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#include <odindata/fileio.h>
#include <odindata/utils.h>
#include <odindata/filter.h>
/**
* \page miconv Conversion utility for medical images
* \verbinclude cmdline-utils/miconv.usage
*
* \section miconv_examples Some examples how to use miconv:
*
* Read a bunch of DICOM files (format 'dcm'), produced by Siemens, from directory 'mosaic' and convert it to NIFTI file 'mosaic.nii'
* with a dialect suitable for FSL:
* \verbatim
miconv -rf dcm -rdialect siemens -wdialect fsl mosaic mosaic.nii
\endverbatim
*
* Converting a short (16 bit) raw data file '2dseq' of size 256x256 to a DICOM file 'image.dcm':
* \verbatim
miconv -nx 256 -ny 256 -rf short 2dseq image.dcm
\endverbatim
*/
struct MiConvOpts : LDRblock {
LDRbool quiet;
LDRstring protfile;
LDRstring parlist;
MiConvOpts() {
quiet.set_cmdline_option("q").set_description("Quiet mode: do not print progress");
append_member(quiet,"quiet");
protfile.set_cmdline_option("p").set_description("Load this protocol for defaults");
append_member(protfile,"protfile");
parlist.set_cmdline_option("l").set_description("Lists space-separated set of protocol parameters and exits. Use '-l help' to get a list of possible parameters and '-l all' to list all parameters. The parameter 'output-file' must be omitted when using this option.");
append_member(parlist,"parlist");
}
};
////////////////////////////////////////
void usage(const Protocol& prot) {
FileReadOpts ropts;
FileWriteOpts wopts;
MiConvOpts mopts;
FilterChain filter;
STD_cout << "miconv: Converts medical image data between formats." << STD_endl;
STD_cout << " File formats are automatically identified by their file extension." << STD_endl;
STD_cout << " It expects at least two filenames/directories (for the input and output file) at the end of the command line." << STD_endl;
STD_cout << " An exception is the option '-l' which requires only one filename/directory to list its content." << STD_endl;
STD_cout << configInfo() << STD_endl;
STD_cout << STD_endl;
STD_cout << "Usage: miconv [options] <input-file> [<output-file>]" << STD_endl;
STD_cout << "General options:" << STD_endl;
STD_cout << mopts.get_cmdline_usage("\t");
STD_cout << "Protocol options (overrides parameters in input data):" << STD_endl;
STD_cout << prot.get_cmdline_usage("\t");
STD_cout << "File read options (will be applied to input data before processing):" << STD_endl;
STD_cout << ropts.get_cmdline_usage("\t");
STD_cout << "File write options (will be applied to output data after processing):" << STD_endl;
STD_cout << wopts.get_cmdline_usage("\t");
STD_cout << "Filters/processing, applied in the order they appear on the command line:" << STD_endl;
STD_cout << filter.get_cmdline_usage("\t");
STD_cout << "Other options:" << STD_endl;
STD_cout << "\t" << LogBase::get_usage() << STD_endl;
STD_cout << "\t" << helpUsage() << STD_endl;
STD_cout << "Supported file extensions(formats):" << STD_endl;
STD_cout << FileIO::autoformats_str("\t") << STD_endl;
}
////////////////////////////////////////
int main(int argc, char* argv[]) {
if(LogBase::set_log_levels(argc,argv)) return 0;
Log<OdinData> odinlog("miconv","main");
char optval[ODIN_MAXCHAR];
Protocol prot_template;
FileReadOpts ropts;
FileWriteOpts wopts;
MiConvOpts mopts;
if(hasHelpOption(argc,argv)) {usage(prot_template); return 0;}
if(argc<3) {usage(prot_template); return 0;}
// set defaults
prot_template.seqpars.set_MatrixSize(readDirection,1);
prot_template.seqpars.set_MatrixSize(phaseDirection,1);
prot_template.seqpars.set_MatrixSize(sliceDirection,1);
mopts.parse_cmdline_options(argc,argv);
if(mopts.quiet) FileIO::set_trace_status(false);
STD_string infile;
STD_string outfile;
if(mopts.parlist!="") {
infile=argv[argc-1];
} else {
infile=argv[argc-2];
outfile=argv[argc-1];
}
if(mopts.parlist=="help") {
STD_cout << "Possible protocol parameters:" << STD_endl;
for(unsigned int i=0; i<prot_template.numof_pars(); i++) {
LDRbase& ldr=prot_template[i];
if(ldr.get_filemode()!=exclude) {
STD_cout << ldr.get_label() << STD_endl;
}
}
return 0;
}
svector pars;
if(mopts.parlist=="all") {
for(unsigned int i=0; i<prot_template.numof_pars(); i++) {
LDRbase& ldr=prot_template[i];
if(ldr.get_filemode()!=exclude) pars.push_back(ldr.get_label());
}
} else {
pars=tokens(mopts.parlist);
}
int npars=pars.size();
if(npars) FileIO::set_trace_status(false);
if(mopts.protfile!="") {
ODINLOG(odinlog,infoLog) << "Loading default protocol " << optval << STD_endl;
prot_template.load(mopts.protfile);
}
// override parameters of protocol file
prot_template.parse_cmdline_options(argc,argv,false); // do not modify argc/argv on 1st pass
FileIO::ProtocolDataMap pdmap_in;
// Read data
ropts.parse_cmdline_options(argc,argv);
ProgressDisplayConsole display;
ProgressMeter progmeter(display);
ProgressMeter* progmeter_ptr=0;
if(!mopts.quiet) progmeter_ptr=&progmeter;
int readresult=FileIO::autoread(pdmap_in, infile, ropts, prot_template, progmeter_ptr);
if(readresult<0) {
ODINLOG(odinlog,errorLog) << "autoread failed" << STD_endl;
return readresult;
}
// If requested, print formatted protocol properties and exit
if(npars) {
int ncols=npars;
int irow=0;
int ndsets=pdmap_in.size();
if(ndsets>1) {
ncols++;
}
int nrows=ndsets;
if(npars>1) nrows++;
sarray table(nrows,ncols);
if(npars>1) {
for(int ipar=0; ipar<npars; ipar++) {
table(0,ipar)=pars[ipar];
}
table(0,npars)="Dataset";
irow++;
}
for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap_in.begin(); pdit!=pdmap_in.end(); ++pdit) {
for(int ipar=0; ipar<npars; ipar++) {
table(irow,ipar)=rmblock(pdit->first.printval(pars[ipar]), "\n", ""); // truncate after first newline
}
if(ndsets>1) {
STD_ostringstream oss;
oss << pdit->second.shape();
table(irow,npars)=oss.str();
}
irow++;
}
STD_cout << print_table(table);
return 0;
}
ODINLOG(odinlog,normalDebug) << "mem(in ): " << Profiler::get_memory_usage() << STD_endl;
// Create copy of protocol-data map, thereby modify protocol
FileIO::ProtocolDataMap pdmap_out;
for(FileIO::ProtocolDataMap::const_iterator pdit=pdmap_in.begin(); pdit!=pdmap_in.end(); ++pdit) {
Protocol prot(pdit->first);
prot.parse_cmdline_options(argc,argv); // override parameters of infile
pdmap_out[prot].reference(pdit->second);
}
ODINLOG(odinlog,normalDebug) << "mem(out): " << Profiler::get_memory_usage() << STD_endl;
// Parse before filters to remove options
wopts.parse_cmdline_options(argc,argv);
FilterChain filterchain(argc,argv);
//apply filters on pdmap_out
if(!filterchain.apply(pdmap_out)) return -1;
// Write data
int result=FileIO::autowrite(pdmap_out, outfile, wopts);
if(result>0) result=0;
return result;
}
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