void ImageSpecClass::ReadFirstImage(Image &img, SystemContext &sys_context, ImageControlOpts &img_control, SpatialContext &loc_context )
{
img.SetImgLoadImmediate ( false );
img.SetNumAcqFiles ( 1 );
img.SetIgnoreChecksumErrors ( img_control.ignoreChecksumErrors );
bool datIsSdat = false;
char *firstAcqFile = ( char * ) malloc ( strlen ( sys_context.dat_source_directory ) + strlen (
img_control.acqPrefix ) + 10 );
sprintf ( firstAcqFile, "%s/%s%04d.dat", sys_context.dat_source_directory, img_control.acqPrefix, 0 );
/* Check to see if our dat file is really an sdat file in disguise, if so updat our suffix and doing sdats. */
if (H5File::IsH5File(firstAcqFile)) {
datIsSdat = true;
img_control.sdatSuffix = "dat";
img_control.doSdat = true;
}
char *firstSdatAcqFile = ( char * ) malloc ( strlen ( sys_context.dat_source_directory ) + strlen (
img_control.acqPrefix ) + 11 );
sprintf ( firstSdatAcqFile, "%s/%s%04d.%s", sys_context.dat_source_directory, img_control.acqPrefix, 0, img_control.sdatSuffix.c_str() );
if (isFile(firstAcqFile) && !datIsSdat) {
if ( !img.LoadRaw ( firstAcqFile, 0, true, false ) )
{
exit ( EXIT_FAILURE );
}
}
else if(isFile(firstSdatAcqFile)) {
TraceChunkSerializer reader;
SynchDat sdat;
reader.Read(firstSdatAcqFile, sdat);
img.InitFromSdat(&sdat);
if (loc_context.regionXSize == 0){ // not explicitly set, set now
loc_context.regionXSize = sdat.GetColStep();
loc_context.regionYSize = sdat.GetRowStep();
}
if ((sdat.GetColStep() != (size_t)loc_context.regionXSize) ||
(sdat.GetRowStep() != (size_t)loc_context.regionYSize)) {
fprintf(stdout, "Warning: Analysis region sizes width=%d, height=%d do not match sdat region sizes width=%d, height=%d\n", loc_context.regionXSize, loc_context.regionYSize, (int)sdat.GetColStep(), (int)sdat.GetRowStep());
}
}
else {
exit ( EXIT_FAILURE );
}
img.SetOffsetFromChipOrigin ( firstAcqFile );
free ( firstAcqFile );
free ( firstSdatAcqFile );
if ( !loc_context.IsSetRegionXYSize() ){ // not yet set, has to be set now
loc_context.SetRegionXYSize(50, 50);
}
img.SetDir ( sys_context.results_folder );
img.SetFlowOffset ( img_control.flowTimeOffset );
}
void ImageSpecClass::ReadFirstImage(Image &img, SystemContext &sys_context, ImageControlOpts &img_control, SpatialContext &loc_context )
{
img.SetImgLoadImmediate ( false );
img.SetNumAcqFiles ( 1 );
img.SetIgnoreChecksumErrors ( img_control.ignoreChecksumErrors );
char *firstAcqFile = ( char * ) malloc ( strlen ( sys_context.dat_source_directory ) + strlen (
img_control.acqPrefix ) + 10 );
sprintf ( firstAcqFile, "%s/%s%04d.dat", sys_context.dat_source_directory, img_control.acqPrefix, 0 );
if ( !img.LoadRaw ( firstAcqFile, 0, true, false ) )
{
exit ( EXIT_FAILURE );
}
img.SetOffsetFromChipOrigin ( firstAcqFile );
free ( firstAcqFile );
if ( !loc_context.IsSetRegionXYSize() ){ // not yet set, has to be set now
loc_context.SetRegionXYSize(50, 50);
}
img.SetDir ( sys_context.results_folder );
img.SetFlowOffset ( img_control.flowTimeOffset );
}
