmac tool: if only two args are specified then squash-and-sum <input1>
- remove rsense tool
- support for cmake (Hans Johnson)
- rename vars.(sh|m) to startup.(sh|m)
- more efficient Matlab interface (Tim Loderhose)
- write BART version and command line into created files
- change fftw to use 64-bit interface
- phase out old wavelet2 code
- library: phase cycling for nufft
- library: support weights in toeplitz mode
- library: fmac operator
- library: cabs: complex magnitude
- library: md_compare
- library: thomas algorithm
- library: inital spline code
- many other bug fixes and enhancements
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David Smith (1):
add option to specify random seed in poisson (#74)
Frank Ong (5):
fix openblas with macports
replace usr with for macports install
fix macports openblas library warning
change fftw to use 64-bit interface
add phase cycling for nufft (#71)
Hans Johnson (24):
ENH: Add initial cmake build script (#51)
ENH: Add a robust FindOpenBLAS.cmake file
ENH: Add a robust FindLAPACKE.cmake file
ENH: Add a robust FindATLAS.cmake file
ENH: Provide support to build against vendor supplied lapack implementations
SQPE FindAtlas fixes.
SQME findATLAST
SQME FindOpenBLAS
ENH: Improved lapack, ATLAS, and OpenBLAS support
ENH: Improve C99 compiler identification
DOC: Provide some documentation for building BART
COMP: Depend on Fortran if LINALG_VENDOR="LAPACKE"
COMP: Add Stage 2 build for bart binaries
STYLE: Sanity check that misc/cppmap.h is not needed
COMP: Ease syncronization of Makefile & CMake
ENH: Added optional matlab dependant functions
ENH: Implement ISMRMRD support for reconstructions
ENH: Allow building of tarballs from CMakeLists.txt.
COMP: Add ability to generate doxygen files.
COMP: Add custom target for building bart.syms file in cmake.
COMP: Add installation rules for bart.
ENH: Add ability to automatically generate doc/commands.txt
DOC: Add some documentation for common failure case
COMP: Fix linker dependancies
Jon Tamir (37):
update copyright
test on osx
move regularization options to separate file
travis: run tests on mac build
Merge pull request #38 from mrirecon/utests2
test frank's homebrew install
pattern: use estimate_pattern_flags
estimate_pattern now takes flags as input
unit tests for estimate_pattern
travis: add numpy/scipy and remove homebrew test (moved to separate repo)
add test for python read/writecfl
add test for join tool
simplify md_zwavg
add num_init() call to standalone tools (#48)
Revert "simplify md_zwavg"
add proper test arrays with 0 entries
rename wavg to avg, add md_zavg, add test for unweighted avg
mip: don't do abs by default
add invert tool
remove extra assert header
mip: fix bug with abs option
README: minor
reshape: fix printf
twixread: change debug level and show -A in help
admm: fix calculation of s norm (broken in 79fa31eb)
admm: make conjgrad tolerance configurable
missing SET_TYPEID
add tool zexpj for complex exponential
add squeeze tool
don't hide some options
threshold: add hard threshold option
add flatten tool
add call to num_init()
indents
fmac tool: if only two args are specified then squash-and-sum <input1>
show tool: option to use custom number formatting
make custom Makefiles dir and README for explanation (#73)
Jonathan Tamir (2):
lowrank: fix call to csyrk
make estimate_pattern_flags function
Joseph Y Cheng (1):
don't re-init cuplan every time (#69)
Martin Uecker (215):
admm: coding style
fix const for conjgrad_hist_prealloc
do not use md-functions in admm.c
admm: Aop_data can be zero
simplify handling of biases
write BART version and command line into created files
minor
there is no reason data must be non-null
use array notation in iter2
does not exit
minor improvements lad/lsqr
_Bool -> bool, _Complex -> complex in c file
make pocs interface more standard
minor
use boolean operator
rewrite blas/lapack interface
use openblas on mac os x, fix build testing
rewrite batch_svthresh
move
comment
use union instead of type-punning with pointer cast
update utests
Merge pull request #32 from mrirecon/lapack
cleanup nlinv
update README
use config struct for nlinv
remove useless casts
xfree, XFREE, PTR_FREE, PTR_PASS
add debug_backtrace
use simpler implementation for free checks
don't use -rdynamic on MacOSX
rewrite test for parallel make
add some missing PTR_PASS
integrate utests into main build system
add missing file
properly generate dependencies
use our own unit test macros
coding style
move and rename stuff
run tests from proper function
remove utests/README.md
rename data file
a bit simpler to use
use linker script to collect unit tests
use PTR_FREE
utests: be more optimistic
utests: be more verbose
use shell script to assemble list of unit tests
Merge pull request #37 from mrirecon/opt-reg
use variable instead of file (makes parallel make work)
add some color
remove some unnecessary includes
add initial spline code
export bernstein
missing copyright header
add casts to avoid warnings for OpenBLAS
remove unnecessary struct members
ops: fix input and output types
fix type error in nufft
missing PTR_PASS
convert more void* to iter_conf
operators: replace void pointers
operators from iter2 functios
operators for lsqr
replace README on GitHub with a link to the homepage
Merge pull request #39 from frankong/master
Merge pull request #41 from mrirecon/pattern-flags
add information for contributors
use cppwrap instead of redefined __VLA
Merge pull request #42 from sidward/master
README fixes
fix formatting, improve readability
simplify md_calc_fmac_dims to md_merge_dims, restore fmac formatting
remove duplicate option
move merge_dims to multind.c
PTR_FREE
start to document coding style
document use of debugger
rename vars.(sh|m) to startup.(sh|m)
move python/matlab scripts into subdirectories
add memory accounting and cache
refactor gpuops
PTR_PASS/PTR_FREE in fft-cuda.c
guard omp includes
improve debugging.txt
document build system
markdown compatibility
nufft: use OPT macros
track inputs + outputs
PTR_PASS
remove Mac OS X build testing for now
add float vector options
OPT macros + copyright
option formatting fix
Merge pull request #47 from timlod/master
cc: reformat options
fix writing of .hdr files
rename sf to specfun
PTR_PASS
pics: remove unneeded headers
debug_trace
convert symbols
add tracing to operators
add auto_scale option to nrmse
fix broken test
add nrmse scale test
Merge branch 'profile'
Revert "remove Mac OS X build testing for now"
add thomas algorithm
test for thomas algorithm
update MacOS X instructions (thanks to Jakob Asslaender)
copyright
renme la.[ch] to linalg.[ch]
remove deprecated function fftmodk
move INSTALL.md to doc/cmake_building.txt
Merge branch 'AllowVendorSuppliedLAPACK' (closes #53)
add optimization for md_axpy, and improve debug info
move optimize_nop to optimize.[ch]
change interface to optimize_nop
move use_gpu
optimization fixes, and improvements
use generic optimization framework for md_copy/md_clear
gpu fix
change debug level for MD time
add md_compare
unit tests for multind
utest for md_zmatmul
fix for md_circular_swap
utest for md_circular_swap
use generic optimization framework for md_swap..
GPU system tests
add test for weights
add test for weights on GPU
convoaa: don't use vecops
remove functions from vecops only needed for vec_iter
md_free takes const void* ptr
operator inferace to sense recon
initialize unknown in itop
pics: use sense_recon_create
debug output for toeplitz mode
support weights in toeplitz mode
operators: add ioflags
add axpy back to vecops
add (two) shared pointer implementations
ops/linops: refactor memory management
UNCONST
Merge pull request #56 from hjmjohnson/AddSecondStageBuild
admm: minor changes
admm: untangle history
admm: minor changes
admm: make dynamic rho independent from fast
relax test criterium
rename rvc linop_realval
improve linop API consistency (closes #64)
no automatic python test
CAST_UP/CAST_DOWN macros with run-time checking of down-casts
admm: refactor xupdate
merge biases into iter2 interface
introduce monitor object
do not use vops->dot in admm
monitor: add history call-back
monitor: make objective value and residuum accessible
admm: use monitor to record history
add missing extern
nudft
add nudft option to nufft
create default normal operator
add nudft tests
gpu reco
make existence of operator_gpu_wrapper independent from USE_CUDA
add gpu option to lsqr
new gpu mode
remove old GPU code path
lsqr: remove old GPU code path
remove use_gpu from operators
debug messages for GPU
implement lad2_create
use lad2_create in sense_recon_create
eliminate grecon and rsense
remove sense_recon
minor
lazy cufft plans
fftw measure
lazy cufft 2
change gpu initialization
non-gpu build fix
CAST_UP/CAST_DOWN
warmstart
ops: copy_wrapper
pics: add batch mode
pics: test for batch mode
missing free
fix use after free
optimize.c: change flags to long
references for ADMM
activate nested parallelism
rof: use MAKE_ARRAY
add FT as sparsity transform
Linux: add libopenblas-dev to README
do not use wavelet2
test case
make it possible to change xref in iter3
remove mac tests (fail due to timeouts)
fix warning
add delta tool
fix warning
fix use of static
test clang builds
add fmac operator
add append mode to join
add copy command
squeeze: remove singletons completely
restrict format strings and do not use sprintf
turn off nested parallelization
bump version
Siddharth Iyer (13):
Update Python wrapper + Python Readme
Minor change to citation.
Automated crop threshold
style changes
Added automate option -a
Removed fmac3 and other stylistic changes.
added a check to avoid divide by zero in soft_weight_singular_vectors
TOOLBOX_PATH check in noise estimation (#44)
covariance_function instead of calmat_svd (estvar) (#52)
Function cabs: Complex magnitude of an array (#57)
Updates to SURE + ESPIRiT (#58)
Use low-resolution maps in auto-espirit (#67)
Added auto-espirit test in ecalib.mk (#68)
timloderhose (2):
Use single precision floats + remove allocation
Format documentation and remove redundant line
-----------------------------------------------------------------------
This annotated tag includes the following new commits:
new 9485ff1 admm: coding style
new 709f416 fix const for conjgrad_hist_prealloc
new 614697a do not use md-functions in admm.c
new 5a180b6 admm: Aop_data can be zero
new b55eb38 simplify handling of biases
new d18e07b write BART version and command line into created files
new 28b5e81 minor
new 5edf51d there is no reason data must be non-null
new fce03ae use array notation in iter2
new 154033a does not exit
new 4ec1f39 minor improvements lad/lsqr
new cb86058 _Bool -> bool, _Complex -> complex in c file
new 540a1cf make pocs interface more standard
new 22d67f4 minor
new 7ce7ad0 use boolean operator
new be8da6b rewrite blas/lapack interface
new d60fd05 use openblas on mac os x, fix build testing
new 0e1f04a rewrite batch_svthresh
new 9d1f129 move
new 1cb877c comment
new 0397161 use union instead of type-punning with pointer cast
new 215cfab update utests
new cd4121b Merge pull request #32 from mrirecon/lapack
new ea4bb61 cleanup nlinv
new c30300c update README
new 48535be use config struct for nlinv
new 1cc6a39 remove useless casts
new 7768a2d xfree, XFREE, PTR_FREE, PTR_PASS
new 19f62e6 add debug_backtrace
new 4abd7f0 use simpler implementation for free checks
new 776a892 don't use -rdynamic on MacOSX
new 891015d rewrite test for parallel make
new f50100b add some missing PTR_PASS
new 4202e52 integrate utests into main build system
new 7dbbf74 add missing file
new c06cb49 properly generate dependencies
new cf14772 use our own unit test macros
new 3867aac coding style
new 08a88f6 move and rename stuff
new d37d17c run tests from proper function
new fa232e4 remove utests/README.md
new 24ad803 rename data file
new 6c568c8 a bit simpler to use
new 7016e2d use linker script to collect unit tests
new 6deae8e use PTR_FREE
new 2e7698a utests: be more optimistic
new 1cc3c4a lowrank: fix call to csyrk
new 2fc608c update copyright
new 799bc31 utests: be more verbose
new c4f51a0 use shell script to assemble list of unit tests
new c153753 test on osx
new e33252c move regularization options to separate file
new fa25625 travis: run tests on mac build
new 0179313 Merge pull request #37 from mrirecon/opt-reg
new 31cbeea use variable instead of file (makes parallel make work)
new cdbf667 Merge pull request #38 from mrirecon/utests2
new 3aeeb27 add some color
new 99d360f remove some unnecessary includes
new 8ba25e1 add initial spline code
new 2a754fe export bernstein
new 1b16540 missing copyright header
new 1775d73 add casts to avoid warnings for OpenBLAS
new c4bfb84 remove unnecessary struct members
new e6ddf55 ops: fix input and output types
new d3b49b0 fix type error in nufft
new 0954a7e missing PTR_PASS
new 3880365 convert more void* to iter_conf
new eca407c operators: replace void pointers
new 68f8ec8 operators from iter2 functios
new ea57e19 operators for lsqr
new c807a5a replace README on GitHub with a link to the homepage
new 28b74a4 fix openblas with macports
new 0c0ebd7 Merge pull request #39 from frankong/master
new f25d152 test frank's homebrew install
new a5b7cce make estimate_pattern_flags function
new a73f046 pattern: use estimate_pattern_flags
new 655a66e estimate_pattern now takes flags as input
new b4be5e4 unit tests for estimate_pattern
new 88ee403 Merge pull request #41 from mrirecon/pattern-flags
new 978ac93 travis: add numpy/scipy and remove homebrew test (moved to separate repo)
new 60d049d add test for python read/writecfl
new 92f4e31 Update Python wrapper + Python Readme
new f8d32ab Minor change to citation.
new 54e09a4 Automated crop threshold
new 812b298 add information for contributors
new af991df use cppwrap instead of redefined __VLA
new f6950cb style changes
new 9e8a95f Added automate option -a
new cdf8f20 Removed fmac3 and other stylistic changes.
new 8da691e Merge pull request #42 from sidward/master
new 694f2b0 README fixes
new 56e3f08 fix formatting, improve readability
new fb30579 simplify md_calc_fmac_dims to md_merge_dims, restore fmac formatting
new 7c5a563 remove duplicate option
new 91f5922 move merge_dims to multind.c
new 68179fc PTR_FREE
new 8b21783 added a check to avoid divide by zero in soft_weight_singular_vectors
new cad4e7d TOOLBOX_PATH check in noise estimation (#44)
new f1ddd3f start to document coding style
new bfe4571 document use of debugger
new 321ac2f rename vars.(sh|m) to startup.(sh|m)
new 242bdf7 move python/matlab scripts into subdirectories
new eee4314 add memory accounting and cache
new 2977434 refactor gpuops
new 9ede8e8 PTR_PASS/PTR_FREE in fft-cuda.c
new a84e70e guard omp includes
new 94ba8d3 improve debugging.txt
new c2ca95e document build system
new 35f1df2 markdown compatibility
new e713263 nufft: use OPT macros
new b816b6b track inputs + outputs
new 38046e0 PTR_PASS
new 263c2d7 remove Mac OS X build testing for now
new 21bcac5 add float vector options
new e7125f2 OPT macros + copyright
new 19a5dd2 option formatting fix
new a7bf8c0 Use single precision floats + remove allocation
new 0152fd7 Format documentation and remove redundant line
new 69fe7df Merge pull request #47 from timlod/master
new f092ea7 add test for join tool
new 6865c4f simplify md_zwavg
new e4794e5 cc: reformat options
new 1cedc3f add num_init() call to standalone tools (#48)
new 938d6af fix writing of .hdr files
new ed004f9 Revert "simplify md_zwavg"
new e242a59 add proper test arrays with 0 entries
new e338569 rename wavg to avg, add md_zavg, add test for unweighted avg
new 538caec rename sf to specfun
new b8804d1 PTR_PASS
new 6b311e3 replace usr with for macports install
new 9ff5a49 pics: remove unneeded headers
new 1290da4 debug_trace
new 169e355 convert symbols
new b613140 add tracing to operators
new 0d17b10 add auto_scale option to nrmse
new 395cb7e fix broken test
new a1cba19 add nrmse scale test
new 1e56230 covariance_function instead of calmat_svd (estvar) (#52)
new 49294e1 ENH: Add initial cmake build script (#51)
new 7b6b170 Merge branch 'profile'
new be6712a Revert "remove Mac OS X build testing for now"
new d870142 mip: don't do abs by default
new d8a7262 ENH: Add a robust FindOpenBLAS.cmake file
new 0f97c3e ENH: Add a robust FindLAPACKE.cmake file
new 929a850 ENH: Add a robust FindATLAS.cmake file
new 55bc91d ENH: Provide support to build against vendor supplied lapack implementations
new 9cd88a7 add thomas algorithm
new 89add9c test for thomas algorithm
new 945a6b4 SQPE FindAtlas fixes.
new bca8caf SQME findATLAST
new 49cdd43 SQME FindOpenBLAS
new 4dddd83 update MacOS X instructions (thanks to Jakob Asslaender)
new 53c401d copyright
new dccb9c2 renme la.[ch] to linalg.[ch]
new d585228 ENH: Improved lapack, ATLAS, and OpenBLAS support
new 5869476 ENH: Improve C99 compiler identification
new dfed1c6 DOC: Provide some documentation for building BART
new 9c4b28f add invert tool
new 60de19b remove extra assert header
new 19f44df remove deprecated function fftmodk
new 11b493a move INSTALL.md to doc/cmake_building.txt
new 459a0ea Merge branch 'AllowVendorSuppliedLAPACK' (closes #53)
new 7fad141 mip: fix bug with abs option
new 1470bc7 add optimization for md_axpy, and improve debug info
new 4136889 move optimize_nop to optimize.[ch]
new 02c800e change interface to optimize_nop
new 6c36759 move use_gpu
new ba969f2 optimization fixes, and improvements
new 6345058 use generic optimization framework for md_copy/md_clear
new 2fae325 gpu fix
new 2799ab8 change debug level for MD time
new 7c9079a add md_compare
new 80e517e unit tests for multind
new b5bac88 utest for md_zmatmul
new 774d9f1 fix for md_circular_swap
new 46b5fef utest for md_circular_swap
new 4894085 use generic optimization framework for md_swap..
new e36911d GPU system tests
new 771ee48 add test for weights
new fecf892 add test for weights on GPU
new bd48afe README: minor
new 3a8b80b convoaa: don't use vecops
new a3c8ce2 remove functions from vecops only needed for vec_iter
new 7cec7e3 md_free takes const void* ptr
new 855243a operator inferace to sense recon
new 58d926d initialize unknown in itop
new fd9dab9 pics: use sense_recon_create
new 4d28f82 debug output for toeplitz mode
new 8d23009 support weights in toeplitz mode
new d35d104 operators: add ioflags
new b0e1ded add axpy back to vecops
new 19e9c8e add (two) shared pointer implementations
new 12fca9e ops/linops: refactor memory management
new d238302 UNCONST
new f80beb5 COMP: Depend on Fortran if LINALG_VENDOR="LAPACKE"
new c880754 COMP: Add Stage 2 build for bart binaries
new 0ff121c STYLE: Sanity check that misc/cppmap.h is not needed
new 33ae164 COMP: Ease syncronization of Makefile & CMake
new 2fad338 ENH: Added optional matlab dependant functions
new 1f24aef ENH: Implement ISMRMRD support for reconstructions
new fb0dc23 ENH: Allow building of tarballs from CMakeLists.txt.
new ac7ac06 COMP: Add ability to generate doxygen files.
new 13d233c COMP: Add custom target for building bart.syms file in cmake.
new b929657 COMP: Add installation rules for bart.
new 26ba655 ENH: Add ability to automatically generate doc/commands.txt
new 8f801bd Merge pull request #56 from hjmjohnson/AddSecondStageBuild
new bbabf55 Function cabs: Complex magnitude of an array (#57)
new 61d5f51 Updates to SURE + ESPIRiT (#58)
new 81ced10 DOC: Add some documentation for common failure case
new ecc862b COMP: Fix linker dependancies
new bad5670 fix macports openblas library warning
new 79fa31e admm: minor changes
new 224049e admm: untangle history
new 46ee1ea admm: minor changes
new 2e1ad40 admm: make dynamic rho independent from fast
new 0db6ae9 relax test criterium
new 5c3dccf reshape: fix printf
new 14631ff rename rvc linop_realval
new c4e4b26 improve linop API consistency (closes #64)
new 1d1615d no automatic python test
new 145df11 CAST_UP/CAST_DOWN macros with run-time checking of down-casts
new c63646b admm: refactor xupdate
new 4a0d602 merge biases into iter2 interface
new 5819b80 introduce monitor object
new 003c76d do not use vops->dot in admm
new 1ad6cb9 monitor: add history call-back
new 813338d monitor: make objective value and residuum accessible
new eb9140f admm: use monitor to record history
new d2a55d0 add missing extern
new 243111c nudft
new ef5ea20 add nudft option to nufft
new a1f1e24 create default normal operator
new ed85936 add nudft tests
new 78e998d twixread: change debug level and show -A in help
new c41fc6b admm: fix calculation of s norm (broken in 79fa31eb)
new 27ed3f3 admm: make conjgrad tolerance configurable
new 95fe8bb missing SET_TYPEID
new a7e6ba3 gpu reco
new 627331c make existence of operator_gpu_wrapper independent from USE_CUDA
new a6ac444 add gpu option to lsqr
new 4ce20ba new gpu mode
new d6dbfd0 remove old GPU code path
new f02e74a lsqr: remove old GPU code path
new acf2b86 remove use_gpu from operators
new c13357c debug messages for GPU
new 1ffa3cd implement lad2_create
new e38458e use lad2_create in sense_recon_create
new 54d2530 eliminate grecon and rsense
new 96502a7 remove sense_recon
new 700ffc1 minor
new 1de0021 lazy cufft plans
new 51a8a88 fftw measure
new 42d669d lazy cufft 2
new ca37bdd change gpu initialization
new e535b49 non-gpu build fix
new e8d4c5d CAST_UP/CAST_DOWN
new c4c5b25 warmstart
new 7ee29a2 ops: copy_wrapper
new 128cb70 pics: add batch mode
new 54d75eb pics: test for batch mode
new 912db9d missing free
new 829bb0c fix use after free
new d3aa658 optimize.c: change flags to long
new 10f0524 references for ADMM
new 797e6f5 Use low-resolution maps in auto-espirit (#67)
new 4fbfaa8 Added auto-espirit test in ecalib.mk (#68)
new 553953a add tool zexpj for complex exponential
new 6660991 don't re-init cuplan every time (#69)
new fde9a66 activate nested parallelism
new 1d240a1 rof: use MAKE_ARRAY
new 1e25d55 add FT as sparsity transform
new 0c30913 Linux: add libopenblas-dev to README
new d69a026 do not use wavelet2
new 6f0267e test case
new f587a7e make it possible to change xref in iter3
new 6c62fad remove mac tests (fail due to timeouts)
new eb435aa change fftw to use 64-bit interface
new af6b01d fix warning
new b53d15b add delta tool
new a191376 fix warning
new 2fcc7ae fix use of static
new b2b764b test clang builds
new 98f5618 add fmac operator
new 27be58a add squeeze tool
new 62989df don't hide some options
new e288a6f threshold: add hard threshold option
new 9b60892 add flatten tool
new d7ed8ad add call to num_init()
new ec6696b indents
new 9c56515 fmac tool: if only two args are specified then squash-and-sum <input1>
new ad2f7b7 show tool: option to use custom number formatting
new 7725ec2 make custom Makefiles dir and README for explanation (#73)
new ea576e2 add phase cycling for nufft (#71)
new c06e2ae add option to specify random seed in poisson (#74)
new 5862f64 add append mode to join
new 81e7ed6 add copy command
new 1547e55 squeeze: remove singletons completely
new e3e5798 restrict format strings and do not use sprintf
new bbca3dc turn off nested parallelization
new f236631 bump version
The 300 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.
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