mris_convert/gifit.cpp

  - gifti.cpp: read/write TAG_GROUP_AVG_SURFACE_AREA/TAG_CMDLINE metadata
  - mris_convert: call MRISaddCommandLine() to save the command line with surface file

Author: yhuang43

mris_convert/mris_convert.cpp

@@ -164,6 +164,8 @@ main(int argc, char *argv[])
   FILE *fp=NULL;
   char *in2_fname=NULL;
 
+  std::string cmdline = getAllInfo(argc, argv, "mris_convert");
+
   nargs = handleVersionOption(argc, argv, "mris_convert");
   if (nargs && argc - nargs == 1)
   {
@@ -330,6 +332,8 @@ main(int argc, char *argv[])
     mris->ncmds = 0;
   }
 
+  MRISaddCommandLine(mris, cmdline);
+
   if(cras_add){
     printf("Adding scanner CRAS to surface xyz\n");
     MRISshiftCRAS(mris, 1);

utils/gifti.cpp

@@ -35,6 +35,8 @@
 #include "timer.h"
 #include "utils.h"  // strcpyalloc
 
+#define TAG_CMDLINE_LEN 1024
+
 /*
  *
  */
@@ -651,6 +653,7 @@ MRIS *mrisReadGIFTIdanum(const char *fname, MRIS *mris, int daNum, MRI *outmri,
         vgvalid++;
       }
 
+      // we got all 18 values
       if (vgvalid == 18) {
         mris->vg.valid = 1;  // finally we can say its valid data
       }
@@ -669,6 +672,50 @@ MRIS *mrisReadGIFTIdanum(const char *fname, MRIS *mris, int daNum, MRI *outmri,
       }
     }
 
+    /* retrieve TAG_GROUP_AVG_SURFACE_AREA info */
+    {
+      char *group_avg_surface_area = gifti_get_meta_value(&coords->meta, "TAG_GROUP_AVG_SURFACE_AREA");
+      if (group_avg_surface_area)
+        sscanf(group_avg_surface_area, "%f", &mris->group_avg_surface_area);
+    }
+
+    /* retrieve TAG_CMDLINE info */
+    {
+      char *ncmds = gifti_get_meta_value(&coords->meta, "NUM_TAG_CMDLINE");
+      if (ncmds)
+        sscanf(ncmds, "%d", &mris->ncmds);
+
+      int numcmds = mris->ncmds;
+      if (mris->ncmds > MAX_CMDS)
+      {
+        printf("[WARN] mrisReadGIFTIdanum():  too many commands (%d) in file. Only last %d will be saved!\n", mris->ncmds, MAX_CMDS);
+        mris->ncmds = MAX_CMDS;
+      }
+
+      int toskip = (numcmds > MAX_CMDS) ? (numcmds - MAX_CMDS) : 0;
+      while (toskip)
+        gifti_get_meta_value(&coords->meta, "TAG_CMDLINE");
+
+      for (int ncmd = 0; ncmd < mris->ncmds; ncmd++)
+      {
+        char tag[20] = {'\0'};
+        sprintf(tag, "%s#%d", "TAG_CMDLINE", ncmd);
+
+        char *cmdline = gifti_get_meta_value(&coords->meta, tag);
+        if (!cmdline)
+	{
+          printf("[ERROR] TAG_CMDLINE out of sync\n");
+          break;
+	}
+
+        mris->cmdlines[ncmd] = (char *)calloc(TAG_CMDLINE_LEN + 1, sizeof(char));
+        if (mris->cmdlines[ncmd] == NULL)
+            ErrorExit(ERROR_NOMEMORY, "mrisReadGIFTIdanum(): could not allocate %d byte cmdline", TAG_CMDLINE_LEN);
+        //mris->cmdlines[ncmd][TAG_CMDLINE_LEN] = 0;
+        memcpy(mris->cmdlines[ncmd], cmdline, TAG_CMDLINE_LEN);
+      }
+    }
+
     /* Copy in the vertices. */
     int vertex_index;
     for (vertex_index = 0; vertex_index < num_vertices; vertex_index++) {
@@ -2194,6 +2241,33 @@ int MRISwriteGIFTISurface(MRIS *mris, gifti_image *image, const char *out_fname)
       gifti_add_to_meta(&coords->meta, "SurfaceCenterZ", stmp, 1);
     }
 
+    // group avg surface area, TAG_GROUP_AVG_SURFACE_AREA
+    if (!FZERO(mris->group_avg_surface_area))
+    {
+      char group_avg_surface_area[100] = {'\0'};
+
+      sprintf(group_avg_surface_area, "%.20f", mris->group_avg_surface_area);
+      gifti_add_to_meta(&coords->meta, "TAG_GROUP_AVG_SURFACE_AREA", group_avg_surface_area, 1);
+    }
+
+    // TAG_CMDLINE
+    if (mris->ncmds > 0)
+    {
+      char ncmds[20] = {'\0'};
+      sprintf(ncmds, "%d", mris->ncmds);
+      gifti_add_to_meta(&coords->meta, "NUM_TAG_CMDLINE", ncmds, 1);
+
+      for (int ncmd = 0; ncmd < mris->ncmds; ncmd++)
+      {
+        char cmdline[TAG_CMDLINE_LEN] = {'\0'};
+        snprintf(cmdline, sizeof(cmdline), "%s", mris->cmdlines[ncmd]);
+
+        char tag[20] = {'\0'};
+        sprintf(tag, "%s#%d", "TAG_CMDLINE", ncmd);
+        gifti_add_to_meta(&coords->meta, tag, cmdline, 1);
+      }
+    }
+
     return NO_ERROR;
 } // end of MRISwriteGIFTISurface()