Codebase list bart / 4124557
Add a script for creating simulated phantoms + tests Nick Scholand authored 1 year, 8 months ago Martin Uecker committed 1 year, 8 months ago
4 changed file(s) with 256 addition(s) and 1 deletion(s). Raw diff Collapse all Expand all
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Makefile less more
340340
341341 ifeq ($(MAKESTAGE),1)
342342 .PHONY: doc/commands.txt $(TARGETS)
343 default all clean allclean distclean doc/commands.txt doxygen test utest utest_gpu gputest testslow pythontest testague shared-lib $(TARGETS):
343 default all clean allclean distclean doc/commands.txt doxygen test utest utest_gpu gputest testslow pythontest testague scripttest shared-lib $(TARGETS):
344344 $(MAKE) MAKESTAGE=2 $(MAKECMDGOALS)
345345
346346 tests/test-%: force
770770 rm -f $(patsubst %, %, $(TARGETS))
771771 rm -f $(srcdir)/misc/version.inc
772772 rm -rf $(root)/tests/tmp/*/
773 rm -rf $(root)/stests/tmp/*/
773774 rm -rf $(root)/doc/dx
774775 rm -f $(root)/doc/commands.txt
775776 rm -f $(root)/save/fftw/*.fftw
813814 TESTS = $(filter-out $(NOT_SUPPORTED),$(TMP_TESTS))
814815 endif
815816
817 # script tests
818
819 SCRIPTDIR=$(root)/scripts
820 STESTS_TMP=$(root)/stests/tmp/$$$$/
821 STESTS_OUT=$(root)/stests/out/
822
823 include $(root)/stests/*.mk
824
816825 test: ${TESTS}
817826
818827 testslow: ${TESTS_SLOW}
822831 gputest: ${TESTS_GPU}
823832
824833 pythontest: ${TESTS_PYTHON}
834
835 scripttest: ${STESTS}
825836
826837 # unit tests
827838
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scripts/phantom.sh less more
0 #!/bin/bash
1 # Copyright 2022. Martin Uecker.
2 # All rights reserved. Use of this source code is governed by
3 # a BSD-style license which can be found in the LICENSE file.
4 #
5 # Author:
6 # 2022 Nick Scholand <scholand@tugraz.at>
7 #
8 # Creation of digital reference object.
9
10 set -e
11
12 LOGFILE=/dev/stdout
13 KSPACE=false
14 SENS=1
15 ROT_ANGLE=0
16 ROT_STEPS=1
17 GEOM=NIST
18
19 title=$(cat <<- EOF
20 Digital Reference Object
21 EOF
22 )
23
24 helpstr=$(cat <<- EOF
25 -S \t\t Diagnostic Sonar geometry (NIST phantom is default)
26 -k \t\t simulate in k-space
27 -a d \t\t angle of rotation
28 -r d \t\t number of rotation steps
29 -s d \t\t number of simulated coils
30 -t <traj> \t define custom trajectory file
31 -l \t\t logfile
32 -h \t\t help
33
34 Please adjust simulation parameters inside the script.
35 EOF
36 )
37
38 usage="Usage: $0 [-h] [-k] [-r d] [-s d] [-t <traj>] <output>"
39
40 echo "$title"
41 echo
42
43 while getopts "hSka:r:s:t:l:" opt; do
44 case $opt in
45 h)
46 echo "$usage"
47 echo
48 echo -e "$helpstr"
49 exit 0
50 ;;
51 S)
52 GEOM=SONAR
53 ;;
54 k)
55 KSPACE=true
56 ;;
57 a)
58 ROT_ANGLE=$OPTARG
59 ;;
60 r)
61 ROT_STEPS=$OPTARG
62 ;;
63 s)
64 SENS=$OPTARG
65 ;;
66 t)
67 TRAJ=$(readlink -f "$OPTARG")
68 ;;
69 l)
70 LOGFILE=$(readlink -f "$OPTARG")
71 ;;
72 \?)
73 echo "$usage" >&2
74 exit 1
75 ;;
76 esac
77 done
78
79 shift $((OPTIND - 1))
80
81 if [ $# != 1 ] ; then
82
83 echo "$usage" >&2
84 exit 1
85 fi
86
87
88 export PATH=$TOOLBOX_PATH:$PATH
89
90 if [ ! -e $TOOLBOX_PATH/bart ] ; then
91 echo "\$TOOLBOX_PATH is not set correctly!" >&2
92 exit 1
93 fi
94
95
96 output=$(readlink -f "$1")
97
98
99 # Tests for usefull input
100
101 if [ ! -z "${TRAJ}" ] && [ "$KSPACE" = false ]; then
102
103 echo "Trajectory only works in k-space domain. Please add [-k]!" >&2
104 exit 1
105 fi
106
107
108 #WORKDIR=$(mktemp -d)
109 # Mac: http://unix.stackexchange.com/questions/30091/fix-or-alternative-for-mktemp-in-os-x
110 WORKDIR=`mktemp -d 2>/dev/null || mktemp -d -t 'mytmpdir'`
111 trap 'rm -rf "$WORKDIR"' EXIT
112 cd $WORKDIR
113
114
115 # start group for redirection of output to the logfile
116 {
117
118 case $GEOM in
119
120 NIST)
121 echo "NIST Phantom Geometry"
122 echo "T2 Sphere of Model 130"
123 echo "Relaxation Paramters for 3 T"
124 echo ""
125
126 ## Relaxation parameters for T2 Sphere of NIST phantom at 3 T (Model 130)
127 ## Stupic, KF, Ainslie, M, Boss, MA, et al.
128 ## A standard system phantom for magnetic resonance imaging.
129 ## Magn Reson Med. 2021; 86: 1194– 1211. https://doi.org/10.1002/mrm.28779
130 T1=(3 2.48 2.173 1.907 1.604 1.332 1.044 0.802 0.609 0.458 0.337 0.244 0.177 0.127 0.091)
131 T2=(1 0.581 0.404 0.278 0.191 0.133 0.097 0.064 0.046 0.032 0.023 0.016 0.011 0.008 0.006)
132 ;;
133
134 SONAR)
135 echo "Diagnostic Sonar Phantom Geometry"
136 echo "Eurospin II"
137 echo "Gels: 3, 4, 7, 10, 14, and 16"
138 echo ""
139
140 ## Relaxation parameters for Diagnostic Sonar phantom
141 ## Eurospin II, gel nos 3, 4, 7, 10, 14, and 16)
142 ## T1 from reference measurements in
143 ## Wang, X., Roeloffs, V., Klosowski, J., Tan, Z., Voit, D., Uecker, M. and Frahm, J. (2018),
144 ## Model-based T1 mapping with sparsity constraints using single-shot inversion-recovery radial FLASH.
145 ## Magn. Reson. Med, 79: 730-740. https://doi.org/10.1002/mrm.26726
146 ## T2 from
147 ## T. J. Sumpf, A. Petrovic, M. Uecker, F. Knoll and J. Frahm,
148 ## Fast T2 Mapping With Improved Accuracy Using Undersampled Spin-Echo MRI and Model-Based Reconstructions With a Generating Function
149 ## IEEE Transactions on Medical Imaging, vol. 33, no. 12, pp. 2213-2222, Dec. 2014, doi: 10.1109/TMI.2014.2333370.
150 T1=(3 0.311 0.458 0.633 0.805 1.1158 1.441 3)
151 T2=(1 0.046 0.081 0.101 0.132 0.138 0.166 1)
152 ;;
153 *)
154 echo -n "Unknown geometry!\n"
155 exit 1
156 ;;
157 esac
158
159
160 # Simulation Parameters
161 # Run `bart sim --seq h` for more details
162 SEQ=ir-flash # Sequence Type
163 TR=0.0034 # Repetition Time [s]
164 TE=0.0021 # Echo Time [s]
165 REP=600 # Number of repetitions
166 IPL=0.01 # Inversion Pulse Length [s]
167 ISP=0.005 # Inversion Spoiler Gradient Length [s]
168 PPL=0 # Preparation Pulse Length [s]
169 TRF=0.001 # Pulse Duration [s]
170 FA=6 # Flip Angle [degree]
171 BWTP=4 # Bandwidth-Time-Product
172 OFF=0 # Off-Resonance [rad/s]
173 MOMSL=0 # Slice Selection Gradient Moment [rad/s]
174
175
176 # Run Simulation
177 for i in `seq 0 $((${#T1[@]}-1))`; do
178
179 echo -e "Tube $i\t T1: ${T1[$i]} s,\tT2[$i]: ${T2[$i]} s"
180
181 bart sim --ODE \
182 --seq $SEQ,tr=$TR,te=$TE,nrep=$REP,ipl=$IPL,isp=$ISP,ppl=$PPL,trf=$TRF,fa=$FA,bwtp=$BWTP,off=$OFF,mom-sl=$MOMSL \
183 -1 ${T1[$i]}:${T1[$i]}:1 -2 ${T2[$i]}:${T2[$i]}:1 \
184 _simu$(printf "%02d" $i)
185 done
186
187
188 # Join individual simulations
189 bart join 7 $(ls _simu*.cfl | sed -e 's/\.cfl//') simu
190
191 # Join simulations in a single dimension (-> 6)
192 bart reshape $(bart bitmask 6 7) ${#T1[@]} 1 simu simu2
193
194
195 # Create Geometry
196 if [ -z "${TRAJ}" ]; then
197
198 if $KSPACE; then
199
200 # Create default trajectory
201 DIM=192
202 SPOKES=$((DIM-1))
203
204 bart traj -x $DIM -y $SPOKES traj
205
206 bart phantom --${GEOM} -b -s $SENS --rotation-steps $ROT_STEPS --rotation-angle $ROT_ANGLE -t traj geom
207 else
208
209 bart phantom --${GEOM} -b -s $SENS --rotation-steps $ROT_STEPS --rotation-angle $ROT_ANGLE geom
210 fi
211 else
212 if $KSPACE; then
213
214 bart phantom --${GEOM} -b -s $SENS --rotation-steps $ROT_STEPS --rotation-angle $ROT_ANGLE -k -t ${TRAJ} geom
215 else
216
217 bart phantom --${GEOM} -b -s $SENS --rotation-steps $ROT_STEPS --rotation-angle $ROT_ANGLE geom
218 fi
219 fi
220
221 # Combine simulated signal and geometry
222
223 bart fmac -s $(bart bitmask 6) geom simu2 $output
224
225 } > $LOGFILE
226
227 [ -d $WORKDIR ] && rm -rf $WORKDIR
228
229 exit 0
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stests/phantom.mk less more
0
1 stests/phantom: sim join reshape traj phantom fmac
2 set -e; mkdir $(STESTS_TMP) ; cd $(STESTS_TMP) ;\
3 $(TOOLDIR)/traj t.ra ;\
4 $(SCRIPTDIR)/phantom.sh -S -k -a 90 -r 3 -s 3 -l log.txt -t t.ra test.ra ;\
5 exit 0 ;\
6 rm *.ra *.txt ; cd .. ; rmdir $(STESTS_TMP)
7 touch $@
8
9 STESTS += stests/phantom⏎
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stests/tmp/.gitignore less more
0 # Ignore everything in this directory
1 *
2 # Except this file
3 !.gitignore