// hkl2ang.cxx
#include<iostream>
#include<fstream>
#include<cmath>
#include<sstream>
#include<vector>
using namespace std;

struct phase_struct{
	double a, b, c, alpha, beta, gamma;
	string MaterialName, Formula, Symmetry;
};


int main(int argc, char* argv[])
{
	// check argument list



	// open file objects
	ifstream hkl(argv[1]);
	ofstream tsl(argv[2]);


	// HKL header data, in order
	string Channel, Prj, Author, JobMode;
	int    XCells, YCells;
	double XStep, YStep, AcqE1, AcqE2, AcqE3;
	int    Mag, Coverage, Device, KV, TiltAngle, TiltAxis;
	int    Phases;

	// TSL header data, in order
	double TEM_PIXperUM, xstar, ystar, zstar, WorkingDistance;
	string GRID;
	double XSTEP, YSTEP;
	int    NCOLS_ODD, NCOLS_EVEN, NROWS;
	string OPERATOR, SAMPLEID, SCANID;

	vector<phase_struct> phases;


	// read HKL header

	cout<<"This converts an HKL .ctf file to a TSL .ang "<<" \n";
	cout<<"note that 30 degrees is subtracted from the "<<" \n";
	cout<<" 3rd Euler angle (phi 2) "<<" \n";
	cout<<"and 90 degrees is added to the 1st Euler angle (phi1) "<<" \n\n";
	cout<<"If you don't want the 30 degr offset, then edit this program!"<<" \n\n";
	cout<<"Mainly written by Jason Gruber, with"<<" \n";
	cout<<" mods by AD Rollett, March 2007"<<"\n";

	while (1) {
	  string line, label;
	  getline(hkl,line);
	  stringstream sstream(line);
	  sstream>>label;
	  if (label=="Channel") sstream>>Channel;
	  if (label=="Prj")     sstream>>Prj;
	  if (label=="Author")  sstream>>Author;
	  if (label=="JobMode") sstream>>JobMode;
	  if (label=="XCells")  sstream>>XCells;
	  if (label=="YCells")  sstream>>YCells;
	  if (label=="XStep")   sstream>>XStep;
	  if (label=="YStep")   sstream>>YStep;
	  if (label=="AcqE1")   sstream>>AcqE1;
	  if (label=="AcqE2")   sstream>>AcqE2;
	  if (label=="AcqE3")   sstream>>AcqE3;
	  if (label=="Euler") {
	    sstream>>label>>label>>label>>label;
	    sstream>>label>>label>>label;
	    sstream>>label>>Mag;
	    sstream>>label>>Coverage;
	    sstream>>label>>Device;
	    sstream>>label>>KV;
	    sstream>>label>>TiltAngle;
	    sstream>>label>>TiltAxis;
	  }
	  if (label=="Phases") {
	    sstream>>Phases;
	    break;
	  }
	}
	phases.resize(Phases+1);
	for (int i=1; i<=Phases; i++) {
	  string line;
	  getline(hkl,line);
	  int p = line.find(',',0);
	  while (p!=string::npos) {line[p]='.'; p=line.find(',',p);}
	  p = line.find(';',0);
	  while (p!=string::npos) {line[p]=' '; p=line.find(';',p);}
	  stringstream sstream(line);
	  sstream>>phases[i].a>>phases[i].b>>phases[i].c;
	  sstream>>phases[i].alpha>>phases[i].beta>>phases[i].gamma;
	  sstream>>phases[i].MaterialName;
	  phases[i].Formula = "";
	  phases[i].Symmetry = "";
	}
	hkl.ignore(1000,'\n');


	// convert HKL header data to TSL header data
	TEM_PIXperUM = 1.0;							// ?
	xstar = AcqE1;
	ystar = AcqE2;
	zstar = AcqE3;
	WorkingDistance = 15.0;						// ?
	GRID = "SqGrid";
	XSTEP = XStep;
	YSTEP = YStep;
	NCOLS_ODD = XCells;
	NCOLS_EVEN = XCells;
	NROWS = YCells;
	OPERATOR = Author;
	SAMPLEID = "";
	SCANID = Prj;


	// write TSL header
	tsl<<"# TEM_PIXperUM			"<<TEM_PIXperUM<<"\n";
	tsl<<"# x-star			"<<xstar<<"\n";
	tsl<<"# y-star			"<<ystar<<"\n";
	tsl<<"# z-star			"<<zstar<<"\n";
	tsl<<"# WorkingDistance		"<<WorkingDistance<<"\n";
	tsl<<"# \n";

	for (int i=1; i<phases.size(); i++) {
	  tsl<<"# Phase "<<i<<"\n";
	  tsl<<"# MaterialName		"<<phases[i].MaterialName<<"\n";
	  tsl<<"# Formula				"<<phases[i].Formula<<"\n";
	  tsl<<"# Info \n";
	  tsl<<"# Symmetry			"<<phases[i].Symmetry<<"\n";
	  tsl<<"# LatticeConstants	";
	  tsl<<phases[i].a<<" "<<phases[i].b<<" "<<phases[i].c<<" ";
	  tsl<<phases[i].alpha<<" "<<phases[i].beta<<" "<<phases[i].gamma<<"\n";
	  tsl<<"# NumberFamilies	"<<"0 \n";
	  tsl<<"# Categories "<<"0 0 0 0 0 \n";
	  tsl<<"# \n";
	}

	tsl<<"# GRID: "<<GRID<<"\n";
	tsl<<"# XSTEP: "<<XSTEP<<"\n";
	tsl<<"# YSTEP: "<<YSTEP<<"\n";
	tsl<<"# NCOLS_ODD: "<<NCOLS_ODD<<"\n";
	tsl<<"# NCOLS_EVEN: "<<NCOLS_EVEN<<"\n";
	tsl<<"# NROWS: "<<NROWS<<"\n";
	tsl<<"# \n";
	tsl<<"# OPERATOR: "<<OPERATOR<<"\n";
	tsl<<"# \n";
	tsl<<"# SAMPLEID: "<<SAMPLEID<<"\n";
	tsl<<"# \n";
	tsl<<"# SCANID: "<<SCANID<<"\n";
	tsl<<"# \n";


	// read, convert, and write record data
	while (!hkl.eof()) {
	  string line;
	  getline(hkl,line);
	  int p = line.find(',',0);
	  while (p!=string::npos) {line[p]='.'; p=line.find(',',p);}	
	  
	  // HKL record data, in order
	  int    Phase;
	  double X, Y;
	  int    Bands, Error;
	  double Euler1, Euler2, Euler3, MAD;
	  int    BC, BS;
	  
	  // TSL record data, in order
	  double phi1, PHI, phi2;
	  double x, y;
	  double IQ, CI;
	  int    A, phase;
	  double B;

	  // read HKL record from string stream
	  stringstream sstream(line);
	  sstream>>Phase>>X>>Y>>Bands>>Error;
	  sstream>>Euler1>>Euler2>>Euler3>>MAD>>BC>>BS;
	  
	  // convert HKL record to TSL record
	  phi1  = M_PI/180.0 * (Euler1 + 90.) ;
	  PHI   = M_PI/180.0 * Euler2 ;
	  phi2  = M_PI/180.0 * (Euler3 - 30.) ;
	  x     = X;
	  y     = Y;
	  IQ    = 1.0;							// ?
	  CI    = 1.0;							// ?
	  A     = 0;								// ?
	  phase = Phase;							// ?
	  B     = 1.0;							// ?
	  
	  // write TSL record to file
	  tsl<<phi1<<"\t"<<PHI<<"\t"<<phi2<<"\t"<<x<<"\t"<<y<<"\t";
	  tsl<<IQ<<"\t"<<CI<<"\t"<<A<<"\t"<<phase<<"\t"<<B<<"\n";
	}
}