Stuff to parse hyperslab parameters.

git-svn-id: http://svn.cactuscode.org/arrangements/CactusPUGHIO/IOStreamedHDF5/trunk@14 0888f3d4-9f52-45d2-93bc-d00801ff5e46

2 files changed, 551 insertions, 0 deletions

diff --git a/src/ParseGeometry.c b/src/ParseGeometry.c
new file mode 100644
index 0000000..8db56f8
--- /dev/null
+++ b/src/ParseGeometry.c
@@ -0,0 +1,347 @@
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+
+#include "cctk.h"
+#include "cctk_Arguments.h"
+#include "cctk_Parameters.h"
+#include "cctk_GNU.h"
+#include "util_String.h"
+
+#include "StreamedHDF5GH.h"
+ 
+/* CCTK_NO_AUTOUSE_MACRO */
+
+/*#define DEBUG*/
+
+
+int GeometryParser(const char *before, char **outname, StreamGeo_t *geo)
+{
+  DECLARE_CCTK_PARAMETERS
+
+  regmatch_t pmatch[3],gmatch[6];
+  int matched,ierr=0,retval=0, verb=0, deb=0;
+
+  const char *argument;
+  char *varname=NULL, *geo_s=NULL, *token=NULL; 
+  char *dim_s=NULL, *ori_s=NULL, *dir_s=NULL;
+  char *len_s=NULL, *down_s=NULL;
+
+  int  dim, idim, iidim;
+  int index;
+
+  char *info;
+  
+  
+  /* Debugging switches */
+  if (CCTK_Equals(h5verbose,"debug")) {
+    deb  =1;
+    verb =1;
+  }
+  if (CCTK_Equals(h5verbose,"yes"))
+    verb =1;
+      
+
+  info = (char*) malloc (8000*sizeof(char));
+  sprintf(info,"\n\nGeometryParser \nargument: >%s<\n",before);
+
+  if((matched = CCTK_RegexMatch(before,
+		"(\\w*:?:?\\w*)\\[?(.*)?\\]?", 3, pmatch)) != 0) {
+
+#ifdef HEAVYDEBUG
+      printf("matched %d rm_so/rm_eo: %d %d;  %d %d\n",
+	     matched,
+	     pmatch[1].rm_so,pmatch[1].rm_eo,
+	     pmatch[2].rm_so,pmatch[2].rm_eo);
+#endif
+      
+      if(pmatch[1].rm_so != -1 &&
+	 (pmatch[1].rm_eo-pmatch[1].rm_so > 0))
+      {
+	varname = (char*) malloc((int)(pmatch[1].rm_eo-pmatch[1].rm_so+1)
+				 *sizeof(char));
+	strncpy(varname,before+pmatch[1].rm_so,
+		(int)(pmatch[1].rm_eo-pmatch[1].rm_so));
+	varname[(int)(pmatch[1].rm_eo-pmatch[1].rm_so)]='\0';
+
+	*outname = varname;
+	sprintf(info,"%sOUTNAME : >%s< \n",info,*outname);
+
+	if ((index = CCTK_VarIndex(varname))>=0) {
+	  geo->vdim  = CCTK_GroupDimI(CCTK_GroupIndexFromVarI(index));
+	  geo->sdim  = geo->vdim;
+	} 
+	else
+	{
+	  sprintf(info,"%sOUTNAME : no appropriate gridfunction found. \n",
+		  info,*outname);
+	  geo->vdim  = -1;
+	  geo->sdim  = -1;
+	}
+      } 
+      else  
+      {
+	CCTK_WARN(1,"No variable name found in StreamedHDF5::out_vars");
+	retval = -1;
+      }
+
+      if(pmatch[2].rm_so != -1 &&
+         (pmatch[2].rm_eo-pmatch[2].rm_so > 0))
+      {
+	geo_s = (char*) malloc((int)(pmatch[2].rm_eo-pmatch[2].rm_so+1)
+			       *sizeof(char));
+	strncpy(geo_s,before+pmatch[2].rm_so,
+		(int)(pmatch[2].rm_eo-pmatch[2].rm_so));
+        geo_s[(int)(pmatch[2].rm_eo-pmatch[2].rm_so)]='\0';
+        sprintf(info,"%sGEOMETRY: >%s< \n",info,geo_s);
+      } else {
+	sprintf(info,"%sGEOMETRY: No geometry specified -> use default\n",info);
+      }
+  }
+  else {
+    retval=-1;
+  }
+
+  /* Pattern match the hyperslab string geo_s*/
+  if (geo_s) {
+    if((matched = CCTK_RegexMatch(geo_s,
+		  "\\{(.*)\\},\\{(.*)\\},\\{(.*)\\},\\{(.*)\\},\\{(.*)\\}",
+		  6, gmatch)) != 0) 
+    {
+
+      /* SLAB DIMENSION */
+      if(gmatch[1].rm_so != -1 &&
+         (gmatch[1].rm_eo-gmatch[1].rm_so > 0))
+      {
+        dim_s = (char*) malloc((int)(gmatch[1].rm_eo-gmatch[1].rm_so+1)
+                                 *sizeof(char));
+        strncpy(dim_s,geo_s+gmatch[1].rm_so,
+                (int)(gmatch[1].rm_eo-gmatch[1].rm_so));
+        dim_s[(int)(gmatch[1].rm_eo-gmatch[1].rm_so)]='\0';
+	
+	if (deb)
+	  sprintf(info,"%sDIMENSION: >%s< \n",info,dim_s);
+
+	dim = atoi(dim_s);
+	geo->sdim = dim;
+      } 
+      else {
+	if (deb)
+	  sprintf(info,"%s","DIMENSION: No dimension\n");
+	retval = -1;
+      }
+      free(dim_s);
+			  
+      /* DIRECTION */
+      ierr = -1;
+      if(gmatch[2].rm_so != -1 &&
+         (gmatch[2].rm_eo-gmatch[2].rm_so > 0))
+	{
+	  dir_s = (char*) malloc((int)(gmatch[2].rm_eo-gmatch[2].rm_so+1)
+                                 *sizeof(char));
+	  strncpy(dir_s,geo_s+gmatch[2].rm_so,
+		  (int)(gmatch[2].rm_eo-gmatch[2].rm_so));
+	  dir_s[(int)(gmatch[2].rm_eo-gmatch[2].rm_so)]='\0';
+
+	  if (deb)
+	    sprintf(info,"%sDIRECTION: >%s< \n",info,dir_s);
+
+	  idim = 0;
+	  argument = dir_s;
+	  while((token = Util_StrSep(&argument,","))) {
+	    geo->direction[idim++]=atoi(token);
+	  }
+	  geo->direction[idim] = atoi(argument);
+	  if (idim==dim-1) ierr = 0;
+	}
+      if (ierr<0) {
+	sprintf(info,"%sDIRECTION: dimension not consistent: >%s< \n",
+		info,dir_s);
+	retval = -1;
+      }
+      free(dir_s);
+
+      /* ORIGIN */
+      ierr = -1;
+      if(gmatch[3].rm_so != -1 &&
+         (gmatch[3].rm_eo-gmatch[3].rm_so > 0))
+      {
+        ori_s = (char*) malloc((int)(gmatch[3].rm_eo-gmatch[3].rm_so+1)
+                                 *sizeof(char));
+        strncpy(ori_s,geo_s+gmatch[3].rm_so,
+                (int)(gmatch[3].rm_eo-gmatch[3].rm_so));
+        ori_s[(int)(gmatch[3].rm_eo-gmatch[3].rm_so)]='\0';
+
+	if (deb)
+	  sprintf(info,"%sDIRECTION: >%s< \n",info,ori_s);
+
+	idim=0;
+	argument = ori_s;
+	while((token = Util_StrSep(&argument,","))) {
+	  geo->origin[idim++]=atoi(token);
+	}
+	geo->origin[idim] = atoi(argument);
+	if (idim==(geo->vdim-1)) ierr = 0;
+	else if (idim==0) {
+	  for (iidim=1;iidim<geo->vdim;iidim++)
+	    geo->origin[iidim] = geo->origin[0];
+	  ierr = 0;
+	}
+      }
+      if (ierr<0) {
+	sprintf(info,"%sORIGIN: dimension not consistent: >%s< \n",
+		info,ori_s);
+	ierr = -1;
+      }
+      free(ori_s);
+
+      /* LENGTH */
+      ierr = -1;
+      if(gmatch[4].rm_so != -1 &&
+         (gmatch[4].rm_eo-gmatch[4].rm_so > 0))
+      {
+        len_s = (char*) malloc((int)(gmatch[4].rm_eo-gmatch[4].rm_so+1)
+                                 *sizeof(char));
+        strncpy(len_s,geo_s+gmatch[4].rm_so,
+                (int)(gmatch[4].rm_eo-gmatch[4].rm_so));
+        len_s[(int)(gmatch[4].rm_eo-gmatch[4].rm_so)]='\0';
+
+	if (deb)
+	  sprintf(info,"%sLENGTH: >%s< \n",info,len_s);
+
+	idim = 0;
+	argument = len_s;
+	while((token = Util_StrSep(&argument,","))) {
+	  geo->length[idim++]=atoi(token);
+	}
+	geo->length[idim] = atoi(argument);
+	if (idim==dim-1) ierr = 0;
+	else if (idim==0) {
+	  for (iidim=1;iidim<dim;iidim++)
+	    geo->length[iidim] = geo->length[0];
+	  ierr = 0;
+	}
+      }
+      if (ierr<0) {
+	sprintf(info,"%sLENGTH: dimension not consistent: >%s< \n",
+		info,len_s);
+	retval =-1;
+      }
+      free(len_s);
+
+      
+      /* DOWNSAMPLING */
+      ierr = -1;
+      if(gmatch[5].rm_so != -1 &&
+         (gmatch[5].rm_eo-gmatch[5].rm_so > 0)) {
+
+        down_s = (char*) malloc((int)(gmatch[5].rm_eo-gmatch[5].rm_so+1)
+                                 *sizeof(char));
+        strncpy(down_s,geo_s+gmatch[5].rm_so,
+                (int)(gmatch[5].rm_eo-gmatch[5].rm_so));
+        down_s[(int)(gmatch[5].rm_eo-gmatch[5].rm_so)]='\0';
+
+	if (deb)
+	  sprintf(info,"%sDOWNSAMPLING: >%s< \n",info,down_s);
+
+
+	idim=0;
+	argument = down_s;
+	while((token = Util_StrSep(&argument,","))) {
+	  geo->downs[idim++]=atoi(token);
+	}
+	geo->downs[idim] = atoi(argument);
+	if (idim==dim-1) ierr =0;
+	else if (idim==0) {
+	  for (iidim=1;iidim<dim;iidim++)
+	   geo->downs[iidim] = geo->downs[0];
+	  ierr = 0;
+	}
+      }
+      if (ierr<0) {
+	sprintf(info,"%sDOWNSAMPLING: dimension not consistent: >%s< \n",
+		info,down_s);
+	ierr =-1;
+      }
+      free(down_s);
+    }
+    if (geo_s) free(geo_s);
+  }
+
+  sprintf(info, "%sGeometry Data: \n",info);
+  sprintf(info, "%s  Argument/Slab dimension: %d / %d \n",
+	  info,geo->vdim,geo->sdim);
+  sprintf(info, "%s  Origin: ",info);
+  for (idim=0;idim<geo->vdim;idim++)
+    sprintf(info,"%s %d ",info,geo->origin[idim]);
+  sprintf(info,"%s\n  Downs : ",info);
+  for (idim=0;idim<geo->sdim;idim++)
+    sprintf(info,"%s %d ",info,geo->downs[idim]);
+  sprintf(info,"%s\n  Length: ",info);
+  for (idim=0;idim<geo->sdim;idim++)
+    sprintf(info,"%s %d ",info,geo->length[idim]);
+  sprintf(info,"%s\n  Dirs  : ",info);
+  for (idim=0;idim<geo->sdim;idim++)
+    sprintf(info,"%s %d ",info,geo->direction[idim]);
+  sprintf(info,"%s\n\n",info);
+
+
+  printf("%s",info);
+  free(info);
+  info=NULL;
+
+  USE_CCTK_PARAMETERS
+    
+  return(retval);
+}
+
+void SetDefaultGeo(StreamGeo_t *geo) {
+  DECLARE_CCTK_PARAMETERS
+
+  int idim;
+  char *argument, *token;
+  
+  geo->vdim = -1;
+  geo->sdim = -1;
+
+  /* Origin */
+  idim=0;
+  argument = origin;
+  while((token = Util_StrSep(&argument,","))) {
+    geo->origin[idim++]=atoi(token);
+  }
+  geo->downs[idim] = atoi(argument);
+
+  /* Direction */
+  idim=0;
+  argument = direction;
+  while((token = Util_StrSep(&argument,","))) {
+    geo->direction[idim++]=atoi(token);
+  }
+  geo->downs[idim] = atoi(argument);
+
+  /* Downsample */
+  idim=0;
+  argument = origin;
+  while((token = Util_StrSep(&argument,","))) {
+    geo->downs[idim++]=atoi(token);
+  }
+  geo->downs[idim] = atoi(argument);
+
+  /* Length */
+  idim=0;
+  argument = origin;
+  while((token = Util_StrSep(&argument,","))) {
+    geo->length[idim++]=atoi(token);
+  }
+  geo->length[idim] = atoi(argument);
+
+  for (idim=0;idim<STREAM_MAXDIM;idim++) {
+    geo->direction[idim] = idim;
+    geo->origin[idim]    = 0;
+    geo->length[idim]    =-1;
+    geo->downs[idim]     = 1;
+  }
+}
+ 
diff --git a/src/ParseVars.c b/src/ParseVars.c
new file mode 100644
index 0000000..f441234
--- /dev/null
+++ b/src/ParseVars.c
@@ -0,0 +1,204 @@
+ /*@@
+   @file      GHExtension.c
+   @date      Tue 9th Feb 1999
+   @author    Gabrielle Allen
+   @desc 
+              IOUtil GH extension stuff.
+   @enddesc 
+   @history
+   @endhistory
+ @@*/
+
+/*#define DEBUG_IO*/
+
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+
+#include "cctk.h"
+#include "util_String.h"
+#include "cctk_Parameters.h"
+
+#include "StreamedHDF5GH.h"
+
+
+static char *rcsid = "$Header$";
+
+
+/* =============================================================== 
+   utility routines used by other IO thorns
+   ===============================================================*/
+
+ /*@@
+   @routine    IOUtil_ParseVarsForOutput
+   @date       Sat March 6 1999
+   @author     Gabrielle Allen
+   @desc 
+               Sets each flag in the do_output[] do_output to true 
+               if var[i] could be found in the list of variable names.
+               var_list my also contain group names of variables as well as the
+               special keyword "all" which indicates that output is requested
+               on all variables.
+   @enddesc 
+   @history 
+   @endhistory 
+   @var        var_list
+   @vdesc      list of variables and/or group names
+   @vtype      const char *
+   @vio        in
+   @endvar 
+   @var        do_output
+   @vdesc      do_output of flags indicating output was requested for var[i]
+   @vtype      char []
+   @vio        out
+   @endvar 
+@@*/
+
+void ParseVarsForOutput (StreamedHDF5GH *h5GH, const char *var_list)
+{
+  char *outname=NULL;
+  char *before=NULL;
+  char *after=NULL;
+  char *splitstring;
+  int first,groupnum,i,last,index,varnum;
+  StreamGeo_t geo_tmp;
+  int ierr=0;
+
+  /* First initialise every variable to no output */
+  for (i=0; i<CCTK_NumVars(); i++)
+  {
+    h5GH->do_output[i] = 0;
+  }
+
+  /* Initialize geometry structure with default */
+  SetDefaultGeo(&geo_tmp);
+
+  splitstring = (char *) var_list;
+
+  /* split string at blanks */
+  while(Util_SplitString(&before,&after,splitstring," ")==0) {
+
+#ifdef DEBUG_IO
+    printf("   String is -%s-\n",splitstring);
+    printf("   Split is -%s- and -%s-\n",before,after);
+#endif
+
+    if (CCTK_Equals(before," ")) continue;
+
+    if (strlen(before) > 0) 
+    {
+      /* Extract geometry information */
+      ierr=GeometryParser(before, &outname, &geo_tmp);
+      if (ierr<0) printf("GeometryParser failed: >%s<\n",before);
+
+      /* Look for any special tokens */
+      if (CCTK_Equals(outname,"all")) 
+      {
+        int ilab;
+        for (ilab=0;ilab<CCTK_NumVars();ilab++) {
+	  h5GH->geo_output[ilab]= geo_tmp;
+	  h5GH->do_output[ilab] = 1;
+	}
+      } 
+      else 
+      {
+        /* See if this name is implementation::variable */
+        varnum = CCTK_VarIndex(outname);
+        if ( varnum < 0 ) 
+        {
+          /* See if this name is implementation::group */
+          groupnum = CCTK_GroupIndex(outname);
+          if (groupnum < 0) 
+          {
+            char *msg;
+            msg = (char *)malloc((100+strlen(outname))*sizeof(char));
+            sprintf(msg,"Ignoring <%s> in IO string (invalid token)",outname);
+            CCTK_WARN(2,msg);
+            free(msg);
+          } 
+          else 
+          {
+            /* We have a group so now need all the variables in the group */
+            first = CCTK_FirstVarIndexI(groupnum);
+            last = first+CCTK_NumVarsInGroupI(groupnum)-1;
+            for (index=first;index<=last;index++) {
+	      h5GH->geo_output[index]=geo_tmp;
+	      h5GH->do_output[index] =1;
+	    }
+          }
+        } 
+        else
+	{
+	  h5GH->geo_output[varnum]= geo_tmp;
+	  h5GH->do_output[varnum] = 1;
+	}
+      }
+    }
+    if(before) 
+    {
+      free(before);
+      before = NULL;
+    }
+    if(outname)
+    {
+      free(outname);
+      outname = NULL;
+    }
+    if(splitstring != var_list)
+    {
+      free(splitstring);
+    }
+     
+    splitstring = after;
+
+  }
+
+  if (strlen(splitstring)>0) {
+
+    /* Extract geometry information */
+    ierr=GeometryParser(splitstring, &outname, &geo_tmp);
+    if (ierr<0) printf("GeometryParser failed: >%s<\n",before);
+
+    /* Special cases */
+    if (CCTK_Equals(splitstring,"all")) {
+      int ilab;
+      for (ilab=0;ilab<CCTK_NumVars();ilab++) {
+	h5GH->geo_output[ilab]=geo_tmp;
+	h5GH->do_output [ilab]=1;
+      }
+    } else {
+
+      varnum = CCTK_VarIndex(splitstring);
+      if (varnum < 0) {
+        groupnum = CCTK_GroupIndex(splitstring);
+        if (groupnum < 0) {
+          char *msg;
+          msg = (char *)malloc((100+strlen(splitstring))*sizeof(char));
+          sprintf(msg,"Ignoring %s in IO string (invalid token)",splitstring);
+          CCTK_WARN(2,msg);
+          free(msg);
+        } else {
+          /* We have a group so now need all the variables in the group */
+          first = CCTK_FirstVarIndexI(groupnum);
+          last = first+CCTK_NumVarsInGroupI(groupnum)-1;
+          for (index=first;index<=last;index++) {
+	    h5GH->geo_output[index]=geo_tmp;
+	    h5GH->do_output[index] =1;
+	  }
+        }
+      } 
+      else {
+	h5GH->geo_output[varnum]=geo_tmp;
+	h5GH->do_output[varnum] =1;
+      }
+    }
+  }
+
+  if (before) free(before);
+  if (after) free(after);
+  if(splitstring != var_list)
+  {
+    free(splitstring);
+  }
+
+}