#define rcmaker_cxx
// This is a standalone root macro that reads in a sequence of tif images
// from the CHESS FLIcam ccd camera corresponding to a single rocking curve
// measurement.  It outputs a root tree containing a sequence of TH1D
// histogram objects, one for each pixel, containing the image intensity
// versus step sequence number. The order of the histogram objects in the
// tree is left-to-right row-wise storage, then top to bottom, as seen in a
// standard tif viewer.  As a cross-check, the pixel coordinates (tif x,y)
// are encoded in the titles of the histograms.
//
// To use this macro, try the following session from within the directory
// containing your tif images, entitled "pristine_007_NNN.tif" in this example,
// where NNN varies from 15 to 155.  This macro is located in the parent dir.
//
//  Root > .L /usr/lib64/libtiff.so
//  Root > .L ../rcmaker.C+O
//  Root > rcmaker("pristine",7,141,15);
//  Root > .ls
//
// Update by RTJ on 11/21/2012:
// I have overhauled this macro to make it work properly with the newer image
// files generated by the ANDOR camera at CHESS.  The files are now quite a
// bit larger (10MB typical) and end with the extension ".tiff" instead of
// ".tif".  There are no changes the usage instructions.  The script should
// be able to recognize automatically which of the image types are being
// analyzed.
//
// Update by RTJ on 8/24/2016:
// I have overhauled this macro to make it work with the different style of
// image files and scan summary files that we collected at the Canadian Light
// Source. The image files themselves have the extension ".tif" and have the
// scan number and scan step number encoded into the filename. The camera is
// the Hammamatsu AA-60 and the scintillator C9300-124.

#include <TClonesArray.h>
#include <TFitResultPtr.h>
#include <TFitResult.h>
#include <TH1D.h>
#include <TH2D.h>
#include <TF1.h>

#include <TFile.h>
#include <TTree.h>

#include <iostream>
#include <iomanip>
#include <sstream>
#include <fstream>
#include <string>

#include <tiffio.h>

void rcmaker(const char *prefix, Int_t seq, Int_t count, Int_t start=0)
{
   bool oldFliCam = true;
   bool AndorCam = false;
   bool HamaCam = false;
   bool is16bit = false;
   bool is8bit = false;

   // read the dimensions of the topographs from the first image file
   std::stringstream ssn;
   ssn << TString(prefix) << "_" 
       << std::setfill('0') << std::setw(3) << seq << "_"
       << std::setfill('0') << std::setw(3) << start << ".tif";
   TIFF* refimg = TIFFOpen(ssn.str().c_str(),"r");

   // the new Andor camera uses a different filename convention
   if (!refimg) {
      ssn.str("");
      ssn << TString(prefix) << "_scan" 
          << std::setfill('0') << std::setw(3) << seq << "_"
          << std::setfill('0') << std::setw(3) << start << ".tiff";
      refimg = TIFFOpen(ssn.str().c_str(),"r");
      oldFliCam = false;
      AndorCam = true;
   }
 
   // the Hamamatsu camera uses yet another filename convention
   if (!refimg) {
      ssn.str("");
      ssn << TString(prefix) << "-" << seq << "_"
          << std::setfill('0') << std::setw(5) << start << ".tif";
      refimg = TIFFOpen(ssn.str().c_str(),"r");
      AndorCam = false;
      HamaCam = true;
   }

   // if none of the above sections succeeded, this image file is not supported
   if (!refimg) {
      std::cerr << "rcmaker error - unable to read from first image file " 
                << ssn.str() << ", unable to continue." << std::endl;
      return;
   }

   UShort_t config;
   TIFFGetField(refimg, TIFFTAG_PLANARCONFIG, &config);
   if (config != 1) {
      std::cerr << "rcmaker error - tiff image has an unfamiliar "
                << "PlanarConfiguration value of " << config
                << ", unable to continue." << std::endl;
      return;
   }

   UInt_t height,width;
   TIFFGetField(refimg, TIFFTAG_IMAGEWIDTH, &width);
   TIFFGetField(refimg, TIFFTAG_IMAGELENGTH, &height);

   // if image file was not found, give up
   if (!(width > 0 && height > 0)) {
      std::cerr << "rcmaker error - zero image dimensions found in "
                << "image file " << ssn.str()
                << ", unable to continue." << std::endl;
      return;
   }
   TIFFClose(refimg);

   // open a tree file to receive the rocking curve histograms
   ssn.str("");
   ssn << TString(prefix) << "_"
       << std::setfill('0') << std::setw(3) << seq << "_"
       << "rocking_curves.root";
   std::stringstream title;
   title << "rocking curves for sample " << TString(prefix)
         << " scan " << std::setfill('0') << std::setw(3) << seq;
   TFile rootfile(ssn.str().c_str(),"RECREATE",title.str().c_str());

   // create a rocking curve histogram and a tree to receive it
   TTree roottree("rctree","Rocking Curves");
   ssn.str("");
   ssn << "rc_" << TString(prefix) << "_" 
       << std::setfill('0') << std::setw(3) << seq;
   TH1D rchist(ssn.str().c_str(),title.str().c_str(),count,start,start+count);
   roottree.Branch("rchist",&rchist,128000,0);

   // loop over the image in horizontal swaths of SwathHeight rows
   const Int_t SwathHeight = 128;
#  define HINDEX(IU, IV0, INDEX) ((((IV0)*width)+(IU))*count)+(INDEX)
   Double_t *harray = new Double_t[width*SwathHeight*count];
   UShort_t *buf = (UShort_t*)_TIFFmalloc(width*sizeof(UShort_t));
   unsigned char *buf8 = (unsigned char*)buf;
   for (Int_t swath=0; swath*SwathHeight < (int)height; ++swath) {
      Int_t startHeight = swath*SwathHeight;
      Int_t stopHeight = (swath+1)*SwathHeight;
      stopHeight = (stopHeight < (int)height)? stopHeight : height;

      // loop over the input image files, filling the rocking curve histograms
      for (Int_t index=0; index < count; index++) {
         ssn.str("");
         if (oldFliCam) {
            ssn << TString(prefix) << "_"
                << std::setfill('0') << std::setw(3) << seq << "_"
                << std::setfill('0') << std::setw(3) << index+start
                << ".tif";
         }
         else if (AndorCam) {
            ssn << TString(prefix) << "_scan"
                << std::setfill('0') << std::setw(3) << seq << "_"
                << std::setfill('0') << std::setw(3) << index+start
                << ".tiff";
         }
         else if (HamaCam) {
            ssn << TString(prefix) << "-" << seq << "_"
                << std::setfill('0') << std::setw(5) << index+start
                << ".tif";
         }
         TIFF *img = TIFFOpen(ssn.str().c_str(),"r");
         if (!img) {
            std::cerr << "rcmaker warning - scan image file "
                      << ssn.str() << " could not be opened, "
                      << "moving on..." << std::endl;
            continue;
         }
         UInt_t linewidth = TIFFScanlineSize(img);
         if (linewidth == width*sizeof(UShort_t)) {
            is16bit = true;
         }
         else if (linewidth == width*sizeof(char)) {
            is8bit = true;
         }
         else {
            std::cerr << "rcmaker error - expecting 16-bit samples "
                      << "but found " << linewidth*8./width
                      << " bits/sample, cannot continue."
                      << std::endl;
            return;
         }
         for (Int_t iv=startHeight,iv0=0; iv < stopHeight; ++iv,++iv0) {
            TIFFReadScanline(img, buf, iv);
            for (Int_t iu=0; iu<(int)width; ++iu) {
               if (is16bit)
                  harray[HINDEX(iu,iv0,index)] = buf[iu];
               else if (is8bit)
                  harray[HINDEX(iu,iv0,index)] = buf8[iu];
               else
                  harray[HINDEX(iu,iv0,index)] = 999;
            }
         }
         TIFFClose(img);
      }

      // save the rocking curves as histograms to the tree
      for (Int_t iv=startHeight,iv0=0; iv < stopHeight; ++iv,++iv0) {
         for (Int_t iu=0; iu<(int)width; ++iu) {
            ssn.str("");
            ssn << "pixel_" << std::setfill('0') << std::setw(3) << iu
                << "_" << std::setfill('0') << std::setw(3) << iv;
            title.str("");
            title << "rocking curve for sample " << TString(prefix)
                  << " scan " << std::setfill('0') << std::setw(3) << seq
                  << " pixel " << std::setfill('0') << std::setw(3) << iu
                  << "," << std::setfill('0') << std::setw(3) << iv;
            rchist.SetNameTitle(ssn.str().c_str(),title.str().c_str());
            rchist.SetContent(&harray[HINDEX(iu,iv0,0)]);
            roottree.Fill();
         }
      }
   }
   _TIFFfree(buf);

   // save the tree to the file and close
   rootfile.Write();
   rootfile.Close();
}