void DoCrop(OptionsCls &options)
{
char name[MAX_PATH_LENGTH];
char destName[MAX_PATH_LENGTH];
int i;
Image loader;
Acq saver;
int mode = 0;
i = 0;
bool allocate = true;
int nameListLen;
char **nameList;
int maxMode=2;
//@WARNING: >must< copy beadfind_post_0000 if it exists, or Analysis will >fail to complete< on PGM run crops
// This is an inobvious bug due to the fact that the Image routine "ReadyToLoad" checks for >the next< acq file
// or explog_final.txt, >or< beadfind_post. If none of those three exist, we wait forever.
// not all runs appear to have explog_final.txt copied around, so can't depend on that.
const char* defaultNameList[] = {"beadfind_pre_0000.dat", "beadfind_pre_0001.dat", "beadfind_pre_0002.dat", "beadfind_pre_0003.dat",
"beadfind_post_0000.dat", "beadfind_post_0001.dat", "beadfind_post_0002.dat", "beadfind_post_0003.dat",
"prerun_0000.dat", "prerun_0001.dat", "prerun_0002.dat", "prerun_0003.dat"
};
// if requested...do not bother waiting for the files to show up
if ( options.dont_retry )
loader.SetTimeout ( 1,1 );
if ( options.oneFile != NULL ) {
nameList = &options.oneFile;
nameListLen = 1;
maxMode=1;
} else {
nameList = const_cast<char**> ( defaultNameList );
nameListLen = sizeof ( defaultNameList ) /sizeof ( defaultNameList[0] );
}
// Create results folder
umask ( 0 ); // make permissive permissions so its easy to delete.
if ( mkdir ( options.destPath, 0777 ) ) {
if ( errno == EEXIST ) {
//already exists? well okay...
} else {
perror ( options.destPath );
exit ( 1 );
}
}
if(!options.skipCopy)
{
// Copy explog.txt file: all .txt files
char cmd[1024];
sprintf ( cmd, "cp -v %s/*.txt %s", options.expPath, options.destPath );
if(system ( cmd ) != 0 )
printf("failed to copy txt files from src\n");
// Copy lsrowimage.txt file
const char *filesToMove[] = {
"lsrowimage.dat",
"gainimage.dat",
"reimage.dat",
"rmsimage.dat"
};
for(int iFile=0; iFile < 4; iFile++) {
sprintf ( cmd, "cp -v %s/%s %s", options.expPath, filesToMove[iFile], options.destPath);
if(system ( cmd ) == 1)
fprintf (stdout, "No %s file found\n",filesToMove[iFile]);
}
}
while ( mode < maxMode ) {
if ( mode == 1 ) {
sprintf ( name, "%s/acq_%04d.dat", options.expPath, i );
sprintf ( destName, "%s/acq_%04d.dat", options.destPath, i );
} else if ( mode == 0 ) {
if ( i >= nameListLen ){
mode++;
i=0;
continue;
}
sprintf ( name, "%s/%s", options.expPath, nameList[i] );
sprintf ( destName, "%s/%s", options.destPath, nameList[i] );
} else
break;
if ( loader.LoadRaw ( name, 0, allocate, false, false ) ) {
allocate = false;
const RawImage *raw = loader.GetImage();
DetermineCropWidthAndHeight ( options.cropx, options.cropy, options.cropw, options.croph, raw->cols, raw->rows );
struct timeval tv;
double startT;
double stopT;
gettimeofday ( &tv, NULL );
startT = ( double ) tv.tv_sec + ( ( double ) tv.tv_usec/1000000 );
if(options.OverSample_skip || options.OverSample_combine)
DoOverSample(options,loader);
if(options.chipType)
ChipIdDecoder::SetGlobalChipId(options.chipType);
if(options.applyXtalkCorrection1){
PairPixelXtalkCorrector xtalkCorrector;
xtalkCorrector.Correct(loader.raw, options.applyXtalkCorrection1);
}
if(options.applyRowCorrection){
printf("Applying row noise correction\n");
CorrNoiseCorrector rnc;
rnc.CorrectCorrNoise(loader.raw,options.applyColCorrection?3:1,true,true,false );
}
else if(options.applyColCorrection){
printf("Applying column noise correction\n");
CorrNoiseCorrector rnc;
rnc.CorrectCorrNoise(loader.raw,0,true,true,false );
}
if(options.applyXtalkCorrection2){
PairPixelXtalkCorrector xtalkCorrector;
xtalkCorrector.Correct(loader.raw, options.applyXtalkCorrection2);
}
if(options.doColumnCorrectionTn)
{
ComparatorNoiseCorrector cnc;
cnc.CorrectComparatorNoiseThumbnail(loader.raw, NULL, 50,50, false);
} else if(options.doColumnCorrection){
ComparatorNoiseCorrector cnc;
bool beadfind = false;//((strstr(name,"beadfind_pre"))?true:false);
cnc.CorrectComparatorNoise(loader.raw, NULL, false, options.cncType,beadfind );
}
if(options.cmpFile){
// subtract this file before continuing
Image loader2;
loader2.LoadRaw ( options.cmpFile, 0, allocate, 2 );
if(options.OverSample_skip || options.OverSample_combine)
DoOverSample(options,loader2);
if(options.doColumnCorrectionTn)
{
ComparatorNoiseCorrector cnc;
cnc.CorrectComparatorNoiseThumbnail(loader2.raw, NULL, 100,100, false);
} else if(options.doColumnCorrection){
ComparatorNoiseCorrector cnc;
bool beadfind = ((strstr(options.cmpFile,"beadfind_pre"))?true:false);
cnc.CorrectComparatorNoise(loader2.raw, NULL, 0, options.cncType,beadfind );
}
{
short int *rawPtr = loader.raw->image;
short int *rawPtr2 = loader2.raw->image;
int frameStride=loader.raw->cols*loader.raw->rows;
for(int frame=0;frame<loader.raw->frames;frame++){
for(int idx=0;idx<frameStride;idx++){
*rawPtr -= *rawPtr2;
*rawPtr += 8192;
rawPtr++;
rawPtr2++;
}
}
}
printf("subtracted %s from the file\n",options.cmpFile);
}
if(options.subtractAverage)
{
// subtract off the mean trace
SubtractOffMean(loader);
printf("subtracted mean from trace\n");
}
// testing of lossy compression
if(!options.pfc && ImageTransformer::PCATest[0]) {
AdvComprTest(name,&loader,ImageTransformer::PCATest,true );
}
saver.SetData ( &loader );
if(options.T0Test)
saver.doT0Compression();
if ( options.regBasedAcq && i == 0 ) {
if ( options.excludeMask )
saver.GenerateExcludeMaskRegions ( ( const char* ) options.excludeMaskFile );
if ( options.useSeparatorT0File )
saver.PopulateCroppedRegionalAcquisitionWindow ( ( const char* ) options.separatorIn, "t0Map.txt",
options.cropx, options.cropy, options.cropw, options.croph, raw->timestamps[0] );
else
saver.ParseT0File ( ( const char* ) options.t0In, "t0Map.txt",
options.cropx, options.cropy, options.cropw, options.croph, raw->timestamps[0] );
}
printf ( "Converting raw data %d %d frames: %d UncompFrames: %d\n", raw->cols, raw->rows, raw->frames, raw->uncompFrames );
if ( options.doAscii ) {
if ( !saver.WriteAscii ( destName, options.cropx, options.cropy, options.cropw, options.croph ) )
break;
} else {
if ( options.vfc ) {
if(options.pfc) {
saver.WritePFV(destName, options.cropx, options.cropy, options.cropw, options.croph, options.PCAOpts);
}
else if ( options.regBasedAcq ) {
if ( !saver.WriteFrameAveragedRegionBasedAcq ( destName, options.cropx, options.cropy, options.cropw, options.croph ) )
break;
} else if ( options.TimeBasedAcq ) {
if ( !saver.WriteTimeBasedAcq ( destName, options.cropx, options.cropy, options.cropw, options.croph ) )
break;
} else {
if ( !saver.WriteVFC ( destName, options.cropx, options.cropy, options.cropw, options.croph ) )
break;
}
} else {
if ( !saver.Write ( destName, options.cropx, options.cropy, options.cropw, options.croph ) )
break;
}
}
gettimeofday ( &tv, NULL );
stopT = ( double ) tv.tv_sec + ( ( double ) tv.tv_usec/1000000 );
printf ( "Converted: %s in %0.2lf sec\n", name,stopT - startT );
fflush ( stdout );
i++;
} else {
if ( ( mode == 0 && i >= 12 ) || ( mode ==1 ) ) {
mode++;
i = 0;
allocate = true;
} else
i++;
}
}
}
int main(int argc, char *argv[])
{
//int cropx = 624, cropy = 125, cropw = 100, croph = 100;
int cropx = 0, cropy = 0, cropw = 0, croph = 0;
char *expPath = const_cast<char*>(".");
char *destPath = const_cast<char*>("./converted");
char *oneFile = NULL;
int alternate_sampling=0;
int doAscii = 0;
int vfc = 1;
int regBasedAcq = 0;
int TimeBasedAcq = 0;
int excludeMask = 0;
int useSeparatorT0File = true;
char* separatorIn = const_cast<char*>("./separator.summary.txt");
char* t0In = const_cast<char*>("./T0file.txt");
char* excludeMaskFile = "/opt/ion/config/exclusionMask_318.bin";
int dont_retry = 0;
if (argc == 1) {
usage(cropx, cropy, cropw, croph);
}
int argcc = 1;
while (argcc < argc) {
switch (argv[argcc][1]) {
case 'a':
doAscii = 1;
break;
case 'x':
argcc++;
cropx = atoi(argv[argcc]);
break;
case 'y':
argcc++;
cropy = atoi(argv[argcc]);
break;
case 'w':
argcc++;
cropw = atoi(argv[argcc]);
break;
case 'h':
argcc++;
// don't segfault if called with -h (user expects help)
if (argcc >= argc) {
usage(cropx, cropy, cropw, croph);
}
croph = atoi(argv[argcc]);
break;
case 's':
argcc++;
expPath = argv[argcc];
break;
case 'f':
argcc++;
oneFile = argv[argcc];
break;
case 'z':
dont_retry = 1;
break;
case 'c':
vfc=1;
cropx=0;
cropy=0;
cropw=0;
croph=0;
break;
case 'n':
vfc=0;
break;
case 'b':
alternate_sampling=1;
break;
case 'v':
fprintf (stdout, "%s", IonVersion::GetFullVersion("Crop").c_str());
exit (0);
break;
case 'H':
usage(cropx, cropy, cropw, croph);
break;
case 'd':
argcc++;
destPath = argv[argcc];
break;
case 'r':
regBasedAcq=1;
break;
case 'l':
TimeBasedAcq=1;
break;
case 't':
argcc++;
separatorIn = argv[argcc];
break;
case 'e':
argcc++;
t0In = argv[argcc];
useSeparatorT0File = false;
break;
case 'g':
argcc++;
excludeMaskFile = argv[argcc];
excludeMask = 1;
break;
default:
argcc++;
fprintf (stdout, "\n");
}
argcc++;
}
char name[MAX_PATH_LENGTH];
char destName[MAX_PATH_LENGTH];
int i;
Image loader;
Acq saver;
int mode = 0;
i = 0;
bool allocate = true;
char **nameList;
char *defaultNameList[] = {"beadfind_post_0000.dat", "beadfind_post_0001.dat", "beadfind_post_0002.dat", "beadfind_post_0003.dat",
"beadfind_pre_0000.dat", "beadfind_pre_0001.dat", "beadfind_pre_0002.dat", "beadfind_pre_0003.dat",
"prerun_0000.dat", "prerun_0001.dat", "prerun_0002.dat", "prerun_0003.dat", "prerun_0004.dat"};
int nameListLen;
// Turn off this feature which sucks the life out of performance.
PWR::PinnedWellReporter::Instance( false );
// if requested...do not bother waiting for the files to show up
if (dont_retry)
loader.SetTimeout(1,1);
if (oneFile != NULL)
{
nameList = &oneFile;
nameListLen = 1;
mode = 1;
}
else
{
nameList = defaultNameList;
nameListLen = sizeof(defaultNameList)/sizeof(defaultNameList[0]);
}
// Create results folder
umask (0); // make permissive permissions so its easy to delete.
if (mkdir (destPath, 0777))
{
if (errno == EEXIST) {
//already exists? well okay...
}
else {
perror (destPath);
exit (1);
}
}
// Copy explog.txt file: all .txt files
char cmd[1024];
sprintf (cmd, "cp -v %s/*.txt %s", expPath, destPath);
assert(system(cmd) == 0);
while (mode < 2) {
if (mode == 0) {
sprintf(name, "%s/acq_%04d.dat", expPath, i);
sprintf(destName, "%s/acq_%04d.dat", destPath, i);
} else if (mode == 1) {
if(i >= nameListLen)
break;
sprintf(name, "%s/%s", expPath, nameList[i]);
sprintf(destName, "%s/%s", destPath, nameList[i]);
} else
break;
if (loader.LoadRaw(name, 0, allocate, false)) {
allocate = false;
const RawImage *raw = loader.GetImage();
DetermineCropWidthAndHeight(cropx, cropy, cropw, croph, raw->cols, raw->rows);
struct timeval tv;
double startT;
double stopT;
gettimeofday(&tv, NULL);
startT = (double) tv.tv_sec + ((double) tv.tv_usec/1000000);
saver.SetData(&loader);
if (regBasedAcq && i == 0) {
if (excludeMask)
saver.GenerateExcludeMaskRegions((const char*)excludeMaskFile);
if (useSeparatorT0File)
saver.PopulateCroppedRegionalAcquisitionWindow((const char*)separatorIn, "t0Map.txt",
cropx, cropy, cropw, croph, raw->timestamps[0]);
else
saver.ParseT0File((const char*)t0In, "t0Map.txt",
cropx, cropy, cropw, croph, raw->timestamps[0]);
}
printf("Converting raw data %d %d frames: %d UncompFrames: %d\n", raw->cols, raw->rows, raw->frames, raw->uncompFrames);
if (doAscii) {
if (!saver.WriteAscii(destName, cropx, cropy, cropw, croph))
break;
}
else {
if(vfc)
{
if (regBasedAcq) {
if (!saver.WriteFrameAveragedRegionBasedAcq(destName, cropx, cropy, cropw, croph))
break;
}
else if (TimeBasedAcq) {
if (!saver.WriteTimeBasedAcq(destName, cropx, cropy, cropw, croph))
break;
}
else {
if (!saver.WriteVFC(destName, cropx, cropy, cropw, croph))
break;
}
}
else
{
if (!saver.Write(destName, cropx, cropy, cropw, croph))
break;
}
}
gettimeofday(&tv, NULL);
stopT = (double) tv.tv_sec + ((double) tv.tv_usec/1000000);
printf("Converted: %s in %0.2lf sec\n", name,stopT - startT);
fflush (stdout);
i++;
} else {
if ((mode == 1 && i >= 12) || (mode == 0)) {
mode++;
i = 0;
allocate = true;
} else
i++;
}
}
}