diff saitools/saisummary.c @ 0:5242703e91d3 tip

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/saitools/saisummary.c	Fri May 20 15:19:45 2011 +0100
@@ -0,0 +1,533 @@
+/*
+    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.
+*/
+/*---------------------------------------------------------------------------*/
+/* 
+* saisummary
+*
+* builds a summary .sai 
+* Output is one channel.
+*
+* M. Akeroyd.   May 1993.  Version 2.0
+*               Revised Winter 1994.
+* revised Autumn 1993.
+* variuos fiddles added Summer 1994.
+* (and some new options)
+* and some more Spring 1995.
+* and more Summer 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 writedata_output (FILE *outputfp, int samples_to_write);
+FILE *open_file (char filefn[], FILE *dir_default, int streamtype);
+void copytooutput_single(int no_peaks, int frame, int channel, int trigger_peak);
+
+int findpeaksreverse();
+int findbigpeaks(int total_peaks);
+void integratebigpeaks(int total_bigpeaks);
+
+void changeheader(int no_frames, int new_pwidth, int new_nwidth, int framewidth_samples_output);
+void changeheader_B(int new_mincf, int new_maxcf, int new_channels);
+
+void write_matrix_hori_time(int framewidth, FILE *outputfigurefp);
+
+
+
+/* Data arrays: global */
+/*--------------------------------------------------------------------------*/
+
+
+short inputdata[MAX_DATA];
+short outputdata[MAX_DATA];
+short outputfiguredata[MAX_DATA];
+short outputgrounddata[MAX_DATA];
+float summary[MAX_DATA];
+float framesummary[MAX_DATA];
+
+short interval[MAX_CHANNELS][MAX_DATA];   /* required for matrix.c */
+short summation[MAX_CHANNELS];            /* required for matrix.c */ 
+
+int clip[MAX_DATA];
+
+/* other variables */
+/*-------------------------------------------------------------------------*/
+
+
+/* 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 */
+
+
+
+
+
+/* misc */
+/*---------------- ---------------------------------------------------------*/
+
+char progname[MAX_STRING_LENGTH];
+char outputfigurefn[MAX_STRING_LENGTH];
+
+
+int verboseflag = OFF;               /* -v */
+int summationflag = OFF;
+int frameflag = OFF;                 /* -f */
+int asciiflag = OFF;
+int greyscaleflag = OFF;
+int divideflag = OFF;
+
+int oppositearchflag = OFF;          /* -oparch : see saigraph.c for info */
+
+int nstopflag = ON;
+int nwarnflag = OFF;
+int n32760flag = OFF;
+int n0flag = OFF;
+int headeroutputflag = ON;
+int singleframeflag = OFF;
+int frameaverageflag = ON;
+int specificchannelflag = OFF;
+int cutchannels[MAX_CHANNELS];
+int nchannels=0;
+
+int framestart;   
+int frameend;
+int cut_framestart;
+int cut_frameend;
+
+
+/* ..............           Main           .............................*/
+/* .....................................................................*/
+/* .....................................................................*/
+
+
+
+
+void main (int argc, char *argv[])
+{
+  int sample;
+  int n;
+
+  int frame, channel;
+  int trigger_peak = 0;
+  int no_peak = 0, total_peaks =0;
+  int total_bigpeaks = 0;
+  int trueframeheight = 0;
+  int header_bytes = 0;
+
+  double temp;
+ 
+  char inputfn[MAX_STRING_LENGTH], 
+       outputbasefn[MAX_STRING_LENGTH];
+
+  FILE *inputfp, *outputfigurefp;
+
+  strcpy(progname, argv[0]);
+  strcpy(inputfn, "");
+  strcpy(outputbasefn, "");
+  strcpy(outputfigurefn, "");
+
+  for (n=0; n<MAX_CHANNELS; n++)
+    cutchannels[n] = OFF;
+
+  /* parse command line */
+  parsecommandline(argc, argv, inputfn, outputbasefn);
+
+/*    for (n=0; n<MAX_CHANNELS; n++)
+      if (cutchannels[n] == ON)
+	fprintf(stderr, "%d\n", n);
+*/
+  if (specificchannelflag == OFF)
+    for (n=0; n<MAX_CHANNELS; n++)
+      cutchannels[n] = ON;
+  
+  if (strcmp(outputbasefn, "") == 0) 
+    strcpy(outputfigurefn, "");
+  else {
+    strcpy(outputfigurefn, outputbasefn);
+  /*  strcat(outputfigurefn, OUTPUT_EXT);*/
+  }
+
+  /* open files */
+  /* default directions are:
+   * input = stdin 
+   * figure = stdout
+   */
+
+  inputfp = open_file(inputfn, stdin, READ);
+  outputfigurefp = open_file(outputfigurefn, stdout, WRITE);
+
+  /* read Header */
+  header_bytes = readheader(inputfp);
+
+  /* do some error-checking on the header, and set the fread 
+   * pointer to the right place */
+  checkheader();
+
+  if (frameflag == ON) {
+    cut_frameend = frameend;
+    cut_framestart = framestart; }
+  else {
+    cut_frameend = no_frames;
+    cut_framestart = 1; }
+
+  if (frameflag == ON)
+    changeheader((cut_frameend - cut_framestart + 1), pwidth, nwidth, framewidth_samples);
+
+  if (singleframeflag == ON)
+    changeheader(1, pwidth, nwidth, framewidth_samples);
+
+  /* reset the variables */
+  /* arguments: mincf  maxcf  channels */
+  changeheader_B(0, 0, 1);  
+  
+  /* write header */
+  if (singleframeflag == OFF) {
+    if ((asciiflag == OFF) && (headeroutputflag == ON))
+      writeheader(outputfigurefp);
+    else ;}
+  else {
+    if ((asciiflag == OFF) && (headeroutputflag == ON))
+      writeheader(outputfigurefp);
+    else if (asciiflag == ON){
+      /* begining of ascii header. The rest depends upon the output format. */
+      fprintf(outputfigurefp, "# saisummary output. %s\n", inputfn);
+      fprintf(outputfigurefp, "# \n");
+      fprintf(outputfigurefp, "# samplerate=%i  pwidth=%d  nwidth=%d  frameheight=%i\n", samplerate, pwidth, nwidth, frameheight);
+      fprintf(outputfigurefp, "# \n");
+    }}
+
+
+/*---------------------------------------------------------------------------*/
+
+  /* Main loop */
+
+
+  if  (verboseflag==ON) { 
+    fprintf(stderr, " frames "); 
+    fflush(stderr);}
+
+  for(sample=0; sample<framewidth_samples; sample++) 
+    framesummary[sample] = 0.0;
+
+  for (frame=1; frame<=no_frames; frame++) {
+    if  (verboseflag==ON) {
+      fprintf(stderr, " %i ", frame);
+      fflush(stderr);}
+
+    for(sample=0; sample<framewidth_samples; sample++) {
+      interval[1][sample] = outputfiguredata[sample] = 0;
+      summary[sample] = 0.0;
+      clip[sample] = OFF;}
+
+/*---------------------------------------------------------------------------*/
+
+    nchannels=0;
+    for (channel=1; channel <=frameheight; channel ++) {
+
+      /* clear arrays */
+      for(sample=0; sample<framewidth_samples; sample++)
+        inputdata[sample] = 0;
+
+      /* load data */
+      fread (inputdata, 2, (size_t) framewidth_samples, inputfp);
+
+      /* This next is a simple input check: */
+      /* revised for various warnings */
+      for(sample=0; sample<framewidth_samples; sample++) {
+/*	  fprintf(stderr, "data: %i  sample: %i channel: %i \n", inputdata[sample], sample, channel);*/
+        if (inputdata[sample] < 0 )  {
+	  if (nstopflag == ON) {
+	    if (verboseflag == ON) fprintf(stderr, "\n");
+	    fprintf(stderr, "%s: negative data: ", progname);
+	    fprintf(stderr, "%i  sample: %i channel: %i \n", inputdata[sample], sample, channel);
+	    fprintf(stderr, "bye.\n");
+	    exit(-1);}
+	  if (nwarnflag == ON){
+	    if (verboseflag == ON) fprintf(stderr, "\n");
+	    fprintf(stderr, "warning: negative data: %i  (sample: %i channel: %i)\n", inputdata[sample], sample, channel);}
+	  if (n0flag == ON)
+	    inputdata[sample] = 0;
+	  else if (n32760flag == ON)
+	    inputdata[sample] = 32760;}}
+
+      /* add data to the summary autoco: outputfigurefp */
+      if ((frame >= cut_framestart) && (frame <= cut_frameend)){
+	if (cutchannels[channel] == ON){
+	  nchannels ++;
+	  /*fprintf(stderr, "c%d ", channel);*/
+	  for(sample=0; sample<framewidth_samples; sample++)
+	    summary[sample] += (double) inputdata[sample];}
+	/*fprintf(stderr, "%d hello\n", channel);*/
+      }
+    } /* channel */
+
+/*    fprintf(stderr, "c%d ", nchannels);*/
+    /* divide everything by no. of channels */
+    if (divideflag == ON) {
+      for(sample=0; sample<framewidth_samples; sample++){
+	temp = (double) summary[sample] / nchannels;
+	if ( ( temp > 32760.0)||( temp < 0)) {
+	  if (clip[sample] == OFF) {
+	    fprintf(stderr, "\nclipping: time interval %i\n", sample);
+	    clip[sample] = ON; }
+	  temp = 32761.0; }
+	interval[1][sample] = outputfiguredata[sample] = (short) temp; }}
+    else {
+      for(sample=0; sample<framewidth_samples; sample++){
+	temp = (double) summary[sample];
+	if (( temp > 32760.0) || (temp < 0.0)){
+	  if (clip[sample] == OFF) {
+	    fprintf(stderr, "\nclipping: time interval %i\n", sample);
+	    clip[sample] = ON; }
+	  temp = 32761.0; }
+	interval[1][sample] = outputfiguredata[sample] = (short) temp; }}
+
+    /* This next is a simple output check: */
+    for(sample=0; sample<framewidth_samples; sample++)
+      if (outputfiguredata[sample] < 0 )  {
+	fprintf(stderr, " %s : something's gone wrong: the output data is negative. \n", progname);
+	exit(-1); }
+
+    /* if required, sum the values */
+    if (summationflag == ON) {
+       /* clear ... */
+       summation[1] = 0;
+       clip[0] = OFF;
+       /* set ... */
+       for (sample=0; sample < framewidth_samples; sample++) {
+         summation[1] += interval[1][sample];
+	 /* clip check */
+	 if (( summation[1] > 32760 )||(summation[1] < 0 )) {
+	   if (clip[0] == OFF) {
+	     fprintf(stderr, "\nclipping: summation\n");
+	     clip[0] = ON; }
+	   summation[1] = 32761;}}
+
+    }
+
+    /* add to frame average */
+    if ((frame >= cut_framestart) && (frame <= cut_frameend)){
+      for (sample=0; sample < framewidth_samples; sample++) 
+	framesummary[sample] += outputfiguredata[sample];
+    }
+
+    /* write output: outputfiguredata[] for the .sai
+     *               interval[] & summation[] for the ascii
+     * Note hack for frameheight
+     * BUT: not if only 1 frame is to be output 
+     */
+
+    if ((frame >= cut_framestart) && (frame <= cut_frameend)){    
+      if (singleframeflag == OFF) {
+	if (asciiflag == OFF)
+	  writedata_output(outputfigurefp, framewidth_samples);
+	else {
+	  trueframeheight=frameheight;
+	  frameheight=1;
+	  write_matrix_hori_time(framewidth_samples, outputfigurefp);
+	  frameheight=trueframeheight; }}
+      else ;
+    }
+
+/* -------------------------------------------------------------------------*/
+
+  }  /* frame */
+
+    if (singleframeflag == ON) {
+      if (verboseflag == ON) {
+	fprintf(stderr, " averaging ");
+	fflush(stderr);}
+      clip[0] = OFF;
+      for (sample=0; sample < framewidth_samples; sample++) {
+	if (frameaverageflag == ON)
+	  temp = framesummary[sample]/(cut_frameend - cut_framestart + 1);
+	else
+	  temp = framesummary[sample];
+	/* clip check */
+	if (temp > 32760) {
+	    if (clip[0] == OFF) {
+	      fprintf(stderr, "\nclipping: frameaverage at sample %i\n", sample);
+	      clip[0] = ON; }
+	    temp = 32760;}
+	outputfiguredata[sample]= (short)temp;
+	interval[1][sample] = outputfiguredata[sample];}
+      if (asciiflag == OFF)
+	writedata_output(outputfigurefp, framewidth_samples);
+      else {
+	trueframeheight=frameheight;
+	frameheight=1;
+	write_matrix_hori_time(framewidth_samples, outputfigurefp);
+	frameheight=trueframeheight; }}
+    else ;
+
+
+  /* Tidy up and exit */
+  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 outputfn[])
+{
+  int x=1, helpflag = OFF;
+  int group;
+
+  while (x < argc){
+    if      (!strcmp(argv[x], "-o")) {strcpy(outputfn, argv[x+1]); x+=2;}
+    else if (!strcmp(argv[x], "-output")) {strcpy(outputfn, argv[x+1]); x+=2;}
+    else if (!strcmp(argv[x], "-i")) {strcpy(inputfn, 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], "-verbose")) {verboseflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-v")) {verboseflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-s")) {summationflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-g")) {greyscaleflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-gray")) {greyscaleflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-grey")) {greyscaleflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-ar")) {asciiflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-d")) {divideflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-channels")) {specificchannelflag = ON; 
+					     x+=1;
+					     while (x<argc){
+					       if ((int) strspn(argv[x], "-") == 0)
+						 cutchannels[atoi(argv[x])]=ON;
+					       else break;
+					       x++;}}
+    else if (!strcmp(argv[x], "-oneframe")) {singleframeflag = ON; frameaverageflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-sumframe")) {singleframeflag = ON; frameaverageflag = OFF; x+=1;}
+    else if (!strcmp(argv[x], "-oparch")) {oppositearchflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-nstop")) {nstopflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-header")) {headeroutputflag = ON; x+=1;}
+    else if (!strcmp(argv[x], "-noheader")) {headeroutputflag = OFF; x+=1;}
+    else if (!strcmp(argv[x], "-nwarn")) {nwarnflag = ON; nstopflag = OFF; x+=1;}
+    else if (!strcmp(argv[x], "-nignore")) {nwarnflag = OFF; nstopflag = OFF; x+=1;}
+    else if (!strcmp(argv[x], "-n0")) {n0flag = ON; n32760flag = OFF; nstopflag = OFF; x+=1;}
+    else if (!strcmp(argv[x], "-n32760")) {n0flag = OFF; n32760flag = ON; nstopflag = OFF; x+=1;}
+    else if (!strcmp(argv[x], "-frames")) {frameflag=ON; framestart=atoi(argv[x+1]); frameend=atoi(argv[x+2]); x+=3;}
+
+    else {fprintf(stderr, "%s: unknown option %s\n", progname, argv[x]);
+	  exit(-1);}
+  }
+  
+  if (helpflag == ON)
+    {
+      fprintf(stderr, "\n");
+      fprintf(stderr, "                         saisummary\n");
+      fprintf(stderr, " -----------------------------------------------------------\n");
+      fprintf(stderr, " Works out a summary image (cf a summary autocorrelogram).\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, "\n");
+      fprintf(stderr, " -i <.sai file>      input file             default = stdin\n");
+      fprintf(stderr, " -o <.sai file>      output file            default = stdout\n");
+      fprintf(stderr, " -oparch          assume input was generated on an opposing architecture cpu\n");
+      fprintf(stderr, "\n");
+      fprintf(stderr, " -frames <start>  <end>   (inclusive) (default=all)\n");
+      fprintf(stderr, " -channels <> <> .....   specify channel numbers to be included (1++)\n");
+      fprintf(stderr, " -d               divide by no. of channels (Warning: precision may be lost).\n");
+      fprintf(stderr, " -ar              ASCII output: rows=time intervals (requires -oneframe)\n");
+      fprintf(stderr, " -s               include summations (ascii only)\n");
+      fprintf(stderr, "\n");
+      fprintf(stderr, " -header          include AIM header in output file (default)\n");
+      fprintf(stderr, " -noheader        don't  ...  ...  ... \n");
+      fprintf(stderr, " -v               verbose output (to stderr)\n");
+      fprintf(stderr, " -g               change .sai format to 'grayscale'\n");
+      fprintf(stderr, " -oneframe        average frames together; one (1) output frame\n");
+      fprintf(stderr, " -sumframe        sum frames together; one (1) output frame\n");
+      fprintf(stderr, "\n");
+      fprintf(stderr, " -nstop           if negative inputs found, stop processing (default)\n");
+      fprintf(stderr, " -nwarn           if negative inputs found, continue (but warn user) \n");
+      fprintf(stderr, " -nignore         if negative inputs found, continue \n");
+      fprintf(stderr, " -n0              if negative inputs found, replace with 0 \n");
+      fprintf(stderr, " -n32760          if negative inputs found, replace with 32760 \n");
+      fprintf(stderr, "\n\n");
+      exit(-1);}
+}  
+
+/* The End. */
+/*------------------------------------------------------------------------------------------------------*/