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sebastic-guest pushed a commit to branch upstream-master
in repository pktools.
commit 8fd9b88f970417bf49e8d2b64234b1393fa2e705
Author: Pieter Kempeneers <kempe...@gmail.com>
Date: Wed Jun 25 23:37:18 2014 +0200
worked on pkkalman, supporting different spatial resolutions for model and
observation
---
src/algorithms/ImgRegression.cc | 10 ++-
src/algorithms/StatFactory.h | 17 +++++
src/apps/pkkalman.cc | 163 +++++++++++++++++++++++++++++++---------
3 files changed, 150 insertions(+), 40 deletions(-)
diff --git a/src/algorithms/ImgRegression.cc b/src/algorithms/ImgRegression.cc
index b945206..df88973 100644
--- a/src/algorithms/ImgRegression.cc
+++ b/src/algorithms/ImgRegression.cc
@@ -30,6 +30,8 @@ ImgRegression::~ImgRegression(void)
{}
double ImgRegression::getRMSE(const ImgReaderGdal& imgReader1, const
ImgReaderGdal& imgReader2, double& c0, double& c1, short verbose) const{
+ c0=0;
+ c1=1;
int icol1=0,irow1=0;
std::vector<double> rowBuffer1(imgReader1.nrOfCol());
std::vector<double> rowBuffer2(imgReader2.nrOfCol());
@@ -74,9 +76,11 @@ double ImgRegression::getRMSE(const ImgReaderGdal&
imgReader1, const ImgReaderGd
std::cout << geox << " " << geoy << " " << icol1 << " " << irow1 << " "
<< icol2 << " " << irow2 << " " << buffer1.back() << " " << buffer2.back() <<
std::endl;
}
}
- statfactory::StatFactory stat;
- double err=stat.linear_regression_err(buffer1,buffer2,c0,c1);
-
+ double err=0;
+ if(buffer1.size()||buffer2.size()){
+ statfactory::StatFactory stat;
+ err=stat.linear_regression_err(buffer1,buffer2,c0,c1);
+ }
if(verbose)
std::cout << "linear regression based on " << buffer1.size() << " points:
" << c0 << "+" << c1 << " * x " << " with rmse: " << err << std::endl;
return err;
diff --git a/src/algorithms/StatFactory.h b/src/algorithms/StatFactory.h
index d8f76a7..abf7640 100644
--- a/src/algorithms/StatFactory.h
+++ b/src/algorithms/StatFactory.h
@@ -184,6 +184,7 @@ public:
// template<class T> void interpolateUp(const std::vector< std::vector<T> >&
input, std::vector< std::vector<T> >& output, double start, double end, double
step, const gsl_interp_type* type);
// template<class T> void interpolateUp(const std::vector< std::vector<T> >&
input, const std::vector<double>& wavelengthIn, std::vector< std::vector<T> >&
output, std::vector<double>& wavelengthOut, double start, double end, double
step, const gsl_interp_type* type);
template<class T> void interpolateUp(const std::vector<T>& input,
std::vector<T>& output, int nbin) const;
+ template<class T> void nearUp(const std::vector<T>& input, std::vector<T>&
output) const;
template<class T> void interpolateUp(double* input, int dim, std::vector<T>&
output, int nbin);
template<class T> void interpolateDown(const std::vector<T>& input,
std::vector<T>& output, int nbin) const;
template<class T> void interpolateDown(double* input, int dim,
std::vector<T>& output, int nbin);
@@ -989,6 +990,22 @@ template<class T> void StatFactory::interpolateUp(const
std::vector<T>& input, s
}
}
+template<class T> void StatFactory::nearUp(const std::vector<T>& input,
std::vector<T>& output) const
+{
+ assert(input.size());
+ assert(output.size()>=input.size());
+ int dimInput=input.size();
+ int dimOutput=output.size();
+
+ for(int iin=0;iin<dimInput;++iin){
+ for(int iout=0;iout<dimOutput/dimInput;++iout){
+ int indexOutput=iin*dimOutput/dimInput+iout;
+ assert(indexOutput<output.size());
+ output[indexOutput]=input[iin];
+ }
+ }
+}
+
template<class T> void StatFactory::interpolateUp(double* input, int dim,
std::vector<T>& output, int nbin)
{
assert(nbin);
diff --git a/src/apps/pkkalman.cc b/src/apps/pkkalman.cc
index 9d31cd9..61d93ef 100644
--- a/src/apps/pkkalman.cc
+++ b/src/apps/pkkalman.cc
@@ -44,7 +44,7 @@ int main(int argc,char **argv) {
Optionpk<string> outputbw_opt("obw", "outputbw", "Output raster dataset for
backward model");
Optionpk<string> outputfb_opt("ofb", "outputfb", "Output raster dataset for
smooth model");
Optionpk<float> threshold_opt("th", "threshold", "threshold for selecting
samples (randomly). Provide probability in percentage (>0) or absolute (<0).",
0);
- // Optionpk<double> modnodata_opt("modnodata", "modnodata", "invalid value
for model input", 0);
+ Optionpk<double> modnodata_opt("modnodata", "modnodata", "invalid value for
model input", 0);
Optionpk<double> obsnodata_opt("obsnodata", "obsnodata", "invalid value for
observation input", 0);
Optionpk<double> eps_opt("eps", "eps", "epsilon for non zero division",
0.00001);
Optionpk<double> uncertModel_opt("um", "uncertmodel", "Multiply this value
with std dev of first model image to obtain uncertainty of model",2);
@@ -69,7 +69,7 @@ int main(int argc,char **argv) {
outputbw_opt.retrieveOption(argc,argv);
outputfb_opt.retrieveOption(argc,argv);
threshold_opt.retrieveOption(argc,argv);
- // modnodata_opt.retrieveOption(argc,argv);
+ modnodata_opt.retrieveOption(argc,argv);
obsnodata_opt.retrieveOption(argc,argv);
eps_opt.retrieveOption(argc,argv);
uncertModel_opt.retrieveOption(argc,argv);
@@ -147,6 +147,7 @@ int main(int argc,char **argv) {
exit(1);
}
+ statfactory::StatFactory stat;
imgregression::ImgRegression imgreg;
// vector<ImgReaderGdal> imgReaderModel(model_opt.size());
// vector<ImgReaderGdal> imgReaderObs(observation_opt.size());
@@ -173,6 +174,8 @@ int main(int argc,char **argv) {
option_opt.push_back(theInterleave);
}
+ imgReaderObs.close();
+
int obsindex=0;
const char* pszMessage;
@@ -194,12 +197,14 @@ int main(int argc,char **argv) {
for(int tindex=0;tindex<tobservation_opt.size();++tindex){
vector<int>::iterator modit;
modit=lower_bound(tmodel_opt.begin(),tmodel_opt.end(),tobservation_opt[tindex]);
- int relpos=modit-tmodel_opt.begin()-1;
- if(relpos<0)
- relpos=0;
+ int relpos=modit-tmodel_opt.begin();
+ // if(relpos<0)
+ // relpos=0;
relobsindex.push_back(relpos);
if(verbose_opt[0])
- cout << "tobservation_opt[tindex] " << tobservation_opt[tindex] << " "
<< relobsindex.back() << endl;
+ cout << "tobservation_opt[tindex] " << tobservation_opt[tindex] << " "
<< relobsindex.back() << " " << observation_opt[tindex] << " " <<
model_opt[relpos] << endl;
+ // if(verbose_opt[0])
+ // cout << "tobservation_opt[tindex] " << tobservation_opt[tindex] << "
" << relobsindex.back() << endl;
}
if(find(direction_opt.begin(),direction_opt.end(),"forward")!=direction_opt.end()){
@@ -231,32 +236,67 @@ int main(int argc,char **argv) {
cout << "There is no next observation" << endl;
}
- imgReaderModel1.open(model_opt[0]);
+ try{
+ imgReaderModel1.open(model_opt[0]);
+ imgReaderModel1.setNoData(modnodata_opt);
+ }
+ catch(string errorString){
+ cerr << errorString << endl;
+ }
+ catch(...){
+ cerr << "Error opening file " << model_opt[0] << endl;
+ }
+
//calculate standard deviation of image to serve as model uncertainty
GDALRasterBand* rasterBand;
rasterBand=imgReaderModel1.getRasterBand(0);
double minValue, maxValue, meanValue, stdDev;
void* pProgressData;
rasterBand->ComputeStatistics(0,&minValue,&maxValue,&meanValue,&stdDev,pfnProgress,pProgressData);
+ double x=0;
+ double y=0;
+ double modRow=0;
+ double modCol=0;
if(relobsindex[0]>0){//initialize output_opt[0] as model[0]
//write first model as output
+ if(verbose_opt[0])
+ cout << "write first model as output" << endl;
for(int irow=0;irow<nrow;++irow){
vector<double> estReadBuffer;
+ vector<double> estWriteBuffer(ncol);
vector<double> uncertWriteBuffer(ncol);
- imgReaderModel1.readData(estReadBuffer,GDT_Float64,irow);
- imgWriterEst.writeData(estReadBuffer,GDT_Float64,irow,0);
- for(int icol=0;icol<ncol;++icol)
- uncertWriteBuffer[icol]=uncertModel_opt[0]*stdDev;
- imgWriterEst.writeData(uncertWriteBuffer,GDT_Float64,irow,1);
+ imgWriterEst.image2geo(0,irow,x,y);
+ imgReaderModel1.geo2image(x,y,modCol,modRow);
+ assert(modRow>=0||modRow<imgReaderModel1.nrOfRow());
+ try{
+ imgReaderModel1.readData(estReadBuffer,GDT_Float64,modRow);
+ //simple nearest neighbor
+ stat.nearUp(estReadBuffer,estWriteBuffer);
+ imgWriterEst.writeData(estWriteBuffer,GDT_Float64,irow,0);
+ for(int icol=0;icol<ncol;++icol)
+ uncertWriteBuffer[icol]=uncertModel_opt[0]*stdDev;
+ imgWriterEst.writeData(uncertWriteBuffer,GDT_Float64,irow,1);
+ }
+ catch(string errorString){
+ cerr << errorString << endl;
+ }
+ catch(...){
+ cerr << "Error writing file " << imgWriterEst.getFileName() << endl;
+ }
}
}
else{//we have an observation at time 0
+ if(verbose_opt[0])
+ cout << "we have an observation at time 0" << endl;
imgReaderObs.open(observation_opt[0]);
imgReaderObs.getGeoTransform(geotransform);
imgReaderObs.setNoData(obsnodata_opt);
for(int irow=0;irow<nrow;++irow){
vector<double> estReadBuffer;
- imgReaderModel1.readData(estReadBuffer,GDT_Float64,irow);
+ imgWriterEst.image2geo(0,irow,x,y);
+ imgReaderModel1.geo2image(x,y,modCol,modRow);
+ assert(modRow>=0||modRow<imgReaderModel1.nrOfRow());
+ imgReaderModel1.readData(estReadBuffer,GDT_Float64,modRow);
vector<double> estWriteBuffer(ncol);
vector<double> uncertWriteBuffer(ncol);
vector<double> uncertObsBuffer;
@@ -265,7 +305,10 @@ int main(int argc,char **argv) {
imgReaderObs.readData(uncertObsBuffer,GDT_Float64,irow,1);
for(int icol=0;icol<ncol;++icol){
if(imgReaderObs.isNoData(estWriteBuffer[icol])){
- estWriteBuffer[icol]=estReadBuffer[icol];
+ imgWriterEst.image2geo(icol,irow,x,y);
+ imgReaderModel1.geo2image(x,y,modCol,modRow);
+ assert(modRow>=0||modRow<imgReaderModel1.nrOfRow());
+ estWriteBuffer[icol]=estReadBuffer[modCol];
uncertWriteBuffer[icol]=uncertModel_opt[0]*stdDev;
}
else{
@@ -273,12 +316,15 @@ int main(int argc,char **argv) {
if(uncertObsBuffer.size()>icol)
uncertObs=uncertObsBuffer[icol];
if(uncertModel_opt[0]*stdDev+uncertObs>eps_opt[0]){
+ imgWriterEst.image2geo(icol,irow,x,y);
+ imgReaderModel1.geo2image(x,y,modCol,modRow);
+ assert(modRow>=0||modRow<imgReaderModel1.nrOfRow());
// double noemer=uncertObs*uncertObs+stdDev*stdDev;//todo:
multiply stdDev with uncertModel_opt[0]
// estWriteBuffer[icol]*=uncertModel_opt[0]*stdDev*stdDev/noemer;
//
estWriteBuffer[icol]+=uncertModel_opt[0]*uncertObs*uncertObs/noemer;//todo:check!
error?
double
kalmanGain=uncertModel_opt[0]*stdDev/(uncertModel_opt[0]*stdDev+uncertObs);
assert(kalmanGain<=1);
-
estWriteBuffer[icol]=estReadBuffer[icol]+kalmanGain*(estWriteBuffer[icol]-estReadBuffer[icol]);
+
estWriteBuffer[icol]=estReadBuffer[modCol]+kalmanGain*(estWriteBuffer[icol]-estReadBuffer[modCol]);
uncertWriteBuffer[icol]=uncertModel_opt[0]*stdDev*(1-kalmanGain);
}
else{
@@ -318,12 +364,13 @@ int main(int argc,char **argv) {
imgWriterEst.open(output,ncol,nrow,2,GDT_Float32,imageType,option_opt);
imgWriterEst.setProjectionProj4(projection_opt[0]);
imgWriterEst.setGeoTransform(geotransform);
-
imgWriterEst.GDALSetNoDataValue(obsnodata_opt[0]);
//calculate regression between two subsequence model inputs
imgReaderModel1.open(model_opt[modindex-1]);
+ imgReaderModel1.setNoData(modnodata_opt);
imgReaderModel2.open(model_opt[modindex]);
+ imgReaderModel2.setNoData(modnodata_opt);
//calculate regression
//we could re-use the points from second image from last run, but
//to keep it general, we must redo it (overlap might have changed)
@@ -350,9 +397,10 @@ int main(int argc,char **argv) {
imgReaderObs.setNoData(obsnodata_opt);
//calculate regression between model and observation
if(verbose_opt[0])
- cout << "Calculating regression for " <<
imgReaderModel1.getFileName() << " " << imgReaderObs.getFileName() << endl;
-
errObs=imgreg.getRMSE(imgReaderModel1,imgReaderObs,c0obs,c1obs,verbose_opt[0]);
+ cout << "Calculating regression for " <<
imgReaderModel2.getFileName() << " " << imgReaderObs.getFileName() << endl;
+
errObs=imgreg.getRMSE(imgReaderModel2,imgReaderObs,c0obs,c1obs,verbose_opt[0]);
}
+ //prediction (also to fill cloudy pixels in update mode)
string input;
if(outputfw_opt.size()==model_opt.size())
input=outputfw_opt[modindex-1];
@@ -369,6 +417,7 @@ int main(int argc,char **argv) {
vector<double> uncertReadBuffer;
vector<double> estWriteBuffer(ncol);
vector<double> uncertWriteBuffer(ncol);
+
for(int irow=0;irow<imgWriterEst.nrOfRow();++irow){
assert(irow<imgReaderEst.nrOfRow());
imgReaderEst.readData(estReadBuffer,GDT_Float64,irow,0);
@@ -429,8 +478,8 @@ int main(int argc,char **argv) {
}
}
if(find(direction_opt.begin(),direction_opt.end(),"backward")!=direction_opt.end()){
- obsindex=relobsindex.size()-1;
///////////////////////////// backward model /////////////////////////
+ obsindex=relobsindex.size()-1;
if(verbose_opt[0])
cout << "Running backward model" << endl;
//initialization
@@ -456,32 +505,68 @@ int main(int argc,char **argv) {
else
cout << "There is no next observation" << endl;
}
- imgReaderModel1.open(model_opt.back());
+
+ try{
+ imgReaderModel1.open(model_opt.back());
+ imgReaderModel1.setNoData(modnodata_opt);
+ }
+ catch(string errorString){
+ cerr << errorString << endl;
+ }
+ catch(...){
+ cerr << "Error opening file " << model_opt[0] << endl;
+ }
+
//calculate standard deviation of image to serve as model uncertainty
GDALRasterBand* rasterBand;
rasterBand=imgReaderModel1.getRasterBand(0);
double minValue, maxValue, meanValue, stdDev;
void* pProgressData;
rasterBand->ComputeStatistics(0,&minValue,&maxValue,&meanValue,&stdDev,pfnProgress,pProgressData);
+ double x=0;
+ double y=0;
+ double modRow=0;
+ double modCol=0;
if(relobsindex.back()<model_opt.size()-1){//initialize output_opt.back()
as model[0]
//write last model as output
+ if(verbose_opt[0])
+ cout << "write last model as output" << endl;
for(int irow=0;irow<imgWriterEst.nrOfRow();++irow){
vector<double> estReadBuffer;
+ vector<double> estWriteBuffer(ncol);
vector<double> uncertWriteBuffer(ncol);
- imgReaderModel1.readData(estReadBuffer,GDT_Float64,irow);
- imgWriterEst.writeData(estReadBuffer,GDT_Float64,irow,0);
- for(int icol=0;icol<imgWriterEst.nrOfCol();++icol)
- uncertWriteBuffer[icol]=uncertModel_opt[0]*stdDev;
- imgWriterEst.writeData(uncertWriteBuffer,GDT_Float64,irow,1);
+ imgWriterEst.image2geo(0,irow,x,y);
+ imgReaderModel1.geo2image(x,y,modCol,modRow);
+ assert(modRow>=0||modRow<imgReaderModel1.nrOfRow());
+ try{
+ imgReaderModel1.readData(estReadBuffer,GDT_Float64,irow);
+ //simple nearest neighbor
+ stat.nearUp(estReadBuffer,estWriteBuffer);
+ imgWriterEst.writeData(estWriteBuffer,GDT_Float64,irow,0);
+ for(int icol=0;icol<imgWriterEst.nrOfCol();++icol)
+ uncertWriteBuffer[icol]=uncertModel_opt[0]*stdDev;
+ imgWriterEst.writeData(uncertWriteBuffer,GDT_Float64,irow,1);
+ }
+ catch(string errorString){
+ cerr << errorString << endl;
+ }
+ catch(...){
+ cerr << "Error writing file " << imgWriterEst.getFileName() << endl;
+ }
}
}
else{//we have an observation at end time
+ if(verbose_opt[0])
+ cout << "we have an observation at end time" << endl;
imgReaderObs.open(observation_opt.back());
imgReaderObs.getGeoTransform(geotransform);
imgReaderObs.setNoData(obsnodata_opt);
for(int irow=0;irow<nrow;++irow){
vector<double> estReadBuffer;
- imgReaderModel1.readData(estReadBuffer,GDT_Float64,irow);
+ imgWriterEst.image2geo(0,irow,x,y);
+ imgReaderModel1.geo2image(x,y,modCol,modRow);
+ assert(modRow>=0||modRow<imgReaderModel1.nrOfRow());
+ imgReaderModel1.readData(estReadBuffer,GDT_Float64,modRow);
vector<double> estWriteBuffer(ncol);
vector<double> uncertWriteBuffer(ncol);
vector<double> uncertObsBuffer;
@@ -490,7 +575,10 @@ int main(int argc,char **argv) {
imgReaderObs.readData(uncertObsBuffer,GDT_Float64,irow,1);
for(int icol=0;icol<imgWriterEst.nrOfCol();++icol){
if(imgReaderObs.isNoData(estWriteBuffer[icol])){
- estWriteBuffer[icol]=estReadBuffer[icol];
+ imgWriterEst.image2geo(icol,irow,x,y);
+ imgReaderModel1.geo2image(x,y,modCol,modRow);
+ assert(modRow>=0||modRow<imgReaderModel1.nrOfRow());
+ estWriteBuffer[icol]=estReadBuffer[modCol];
uncertWriteBuffer[icol]=uncertModel_opt[0]*stdDev;
}
else{
@@ -498,19 +586,17 @@ int main(int argc,char **argv) {
if(uncertObsBuffer.size()>icol)
uncertObs=uncertObsBuffer[icol];
if(uncertModel_opt[0]*stdDev+uncertObs>eps_opt[0]){
+ imgWriterEst.image2geo(icol,irow,x,y);
+ imgReaderModel1.geo2image(x,y,modCol,modRow);
+ assert(modRow>=0||modRow<imgReaderModel1.nrOfRow());
// double noemer=uncertObs*uncertObs+stdDev*stdDev;//todo:
multiply stdDev with uncertModel_opt[0]
// estWriteBuffer[icol]*=uncertModel_opt[0]*stdDev*stdDev/noemer;
//
estWriteBuffer[icol]+=uncertModel_opt[0]*uncertObs*uncertObs/noemer;//todo:check!
error?
double
kalmanGain=uncertModel_opt[0]*stdDev/(uncertModel_opt[0]*stdDev+uncertObs);
assert(kalmanGain<=1);
-
estWriteBuffer[icol]=estReadBuffer[icol]+kalmanGain*(estWriteBuffer[icol]-estReadBuffer[icol]);
+
estWriteBuffer[icol]=estReadBuffer[modCol]+kalmanGain*(estWriteBuffer[icol]-estReadBuffer[modCol]);
uncertWriteBuffer[icol]=uncertModel_opt[0]*stdDev*(1-kalmanGain);
}
- // if(uncertObs>eps_opt[0]){
- // double noemer=uncertObs*uncertObs+stdDev*stdDev;
- // estWriteBuffer[icol]*=uncertModel_opt[0]*stdDev*stdDev/noemer;
- //
estWriteBuffer[icol]+=uncertModel_opt[0]*uncertObs*uncertObs/noemer;//todo:
check error?
- // }
else{
//no need to fill write buffer (already done in
imgReaderObs.readData
uncertWriteBuffer[icol]=uncertObs;
@@ -543,6 +629,7 @@ int main(int argc,char **argv) {
// outputstream << output_opt[0] << "_" << modindex+1 << ".tif";
output=outputstream.str();
}
+
//two band output band0=estimation, band1=uncertainty
imgWriterEst.open(output,ncol,nrow,2,GDT_Float32,imageType,option_opt);
imgWriterEst.setProjectionProj4(projection_opt[0]);
@@ -551,7 +638,9 @@ int main(int argc,char **argv) {
//calculate regression between two subsequence model inputs
imgReaderModel1.open(model_opt[modindex+1]);
+ imgReaderModel1.setNoData(modnodata_opt);
imgReaderModel2.open(model_opt[modindex]);
+ imgReaderModel2.setNoData(modnodata_opt);
//calculate regression
//we could re-use the points from second image from last run, but
//to keep it general, we must redo it (overlap might have changed)
@@ -572,19 +661,19 @@ int main(int argc,char **argv) {
if(update){
if(verbose_opt[0])
cout << "***update " << relobsindex[obsindex] << " = " << modindex <<
" " << observation_opt[obsindex] << " ***" << endl;
+
imgReaderObs.open(observation_opt[obsindex]);
imgReaderObs.getGeoTransform(geotransform);
imgReaderObs.setNoData(obsnodata_opt);
//calculate regression between model and observation
if(verbose_opt[0])
- cout << "Calculating regression for " <<
imgReaderModel1.getFileName() << " " << imgReaderObs.getFileName() << endl;
-
errObs=imgreg.getRMSE(imgReaderModel1,imgReaderObs,c0obs,c1obs,verbose_opt[0]);
+ cout << "Calculating regression for " <<
imgReaderModel2.getFileName() << " " << imgReaderObs.getFileName() << endl;
+
errObs=imgreg.getRMSE(imgReaderModel2,imgReaderObs,c0obs,c1obs,verbose_opt[0]);
}
//prediction (also to fill cloudy pixels in update mode)
string input;
- if(outputbw_opt.size()==model_opt.size()){
+ if(outputbw_opt.size()==model_opt.size())
input=outputbw_opt[modindex+1];
- }
else{
ostringstream outputstream;
outputstream << outputbw_opt[0] << "_" << tmodel_opt[modindex+1] <<
".tif";
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