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Old 05-07-2006, 06:50 AM   #1
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Registered: Apr 2004
Posts: 6

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What is pgm.h and how do I install?

Hallo everyone,

I am having some trouble compiling C code written for me. I working on cygwin (at work) at the moment but would like to compile the software on a machine running Mandriva 2006 (at home: no i-net access).

I get an error when I try and compile using the following command (cygwin work and at home).

gcc -O4 -o tempspatcorrel tempspatcorrel.c -lm -lpgm -lpbm

The error states that pgm.h: No such file or directory

When I add pgm.h to /usr/local/include I get an error asking for pbm.h
So I put pbm.h in /usr/local/include and get an error asking for pbmplus.h
After that I get new errors regarding conflicting types for srandom and random in stdlib.h and pbm.h.

I know that it would be useful to include the error messages but my efforts to write the error output to a file under cygwin have met with scant success and copying cygwin command line to windows notepad just doesnt work. Apologies.

The source code is below. As I said I did not write the code and I have little or no experience writing and compiling c code.

I would really appreciate some help on this as I need to get the code compiled to run some analysis.

Many thanks in advance for your help and input


#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include <pgm.h>

// Some basic parameters that won't change often
#define MAXFILES 600
#define MAXSTR 100
#define KERNEL_SIZE 2
// Function declaration for basic Pearson Correlation calc
float correl(float *series1, float *series2, int n);
int main(int argc, char **argv)

char tempfilename[MAXSTR], filename[MAXSTR], command[500];
FILE *infiles[MAXFILES], *filelist, *outfile;
int fileno, xsize, ysize, xpos, ypos, xi, yi, zi, img;
gray **sourceimages[MAXFILES], **outimage, maxval;
float cntr_series[MAXFILES], series[MAXFILES], r;

// Check command line parameters

if (argc != 3)

printf("Usage: %s filelist outfile\n", argv[0]);

// Open the file list file
if (!(filelist = fopen(argv[1], "r")))
printf("Error opening filelist: %s\n", argv[1]);

printf("Opened filelist: %s\n", argv[1]);

outfile = fopen(argv[2], "w");

// Open all the input image files and read in the image data

fileno = 0;

while (!feof(filelist))


// Get the file name

fscanf(filelist, "%s\n", filename);

printf("file %d: %s\n", fileno, filename);

// Convert to pgm format

sprintf(tempfilename, "temp%d.pgm", fileno);

sprintf(command, "/usr/X11R6/bin/convert %s %s >& /dev/null", filename, tempfilename);


// Open the file and read in the data

if (!(infiles[fileno] = fopen(tempfilename, "r"))) printf("Oops!\n");

sourceimages[fileno] = pgm_readpgm(infiles[fileno], &xsize, &ysize,&maxval);



// Allocate space for the new image

outimage = pgm_allocarray(xsize-(KERNEL_SIZE*2), ysize-(KERNEL_SIZE*2));

// Now scan the source images and calc correlations

for (ypos = KERNEL_SIZE; ypos < ysize - KERNEL_SIZE; ypos++)


printf("Processing row %d \r", ypos);

for (xpos = KERNEL_SIZE; xpos < xsize - KERNEL_SIZE; xpos++)


r = 0;

// Pull out the kernel central time series

for (img = 0; img < fileno; img++)

cntr_series[img] = (float)sourceimages[img][ypos][xpos];

// For each pixel in the kernel

for (xi = xpos-KERNEL_SIZE; xi <= xpos+KERNEL_SIZE; xi++)

for (yi = ypos-KERNEL_SIZE; yi <= ypos+KERNEL_SIZE; yi++)


// .. except the central pixel!

if (xi == xpos && yi == ypos) continue;

// Pull out the time series

for (img = 0; img < fileno; img++)

series[img] = (float)sourceimages[img][yi][xi];

// Accumulate the correlation coefficients

r += correl(cntr_series, series, fileno);


// Now calculate the average coefficient and write to the new image

r = r/((KERNEL_SIZE*2 + 1)*((KERNEL_SIZE*2)+1) - 1);

outimage[ypos-KERNEL_SIZE][xpos-KERNEL_SIZE] = (int)(r*255);



// Write out the image file

pgm_writepgm(outfile, outimage, xsize-(KERNEL_SIZE*2), ysize-(KERNEL_SIZE*2), 255, 1);

return 0;


// Calculate Pearson correlatoin coefficient

float correl(float *series1, float *series2, int n)


float xm=0, ym=0, xx=0, yy=0, xy=0;

int i;

float r;

// Means

for (i = 0; i < n; i++)


xm += series1[i];

ym += series2[i];


xm = xm/n;

ym = ym/n;

// Sum of normalised squares

for (i = 0; i < n; i++)


xx += pow((series1[i]-xm),2);

yy += pow((series2[i]-ym),2);

xy += (series1[i] - xm)*(series2[i] - ym);


// We don't want div by zero

if (xx*yy == 0.0)

r = 0;

// The final formula...


r = pow(xy,2)/(xx*yy);

// And back we go

return r;

Old 05-07-2006, 09:16 AM   #2
Registered: Jun 2001
Location: UK
Distribution: Gentoo, RHEL, Fedora, Centos
Posts: 43,417

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install netpbm-devel.


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