annotate saitools/saicut.c @ 0:5242703e91d3 tip

Initial checkin for AIM92 aimR8.2 (last updated May 1997).

/*
    Copyright (c) Applied Psychology Unit, Medical Research Council. 1993
    ===========================================================================

    Permission to use, copy, modify, and distribute this software without fee 
    is hereby granted for research purposes, provided that this copyright 
    notice appears in all copies and in all supporting documentation, and that 
    the software is not redistributed for any fee (except for a nominal 
    shipping charge). Anyone wanting to incorporate all or part of this 
    software in a commercial product must obtain a license from the Medical 
    Research Council.

    The MRC makes no representations about the suitability of this 
    software for any purpose.  It is provided "as is" without express or 
    implied warranty.
 
    THE MRC DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING 
    ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL 
    THE A.P.U. BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES 
    OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, 
    WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, 
    ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS 
    SOFTWARE.
*/
/*    saicut.c
*   ------------
*
*  Cuts out frames or channels (or both) from a .sai
*  output= .sai
*   
*  options:  -frame <start> <end>   (units=frame numbers; INCLUSIVE).
*            -channel <low> <high>  (units=channel nos; INCLUSIVE).
*          (both arguments are needed).
*
*  When using verbose, those frame numbers that are NOT kept are put in
*  round brackets ().
*
*
*  M Akeroyd.  June 1993. v1.00  Revised Spring 1994.
*  Lots of extra options Winter 1995.
*/



#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include "tip.h"




/* Function declarations */
/*-------------------------------------------------------------------------*/

void parsecommandline (int argc, char *argv[], char inputfn[], char outputfn[]);
int readheader(FILE *inputfp);
void checkheader();
void writeheader(FILE *outputfp);
void changeheader(int no_frames, int new_pwidth, int new_nwidth, int framewidthsamples_output);
void changeheader_B(int new_mincf, int new_maxcf, int new_channels);

void writedata_output (FILE *outputfp, int samples_to_write);
FILE *open_file (char filefn[], FILE *dir_default, int streamtype);


/* Data Arrays */
/* ------------------------------------------------------------------------*/
short inputdata[MAX_DATA];
short inputbychannel[MAX_CHANNELS][MAX_DATA];
short outputfiguredata[MAX_DATA];
short outputgrounddata[MAX_DATA];

#define MAX_STROBES 2000
int strobelocation[MAX_STROBES];       

/* variables read from header */
/*-------------------------------------------------------------------------*/
char header[MAX_LINES_HEADER][MAX_LINE_LENGTH];
int header_lines;

/* .sai parameters */
int no_frames;
int frameheight;             /* number of channels */
int framewidth_samples;      /* pwidth + nwidth * samplerate */
int frameshift_samples;      /* frstep_aid * samplerate */
int pwidth;                  /* in msecs */
int nwidth;                  /* in msecs: NEGATIVE */
int width_win;               /* pixels */
int height_win;              /* pixels */
long samplerate;             /* samples per sec */
int mincf;                   /* Hz */
int maxcf;                   /* Hz */

/* parameters read from command line*/
int framestart;
int frameend;
int minchannel;
int maxchannel;

int cut_timestart;
int cut_timeend;
int counter;
float sum;
float tempf;
float timestart, timeend;

/* misc */
/*-----------------------------------------------------------------------*/

char progname[MAX_STRING_LENGTH];
char outputfigurefn[MAX_STRING_LENGTH];
char strobefn[MAX_STRING_LENGTH];


int verboseflag = OFF;               /* -v */
int frameflag = OFF;                 /* -f */
int channelflag = OFF;               /* -c */
int greyscaleflag = OFF;             /* Not used: required for compilation */
int oppositearchflag = OFF;          /* -oparch : see saigraph.c for info */
int sumflag = OFF;
int averageflag = OFF;
int timeflag = OFF;
int headerflag = ON;
int strobeflag = OFF;
int strobevalue = 1;                /* the value used to mark a strobe event in 
				       the .trigger file */
int cutthisframe = OFF;
int infoflag = OFF;
int forceframeflag = OFF;
int forceframe = 0;
int successforceflag = OFF;

/* ...................         Main         ................................*/
/* .........................................................................*/
/* .........................................................................*/



void main (int argc, char *argv[])
{
  int n, sample;
  int frame, channel;
  int trigger_peak = 0;
  int header_bytes = 0;
  int cut_framestart, cut_frameend, cut_no_frames;
  int cut_minchannel, cut_maxchannel, cut_frameheight;
  char inputfn[MAX_STRING_LENGTH],  outputbasefn[MAX_STRING_LENGTH];
  FILE *inputfp, *outputfigurefp;
  FILE *strobefp;
  int x, counter, previousx;
  int nstrobes;
  short sampledata[2];

/*-------------------------------------*/
  strcpy(progname, argv[0]);
  strcpy(inputfn, "");
  strcpy(outputbasefn, "");
  strcpy(outputfigurefn, "");

  parsecommandline(argc, argv, inputfn, outputbasefn);

  if (strcmp(outputbasefn, "") == 0) 
    strcpy(outputfigurefn, "");
  else {
    strcpy(outputfigurefn, outputbasefn);
/*    strcat(outputfigurefn, OUTPUT_EXT);*/
  }

/*--------------------------------------*/
  /* open files, read and check header */
  inputfp = open_file(inputfn, stdin, READ);
  outputfigurefp = open_file(outputfigurefn, stdout, WRITE);
  header_bytes = readheader(inputfp);
  checkheader();

/*-------------------------------------*/
  /* strobe code */
  if (strobeflag == ON){
    strobefp = open_file(strobefn, stderr, READ);
    /* note 
     *   add (nwidth * samplerate) to the index
     *   the frame number is the floor of that + 1 (because it seems to give the correct answer)
     *   some versions of gensai return a triggerpoint 3 samples across; take the first.
     */
    for (x=0; x<MAX_STROBES; x++)
      strobelocation[x] = 0;
    x=0; counter=1;
    previousx=0;
    while( feof(strobefp) ==0) {
      fread(sampledata, 2, 1, strobefp);
      if (sampledata[0] >= strobevalue){
	if (((x-previousx) <= 2) && (previousx != 0))
	  /* don't need this trigger */
	  continue;
	strobelocation[counter] = x;
	tempf = (float) strobelocation[counter] + (-1.0 * nwidth * samplerate / 1000.0);
	tempf = tempf * 1.0 / frameshift_samples;
	/* tempf = floor(tempf);*/
	strobelocation[counter] = (int) tempf + 1.0;
/*	if (verboseflag == ON) 
	  fprintf(stderr, "strobe %i: %i samples %f (%i frames)\n", counter, x, tempf, (int)strobelocation[counter]);*/
	previousx=x;
	counter++;}
      x++;
      if (counter >= MAX_STROBES){
	fprintf(stderr, " %s : too many strobes in .trigger file.\n", progname);
	exit(-1);}
    }
    nstrobes=counter-1;
    if (infoflag == ON){
      fprintf(stderr, "using %i frames ", nstrobes);
      for (counter=1; counter <=nstrobes; counter ++)  
	fprintf(stderr, " %i", strobelocation[counter]);
      fprintf(stderr, "\n");}
    fclose(strobefp);
  }

/*--------------------------------------*/

  /* reset the frame/channel counters */
  if (frameflag == ON) {
    cut_frameend = frameend;
    cut_framestart = framestart; }
  else {
    cut_frameend = no_frames;
    cut_framestart = 1; }

  if (channelflag == ON) {
    cut_maxchannel = maxchannel;
    cut_minchannel = minchannel; }
  else {
    cut_maxchannel = frameheight;
    cut_minchannel = 1; }

  if (timeflag == ON) {
    cut_timestart = samplerate * timestart/1000;
    cut_timeend = samplerate * timeend/1000;}
  else{
    cut_timestart = 0;
    cut_timeend = framewidth_samples;}

/*  fprintf(stderr, "%d \n", cut_timestart);*/
/*  fprintf(stderr, "%d \n", cut_timeend);*/

  cut_no_frames = cut_frameend - cut_framestart + 1;     /* inclusive, so +1 */
  cut_frameheight = cut_maxchannel - cut_minchannel + 1; /* inclusive, so +1 */
  if (strobeflag == ON)
    cut_no_frames = nstrobes;

/*--------------------------------------*/
/* WARNING: 'time' options are NOT built into the headers yet */

  changeheader(cut_no_frames, pwidth, nwidth, framewidth_samples); 
  changeheader_B(mincf, maxcf, cut_frameheight);
  if (headerflag == ON)
    writeheader(outputfigurefp);

/*--------------------------------------*/

  if  (verboseflag==ON) { 
    fprintf(stderr, " frames "); 
    fflush(stderr);}

/*------------------------------------------------------------------------*/

  for (frame=1; frame<=no_frames; frame++) {

    if (strobeflag == OFF) {
      if ((frame < cut_framestart) || (frame > cut_frameend )) 
	cutthisframe = OFF;
      else 
	cutthisframe = ON;}
    else {
      cutthisframe = OFF;
      for (counter=1; counter <= nstrobes; counter ++){
	if (frame == strobelocation[counter])
	  cutthisframe = ON;}}

    if (forceframeflag == ON){
      if (frame < forceframe){
	cutthisframe = OFF;}
      else {
	if (successforceflag == OFF){
	  if (cutthisframe == ON){
	    successforceflag = ON;
	    fprintf(stdout, "%d\n", frame);}}
	else 
	  cutthisframe = OFF;}}

    if (verboseflag == ON) {
      if (cutthisframe == ON){
	fprintf(stderr, " %i ", frame); fflush(stderr);}
      else {
	fprintf(stderr, " (%i) ", frame); fflush(stderr);}}

    /*--------------------------------------*/

    for (channel=1; channel <=frameheight; channel ++) {

      for(sample=0; sample<framewidth_samples; sample++) 
	inputdata[sample] = 0;

      fread (inputdata, 2, framewidth_samples, inputfp);

      /* input check */
      for(sample=0; sample<framewidth_samples; sample++)
	if (inputdata[sample] < 0 )  {
	  fprintf(stderr, "%s: something's gone wrong: the data is negative.\n", progname);
	  exit(-1); }

      for(sample=0; sample<framewidth_samples; sample++) 
	inputbychannel[channel][sample] = inputdata[sample];
     
    } /* (loading of) channel */

    /*--------------------------------------*/

    /* Is this frame to be output? If not, next frame. */
    if (strobeflag == OFF){
      if ((frame < cut_framestart) || (frame > cut_frameend ))
	continue;}
    else {
      if (cutthisframe == OFF)
	continue;}
       
    /* output all required channels */
    for (channel = cut_minchannel; channel <= cut_maxchannel; channel++) {
      sum = 0.0;
      counter=0;
      for(sample=cut_timestart; sample<cut_timeend; sample++) {
	outputfiguredata[counter] = inputbychannel[channel][sample];
	if ((sumflag == ON) || (averageflag == ON))
	  sum += inputbychannel[channel][sample];
	counter++;}

      if (sumflag == ON){
	outputfiguredata[0] = (short) sum;
	counter=1;}
      if (averageflag == ON){
	tempf = (float) sum/counter;
	outputfiguredata[0] = (short) tempf;
	counter=1;}
/*      fprintf(stderr, "%f %d \n", sum, outputfiguredata[0]);*/

      writedata_output(outputfigurefp, counter); }

    /*--------------------------------------*/

  } /* frame */

/*----------------------------------------------------------------------*/

  /* Tidy up and exit */
  if (verboseflag == ON) 
    fprintf(stderr, "\n");
  fclose(inputfp);   fclose(outputfigurefp); 

  if ( ferror(inputfp) != 0) {
    fprintf(stderr, " %s : error closing input file.\n", progname);
    exit(-1);}

  if ( ferror(outputfigurefp) != 0) {
    fprintf(stderr, " %s : error closing figure file.\n", progname);
    exit(-1);}

  exit(0);

} /* Main */




/*......................................................................*/
/*......................................................................*/





void parsecommandline(int argc, char *argv[], char inputfn[], char outputbasefn[])
{
  int x=1, helpflag = OFF;

  while (x < argc){
    if      (!strcmp(argv[x], "-o")) {strcpy(outputbasefn, argv[x+1]); x+=2;}
    else if (!strcmp(argv[x], "-output")) {strcpy(outputbasefn, argv[x+1]); x+=2;}
    else if (!strcmp(argv[x], "-i")) {strcpy(inputfn, argv[x+1]); x+=2;}
    else if (!strcmp(argv[x], "-t")) {strobeflag=ON; frameflag=OFF;strcpy(strobefn, argv[x+1]); x+=2;}
    else if (!strcmp(argv[x], "-input")) {strcpy(inputfn, argv[x+1]); x+=2;}
    else if (!strcmp(argv[x], "-help")) {helpflag = ON; x+=1;}
    else if (!strcmp(argv[x], "-h")) {helpflag = ON; x+=1;}
    else if (!strcmp(argv[x], "-triggerinfo")) {infoflag = ON; x+=1;}
    else if (!strcmp(argv[x], "-sum")) {sumflag = ON; averageflag=OFF; x+=1;}
    else if (!strcmp(argv[x], "-average")) {sumflag = OFF; averageflag=ON; x+=1;}
    else if (!strcmp(argv[x], "-header")) {headerflag = ON; x+=1;}
    else if (!strcmp(argv[x], "-noheader")) {headerflag = OFF; x+=1;}
    else if (!strcmp(argv[x], "-verbose")) {verboseflag = ON; x+=1;}
    else if (!strcmp(argv[x], "-v")) {verboseflag = ON; x+=1;}
    else if (!strcmp(argv[x], "-n")) {forceframeflag=ON; forceframe=atoi(argv[x+1]); x+=2;}
    else if (!strcmp(argv[x], "-f")) {frameflag=ON; framestart=atoi(argv[x+1]); frameend=atoi(argv[x+2]); x+=3;}
    else if (!strcmp(argv[x], "-frames")) {frameflag=ON; framestart=atoi(argv[x+1]); frameend=atoi(argv[x+2]); x+=3;}
    else if (!strcmp(argv[x], "-c")) {channelflag=ON; minchannel=atoi(argv[x+1]); maxchannel=atoi(argv[x+2]); x+=3;}
    else if (!strcmp(argv[x], "-channel")) {channelflag=ON; minchannel=atoi(argv[x+1]); maxchannel=atoi(argv[x+2]); x+=3;}
    else if (!strcmp(argv[x], "-time")) {timeflag=ON; timestart=atof(argv[x+1]); timeend=atof(argv[x+2]); x+=3;}
    else if (!strcmp(argv[x], "-oparch")) {oppositearchflag = ON; x+=1;}
    else {fprintf(stderr, "%s: unknown option %s\n", progname, argv[x]);
	  exit(-1);}
  }
    
  if (helpflag == ON)
    {
      fprintf(stderr, "\n");
      fprintf(stderr, "                         %s\n", progname);
      fprintf(stderr, " -----------------------------------------------------------\n");
      fprintf(stderr, " Cuts a .sai by frame or channel, and (if necessary) just some\n");
      fprintf(stderr, " of the input image\n");
      fprintf(stderr, " The -oparch option is REQUIRED if reading a Sun .sai files \n");
      fprintf(stderr, " on a DEC cpu or vice-versa.\n");
      fprintf(stderr, " Add .sai to both input and output filenames.\n");
      fprintf(stderr, " WARNING: the header is not rebuilt properly for the\n");
      fprintf(stderr, " '-time' options.\n");
      fprintf(stderr, " -----------------------------------------------------------\n");
      fprintf(stderr, " -i <.sai file>      input file             default = stdin\n");
      fprintf(stderr, " -o <.sai file>      output file            default = stdout\n");
      fprintf(stderr, " -t <.trigger file>  trigger location file\n");
      fprintf(stderr, " -oparch          assume input was generated on an opposing architecture cpu\n");
      fprintf(stderr, "\n");
      fprintf(stderr, " -n <frame>       take first frame after <frame>\n");
      fprintf(stderr, " -frames <start>  <end>   (inclusive) (default=all)\n");
      fprintf(stderr, " -time   <start>  <end>   (inclusive; ms from leftedge)\n");
      fprintf(stderr, " -channel <low>  <high>   (inclusive) (default=all)\n");
      fprintf(stderr, " -sum             sum and output 1 value per frame\n");
      fprintf(stderr, " -average         sum, average & output 1 value per frame\n");
      fprintf(stderr, " -noheader        don't output a .sai header\n");
      fprintf(stderr, " -header          do output a .sai header (default)\n");
      fprintf(stderr, "\n");
      fprintf(stderr, " -v               verbose output (to stderr)\n");
      fprintf(stderr, " -triggerinfo     report the 'trigger' frames (to stderr)");
      fprintf(stderr, "\n\n");
      exit(-1);}

}