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Process.cc
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/*! \file
\brief Processing commands */
#include "simpsonio.h"
#include "matlabio.h"
#include "cmatrix_utils.h"
#include "NMRsim_Process.h"
#include "NMRsim_logfile.h"
#include "Histogram.h"
#include <sys/stat.h>
#include <sstream>
static const double deg_to_rad=M_PI/180.0;
static const double rad_to_deg=180.0/M_PI;
static const double TWOPI=M_PI*2.0;
BaseList<complex> current_data_row;
void real(ListList<double>& d, const ListList<complex>& s)
{
d.duplicate_structure(s);
BaseList<double> drow(d.row());
real(drow,s.row());
}
// maximum length of Matlab variables
#define NMRSIM_SAVEMAX NMRSIM_MATLAB_VARMAX
static const double sfrq_factor=1e-6; //!< factor for converting pNMRsim sfrq (always in Hz) to external (by default MHz)
double convert_sfrq(double x, int saveflags =0)
{
if (saveflags & ProcessSave::NOSFRQ)
return 0.0;
return sfrq_factor*((saveflags & ProcessSave::POSITIVESFRQ) ? fabs(x) : x);
}
option optsaveprotect("preventoverwrite","prevent file overwrite");
void filestruct::clear()
{
domain=domain1=D_UNKNOWN;
sw=sw1=sfrq=sfrq1=ref=ref1=0.0;
}
static bool allow_proc_sum=true;
//! flag whether sum allowed in this context
int defsumflags() {
return allow_proc_sum ? 0 : F_DENYSUM;
}
//! normal flags, allowing sum only if allow_proc_sum set and blocking array / expression variables if 2D active
int defflags() {
const static int result=active2D ? (F_DENYEXPR | F_DENYARRAY) : 0;
return result | defsumflags();
}
ContextWarning<> process_groupsvary_warning("number of processing groups varies between processing stage - this may create very odd results!",&NMRsim_repeat_warning);
bool read_proc_block(procstack_t& pstack, const char* name, const Process_Factory_t& factory, bool allowsum)
{
allow_proc_sum=allowsum;
return factory_read(pstack,name,factory,Type2Type<ProcessCommand>(),Type2Type<NullType>());
}
size_t read_proc_blocks(LIST<procstack_t>& pstacks, size_t& accstacks, const char* name, const Process_Factory_t& factory, bool allowsum)
{
allow_proc_sum=allowsum;
const size_t nstacks=multiple_factory_read(pstacks,name,factory,Type2Type<ProcessCommand>(),Type2Type<NullType>());
if (nstacks) {
if (accstacks<2)
accstacks=nstacks;
else {
if (nstacks!=accstacks)
process_groupsvary_warning.raise();
}
}
return nstacks;
}
bool try_merge_proc_blocks(LIST<procstack_t>& initialstacks, LIST<procstack_t>& procstacks)
{
const size_t n=initialstacks.size();
if ((n==0) || ((n!=procstacks.size()) && !(procstacks.empty())))
return false;
const int uses=multiple_overall_attributes(initialstacks);
const bool mergestacks=((uses & A_SUM)==0);
if (verbose & VER_PARSE)
std::cout << "Merging initialproc and proc: " << (mergestacks ? "Yes\n" : "No\n");
if (!mergestacks)
return false;
if (procstacks.empty())
procstacks.create(n);
for (size_t i=n;i--;) {
procstack_t& source(initialstacks(i));
procstack_t& dest(procstacks(i));
// dest.reserve(dest.size()+source.size());
while (!source.empty()) {
dest.push_front(source.back());
source.pop_back();
}
}
initialstacks.clear();
return true;
}
static char scr_fname[2048];
static const int SAVE_FORMATS = ProcessSave::MATLAB | ProcessSave::ASCII | ProcessSave::SIMPSON | ProcessSave::SIMPLOT;
bool ProcessSave::defaultstopoverwrite=false;
Process_Factory_t& get_Process_Factory()
{
static Process_Factory_t Process_Factory;
return Process_Factory;
}
Process_Factory_t& get_Finalise_Factory()
{
static Process_Factory_t Finalise_Factory;
return Finalise_Factory;
}
typedef std::map<size_t,SaveCommand_function> Save_Factory_t;
Save_Factory_t& get_Save_Factory()
{
static Save_Factory_t save_Factory;
return save_Factory;
}
flagsmap_type& get_Save_flags()
{
static flagsmap_type saveflags;
return saveflags;
}
void register_save_function(const char* name, SaveCommand_function funcp)
{
static size_t curflag=ProcessSave::USERFLAGS;
if (curflag==0)
throw Failed("register_save_function: flags exhausted");
get_Save_Factory()[curflag]=funcp;
get_Save_flags()[name]=curflag;
curflag<<=1;
}
bool havescale=false;
// procflags::procflags()
// : istimedomain(!isfrequency()),
// istimedomain1(true),
// scalevalid(true)
// {}
// void procflags::invalidatescale()
// {
// scalevalid=false;
// }
processing_state::processing_state(double swv, bool istdv, double sfrqv, double refv)
: sw(swv),
istimedomain(istdv),
sfrq(sfrqv),
ref(refv)
{}
//Warning<> ProcessSave::matlabname_warning("data set name does not start with letter. This may confuse Matlab: ",&NMRsim_once_warning);
namespace {
smartptr<matlab_controller,false> matlabrawp;
smartptr<matlab_controller::composite,false> matlabp;
std::string strbuffer;
void write_simpson_rows(const char* fnamep, const ListList<complex>& FID, const BaseList<processing_state>& pflags, int saveflags)
{
simpson_controller ctrl(fnamep,FID.size());
for (size_t i=FID.size();i--;) {
simpsonFD spec(FID(i),pflags(i).sw,!(pflags(i).istimedomain));
spec.sfrq=convert_sfrq(pflags(i).sfrq, saveflags);
spec.ref=pflags(i).ref;
ctrl.write(i,spec);
}
}
void scalefirst(cmatrix& FID, double scale, double scale1)
{
if (scale1!=1.0) {
for (size_t n=skips.front();n--;)
FID.row(n)*=scale1;
}
for (size_t n=FID.rows();n--;)
FID(n,0U)*=scale;
}
template<class T> LIST<T> project_row(const Matrix<T>& a)
{
const size_t n=a.rows();
if (!n)
throw Undefined("project_row");
LIST<T> d(a.row(0),mxflag::temporary);
for (size_t j=1;j<n;j++)
d+=a.row(j);
return d;
}
template<class T> LIST<T> project_col(const Matrix<T>& a)
{
size_t n=a.rows();
LIST<T> d(n,T(0),mxflag::temporary);
for (;n--;)
d(n)=sum(a.row(n));
return d;
}
void doshift(BaseList<complex> FID, size_t shift)
{
for (size_t c=shift;c--;)
::std::swap(FID(c),FID(c+shift));
}
void shifthalf(cmatrix& FID, bool is2D)
{
size_t shift,r;
if (FID.cols()>1) {
if (FID.cols() & 1)
throw Failed("shifthalf can only be applied to data sets with an even number of points");
shift=FID.cols()/2;
for (r=FID.rows();r--;)
doshift(FID.row(r),shift);
}
if (is2D) {
if ((FID.rows()/skips.front()) & 1)
throw Failed("shifthalf can only be applied to data sets with an even number of rows");
shift=FID.rows()/2;
for (r=shift;r--;) {
BaseList<complex> FIDr(FID.row(r));
BaseList<complex> FIDs(FID.row(r+shift));
for (size_t c=FIDr.size();c--;)
::std::swap(FIDr(c),FIDs(c));
}
}
}
}
void ProcessCommand::print_ftflags(std::ostream& ostr, size_t flags)
{
if (flags & FT_INV)
ostr << " -inv";
if (flags & FT_NOFIRST)
ostr << " -noscalefirst";
if (flags & FT_NOSHIFT)
ostr << " -noshift";
}
bool ProcessSave::openmatlab(const char* rawname) const
{
const char* basename=getbasename(rawname);
const size_t rootlength=basename-rawname;
char tmpname[MAXPATH];
strncpy(tmpname,rawname,rootlength); //!< copy root
char* cleanbuf = tmpname+rootlength;
const char* outp=sanitise_varname(basename,cleanbuf);
if (outp!=cleanbuf)
throw InternalError("ProcessSave::openmatlab");
// if (!isalpha(basename[0]))
// ProcessSave::matlabname_warning.raise(basename);
char* endp=strchr(tmpname,'\0');
strcpy(endp,".mat");
if (checkoverwrite(tmpname))
return false;
*endp='\0'; //suppress temporarily added .mat
matlabrawp.reset(new matlab_controller(tmpname,5));
matlabp.reset(new matlab_controller::composite(*matlabrawp,cleanbuf,matlab_controller::STRUCT));
return true;
}
struct Process_Proxy_ {
Process_Proxy_() {
Process_Factory_t& Process_Factory(get_Process_Factory());
Process_Factory["addlb"]=&ProcessAddLB::create;
Process_Factory["addnoise"]=&ProcessAddNoise::create;
Process_Factory["apply"]=&ProcessApply::create;
Process_Factory["addsignals"]=&ProcessAddSignals::create;
Process_Factory["conjugate"]=&ProcessConjugate::create;
Process_Factory["echo"]=&ProcessEcho::create;
Process_Factory["extract"]=&ProcessExtract::create;
Process_Factory["fill"]=&ProcessFill::create;
Process_Factory["ft"]=&ProcessFT::create;
Process_Factory["ft2d"]=&ProcessFT2d::create;
Process_Factory["log_file"]=&ProcessLogFile::create;
Process_Factory["magnitude"]=&ProcessMagnitude::create;
Process_Factory["newnp"]=&ProcessResample::create;
Process_Factory["normalise"]=&ProcessNormalise::create;
Process_Factory["normalize"]=&ProcessNormalise::create;
Process_Factory["offset"]=&ProcessOffset::create;
Process_Factory["phase"]=&ProcessPhase::create;
Process_Factory["resample"]=&ProcessResample::create;
Process_Factory["rev"]=&ProcessReverse::create;
Process_Factory["save"]=&ProcessSave::create;
Process_Factory["scale"]=&ProcessScale::create;
Process_Factory["scalefirst"]=&ProcessScaleFirst::create;
Process_Factory["set"]=&ProcessSet::create;
Process_Factory["setdomain"]=&ProcessSetDomain::create;
Process_Factory["shifthalf"]=&ProcessShiftHalf::create;
Process_Factory["transpose"]=&ProcessTranspose::create;
// Process_Factory["sw"]=&ProcessSW::create;
Process_Factory["zerofill"]=&ProcessZeroFill::create;
Process_Factory_t& Finalise_Factory(get_Finalise_Factory());
Finalise_Factory["echo"]=&ProcessEcho::create;
// Finalise_Factory["puts"]=&ProcessEcho::create_puts;
Finalise_Factory["rev"]=&ProcessReverse::create;
Finalise_Factory["save"]=&ProcessSave::create;
Finalise_Factory["setdomain"]=&ProcessSetDomain::create;
Finalise_Factory["system"]=&ProcessSystem::create;
Finalise_Factory["log_file"]=&ProcessLogFile::create;
// optional_map_t& optional_map(get_optional_map());
add_option(optsaveprotect);
// optional_map["preventoverwrite"]=&optsaveprotect;
}
};
//declare ProcessCommands
static Process_Proxy_ process_proxy_;
void FTObject::negate_alternate(BaseList<complex> FID)
{
IndirectList<complex,slice> indFID(FID,slice(1,FID.size()/2,2));
negate_ip(indFID);
}
ThreadWarning<> ProcessFT::doesnothing_warning("FT applied to data set with single point does nothing!",&NMRsim_once_warning);
ThreadWarning<> ProcessFT::nonpowerof2_warning("data set length is not a power of 2 and so not using Fast FT; use zerofill to pad to power of 2?",&NMRsim_once_warning);
ThreadWarning<> ProcessFT::expectingfid_warning("Forward ft applied to spectrum rather than FID may result in reversed data (-nochecks will suppress warning)",&NMRsim_once_warning);
ThreadWarning<> ProcessFT::expectingspectrum_warning("ft -inv applied to FID rather than spectrum may result in reversed data (-nochecks will suppress warning)",&NMRsim_once_warning);
FTObject::FTObject(size_t nv, int flagsv)
: n(nv), flags(flagsv)
{
if (n<2)
ProcessFT::doesnothing_warning.raise();
doshift=!(flags & ProcessCommand::FT_NOSHIFT);
doscale=!(flags & ProcessCommand::FT_NOFIRST);
// static const int dirmask=(ProcessCommand::FT_INV | ProcessCommand::FT_FID | ProcessCommand::FT_SPECTRUM);
//switch (flags & dirmask) {
//case 0: case ProcessCommand::FT_SPECTRUM: case ProcessCommand::FT_INV: case ProcessCommand::FT_FID:
// break;
//default:
// error_abort("ft: can only specify one of -inv, -fid or -spectrum");
//}
fastft=ispowerof2(n);
if (!fastft)
ProcessFT::nonpowerof2_warning.raise();
}
void FTObject::exec(BaseList<complex> FID, const processing_state& pflags) const
{
if (n<2)
return;
int dir=0;
static const int dirmask=(ProcessCommand::FT_INV | ProcessCommand::FT_FID | ProcessCommand::FT_SPECTRUM);
switch (flags & dirmask) {
case 0:
dir=1;
if (!nochecks && !(pflags.istimedomain))
ProcessFT::expectingfid_warning.raise();
break;
case ProcessCommand::FT_INV:
dir=-1;
if (!nochecks && pflags.istimedomain)
ProcessFT::expectingspectrum_warning.raise();
break;
// case ProcessCommand::FT_SPECTRUM:
// dir=1;
// if (pflags.istimedomain)
// ProcessFT::expectingspectrum_warning.raise();
// break;
// case ProcessCommand::FT_FID:
// dir=-1;
// if (!(pflags.istimedomain))
// ProcessFT::expectingfid_warning.raise();
// break;
default:
throw InternalError("FT: unexpected direction flag");
}
if (pflags.istimedomain) {
if (doshift)
negate_alternate(FID);
if (doscale)
FID.front()*=0.5;
}
if (fastft)
fft_ip(FID,dir);
else
FID=ft(FID,dir);
if (!(pflags.istimedomain)) { //ensure that TD->FD and FD->TD are inverses
if (doshift)
negate_alternate(FID);
if (doscale)
FID.front()*=2.0;
}
}
void ProcessFT::exec(BaseList<complex> FID, processing_state& pflags) const
{
FTObject obj(FID.size(),ftflags);
obj.exec(FID,pflags);
pflags.istimedomain=!pflags.istimedomain;
}
static void split(cmatrix& FIDc, cmatrix& FIDs, const cmatrix& a)
{
const size_t nrows=a.rows();
if (!nrows)
throw Undefined("split");
if (nrows % 2)
throw Failed("Hypercomplex signal must have even number of rows");
const size_t nrows2=nrows/2;
FIDc.create(nrows2,a.cols());
FIDs.create(nrows2,a.cols());
size_t ai=0;
for (size_t i=0;i<nrows2;i++) {
FIDc.row(i)=a.row(ai++);
FIDs.row(i)=a.row(ai++);
}
}
// void ProcessConjugate::checktd(const processing_state& pflags)
// {
// static bool donewarn=!allowwarnings();
// if (!(pflags.istimedomain) && !donewarn) {
// std::cerr << "Warning (first): conjugate applied to frequency domain data\n";
// donewarn=true;
// }
// }
void ProcessMagnitude::exec(BaseList<complex>& FID)
{
for (size_t i=FID.size();i--;)
FID(i)=abs(FID(i));
}
void ProcessMagnitude::exec(BaseList<complex> FID, processing_state&) const
{
exec(FID);
}
void ProcessMagnitude::exec(cmatrix& FID, LIST<processing_state>&) const
{
// checktd(pflags.back());
BaseList<complex> asrow(FID.row());
exec(asrow);
}
void ProcessConjugate::exec(BaseList<complex> FID, processing_state&) const
{
// checktd(pflags);
exec(FID);
}
void ProcessConjugate::exec(cmatrix& FID, LIST<processing_state>&) const
{
// checktd(pflags.back());
FID.conj();
}
void ProcessShiftHalf::exec(BaseList<complex> FID, processing_state& pflag) const
{
if (FID.size() & 1)
throw Failed("shifthalf can only be applied to data sets with an even number of points");
doshift(FID,FID.size()/2);
// if (pflag.ref) {
// refreset_warning.raise();
// pflag.ref=0.0;
// }
}
void ProcessShiftHalf::exec(cmatrix& FID, LIST<processing_state>& pflags) const
{
shifthalf(FID,process2D);
// bool donereset=false;
// for (size_t i=pflags.size();i--;) {
// if (pflags(i).ref) {
// donereset=true;
// pflags(i).ref=0.0;
// }
// }
// if (donereset)
// refreset_warning.raise();
}
void process_set_n(int dim, int n, int ni_skip)
{
raw_set_n(dim,n,ni_skip);
ensure_array();
}
void ProcessFT2d::exec(cmatrix& FID, LIST<processing_state>& pflags) const
{
const int dir=(ftflags & FT_INV) ? -1 : 1;
if (pflags.size()!=2)
throw Failed("2D FT only valid for 2D data");
if (!pflags(0U).istimedomain || !pflags(1U).istimedomain)
throw Failed("2D FT only valid for time-domain data");
if (!ispowerof2(FID.cols()) || !ispowerof2(FID.rows()))
error_abort("ft2d only applicable when acquisition dimensions are powers of 2",ERR_FAILED);
if (!(ftflags & FT_NOFIRST))
scalefirst(FID,0.5,0.5);
switch (skips.front()) {
case 2: {
cmatrix FIDc,FIDs;
split(FIDc,FIDs,FID);
ampfft_ip(FIDc,FIDs,dir);
if (needphase)
ampphase_correct_ip(FIDc,FIDs,zero2*deg_to_rad,first2*deg_to_rad,0.0,zero1*deg_to_rad,first1*deg_to_rad,0.0);
FID.swap(FIDc); //!< 'sin' component is discarded after phasing
process_set_n(1,FID.rows(),1); //!< change number of rows
}
break;
case 1:
if (FID.cols()==1) {
BaseList<complex> FIDr(FID.row());
fft_ip(FIDr,dir);
}
else
phasefft_ip(FID,dir);
if (needphase)
phase_correct_ip(FID,zero2*deg_to_rad,first2*deg_to_rad,0.0,zero1*deg_to_rad,first1*deg_to_rad,0.0);
break;
default:
parser_printthread(std::cerr) << "ft2d only valid with skip of 1 or 2 (" << skips.front() << ")\n";
error_abort();
}
if (!(ftflags & FT_NOSHIFT))
shifthalf(FID,true);
pflags(0U).istimedomain=false;
pflags(1U).istimedomain=false;
}
void ProcessPhase::exec(BaseList<complex> data, processing_state&) const
{
phase_correct_ip(data,zero*deg_to_rad,first*deg_to_rad,pivot);
}
void
ProcessFT2d::print(std::ostream& ostr) const
{
// assert(subsid==S_NONE);
ostr << "ft2d ";
print_ftflags(ostr,ftflags);
if (needphase)
ostr << first2 << ' ' << zero2 << ' ' << first1 << ' ' << zero1;
}
void
ProcessPhase::print(std::ostream& ostr) const
{
ostr << "phase " << first << ' ' << zero << ' ' << "(pivot: " << pivot << ')';
}
void
ProcessPhase::printvariablename(std::ostream& ostr, subsid_t subsid) const
{
ostr << "phase_";
switch (subsid) {
case S_ARG1:
ostr << "first";
break;
case S_ARG2:
ostr << "zero";
break;
default:
throw InvalidParameter("ProcessPhase::printvariablename");
}
}
void
ProcessPhase::set(double v, subsid_t subsid)//, bool)
{
switch (subsid) {
case S_ARG1:
first=v;
break;
case S_ARG2:
zero=v;
break;
default:
throw InternalError("ProcessPhase::set");
}
}
const char* ProcessSave::makefilename(const char* fnamep, const char* name) const
{
// const char* bname=name; //!< something odd here - bname not used?
char* scrp(scr.vector());
if (name) {
if (strlen(name)>=NMRSIM_SAVEMAX)
throw Failed("makefilename: filename too long");
switch (saveflags_ & SAVE_FORMATS) {
case SIMPLOT: case SIMPSON:
strcpy(scrp,insert_simpson(fnamep,name,'_').vector());
break;
default:
if (*fnamep)
sprintf(scrp,"%s_%s",fnamep,name);
else
strcpy(scrp,name);
}
}
else {
if (fnamep==NMRSIM_NULL)
throw InternalError("makefilename");
strncpy(scrp,fnamep,scr.size());
// bname=getbasename(fnamep);
}
return scrp;
}
bool ProcessSave::checkoverwrite(const char* scrp) const
{
if ((saveflags_ & STOPOVERWRITE) && isreadable(scrp)) {
parser_printthread(std::cerr) << "Refusing to overwrite existing file: " << scrp << "\nUse -disable:preventoverwrite to force overwriting\n";
if (abortonwarning)
error_abort();
return true;
}
return false;
}
ThreadWarning<> ProcessSave::simpson_notfid_warning("saving freqency-domain data to file with .fid extension",&NMRsim_once_warning);
ThreadWarning<> ProcessSave::simpson_notspec_warning("saving time-domain data to file with .spe extension",&NMRsim_once_warning);
void check_simpson(const char* fname, bool isspec)
{
if (nochecks)
return;
const char* term=fname+strlen(fname)-4;
if (term<fname)
return;
if (strcmp(term,".fid")==0) {
if (isspec)
ProcessSave::simpson_notfid_warning.raise();
}
else {
if (!isspec)
ProcessSave::simpson_notspec_warning.raise();
}
}
void write_simpson_wrapper(const char* scrp, const BaseList<complex>& data, double sw, bool isspec, double sfrq, double ref)
{
simpsonFD simpinfo(data,sw,isspec);
simpinfo.sfrq=sfrq;
simpinfo.ref=ref;
check_simpson(scrp,isspec);
write_simpson(scrp,simpinfo);
}
void write_simpson_wrapper(const char* scrp, const Matrix<complex>& data, double sw, double sw1, bool isspec, double sfrq, double sfrq1, double ref, double ref1)
{
simpsonFD simpinfo(data,sw,sw1,isspec);
// if (detect_freq)
// simpinfo.sfrq=detect_freq;
// if (sw1)
// simpinfo.sfrq1=getsfrq1();
simpinfo.sfrq=sfrq;
simpinfo.sfrq1=sfrq1;
simpinfo.ref=ref;
simpinfo.ref1=ref1;
check_simpson(scrp,isspec);
write_simpson(scrp,simpinfo);
}
void ProcessSave::save(const BaseList<complex>& data, const processing_state& pflags, const ProcessSave_state& state, const char* name) const
{
const char* scrp=makefilename(state.fname,name);
if (!compositesave() && checkoverwrite(scrp))
return;
switch (saveflags_ & SAVE_FORMATS) {
case MATLAB:
if (matlabp.get())
matlabp->write(data,name);
else
WriteMATLAB(scrp,data,name);
break;
case SIMPLOT: case SIMPSON:
write_simpson_wrapper(scrp,data,pflags.sw,!pflags.istimedomain,convert_sfrq(pflags.sfrq,saveflags_),pflags.ref);
break;
default:
write_vector(scrp,data,mxflag::rmat);
}
}
void ProcessSave::print(std::ostream& ostr) const
{
ostr << "save " << fname.vector();
}
namespace {
inline void write_ascii(const char* name, const rmatrix& a) { write_matrix(name,a); }
inline void write_ascii(const char* name, const BaseList<double>& a) { write_vector(name,a); }
inline void write_ascii(const char*, const BaseList<bool>&) { throw InternalError("write_ascii"); }
}
void ProcessSave::makescale(LIST<double>& scale, const processing_state& pflags, size_t np, size_t skip) const
//, bool istimedomain)
{
const double locsw=pflags.sw;
scale.create(np);
if (pflags.istimedomain) {
// ignore rev flag - will have generated warning elsewhere
const double dt=1/(skip*locsw); //fudge dt for skip factor
for (size_t i=0;i<np;i+=skip) {
for (size_t j=0;j<skip;j++)
scale(i+j)=i*dt*1e6;
}
}
else {
// const int offset=np/2;
// const double df=locsw/np;
const bool rev= (saveflags_ & REVERSEFREQ);
const double invN=1.0/double(np);
for (size_t i=0;i<np;i++) {//no skip if transformed
const size_t desti = rev ? np-1-i : i;
scale(desti)=locsw*(invN*i-0.5)+pflags.ref;
// scale(i)=(i-offset)*df;
}
}
}
ThreadWarning<> ProcessSave::simpsonunsuitable_warning("SIMPLOT/SIMPSON format not suitable for data set (ignored): ",&NMRsim_once_warning);
template<class T> void ProcessSave::save(const T& data, const ProcessSave_state& state, const char* name) const
{
const char* scrp=makefilename(state.fname,name);
if (!compositesave() && checkoverwrite(scrp))
return;
switch (saveflags_ & SAVE_FORMATS) {
case MATLAB:
if (matlabp.get())
matlabp->write(data,name);
else
WriteMATLAB(scrp,data,name);
break;
case SIMPLOT: case SIMPSON:
simpsonunsuitable_warning.raise(name);
break;
default:
write_ascii(scrp,data);
}
}
namespace {
size_t save_cols=-1;
bool save_isspec,save_isrealnD;
}
FILE* ProcessSave::opencomments(const char* outname, const char* mode) const
{
if (saveflags_ & MATLAB) {
strbuffer="";
return NMRSIM_NULL;
}
FILE* fp=NMRSIM_NULL;
if (!checkoverwrite(outname))
fp=fopen(outname,mode);
if (fp==NMRSIM_NULL)
throw Failed("opencomments: failed to open output file");
return fp;
}
void ProcessSave::writeline(FILE* foutp, const char* str, char comchar) const
{
if (saveflags_ & MATLAB) {
strbuffer+=str;
strbuffer+='\n';
}
else {
if ((saveflags_ & ASCII) && comchar)
fputc('#',foutp);
fprintf(foutp,"%s\n",str);
}
}
void ProcessSave::closecomments(FILE* fp, const char* name) const
{
if (saveflags_ & MATLAB) {
matlabp->write(strbuffer.c_str(),name);
return;
}
if (fp)
fclose(fp);
}
bool ProcessSave::original_isflipped() const
{
if (original_revguardp)
return original_revguardp->isflipped();
return false;
}
void ProcessSave::savesource(const char* outname) const
{
const char* origin(parser_getfname());
FILE* finp=fopen(origin,"r");
FILE* foutp=NMRSIM_NULL;
if (!finp)
throw Failed("ProcessSave::savesource: can't open original input file!");
try {
foutp=opencomments(outname);
std::ostringstream envline(std::ostringstream::out);
dumpenvironment(envline);
std::string comline(envline.str());
comline.insert(0,"Command line: ");
if (global_argc==0)
throw InternalError("savesource");
for (size_t i=0;i<global_argc;i++) {
comline+=global_argv[i];
comline+=' ';
}
writeline(foutp,comline.c_str());
comline="Input file: ";
comline+=origin;
writeline(foutp,comline.c_str());
char linebuf[MAXLINE];
while (fgets(linebuf,MAXLINE,finp)) {
char* p=linebuf+strlen(linebuf)-1; //!< strip trailing whitespace
while (isspace(*p) && (p>=linebuf))
--p;
p[1]='\0';
writeline(foutp,linebuf);
}
closecomments(foutp,"source");
} catch (...) {
fclose(finp);
closecomments(foutp,"source");
throw;
}
fclose(finp);
}
ThreadWarning<> ProcessSave::notnd_warning("File format does not support >2D data",&NMRsim_once_warning);
ThreadWarning<> ProcessSave::notirregular_warning("ASCII format does not support irregular data",&NMRsim_once_warning);
ThreadWarning<> ProcessSave::nosource_warning("can't save source to this format (ignored)",&NMRsim_once_warning);
ThreadWarning<> ProcessSave::realnotvalid_warning("-realonly flag is ignored for this format",&NMRsim_once_warning);
template<class TC, class TR> void raw_matlab_write(matlab_controller::composite& matlabc, const TC& data, const char* bname, const Type2Type<TR>, bool savereal)
{
if (savereal) {
TR rdata;
real(rdata,data);
matlabc.write(rdata,bname);
}
else
matlabc.write(data,bname);
}
void ProcessSave::save(const DataStore& a, const ProcessSave_state& state, const char* bname) const
{
if (a.empty()) {
nothingtosave_warning.raise(bname);
return;
}
//const char* scrp=NMRSIM_NULL;
// if (bname)
const char* scrp=makefilename(state.fname,bname);
// else {
// scrp=state.fname;
// bname=getbasename(state.fname);
// }
if (!compositesave() && checkoverwrite(scrp))
return;
const processing_state statedir(a.states().back());
const double lsw=statedir.sw;
const double lsfrq=convert_sfrq(statedir.sfrq, saveflags_);
const double lref=statedir.ref;
double save_sw1=0;
double save_sfrq1=0;
double save_ref1=0;
if (a.isnD() && (ndims>1)) {
const processing_state& stateind(a.state(ndims-2));
save_sw1=stateind.sw;
save_sfrq1=convert_sfrq(stateind.sfrq, saveflags_);
save_ref1=stateind.ref;
}
const bool savereal=(saveflags_ & REALONLY);
try {
switch (saveflags_ & SAVE_FORMATS) {
case MATLAB: {
if (a.rows()==1)
raw_matlab_write(*matlabp,a.row(),bname,Type2Type< List<double> >(),savereal);
else {
if (a.isnD()) {
switch (ndims) {
case 1: case 2:
raw_matlab_write(*matlabp,a.matrix(),bname,Type2Type< Matrix<double> >(),savereal);
break;
case 3:
if (save_cols==1)
raw_matlab_write(*matlabp,a.matrix(),bname,Type2Type< Matrix<double> >(),savereal);
else { //copying out is wasteful, but not worth optimising
const MultiMatrix<complex,3> mm(save_cols,array_ns.front(),array_ns(1U),a.row().vector());
raw_matlab_write(*matlabp,mm,bname,Type2Type< MultiMatrix<double,3> >(),savereal);
}
break;
case 4:
if (save_cols==1) {
const MultiMatrix<complex,3> mm(array_ns.front(),array_ns(1U),array_ns(2U),a.row().vector());
raw_matlab_write(*matlabp,mm,bname,Type2Type< MultiMatrix<double,3> >(),savereal);
}
else {
const MultiMatrix<complex,4> mm(save_cols,array_ns.front(),array_ns(1U),array_ns(2U),a.row().vector());
raw_matlab_write(*matlabp,mm,bname,Type2Type< MultiMatrix<double,4> >(),savereal);
}
break;
// case 4: {
// const MultiMatrix<complex,5> mm(cols,array_ns.front(),array_ns(1U),array_ns(2U),array_ns(3U),a.row());
// matlabp->write(mm,bname);
// }
// break;
default:
throw Failed("save: unhandled Matlab dimensionality");
}
}
else
raw_matlab_write(*matlabp,a.listlist(),bname,Type2Type< ListList<double> >(),savereal);
// matlabp->write(a.listlist(),bname);
}
}
break;
case SIMPSON:
if (savereal)
realnotvalid_warning.raise();
if (a.isnD()) {
if (ndims>2)
notnd_warning.raise();
write_simpson_wrapper(scrp,a.matrix(),lsw,save_sw1,save_isspec,lsfrq,save_sfrq1,lref,save_ref1);
}
else {
if (a.rows()==1)
write_simpson_wrapper(scrp,a.row(),lsw,save_isspec,lsfrq,lref);
else
write_simpson_rows(scrp,a.listlist(),a.states(),saveflags_);
}
break;
case SIMPLOT:
if (savereal)
realnotvalid_warning.raise();
if (save_isrealnD) {
write_simpson_rows(scrp,a.matrix(),lsw,save_isspec,lsfrq);
scrp=NMRSIM_NULL;
}
else {
if (a.isnD() || (a.rows()==1))
write_simpson_wrapper(scrp,a.row(),lsw,save_isspec,lsfrq,lref);
else {
write_simpson_rows(scrp,a.listlist(),a.states(),saveflags_);
scrp=NMRSIM_NULL; //!< flag can't write
}
}
break;
case ASCII:
try {
if (save_isrealnD) {
if (ndims>2)
notnd_warning.raise();
if (savereal) {
rmatrix rdata;
real(rdata,a.matrix());
write_matrix(scrp,rdata);
}
else
write_matrix(scrp,a.matrix());
}
else {
if (!a.isnD() && (a.rows()>1))
notirregular_warning.raise();