arguments* parse_args(int argc, char* argv[]) {
/* Parse the command line argument array into a convienent structure. */
FILE* csv;
arguments* args = calloc(1, sizeof(arguments));
args->delim = *argv[2];
args->quo = *argv[3];
// Parse sequence of integers passed as command line arguments into an
// integer array.
args->n_fields = argc - 4;
if(args->n_fields > MAX_N_FIELDS) {
raise_too_many_fields_error();
}
for(int i = 4; i < argc; i++) {
args->field_idxs[i-4] = atoi(argv[i]);
}
if(!check_increasing(args->field_idxs, args->n_fields)) {
raise_not_increasing_error();
}
// Open a connection to the delimited file.
if(strcmp(argv[1], "stdin") == 0) {
csv = stdin;
}
else {
csv = fopen(argv[1], "r");
}
if(csv == NULL) {
raise_file_error();
}
args->csv = csv;
return args;
}
/* BIN
* ---
* Input parameters:
* dataCol - the column with the channel data
* numChans - number of channels in groupCol and qualCol
* binLow - array of lower group boundaries
* binHigh - array of higher group boundaries
* numBins - number of binLow-binHigh group pairs
* groupCol - the GROUPING column
* qualCol - the QUALITY column
* tabStops - array giving channels with tabs or stops
*/
int grp_do_bin(double *dataCol, long numChans, double *binLow,
double *binHigh, long numBins, short *groupCol,
short *qualCol, short *tabStops, dsErrList *errList,
short partialBin, int isColReal){
long ii, jj, binLength, counter, tempLow, tempHigh, chanHigh;
short isComplete;
double maxVal, dataHigh;
int tmpVar = 0;
int isAscending = 0;
/* Check for obviously bad inputs */
if(!dataCol || (numChans <= 0) || !binLow || !binHigh
|| (numBins < 0) || !groupCol || !qualCol || !tabStops){
if(errList)
dsErrAdd(errList, dsDMGROUPBADPARAMERR, Accumulation,
Generic);
else
err_msg("ERROR: At least one input parameter has an "
"invalid value.\n");
return(GRP_ERROR);
}
/* Check for monotonically increasing or decreasing data */
if (check_increasing(dataCol, numChans) == 0) {
isAscending = 1;
} else {
if ( check_decreasing(dataCol, numChans) != 0 ) {
if(errList)
dsErrAdd(errList, dsDMGROUPBADDATAORDERERR, Accumulation,
Generic);
else
err_msg("ERROR: Data column is not increasing/decreasing.\n");
return(GRP_ERROR);
}
}
if (isAscending) {
dataHigh = dataCol[numChans - 1];
maxVal = binHigh[numBins - 1];
} else {
dataHigh = dataCol[0];
maxVal = binLow[0];
}
chanHigh = upper_bound(maxVal, dataCol, numChans, isAscending, isColReal, errList);
/* Check if any bins overlap */
if(check_overlap(binLow, binHigh, numBins)){
if(errList)
dsErrAdd(errList, dsDMGROUPOVERLAPBINSPECERR, Accumulation,
Generic);
else
err_msg("ERROR: At least two bins in binspec overlap.\n");
return(GRP_ERROR);
}
/* Go through all binLow-binHigh pairs */
for(ii = 0; ii < numBins; ii++){
tempLow = lower_bound(binLow[ii], dataCol, numChans, isAscending,
errList);
tempHigh = upper_bound(binHigh[ii], dataCol, numChans, isAscending,
isColReal, errList);
if (!isAscending) {
tmpVar = tempLow;
tempLow = tempHigh;
tempHigh = tmpVar;
}
if((tempLow == GRP_ERROR) || (tempHigh == GRP_ERROR))
continue;
/* return(GRP_ERROR); */
/* If there are no data within the pair, skip to next pair */
if((tempHigh - tempLow) < 0)
continue;
binLength = tempHigh - tempLow;
if(binLow[ii] > dataHigh){
if(errList)
dsErrAdd(errList, dsDMGROUPINVALIDBINERR, Accumulation,
Generic);
else
err_msg("ERROR: A bin boundary is invalid.\nMake "
"sure the binspec fits within the bounds "
"of the data.\n");
return(GRP_ERROR);
}
isComplete = GRP_TRUE;
/* Check for a complete group */
for(jj = tempLow; jj <= tempHigh; jj++){
if ( (jj > chanHigh) || tabStops[jj] ) {
isComplete = GRP_FALSE;
break;
}
}
/* If it's the last group, and partialBin is TRUE, then it's
not complete. */
if( (partialBin && (ii == (numBins - 1))) ||
((!isAscending) && (binLength < (numBins-1))) )
isComplete = GRP_FALSE;
counter = 0;
/* Create group - good or bad */
for(jj = tempLow; jj <= tempHigh; jj++){
/* Are we in a tab or stop? */
if(tabStops[jj]){
counter = 0;
}
/* Are we at the end of the table? */
else if(jj == (numChans - 1)){
/* Is this a single-element group? */
if(counter == 0){
if(isComplete){
groupCol[jj] = GRP_BEGIN;
qualCol[jj] = GRP_GOOD;
break;
}
else{
groupCol[jj] = GRP_BEGIN;
qualCol[jj] = GRP_POOR;
break;
}
}
/* Does this complete the group? */
if(isComplete){
groupCol[jj] = GRP_MIDDLE;
qualCol[jj] = GRP_GOOD;
break;
}
else{
groupCol[jj] = GRP_MIDDLE;
qualCol[jj] = GRP_POOR;
break;
}
}
/* Are we at the beginning of a group? */
else if(counter == 0){
if(isComplete){
groupCol[jj] = GRP_BEGIN;
qualCol[jj] = GRP_GOOD;
counter++;
}
else{
groupCol[jj] = GRP_BEGIN;
qualCol[jj] = GRP_POOR;
counter++;
}
}
/* We must be in the middle of a group */
else{
if(isComplete){
groupCol[jj] = GRP_MIDDLE;
qualCol[jj] = GRP_GOOD;
counter++;
}
else{
groupCol[jj] = GRP_MIDDLE;
qualCol[jj] = GRP_POOR;
counter++;
}
}
} /* end for(jj) */
} /* end for(ii) */
return(GRP_SUCCESS);
}
