Merge pull request #2 from hcmh/master

revision

04_newton_noise/brain/1_create_figure.sh

@@ -17,6 +17,41 @@ TMP=tmp
 mkdir ${TMP} || true
 cd $TMP
 
+
+
+#add arrow
+arrow_head="l 0,0  +200,+500  -200,+500  +1500,-500 z"
+
+convert -size 1500x1000 xc:None \
+	        -draw "stroke white fill white scale 1,1 rotate 0
+               path 'M 000,000  $arrow_head' " \
+		               arrow.png
+
+declare -A uARROWS
+uARROWS["22_0.05"]="+218+219 +541+641"
+uARROWS["25_0.01"]="+240+240 +224+286 +175+583"
+uARROWS["25_0.025"]="+230+195 +180+233 +141+390 +100+605"
+uARROWS["25_0.05"]="+241+125 +190+195 +130+295 +100+347 +141+588 +130+673 +460+823"
+
+
+#add offsets
+offsetx=54
+offsety=59
+declare -A ARROWS
+for i in "${!uARROWS[@]}"
+do
+	arrow=""
+	for uarrow in ${uARROWS[$i]}
+	do
+		X=$(echo $uarrow | cut -f2 -d"+")
+		Y=$(echo $uarrow | cut -f3 -d"+")
+		(( X = X - offsetx ))
+		(( Y = Y - offsety ))
+		arrow="$arrow +$X+$Y"
+	done
+	ARROWS[$i]="$arrow"
+done
+
 scale_and_text()
 {
 	IF="$1"
@@ -40,6 +75,17 @@ do
 		else
 			cp ../r_mm_${N}_${NOISE}.png ${N}_${NOISE}.png
 		fi
+
+		arg="${N}_${NOISE}"
+		arrows=${ARROWS[$arg]+"${ARROWS[$arg]}"}
+		if [ ! -z "$arrows" ]
+		then
+			for arrow in ${arrows[@]}
+ 			do	
+				convert ${N}_${NOISE}.png \( ./arrow.png -scale 04\% -geometry "$arrow" -background None -rotate 50 \) -composite ${N}_${NOISE}.png
+			done
+		fi
+
 	done
 
 	convert -interword-spacing 1  -rotate -90 -density ${DENSITY} -pointsize ${FONTSIZE} -font ${FONT} caption:"${NSTRING}" -gravity Center ../r_mm_${NEWTONS[0]}_${NOISE}.png +append -gravity east -splice x0 N_tmp.png

04_newton_noise/brain/doit.sh

@@ -2,7 +2,6 @@
 set -euo pipefail
 set -B
 
-# ENLIVE reco first:
 # param is output directory
 ./0_reco_enlive.sh reco_ENLIVE
 

07_phase_singularities/create_HeadvPhantom.sh → 07_phase_singularities/create_Phantom_Head_Heart.sh

@@ -6,6 +6,7 @@ source head/opts.sh
 DIR=reco
 SL1=phantom/${DIR}/${DIR}.png
 SL2=head/${DIR}/${DIR}.png
+SL3=heart/${DIR}/${DIR}.png
 
 Y=$(identify -format "%[fx:h]" phantom/${DIR}/r_sm.png)
 DENSITY=$( echo 'scale=5; 72/192*'$Y | bc)
@@ -29,22 +30,27 @@ scale_and_text()
 #the space after a and b is a unicode  U+2009 THIN SPACE
 scale_and_text ../${SL1} "a " 1.png
 scale_and_text ../${SL2} "b " 2.png
+W=$(identify -format "%[fx:w]" ../${SL2})
+convert -geometry ${W}x ../${SL3} tmp3.png
+scale_and_text tmp3.png "c " 3.png
 
-montage -background white -alpha remove 1.png 2.png -tile 1x2 \
+
+montage -background white -alpha remove 1.png 2.png 3.png -tile 1x3 \
 	-geometry "1x1+0+${SPACING}<" -border 0 tmp.png
 
 H=$(identify -format "%[fx:h]" tmp.png)
+H2=$(echo "$H/2" | bc)
 
-convert ../../MYGBM_colorbar.png -geometry x${H} cb_tmp.png
+convert ../../MYGBM_colorbar.png -geometry x${H2} cb_tmp.png
 
-convert tmp.png cb_tmp.png +append -layers mosaic tmp2.png
+convert tmp.png cb_tmp.png -gravity east +append -layers mosaic tmp2.png
 
 
 #remove whitespace around final image:
-convert tmp2.png -density ${DENSITY} -units PixelsPerInch -crop +0+${SPACING} +repage -crop -0-${SPACING} +repage ../bh_headvphantom.png
+convert tmp2.png -density ${DENSITY} -units PixelsPerInch -crop +0+${SPACING} +repage -crop -0-${SPACING} +repage ../bh_phan_head_heart.png
 
 
 cd ..
 rm -r ${TMP}
 
-cp bh_headvphantom.png ../output/07_fig_blackholes.png
+cp bh_phan_head_heart.png ../output/07_fig_blackholes.png

10_noncart/heart/.gitignore → 07_phase_singularities/heart/.gitignore

@@ -1,3 +1,3 @@
-reco_*/
+reco/
 data/*
 !data/unders.*

10_noncart/heart/0_prep.sh → 07_phase_singularities/heart/0_prep.sh

@@ -4,26 +4,36 @@ source opts.sh
 set -euo pipefail
 set -B
 
-#if false; then
-#	# generate undersampled data
-#	# T6439, sl2, 21-25
-#	RAW=/home/ague/archive/2016/2016-08-30_Sequence_bSSFP/T006439/T006439_raw.coo
-#	$BART extract 11 2 2 $RAW data/tmp
-#	$BART extract 10 21 25 data/tmp{,2}
-#	$BART transpose 2 10 data/tmp{2,}
-#	$BART circshift 2 4 data/tmp{,2}
-#	$BART reshape 6 $NSPK 1 data/tmp{2,}
-#	$BART transpose 1 2 data/tmp{,2}
-#	$BART transpose 0 1 data/tmp2 data/unders
-#fi
+if false; then
+	# generate undersampled data
+
+	# TT10740, sl9, 15-20
+	DAT=/home/ague/archive/volunteers/2018-09-07_MRT5_ADVM_0004/2018-09-07_SA_BlackHoles/meas_MID00268_FID25607_mpi_rfl40_33ms_SA_mit_VH_20_3.dat
+	RAW=data/raw_T10740
+	$BART twixread -A $DAT $RAW 
+	NSPK=$(echo "$NSSPK"*"$NTURN" | bc)
+	$BART slice 13 07 $RAW data/tmp
+	$BART extract 10 80 85 data/tmp{,2}
+	$BART transpose 2 10 data/tmp{2,}
+	$BART circshift 2 3 data/tmp{,2}
+
+	$BART reshape 6 $NSPK 1 data/tmp{2,}
+	$BART transpose 1 2 data/tmp{,2}
+	$BART transpose 0 1 data/tmp2 data/unders
+fi
+
+NSSPK=15
+NTURN=5
+NSPK=$(echo "$NSSPK"*"$NTURN" | bc)
+NC=$($BART show -d3 data/unders)
 
 $BART traj -x$NSMPL -y$NSPK -t5 -D data/traj_uncorr
 
 # gradient delays
 GD=$($BART estdelay data/traj_uncorr data/unders)
 
 $BART traj -x$NSMPL -y$NSPK -t5 -D -q${GD} data/tmp
-$BART reshape 12 13 5 data/tmp{,2}
+$BART reshape 12 $NSSPK $NTURN data/tmp{,2}
 $BART circshift 3 3 data/tmp{2,}
 $BART reshape 12 $NSPK 1 data/tmp data/traj
 
@@ -35,9 +45,9 @@ $BART scale $OG data/traj data/traj_scaled
 SCALE=$(echo "scale=5;1./"$NSPK | bc -l)
 $BART nufft -d$S:$S:1 -a data/traj_scaled data/unders data/tmp_grid > /dev/null
 $BART fft -u 7 data/tmp_grid data/tmp
-$BART scale $SCALE data/tmp data/grid
-
+$BART scale 1. data/tmp data/grid
 
+#PSF
 $BART ones 3 1 $NSMPL $NSPK data/tmp_o
 $BART nufft -d$S:$S:1 -a data/traj_scaled data/tmp_o data/tmp > /dev/null
 $BART fft -u 7 data/tmp{,2}

10_noncart/heart/1_reco_enlive.sh → 07_phase_singularities/heart/1_reco_enlive.sh

@@ -13,13 +13,14 @@ out=$1
 DEBUG=4
 
 #resize to: 
-CROP=$(echo "scale=0;"$NSMPL"*"$OG"/3" | bc -l)
+CROP=$(echo "scale=0;"$NSMPL"/2*1.1" | bc -l)
 for ((m=1; m<=$COMP_MAPS; m++))
 do
     $BART nlinv -d$DEBUG -m$m $NLINV_OPTS $DATA $out/tmp_${m} >$out/log_r_mm_${m} 2>&1
     $BART resize -c 0 $CROP 1 $CROP $out/tmp_${m} $out/r_mm_${m}
     $BART rss 4096 $out/r_mm_${m} $out/tmp_rss_${m}
     $CFL2PNG $CFLCOMMON $out/tmp_rss_${m} $out/r_mm_${m}.png
+    $CFL2PNG -C Y $CFLCOMMON $out/r_mm_${m} $out/r_mm_${m}_phase.png
 
     if [ "$m" -eq "$COMP_MAPS" ]
     then

07_phase_singularities/heart/2_create_figure.sh

@@ -0,0 +1,47 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+source ../../FONT.sh
+source opts.sh
+
+#first argument is both dir name and output name
+DIR="$1"
+cd ${DIR}
+
+Y=$(identify -format "%[fx:h]" ./r_mm_1.png)
+#set density. 72 means 1pt is 1 pxl
+DENSITY=$( echo 'scale=5; 72/192*'$Y | bc)
+FONTSIZE=$( echo 'scale=0; 192/6' | bc)
+SPACING=$( echo 'scale=0; '${Y}'/48' | bc)
+STRW=3
+
+TMP=tmp
+mkdir ${TMP} || true
+cd $TMP
+
+scale_and_text()
+{
+	IF="$1"
+	T="$2"
+	OF="$3"
+	convert ${IF} -stroke red -strokewidth ${STRW} -fill none -draw "translate ${circle_x},${circle_y} circle 0,0 ${circle_r},0" tmp.png
+	convert tmp.png -density ${DENSITY} -pointsize ${FONTSIZE} -font ${FONT} label:"${T}" -gravity Center -append ${OF}
+	rm tmp.png
+
+}
+
+
+scale_and_text "../r_mm_1.png" "1 map" 1m.png 
+scale_and_text "../r_mm_2.png" "2 maps" 2m.png 
+scale_and_text "../r_mm_1_phase.png" "1 map phase" phase.png
+
+scale_and_text ../r_mmu_2_map_0000.png "map #1" m0.png 
+scale_and_text ../r_mmu_2_map_0001.png "map #2" m1.png 
+montage -background white -alpha remove phase.png 1m.png 2m.png m0.png m1.png -tile 5x1 -geometry "1x1+${SPACING}+0<" tmp.png
+
+#remove whitespace around final image:
+convert tmp.png -density ${DENSITY} -units PixelsPerInch -crop +${SPACING}+0 +repage -crop -${SPACING}-0 +repage ../${DIR}.png
+
+cd ..
+rm -r ${TMP}
+cd ..

10_noncart/heart/data/unders.hdr → 07_phase_singularities/heart/data/unders.hdr

@@ -1,8 +1,8 @@
 # Dimensions
-1 320 65 30 1 1 1 1 1 1 1 1 1 1 1 1 
+1 320 75 30 1 1 1 1 1 1 1 1 1 1 1 1 
 # Command
 transpose 0 1 data/tmp2 data/unders 
 # Files
  >data/unders <data/tmp2
 # Creator
-BART v0.4.01-62-gba56e21
+BART v0.4.03

07_phase_singularities/heart/doit.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+./0_prep.sh
+
+./1_reco_enlive.sh reco
+
+./2_create_figure.sh reco

10_noncart/heart/opts.sh → 07_phase_singularities/heart/opts.sh

@@ -1,16 +1,20 @@
 ZOOM=3
 DATA=data/grid
 REF=data/ref
-WMAX=0.4
+WMAX=0.3
 CFLCOMMON="-z$ZOOM -u$WMAX -FZ -x0 -y1"
 
-NEWTON=11
-REDU=2
+NEWTON=17
+REDU=1.5
 
 NLINV_OPTS="-a240 -b40  -i${NEWTON} -R${REDU} -S -f0.5 -pdata/psf"
 MAPS=2
 COMP_MAPS=2
 
 NSMPL=320
-NSPK=65
 OG=1.5
+
+
+circle_r=$((  12 * $ZOOM ))
+circle_x=$(( ( 176 - 163 ) * $ZOOM ))
+circle_y=$(( ( 176 - 45 ) * $ZOOM ))

08_09_lowrank/knee/.gitignore

@@ -0,0 +1,3 @@
+reco*/
+data/*
+!data/single_slice.*

08_09_lowrank/knee/0_prep.sh

@@ -0,0 +1,26 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+source ../../BART.sh
+
+if false;
+then
+	cd data
+	wget http://old.mridata.org/knees/fully_sampled/p3/e1/s1/P3.zip
+	unzip P3.zip
+	cd ..
+
+	#extract single slice
+	$BART fft -u -i 1 data/kspace data/tmp_fft
+	$BART slice 0 160 data/tmp_fft data/single_slice
+fi
+
+$BART rss 8 data/single_slice data/tmp_rss
+$BART threshold -H 21 data/tmp_rss data/tmp_pat
+$BART pattern data/tmp_pat data/pat
+$BART fmac data/pat data/single_slice data/tmp_full
+#scale maximum to about 1
+$BART scale 1e-8 data/tmp_full data/full
+
+
+rm data/tmp_*

08_09_lowrank/knee/1_gen_unders.sh

@@ -0,0 +1,40 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+source ../../BART.sh
+
+US=$1
+
+SEED=20869
+
+# VD-PD for total undersampling of $US:
+$BART poisson -Y320 -Z256 -y$US -z$US -v -V05 -s$SEED data/tmp_pat_${US} > /dev/null
+$BART pattern data/full data/s_${US}
+$BART fmac data/tmp_pat_${US} data/s_${US} data/pat_${US}
+rm data/tmp_pat_${US}.*
+
+#calculate undersampling
+$BART fmac -s 65535 data/s_${US} data/s_${US} data/ns_${US}
+$BART fmac -s 65535 data/pat_${US} data/pat_${US} data/npat_${US}
+ALL=$($BART show -f "%+f%+fi" data/ns_${US} | cut -f1 -d"." | cut -f2 -d"+")
+PAT=$($BART show -f "%+f%+fi" data/npat_${US} | cut -f1 -d"." | cut -f2 -d"+")
+rm data/ns_${US}.* data/npat_${US}.* data/s_${US}.*
+
+UNDERS=$(echo "scale=1;"$ALL"/"$PAT | bc -l)
+echo $UNDERS > data/undersampling_factor_${US}.txt
+
+source opts.sh
+US_NAME=$(GET_US $US)
+
+mv data/pat_${US}.cfl data/pat_${US_NAME}.cfl
+mv data/pat_${US}.hdr data/pat_${US_NAME}.hdr
+$BART fmac data/full data/pat_${US_NAME} data/unders_${US_NAME}
+
+# rss reco:
+mkdir -p reco_zerofill
+$BART fft -u -i 7 data/unders_${US_NAME} data/tmp_${US_NAME}
+$BART rss 8 data/tmp_${US_NAME} reco_zerofill/zf_${US_NAME}
+$CFL2PNG $CFLCOMMON reco_zerofill/zf_${US_NAME}{,.png}
+
+rm data/tmp_${US_NAME}.*
+

08_09_lowrank/knee/2_reco_enlive.sh

@@ -0,0 +1,27 @@
+#!/usr/bin/env bash
+source ../../BART.sh
+source opts.sh
+
+set -euo pipefail
+# brace expand
+set -B
+
+out=$1
+US=$(GET_US $2)
+
+DEBUG=4
+MAPS=2
+
+export OMP_NUM_THREADS=1
+
+# regular
+{ time $BART nlinv -d$DEBUG -m$MAPS -U $NLINV_OPTS ${DATA}_${US} $out/r_mmu_${US}; } \
+	>$out/log_r_mmu_${US} 2>$out/timelog_r_mmu_${US}
+$CFL2PNG $CFLCOMMON $out/r_mmu_${US}{,}
+
+$BART nlinv -d$DEBUG -m$MAPS $NLINV_OPTS ${DATA}_${US} $out/r_mm_${US} >$out/log_r_mm_${US}
+$CFL2PNG $CFLCOMMON $out/r_mm_${US}{,}
+
+$BART nlinv -d$DEBUG -m1 $NLINV_OPTS ${DATA}_${US} $out/{r,s}_sm_${US} >$out/log_r_sm_${US}
+$CFL2PNG $CFLCOMMON $out/r_sm_${US}{,}
+$CFL2PNG -C Y $CFLCOMMON $out/r_sm_${US} $out/r_sm_phase_${US}.png