// zfinder.cc - tool for use with Zygo's MetroPro package,
//              a component of the "restitch" extensions
//              to the standard stitch application.
//
// purpose: Reads in a standard coords.crd file from the MetroPro
//          stitch script, and writes it out with the z coordinate
//          adjusted relative to the mean z-height in each frame.
//
// author: richard.t.jones at uconn.edu
// version: November 12, 2011

#include <fstream>
#include <string>
#include <sstream>
#include <iomanip>
#include "MetroProMap.h"

#define REWRITE_ABSOLUTE_TO_LOCAL_PATHS 1

// this must be half the scan distance of the original stitching run
double zdelta = 50e-3/MetroProMap::inches2mm;

void usage()
{
   std::cerr << "Usage: zfinder [-zshift <offset>] <input file>"
             << std::endl
             << " where <offset>=floating point offset in z with units,"
             << std::endl
             << " eg. -0.115mm or 0.00176in, and <input file> is a text"
             << std::endl
             << " file in .crd format, as in \"coords.crd\"."
             << std::endl;
}

int main(int argc, char *argv[])
{
   double zshift = 0;
   if (argc == 1) {
      usage();
      exit(1);
   }
   for (int arg=1; arg<argc; ++arg) {
      std::string args(argv[arg]);
      if (args.compare("-zshift") == 0) {
         std::string shifts(argv[++arg]);
         int upos;
         if ((upos = shifts.find("mm")) != std::string::npos) {
            zshift = atof(shifts.substr(0,upos).c_str())/MetroProMap::inches2mm;
         }
         else if ((upos = shifts.find("in")) != std::string::npos) {
            zshift = atof(shifts.substr(0,upos).c_str());
         }
         else {
            usage();
            exit(1);
         }
         continue;
      }
      std::ifstream infile(args.c_str());
      if (! infile.is_open()) {
         std::cerr << "Error - unable to open input file "
                   << args << std::endl;
         continue;
      }
      std::string inpath(args.c_str());
      inpath = inpath.substr(0,inpath.find("/stch_"));
      int frame=0;
      std::string dfilename;
      while (! infile.eof()) {
         std::string line;
         getline(infile,line);
         int epos = line.rfind(".dat");
         if (epos != std::string::npos) {
            std::cout << line << std::endl;
            dfilename = line;
            if (dfilename.substr(dfilename.length()-1) == "\r") {
               dfilename = dfilename.substr(0,dfilename.length()-1);
            }
#if REWRITE_ABSOLUTE_TO_LOCAL_PATHS
            int rpos = dfilename.find("MetroPro");
            if (rpos != std::string::npos) {
               dfilename = dfilename.substr(rpos);
               for (int pos=dfilename.find("\\"); pos != std::string::npos;
                        pos=dfilename.find("\\")) {
                  dfilename[pos] = '/';
               }
               dfilename = dfilename.replace(0,8,inpath);
            }
#endif
            continue;
         }
         if (line.find("x y and z position in inches") == std::string::npos) {
            continue;
         }
         ++frame;
         double x,y,z;
         std::stringstream ss(line);
         ss >> x >> y >> z;
         std::ifstream dfile(dfilename.c_str());
         if (! dfile.is_open()) {
            std::cerr << "Error - unable to open data file "
                      << dfilename << std::endl;
            exit(2);
         }
         MetroProMap map;
         dfile >> map;
         double zave = map.getAverageHeight(0);
         double zmin = map.getMinimumHeight(0);
         double zmax = map.getMaximumHeight(0);
         double zmid = (zmin+zmax)/2;
         if (zshift) {
            if (zshift > 0 && zmin+zshift < zmax) {
               std::cerr << "Warning: zshift is not sufficient"
                         << " to exclude original surface in frame "
                         << frame << std::endl
                         << "  zmin,zave,zmax = "
                         << (zmin+z-zdelta)*MetroProMap::inches2mm << ","
                         << (zave+z-zdelta)*MetroProMap::inches2mm << ","
                         << (zmax+z-zdelta)*MetroProMap::inches2mm
                         << " mm" << std::endl;
            }
            else if (zshift > 0 && zmin+zshift < zmax-zdelta) {
               std::cerr << "Warning: zshift may not be sufficient"
                         << " to exclude original surface in frame "
                         << frame << std::endl
                         << "  zmin,zave,zmax = "
                         << (zmin+z-zdelta)*MetroProMap::inches2mm << ","
                         << (zave+z-zdelta)*MetroProMap::inches2mm << ","
                         << (zmax+z-zdelta)*MetroProMap::inches2mm
                         << " mm" << std::endl;
            }
            else if (zshift < 0 && zmax+zshift > zmin) {
               std::cerr << "Warning: zshift is not sufficient"
                         << " to exclude original surface in frame "
                         << frame << std::endl
                         << "  zmin,zave,zmax = "
                         << (zmin+z-zdelta)*MetroProMap::inches2mm << ","
                         << (zave+z-zdelta)*MetroProMap::inches2mm << ","
                         << (zmax+z-zdelta)*MetroProMap::inches2mm
                         << " mm" << std::endl;
            }
            else if (zshift < 0 && zmax+zshift > zmin-zdelta) {
               std::cerr << "Warning: zshift may not be sufficient"
                         << " to exclude original surface in frame "
                         << frame << std::endl
                         << "  zmin,zave,zmax = "
                         << (zmin+z-zdelta)*MetroProMap::inches2mm << ","
                         << (zave+z-zdelta)*MetroProMap::inches2mm << ","
                         << (zmax+z-zdelta)*MetroProMap::inches2mm
                         << " mm" << std::endl;
            }
         }
         std::cout << std::setprecision(8)
                   << x << " " << y << " " << z+zmid-zdelta+zshift
                   << "   #      x y and z position in inches"
                   << std::endl;
      }
   }
   return 0;
}