[med-svn] [Git][med-team/bart][master] 687 commits: Fix versioning
Martin Uecker (@uecker-guest)
gitlab at salsa.debian.org
Sun Sep 25 12:59:36 BST 2022
Martin Uecker pushed to branch master at Debian Med / bart
Commits:
0973af65 by Philip Schaten at 2021-03-12T07:28:36+01:00
Fix versioning
- correctly sorting main releases
- follow fedora versioning guidelines
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9fe5b6e4 by Philip Schaten at 2021-03-12T07:28:36+01:00
bart for centos 7
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d1799fab by Martin Uecker at 2021-03-24T11:02:39+01:00
quicksort with nested functions
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0585ffe6 by Martin Uecker at 2021-03-24T11:02:39+01:00
minor
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2de61b24 by Martin Uecker at 2021-03-25T12:15:23+01:00
clang workarounds
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2d067289 by Martin Uecker at 2021-03-25T12:15:50+01:00
relax test for clang
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b4057a81 by Martin Uecker at 2021-03-25T15:44:37+01:00
add ubsan option
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7825df89 by Martin Uecker at 2021-03-25T21:24:19+01:00
make more variables signed
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e5ce9fa7 by Moritz Blumenthal at 2021-04-07T14:08:10+02:00
Update vecops
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522bd1d9 by Moritz Blumenthal at 2021-04-07T14:08:50+02:00
Add hyperbolic functions
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b1619570 by Moritz Blumenthal at 2021-04-07T14:12:33+02:00
More efficient use of memcache
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5c4bd6ff by Moritz Blumenthal at 2021-04-07T14:27:22+02:00
Add name string to types
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63f389cf by Martin Uecker at 2021-04-07T14:38:47+02:00
allow additional ones in dims for ra files
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be1a35cd by Moritz Blumenthal at 2021-04-07T14:40:06+02:00
Reduce calls of cuda_ondevice
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ebd83ff4 by Moritz Blumenthal at 2021-04-07T14:42:28+02:00
reduce memory for linop_fftc
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0cd2274e by Martin Uecker at 2021-04-08T20:36:15+02:00
fix compilation errors
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1b142f6a by Martin Uecker at 2021-04-08T21:26:36+02:00
POSIX shared memory files
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0a80ffe7 by aTrotier at 2021-04-08T21:43:50+02:00
traj test default vs custom angles
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1d7ab0b0 by Moritz Blumenthal at 2021-04-12T09:55:36+02:00
Add test for comparing cpu with gpu
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08fbb520 by Martin Uecker at 2021-04-12T10:14:29+02:00
simplify test
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5bc24606 by Martin Uecker at 2021-04-12T21:38:30+02:00
support Data flag and stdin
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7d0fa021 by Martin Uecker at 2021-04-12T21:38:30+02:00
make reading from pipe robust
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8ed4fab7 by Martin Uecker at 2021-04-12T21:38:30+02:00
support writing pipe files & delete read pipe files
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c1a47f01 by Martin Uecker at 2021-04-12T21:38:30+02:00
protect against multiple io from pipe
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eb0a3a1b by Martin Uecker at 2021-04-12T21:55:26+02:00
remove old mem cfl framework
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2b6f82d5 by Martin Uecker at 2021-04-12T23:43:33+02:00
add new memcfl framework
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644f71e9 by Martin Uecker at 2021-04-12T23:58:53+02:00
refactor and use mkstemp for temp file
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1922723b by Volkert Roeloffs at 2021-04-14T13:37:52+02:00
add initial framework to do Cramér-Rao bound analysis
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8053fea2 by Volkert Roeloffs at 2021-04-14T13:37:52+02:00
epg command with utest
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eb947323 by Volkert Roeloffs at 2021-04-14T13:37:52+02:00
ADD bSSFP sequence and change M_ini to -M_0 for FLASH
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36875671 by Volkert Roeloffs at 2021-04-14T13:37:52+02:00
ADD more details in help strings
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78aa1c47 by Martin Uecker at 2021-04-14T13:37:52+02:00
coding style
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6d6c0df9 by Martin Uecker at 2021-04-14T13:37:52+02:00
coding style
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2b6a234f by Martin Uecker at 2021-04-15T00:05:16+02:00
fix test
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95dc57fc by Martin Uecker at 2021-04-15T09:25:06+02:00
C++ compilation fix
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ebca599a by Christian Holme at 2021-04-22T11:35:26+02:00
noir/model.c: fix pattern_for_each_coil
fix linop_fmac for a pattern which is different in each coil
and add a test for pattern_for_each_coil using vcc.
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d698e01f by Martin Uecker at 2021-04-22T13:17:00+02:00
add unmap_raw
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eaa37dda by Martin Uecker at 2021-04-22T13:17:00+02:00
add const
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9b542cfc by Martin Uecker at 2021-04-22T13:17:00+02:00
and md_ random functions
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23edfa4a by Martin Uecker at 2021-04-22T13:17:00+02:00
nlop reshape function
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b533cb36 by Martin Uecker at 2021-04-22T13:17:00+02:00
linear operators and padding operator
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2c237371 by Martin Uecker at 2021-04-22T13:17:00+02:00
update copyright year
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45f8c5a5 by Martin Uecker at 2021-04-25T16:33:29+02:00
sum: free dimensions and strides
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a4ac6608 by Martin Uecker at 2021-04-25T16:33:45+02:00
avoid out-of-bounds read
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d744c850 by Martin Uecker at 2021-04-25T16:34:32+02:00
avoid leaks in moba regularizations
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22cd040a by Martin Uecker at 2021-04-25T16:34:54+02:00
avoid leak of io_flags
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9f339b4c by Martin Uecker at 2021-04-25T16:36:07+02:00
free things in main (for easier debugging)
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21a10de8 by Martin Uecker at 2021-04-25T16:36:42+02:00
free things in utests (for easier debugging)
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3f76f2f4 by Christian Holme at 2021-04-26T15:52:15+02:00
make cuda lib directory configurable
This is necessary e.g. for Google colab, where CUDA lives in lib64/
instead of lib/
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a60dfe4e by Martin Uecker at 2021-04-28T10:10:01+02:00
makefile support for tensorflow
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13042d3a by Martin Uecker at 2021-04-28T10:10:01+02:00
add tensorflow build test
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899e8dd2 by Martin Uecker at 2021-04-28T10:10:01+02:00
document build
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babb3ff7 by Martin Uecker at 2021-05-02T23:22:37+02:00
tensor flow wrapper
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3c3eda9d by Christian Holme at 2021-05-03T17:06:07+02:00
epg.c: use logical-or instead of bitwise-or
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078434e5 by Tamás Hakkel at 2021-05-05T22:12:38+02:00
add memcfl_register
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4f2a7416 by Tamás Hakkel at 2021-05-05T22:12:38+02:00
test added for memcfl_register
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a697c3b0 by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.h: remove unused macro OPTL_CFLOAT
This was added by accident in commit 1f99a8718
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ca6ff6e6 by Christian Holme at 2021-05-07T12:32:13+02:00
option handling: add option type enum
Instead of having a pointer to the conversion function, we now include
the option type (as an enum specified in misc/opts.h) in the struct
opt_s. This has the following benefits:
* It will enable a clearer interface description, by e.g.
allowing us to specify which string arguments are filenames and if they
are for input or output
* It will allow checking if the file arguments are used
correctly
Furthermore, this commit now specifies what is special about
OPT_SPECIAL: From now on, OPT_SPECIAL means that the conversion function
pointer is specified in the struct opt_s, for alle other arguments that
function pointer is NULL.
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5602f0cf by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.c: change usage string for vector arguments
We now show the specific way we want to specifiy the arguments in vec2
and vec3.
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5c861d66 by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.c: move length check for long options
This check should really be done in the loop, as otherwise we might
write beyond the end of the longopts array
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a4be2f19 by Christian Holme at 2021-05-07T12:32:13+02:00
remove mini_cmdline_bool
mini_cmdline_bool just introduces undocumented options, something we
want to avoid for a proper interface description
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849e8d8c by Christian Holme at 2021-05-07T12:32:13+02:00
add first version of --interface
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cf2e94dc by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.c: check_options for interface and help
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3edc7a70 by Christian Holme at 2021-05-07T12:32:13+02:00
slightly improved --interface
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04079a45 by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts: allow full range of char
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a5b12ca9 by Christian Holme at 2021-05-07T12:32:13+02:00
add new IN, OUT and INOUTFILE options
For now, they just annotate intent. In the future, they can be used to
detect incorrect usage
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02b39176 by Christian Holme at 2021-05-07T12:32:13+02:00
check OPT_{IN,OUT}FILE for correct use
and abort with an error when we do things wrong
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e8f643d6 by Christian Holme at 2021-05-07T12:32:13+02:00
misc/opts.c: properly support full range of char for longopts
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70845e22 by Christian Holme at 2021-05-07T13:03:22+02:00
misc/opts: properly space help string
and remove the unneeded \t from fftmod
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b6c1de19 by Christian Holme at 2021-05-07T13:03:22+02:00
opts: add default argname if argname is empty
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9955a26d by Christian Holme at 2021-05-07T13:03:22+02:00
opts: interface update
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5857940d by Christian Holme at 2021-05-07T13:03:22+02:00
style
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63ad793c by Martin Uecker at 2021-05-08T09:35:36+02:00
prox for arbitrary differentiable loss
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dd40a35f by Martin Uecker at 2021-05-08T09:35:47+02:00
refactor prox operators
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fa4ab36f by Martin Uecker at 2021-05-08T09:35:48+02:00
refactor complex sort
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0a438e4f by Martin Uecker at 2021-05-08T09:35:48+02:00
md_zmaxnorm
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f5b9cab7 by Martin Uecker at 2021-05-08T09:35:48+02:00
add option to choose norm
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4077ba69 by Martin Uecker at 2021-05-08T09:35:48+02:00
add op_p_conjugate
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68b26fbe by Martin Uecker at 2021-05-08T09:35:49+02:00
add zselect
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adab2714 by Martin Uecker at 2021-05-08T16:55:41+02:00
not a nested function
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ec34c6c6 by Martin Uecker at 2021-05-09T17:38:33+02:00
increase tolerance of nufft batch test
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d7382d07 by Christian Holme at 2021-05-11T11:02:42+02:00
update gitlab-ci to make all
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3f200b43 by Martin Uecker at 2021-05-11T23:15:25+02:00
split lambda and stepsize
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a9d3a873 by Martin Uecker at 2021-05-11T23:15:25+02:00
debug output for auto scaling
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8b8d4ed2 by Martin Uecker at 2021-05-11T23:18:54+02:00
tensorflow loss (thx to Guanxiong 'Jason' Luo)
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d7b4dcd1 by Martin Uecker at 2021-05-12T09:17:52+02:00
missing library
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fcffe716 by Martin Uecker at 2021-05-12T10:49:14+02:00
remove warnings
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9d66c09e by Martin Uecker at 2021-05-12T12:40:06+02:00
update references
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bef0317e by Tamás Hakkel at 2021-05-17T10:40:41+02:00
Windows support by MSYS2
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cbc10b60 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: rename OPT_ARG_TYPE to OPT_TYPE
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8ac71e0c by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts.c: fix opt_long
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2c85286d by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts.c: make opt_dispatch more general
Making opt_dispatch more general is necessary so that we can reuse it
for handling positional arguments.
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0934de86 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts.c: check result of opt_uint
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4ef0074d by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: add opt_cfl for parsing complex float
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e543ff55 by Christian Holme at 2021-05-18T16:02:09+02:00
tests/test-join: preserve order in join
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7da35690 by Christian Holme at 2021-05-18T16:02:09+02:00
add test for vec tool
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8af3c9e0 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: check success of parse_cfl
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422b1872 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: OPT_INOUTFILE is just a string for now
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26adfe08 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/opts: add fist version for positional arguments
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2317da92 by Christian Holme at 2021-05-18T16:02:09+02:00
misc/io: only warn for "incorrect" usage
With options, opening an output for reading or an input for writing is
clearly wrong. But with positional arguments, this can be legitimate,
e.g. when overwriting a file: "bart slice 0 0 a.ra a.ra" is a legitimate
use case. So for now, we just warn about it.
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3134d286 by Christian Holme at 2021-05-18T16:02:10+02:00
migrate some tools to declared positional arguments
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0c45849f by Christian Holme at 2021-05-19T10:03:00+02:00
positional arguemnts: migrate first batch of tools
and remove mini_cmdline, add OPT_ULONG
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43d9065b by Christian Holme at 2021-05-19T10:51:28+02:00
migrate more tools, changes for fmac
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4d3340e8 by Christian Holme at 2021-05-19T18:06:01+02:00
migrate remaining commands
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5e29ca55 by Christian Holme at 2021-05-20T10:01:41+02:00
add positional arguments to --interface
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cc4121a8 by Christian Holme at 2021-05-20T10:30:06+02:00
switch from "optional" to "required
so we switch true and false in every single ARG_*() macro
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f9074934 by Christian Holme at 2021-05-20T13:53:42+02:00
bugfixes
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1d61371b by Christian Holme at 2021-05-20T15:56:01+02:00
properly support inoutfiles
Additionally, it is now an error to open a file for either reading or
writing without first registering its use as an output, input, or inout
file. With declared OPT{IN,OUT}FILE and ARG_{IN,OUT}FILE options, there
should be no need now to open a file without an earlier declaration of
intended use.
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478afdae by Christian Holme at 2021-05-20T15:59:58+02:00
misc/io.c: improve error condition
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87250e7d by Christian Holme at 2021-05-20T16:17:53+02:00
fix utest test_memcfl
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82988d66 by Christian Holme at 2021-05-21T09:47:38+02:00
misc/io: error into warning
on opening files which were not previously reserved as input or output.
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a8c0a74f by Christian Holme at 2021-05-21T09:48:44+02:00
misc/opts.c: style
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96ce1d67 by Christian Holme at 2021-05-21T10:03:47+02:00
more style
nicer interface, remove remaining usage_str, never end help_str with a
newline
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f071aebf by Martin Uecker at 2021-05-21T12:47:45+02:00
minor style changeS
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676b41c8 by Martin Uecker at 2021-05-23T11:48:35+02:00
don't create doc/commands.txt by default
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f64c7b61 by Martin Uecker at 2021-05-23T18:33:28+02:00
style
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8ebb989d by Martin Uecker at 2021-05-23T18:33:28+02:00
avoid pointer arithmetic
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e9bb7eb4 by Martin Uecker at 2021-05-23T18:33:28+02:00
string handling
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a477a809 by Martin Uecker at 2021-05-26T12:55:23+02:00
typo
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49620750 by Zhengguo Tan at 2021-05-26T12:55:23+02:00
mobafit: init output with 0
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0d431414 by Philip Schaten at 2021-05-26T12:55:23+02:00
Store meco scaling factor array in CPU memory for compatibility with older GPUs
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f09d5d96 by tan4 at 2021-05-27T10:27:21+02:00
bitmask: loop over dims based on count (thanks to Christian Holme)
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b80d802a by Philip Schaten at 2021-05-27T10:30:08+02:00
fix bart.spec
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3ed31530 by Christian Holme at 2021-05-31T10:25:01+02:00
fix bench and bitmask
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f6bd2149 by Christian Holme at 2021-05-31T12:25:31+02:00
moba: fix output of sensitivities
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4e2b0c85 by Christian Holme at 2021-05-31T16:08:00+02:00
fix memleaks of ARG_TUPLE
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3b5c228d by Christian Holme at 2021-05-31T16:08:25+02:00
poly: do not use argc, and style
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be220b0c by Christian Holme at 2021-05-31T16:15:48+02:00
add test for bitmask tool
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d4fb3950 by Christian Holme at 2021-05-31T16:17:56+02:00
misc/opts.c: fix string handling
fixes usage string of poly, for example
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dd40a4df by Christian Holme at 2021-05-31T17:03:54+02:00
misc/opts.c: fix skipping of optional args, better style
better variable names and more informative (I hope) comments
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0bfb0d39 by Moritz Blumenthal at 2021-06-05T14:18:17+02:00
Fix tf_wrapper
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02d22826 by Moritz Blumenthal at 2021-06-05T14:18:17+02:00
Test gradients
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757401d2 by Moritz Blumenthal at 2021-06-05T14:18:17+02:00
tf wrapper force equal dims for gradient and input
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e2fc09a3 by Moritz Blumenthal at 2021-06-05T14:18:17+02:00
Automatically annotate tf graph with gradients
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a164650a by Martin Uecker at 2021-06-05T14:25:26+02:00
BART coding style
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d24ac66f by Christian Holme at 2021-06-05T14:48:15+02:00
don't install doc/commands.txt by default
since, as of commit 676b41c8 , we don't create it by default anymore
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cbf797b3 by Moritz Blumenthal at 2021-06-05T17:50:49+02:00
Add kernels for efficient reduction
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647c0c75 by Moritz Blumenthal at 2021-06-05T17:50:49+02:00
Add basic convolution algorithm
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954434f1 by Martin Uecker at 2021-06-05T17:50:49+02:00
coding style
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9ef9034f by Martin Uecker at 2021-06-05T18:28:41+02:00
missing variable
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54bf67c3 by Martin Uecker at 2021-06-05T19:45:15+02:00
no cuda for tensorflow test
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29f4d05b by Moritz Blumenthal at 2021-06-05T21:09:28+02:00
Fix linop_plus normal
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046a7941 by Moritz Blumenthal at 2021-06-05T21:10:12+02:00
Allow NULL for nlop derivative (fallback to "not implemented")
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41ca8e79 by Moritz Blumenthal at 2021-06-05T21:12:30+02:00
Add linops
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955187c7 by Moritz Blumenthal at 2021-06-05T21:13:05+02:00
introduce flag to allow non-deterministic functions
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52604f9a by Moritz Blumenthal at 2021-06-05T21:17:29+02:00
Make blas in vecops an optional optimization
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d3873701 by mblum at 2021-06-05T21:20:58+02:00
Use memcache for cufft workingspace
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cfb56bd8 by Moritz Blumenthal at 2021-06-05T21:21:18+02:00
Async cuda calls
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dae8f735 by Moritz Blumenthal at 2021-06-05T21:21:34+02:00
reduce tenmul to zmul if possible
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a62d72d4 by Moritz Blumenthal at 2021-06-05T21:22:06+02:00
activate zpow on gpu
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610f7799 by Moritz Blumenthal at 2021-06-05T21:22:19+02:00
permute for strided_vecops
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b9ea29f2 by Moritz Blumenthal at 2021-06-05T21:26:15+02:00
Merge dims again after sorting
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cd210f24 by Moritz Blumenthal at 2021-06-05T21:28:47+02:00
Add cudnn support for convolutions
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86ac911d by Moritz Blumenthal at 2021-06-05T21:37:23+02:00
rename linop_avg to add real linop_avg
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c9a7aa0b by Martin Uecker at 2021-06-07T10:40:08+02:00
silence debug output in test
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f0657fe7 by Christian Holme at 2021-06-15T11:15:50+02:00
return 0 instead of exit(0) in some tools
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93fbdedb by Christian Holme at 2021-06-15T11:16:34+02:00
nlinv.c: fix memleak
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f0e12f8e by Christian Holme at 2021-06-15T11:16:43+02:00
misc/io.c: fix bug in io_unregister
introduced by me in 11b0a3c0
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61a3b832 by Martin Uecker at 2021-06-26T16:16:57+02:00
add target for a shared lib on Linux
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109536a2 by Christian Holme at 2021-06-29T10:23:41+02:00
improve parsing of int, long and float
atoi, atol and family hide errors by returning 0 when they cannot parse
their string argument. This can lead to bugs when not giving an argument
to e.g. OPT_INT:
bart nlinv -i -d4
would set the number of iteration (-i) to zero, as it cannot parse -d4
as an integer.
Now, such cases lead to an error.
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e0c4de09 by Christian Holme at 2021-06-29T10:35:42+02:00
tests: fix noise -s
noise -s always parsed its argument as an integer, so noise -s1. was
always invalid (but hidden)
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04cc35ca by Jon Tamir at 2021-07-09T20:45:31+02:00
fix some errors under MacOS:
1b142f6a (librt)
cbf797b3 (uint)
950b3a5d (test-roistat-mean)
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125a8a2c by Jon Tamir at 2021-07-09T14:05:25-05:00
change default Mac gcc version to gcc10
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65cb4a3c by Christian Holme at 2021-08-09T16:04:14+02:00
add compat for RING paper
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29f303b2 by Christian Holme at 2021-08-16T12:24:25+02:00
update CI for new debian stable
Additionally, start documenting that we only support python 3
- - - - -
4ffaebeb by Sidharth Kumar at 2021-10-17T01:03:47+02:00
Added a simple example in the end of file (#273)
Added a simple example of bart resize with and without -c flag. Recommended the user to look at the doc/resize.txt file to get more help.
- - - - -
0d70cdd6 by Martin Uecker at 2021-10-24T23:34:53+02:00
fix compiler version check for dissecting trampolines
- - - - -
59d89cde by Martin Uecker at 2021-10-24T23:34:53+02:00
add resize.txt to bart.spec
- - - - -
6068509d by Moritz Blumenthal at 2021-10-26T16:37:15+02:00
Relax tests
- - - - -
568cc98d by Moritz Blumenthal at 2021-10-26T16:37:43+02:00
fix zpow on gpu
- - - - -
8ec67706 by Moritz Blumenthal at 2021-10-26T16:38:23+02:00
Refactor test for convcorr
- - - - -
c51f33d7 by Moritz Blumenthal at 2021-10-26T16:38:55+02:00
Activate gputest for convcorr
- - - - -
dccb9258 by Moritz Blumenthal at 2021-10-26T16:56:33+02:00
pass non-deterministic flag to nvcc
- - - - -
87eec682 by Moritz Blumenthal at 2021-10-26T16:58:41+02:00
pass debug flag to nvcc
- - - - -
2f71325d by Moritz Blumenthal at 2021-10-26T16:59:05+02:00
fix linop stack (P. Schaten)
- - - - -
b90f2cf3 by Moritz Blumenthal at 2021-10-26T17:01:45+02:00
Use optimizatios from vecops strided
- - - - -
f48f5d24 by Moritz Blumenthal at 2021-10-26T17:04:31+02:00
linop get normal (P Schaten)
- - - - -
75dc75d1 by Moritz Blumenthal at 2021-10-26T17:05:16+02:00
Refactor reduction kernels
- - - - -
f9cb03a6 by Moritz Blumenthal at 2021-10-26T17:05:42+02:00
md_parallel_nary: allow flags exceeding D
- - - - -
d33961cd by Moritz Blumenthal at 2021-10-26T17:31:33+02:00
add struct holding data at multiple places (gpu + cpu)
- - - - -
36ebc331 by Moritz Blumenthal at 2021-10-26T17:31:57+02:00
multiplace and lazy initialization for linop_fmac linop_gdiag
- - - - -
b681b8fc by Martin Uecker at 2021-10-26T19:19:49+02:00
fix multiplace patch
- - - - -
8e8943c4 by Martin Uecker at 2021-10-26T19:42:24+02:00
refactor multiplace
- - - - -
92f2b139 by Moritz Blumenthal at 2021-10-26T20:01:29+02:00
Stop gradient by replacing derivative with null-linop
- - - - -
5fffafda by Moritz Blumenthal at 2021-10-26T20:02:18+02:00
add function to flatten(by reshape) input/output of nlop
- - - - -
55761b60 by Moritz Blumenthal at 2021-10-26T20:03:37+02:00
Extend nlop framework
- - - - -
535b1ed5 by Martin Uecker at 2021-10-26T20:05:45+02:00
remove unused headers
- - - - -
a0d6f4c8 by Martin Uecker at 2021-10-26T20:21:11+02:00
formalities & style
- - - - -
368d244e by Moritz Blumenthal at 2021-10-26T21:33:57+02:00
make make_z3op_scalar fast
- - - - -
6277e52b by Moritz Blumenthal at 2021-10-26T21:41:38+02:00
Add function to apply nlop in loop
- - - - -
8b494d5c by Moritz Blumenthal at 2021-10-26T22:18:04+02:00
Add batch dim
- - - - -
21fbbb1f by Moritz Blumenthal at 2021-10-26T22:25:34+02:00
Add linop repmat (adjoing sum)
- - - - -
a72c9d98 by Martin Uecker at 2021-10-26T22:25:34+02:00
formalities
- - - - -
95df246e by Moritz Blumenthal at 2021-10-26T22:26:49+02:00
add tenmul
- - - - -
9e3fce01 by Moritz Blumenthal at 2021-10-26T22:42:17+02:00
functions to get highest and lowest selected dim
- - - - -
ef5294d7 by Moritz Blumenthal at 2021-10-26T22:42:17+02:00
simplify code for fill like copies
- - - - -
495295db by Martin Uecker at 2021-10-26T22:42:17+02:00
style
- - - - -
b7162f66 by Moritz Blumenthal at 2021-10-26T22:59:02+02:00
Reduce memory usage
- - - - -
d7ab615b by Christian Holme at 2021-10-27T10:32:47+02:00
shared-lib: preserve CFLAGS & move to MAKESTAGE=2
We do not want to override the CFLAGS, so just add -fPIC to the normal
initialization of CFLAGS.
Additionally, the target needs to be defined in MAKESTAGE=2,
because the necessary variables are only defined in there.
- - - - -
a4df6b06 by Martin Uecker at 2021-10-28T21:12:36+02:00
ubsan workaround for zero sized array
- - - - -
8a5533fa by Moritz Blumenthal at 2021-11-03T09:23:05+01:00
Add support for multi cfl
- - - - -
6ae13fca by Moritz Blumenthal at 2021-11-03T09:42:26+01:00
Update python cfl + multicfl
- - - - -
8ec0ebdd by Martin Uecker at 2021-11-03T09:42:26+01:00
copyright update, spelling, style
- - - - -
970be458 by Moritz Blumenthal at 2021-11-03T11:46:55+01:00
Add generic list
- - - - -
c0ea904a by Moritz Blumenthal at 2021-11-03T11:49:00+01:00
Add generic graphs
- - - - -
70776fba by Moritz Blumenthal at 2021-11-04T11:51:04+01:00
Add function to create ptr and printf in it
- - - - -
a5241548 by Moritz Blumenthal at 2021-11-04T11:51:04+01:00
Add graphs to ops/linops/nlops
- - - - -
b0a63f22 by Moritz Blumenthal at 2021-11-04T14:20:24+01:00
Managed nlops for save memory of unused derivatives
- - - - -
89844ddf by Martin Uecker at 2021-11-04T15:03:51+01:00
updates
- - - - -
d9c36d42 by Moritz Blumenthal at 2021-11-04T15:06:04+01:00
Add nlops based on jacobians
- - - - -
fe6434da by Moritz Blumenthal at 2021-11-04T15:06:04+01:00
Adapt tenmul to managed interface
- - - - -
19df772d by Moritz Blumenthal at 2021-11-04T15:06:04+01:00
Add some nlops
- - - - -
a6b1f1ec by Moritz Blumenthal at 2021-11-04T15:22:11+01:00
checkpointing
- - - - -
910790fb by Martin Uecker at 2021-11-06T09:06:00+01:00
fix python->python3
- - - - -
f8b302a8 by Moritz Blumenthal at 2021-11-06T09:06:00+01:00
Add convolution
- - - - -
f3e7f790 by Moritz Blumenthal at 2021-11-06T09:06:00+01:00
Update iterative algorithms
- - - - -
e82eb431 by Martin Uecker at 2021-11-06T09:17:17+01:00
style
- - - - -
b88f5cd7 by Christian Holme at 2021-11-08T14:20:19+01:00
multicfl: fix interface
Now, when combining, the last argument is the multicfl;
and when splitting / separatingg, the first argument is the multicfl.
This is to maintain standard bart usage, with the input coming first
and output last in command-line tools.
- - - - -
8ba111bb by Christian Holme at 2021-11-08T14:46:33+01:00
tests/multicfl.mk: adapt to interface changes
As the input is now in the beginning, the test needs to be adapted
- - - - -
2a2cf0bb by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Add projections
- - - - -
bbd9ab36 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Add nn framework
- - - - -
14b51ff6 by Martin Uecker at 2021-11-09T14:58:18+01:00
macros for real dims and strides
- - - - -
c187fc42 by Martin Uecker at 2021-11-09T14:58:18+01:00
ubsan fix
- - - - -
ab5b187c by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Allow comma separated list for subopts
- - - - -
6d316276 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Command line opts for iter6
- - - - -
8046cb22 by Martin Uecker at 2021-11-09T14:58:18+01:00
copyright & indentation
- - - - -
9428c2c7 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Add function to check if linop is null
- - - - -
d846cba0 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Optimize operators based on graphs
- - - - -
67869b34 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Arbitrary number of inputs for operator zadd
- - - - -
66f710a0 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Make sums with multiple permuted inputs identifyable
- - - - -
a878e0db by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
nlop_no_der for checkpointing
- - - - -
d0f21e2d by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Optimize linear operators Ax+Ay ->A(x+y) i
- - - - -
724e9da8 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
Add functions to optimize linops by graph
- - - - -
a0489d83 by Martin Uecker at 2021-11-09T14:58:18+01:00
fix test
- - - - -
0f0f1061 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
add utassert only returning when false
- - - - -
0817d71f by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
add md_is_sameplace
- - - - -
65c5bd4c by Martin Uecker at 2021-11-09T14:58:18+01:00
fix comment
- - - - -
864c2446 by Moritz Blumenthal at 2021-11-09T14:58:18+01:00
add generic copy wrapper function and return inner operator in list
- - - - -
8f12c040 by Philipp Ehses at 2021-11-12T08:22:14+01:00
poisson.c: fix calreg position for odd calreg size (#274)
- - - - -
4f6da5df by Moritz Blumenthal at 2021-11-12T08:28:35+01:00
Multiplace for nufft + later update of traj and psf
- - - - -
18b818a9 by Martin Uecker at 2021-11-12T08:28:35+01:00
don't initialize
- - - - -
f842fbcc by Moritz Blumenthal at 2021-11-12T08:28:35+01:00
Add nlops mri
- - - - -
e54982d8 by Martin Uecker at 2021-11-12T08:28:35+01:00
reduce output
- - - - -
63f51488 by Moritz Blumenthal at 2021-11-12T08:28:35+01:00
Add nnet and reconet
- - - - -
a6dd97a9 by Martin Uecker at 2021-11-12T08:28:35+01:00
fix memory leak
- - - - -
4ff0379f by Martin Uecker at 2021-11-12T08:28:35+01:00
fix ubsan zero array issue
- - - - -
490ee042 by Martin Uecker at 2021-11-12T08:28:35+01:00
nlinv: fix resource leak
- - - - -
0e1fdb16 by Martin Uecker at 2021-11-12T08:28:35+01:00
zinv: fix leak
- - - - -
a9bde381 by Martin Uecker at 2021-11-12T08:28:35+01:00
fix memory leak in test
- - - - -
3b8a4294 by Martin Uecker at 2021-11-12T08:28:35+01:00
turn off broken tests
- - - - -
59549982 by Martin Uecker at 2021-11-12T08:28:35+01:00
revise tuple ops and fix some issues
- - - - -
b57ef427 by Moritz Blumenthal at 2021-11-12T15:19:44+01:00
Add tool to transform onehotencoded data to integer encoded
- - - - -
e21abdf6 by Moritz Blumenthal at 2021-11-12T15:20:35+01:00
Add attention for unet combine
- - - - -
53299e1b by Moritz Blumenthal at 2021-11-12T15:20:42+01:00
fix test_nlop for linear optimization
- - - - -
3abe32d7 by Moritz Blumenthal at 2021-11-12T15:23:42+01:00
copy wrapper at sameplace
- - - - -
865c8364 by Moritz Blumenthal at 2021-11-12T15:26:30+01:00
improve linop optimization
- - - - -
5dd970cd by Moritz Blumenthal at 2021-11-12T15:27:13+01:00
fix unsigned int in cudnn wrapper
- - - - -
555c044c by Moritz Blumenthal at 2021-11-12T15:27:21+01:00
unsigned int gpu conv
- - - - -
ea6ecc3d by Moritz Blumenthal at 2021-11-12T15:27:32+01:00
test cuda flpmath test for nan
- - - - -
6793d5b9 by Moritz Blumenthal at 2021-11-12T15:57:55+01:00
fix scaling
- - - - -
a3f98500 by Moritz Blumenthal at 2021-11-12T16:00:12+01:00
refactor mad loss
- - - - -
a3babf69 by Moritz Blumenthal at 2021-11-12T16:03:11+01:00
fix mri_ops: allow for shared patterns
- - - - -
4fcfbb24 by Moritz Blumenthal at 2021-11-12T16:04:31+01:00
fix: "Add nnet and reconet" delete unused options
- - - - -
c0bdf52e by Martin Uecker at 2021-11-12T16:07:01+01:00
minor
- - - - -
b3a53546 by Moritz Blumenthal at 2021-11-13T07:24:10+01:00
add mask to loss functions
- - - - -
5bf58839 by Moritz Blumenthal at 2021-11-13T07:24:20+01:00
update mri ops
- - - - -
bae11ed9 by Moritz Blumenthal at 2021-11-13T07:24:32+01:00
updates nn
- - - - -
2b59c312 by Moritz Blumenthal at 2021-11-13T07:24:44+01:00
add list for data passed to training etc ...
- - - - -
0f768020 by Moritz Blumenthal at 2021-11-13T07:24:57+01:00
refactor reconet dc ops + add mask
- - - - -
0b16ca02 by Martin Uecker at 2021-11-13T08:12:55+01:00
fix another ubsan issue
- - - - -
f14ab6fc by Moritz Blumenthal at 2021-11-13T08:24:07+01:00
fix test
- - - - -
1a97ed62 by Martin Uecker at 2021-11-13T08:24:23+01:00
update BART references
- - - - -
dc7e8d92 by Martin Uecker at 2021-11-13T09:10:43+01:00
integration with ubsan
- - - - -
2eba6de1 by Martin Uecker at 2021-11-13T09:10:53+01:00
fixup
- - - - -
dff5cd25 by Martin Uecker at 2021-11-13T09:10:53+01:00
machine learning references
- - - - -
86d33b57 by ecat at 2021-11-14T13:20:11+01:00
Added usage notes that may cause issues in pics reconstruction. (#272)
- - - - -
68758957 by Martin Uecker at 2021-11-14T13:22:10+01:00
move to doc
- - - - -
84cc4b7d by aTrotier at 2021-11-14T13:28:16+01:00
add 3D uniform traj
- - - - -
e62c6975 by aTrotier at 2021-11-14T13:28:23+01:00
add 3D uniform half-sphere
- - - - -
74d22b43 by Martin Uecker at 2021-11-14T14:23:44+01:00
fixes for show command
- - - - -
af791034 by Martin Uecker at 2021-11-14T15:09:35+01:00
refactor 3D trajectory
- - - - -
480509c4 by Christian Holme at 2021-11-15T16:09:54+01:00
calib/delays.c: output to stdout for RING paper
Previously, this used files and a specific define during compilation.
Now, we use the environment variable RING_PAPER and output projection
angles and offsets when RING_PAPER=1
- - - - -
041df1ee by Christian Holme at 2021-11-16T11:29:14+01:00
num/multind: add pointer for clang
For now, this shouldn't change anything. But if we ever support
clang+cuda, it is one thing less to fix
- - - - -
55e0f8cc by Christian Holme at 2021-11-16T11:56:25+01:00
rtnlinv.c: properly free pattern
by ensuring that it is always allocated by md_alloc
- - - - -
470ae52e by Moritz Blumenthal at 2021-11-16T14:17:09+01:00
fix overflow
- - - - -
53e5886a by Moritz Blumenthal at 2021-11-16T14:17:09+01:00
fix basis
- - - - -
0ce4a4c5 by Moritz Blumenthal at 2021-11-16T14:18:20+01:00
Add function to get nufft_normal op only (toeplitz)
- - - - -
0227886f by Moritz Blumenthal at 2021-11-16T14:18:20+01:00
use nufft normal op in reconet
- - - - -
cf69bcc7 by Moritz Blumenthal at 2021-11-16T14:28:33+01:00
optimize coil/psf tenmul on GPU
- - - - -
578ac9ae by Martin Uecker at 2021-11-16T15:20:03+01:00
merge reorder/label binning
- - - - -
8f4ee6ef by rosenzweig at 2021-11-17T11:31:18+01:00
bin: Introduce config struct
- - - - -
c0f025d5 by rosenzweig at 2021-11-17T11:32:14+01:00
bin: Offset option
- - - - -
ce95a673 by Christian Holme at 2021-11-17T11:32:14+01:00
bin.c: add missing unmap_cfl
- - - - -
99b781fe by rosenzweig at 2021-11-17T11:32:14+01:00
bin, calib/bin, tests: Amplitude respiratory binning
- - - - -
2ce3608f by rosenzweig at 2021-11-17T11:32:14+01:00
bin: assertion to avoid mov_avg in amplitude binning
- - - - -
82a25a6b by Martin Uecker at 2021-11-17T11:48:07+01:00
add geometric median
- - - - -
006a96c9 by rosenzweig at 2021-11-17T11:48:07+01:00
num/filter: Add moving average
- - - - -
2abb6f49 by Martin Uecker at 2021-11-17T11:48:07+01:00
rewrite moving average
- - - - -
30f6563f by rosenzweig at 2021-11-17T11:48:07+01:00
num/filter: median calculation safe for large arrays
- - - - -
b7ebe767 by rosenzweig at 2021-11-17T11:48:07+01:00
filter: Moving average option
- - - - -
4df883d2 by Martin Uecker at 2021-11-17T12:05:06+01:00
fix test and coding style
- - - - -
1f0f7d82 by Christian Holme at 2021-11-17T13:49:52+01:00
tests/bin.mk: clean up after test
- - - - -
d9fe30bd by schaten at 2021-11-22T18:01:40+01:00
Fix bart.spec - all files matching doc/*.txt are installed as documentation (#275)
- - - - -
6b6adff8 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
fixes for scaling maxeigen
- - - - -
03cbda22 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
fix: allow help ('h') in subopts
- - - - -
b04ca9b4 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
Fix: real from complex strides for double
- - - - -
325177b8 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
make eval numerically more stable
- - - - -
64c1d14c by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
fix bufferoverflow
- - - - -
e1e766f6 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
networks/misc.c: fix memleak
- - - - -
411dc751 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
nn/nn.c: fix memleak
- - - - -
101c4725 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
rtnlinv.c: fix memleak
- - - - -
d260da12 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
fix memleak in opts
- - - - -
18ad4038 by Moritz Blumenthal at 2021-11-22T22:39:55+01:00
calib/bin.c: fix memleak
- - - - -
4ed5821b by Moritz Blumenthal at 2021-11-22T22:43:29+01:00
add fsanitize=address
- - - - -
6646e06c by Martin Uecker at 2021-11-23T13:18:16+01:00
minor fix to call to xargs
- - - - -
8bc8ad7a by Martin Uecker at 2021-12-16T10:16:59+01:00
typo
- - - - -
2ba88902 by Martin Uecker at 2021-12-16T10:17:05+01:00
add target for slow tests
- - - - -
509237af by Martin Uecker at 2021-12-16T10:17:09+01:00
run slow tests
- - - - -
be5b70c8 by Jon Tamir at 2021-12-16T20:19:10+01:00
Create c-cpp.yml (#276)
*
- - - - -
5f1679dc by Martin Uecker at 2021-12-16T20:19:36+01:00
refactor & unmap trajectory
- - - - -
a95f1522 by Martin Uecker at 2021-12-16T20:19:36+01:00
fix trajectory scaling in moba
- - - - -
df7697a2 by Martin Uecker at 2021-12-16T20:19:36+01:00
set default oversampling to 1.
- - - - -
7d15691f by Martin Uecker at 2021-12-16T21:25:25+01:00
fix help
- - - - -
f7e84879 by Martin Uecker at 2021-12-16T21:39:02+01:00
fix clang build
- - - - -
348e1f17 by Moritz Blumenthal at 2021-12-17T12:06:24+01:00
Fix scaling of nlinv
- - - - -
26417969 by Moritz Blumenthal at 2021-12-17T12:06:33+01:00
fix scaling of psf with basis
- - - - -
7181e397 by Martin Uecker at 2021-12-18T15:39:04+01:00
set error to zero for tests which should be exact
- - - - -
012acdf7 by Martin Uecker at 2021-12-18T19:04:51+01:00
tighten some tests
- - - - -
83c090e9 by Martin Uecker at 2021-12-18T19:04:51+01:00
tell about loose tests
- - - - -
22d2b4fc by Martin Uecker at 2021-12-18T19:46:20+01:00
use of uninitialized variable
- - - - -
63a6b28e by Martin Uecker at 2021-12-18T19:46:47+01:00
reduce default optimization
- - - - -
7aeae14c by Martin Uecker at 2021-12-23T15:39:02+01:00
style & copyright
- - - - -
12711590 by Christian Holme at 2022-01-04T13:46:55+01:00
allclean now removes saved fftw wisdowm and estvar simulations
since allclean should give you an actually clean repository
- - - - -
e2e3cc68 by Christian Holme at 2022-01-04T13:47:12+01:00
fftw: use of wisdom now configurable in Makefile
and disabled by default
- - - - -
d7192dcf by Jon Tamir at 2022-01-14T08:50:07+01:00
fix path finding for bart + WSL in Matlab (#277)
- - - - -
f82cf94d by Christian Holme at 2022-01-26T12:33:04+01:00
noir/misc: clear correct length for img_output
- - - - -
92dd921a by Christian Holme at 2022-01-26T12:35:04+01:00
nlinv: fix noncart ENLIVE
Commit 9ea47b4ae66af rewrote part of the image size estimation for
noncartesian nlinv, and overwrote the number of maps in the `dims`
array, breaking noncartesian ENLIVE.
- - - - -
fc1930ee by Christian Holme at 2022-01-26T13:08:24+01:00
add tests to check ENLIVE maps dimensions
- - - - -
20ffadae by Jon Tamir at 2022-02-02T16:31:58+01:00
tests: reduce tolerance a little (Mac Intel 12.1 gcc11) (#279)
- - - - -
33c56b7c by Philipp Ehses at 2022-02-02T16:51:46+01:00
faster write_cfl (#280)
- - - - -
99b39c4b by Martin Uecker at 2022-02-06T12:19:24+01:00
style
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ec016f56 by Martin Uecker at 2022-02-06T15:09:03+01:00
coding style, filename handling
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350dec93 by Martin Uecker at 2022-02-06T15:09:48+01:00
protect some macros against double evaluation
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50936751 by Jon Tamir at 2022-02-07T11:22:34-06:00
matlab test: comment out TOOLBOX_PATH test (not strictly needed)
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237f9fec by Martin Uecker at 2022-02-13T12:02:42+01:00
Update README.md
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c84712c9 by Martin Uecker at 2022-02-15T10:35:15+01:00
error message for cuda plan
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e1adf2a5 by Philip Schaten at 2022-02-16T21:12:42+01:00
Added rpkg.conf and moved anything rpm-related to pkg/rpm
copr-build broke because rpkg-util does not read rpkg.macros by default anymore.
Instead it looks for a file rpkg.conf which points to the file
containing user-defined macros.
https://www.mail-archive.com/devel@lists.fedoraproject.org/msg170768.html
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fcd368fd by Philip Schaten at 2022-02-16T21:12:42+01:00
Moved anything rpm-related to pkg/rpm: Fix a path in libbart-devel.spec
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1b62b6cd by Martin Uecker at 2022-02-16T22:44:56+01:00
fix some warnings
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4c2f2695 by Christian Holme at 2022-02-17T10:48:51+01:00
add strict array bounds to main-functions
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a4765911 by Moritz Blumenthal at 2022-02-22T00:04:25+01:00
softsense for varnet
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c75b33ee by Moritz Blumenthal at 2022-02-22T00:06:40+01:00
give numeric index to lambda
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36100b91 by Moritz Blumenthal at 2022-02-22T00:07:03+01:00
fix normalization for coil images
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f5e4f0ce by Moritz Blumenthal at 2022-02-22T00:07:18+01:00
Update ISMRMRD tool
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39283237 by Moritz Blumenthal at 2022-02-22T15:56:40+01:00
more iterations for eigenmapscu
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568bccef by Moritz Blumenthal at 2022-02-22T15:56:40+01:00
sure_crop on gpu
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cf0baa7e by Moritz Blumenthal at 2022-02-23T10:01:49+01:00
only use first map for reconet by default
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e35c79cb by Martin Uecker at 2022-03-13T15:21:44+01:00
coding style
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53583a05 by Christian Holme at 2022-04-06T11:39:47+02:00
add tests for fakeksp
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7d4cd510 by Christian Holme at 2022-04-06T11:39:47+02:00
fakeksp: fix output argument
output should really be an ARG_OUTFILE
Fixes #283
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432a7775 by Christian Holme at 2022-04-07T11:13:35+02:00
add tests for pocsense
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c5efbab8 by Christian Holme at 2022-04-07T12:00:48+02:00
pocsense: fix infinite loop in linop_wavelet_create
The previous code would lead to in infinite loop in
`wavelet_num_levels`.
This code builds both the flags and minsize correctly.
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9daa033b by Christian Holme at 2022-04-07T12:00:48+02:00
pocsense: use more common wavthresh interface
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193c849e by Christian Holme at 2022-04-07T12:07:20+02:00
grecon/optreg: remove unnecessary initialization
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4cc95c46 by Christian Holme at 2022-04-07T14:13:36+02:00
misc/opts.c: remove unused forward declaration
The function does not exist anymore as of commit
5954998216ff81bd4e06c535179b15f3d79a7099
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7992b244 by Martin Uecker at 2022-04-10T12:54:42+02:00
remove dead code
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e5a0c6dc by Martin Uecker at 2022-04-10T12:54:42+02:00
join: rename idata -> in_data
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71a90847 by Martin Uecker at 2022-04-10T12:54:43+02:00
coding style
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21c71e1d by Martin Uecker at 2022-04-10T12:54:43+02:00
improve readability
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757e47e0 by Martin Uecker at 2022-04-10T12:54:43+02:00
turn off failing test
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6e2fdf08 by Christian Holme at 2022-04-13T16:37:50+02:00
gitlab-ci: correct dependencies for UBSan integration test
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863cd9ab by Martin Uecker at 2022-04-15T15:09:04+02:00
new tool: fovshift
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1aac884a by Martin Uecker at 2022-04-15T16:13:05+02:00
flag to create oversampled trajectory
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2fe3b941 by Martin Uecker at 2022-04-15T17:42:56+02:00
test for trajectory rotation
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33eb09dc by Martin Uecker at 2022-04-15T18:21:55+02:00
tests for centered radial trajectory
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58095e29 by Martin Uecker at 2022-04-15T21:13:20+02:00
make estdelay more generic regarding un-/centered trajectories
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9e361cbe by Martin Uecker at 2022-04-15T21:25:41+02:00
tests for zexp
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087ab38f by rosenzweig at 2022-04-15T21:43:18+02:00
tests/filter: Moving average
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17bbcb84 by Martin Uecker at 2022-04-15T21:52:50+02:00
radial DCF examples
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717bca81 by Martin Uecker at 2022-04-16T17:45:07+02:00
coding style
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79647b83 by Martin Uecker at 2022-04-16T21:22:29+02:00
make config constant
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e4572759 by Martin Uecker at 2022-04-17T16:31:59+02:00
fix memory leak
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c5726533 by Martin Uecker at 2022-04-17T16:38:06+02:00
add missing copyright header
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07ed3a63 by Tamás Hakkel at 2022-04-17T17:22:44+02:00
Og flag for debug mode + memcfl_exists
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acc83578 by Tamás Hakkel at 2022-04-17T17:24:00+02:00
bugfix
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7578c4d3 by Christian Holme at 2022-04-20T11:55:07+02:00
calib/calib.c: use designated initialization for ecalib_defaults
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a8302cbd by Christian Holme at 2022-04-20T11:55:07+02:00
ecalib: make number of iterations for orthiter configurable
This reverts 392832378365df541ccb96fb521ad02750152be5
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bd4ae41a by Christian Holme at 2022-04-20T14:59:33+02:00
gitlab-ci: add GPU tests running in our system
Using the nvidia cuda docker image
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97779c68 by Christian Holme at 2022-04-20T14:59:33+02:00
gitlab-ci: OMP threads to 1, no more tags
tags should come back once we need them or once the gwdg is no longer
relevant
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6f1bbac2 by Sebastian Rosenzweig at 2022-04-25T08:04:59+02:00
num/qform: Add bilinear form
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f16e5e02 by Martin Uecker at 2022-04-25T08:04:59+02:00
rename gradient_form in quadratic_form
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69a67aa4 by Martin Uecker at 2022-04-25T08:04:59+02:00
harmonic fit + tests
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fbcde693 by Martin Uecker at 2022-04-25T08:04:59+02:00
move estimate_im_dims to misc/mri.c
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075dea69 by Martin Uecker at 2022-04-25T08:04:59+02:00
function to extact angles from radial trajectory
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a62a3a6d by Martin Uecker at 2022-04-25T08:04:59+02:00
move some helper functions to misc/mri.c
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5be7829d by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
add measure tool
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54f9c24e by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
add test ideal for measure tool
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451a76c6 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
fixup learned tickhonov init
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f2b00d41 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
let linop_sum use md_zsum
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6905ef40 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
refactor batch generator
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ed6ac838 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
more flexible batch generator configuration in reconet
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55467da8 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
move scaling and preprocessing to network data
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7dff7588 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
add functions to data list
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8ff90ada by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
reconstruction as output name
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a7f838cd by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
apply/eval with datalist
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17ec0b83 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
move sense initialization to preprocessing
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8e3e39a8 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
rename tikhonov->sense
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27254cea by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
assert no identical argument names in nn_chain2
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c8592bf7 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
update reconet tests
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6d7a6762 by Moritz Blumenthal at 2022-04-28T08:49:24+02:00
add warmup to learning rate scheduling
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2f3bdbd3 by Martin Uecker at 2022-04-28T11:25:16+02:00
add missing workaround for C++
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3dc2c17a by Christian Holme at 2022-04-28T12:11:31+02:00
fix measure tests
* Use --mse-mag instead of --mse in the test named mse-mag
* No line continuation before the "touch"
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d4db0a1d by Christian Holme at 2022-04-28T12:11:41+02:00
fully reduce default optimization
In line with 63a6b28ea7f5eb85eca8bcccf2ee57bf9658f318, default
optimization is now -O2 without -ffast-math, for CUDA and also for the
automatic tests
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9bf00c25 by Christian Holme at 2022-04-28T12:52:33+02:00
gitlab-ci: use UBSAN=1 instead of CFLAGS
and switch Integration_Test_UBSan to debian:testing, as Build_UBSan and
Unit_Test_UBSan also use debian:testing
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fe27fa95 by Christian Holme at 2022-04-29T11:31:48+02:00
Makefile: re-add -fsanitize=address
As it was included in the .gitlab-ci.yml, it should also be part of
UBSAN=1
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4bc44901 by Martin Uecker at 2022-05-02T21:46:05+02:00
refactor
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24a3ca45 by Martin Uecker at 2022-05-02T21:46:05+02:00
merge two functions always used together
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9ef31f72 by Martin Uecker at 2022-05-02T21:46:05+02:00
use tenmul instead of clear/fmac
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77220b7d by Martin Uecker at 2022-05-02T21:46:05+02:00
copyright + typos
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bdfd7d85 by Martin Uecker at 2022-05-02T21:46:05+02:00
allow forward nufft with toeplitz
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9d018753 by Martin Uecker at 2022-05-02T21:46:05+02:00
refactor
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6d943598 by Martin Uecker at 2022-05-02T21:46:05+02:00
refactor
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a77fdf96 by Martin Uecker at 2022-05-02T21:46:05+02:00
copyright, remove unused variable
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431c6d45 by Moritz Blumenthal at 2022-05-03T17:26:00+02:00
tenmul for linop_fmac
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5145d84b by Moritz Blumenthal at 2022-05-03T17:27:02+02:00
merge fftmod and coils in mriops
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2558d8a6 by Moritz Blumenthal at 2022-05-03T17:48:00+02:00
update im2col code
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38d6983a by Martin Uecker at 2022-05-03T18:23:38+02:00
minor changes
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89cbb85a by Nick Scholand at 2022-05-04T12:16:23+02:00
Add approximation of sine integral with test
Fix date
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71210f83 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add windowed sinc functions with utests
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f041c80b by Nick Scholand at 2022-05-04T12:16:25+02:00
Add rotation matrices
Defining direction of rotation becomes easier.
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49efbb95 by Nick Scholand at 2022-05-04T12:16:25+02:00
Reformulate relaxation and rotation with rotation matrices + utests
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d1c6e76b by Nick Scholand at 2022-05-04T12:16:25+02:00
Add rf excitation wrapper for phase and FA + utest
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7fb0ebe4 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add excitation with RF phase utest
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4bc6c99d by Nick Scholand at 2022-05-04T12:16:25+02:00
Add B1 partial derivative + utests
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9b2b45b4 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add ODE based simulation tool with first utests
Utests:
- Test partial derivatives for an IR bSSFP sequence
- Compare simulated IR bSSFP signal with analytical model
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9e018e9a by Nick Scholand at 2022-05-04T12:16:25+02:00
Add structural elements for simulation
Increases the flexibility for later extensions.
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a3f7fb4c by Nick Scholand at 2022-05-04T12:16:25+02:00
Add ODE simulation offresonance and gradient utests
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05f941f5 by Nick Scholand at 2022-05-04T12:16:25+02:00
No inversion
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4c9506a2 by Nick Scholand at 2022-05-04T12:16:25+02:00
Avoid case conflict
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8eafc33b by Nick Scholand at 2022-05-04T12:16:25+02:00
Add utest linking Bloch simulation and EPG
Idea: Loop through Fourier coefficients by changing the off-resonance of
isochromates.
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cde00743 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add hard pulse option with utests
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e084b4b8 by Nick Scholand at 2022-05-04T12:16:25+02:00
Remove unused variable
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049a636b by Nick Scholand at 2022-05-04T12:16:25+02:00
Fix smooth spoiling for rotation matrix relaxation
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b070fe78 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add function for simulation debug output
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58c4d3d4 by Nick Scholand at 2022-05-04T12:16:25+02:00
Avoid unnecessary computation
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5af80d93 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add simulation interface with tests
Separated in a new tool (sim.c)
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ff4db60b by Nick Scholand at 2022-05-04T12:16:25+02:00
Add test for relaxation parameter grid simulation
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ba69bc42 by Nick Scholand at 2022-05-04T12:16:25+02:00
Make slice-profile gradient moment accessible from sim interface
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8c3fa86a by Nick Scholand at 2022-05-04T12:16:25+02:00
Add NIST phantom (T2 sphere)
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bd9ec293 by Nick Scholand at 2022-05-04T12:16:25+02:00
Balance z gradient for bSSFP type sequences
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d8db8ea6 by Nick Scholand at 2022-05-04T12:16:25+02:00
Specify pulse type
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e74c1e9e by Nick Scholand at 2022-05-04T12:16:25+02:00
style
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5065fe6a by Nick Scholand at 2022-05-04T12:16:25+02:00
Add hyperbolic secant inversion pulse with utest
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57e3d5a2 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add perfect inversion and inversion spoiler duration
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2dd3541a by Nick Scholand at 2022-05-04T12:16:25+02:00
Turn off output
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29a9f91f by Nick Scholand at 2022-05-04T12:16:25+02:00
Set hyperbolic secant inversion default
- Tests and utests comparing with analytical models still require
perfect inversion models
- - - - -
9a6d0827 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add simulation type
- - - - -
4ac830cb by Nick Scholand at 2022-05-04T12:16:25+02:00
style
- - - - -
7a255cbe by Nick Scholand at 2022-05-04T12:16:25+02:00
Split Bloch function
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76784609 by Nick Scholand at 2022-05-04T12:16:25+02:00
Rename Bloch function
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b838ef58 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add matrix exponential estimation
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63d9b7f0 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add Bloch system matrices including SAB
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161908d4 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add debug output for hyperbolic secant pulse
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b12ae3fa by Nick Scholand at 2022-05-04T12:16:25+02:00
Make type for obvious
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21f2882f by Nick Scholand at 2022-05-04T12:16:25+02:00
Add functions for STM matrix simulation
- - - - -
dc53b9ac by Nick Scholand at 2022-05-04T12:16:25+02:00
Integrate STM in ODE simulation interface with utests
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4fa11246 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add initialization of hyperbolic secant pulses to sim.c
- - - - -
6227bc1a by Nick Scholand at 2022-05-04T12:16:25+02:00
Make simulation types accessible from CLI + tests
- - - - -
77317450 by Nick Scholand at 2022-05-04T12:16:25+02:00
Reorder functions
- - - - -
0aae05c3 by Nick Scholand at 2022-05-04T12:16:25+02:00
style
- - - - -
632aba85 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add slice selection rewinder with utests for ODE and STM
- - - - -
e8b39326 by Nick Scholand at 2022-05-04T12:16:25+02:00
style
- - - - -
df4649b2 by Nick Scholand at 2022-05-04T12:16:25+02:00
Fix terminology
- - - - -
42ccc9fd by Nick Scholand at 2022-05-04T12:16:25+02:00
Add missing header file
- - - - -
5b8f4ff0 by Nick Scholand at 2022-05-04T12:16:25+02:00
True B1
- - - - -
b88e3e6a by Nick Scholand at 2022-05-04T12:16:25+02:00
Fix dimension
- - - - -
d9b325aa by Nick Scholand at 2022-05-04T12:16:25+02:00
Add simulation type debug output
- - - - -
76c9aec1 by Nick Scholand at 2022-05-04T12:16:25+02:00
Reuse temporary arrays
- - - - -
42d8135e by Nick Scholand at 2022-05-04T12:16:25+02:00
Specify struct type
- - - - -
fa09ee08 by Nick Scholand at 2022-05-04T12:16:25+02:00
Style
- - - - -
52c57ff5 by Nick Scholand at 2022-05-04T12:16:25+02:00
Add rectangle geometry to phantom tool
- - - - -
973139ae by Nick Scholand at 2022-05-04T12:16:25+02:00
Add tool for morphological operations with tests
- - - - -
b796b781 by Nick Scholand at 2022-05-04T12:16:25+02:00
Make inversion spoiler duration accessible from CLI
- - - - -
fdc4e57d by Nick Scholand at 2022-05-04T12:16:25+02:00
Rename simulation interface
- - - - -
c320d839 by Nick Scholand at 2022-05-04T12:16:25+02:00
Generalize initialization
- - - - -
a0b73c90 by Nick Scholand at 2022-05-04T12:16:25+02:00
More accurate terminology
- - - - -
b8dd2d92 by Moritz Blumenthal at 2022-05-04T20:54:55+02:00
reconstruct coil images
- - - - -
7e311142 by Martin Uecker at 2022-05-13T14:33:34+02:00
warn about incorrectly scaled trajectories
- - - - -
411f0b88 by Martin Uecker at 2022-05-13T15:53:42+02:00
update directories described in README
- - - - -
900bb5f7 by Martin Uecker at 2022-05-14T19:26:18+02:00
better backwards compatibility for moba
- - - - -
2bf1f14c by Martin Uecker at 2022-05-15T15:37:52+02:00
import/export of PSF in pics
- - - - -
03be2259 by Martin Uecker at 2022-05-15T17:08:39+02:00
ubsan fix
- - - - -
8dd61e15 by Martin Uecker at 2022-05-17T13:44:07+02:00
remove unused variable
- - - - -
d795626e by Martin Uecker at 2022-05-17T13:56:57+02:00
update copyright year
- - - - -
eafe40ab by Martin Uecker at 2022-05-17T15:01:51+02:00
tests for rof / tgv denoising
- - - - -
a1cd998b by Martin Uecker at 2022-05-17T18:38:46+02:00
refactor rof/tgv
- - - - -
5f1a6da4 by Martin Uecker at 2022-05-17T18:49:08+02:00
move tgv code into library
- - - - -
79f98930 by Martin Uecker at 2022-05-17T20:03:31+02:00
implement TGV for pics
- - - - -
564766d6 by Martin Uecker at 2022-05-17T21:17:09+02:00
multiple reglarization parameters + minor changes
- - - - -
873ab951 by Martin Uecker at 2022-05-18T07:13:57+02:00
better test for pics with tgv
- - - - -
f1a66b17 by Martin Uecker at 2022-05-18T07:15:37+02:00
fix copyright
- - - - -
75007b3c by Martin Uecker at 2022-05-18T07:15:37+02:00
minor
- - - - -
4e0caed4 by Martin Uecker at 2022-05-18T07:15:37+02:00
rename variable, remove unused
- - - - -
c9afc50d by Martin Uecker at 2022-05-18T07:15:37+02:00
reduce memory usage
- - - - -
7ccc8008 by Martin Uecker at 2022-05-18T08:51:02+02:00
partially separable function reference
- - - - -
5d48102b by Martin Uecker at 2022-05-21T13:50:42+02:00
fix some warnings
- - - - -
b233b653 by Martin Uecker at 2022-05-21T14:11:48+02:00
rename some set_ to get_ in moba
- - - - -
82f1c1c5 by Martin Uecker at 2022-05-21T14:19:42+02:00
refactor
- - - - -
78e39a91 by Martin Uecker at 2022-05-21T17:26:04+02:00
moba refactoring
- - - - -
834e681e by Martin Uecker at 2022-05-21T23:26:00+02:00
refactoring
- - - - -
e0618861 by Martin Uecker at 2022-05-27T21:37:20+02:00
fix typo in reference
- - - - -
9bfca34f by Martin Uecker at 2022-05-27T21:37:20+02:00
clarfications in mobafit
- - - - -
a8138506 by Martin Uecker at 2022-05-27T21:37:20+02:00
refactor
- - - - -
a5eac34c by Martin Uecker at 2022-05-27T21:37:20+02:00
coding style
- - - - -
afb7d401 by Martin Uecker at 2022-05-27T21:37:20+02:00
generic exponential model
- - - - -
c9e85d2e by Martin Uecker at 2022-05-27T21:37:20+02:00
mobafit: T2
- - - - -
a57a79b0 by Martin Uecker at 2022-05-27T21:37:20+02:00
nlop_attach, for attaching a random data pointer
- - - - -
aa65b9ab by Martin Uecker at 2022-05-27T21:37:20+02:00
remove unneeded headers and outputs
- - - - -
10414893 by Martin Uecker at 2022-05-27T21:37:20+02:00
initial code for using generic exp model in moba
- - - - -
96be7f84 by Martin Uecker at 2022-05-27T21:37:20+02:00
minor
- - - - -
9d319a52 by Martin Uecker at 2022-05-27T21:37:20+02:00
missing test prerequisite
- - - - -
66d1f4cc by Jon Tamir at 2022-06-01T08:31:18+02:00
fix basis pursuit pics when using a sampling pattern (#285)
* re-initialize sense op even if no loop flags
* re-initialize sense op if Cartesian bpsense is active
* test-pics-bpwavl1: check data consistency error
* style
- - - - -
53935168 by Martin Uecker at 2022-06-01T09:39:58+02:00
tgv/ictv + multiple penalties + 3D
- - - - -
ff9de4fe by Jon Tamir at 2022-06-02T22:02:15+02:00
don't change path for main part of bart command (fixes #284)
- - - - -
e782b930 by Jon Tamir at 2022-06-02T22:02:15+02:00
refactor matlab functions and fix failing test
- - - - -
093559fd by Nick Scholand at 2022-06-03T13:38:33+02:00
Add function to pass 4 element vector to CLI
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1d82e5e4 by Christian Holme at 2022-06-20T13:16:56+02:00
twixread: updates for VD/VE
- - - - -
d637a5e3 by Christian Holme at 2022-06-20T13:16:56+02:00
twixread: add option for debug_level
- - - - -
50905f7f by Christian Holme at 2022-06-20T13:16:56+02:00
Makefile: add testague for twixread
- - - - -
3efad151 by Christian Holme at 2022-06-23T12:07:16+02:00
tests/twixread: better datasets, better paths
and controlled by an environment variable, so that they are no longer
random paths on our systems
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1b8f7541 by Philip Schaten at 2022-06-23T18:28:51+02:00
Fix Fedora Packages
Since Fedora 36, distribution default compiler and linker flags are added implicitly: https://fedoraproject.org/wiki/Changes/SetBuildFlagsBuildCheck#How_To_Test
This includes -Wl,--as-needed ; results in undefined cblas symbols.
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1a3e77ef by Christian Holme at 2022-07-01T11:42:17+02:00
twixread: add full adc_flags, more changes for VE
Closes #288
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4743aff7 by Martin Uecker at 2022-07-01T22:22:55+02:00
coding style
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7316ac44 by Martin Uecker at 2022-07-01T22:22:55+02:00
update gcc version in the README for Macs
- - - - -
c23ab116 by Nick Scholand at 2022-07-01T22:29:35+02:00
Simplify parameter passing
- - - - -
6be1997c by Martin Uecker at 2022-07-02T10:53:07+02:00
README updates
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5f214da9 by Martin Uecker at 2022-08-02T21:45:10+02:00
fix for other wavelet types
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43146dda by Martin Uecker at 2022-08-02T21:45:10+02:00
support for different wavelets
- - - - -
e0fe7c0e by Martin Uecker at 2022-08-02T22:26:33+02:00
also update cuda
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f0112dd0 by Alexander Fyrdahl at 2022-08-03T22:23:40+02:00
adjoint nufft example used wrong dcf
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c56d3080 by Martin Uecker at 2022-08-04T10:18:47+02:00
coding style
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2d0a4c2d by Martin Uecker at 2022-08-04T10:21:54+02:00
option to select wavelets in pics
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d6ae5521 by Nick Scholand at 2022-08-12T17:43:27+02:00
Add arccos md functions
- - - - -
24d43484 by Nick Scholand at 2022-08-12T19:21:22+02:00
Add rotational matrices simulation option with utest
based on homogeneously discretized sinc shaped rf pulses
- - - - -
af428395 by Nick Scholand at 2022-08-12T19:21:22+02:00
Single hard pulse is special case of rotational matrix based simulation
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55204e26 by Martin Uecker at 2022-08-12T19:31:33+02:00
coding style
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1ffeb48c by Nick Scholand at 2022-08-12T19:33:22+02:00
Change default pulse duration
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ab2904b0 by Nick Scholand at 2022-08-12T19:47:19+02:00
Add option to pass ODE solver tolerance to simulation
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46270b18 by Nick Scholand at 2022-08-12T20:28:56+02:00
Add option to remove coeff maps from joint wavelet denoising
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badf3b12 by Nick Scholand at 2022-08-12T20:33:09+02:00
More precise description
- - - - -
1008b1dc by Martin Uecker at 2022-08-13T09:44:53+02:00
output number of failing test
- - - - -
959fc981 by Martin Uecker at 2022-08-13T09:45:06+02:00
do not use -fsantize=address in UBSAN=1, introduce ASAN
- - - - -
9d4726ae by Nick Scholand at 2022-08-13T10:33:55+02:00
Copy sim struct
Ensures that the original data is not changed
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7cc0864a by Martin Uecker at 2022-08-13T10:34:55+02:00
add blochfun and test
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29738920 by Martin Uecker at 2022-08-13T11:20:01+02:00
coding style
- - - - -
e3607c8d by Martin Uecker at 2022-08-13T11:35:00+02:00
coding style
- - - - -
8ad7bd43 by Martin Uecker at 2022-08-13T13:50:18+02:00
Bloch model recon with tests
- - - - -
cb2c99f6 by Martin Uecker at 2022-08-17T11:15:54+02:00
update help str.
- - - - -
97abf8f4 by Martin Uecker at 2022-08-17T11:26:48+02:00
psf test error
- - - - -
8cfd7760 by Nick Scholand at 2022-08-17T13:18:59+02:00
Add reparameterized Look-Locker model (MDB_T1_PHY) with tests
Parameters (M0, R1, FA) are closer to Bloch equations
- - - - -
6a1d3c02 by Martin Uecker at 2022-08-17T15:14:28+02:00
merge functions for sobolev norm weights
- - - - -
3ed1d4c7 by Nick Scholand at 2022-08-17T15:25:15+02:00
Fix R2 map and B1 map tests
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b15192f2 by Nick Scholand at 2022-08-17T15:25:15+02:00
Increase strength of Bloch moba IR FLASH tests
Add and set test for flip angle accuracy default
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bb07ca8c by Nick Scholand at 2022-08-17T15:32:31+02:00
Reduce debug value for simplified moba debugging
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26bb2fed by Martin Uecker at 2022-08-17T15:43:03+02:00
comment
- - - - -
90e93a08 by Nick Scholand at 2022-08-17T16:14:32+02:00
Set constraint maps with flags
allows setting multiple (also non consecutive) dimensions
- - - - -
bdee9153 by Martin Uecker at 2022-08-17T16:14:32+02:00
rewrite positivity constraint
- - - - -
abbeae3c by Nick Scholand at 2022-08-17T16:14:32+02:00
Generalize Bloch moba interface to support IR bSSFP with tests
- - - - -
6f7eb592 by Nick Scholand at 2022-08-17T16:16:01+02:00
minor
- - - - -
61491a52 by Nick Scholand at 2022-08-18T12:00:08+02:00
Add B1 input file option to Bloch model moba with test
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34a32cf2 by Christian Holme at 2022-08-18T13:25:50+02:00
ictv.c: typo
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0d97a717 by Christian Holme at 2022-08-18T13:25:50+02:00
estdelay.c: warn on unexpected shifts, rename shift1 -> scale
- - - - -
f7e02b2b by Christian Holme at 2022-08-18T13:25:50+02:00
estdelay.c: only add 0.5 for trajs with even number of samples
and add tests for odd number of samples
- - - - -
41dd6bda by Nick Scholand at 2022-08-18T16:06:30+02:00
Add spoke averaging option to simulation interface and integrate option
to moba, sim, and signal with tests
- - - - -
e45e5cdf by Martin Uecker at 2022-08-18T16:06:30+02:00
remove duplicated prepare call
- - - - -
38f32f65 by Martin Uecker at 2022-08-18T16:06:30+02:00
rewrite spoke averaging
- - - - -
13ec7d41 by Martin Uecker at 2022-08-18T16:06:30+02:00
refactor
- - - - -
33bd1afb by Nick Scholand at 2022-08-18T17:11:57+02:00
Add Fourier based slice profile to Bloch moba and sim with tests
(refactored -- MU)
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2e5515cd by Nick Scholand at 2022-08-18T17:22:51+02:00
Add option to simulation tool to output partial derivatives
- - - - -
9f4e0e2d by Nick Scholand at 2022-08-18T17:24:03+02:00
Add rotational matrix simulation option to sim CLI with tests
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699b47dc by Martin Uecker at 2022-08-18T18:28:18+02:00
bounds fix & minor changes
- - - - -
ab0dd4b3 by Martin Uecker at 2022-08-18T18:32:29+02:00
debug mode for UBSan
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67a6e689 by Martin Uecker at 2022-08-18T21:30:53+02:00
relax test some more
- - - - -
19f03ac3 by mavel101 at 2022-08-23T17:22:25+02:00
allow multiple files with the correct option string via keyworded arguments
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faac3b9f by Christian Holme at 2022-08-24T13:41:59+02:00
tests/pythoncfl.mk: typo
- - - - -
259cf391 by Christian Holme at 2022-08-24T13:45:48+02:00
tests/python_bart.mk: add tests for python interface
- - - - -
3eb7df53 by Christian Holme at 2022-08-24T13:54:40+02:00
tests/python_bart: fix tolerance
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1db46666 by Christian Holme at 2022-08-24T16:09:44+02:00
tests/python_bart: remove superfluous test
this is already tested in tests/pythoncfl.mk
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297194d3 by Christian Holme at 2022-08-24T16:21:59+02:00
github action: `make all` instead of `make`
This tests if all commands can be built, and not only if the combined
`bart` command can be built
- - - - -
55b04b44 by Christian Holme at 2022-08-24T16:21:59+02:00
add pythontest to github action
- - - - -
a540f9ed by Nick Scholand at 2022-08-25T20:05:34+02:00
Add rotational matrix simulation option to sim CLI with tests
- - - - -
a6e4f90a by Nick Scholand at 2022-08-25T20:05:34+02:00
Add option to split dimensions to sim tool with tests
- - - - -
d83c13b7 by Nick Scholand at 2022-08-25T20:05:34+02:00
Fix STM simulation for TE equal TRF with test
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1816a084 by Nick Scholand at 2022-08-25T20:05:34+02:00
Add output of simulation time
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a111af0f by Nick Scholand at 2022-08-25T20:05:34+02:00
Generalize STM matrix creation + utest
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8c7e8ba6 by Nick Scholand at 2022-08-25T20:05:34+02:00
Do not estimate STM matrix twice for bSSFP
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37bd2332 by Martin Uecker at 2022-08-25T20:05:34+02:00
better array bounds
- - - - -
8cda659a by Nick Scholand at 2022-08-25T20:05:34+02:00
Balance z gradient moment for bSSFP + fix tests and default parameters
- - - - -
1ba1a768 by Nick Scholand at 2022-08-25T20:05:34+02:00
Set all realistic inversion simulations to non slice-selective
- - - - -
33e3d3ff by Martin Uecker at 2022-08-25T20:05:34+02:00
rework fix for timing issue
- - - - -
9a71ae37 by Martin Uecker at 2022-08-25T20:05:34+02:00
tests for LTO builds
- - - - -
3b24afc8 by Nick Scholand at 2022-08-25T20:05:34+02:00
Fix md_zsum hack
Provide correct dimensions
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b7e7d9f4 by Nick Scholand at 2022-08-25T20:05:34+02:00
Move special cases of config to separate function
- - - - -
0aa5bbf9 by Nick Scholand at 2022-08-25T20:05:34+02:00
Move postprocessing out of moba's recon
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dd84edf8 by Xiaoqing Wang at 2022-08-25T20:05:34+02:00
add the time dim to the moba T1
- - - - -
0934a05b by Xiaoqing Wang at 2022-08-25T20:05:34+02:00
moba T1: add configuration options for ADMM
- - - - -
44644795 by rosenzweig at 2022-08-25T20:05:34+02:00
rmfreq: contrast change option
- - - - -
7999d253 by Martin Uecker at 2022-08-25T20:05:34+02:00
coding style
- - - - -
71eed1c5 by rosenzweig at 2022-08-25T20:05:34+02:00
rmfreq: coilwise contrast
- - - - -
cb8d1723 by wang53 at 2022-08-25T20:05:34+02:00
set the edge filter strength as an input
- - - - -
f2bd9c6e by Moritz Blumenthal at 2022-08-27T12:43:20+02:00
Add simple mnist network for demonstration
- - - - -
f7092ba4 by Christian Holme at 2022-08-31T15:56:22+02:00
misc/opts.c: use correct code path & silence warning
For long-only options using vec2 or vec3, char c is a random,
unprintable letter. Therefore, not a lower-case letter, leading to the
incorrect warning: "the upper-case options for specifying dimensions are
deprecated.".
This fixes that, and uses the new and improved way of reading vec2 and
vec3 arguments.
- - - - -
b65faa9b by Christian Holme at 2022-08-31T15:57:42+02:00
moba/iter_l1.c: fix segfault using some T1 models
- - - - -
85ee9d47 by Christian Holme at 2022-09-01T11:02:13+02:00
moba.c: fix flow reproducibility with MECO_PI model
- - - - -
d1c6a084 by Martin Uecker at 2022-09-05T13:20:13+02:00
rename function
- - - - -
dd8d10e9 by Nick Scholand at 2022-09-05T13:25:23+02:00
Unify and comment rotation systems + fix tests
- Bloch equations and rotation matrices clockwise in right-handed system
- FIXME: Unify with EPGs currently defined in counter clockwise system
- - - - -
d3a4dfc9 by Nick Scholand at 2022-09-05T13:25:23+02:00
Add rotation to TUBE and NIST phantom geometries with tests
- - - - -
ecaf8874 by Nick Scholand at 2022-09-05T13:25:23+02:00
Add diagnostic sonar phantom geometry with tests
- - - - -
41245578 by Nick Scholand at 2022-09-05T13:25:23+02:00
Add a script for creating simulated phantoms + tests
- - - - -
1e67b2ed by Nick Scholand at 2022-09-05T13:25:23+02:00
Update slice profile simulation + fix tests
- Normalize simulation output by spin density
- Remove option for Fourier based slice profile approximation
- Define slice profile simulation with slice-selection gradient strength
and slice thickness
- - - - -
3e8fd94c by Nick Scholand at 2022-09-05T13:25:23+02:00
Allow changing the ODE solver tolerance
- - - - -
dfa21c07 by Nick Scholand at 2022-09-05T13:25:23+02:00
Fix derivative output with tests
- - - - -
946f3197 by wang53 at 2022-09-05T14:19:38+02:00
moba T1: bug fix (thanks to Moritz)
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61a047c5 by Martin Uecker at 2022-09-05T20:42:01+02:00
relax test
- - - - -
85a9a517 by Martin Uecker at 2022-09-05T20:47:38+02:00
remove hard-coded scaling from moba
- - - - -
c6ec3e8a by Martin Uecker at 2022-09-05T22:50:51+02:00
parametrize scaling for M0/R1s in T1_fun
- - - - -
01c320f4 by Martin Uecker at 2022-09-05T22:50:51+02:00
remove scaling from looklocker
- - - - -
c2529892 by Martin Uecker at 2022-09-05T23:00:38+02:00
remove hard-coded initialization and scaling from moba
- - - - -
ba80ee61 by Xiaoqing Wang at 2022-09-05T23:00:38+02:00
moba/iter_l1.c: add the ADMM part
- - - - -
e731b123 by Xiaoqing Wang at 2022-09-05T23:00:38+02:00
moba T1: add the optreg for IRLL
- - - - -
09bdf937 by wang53 at 2022-09-06T10:17:10+02:00
moba T1: make the real-constraint compatible with version 0.7.0 (thanks to Christian Holme)
- - - - -
cd394399 by Moritz Blumenthal at 2022-09-06T10:19:07+02:00
transparent allocation for t1fun
- - - - -
d6a6162f by Moritz Blumenthal at 2022-09-06T10:20:10+02:00
fix t1fun (+test)
- - - - -
7560e57f by Moritz Blumenthal at 2022-09-06T10:27:20+02:00
split inversion and adjoint + gpuwrapper if gpu is initialized
- - - - -
2f5c14ac by Moritz Blumenthal at 2022-09-06T10:34:07+02:00
Fix gpuops for large vectors
- - - - -
02a81f2d by Moritz Blumenthal at 2022-09-06T10:44:36+02:00
fix bloch derivative
- - - - -
bb18fe36 by Moritz Blumenthal at 2022-09-06T10:46:35+02:00
transparent gpu allocation
- - - - -
de4e042b by Moritz Blumenthal at 2022-09-06T10:46:43+02:00
simplify copy to gpu
- - - - -
bfc550c2 by Moritz Blumenthal at 2022-09-06T10:46:50+02:00
use pos/dims from compute_mask
- - - - -
c6d76ba3 by Martin Uecker at 2022-09-06T11:21:37+02:00
comment out GPU mode
- - - - -
a0646d55 by Moritz Blumenthal at 2022-09-06T11:48:29+02:00
refactor gpu initialization (with Christian Holme)
- - - - -
07c7d130 by Moritz Blumenthal at 2022-09-06T11:48:37+02:00
refactor cuda errors
- - - - -
77b318d4 by Martin Uecker at 2022-09-06T17:51:49+02:00
fix power iteration issue
- - - - -
a2fd94f7 by Martin Uecker at 2022-09-06T17:51:49+02:00
add alpha to maxeigenval + reduce number of iterations in tests
- - - - -
037e3d8a by Martin Uecker at 2022-09-06T17:51:49+02:00
invert autonorm logic
- - - - -
2c4a4dc2 by Martin Uecker at 2022-09-06T17:51:49+02:00
parameter description
- - - - -
68ea5c4d by Martin Uecker at 2022-09-06T18:05:57+02:00
add GPU test for moba
- - - - -
0c66ebff by Christian Holme at 2022-09-09T09:43:54+02:00
moba: use ! for bool instead of == 0
- - - - -
68e5fcc3 by Christian Holme at 2022-09-09T09:44:05+02:00
moba: compat to old version
- - - - -
4d4a5396 by Christian Holme at 2022-09-09T09:44:05+02:00
moba/iter_l1: keep incorrect eigenvalue calc for compat
- - - - -
910053eb by Martin Uecker at 2022-09-10T11:25:44+02:00
remove script tests
- - - - -
088d4de0 by Martin Uecker at 2022-09-10T14:24:58+02:00
describe more directories
- - - - -
5fe45807 by Martin Uecker at 2022-09-10T14:24:58+02:00
update acknowledgements
- - - - -
923ed7e7 by Martin Uecker at 2022-09-10T14:24:58+02:00
coding style & copyright
- - - - -
006b24e0 by Martin Uecker at 2022-09-10T14:24:58+02:00
fix warning
- - - - -
8a401c45 by Nick Scholand at 2022-09-14T13:23:32+02:00
Divide multi spin simulation output by nominal slice thickness
This change keeps the nlop output similar to the single isochromate
simulation. This ensures a comparable regularization strength for single
and multi isochromate signal models.
- - - - -
e641e74b by Nick Scholand at 2022-09-14T13:23:46+02:00
Capital letters for sequence parameters
- - - - -
0cb1c771 by Moritz Blumenthal at 2022-09-15T10:36:13+02:00
set l2flags for moba l1
- - - - -
1b34f899 by Martin Uecker at 2022-09-16T09:51:43+02:00
reactivate test
- - - - -
6a0dd4d0 by Moritz Blumenthal at 2022-09-16T19:02:29+02:00
multi-gpu option for moba
- - - - -
3b32c90c by wang53 at 2022-09-16T19:04:13+02:00
moba/optreg.c: use a scaling operator for isotropic TV
- - - - -
02947c01 by Martin Uecker at 2022-09-16T20:53:10+02:00
scaling of TV derivatives in moba
- - - - -
6f94ac7a by Martin Uecker at 2022-09-16T20:53:36+02:00
remove pointless variables
- - - - -
894b02dc by Martin Uecker at 2022-09-16T21:20:44+02:00
remove unsigned
- - - - -
4791b2e0 by Moritz Blumenthal at 2022-09-17T14:12:57+02:00
add test dependency
- - - - -
3f65c4e0 by Moritz Blumenthal at 2022-09-17T14:40:44+02:00
sameplace for compute psf
- - - - -
845bfe53 by Moritz Blumenthal at 2022-09-17T14:48:46+02:00
extend linops
- - - - -
774b65aa by Moritz Blumenthal at 2022-09-17T15:12:31+02:00
release memory
- - - - -
4d10f927 by Moritz Blumenthal at 2022-09-18T14:41:30+02:00
provide function to get cuda stream
- - - - -
4ad4700c by Moritz Blumenthal at 2022-09-18T14:44:13+02:00
threadsafe initialization and stream selection for cuDNN wrapper
- - - - -
8e7b8e45 by Moritz Blumenthal at 2022-09-18T14:44:29+02:00
multigpu/streams for cuBLAS
- - - - -
709a235d by Moritz Blumenthal at 2022-09-18T17:29:29+02:00
rename operator_apply_joined_unchecked
- - - - -
f1142310 by Moritz Blumenthal at 2022-09-18T17:29:29+02:00
add function to apply operators in parallel
- - - - -
c732a925 by Moritz Blumenthal at 2022-09-18T17:29:29+02:00
nlop copy wrapper
- - - - -
e51caa36 by Moritz Blumenthal at 2022-09-18T17:29:29+02:00
get nlop/linop data from reshaped nlop/linop
- - - - -
c2703853 by Moritz Blumenthal at 2022-09-18T19:43:58+02:00
add nlop stack container
- - - - -
08928a21 by Moritz Blumenthal at 2022-09-18T19:43:58+02:00
optimize flattening of stacked operator (flatten all stacked operators independently)
- - - - -
365ee11a by Moritz Blumenthal at 2022-09-18T19:43:58+02:00
fix nlop_flatten_F to actually free nlop
- - - - -
019095c2 by Moritz Blumenthal at 2022-09-18T19:44:20+02:00
add nlop_flatten_F
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916af4c4 by Moritz Blumenthal at 2022-09-18T19:44:20+02:00
stacking for model_T1
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d335fa49 by Moritz Blumenthal at 2022-09-18T19:44:20+02:00
correct fov reduction factor in all models
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3f6ebb12 by Moritz Blumenthal at 2022-09-18T20:30:42+02:00
let utestgpu init gpu
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b6967ac0 by Martin Uecker at 2022-09-23T19:48:59+02:00
coding style
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eacc67b9 by Martin Uecker at 2022-09-24T21:42:23+02:00
bump version
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5fdb82e3 by Martin Uecker at 2022-09-25T13:44:40+02:00
Merge tag 'v0.8.00'
version 0.8.00
Changes:
- new tools: epg ictv sim reconet onehotenc measure mnist multicfl morphop fovshift
- epg: EPG simulations
- ictv: infimal convolution TV (experimental)
- sim: Bloch simulations
- reconet: deep learning reconstruction (MoDL, VarNET)
- onehotenc: transform onehotencoded data to integer encoded
- measure: compute MSE, SSIM, PSNR
- mnist: simple mnist network for demonstration
- multicfl: combine/split cfl files
- morphop: morphological operations
- fovshift: retrospectively shift the FOV
- pics: tensorflow loss
- pics: select wavelet type
- pics: TGV/ICTV regularization (experimental)
- moba: scaling parameters via command-line parameters
- moba: various numerical fixes
- moba: time timensions
- moba: support for ADMM
- moba: Bloch model recon with tests
- moba: multi-gpu option
- moba: scaling of TV derivatives
- phantom: NIST phantom and others
- phantom: rotation for TUBE and NIST phantom geometries
- phantom: rectangle geometry
- traj: flag for oversampled trajectory
- traj: 3D uniform (half-sphere) trajectory
- sim: output partial derivatives
- twixread: updates for VD/VE versions
- ismrmd: support for reading XML metadata
- estdelay: more generic regarding un-/centered trajectories
- tgv: for rof / tgv denoising
- rmfreq: support for contrast changes and coilwise contrast
- mobafit: T2 and diffusion fit
- ecalib: make number of iterations for orthiter configurable
- nufft: warn about incorrectly scaled trajectories
- nlinv: fix noncart ENLIVE
- pics: fix basis pursuit pics when using a sampling pattern (#285)
- fakeksp: fix output argument
- python interface: allow multiple files with the correct option string
- python interface: faster write_cfl
- library: New md functions: zacos, zsinh, zcosh, pdf_gauss, zmaxnorm, zcorr, tenmul
- library: framework for neural networks
- library: optimization algorithms: SGD, Adam, Adadelta, iPALM
- library: linear operators: scale, zconj, zreal, permute, padding, repmat, scaled_sum
- library: many new non-linear operators
- library: support for using different wavelet type
- library: nlop_attach, for attaching a random data pointer
- library: nlop reshape function
- library: allow forward nufft with toeplitz
- library: tgv/ictv + multiple penalties + 3D
- generic: radial DCF examples
- generic: Add support for multi cfl
- generic: POSIX shared memory files
- generic: improve determinism
- generic: improved parallelization and multi-gpu support
- generic: add better support for use as shared libray
- generic: bart for centos 7
- generic: Fix Fedora Packages
- generic: Windows support by MSYS2
- generic: support for linking with cudann
- generic: support for linking with tensorlfow
- generic: add pythontest to github action
- generic: LTO test builts
- many other bug fixes and improvements
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06b01678 by Martin Uecker at 2022-09-25T13:46:35+02:00
update patches
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cd48dfe8 by Martin Uecker at 2022-09-25T13:52:46+02:00
update changelog
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30 changed files:
- + .github/workflows/c-cpp.yml
- .gitignore.main
- .gitlab-ci.yml
- − .travis.yml
- ACKNOWLEDGEMENTS
- LICENSE
- Makefile
- README
- README.md
- debian/changelog
- debian/patches/0002-remove-empty-directory.patch → debian/patches/0001-remove-empty-directory.patch
- debian/patches/0003-deactivate-ode-unit-tests.patch → debian/patches/0002-deactivate-ode-unit-tests.patch
- debian/patches/0004-relax-failing-unit-test.patch → debian/patches/0003-relax-failing-unit-test.patch
- debian/patches/0005-workaround-for-compiler-bug.patch → debian/patches/0004-workaround-for-compiler-bug.patch
- debian/patches/0006-do-not-update-doc-commands.txt-automatically.patch → debian/patches/0005-do-not-update-doc-commands.txt-automatically.patch
- debian/patches/0008-on-Deban-never-use-git-version.patch → debian/patches/0006-on-Deban-never-use-git-version.patch
- debian/patches/0009-add-CXXFLAGS-to-nvcc-to-fix-C-build-issue.patch → debian/patches/0007-add-CXXFLAGS-to-nvcc-to-fix-C-build-issue.patch
- − debian/patches/0007-backported-test-fixes.patch
- debian/patches/series
- doc/building.txt
- + doc/pics.txt
- doc/references.txt
- + doc/resize.txt
- matlab/bart.m
- + matlab/get_bart_path.m
- matlab/test_bart.m
- matlab/wslPathCorrection.m
- + msys_setup.sh
- bart.spec → pkg/rpm/bart.spec
- libbart-dev.install → pkg/rpm/libbart-dev.install
The diff was not included because it is too large.
View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/0916b19429150590cceaeb8ced571ed6b95272b1...cd48dfe85dd8b4b94db5839e50cd900a65fd69d3
--
View it on GitLab: https://salsa.debian.org/med-team/bart/-/compare/0916b19429150590cceaeb8ced571ed6b95272b1...cd48dfe85dd8b4b94db5839e50cd900a65fd69d3
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