Files @ 6bcb69712a0e
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Location: EI/VirtualLeaf/src/output.cpp - annotation

Roeland Merks
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
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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 <string>
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <errno.h>
#include <sys/types.h>
#include <sys/stat.h>
#include "warning.h"
#include "parameter.h"
#include "output.h"


#include <QDir>
#include <QFileInfo>

static const std::string _module_id("$Id$");

using namespace MyWarning;

#define FNAMESIZE 100

int OpenFileAndCheckExistance(FILE **fp,const char *fname,char *ftype) {

  *fp=fopen(fname,ftype);
  if (*fp==NULL) 
    return FALSE;

  if (!strncmp(ftype,"a",1)) {
    if (ftell(*fp)>0L) return TRUE;
    else return FALSE;
  } else return TRUE;
}

int FileExistsP(const char *fname) {

  FILE *fp;
  fp=fopen(fname,"r");
  if (fp==NULL)
    return FALSE;

  fclose(fp);
  return TRUE;
}

int YesNoP(const char *message) {

  char answer[100];

  fprintf(stderr,"%s (y/n) ",message);
  fflush(stderr);

  scanf("%s",answer);
  while (strcmp(answer,"y") && strcmp(answer,"n")) {
    fprintf(stderr,"\n\bPlease answer 'y' or 'n'. ");
    fflush(stderr);
    scanf("%s",answer);
  }

  if (!strcmp(answer,"y")) return TRUE;

  return FALSE;
}


FILE *OpenWriteFile(const char *filename) 
{
  char fname[FNAMESIZE];

  FILE *fp;

  fprintf(stderr,"Opening %s for writing\n",filename);

  if(FileExistsP(filename)==TRUE) {

    if (false/*par.interactive*/) {
      char *message=(char *)malloc(2000*sizeof(char));
      if (!YesNoP("File exists, overwrite?")) {
	sprintf(message," Could not open file %s for writing, exiting... \n"
		,filename);
	//exit(0);
	throw(message);
      }
    } else {
      /* Rename old file */
      sprintf(fname, "%s~",filename);
      rename(filename, fname);
    }
  }

  strncpy(fname, filename, FNAMESIZE-1);

  if ((fp=fopen(fname,"w"))==NULL) {
    char *message=(char *)malloc(2000*sizeof(char));
    sprintf(message," Could not open file %s for writing: "
	    ,fname);
    perror("");
    throw(message);
  }
  return fp;
}


FILE *OpenReadFile(const char *filename) 
{
  FILE *fp;

  fprintf(stderr,"Opening %s for reading\n",filename);

  if((OpenFileAndCheckExistance(&fp,filename,"r"))==FALSE) {	
    char *message=(char *)malloc(2000*sizeof(char));
    sprintf(message," File %s not found or empty, exiting... \n" ,filename);
    throw(message);
  }
  return fp;
}


char *ReadLine(FILE *fp) 
{
  /* does almost the same as fgetln(), but DEC Unix doesn't understand
     fgetln(). Also I want my function to return a real C string,
     terminated by a \0. */

  /* The function reads a line from file *fp, and returns a pointer to the
     line read, which can be freed with a normal free(). The length of the
     string is written in *len */

#define INITIAL_BUFSIZE 100

  char *tmpstring;
  int character;
  long bufsize;
  char *line;
  int pos;

  CheckFile(fp);

  /* first allocate a string with a standard length */
  bufsize=INITIAL_BUFSIZE;
  MEMORYCHECK(tmpstring=(char *)malloc(bufsize*sizeof(char)));

  pos=0;

  while ((character=getc(fp))!=EOF && /* read a character and check */
	 character!='\n') {

    tmpstring[pos]=(char)character;
    (pos)++;

    if (pos >= bufsize) {
      /* line is longer than initial_bufsize, reallocate space */
      bufsize+=INITIAL_BUFSIZE;
      MEMORYCHECK(tmpstring=(char *)realloc(tmpstring,bufsize*sizeof(char)));
    }
  }

  if (character==EOF) {

    if (pos==0) {
      /* EOF was reached, while no characters were read */
      free(tmpstring);
      return NULL;
    }
    if (ferror(fp)) {
      error("I/O error in ReadLine(%ld): %s\n",fp, strerror(errno));
    }
  }

  /* Allocate enough memory for the line */
  MEMORYCHECK(line=(char *)malloc((++(pos))*sizeof(char)));

  strncpy(line,tmpstring,(pos)-1);
  free(tmpstring);

  line[pos-1]='\0';
  return line;
}


void CheckFile(FILE *fp) 
{
  if (ftell(fp)<0) {
    /* file is probably not open, or another error occured */
    error("File error (fp=%ld): %d %s\n",fp,errno,strerror(errno));
  }
  /* File pointer is ok */
}

char *Chext(char *filename) {

  /* Chop the extension from a filename */

  /* Search backwards until a dot */

  /* Remember to free the memory allocated by this function */
  /* ( free(result) ) */

  /* not yet tested */

  int i;
  char *result;

  for (i=strlen(filename)-1;i>=0;i--) {
    if (filename[i]=='.') 
      break;
  }

  /* No . found */
  if (i==0) {

    result=strdup(filename);
  } else {

    /* . found */
    result=(char *)malloc((i+1)*sizeof(char));
    strncpy(result, filename, i);
  }
  return result;
}

void MakeDir(const char *dirname) {

#ifdef QTGRAPHICS
  QFileInfo file_info(dirname);

  //check for existance
  if (file_info.exists()) {

    if (file_info.isDir()) {
      // OK 
      cerr << "Using existing directory " << dirname << " for data storage." << endl;
      return;
    } else {
      char *message = new char[MESS_BUF_SIZE+1];
      snprintf(message, MESS_BUF_SIZE, "%s is not a directory", dirname);
      cerr << message << endl;
      throw(message);
    }
  }

  // make directory
  QDir dir;
  if (!dir.mkdir(QString(dirname))) {
    char *message = new char[MESS_BUF_SIZE+1];
    snprintf(message,MESS_BUF_SIZE,"%s: Error in making directory %s",strerror(errno),dirname);
    warning(message);
    //strerror(message);
    //exit(1);
    return;
  }

  // check


#else

  int status;
  char message[MESS_BUF_SIZE];

  status=mkdir(dirname, S_IRWXU); // S_IRWXU: Read, Write, Execute by Owner 

  if (status<0) { // error occurred

    //check for existance

    if (errno==EEXIST) {

      // Check whether it is a directory 
      struct stat buf;
      stat(dirname, &buf);
      if (S_ISDIR(buf.st_mode)) {
	// OK 
	extern  Parameter par;
	if (false /* && par.interactive*/) {
	  fprintf(stderr,"Using existing directory %s for data storage.\n",dirname);
	  if (!YesNoP("OK?")) {
	    // User doesn't agree. Exit
	    exit(1);
	  }
	} else {
	  fprintf(stderr,"Using existing directory %s for data storage.\n",dirname);
	}
      } else {
	snprintf(message, MESS_BUF_SIZE, "%s is not a directory", dirname);
	perror(message);
	exit(1);
      }
    } else {
      // a different error occurred. Print error and quit 

      snprintf(message,MESS_BUF_SIZE,"Error in making directory %s",dirname);
      perror(message);
      exit(1);
    }
  }

#endif
}


char* AppendHomeDirIfPathRelative(char *datadir) {
  QDir dataDir(datadir);
  if (dataDir.isRelative()){
    if (datadir) { 
      free(datadir); 
    }
    QStringList path;
    path << QDir::homePath() << dataDir.dirName();
    return strdup((char *) path.join("/").toStdString().c_str());
  } else return datadir;
}

/* finis */