added option -noneg

v1/mtga/imgki.c

@@ -63,6 +63,8 @@ static char *info[] = {
   "     default is 0%.",
 //  "     Pixels with AUC less than (threshold/100 x max AUC) are set to zero.",
 //  "     Default is 0 %.",
+  " -noneg",
+  "     Pixels with negative Ki are set to zero.",
   " -max=<Max value>",
   "     Upper limit for Ki values.",
   " -filter",
@@ -131,6 +133,7 @@ int main(int argc, char **argv)
   int           ai, help=0, version=0, verbose=1;
   int           fi, ret;
   int           param_filt=0;
+  int           noneg=0; // 0=negative values are kept, 1=negative values set to zero
   char          inpfile[FILENAME_MAX], petfile[FILENAME_MAX];
   char          icfile[FILENAME_MAX], nrfile[FILENAME_MAX], outfile[FILENAME_MAX];
   char          tmp[1024], *cptr;
@@ -166,6 +169,8 @@ int main(int argc, char **argv)
       density=atof_dpi(cptr+2); if(density>0.0) continue;
     } else if(strncasecmp(cptr, "DENSITY=", 8)==0) {
       density=atof_dpi(cptr+8); if(density>0.0) continue;
+    } else if(strncasecmp(cptr, "NONEGATIVES", 5)==0) {
+      noneg=1; continue;
     } else if(strncasecmp(cptr, "MAX=", 4)==0) {
       upperLimit=atof_dpi(cptr+4); if(upperLimit>0.0) continue;
     } else if(strncasecmp(cptr, "E=", 2)==0) {
@@ -233,6 +238,7 @@ int main(int argc, char **argv)
     printf("density := %g\n", density);
     printf("param_filt := %d\n", param_filt);
     printf("calcThreshold := %g%%\n", 100.*calcThreshold);
+    printf("noneg := %d\n", noneg);
     fflush(stdout);
   }
   if(verbose>9) IMG_TEST=verbose-9; else IMG_TEST=0;
@@ -328,6 +334,11 @@ int main(int argc, char **argv)
     if(verbose>0) fprintf(stdout, "filtering out Ki values exceeding %g\n", upperLimit);
     imgCutoff(&out, (float)upperLimit, 0);
   }
+  /* Remove negative Ki values, if requested */
+  if(noneg) {
+    if(verbose>0) fprintf(stdout, "filtering out negative Ki values\n");
+    imgCutoff(&out, 0.0, 1);
+  }
   /*
    *  Filter out pixels that are over 4x higher than their
    *  closest neighbours

v1/mtga/test/imgki/test_imgki.sh

 #!/bin/bash
 #: Title      : test_imgki
-#: Date       : 2019-06-26
+#: Date       : 2019-09-18
 #: Author     : "Vesa Oikonen" <vesa.oikonen@utu.fi>
 #: Options    : None
 
@@ -298,7 +298,7 @@ printf "===================================================================\n"
 
 
 printf "\n 2.0.0 \n"
-printf " Test case: Dynamic ECAT7 image, starting fit from 30 min. \n"
+printf " Test case 1: Dynamic ECAT7 image, starting fit from 30 min. \n"
 printf " Expected result: Correct result. \n\n"
 
 rm -f output.v output.dft output.res stdout.txt
@@ -321,9 +321,9 @@ printf "\n ok \n"
 dft2res output.dft
 if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
 printf "\n ok \n"
-resmatch -res=1 -abs=0.0005 patlak.res output.res
 if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
 printf "\n passed. \n\n"
+resmatch -res=1 -abs=0.0005 patlak.res output.res
 
 printf "\n comparing computed ki image to correct ki image \n\n"
 imgmatch -frames=n -abs=0.005 -rel=10 correct_ki.v output.v
@@ -426,6 +426,37 @@ if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
 printf "\n passed. \n\n"
 
 
+printf "\n-----------------------------------------------------------------\n\n"
+
+
+
+printf "\n 2.3.0 \n"
+printf " Test case 1: Dynamic ECAT7 image, starting fit from 30 min. \n"
+printf " Test case 2: Option -noneg sets negative values to zero. \n"
+printf " Expected result: Correct result. \n\n"
+
+rm -f output.v output.dft output.res stdout.txt
+
+$PROGRAM -noneg plasma.dat dynamic.v 30 output.v
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+printf "\n ok \n"
+
+img2dft -P output.v plane1.roi output.dft 
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+printf "\n ok \n"
+dftmax -min -x=y -y=y output.dft > stdout.txt
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+printf "\n ok \n"
+iftisval stdout.txt "overall_min_value" 0
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+printf "\n passed. \n\n"
+
+printf "\n comparing computed ki image to correct ki image \n\n"
+imgmatch -frames=n -abs=0.005 -rel=10 correct_ki.v output.v
+if [ $? -ne 0 ] ; then printf "Failed!\n" ; exit 1 ; fi
+printf "\n passed. \n\n"
+
+
 
 printf "\n===================================================================\n"
 printf "   Other image formats \n"