[med-svn] [Git][med-team/bart][master] 129 commits: some more memory leaks
Martin Uecker
gitlab at salsa.debian.org
Tue Aug 27 14:16:58 BST 2019
Martin Uecker pushed to branch master at Debian Med / bart
Commits:
66711cc7 by Martin Uecker at 2018-12-11T08:45:43Z
some more memory leaks
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a51a137f by Martin Uecker at 2018-12-11T08:45:43Z
fix bart script
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4d835a66 by Martin Uecker at 2018-12-11T08:45:43Z
relax unit test
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c4e9c535 by Jon Tamir at 2019-01-07T13:19:12Z
replace deprecated cudaThread functions
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f95d4abc by Martin Uecker at 2019-01-13T12:20:35Z
convolution based on tenmul
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624115fc by Siddharth Iyer at 2019-01-15T17:40:28Z
Edit help string for wave.c
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5ffb8969 by Martin Uecker at 2019-01-17T13:52:54Z
GPU performance workaround for md_zaxpy
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692d7fcd by Jon Tamir at 2019-01-17T19:11:52Z
pics: add back comparison to image_truth
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1d254dfd by Martin Uecker at 2019-01-19T17:39:41Z
vector operation: zsum
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e8872413 by Martin Uecker at 2019-01-19T17:39:41Z
accelerate md_zscalar2 on the GPU
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97d2ec70 by Martin Uecker at 2019-01-19T17:39:41Z
allow enlive on the gpu
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dca1cd4c by Yuxin Hu at 2019-03-12T08:10:30Z
fix the issue that 'warm_start' won't be used if pics.c uses ADMM (#187)
* propagate warmstart flag to ADMM
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e9bb015f by Siddharth Iyer at 2019-03-12T17:39:08Z
Decompose Complex LinOp
Add `decompose_complex` as a linear operator so as to allow locally-low rank across
the real-imaginary dimension for calibration-less partial Fourier.
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ae1ee620 by Siddharth Iyer at 2019-03-12T17:39:08Z
Add decompose_complex to wave and wshfl
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41aa9b3d by Martin Uecker at 2019-03-15T18:20:27Z
fix crop == 0. case
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e2f17ca6 by Martin Uecker at 2019-03-15T20:56:34Z
add missing typeid
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926d6ab8 by Martin Uecker at 2019-03-15T20:56:51Z
fix sum operator
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eab6eb26 by Martin Uecker at 2019-03-15T20:57:01Z
fix input
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5ea666ba by Martin Uecker at 2019-03-15T21:05:45Z
low-rank + sparse test
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0852d09b by Martin Uecker at 2019-03-16T22:00:59Z
style
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266ebd7d by Martin Uecker at 2019-03-16T22:08:36Z
check ring centering constraint
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ac48b2dd by Martin Uecker at 2019-03-16T23:35:28Z
estdelay tests
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de165122 by Martin Uecker at 2019-03-17T07:26:38Z
add missing scale precondition
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0661fe9b by jschoormans at 2019-03-18T18:20:42Z
small golden angles (#190)
* small golden angles
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3fcf576a by Martin Uecker at 2019-03-22T16:35:46Z
twixread mode for radials
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f5ea37a3 by Martin Uecker at 2019-03-22T16:37:48Z
twixread: add option for multi-slice MPI data
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3c253fd2 by Martin Uecker at 2019-03-22T17:01:18Z
option to rotate trajectory
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c7a1d8ec by Martin Uecker at 2019-03-22T17:04:02Z
style issues
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3eb9f82f by Christian Holme at 2019-03-24T12:54:56Z
scripts/grash.sh: update script to new extract
current versions of bart extract exclude the end index.
This commit updates the script to be compatible with
newer versions of bart.
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61b6cb31 by Martin Uecker at 2019-03-24T18:44:57Z
check compatibility of trajectory
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d27234ca by Martin Uecker at 2019-03-24T18:44:57Z
median fix and tests
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e08f7488 by Martin Uecker at 2019-03-24T18:44:57Z
improve gridding code
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47fce6bb by Martin Uecker at 2019-03-24T19:27:22Z
check for beta
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29152e8e by Martin Uecker at 2019-04-01T08:28:19Z
dicom export fix
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c869a183 by Martin Uecker at 2019-04-01T08:33:12Z
delete residual temporary test files
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f622823f by Martin Uecker at 2019-04-01T10:04:36Z
read multi-raid files
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95bad642 by Martin Uecker at 2019-04-03T20:04:11Z
style
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0aa68e75 by Martin Uecker at 2019-04-23T10:01:42Z
add .._chain_FF set of functions
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94aaa3ed by Martin Uecker at 2019-04-23T10:01:42Z
rotations using ffts
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b7e4e75b by Martin Uecker at 2019-04-23T10:01:42Z
iter4_irgnm: check operator type
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039fb072 by Martin Uecker at 2019-04-23T10:01:42Z
add test for transverse delays
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24d65bc7 by Martin Uecker at 2019-04-26T10:24:09Z
cc: warn if calibration region is empty.
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827c18e3 by Martin Uecker at 2019-04-30T06:43:49Z
add noexec-stack hack
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97256c83 by Martin Uecker at 2019-04-30T20:00:50Z
add missing NESTED_CALL (thanks to Simon Yeung)
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41b867fc by Martin Uecker at 2019-04-30T20:10:44Z
NOEXEC_FLAG: makefile and README
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25f517aa by Siddharth Iyer at 2019-05-01T06:56:42Z
changed kern_adj in wshfl to be faster (#191)
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e1cf25fb by Jon Tamir at 2019-05-01T06:57:00Z
fix missing isnanf for Mac (#192)
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b83d8507 by aTrotier at 2019-05-06T13:54:56Z
Add custom angle to traj (#193)
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e9ef4036 by Christian Holme at 2019-05-30T18:02:07Z
src/slice.c: extend to allow multiple dims and pos
Similar to resize, slice now accepts an arbitrary number of dims and
positions.
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b4400c69 by Christian Holme at 2019-05-30T18:02:07Z
add test for new multidimensional slice
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824129b0 by Christian Holme at 2019-06-04T15:44:29Z
src/extract.c: update to new #ifndef's
all other tools use this construction with #ifndef,
so extract should, too
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7344fb69 by Christian Holme at 2019-06-04T15:44:29Z
src/extract.c: add test and extend to multiple dims
Similar to resize and slice, extract now accepts an
arbitrary number of dims and positions (starts and ends).
Additionally, there are now tests for the old and new behavior of
extract
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9a74a8bb by Martin Uecker at 2019-06-13T18:28:05Z
automatic rebuilds for makefile changes
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a720b50f by Siddharth Iyer at 2019-06-14T09:06:00Z
calloc -> alloc_sameplace in kern_adj
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6957d45f by Siddharth Iyer at 2019-06-14T09:06:00Z
Search for crop threshold in sure-espirit.
- Implemented a bisection-like search for sure-ecalib.
- This avoids the need to search a grid of crop values.
- Fix: Cast to floats for div and mse in sure_crop.
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90b7fcef by Siddharth Iyer at 2019-06-18T05:47:46Z
fix: Missing clears added to sure_calib
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db13c86a by rosenzweig at 2019-06-18T12:42:20Z
pics: SMS bugfix
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4d6bc064 by rosenzweig at 2019-06-18T12:42:20Z
pics: Allow toeplitz for sms
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465c9045 by rosenzweig at 2019-06-18T12:42:20Z
pics: Allow pattern for non-Cartesian trajectories
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b7b322c8 by rosenzweig at 2019-06-18T12:42:20Z
pics, noncart/nufft: Efficient basis function implementation
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1252b6dd by rosenzweig at 2019-06-18T12:42:20Z
tests: Test memory efficient basis approach
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ec434c7a by Martin Uecker at 2019-06-24T19:22:12Z
fix warning
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34aaeb88 by Martin Uecker at 2019-06-24T19:30:40Z
new trampoline code for GCC >= 10
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fa531930 by rosenzweig at 2019-06-25T12:07:08Z
misc/opts: vec2 options
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d4e6e2e3 by rosenzweig at 2019-06-25T18:32:04Z
rewrite traj tool
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e2086900 by Martin Uecker at 2019-06-30T18:53:56Z
nufft: style and minor changes
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2a949a79 by xwang at 2019-07-08T18:18:38Z
add zsmax functions for cpu and gpu
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b70b41e4 by Martin Uecker at 2019-07-08T18:19:01Z
fix prerequesites for some test cases
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a123293b by Martin Uecker at 2019-07-08T18:19:51Z
shared_obj_unref wich does not delete
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50e3e290 by Martin Uecker at 2019-07-08T18:51:19Z
remove unnecessary CMPLX
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f54e2055 by Martin Uecker at 2019-07-14T19:01:43Z
update operator framework
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a3f80ba9 by Martin Uecker at 2019-07-14T19:03:24Z
mat_pinv
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d8f0f496 by Martin Uecker at 2019-07-14T19:03:24Z
mat_pinv utest
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ec3e71dc by Martin Uecker at 2019-07-14T19:07:40Z
sync some files with internal version
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817802f6 by Martin Uecker at 2019-07-14T19:22:23Z
sync all linops to internal version
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fec3d935 by Martin Uecker at 2019-07-14T19:29:17Z
change TYPES macros
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60bb07d3 by Martin Uecker at 2019-07-14T19:29:17Z
top-level regularization parameter
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00222a19 by Martin Uecker at 2019-07-14T19:29:17Z
itop_p_create
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f5b4359a by Martin Uecker at 2019-07-14T19:29:18Z
lsqr/lad return operator_p
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1c48f326 by Martin Uecker at 2019-07-14T19:38:44Z
unit tests for operators
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537520a7 by Martin Uecker at 2019-07-14T20:42:45Z
fix ubsan error
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cee9c2e0 by Martin Uecker at 2019-07-14T20:44:05Z
temporarily deactivate tests on clang
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1a0bc8bb by Siddharth Iyer at 2019-07-15T09:58:46Z
Change complicated bisection-like search to a simpler line search in sure_crop
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5b893e54 by Siddharth Iyer at 2019-07-15T09:58:46Z
Stricter auto-espirit test
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ac1ea4a1 by Martin Uecker at 2019-07-16T18:44:53Z
update coil simulation
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30dc3b09 by Martin Uecker at 2019-07-16T18:44:53Z
fix whitening bug
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aca6f78c by Martin Uecker at 2019-07-16T19:56:26Z
tgv denoiser
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b4bd20f1 by Siddharth Iyer at 2019-07-16T19:58:54Z
Rename Xlinop_reshape to linop_wavereshape
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1dc2cc28 by Siddharth Iyer at 2019-07-16T19:58:54Z
Modify wshfl to apply ESPIRiT coil by coil.
This should allow for the GPU to be used per channel.
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b479b804 by Siddharth Iyer at 2019-07-16T19:58:54Z
Minor formatting change for printdims in wshfl
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edd0df3b by Siddharth Iyer at 2019-07-18T15:09:40Z
Change complicated spacing to simple printf
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5b15d50f by Siddharth Iyer at 2019-07-18T15:09:40Z
bug fix: missed typed dims for multi-set espirit map case
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7f1dd815 by Siddharth Iyer at 2019-07-18T15:09:40Z
formatting
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38734385 by Martin Uecker at 2019-07-22T07:23:50Z
refactor compute_kern
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7cd3dfb3 by Martin Uecker at 2019-07-22T07:23:50Z
guard dims manipulation by check for basis
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8705289e by Martin Uecker at 2019-07-22T22:44:53Z
make it possible to run individual tests
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e5c12b3a by Siddharth Iyer at 2019-07-22T22:56:53Z
Move noise calreg to md_calloc for 3D estvar
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f86441b7 by Siddharth Iyer at 2019-07-22T22:56:53Z
Formatting changes to estvar.c
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88d584ba by Martin Uecker at 2019-07-27T13:18:58Z
fix CUDA strided memcpy
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1ce3ed79 by Martin Uecker at 2019-07-27T13:19:12Z
update md functions
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de4c1bfb by Martin Uecker at 2019-07-27T13:22:50Z
types.h more self-sustaining
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57ac07ef by Martin Uecker at 2019-07-27T13:52:58Z
update iterative algorithms and nonlinear inversion
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d720f40e by Martin Uecker at 2019-07-27T14:01:36Z
document gfortran dependency
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02afdecd by Martin Uecker at 2019-08-09T19:51:44Z
function for setting random initial state in wavthresh
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f7671445 by Martin Uecker at 2019-08-09T19:53:25Z
iter3: add step config variable
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9bf7ec1c by Martin Uecker at 2019-08-09T20:27:04Z
model-based reconstruction for look-locker experiments
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1fc89d24 by Martin Uecker at 2019-08-16T12:22:30Z
use long for index in gridding code
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03e4559f by Martin Uecker at 2019-08-19T21:37:34Z
rewrite memory-efficient basis
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f32b2342 by Martin Uecker at 2019-08-19T21:37:34Z
reduce memory
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4b75a0cc by Martin Uecker at 2019-08-19T21:37:34Z
minor fixes
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b4421ea6 by Martin Uecker at 2019-08-19T21:37:34Z
automatic choice
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6edc7b13 by Martin Uecker at 2019-08-19T21:37:34Z
fix bug in basis approach, add test, change debug output
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921931ed by Martin Uecker at 2019-08-19T21:37:34Z
use low-mem flag for basis computation
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665f6f14 by Martin Uecker at 2019-08-19T21:37:34Z
low-mem flag for pics
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9c572fd7 by Martin Uecker at 2019-08-19T22:28:55Z
use low-mem in test
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d0e66487 by Martin Uecker at 2019-08-20T06:12:33Z
update and reorganize references
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a201218d by Martin Uecker at 2019-08-22T13:04:13Z
model-based change parameter
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8ade579b by Martin Uecker at 2019-08-22T13:04:17Z
look locker post-processing
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6380e593 by Martin Uecker at 2019-08-22T13:07:05Z
license year
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f7f9ba35 by Siddharth Iyer at 2019-08-23T12:07:19Z
Allow multi-coeff wave psf
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807ac4b2 by Siddharth Iyer at 2019-08-23T12:07:19Z
Reorder nrmse command in wshfl.mk
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3e84c221 by Martin Uecker at 2019-08-25T06:04:27Z
join: append to non-existing file
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26225a60 by Martin Uecker at 2019-08-25T06:04:27Z
generalize cuda fft a bit
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5efc0a95 by Martin Uecker at 2019-08-25T11:21:21Z
bump version
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3f8d82ca by Martin Uecker at 2019-08-27T12:41:29Z
Merge tag 'v0.5.00'
version 0.5.00
Changes:
- new tools: moba, looklocker, tgv, extract, fftrot
- moba: non-linear model-based recon for T1 mapping (Xiaoqing Wang)
- looklocker: post-processing for moba
- extract: extract ranges from multi-dim. arrays
- tgv: a tgv denoiser
- fftrot: perform rotations using FFTs
- join: append to non-existing file
- pics: low-mem flag (-U)
- pics: efficient basis functions (Sebastian Rosenzweig)
- pics: pattern for non-Cartesian trajectories
- nlinv: enlive on the gpu
- twixread: read multi-raid files
- twixread: mode for radial
- traj: custom angle to traj (Aurélien Trotier)
- traj: small golden angles (Jasper Schoormans)
- traj: option to rotate trajectory
- extract: multiple dims (Christian Holme)
- slice: multiple dims (Christian Holme)
- generic: NOEXEC_FLAG flag for non-executable stacks
- generic: automatic rebuilds for makefile changes
- generic: make it possible to run individual tests
- library: use long in gridding code to support larger grids
- library: zsmax functions for cpu and gpu
- library: function for setting random initial state in wavthresh
- library: lsqr/lad return operator_p to select regularization
- library: generalize cuda fft a bit for efficiency
- library: fix for CUDA strided memcpy
- many other bug fixes and improvements
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1743c80a by Martin Uecker at 2019-08-27T12:41:52Z
update patches
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f7945afc by Martin Uecker at 2019-08-27T12:41:53Z
update copyright
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4ff792d5 by Martin Uecker at 2019-08-27T12:41:53Z
update changelog
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f2a05958 by Martin Uecker at 2019-08-27T13:11:01Z
Standards-Version: 4.4.0
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30 changed files:
- .travis.yml
- LICENSE
- Makefile
- README
- build_targets.mk
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/0004-makefile-change-for-compatibility-with-debian.patch → debian/patches/0001-makefile-change-for-compatibility-with-debian.patch
- − debian/patches/0001-some-more-memory-leaks.patch
- − debian/patches/0002-fix-bart-script.patch
- debian/patches/0005-remove-empty-directory.patch → debian/patches/0002-remove-empty-directory.patch
- debian/patches/0006-deactivate-ode-unit-tests.patch → debian/patches/0003-deactivate-ode-unit-tests.patch
- − debian/patches/0003-relax-unit-test.patch
- debian/patches/series
- + doc/applications.txt
- doc/references.txt
- matlab/bart.m
- + rules/moba.mk
- rules/num.mk
- scripts/grasp.sh
- src/bench.c
- src/calib/calib.c
- src/calib/calibcu.cu
- src/calib/estvar.c
- src/cc.c
- src/dfwavelet/dfwavelet_kernels.cu
- src/dfwavelet/prox_dfwavelet.c
- src/ecalib.c
- src/estdelay.c
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/bart/compare/3bc0e34e05dfe7225b30794d8121c52c7241e9c2...f2a05958f2d68b23897a8bd5a6b5227a0f91e715
--
View it on GitLab: https://salsa.debian.org/med-team/bart/compare/3bc0e34e05dfe7225b30794d8121c52c7241e9c2...f2a05958f2d68b23897a8bd5a6b5227a0f91e715
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