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mzXML2stl.c
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/* */ /* mzXML2stl - convert (region of) mzXML file to STL */
/* */
/* (c) Magnus Palmblad, The University of Reading, 2007- */
/* */
/* */
/* This program 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. */
/* */
/* Contact information: [email protected] */
/* */
/* */
/* compile with e.g. gcc -o mzXML2stl mzXML2stl.c base64.c ramp.c -I. -lgd -lm -lz */
/* */
/* */
#include <stdio.h>
#include <stdlib.h>
#include <ctype.h>
#include <string.h>
#include <math.h>
#include "ramp.h"
#include "base64.h"
/* mzXML read functions adopted from Pep3D */
typedef struct {
int size;
double * xval;
double * yval;
} spectStrct;
void freeSpectStrct(spectStrct spectrum)
{
free(spectrum.xval);
free(spectrum.yval);
return;
}
ramp_fileoffset_t *pScanIndex;
int iLastScan;
struct ScanHeaderStruct scanHeader;
struct RunHeaderStruct runHeader;
ramp_fileoffset_t indexOffset;
spectStrct *spects;
double *wghs;
int spectNum;
int **z, **stl_height, **smooth, **smooth2, *new_spectrum;
long i;
RAMPREAL *pPeaks;
int n, n_MS_spectra=0;
RAMPFILE *pFI;
float SG[5][5] = {{-0.0743,0.0114,0.0400,0.0114,-0.0743},
{0.0114,0.0971,0.1257,0.0971,0.0114},
{0.0400,0.1257,0.1543,0.1257,0.0400},
{0.0114,0.0971,0.1257,0.0971,0.0114},
{-0.0743,0.0114,0.0400,0.0114,-0.0743}};
int getMsSpect(spectStrct *msSpect, RAMPFILE *pFI, int scanNum[2])
{
void getCmbSpect(spectStrct *cmbSpect, int spectNum, spectStrct *spects, double *wghs);
msSpect->size = -1;
scanNum[0]=scanNum[0]>1?scanNum[0]:1;
scanNum[1]=scanNum[1]<iLastScan?scanNum[1]:iLastScan;
spectNum=scanNum[1]-scanNum[0]+1;
if(spectNum < 1){
printf("invalid scan number: %d-%d (full scan range: 1-%d)\n",scanNum[0], scanNum[1], iLastScan);
fflush(stdout);
free (pScanIndex);
return -1;
}
spects=(spectStrct *) calloc(spectNum, sizeof(spectStrct));
spectNum=0;
for(i=scanNum[0];i<=scanNum[1];++i)
{
if((scanHeader.msLevel==1)&&(scanHeader.peaksCount>0)) /* MS ? */
{
spects[spectNum].size=scanHeader.peaksCount;
spects[spectNum].xval=(double *) calloc(spects[spectNum].size, sizeof(double));
spects[spectNum].yval=(double *) calloc(spects[spectNum].size, sizeof(double));
pPeaks=readPeaks(pFI,pScanIndex[i]);
spects[spectNum].size=0;
n = 0;
while(pPeaks[n]!=-1)
{
spects[spectNum].xval[spects[spectNum].size]=pPeaks[n];
n++;
spects[spectNum].yval[spects[spectNum].size]=pPeaks[n];
n++;
++(spects[spectNum].size);
}
free (pPeaks);
n_MS_spectra++;
if(spects[spectNum].size>0) ++spectNum;
else freeSpectStrct(spects[spectNum]);
}
}
if(spectNum>0)
{
wghs= (double *) calloc(spectNum, sizeof(double));
for (i=0;i<spectNum;++i)
wghs[i]=1.;
getCmbSpect(msSpect, spectNum, spects, wghs);
free(wghs);
}
else
{
printf("cannot find an MS spectrum..."); fflush(stdout);
for(i=0;i<spectNum;++i) freeSpectStrct(spects[i]);
free(spects);
return -1;
}
for(i=0;i<spectNum;++i) freeSpectStrct(spects[i]);
free(spects);
return 0;
}
void getCmbSpect(spectStrct *cmbSpect, int spectNum, spectStrct *spects, double *wghs)
{
void copySpectStrct(spectStrct * tgtSpect, spectStrct srcSpect);
spectStrct tmpSpect[2];
int indx, indx1, indx2;
double tmpWghs[2]={1.,1.};
int i;
if(spectNum<1) return;
if(spectNum==1)
{
copySpectStrct(cmbSpect,spects[0]);
if(wghs[0]!=1.) for(i=0;i<cmbSpect->size;++i) cmbSpect->yval[i]*=wghs[0];
return;
}
return;
}
void copySpectStrct(spectStrct * tgtSpect, spectStrct srcSpect)
{
int i;
tgtSpect->size=srcSpect.size;
tgtSpect->xval=(double *) calloc(tgtSpect->size, sizeof(double));
tgtSpect->yval=(double *) calloc(tgtSpect->size, sizeof(double));
for(i=0;i<tgtSpect->size;++i)
{
tgtSpect->xval[i]=srcSpect.xval[i];
tgtSpect->yval[i]=srcSpect.yval[i];
}
return;
}
/* main program starts here */
int main(int argc, char *argv[])
{
FILE *inp, *outp;
spectStrct mzXML_spectrum, temp_spectrum;
RAMPFILE *mzXML_file;
char *p, mzXML_filename[100], stl_filename[100], scan_range[100], mass_range[100], pixels[100], s[200];
int range[2];
ramp_fileoffset_t offset, *scan_index;
struct ScanHeaderStruct scan_header;
struct RunHeaderStruct run_header;
int *scan_number;
int XWIDTH,YWIDTH;
int mzXML_MS_scan, scan, first_scan, last_scan, n_scans, x, y, c, lowest_mass, highest_mass, mz_range, horizontal_pixels, vertical_pixels, n_horizontal_labels, n_vertical_labels, horizontal_label_interval, vertical_label_interval, first_horizontal_label, first_vertical_label, MS_scans, noaxes;
long i,j,k;
float min_yval, max_yval, log_min_yval, log_max_yval, power, mz_per_pixel, scans_per_pixel, background, saturation, xscale, yscale, zscale, zbase, upper, lower, xmin, xmax, box_height, box_base;
/* parsing command line parameters */
if( (argc==2) && ( (strcmp(argv[1],"--help")==0) || (strcmp(argv[1],"-help")==0) || (strcmp(argv[1],"-h")==0)) ) /* want help? */
{
printf("mzXML2stl - (c) Magnus Palmblad 2007-\n\nusage: mzXML2stl -i<mzXML file> -o<STL filename> -s<first scan>,<last scan> -m<lowest mass>,<highest mass> [-c<color scheme> -p<horizontal pixels>,<vertical pixels> -B<background (absolute value)> -S<saturation (as fraction of maximum)>].\n\nfor more information, see http://www.ms-utils.org/mzXML2stl or e-mail [email protected]\n");
return 0;
}
if (argc<5 || argc>22) /* incorrect number of parameters */
{
printf("usage: mzXML2stl -i<mzXML file> -o<STL filename> -s<first scan>,<last scan> -m<lowest mass>,<highest mass> [-p<horizontal pixels>,<vertical pixels> -B<background (absolute value)> -S<saturation (as fraction of maximum)>] (type mzXML2stl --help for more information)\n");
return -1;
}
/* set default values and parse flags */
background=0.0; saturation=1.0; noaxes=1; /* linear, m/z on horizontal axis, noaxis yet */
for(i=1;i<argc;i++) {
if( (argv[i][0]=='-') && (argv[i][1]=='i') ) strcpy(mzXML_filename,&argv[strlen(argv[i])>2?i:i+1][strlen(argv[i])>2?2:0]);
if( (argv[i][0]=='-') && (argv[i][1]=='o') ) strcpy(stl_filename,&argv[strlen(argv[i])>2?i:i+1][strlen(argv[i])>2?2:0]);
if( (argv[i][0]=='-') && (argv[i][1]=='s') )
{
strcpy(scan_range,&argv[strlen(argv[i])>2?i:i+1][strlen(argv[i])>2?2:0]); p=strtok(scan_range,",");
first_scan=atoi(p); p=strtok('\0',","); last_scan=atoi(p);
}
if( (argv[i][0]=='-') && (argv[i][1]=='m') )
{
strcpy(mass_range,&argv[strlen(argv[i])>2?i:i+1][strlen(argv[i])>2?2:0]); p=strtok(mass_range,",");
lowest_mass=atoi(p); p=strtok('\0',","); highest_mass=atoi(p);
}
if( (argv[i][0]=='-') && (argv[i][1]=='p') )
{
strcpy(pixels,&argv[strlen(argv[i])>2?i:i+1][strlen(argv[i])>2?2:0]); p=strtok(pixels,",");
horizontal_pixels=atoi(p); p=strtok('\0',","); vertical_pixels=atoi(p);
}
if( (argv[i][0]=='-') && (argv[i][1]=='B') ) background=atof(&argv[strlen(argv[i])>2?i:i+1][strlen(argv[i])>2?2:0]);
if( (argv[i][0]=='-') && (argv[i][1]=='S') ) saturation=atof(&argv[strlen(argv[i])>2?i:i+1][strlen(argv[i])>2?2:0]);
if( strcmp(argv[i],"-noaxes")==0 ) noaxes=1;
}
XWIDTH=horizontal_pixels+(1-noaxes)*40; YWIDTH=vertical_pixels+(1-noaxes)*20; /* add pixels for axes */
printf("checking mzXML dataset %s...",mzXML_filename); fflush(stdout);
mzXML_file=rampOpenFile(mzXML_filename);
indexOffset = getIndexOffset (mzXML_file); /* read the index offset */
pScanIndex = readIndex(mzXML_file, indexOffset, &iLastScan); /* read the scan index into a vector and get LastScan */
readRunHeader(mzXML_file, pScanIndex, &runHeader, iLastScan);
printf("done\n"); fflush(stdout);
printf("allocating memory..."); fflush(stdout);
n_scans=last_scan-first_scan+1;
z=malloc((n_scans>vertical_pixels?n_scans:vertical_pixels)*sizeof(int *));
if(z==NULL) {fprintf(stderr,"out of memory (terminating)\n"); return -1;}
stl_height=malloc(vertical_pixels*sizeof(int *));
if(stl_height==NULL) {fprintf(stderr,"out of memory (terminating)\n"); return -1;}
smooth=malloc(vertical_pixels*sizeof(int *));
if(smooth==NULL) {fprintf(stderr,"out of memory (terminating)\n"); return -1;}
smooth2=malloc(vertical_pixels*sizeof(int *));
if(smooth2==NULL) {fprintf(stderr,"out of memory (terminating)\n"); return -1;}
new_spectrum=malloc(horizontal_pixels*sizeof(int));
scan_number=malloc(n_scans*sizeof(int));
for(y=0;y<(n_scans>vertical_pixels?n_scans:vertical_pixels);y++)
{
z[y]=malloc(horizontal_pixels*sizeof(int));
if(z[y]==NULL) {fprintf(stderr,"out of memory (terminating)\n"); return -1;}
}
for(y=0;y<vertical_pixels;y++)
{
stl_height[y]=malloc(horizontal_pixels*sizeof(int));
if(stl_height[y]==NULL) {fprintf(stderr,"out of memory (terminating)\n"); return -1;}
}
for(y=0;y<vertical_pixels;y++)
{
smooth[y]=malloc(horizontal_pixels*sizeof(int));
if(smooth[y]==NULL) {fprintf(stderr,"out of memory (terminating)\n"); return -1;}
}
for(y=0;y<vertical_pixels;y++)
{
smooth2[y]=malloc(horizontal_pixels*sizeof(int));
if(smooth2[y]==NULL) {fprintf(stderr,"out of memory (terminating)\n"); return -1;}
}
printf("done\nscanning mzXML data for yval range..."); fflush(stdout);
/* get min_yval and max_yval */
min_yval=1E10; max_yval=0; y=-1;
for(scan=first_scan;scan<last_scan;scan++)
{
range[0]=scan;
readHeader(mzXML_file, pScanIndex[range[0]], &scanHeader);
if(scanHeader.msLevel==1) /* MS spectrum */
{
y++;
scan_number[y]=scan; /* store scan numbers for axis */
range[1]=range[0];
if(getMsSpect(&mzXML_spectrum,mzXML_file,range)<0) continue; /* MS spectrum not found in mzXML *** */
for(i=0;i<mzXML_spectrum.size;i++) /* # of peaks in peaklist in line spectra */
{
if(mzXML_spectrum.yval[i]>min_yval) min_yval=mzXML_spectrum.yval[i];
if(mzXML_spectrum.yval[i]>max_yval) max_yval=mzXML_spectrum.yval[i];
}
}
}
printf("done\nparsing mzXML data..."); fflush(stdout);
if(min_yval>0) log_min_yval=log(min_yval); log_max_yval=log(max_yval);
/* read in spectrum by spectrum, store in temporary array */
mz_per_pixel=(float)(highest_mass-lowest_mass)/(float)horizontal_pixels;
for(y=0;y<vertical_pixels;y++) for(x=0;x<horizontal_pixels;x++) stl_height[y][x]=0; /* initialize */
for(y=0;y<(n_scans>vertical_pixels?n_scans:vertical_pixels);y++) for(x=0;x<(highest_mass-lowest_mass)/mz_per_pixel;x++) z[y][x]=0;
y=-1;
/* linear - add log and nth root later */
for(scan=first_scan;scan<last_scan;scan++)
{
range[0]=scan;
readHeader(mzXML_file, pScanIndex[range[0]], &scanHeader);
if(scanHeader.msLevel==1) /* MS spectrum */
{
y++;
range[1]=range[0];
if(getMsSpect(&mzXML_spectrum,mzXML_file,range)<0) continue; /* MS spectrum not found in mzXML *** */
for(i=0;i<mzXML_spectrum.size;i++) /* # of peaks in peaklist in line spectra */
{
if(mzXML_spectrum.xval[i]<lowest_mass) continue;
if(mzXML_spectrum.xval[i]>highest_mass) break;
if(mzXML_spectrum.yval[i]>background) c=round(255*(mzXML_spectrum.yval[i]-background)/(max_yval*saturation));
else c=0;
if(c>255) c=255; /* saturated */
x=(int)round((mzXML_spectrum.xval[i]-lowest_mass)/mz_per_pixel);
if(c>z[y][x]) z[y][x]=c; /* store maximum in each pixel interval */
}
}
}
printf("done\n"); fflush(stdout);
MS_scans=y; scans_per_pixel=(float)MS_scans/(float)vertical_pixels;
printf("generating STL file from mzXML..."); fflush(stdout);
/* plot data */
if(scans_per_pixel>=1) /* when looking at a whole scene, e.g. LC-MS run with 2000 MS scans = 20 cm with 0.1 mm pixels */
{
for(y=0;y<MS_scans;y++)
{
for(x=0;x<horizontal_pixels;x++) stl_height[x+(1-noaxes)*40][YWIDTH-(1-noaxes)*20-(int)round((float)y/(float)scans_per_pixel)]=z[y][x];
}
}
else /* for STL, one would typically expect more than one "pixel" (0.1 mm) per scan for zooms into one isotopic distribution - interpolate here or later? */
{
for(y=0;y<MS_scans;y++)
{
for(i=0;i<=ceil(1/scans_per_pixel);i++)
{
for(x=0;x<horizontal_pixels;x++) stl_height[x+(1-noaxes)*40][YWIDTH-(1-noaxes)*20-i-(int)round((float)y/(float)scans_per_pixel)]=z[y][x];
}
}
}
printf("done\nwriting STL...",stl_filename); fflush(stdout); /* add axes later, if at all */
//xscale=0.7;
//yscale=0.1;
//zscale=0.13;
xscale=1.0;
yscale=0.12;
zscale=0.17;
/*
if ((outp=fopen(stl_filename, "wb"))==NULL) {printf("\nerror opening output file %s\n",stl_filename); return -1;}
fprintf(outp,"solid ms_data\n");
for(y=0;y<vertical_pixels-1;y++)
{
for(x=1;x<horizontal_pixels;x++)
{
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.1f %.1f %.1f\n",(float)x*xscale,(float)y*yscale,(float)stl_height[x][y]*zscale);
fprintf(outp," vertex %.1f %.1f %.1f\n",(float)(x-1)*xscale,(float)(y+1)*yscale,(float)stl_height[x-1][y+1]*zscale);
fprintf(outp," vertex %.1f %.1f %.1f\n",(float)(x-1)*xscale,(float)y*yscale,(float)stl_height[x-1][y]*zscale);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.1f %.1f %.1f\n",(float)x*xscale,(float)y*yscale,(float)stl_height[x][y]*zscale);
fprintf(outp," vertex %.1f %.1f %.1f\n",(float)x*xscale,(float)(y+1)*yscale,(float)stl_height[x][y+1]*zscale);
fprintf(outp," vertex %.1f %.1f %.1f\n",(float)(x-1)*xscale,(float)(y+1)*yscale,(float)stl_height[x-1][y+1]*zscale);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
}
}
fprintf(outp,"endsolid\n");
fclose(outp);
*/
strcpy(stl_filename,strcat(stl_filename,"_smoothed.stl"));
if ((outp=fopen(stl_filename, "wb"))==NULL) {printf("\nerror opening output file %s\n",stl_filename); return -1;}
zbase=5.0; /* 5 mm base */
fprintf(outp,"solid ms_data_SG_smoothed\n");
/* draw box, first bottom, than 4 sides */
/*
fprintf(outp," facet normal 0.0 0.0 0.0\n"); //bottom
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,0.0,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,0.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,vertical_pixels*yscale,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,0.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n"); //top
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,0.0,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,5.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,vertical_pixels*yscale,5.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,0.0,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,0.0,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,0.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,0.0,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,0.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,(float)vertical_pixels*yscale,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,5.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,(float)vertical_pixels*yscale,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,(float)vertical_pixels*yscale,5.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,0.0,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,0.0,5.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,0.0,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,0.0,5.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,0.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,(float)vertical_pixels*yscale,0.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",0.0,(float)vertical_pixels*yscale,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,(float)vertical_pixels*yscale,5.0);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)horizontal_pixels*xscale,(float)vertical_pixels*yscale,0.0);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
*/
/* absolute box */
xmin=530; xmax=650;
box_height=5.0;
box_base=3.0;
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,0.0,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_base);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,vertical_pixels*yscale,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_base);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,0.0,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_height);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,vertical_pixels*yscale,box_height);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,0.0,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,0.0,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,0.0,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_height);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,(float)vertical_pixels*yscale,box_height);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,0.0,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,0.0,box_height);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,0.0,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,0.0,box_height);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n");
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmin*xscale,(float)vertical_pixels*yscale,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,(float)vertical_pixels*yscale,box_height);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)xmax*xscale,(float)vertical_pixels*yscale,box_base);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
/*
// window smoothing
for(y=0;y<vertical_pixels;y++)
{
for(x=1;x<horizontal_pixels-1;x++)
{
new_spectrum[x]=0.25*stl_height[x-1][y]+0.5*stl_height[x][y]+0.25*stl_height[x+1][y];
}
for(x=1;x<horizontal_pixels-1;x++)
{
stl_height[x][y]=new_spectrum[x];
}
}
*/
/* interpolation in zooms k = spikiness factor? */
/*
k=4;
for(y=0;y<vertical_pixels;y++)
{
for(x=1;x<horizontal_pixels-k;x++)
{
if( (stl_height[x+1][y]<stl_height[x][y]) && (stl_height[x-1][y]<stl_height[x][y]) ) // x local maximum - interpolate to next local maximum
{
for(i=x+k;i<horizontal_pixels-1;i++) {if( (stl_height[i-1][y]<stl_height[i][y]) && (stl_height[i+1][y]<stl_height[i][y]) ) break;} // found next local maximum i
for(j=x+1;j<i;j++) {stl_height[j][y]=((float)(j-x)/(float)(i-x))*(float)stl_height[i][y]+(1.0-((float)(j-x)/(float)(i-x)))*(float)stl_height[x][y];} // interpolate
}
x+=k;
}
}
k=4;
for(y=0;y<vertical_pixels;y++)
{
for(x=1;x<horizontal_pixels-k;x++)
{
if( (stl_height[x+1][y]<stl_height[x][y]) && (stl_height[x-1][y]<stl_height[x][y]) ) // x local maximum - interpolate to next local maximum
{
for(i=x+k;i<horizontal_pixels-1;i++) {if( (stl_height[i-1][y]<stl_height[i][y]) && (stl_height[i+1][y]<stl_height[i][y]) ) break;} // found next local maximum i
for(j=x+1;j<i;j++) {stl_height[j][y]=((float)(j-x)/(float)(i-x))*(float)stl_height[i][y]+(1.0-((float)(j-x)/(float)(i-x)))*(float)stl_height[x][y];} // interpolate
}
x+=k;
}
}
k=10;
for(y=0;y<vertical_pixels;y++)
{
for(x=horizontal_pixels-k;x>k+1;x--) // run the same thing but backwards?
{
if( (stl_height[x+1][y]<stl_height[x][y]) && (stl_height[x-1][y]<stl_height[x][y]) ) // x local maximum - interpolate to next local maximum
{
for(i=x-k;i<horizontal_pixels-1;i++) {if( (stl_height[i-1][y]<stl_height[i][y]) && (stl_height[i+1][y]<stl_height[i][y]) ) break;} // found next local maximum i
for(j=x-1;j<i;j++) {stl_height[j][y]=((float)(j-x)/(float)(i-x))*(float)stl_height[i][y]+(1.0-((float)(j-x)/(float)(i-x)))*(float)stl_height[x][y];} // interpolate
}
x-=k;
}
}
*/
for(y=6;y<vertical_pixels-6;y++)
{
for(x=6;x<horizontal_pixels-6;x++) {
smooth[x][y]=(stl_height[x-6][y]*(-11)+stl_height[x-5][y]*0+stl_height[x-4][y]*9+stl_height[x-3][y]*16+stl_height[x-2][y]*21+stl_height[x-1][y]*24+stl_height[x][y]*25 +
stl_height[x+6][y]*(-11)+stl_height[x+5][y]*0+stl_height[x+4][y]*9+stl_height[x+3][y]*16+stl_height[x+2][y]*21+stl_height[x+1][y]*24)/143;
}
}
/* for(y=5;y<vertical_pixels-5;y++)
{
for(x=5;x<horizontal_pixels-5;x++) {
smooth[x][y]=(stl_height[x-5][y]*(-36)+stl_height[x-4][y]*9+stl_height[x-3][y]*44+stl_height[x-2][y]*69+stl_height[x-1][y]*84+stl_height[x][y]*89 +
stl_height[x+5][y]*(-36)+stl_height[x+4][y]*9+stl_height[x+3][y]*44+stl_height[x+2][y]*69+stl_height[x+1][y]*84)/429;
}
}*/
/*for(y=4;y<vertical_pixels-4;y++)
{
for(x=4;x<horizontal_pixels-4;x++) {
smooth[x][y]=(stl_height[x-4][y]*(-21)+stl_height[x-3][y]*14+stl_height[x-2][y]*39+stl_height[x-1][y]*54+stl_height[x][y]*59 +
stl_height[x+4][y]*(-21)+stl_height[x+3][y]*14+stl_height[x+2][y]*39+stl_height[x+1][y]*54)/231;
}
}*/
for(x=2;x<horizontal_pixels-2;x++)
{
for(y=2;y<vertical_pixels-2;y++) {
smooth2[x][y]=(smooth[x-2][y-2]*SG[0][0]+smooth[x-2][y-1]*SG[0][1]+smooth[x-2][y]*SG[0][2]+smooth[x-2][y+1]*SG[0][3]+smooth[x-2][y+2]*SG[0][4] +
smooth[x-1][y-2]*SG[1][0]+smooth[x-1][y-1]*SG[1][1]+smooth[x-1][y]*SG[1][2]+smooth[x-1][y+1]*SG[1][3]+smooth[x-1][y+2]*SG[1][4] +
smooth[x ][y-2]*SG[2][0]+smooth[x ][y-1]*SG[2][1]+smooth[x ][y]*SG[2][2]+smooth[x ][y+1]*SG[2][3]+smooth[x ][y+2]*SG[2][4] +
smooth[x+1][y-2]*SG[3][0]+smooth[x+1][y-1]*SG[3][1]+smooth[x+1][y]*SG[3][2]+smooth[x+1][y+1]*SG[3][3]+smooth[x+1][y+2]*SG[3][4] +
smooth[x+2][y-2]*SG[4][0]+smooth[x+2][y-1]*SG[4][1]+smooth[x+2][y]*SG[4][2]+smooth[x+2][y+1]*SG[4][3]+smooth[x+2][y+2]*SG[4][4]);
}
}
for(y=0;y<vertical_pixels-1;y++)
{
for(x=2;x<horizontal_pixels-1;x++)
{
if( (x>xmin) && (x<=xmax) )
{
fprintf(outp," facet normal 0.0 0.0 0.0\n"); /* in most software, <0,0,0> makes the program calculate the normal using the right hand rule */
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)x*xscale,(float)y*yscale,(float)smooth2[horizontal_pixels-x][y]*zscale+zbase);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)(x-1)*xscale,(float)(y+1)*yscale,(float)smooth2[horizontal_pixels-(x-1)][y+1]*zscale+zbase);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)(x-1)*xscale,(float)y*yscale,(float)smooth2[horizontal_pixels-(x-1)][y]*zscale+zbase);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
fprintf(outp," facet normal 0.0 0.0 0.0\n"); /* in most software, <0,0,0> makes the program calculate the normal using the right hand rule */
fprintf(outp," outer loop\n");
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)x*xscale,(float)y*yscale,(float)smooth2[horizontal_pixels-x][y]*zscale+zbase);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)x*xscale,(float)(y+1)*yscale,(float)smooth2[horizontal_pixels-x][y+1]*zscale+zbase);
fprintf(outp," vertex %.3f %.3f %.3f\n",(float)(x-1)*xscale,(float)(y+1)*yscale,(float)smooth2[horizontal_pixels-(x-1)][y+1]*zscale+zbase);
fprintf(outp," endloop\n");
fprintf(outp," endfacet\n");
}
}
}
fprintf(outp,"endsolid\n");
fclose(outp);
printf("done (STL saved to '%s')\n",stl_filename); fflush(stdout);
return 0;
}