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In response to referee's comment:
"However, (although it is probably not important for model developers), I was
still unable to load the model ‘Meinhardt 1976 with growth’ example from the
‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in
rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected
the Meinhardt model in both the Models and the File -> Read leaf menus together,
it would be preferable if the models loaded from the Models menu worked
automatically. I am not sure that the update referred to in the author’s
response permits the loading of ‘My First Model in Virtual Leaf’ from the
‘Models’ drop down menu; I only got a cell that wiggled."
I made the following changes:
- meinhardt_plugin now reads "meinhardt_init.xml" by default
- changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example.
- Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used.
--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added data/leaves/tutorial1_init.xml
added data/leaves/tutorial2_init.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed src/TutorialCode/Tutorial0/tutorial0.cpp
changed src/TutorialCode/Tutorial1A/tutorial1A.h
changed src/TutorialCode/Tutorial1B/tutorial1B.h
changed src/TutorialCode/Tutorial1C/tutorial1C.h
changed src/TutorialCode/Tutorial1D/tutorial1D.h
changed src/TutorialCode/Tutorial2/tutorial2.h
changed src/build_models/meinhardtplugin.h
"However, (although it is probably not important for model developers), I was
still unable to load the model ‘Meinhardt 1976 with growth’ example from the
‘Models’ drop down menu, I got the ‘Fatal error’ message ‘stepwise underflow in
rkqs, with h=0.000000 and htry = 0.100000’. The model did work when I selected
the Meinhardt model in both the Models and the File -> Read leaf menus together,
it would be preferable if the models loaded from the Models menu worked
automatically. I am not sure that the update referred to in the author’s
response permits the loading of ‘My First Model in Virtual Leaf’ from the
‘Models’ drop down menu; I only got a cell that wiggled."
I made the following changes:
- meinhardt_plugin now reads "meinhardt_init.xml" by default
- changed the name of 'My First Model in Virtual Leaf’ to '0: Empty model template (does nothing)' to make it clear that the wiggle cell is the intended behavior for this model example.
- Added default parameter files for Tutorial1A-D and Tutorial2 to prevent variable behavior depending on the last parameter settings used.
--
user: Roeland Merks <roeland.merks@cwi.nl>
branch 'default'
added data/leaves/tutorial1_init.xml
added data/leaves/tutorial2_init.xml
changed data/leaves/auxin_growth.xml
changed data/leaves/meinhardt_init.xml
changed src/TutorialCode/Tutorial0/tutorial0.cpp
changed src/TutorialCode/Tutorial1A/tutorial1A.h
changed src/TutorialCode/Tutorial1B/tutorial1B.h
changed src/TutorialCode/Tutorial1C/tutorial1C.h
changed src/TutorialCode/Tutorial1D/tutorial1D.h
changed src/TutorialCode/Tutorial2/tutorial2.h
changed src/build_models/meinhardtplugin.h
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*
* This file is part of the Virtual Leaf.
*
* VirtualLeaf is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* VirtualLeaf is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with the Virtual Leaf. If not, see <http://www.gnu.org/licenses/>.
*
* Copyright 2010 Roeland Merks.
*
*/
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <errno.h>
#include <string.h>
#include "warning.h"
#include "parse.h"
#include "output.h"
#include <string>
static const std::string _module_id("$Id$");
using namespace MyWarning;
char *ParsePar(FILE *fp, char *parameter, bool wrapflag)
{
char *line,*token;
char *value;
line=SearchToken(fp,parameter, wrapflag);
if (line==NULL) {
warning("Warning: Token %s not found.",parameter);
value=0;
return value;
}
/* parse the line on = sign */
token=strtok(line,"=");
if (token==NULL) {
error("Parse error: no '=' sign found next to token %s, in line: \n %s.",
parameter,line);
}
// warning("Reading value for token %s...",token);
fprintf(stderr, "[%s = ",token);
token=strtok(NULL,"=");
if (token==NULL)
error("\nParse error: no value found after '=' sign, in line: \n %s",
line);
value=strdup(token);
free(line);
return value;
}
int igetpar(FILE *fp,char *parameter, bool wrapflag) {
// overloaded compatibility function. Doesn't need default parameter
return igetpar(fp, parameter, 0, wrapflag);
}
int igetpar(FILE *fp,char *parameter, int default_val, bool wrapflag)
{
char *token;
int value;
/* Get token representing the value */
token=ParsePar(fp,parameter, wrapflag);
if (token==0) {
/* default value */
warning("No token %s found. Using default value %d.\n", parameter, default_val);
return default_val;
}
/* read it */
sscanf(token,"%d",&value);
fprintf(stderr, "%d]\n",value);
free(token);
return value;
}
float fgetpar(FILE *fp,char *parameter, bool wrapflag) {
// overloaded compatibility function. Doesn't need default parameter
return fgetpar(fp, parameter, 0., wrapflag);
}
float fgetpar(FILE *fp, char *parameter, double default_val, bool wrapflag)
{
char *token;
float value;
/* Get token representing the value */
token=ParsePar(fp,parameter, wrapflag);
if (token==0) {
/* default value */
warning("No token %s found. Using default value %f.\n", parameter, default_val);
return default_val;
}
/* read it */
sscanf(token,"%e",&value);
fprintf(stderr,"%e]\n",value);
free(token);
return value;
}
double *dgetparlist(FILE *fp,char *parameter, int n, bool wrapflag)
{
/* Get a list of n comma separated doubles */
char *token;
double *value;
char *number;
int i;
value=(double *)malloc(n*sizeof(double));
/* Get token representing the value */
token=ParsePar(fp,parameter, wrapflag);
if (token==0) {
error("No token %s found.\n", parameter);
}
/* parse it */
number=strtok(token,","); /* make a pointer to "token" */
i=0;
while (number!=NULL) {
if (i>=n) {
error("\nToo many values found for parameterlist '%s' (%d expected).",parameter,n);
}
sscanf(number,"%le",&value[i]);
fprintf(stderr,"[%f]",value[i]);
/* next value */
number=strtok(NULL,",");
i++;
}
fprintf(stderr,"]\n");
if (i<n) {
warning("Too few values found for parameterlist '%s' (%d expected).", parameter,n);
warning("Padding with 0.");
for (int j=i;j<n;j++)
value[j]=0.;
fprintf(stderr, "Full array is ");
for (int i=0;i<n;i++) {
fprintf(stderr," %lf ",value[i]);
}
fprintf(stderr, "\n");
}
return value;
}
char *sgetpar(FILE *fp,char *parameter, bool wrapflag)
{
return sgetpar(fp, parameter, " ", wrapflag);
}
char *sgetpar(FILE *fp, char *parameter, const char *default_val, bool wrapflag) {
char *token;
char *value;
int pos;
/* Get token representing the value */
token=ParsePar(fp,parameter, wrapflag);
if (token==0) {
/* default value */
warning("No token %s found. Using default value '%s'.\n", parameter, default_val);
value=strdup(default_val);
return value;
}
/* strip leading spaces and duplicate string */
pos=strspn(token," \t\n");
value=(char *)malloc((strlen(&token[pos])+1)*sizeof(char));
sprintf(value,"%s",&token[pos]);
free(token);
fprintf(stderr,"%s]\n",value);
return value;
}
char *bool_str(bool bool_var) {
/* Return string "true" if bool_var=true */
/* Return string "false" if bool_var=false */
static char t[5] = "true";
static char f[6] = "false";
if (bool_var) {
return t;
} else {
return f;
}
}
bool bgetpar(FILE *fp, char *parameter, bool wrapflag) {
// overloaded compatibility function. Doesn't need default parameter
// default = false
return bgetpar(fp, parameter, 0, wrapflag);
}
bool bgetpar(FILE *fp, char *parameter, int default_val, bool wrapflag) {
/* Get boolean parameter. */
/* if "true" or "yes", return 1 */
/* if "false" or "no", return 0 */
/* else complain */
char *token;
int value=0;
int pos;
/* Get token representing the value */
token=ParsePar(fp,parameter, wrapflag);
if (token==0) {
/* default value */
warning("No token %s found. Using default value %s.\n", parameter, bool_str(default_val));
return default_val;
}
/* strip leading spaces */
pos=strspn(token," \t\n");
if (!strcmp(&token[pos],"yes") || !strcmp(&token[pos],"true") || !strcmp(&token[pos],"1"))
value=1;
else
if (!strcmp(&token[pos],"no") || !strcmp(&token[pos],"false") || !strcmp(&token[pos],"0"))
value=0;
else
error("Keyword '%s' not recognized. Try yes/no or true/false.\n",&token[pos]);
fprintf(stderr, "%s]\n",bool_str(value));
return value;
}
char *SearchToken(FILE *fp, char *token,bool wrapflag)
{
/* This function returns the next line of FILE *fp that contains
the string stored in the null terminated string token */
/* remember to free the memory allocated for line */
unsigned int len;
char *line;
int wrapped=false;
long initial_position;
char *tokenplusspace = (char *)malloc( (strlen(token)+3)*sizeof(char));
strcpy(tokenplusspace, token);
strcat(tokenplusspace," ");
initial_position=ftell(fp);
if (ferror(fp)) /* error occured */
{
error("%s",strerror(errno));
}
if (feof(fp)) {
warning("End of file\n");
}
while (!(wrapped && ftell(fp)>=initial_position)) {
/* As long as the search was not wrapped and we are not
* back to where we were, continue searching */
/* Read a line, and check whether an EOF was found */
if ((line=ReadLine(fp))==NULL) {
/* Yes? wrapflag on? => Wrap. */
if (wrapflag) {
wrapped=true;
fseek(fp,0L,SEEK_SET);
continue;
} else
break;
}
/* strip leading spaces */
int pos=strspn(line," \t\n");
if (line[pos]=='#') {
continue;
}
len=strlen(line);
if (strlen(tokenplusspace)<=len) {
/* only if the line is longer than the token, it might be found */
// if (strstr(line,tokenplusspace)!=NULL) /* FOUND */
if (strstr(line,tokenplusspace)==(&line[pos])) /* FOUND */
{
free(tokenplusspace);
return line;
}
}
free(line);
}
free(tokenplusspace);
return NULL; /* Token Not Found in the file */
}
int TokenInLineP(char *line,char *token)
{
if (strstr(token, line)!=NULL)
return true;
else
return false;
}
void SkipLine(FILE *fp) {
/* Just skips a line in FILE *fp */
char *tmpstring;
tmpstring=ReadLine(fp);
free(tmpstring);
}
void SkipToken(FILE *fp,char *token, bool wrapflag)
{
/* A very simple function:
call SearchToken() and get rid of the memory returned by
it.
Also, return an error if the desired token was not found in the file.
*/
char *tmppointer;
tmppointer=SearchToken(fp,token, wrapflag);
if (tmppointer==NULL) {
error("Token `%s' not found by function SkipToken.\n",token);
}
free(tmppointer);
}
/* finis */
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