diff saitools/saicut.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/saicut.c	Fri May 20 15:19:45 2011 +0100
@@ -0,0 +1,450 @@
+/*
+    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);}
+
+}  
+
+
+
+
+
+
+