pkfilter.cc

/**********************************************************************
pkfilter.cc: program to filter raster images: median, min/max, morphological, filtering
Copyright (C) 2008-2014 Pieter Kempeneers

This file is part of pktools

pktools is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

pktools is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with pktools.  If not, see <http://www.gnu.org/licenses/>.
***********************************************************************/
#include <assert.h>
#include <iostream>
#include <string>
#include <fstream>
#include <math.h>
#include <sys/types.h>
#include <stdio.h>
#include "base/Optionpk.h"
#include "base/Vector2d.h"
#include "algorithms/Filter2d.h"
#include "algorithms/Filter.h"
#include "fileclasses/FileReaderAscii.h"
#include "imageclasses/ImgReaderGdal.h"
#include "imageclasses/ImgWriterGdal.h"
#include "algorithms/StatFactory.h"

/******************************************************************************/
using namespace std;
/*------------------
  Main procedure
  ----------------*/
int main(int argc,char **argv) {
  Optionpk<std::string> input_opt("i","input","input image file");
  Optionpk<std::string> output_opt("o", "output", "Output image file");
  // Optionpk<std::string> tmpdir_opt("tmp", "tmp", "Temporary directory","/tmp",2);
  Optionpk<bool> disc_opt("circ", "circular", "circular disc kernel for dilation and erosion", false);
  // Optionpk<double> angle_opt("a", "angle", "angle used for directional filtering in dilation (North=0, East=90, South=180, West=270).");
  Optionpk<std::string> method_opt("f", "filter", "filter function (nvalid, median, var, min, max, sum, mean, dilate, erode, close, open, homog (central pixel must be identical to all other pixels within window), heterog (central pixel must be different than all other pixels within window), sauvola, sobelx (horizontal edge detection), sobely (vertical edge detection), sobelxy (diagonal edge detection NE-SW),sobelyx (diagonal edge detection NW-SE), density, countid, mode (majority voting), only for classes), smoothnodata (smooth nodata values only) values, ismin, ismax, order (rank pixels in order), stdev, mrf, dwt, dwti, dwt_cut, dwt_cut_from, scramble, shift, savgolay, percentile, proportion)");
  Optionpk<std::string> resample_opt("r", "resampling-method", "Resampling method for shifting operation (near: nearest neighbour, bilinear: bi-linear interpolation).", "near");
  Optionpk<double> dimX_opt("dx", "dx", "filter kernel size in x, use odd values only", 3);
  Optionpk<double> dimY_opt("dy", "dy", "filter kernel size in y, use odd values only", 3);
  Optionpk<int> dimZ_opt("dz", "dz", "filter kernel size in z (spectral/temporal dimension), must be odd (example: 3).. Set dz>0 if 1-D filter must be used in band domain");
  Optionpk<std::string> wavelet_type_opt("wt", "wavelet", "wavelet type: daubechies,daubechies_centered, haar, haar_centered, bspline, bspline_centered", "daubechies");
  Optionpk<int> family_opt("wf", "family", "wavelet family (vanishing moment, see also http://www.gnu.org/software/gsl/manual/html_node/DWT-Initialization.html)", 4);
  Optionpk<int> savgolay_nl_opt("nl", "nl", "Number of leftward (past) data points used in Savitzky-Golay filter)", 2);
  Optionpk<int> savgolay_nr_opt("nr", "nr", "Number of rightward (future) data points used in Savitzky-Golay filter)", 2);
  Optionpk<int> savgolay_ld_opt("ld", "ld", "order of the derivative desired in Savitzky-Golay filter (e.g., ld=0 for smoothed function)", 0);
  Optionpk<int> savgolay_m_opt("m", "m", "order of the smoothing polynomial in Savitzky-Golay filter, also equal to the highest conserved moment; usual values are m = 2 or m = 4)", 2);
  Optionpk<short> class_opt("class", "class", "class value(s) to use for density, erosion, dilation, openening and closing, thresholding");
  Optionpk<double> threshold_opt("t", "threshold", "threshold value(s) to use for threshold filter (one for each class), or threshold to cut for dwt_cut (use 0 to keep all) or dwt_cut_from, or sigma for shift", 0);
  Optionpk<double> nodata_opt("nodata", "nodata", "nodata value(s) (used for smoothnodata filter)");
  Optionpk<std::string> tap_opt("tap", "tap", "text file containing taps used for spatial filtering (from ul to lr). Use dimX and dimY to specify tap dimensions in x and y. Leave empty for not using taps");
  Optionpk<double> tapz_opt("tapz", "tapz", "taps used for spectral filtering");
  Optionpk<string> padding_opt("pad","pad", "Padding method for filtering (how to handle edge effects). Choose between: symmetric, replicate, circular, zero (pad with 0).", "symmetric");
  Optionpk<double> fwhm_opt("fwhm", "fwhm", "list of full width half to apply spectral filtering (-fwhm band1 -fwhm band2 ...)");
  Optionpk<std::string> srf_opt("srf", "srf", "list of ASCII files containing spectral response functions (two columns: wavelength response)");
  Optionpk<double> wavelengthIn_opt("win", "wavelengthIn", "list of wavelengths in input spectrum (-win band1 -win band2 ...)");
  Optionpk<double> wavelengthOut_opt("wout", "wavelengthOut", "list of wavelengths in output spectrum (-wout band1 -wout band2 ...)");
  Optionpk<std::string> interpolationType_opt("interp", "interp", "type of interpolation for spectral filtering (see http://www.gnu.org/software/gsl/manual/html_node/Interpolation-Types.html)","akima");
  Optionpk<std::string>  otype_opt("ot", "otype", "Data type for output image ({Byte/Int16/UInt16/UInt32/Int32/Float32/Float64/CInt16/CInt32/CFloat32/CFloat64}). Empty string: inherit type from input image","");
  Optionpk<string>  oformat_opt("of", "oformat", "Output image format (see also gdal_translate).","GTiff");
  Optionpk<string>  colorTable_opt("ct", "ct", "color table (file with 5 columns: id R G B ALFA (0: transparent, 255: solid). Use none to omit color table");
  Optionpk<string> option_opt("co", "co", "Creation option for output file. Multiple options can be specified.");
  Optionpk<short> down_opt("d", "down", "down sampling factor. Use value 1 for no downsampling). Use value n>1 for downsampling (aggregation)", 1);
  Optionpk<string> beta_opt("beta", "beta", "ASCII file with beta for each class transition in Markov Random Field");
  // Optionpk<double> eps_opt("eps","eps", "error marging for linear feature",0);
  // Optionpk<bool> l1_opt("l1","l1", "obtain longest object length for linear feature",false);
  // Optionpk<bool> l2_opt("l2","l2", "obtain shortest object length for linear feature",false,2);
  // Optionpk<bool> a1_opt("a1","a1", "obtain angle found for longest object length for linear feature",false);
  // Optionpk<bool> a2_opt("a2","a2", "obtain angle found for shortest object length for linear feature",false);
  Optionpk<short> verbose_opt("v", "verbose", "verbose mode if > 0", 0,2);

  resample_opt.setHide(1);
  option_opt.setHide(1);
  wavelet_type_opt.setHide(1);
  family_opt.setHide(1);
  savgolay_nl_opt.setHide(1);
  savgolay_nr_opt.setHide(1);
  savgolay_ld_opt.setHide(1);
  savgolay_m_opt.setHide(1);
  class_opt.setHide(1);
  threshold_opt.setHide(1);
  tap_opt.setHide(1);
  tapz_opt.setHide(1);
  padding_opt.setHide(1);
  wavelengthIn_opt.setHide(1);
  wavelengthOut_opt.setHide(1);
  down_opt.setHide(1);
  beta_opt.setHide(1);
  // eps_opt.setHide(1);
  // l1_opt.setHide(1);
  // l2_opt.setHide(1);
  // a1_opt.setHide(1);
  // a2_opt.setHide(1);
  interpolationType_opt.setHide(1);
  otype_opt.setHide(1);
  oformat_opt.setHide(1);
  colorTable_opt.setHide(1);
  disc_opt.setHide(1);

  bool doProcess;//stop process when program was invoked with help option (-h --help)
  try{
    doProcess=input_opt.retrieveOption(argc,argv);
    output_opt.retrieveOption(argc,argv);
    // tmpdir_opt.retrieveOption(argc,argv);
    // angle_opt.retrieveOption(argc,argv);
    method_opt.retrieveOption(argc,argv);
    srf_opt.retrieveOption(argc,argv);
    fwhm_opt.retrieveOption(argc,argv);
    dimX_opt.retrieveOption(argc,argv);
    dimY_opt.retrieveOption(argc,argv);
    dimZ_opt.retrieveOption(argc,argv);
    nodata_opt.retrieveOption(argc,argv);
    resample_opt.retrieveOption(argc,argv);
    option_opt.retrieveOption(argc,argv);
    wavelet_type_opt.retrieveOption(argc,argv);
    family_opt.retrieveOption(argc,argv);
    savgolay_nl_opt.retrieveOption(argc,argv);
    savgolay_nr_opt.retrieveOption(argc,argv);
    savgolay_ld_opt.retrieveOption(argc,argv);
    savgolay_m_opt.retrieveOption(argc,argv);
    class_opt.retrieveOption(argc,argv);
    threshold_opt.retrieveOption(argc,argv);
    tap_opt.retrieveOption(argc,argv);
    tapz_opt.retrieveOption(argc,argv);
    padding_opt.retrieveOption(argc,argv);
    wavelengthIn_opt.retrieveOption(argc,argv);
    wavelengthOut_opt.retrieveOption(argc,argv);
    down_opt.retrieveOption(argc,argv);
    beta_opt.retrieveOption(argc,argv);
    // eps_opt.retrieveOption(argc,argv);
    // l1_opt.retrieveOption(argc,argv);
    // l2_opt.retrieveOption(argc,argv);
    // a1_opt.retrieveOption(argc,argv);
    // a2_opt.retrieveOption(argc,argv);
    interpolationType_opt.retrieveOption(argc,argv);
    otype_opt.retrieveOption(argc,argv);
    oformat_opt.retrieveOption(argc,argv);
    colorTable_opt.retrieveOption(argc,argv);
    disc_opt.retrieveOption(argc,argv);
    verbose_opt.retrieveOption(argc,argv);
  }
  catch(string predefinedString){
    std::cout << predefinedString << std::endl;
    exit(0);
  }
  if(!doProcess){
    cout << endl;
    cout << "Usage: pkfilter -i input -o output [-f filter | -perc value | -srf file [-srf file]* -win wavelength [-win wavelength]* | -wout wavelength -fwhm value [-wout wavelength -fwhm value]* -win wavelength [-win wavelength]*]" << endl;
    cout << endl;
    std::cout << "short option -h shows basic options only, use long option --help to show all options" << std::endl;
    exit(0);//help was invoked, stop processing
  }

  //not implemented yet, must debug first...
  vector<double> angle_opt;

  ImgReaderGdal input;
  ImgWriterGdal output;
  if(input_opt.empty()){
    cerr << "Error: no input file selected, use option -i" << endl;
    exit(1);
  }
  if(output_opt.empty()){
    cerr << "Error: no output file selected, use option -o" << endl;
    exit(1);
  }
  input.open(input_opt[0]);
  GDALDataType theType=GDT_Unknown;
  if(verbose_opt[0])
    cout << "possible output data types: ";
  for(int iType = 0; iType < GDT_TypeCount; ++iType){
    if(verbose_opt[0])
      cout << " " << GDALGetDataTypeName((GDALDataType)iType);
    if( GDALGetDataTypeName((GDALDataType)iType) != NULL
        && EQUAL(GDALGetDataTypeName((GDALDataType)iType),
                 otype_opt[0].c_str()))
      theType=(GDALDataType) iType;
  }
  if(theType==GDT_Unknown)
    theType=input.getDataType();

  if(verbose_opt[0])
    std::cout << std::endl << "Output pixel type:  " << GDALGetDataTypeName(theType) << endl;

  string imageType;//=input.getImageType();
  if(oformat_opt.size())
    imageType=oformat_opt[0];

  if(option_opt.findSubstring("INTERLEAVE=")==option_opt.end()){
    string theInterleave="INTERLEAVE=";
    theInterleave+=input.getInterleave();
    option_opt.push_back(theInterleave);
  }

  try{
    string errorString;
    int nband=input.nrOfBand();

    if(fwhm_opt.size())
      nband=fwhm_opt.size();
    else if(srf_opt.size())
      nband=srf_opt.size();
    else if(tap_opt.size()||tapz_opt.size())
      nband=input.nrOfBand();
    else{
      if(method_opt.empty()){
        errorString="Error: no filter selected, use option -f";
        throw(errorString);
      }
      switch(filter2d::Filter2d::getFilterType(method_opt[0])){
      case(filter2d::dilate):
      case(filter2d::erode):
      case(filter2d::close):
      case(filter2d::open):
      case(filter2d::smooth):
    //implemented in spectral/temporal domain (dimZ>1) and spatial domain
    if(dimZ_opt.size())
      assert(dimZ_opt[0]>1);
      nband=input.nrOfBand();
      break;
      case(filter2d::dwt):
      case(filter2d::dwti):
      case(filter2d::dwt_cut):
      case(filter2d::smoothnodata):
    //implemented in spectral/temporal/spatial domain and nband always input.nrOfBand()
    nband=input.nrOfBand();
    break;
      case(filter2d::savgolay):
    nband=input.nrOfBand();
    if(dimZ_opt.empty())
      dimZ_opt.push_back(1);
      case(filter2d::dwt_cut_from):
    //only implemented in spectral/temporal domain
    if(dimZ_opt.size()){
      nband=input.nrOfBand();
      assert(threshold_opt.size());
    }
    else{
          errorString="filter not implemented in spatial domain";
          throw(errorString);
    }
    break;
      case(filter2d::mrf)://deliberate fall through
    assert(class_opt.size()>1);
    if(verbose_opt[0])
      std::cout << "opening output image " << output_opt[0] << std::endl;
    nband=class_opt.size();
      case(filter2d::ismin):
      case(filter2d::ismax):
      case(filter2d::shift):
      case(filter2d::scramble):
      case(filter2d::mode):
      case(filter2d::sobelx):
      case(filter2d::sobely):
      case(filter2d::sobelxy):
      case(filter2d::countid):
      case(filter2d::order):
      case(filter2d::density):
      case(filter2d::homog):
      case(filter2d::heterog):
      case(filter2d::sauvola):
    //only implemented in spatial domain
    if(dimZ_opt.size()){
          errorString="filter not implemented in spectral/temporal domain";
          throw(errorString);
    }
    break;
      // case(filter2d::percentile):
      //    //implemented in spectral/temporal/spatial domain and nband 1 if dimZ>0
      //    if(dimZ_opt.size()){
      //      dimZ_opt[0]=1;
      //      nband=1;
      //    }
      //    else
      //      nband=input.nrOfBand();
      //    break;
      case(filter2d::sum):
      case(filter2d::mean):
      case(filter2d::min):
      case(filter2d::max):
      case(filter2d::var):
      case(filter2d::stdev):
      case(filter2d::nvalid):
      case(filter2d::median):
      case(filter2d::percentile):
      case(filter2d::proportion):
    //implemented in spectral/temporal/spatial domain and nband 1 if dimZ==1
    if(dimZ_opt.size()==1)
      if(dimZ_opt[0]==1)
        nband=1;
    else
      nband=input.nrOfBand();
    break;
      default:
    errorString="filter not implemented";
        throw(errorString);
    break;
      }
    }
    std::cout << "opening output image " << output_opt[0] << " with " << nband << " bands" << std::endl;
    output.open(output_opt[0],(input.nrOfCol()+down_opt[0]-1)/down_opt[0],(input.nrOfRow()+down_opt[0]-1)/down_opt[0],nband,theType,imageType,option_opt);
  }
  catch(string errorstring){
    cerr << errorstring << endl;
    exit(1);
  }
  output.setProjection(input.getProjection());
  double gt[6];
  input.getGeoTransform(gt);
  gt[1]*=down_opt[0];//dx
  gt[5]*=down_opt[0];//dy
  output.setGeoTransform(gt);
  
  if(colorTable_opt.size()){
    if(colorTable_opt[0]!="none"){
      if(verbose_opt[0])
    cout << "set colortable " << colorTable_opt[0] << endl;
      assert(output.getDataType()==GDT_Byte);
      output.setColorTable(colorTable_opt[0]);
    }
  }
  else if(input.getColorTable()!=NULL)
    output.setColorTable(input.getColorTable());
  
  if(nodata_opt.size()){
      for(int iband=0;iband<output.nrOfBand();++iband)
    output.GDALSetNoDataValue(nodata_opt[0],iband);
  }

  filter2d::Filter2d filter2d;
  filter::Filter filter1d;
  if(verbose_opt[0])
    cout << "Set padding to " << padding_opt[0] << endl;
  filter1d.setPadding(padding_opt[0]);
  if(class_opt.size()){
    if(verbose_opt[0])
      std::cout<< "class values: ";
    for(int iclass=0;iclass<class_opt.size();++iclass){
      if(!dimZ_opt.size())
        filter2d.pushClass(class_opt[iclass]);
      else
        filter1d.pushClass(class_opt[iclass]);
      if(verbose_opt[0])
        std::cout<< class_opt[iclass] << " ";
    }
    if(verbose_opt[0])
      std::cout<< std::endl;
  }

  if(nodata_opt.size()){
    if(verbose_opt[0])
      std::cout<< "mask values: ";
    for(int imask=0;imask<nodata_opt.size();++imask){
      if(verbose_opt[0])
        std::cout<< nodata_opt[imask] << " ";
      filter1d.pushNoDataValue(nodata_opt[imask]);
      filter2d.pushNoDataValue(nodata_opt[imask]);
    }
    if(verbose_opt[0])
      std::cout<< std::endl;
  }
  filter1d.setThresholds(threshold_opt);
  filter2d.setThresholds(threshold_opt);

  if(tap_opt.size()){
    ifstream tapfile(tap_opt[0].c_str());
    assert(tapfile);
    Vector2d<double> taps(dimY_opt[0],dimX_opt[0]);

    for(int j=0;j<dimY_opt[0];++j){
      for(int i=0;i<dimX_opt[0];++i){
        tapfile >> taps[j][i];
      }
    }
    if(verbose_opt[0]){
      std::cout << "taps: ";
      for(int j=0;j<dimY_opt[0];++j){
        for(int i=0;i<dimX_opt[0];++i){
          std::cout<< taps[j][i] << " ";
        }
        std::cout<< std::endl;
      }
    }
    filter2d.setTaps(taps);
    try{
      filter2d.filter(input,output);
    }
    catch(string errorstring){
      cerr << errorstring << endl;
    }
    tapfile.close();
  }
  else if(tapz_opt.size()){
    if(verbose_opt[0]){
      std::cout << "taps: ";
      for(int itap=0;itap<tapz_opt.size();++itap)
    std::cout<< tapz_opt[itap] << " ";
      std::cout<< std::endl;
    }
    filter1d.setTaps(tapz_opt);
    filter1d.filter(input,output);
  }
  else if(fwhm_opt.size()){
    if(verbose_opt[0])
      std::cout << "spectral filtering to " << fwhm_opt.size() << " bands with provided fwhm " << std::endl;
    assert(wavelengthOut_opt.size()==fwhm_opt.size());
    assert(wavelengthIn_opt.size());

    Vector2d<double> lineInput(input.nrOfBand(),input.nrOfCol());
    Vector2d<double> lineOutput(wavelengthOut_opt.size(),input.nrOfCol());
    const char* pszMessage;
    void* pProgressArg=NULL;
    GDALProgressFunc pfnProgress=GDALTermProgress;
    double progress=0;
    pfnProgress(progress,pszMessage,pProgressArg);
    for(int y=0;y<input.nrOfRow();++y){
      if((y+1+down_opt[0]/2)%down_opt[0])
        continue;
      for(int iband=0;iband<input.nrOfBand();++iband)
        input.readData(lineInput[iband],y,iband);
      filter1d.applyFwhm<double>(wavelengthIn_opt,lineInput,wavelengthOut_opt,fwhm_opt, interpolationType_opt[0], lineOutput, down_opt[0], verbose_opt[0]);
      for(int iband=0;iband<output.nrOfBand();++iband){
        try{
          output.writeData(lineOutput[iband],y/down_opt[0],iband);
        }
        catch(string errorstring){
          cerr << errorstring << "in band " << iband << ", line " << y << endl;
        }
      }
      progress=(1.0+y)/output.nrOfRow();
      pfnProgress(progress,pszMessage,pProgressArg);
    }
  }
  else if(srf_opt.size()){
    if(verbose_opt[0])
      std::cout << "spectral filtering to " << srf_opt.size() << " bands with provided SRF " << std::endl;
    assert(wavelengthIn_opt.size());
    vector< Vector2d<double> > srf(srf_opt.size());//[0] srf_nr, [1]: wavelength, [2]: response
    ifstream srfFile;
    for(int isrf=0;isrf<srf_opt.size();++isrf){
      srf[isrf].resize(2);
      srfFile.open(srf_opt[isrf].c_str());
      double v;
      //add 0 to make sure srf is 0 at boundaries after interpolation step
      srf[isrf][0].push_back(0);
      srf[isrf][1].push_back(0);
      srf[isrf][0].push_back(1);
      srf[isrf][1].push_back(0);
      while(srfFile >> v){
        srf[isrf][0].push_back(v);
        srfFile >> v;
        srf[isrf][1].push_back(v);
      }
      srfFile.close();
      //add 0 to make sure srf[isrf] is 0 at boundaries after interpolation step
      srf[isrf][0].push_back(srf[isrf][0].back()+1);
      srf[isrf][1].push_back(0);    
      srf[isrf][0].push_back(srf[isrf][0].back()+1);
      srf[isrf][1].push_back(0);
      if(verbose_opt[0])
        cout << "srf file details: " << srf[isrf][0].size() << " wavelengths defined" << endl;    
    }
    assert(output.nrOfBand()==srf.size());
    double centreWavelength=0;
    Vector2d<double> lineInput(input.nrOfBand(),input.nrOfCol());
    const char* pszMessage;
    void* pProgressArg=NULL;
    GDALProgressFunc pfnProgress=GDALTermProgress;
    double progress=0;
    pfnProgress(progress,pszMessage,pProgressArg);
    for(int y=0;y<input.nrOfRow();++y){
      if((y+1+down_opt[0]/2)%down_opt[0])
        continue;
      for(int iband=0;iband<input.nrOfBand();++iband)
        input.readData(lineInput[iband],y,iband);
      for(int isrf=0;isrf<srf.size();++isrf){
        vector<double> lineOutput(output.nrOfCol());
        double delta=1.0;
        bool normalize=true;
    centreWavelength=filter1d.applySrf<double>(wavelengthIn_opt,lineInput,srf[isrf], interpolationType_opt[0], lineOutput, delta, normalize);
        if(verbose_opt[0])
          std::cout << "centre wavelength srf " << isrf << ": " << centreWavelength << std::endl;
        try{
          output.writeData(lineOutput,GDT_Float64,y/down_opt[0],isrf);
        }
        catch(string errorstring){
          cerr << errorstring << "in srf " << srf_opt[isrf] << ", line " << y << endl;
        }

      }
      progress=(1.0+y)/output.nrOfRow();
      pfnProgress(progress,pszMessage,pProgressArg);
    }

  }
  else{
    switch(filter2d::Filter2d::getFilterType(method_opt[0])){
    case(filter2d::dilate):
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for morphological operator" << std::endl;
    exit(1);
      }
      try{
    if(dimZ_opt.size()){
      if(verbose_opt[0])
          std::cout<< "1-D filtering: dilate" << std::endl;
      filter1d.morphology(input,output,"dilate",dimZ_opt[0],verbose_opt[0]);
    }
    else
      filter2d.morphology(input,output,"dilate",dimX_opt[0],dimY_opt[0],angle_opt,disc_opt[0]);
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    case(filter2d::erode):
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for morphological operator" << std::endl;
    exit(1);
      }
      try{
    if(dimZ_opt.size()>0){
      if(verbose_opt[0])
        std::cout<< "1-D filtering: dilate" << std::endl;
      filter1d.morphology(input,output,"erode",dimZ_opt[0]);
    }
    else{
      filter2d.morphology(input,output,"erode",dimX_opt[0],dimY_opt[0],angle_opt,disc_opt[0]);
    }
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
    break;
    case(filter2d::close):{//closing
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for morphological operator" << std::endl;
    exit(1);
      }

      ImgWriterGdal tmpout;
      tmpout.open("/vsimem/dilation.tif",input.nrOfCol(),input.nrOfRow(),input.nrOfBand(),input.getDataType(),input.getImageType());
      try{
        if(dimZ_opt.size()){
          filter1d.morphology(input,tmpout,"dilate",dimZ_opt[0]);
        }
        else{
      filter2d.morphology(input,tmpout,"dilate",dimX_opt[0],dimY_opt[0],angle_opt,disc_opt[0]);
        }
      }
      catch(std::string errorString){
    std::cout<< errorString;
    exit(1);
      }
      tmpout.close();
      ImgReaderGdal tmpin;
      tmpin.open("/vsimem/dilation.tif");
      try{
    if(dimZ_opt.size()){
      filter1d.morphology(tmpin,output,"erode",dimZ_opt[0]);
    }
    else{
      filter2d.morphology(tmpin,output,"erode",dimX_opt[0],dimY_opt[0],angle_opt,disc_opt[0]);
    }
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      tmpin.close();
      break;
    }
    case(filter2d::open):{//opening
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for morphological operator" << std::endl;
    exit(1);
      }
      ImgWriterGdal tmpout;
      tmpout.open("/vsimem/erosion.tif",input.nrOfCol(),input.nrOfRow(),input.nrOfBand(),input.getDataType(),input.getImageType());
      try{
    if(dimZ_opt.size()){
      filter1d.morphology(input,tmpout,"erode",dimZ_opt[0]);
    }
    else{
      filter2d.morphology(input,tmpout,"erode",dimX_opt[0],dimY_opt[0],angle_opt,disc_opt[0]);
    }
      }
      catch(std::string errorString){
    std::cout<< errorString;
    exit(1);
      }
      tmpout.close();
      ImgReaderGdal tmpin;
      try{
    tmpin.open("/vsimem/erosion.tif");
    if(dimZ_opt.size()){
      filter1d.morphology(tmpin,output,"dilate",dimZ_opt[0]);
    }
    else{
      filter2d.morphology(tmpin,output,"dilate",dimX_opt[0],dimY_opt[0],angle_opt,disc_opt[0]);
    }
    tmpin.close();
    tmpout.close();
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::homog):{//spatially homogeneous
      try{
    filter2d.doit(input,output,"homog",dimX_opt[0],dimY_opt[0],down_opt[0],disc_opt[0]);
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
    break;
    }
    case(filter2d::heterog):{//spatially heterogeneous
      try{
    filter2d.doit(input,output,"heterog",dimX_opt[0],dimY_opt[0],down_opt[0],disc_opt[0]);
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::sauvola):{//Implements Sauvola's thresholding method (http://fiji.sc/Auto_Local_Threshold)

  //test
      Vector2d<unsigned short> inBuffer;
      for(int iband=0;iband<input.nrOfBand();++iband){
        input.readDataBlock(inBuffer,0,input.nrOfCol()-1,0,input.nrOfRow()-1,iband);
      }
      try{
    filter2d.doit(input,output,"sauvola",dimX_opt[0],dimY_opt[0],down_opt[0],disc_opt[0]);
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::shift):{//shift
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for shift operator" << std::endl;
    exit(1);
      }
      assert(input.nrOfBand());
      assert(input.nrOfCol());
      assert(input.nrOfRow());
      try{
        filter2d.shift(input,output,dimX_opt[0],dimY_opt[0],threshold_opt[0],filter2d::Filter2d::getResampleType(resample_opt[0]));
      }
      catch(string errorstring){
        cerr << errorstring << endl;
      }
      break;
    }
    // case(filter2d::linearfeature):{
    //   if(down_opt[0]!=1){
    //  std::cerr << "Error: down option not supported for linear feature" << std::endl;
    //  exit(1);
    //   }
    //   assert(input.nrOfBand());
    //   assert(input.nrOfCol());
    //   assert(input.nrOfRow());
    //   float theAngle=361;
    //   if(angle_opt.size())
    //  theAngle=angle_opt[0];
    //   if(verbose_opt[0])
    //  std::cout << "using angle " << theAngle << std::endl;
    //   try{
    //  //using an angle step of 5 degrees and no maximum distance
    //     filter2d.linearFeature(input,output,theAngle,5,0,eps_opt[0],l1_opt[0],a1_opt[0],l2_opt[0],a2_opt[0],0,verbose_opt[0]);
    //   }
    //   catch(string errorstring){
    //     cerr << errorstring << endl;
    //   }
    //   break;
    // }
    case(filter2d::mrf):{//Markov Random Field
      if(verbose_opt[0])
    std::cout << "Markov Random Field filtering" << std::endl;
      try{
    if(beta_opt.size()){
      //in file: classFrom classTo
      //in variable: beta[classTo][classFrom]
      FileReaderAscii betaReader(beta_opt[0]);
      Vector2d<double> beta(class_opt.size(),class_opt.size());
      vector<int> cols(class_opt.size());
      for(int iclass=0;iclass<class_opt.size();++iclass)
        cols[iclass]=iclass;
      betaReader.readData(beta,cols);
      if(verbose_opt[0]){
        std::cout << "using values for beta:" << std::endl;
        for(int iclass1=0;iclass1<class_opt.size();++iclass1)
          std::cout << "      " << iclass1 << " (" << class_opt[iclass1] << ")";
        std::cout << std::endl;
        for(int iclass1=0;iclass1<class_opt.size();++iclass1){
          std::cout << iclass1 << " (" << class_opt[iclass1] << ")";
          for(int iclass2=0;iclass2<class_opt.size();++iclass2)
        std::cout << " " << beta[iclass2][iclass1] << " (" << class_opt[iclass2] << ")";
          std::cout << std::endl;
        }
      }
      filter2d.mrf(input, output, dimX_opt[0], dimY_opt[0], beta, true, down_opt[0], verbose_opt[0]);
    }
    else
      filter2d.mrf(input, output, dimX_opt[0], dimY_opt[0], 1, true, down_opt[0], verbose_opt[0]);
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::sobelx):{//Sobel edge detection in X
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for sobel edge detection" << std::endl;
    exit(1);
      }
      Vector2d<double> theTaps(3,3);
      theTaps[0][0]=-1.0;
      theTaps[0][1]=0.0;
      theTaps[0][2]=1.0;
      theTaps[1][0]=-2.0;
      theTaps[1][1]=0.0;
      theTaps[1][2]=2.0;
      theTaps[2][0]=-1.0;
      theTaps[2][1]=0.0;
      theTaps[2][2]=1.0;
      filter2d.setTaps(theTaps);
      try{
    filter2d.filter(input,output,true,true);//absolute and normalize
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::sobely):{//Sobel edge detection in Y
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for sobel edge detection" << std::endl;
    exit(1);
      }
      Vector2d<double> theTaps(3,3);
      theTaps[0][0]=1.0;
      theTaps[0][1]=2.0;
      theTaps[0][2]=1.0;
      theTaps[1][0]=0.0;
      theTaps[1][1]=0.0;
      theTaps[1][2]=0.0;
      theTaps[2][0]=-1.0;
      theTaps[2][1]=-2.0;
      theTaps[2][2]=-1.0;
      filter2d.setTaps(theTaps);
      try{
    filter2d.filter(input,output,true,true);//absolute and normalize
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::sobelxy):{//Sobel edge detection in XY
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for sobel edge detection" << std::endl;
    exit(1);
      }
      Vector2d<double> theTaps(3,3);
      theTaps[0][0]=0.0;
      theTaps[0][1]=1.0;
      theTaps[0][2]=2.0;
      theTaps[1][0]=-1.0;
      theTaps[1][1]=0.0;
      theTaps[1][2]=1.0;
      theTaps[2][0]=-2.0;
      theTaps[2][1]=-1.0;
      theTaps[2][2]=0.0;
      filter2d.setTaps(theTaps);
      try{
    filter2d.filter(input,output,true,true);//absolute and normalize
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::sobelyx):{//Sobel edge detection in XY
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for sobel edge detection" << std::endl;
    exit(1);
      }
      Vector2d<double> theTaps(3,3);
      theTaps[0][0]=2.0;
      theTaps[0][1]=1.0;
      theTaps[0][2]=0.0;
      theTaps[1][0]=1.0;
      theTaps[1][1]=0.0;
      theTaps[1][2]=-1.0;
      theTaps[2][0]=0.0;
      theTaps[2][1]=-1.0;
      theTaps[2][2]=-2.0;
      filter2d.setTaps(theTaps);
      try{
    filter2d.filter(input,output,true,true);//absolute and normalize
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::smooth):{//Smoothing filter
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for this filter" << std::endl;
    exit(1);
      }
      try{
    if(dimZ_opt.size()){
      if(verbose_opt[0])
        std::cout<< "1-D filtering: smooth" << std::endl;
      filter1d.smooth(input,output,dimZ_opt[0]);
    }
    else{
      filter2d.smooth(input,output,dimX_opt[0],dimY_opt[0]);
    }
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::smoothnodata):{//Smoothing filter
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for this filter" << std::endl;
    exit(1);
      }
      try{
    if(dimZ_opt.size()){
      if(verbose_opt[0])
        std::cout<< "1-D filtering: smooth" << std::endl;
      filter1d.smoothNoData(input,interpolationType_opt[0],output);
    }
    else{
      if(verbose_opt[0])
        std::cout<< "2-D filtering: smooth" << std::endl;
      filter2d.smoothNoData(input,output,dimX_opt[0],dimY_opt[0]);
    }
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
    case(filter2d::dwt):
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for this filter" << std::endl;
    exit(1);
      }
      try{
    if(dimZ_opt.size()){
      if(verbose_opt[0])
        std::cout<< "DWT in spectral domain" << std::endl;
      filter1d.dwtForward(input, output, wavelet_type_opt[0], family_opt[0]);
    }
    else
      filter2d.dwtForward(input, output, wavelet_type_opt[0], family_opt[0]);
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    case(filter2d::dwti):
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for this filter" << std::endl;
    exit(1);
      }
      try{
    if(dimZ_opt.size()){
      if(verbose_opt[0])
        std::cout<< "inverse DWT in spectral domain" << std::endl;
      filter1d.dwtInverse(input, output, wavelet_type_opt[0], family_opt[0]);
    }
    else
      filter2d.dwtInverse(input, output, wavelet_type_opt[0], family_opt[0]);
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    case(filter2d::dwt_cut):
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for this filter" << std::endl;
    exit(1);
      }
      if(dimZ_opt.size()){
        if(verbose_opt[0])
          std::cout<< "DWT approximation in spectral domain" << std::endl;
    filter1d.dwtCut(input, output, wavelet_type_opt[0], family_opt[0], threshold_opt[0]);
      }
      else
    filter2d.dwtCut(input, output, wavelet_type_opt[0], family_opt[0], threshold_opt[0]);
      break;
    case(filter2d::dwt_cut_from):
      if(down_opt[0]!=1){
    std::cerr << "Error: down option not supported for this filter" << std::endl;
    exit(1);
      }
      try{
    if(dimZ_opt.size()){
      if(verbose_opt[0])
        std::cout<< "DWT approximation in spectral domain" << std::endl;
      filter1d.dwtCutFrom(input, output, wavelet_type_opt[0], family_opt[0], static_cast<int>(threshold_opt[0]));
    }
    else{
      string errorString="Error: this filter is not supported in 2D";
      throw(errorString);
    }
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    case(filter2d::savgolay):{
      assert(savgolay_nl_opt.size());
      assert(savgolay_nr_opt.size());
      assert(savgolay_ld_opt.size());
      assert(savgolay_m_opt.size());
      if(verbose_opt[0])
        std::cout << "Calculating Savitzky-Golay coefficients: " << endl;
      filter1d.getSavGolayCoefficients(tapz_opt, input.nrOfBand(), savgolay_nl_opt[0], savgolay_nr_opt[0], savgolay_ld_opt[0], savgolay_m_opt[0]);
      if(verbose_opt[0]){
        std::cout << "taps (size is " << tapz_opt.size() << "): ";
        for(int itap=0;itap<tapz_opt.size();++itap)
          std::cout<< tapz_opt[itap] << " ";
        std::cout<< std::endl;
      }
      filter1d.setTaps(tapz_opt);
      filter1d.filter(input,output);
      break;
    }
    case(filter2d::percentile)://deliberate fall through
    case(filter2d::threshold)://deliberate fall through
      assert(threshold_opt.size());
      if(dimZ_opt.size())
    filter1d.setThresholds(threshold_opt);
      else
    filter2d.setThresholds(threshold_opt);
    case(filter2d::density)://deliberate fall through
      filter2d.setClasses(class_opt);
      if(verbose_opt[0])
    std::cout << "classes set" << std::endl;
    default:
      try{
    if(dimZ_opt.size()){
      if(dimZ_opt[0]==1)
        filter1d.stat(input,output,method_opt[0]);
      else{
        assert(down_opt[0]==1);//not implemented yet...
        filter1d.filter(input,output,method_opt[0],dimZ_opt[0]);
      }
    }
    else
      filter2d.doit(input,output,method_opt[0],dimX_opt[0],dimY_opt[0],down_opt[0],disc_opt[0]);
      }
      catch(string errorstring){
    cerr << errorstring << endl;
      }
      break;
    }
  }
  input.close();
  output.close();
  return 0;
}