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Copy pathRSGISEliminateSmallClumps.cpp
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RSGISEliminateSmallClumps.cpp
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/*
* RSGISEliminateSmallClumps.cpp
* RSGIS_LIB
*
* Created by Pete Bunting on 17/01/2012.
* Copyright 2012 RSGISLib.
*
* RSGISLib 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.
*
* RSGISLib 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 RSGISLib. If not, see <http://www.gnu.org/licenses/>.
*
*/
#include "RSGISEliminateSmallClumps.h"
namespace rsgis{namespace segment{
RSGISEliminateSmallClumps::RSGISEliminateSmallClumps()
{
}
void RSGISEliminateSmallClumps::eliminateSmallClumps(GDALDataset *spectral, GDALDataset *clumps, unsigned int minClumpSize, float specThreshold)
{
if(spectral->GetRasterXSize() != clumps->GetRasterXSize())
{
throw rsgis::img::RSGISImageCalcException("Widths are not the same");
}
if(spectral->GetRasterYSize() != clumps->GetRasterYSize())
{
throw rsgis::img::RSGISImageCalcException("Heights are not the same");
}
unsigned int width = spectral->GetRasterXSize();
unsigned int height = spectral->GetRasterYSize();
unsigned int numSpecBands = spectral->GetRasterCount();
unsigned int *clumpIdxs = new unsigned int[width];
float **spectralVals = new float*[numSpecBands];
GDALRasterBand **spectralBands = new GDALRasterBand*[numSpecBands];
for(unsigned int n = 0; n < numSpecBands; ++n)
{
spectralBands[n] = spectral->GetRasterBand(n+1);
spectralVals[n] = new float[width];
}
GDALRasterBand *clumpBand = clumps->GetRasterBand(1);
unsigned int uiPxlVal = 0;
rsgis::rastergis::RSGISRasterAttUtils ratUtils;
long minVal = 0;
long maxVal = 0;
ratUtils.getImageBandMinMax(clumps, 1, &minVal, &maxVal);
unsigned long maxClumpIdx = boost::lexical_cast<unsigned long>(maxVal);
std::vector<rsgis::img::ImgClump*> *clumpTable = new std::vector<rsgis::img::ImgClump*>();
clumpTable->reserve(maxClumpIdx);
std::deque<rsgis::img::ImgClump*> smallClumps;
rsgis::img::ImgClump *cClump = NULL;
rsgis::img::ImgClump *tClump = NULL;
for(unsigned int i = 0; i < maxClumpIdx; ++i)
{
cClump = new rsgis::img::ImgClump(i+1);
cClump->sumVals = new float[numSpecBands];
cClump->meanVals = new float[numSpecBands];
cClump->pxls = new std::vector<rsgis::img::PxlLoc>();
cClump->active = true;
for(unsigned int n = 0; n < numSpecBands; ++n)
{
cClump->sumVals[n] = 0;
cClump->meanVals[n] = 0;
}
clumpTable->push_back(cClump);
}
std::cout << "Calculate Initial Clump Means\n";
for(unsigned int i = 0; i < height; ++i)
{
clumpBand->RasterIO(GF_Read, 0, i, width, 1, clumpIdxs, width, 1, GDT_UInt32, 0, 0);
for(unsigned int n = 0; n < numSpecBands; ++n)
{
spectralBands[n]->RasterIO(GF_Read, 0, i, width, 1, spectralVals[n], width, 1, GDT_Float32, 0, 0);
}
for(unsigned int j = 0; j < width; ++j)
{
if(clumpIdxs[j] != 0)
{
cClump = clumpTable->at(clumpIdxs[j] - 1);
for(unsigned int n = 0; n < numSpecBands; ++n)
{
cClump->sumVals[n] += spectralVals[n][j];
}
cClump->pxls->push_back(rsgis::img::PxlLoc(j, i));
}
}
}
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
for(unsigned int n = 0; n < numSpecBands; ++n)
{
(*iterClumps)->meanVals[n] = (*iterClumps)->sumVals[n] / (*iterClumps)->pxls->size();
}
if((*iterClumps)->pxls->size() < minClumpSize)
{
smallClumps.push_back((*iterClumps));
}
}
std::cout << "There are " << clumpTable->size() << " clumps. " << smallClumps.size() << " are too small\n";
rsgis::img::PxlLoc tLoc;
std::list<unsigned long> neighbours;
unsigned long closestNeighbour = 0;
bool firstNeighbourTested = true;
float closestNeighbourDist = 0;
float distance = 0;
std::cout << "Eliminating Small Clumps." << std::endl;
long smallClumpsCounter = 0;
while(smallClumps.size() > 0)
{
if((smallClumpsCounter % 10000) == 0)
{
std::cout << "Eliminated " << smallClumpsCounter << " > " << smallClumps.size() << " to go...\r";
}
cClump = smallClumps.front();
smallClumps.pop_front();
// Check that the clump was not selected for a merging already and therefore over minimum size...
if((cClump->active) & (cClump->pxls->size() < minClumpSize))
{
// Get std::list of neighbours.
neighbours.clear();
for(std::vector<rsgis::img::PxlLoc>::iterator iterPxls = cClump->pxls->begin(); iterPxls != cClump->pxls->end(); ++iterPxls)
{
// Above
if(((long)(*iterPxls).yPos)-1 >= 0)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos, (*iterPxls).yPos-1, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Below
if(((long)(*iterPxls).yPos)+1 < height)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos, (*iterPxls).yPos+1, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Left
if(((long)(*iterPxls).xPos-1) >= 0)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos-1, (*iterPxls).yPos, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Right
if(((long)(*iterPxls).xPos+1) < width)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos+1, (*iterPxls).yPos, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
}
neighbours.sort();
neighbours.unique();
// Decide on which neighbour to measure with.
firstNeighbourTested = true;
for(std::list<unsigned long>::iterator iterClumps = neighbours.begin(); iterClumps != neighbours.end(); ++iterClumps)
{
for(unsigned int b = 0; b < numSpecBands; ++b)
{
if(b == 0)
{
distance = (cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b])*(cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b]);
}
else
{
distance += (cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b])*(cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b]);
}
}
distance = sqrt(distance);
if(firstNeighbourTested)
{
closestNeighbour = *iterClumps;
closestNeighbourDist = distance;
firstNeighbourTested = false;
}
else if(distance < closestNeighbourDist)
{
closestNeighbour = *iterClumps;
closestNeighbourDist = distance;
}
}
// Perform Merge
if(!firstNeighbourTested)
{
if(closestNeighbourDist < specThreshold)
{
// Update Clump Table
tClump = clumpTable->at(closestNeighbour-1);
for(size_t n = 0; n < cClump->pxls->size(); ++n)
{
tLoc = cClump->pxls->at(n);
tClump->pxls->push_back(tLoc);
// Update Pixel Values - in clump image.
clumpBand->RasterIO(GF_Write, tLoc.xPos, tLoc.yPos, 1, 1, &closestNeighbour, 1, 1, GDT_UInt32, 0, 0);
}
for(unsigned int b = 0; b < numSpecBands; ++b)
{
tClump->sumVals[b] += cClump->sumVals[b];
tClump->meanVals[b] = tClump->sumVals[b]/tClump->pxls->size();
}
delete cClump->sumVals;
delete cClump->meanVals;
delete cClump->pxls;
cClump->active = false;
// Is the new clump still to small?
// YES - add to queue...
if(tClump->pxls->size() < minClumpSize)
{
smallClumps.push_back(tClump);
}
}
}
}
++smallClumpsCounter;
}
std::cout << "Eliminated " << smallClumpsCounter << " small clumps\n";
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
if((*iterClumps) != NULL)
{
if((*iterClumps)->active)
{
delete (*iterClumps)->sumVals;
delete (*iterClumps)->meanVals;
delete (*iterClumps)->pxls;
}
delete (*iterClumps);
}
}
delete clumpTable;
delete[] spectralBands;
delete[] clumpIdxs;
for(unsigned int n = 0; n < numSpecBands; ++n)
{
delete[] spectralVals[n];
}
delete[] spectralVals;
}
void RSGISEliminateSmallClumps::stepwiseEliminateSmallClumps(GDALDataset *spectral, GDALDataset *clumps, unsigned int minClumpSize, float specThreshold, std::vector<rsgis::img::BandSpecThresholdStats> *bandStretchStats, bool bandStatsAvail)
{
if(spectral->GetRasterXSize() != clumps->GetRasterXSize())
{
throw rsgis::img::RSGISImageCalcException("Widths are not the same");
}
if(spectral->GetRasterYSize() != clumps->GetRasterYSize())
{
throw rsgis::img::RSGISImageCalcException("Heights are not the same");
}
unsigned int width = spectral->GetRasterXSize();
unsigned int height = spectral->GetRasterYSize();
unsigned int numSpecBands = spectral->GetRasterCount();
double *stretch2reflOffs = NULL;
double *stretch2reflGains = NULL;
if(bandStatsAvail && (numSpecBands != bandStretchStats->size()))
{
throw rsgis::img::RSGISImageCalcException("The number of image bands and the number band statistics are not the same.");
}
else if(bandStatsAvail)
{
stretch2reflOffs = new double[numSpecBands];
stretch2reflGains = new double[numSpecBands];
for(unsigned int i = 0; i < numSpecBands; ++i)
{
stretch2reflOffs[i] = bandStretchStats->at(i).origMin;
stretch2reflGains[i] = (bandStretchStats->at(i).origMax - bandStretchStats->at(i).origMin) / (bandStretchStats->at(i).imgMax - bandStretchStats->at(i).imgMin);
}
}
GDALRasterBand *clumpBand = clumps->GetRasterBand(1);
unsigned int uiPxlVal = 0;
std::cout << "Calc Number of clumps\n";
rsgis::rastergis::RSGISRasterAttUtils ratUtils;
long minVal = 0;
long maxVal = 0;
ratUtils.getImageBandMinMax(clumps, 1, &minVal, &maxVal);
unsigned long maxClumpIdx = boost::lexical_cast<unsigned long>(maxVal);
std::vector<rsgis::img::ImgClump*> *clumpTable = new std::vector<rsgis::img::ImgClump*>();
clumpTable->reserve(maxClumpIdx);
std::cout << "Build clump table\n";
rsgis::img::ImgClump *cClump = NULL;
rsgis::img::ImgClump *tClump = NULL;
for(unsigned int i = 0; i < maxClumpIdx; ++i)
{
cClump = new rsgis::img::ImgClump(i+1);
cClump->sumVals = new float[numSpecBands];
cClump->meanVals = new float[numSpecBands];
cClump->pxls = new std::vector<rsgis::img::PxlLoc>();
cClump->active = true;
for(unsigned int n = 0; n < numSpecBands; ++n)
{
cClump->sumVals[n] = 0;
cClump->meanVals[n] = 0;
}
clumpTable->push_back(cClump);
}
std::deque<rsgis::img::ImgClump*> smallClumps;
std::vector< std::pair<rsgis::img::ImgClump*, rsgis::img::ImgClump*> > mergeLookupTab;
std::cout << "Calculate Initial Clump Means\n";
RSGISPopulateMeansPxlLocs *calcMeans = new RSGISPopulateMeansPxlLocs(clumpTable, numSpecBands);
rsgis::img::RSGISCalcImage calcImg = rsgis::img::RSGISCalcImage(calcMeans);
GDALDataset **datasets = new GDALDataset*[2];
datasets[0] = clumps;
datasets[1] = spectral;
calcImg.calcImagePosPxl(datasets, 2);
delete[] datasets;
delete calcMeans;
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
for(unsigned int n = 0; n < numSpecBands; ++n)
{
(*iterClumps)->meanVals[n] = (*iterClumps)->sumVals[n] / (*iterClumps)->pxls->size();
}
}
std::cout << "There are " << clumpTable->size() << " clumps.\n";
rsgis::img::PxlLoc tLoc;
std::list<unsigned long> neighbours;
unsigned long closestNeighbour = 0;
bool firstNeighbourTested = true;
float closestNeighbourDist = 0;
float distance = 0;
std::cout << "Eliminating Small Clumps." << std::endl;
long smallClumpsCounter = 0;
for(unsigned int clumpArea = 1; clumpArea <= minClumpSize; ++clumpArea)
{
std::cout << "Eliminating clumps of size " << clumpArea << std::endl;
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
if(((*iterClumps) != NULL) && ((*iterClumps)->active))
{
if((*iterClumps)->pxls->size() <= clumpArea)
{
smallClumps.push_back(*iterClumps);
}
}
}
std::cout << "Found " << smallClumps.size() << " small clumps to be eliminated." << std::endl;
mergeLookupTab.clear();
while(smallClumps.size() > 0)
{
cClump = smallClumps.front();
smallClumps.pop_front();
// Check that the clump was not selected for a merging already and therefore over minimum size...
if((cClump->active) & (cClump->pxls->size() < minClumpSize))
{
// Get std::list of neighbours.
neighbours.clear();
for(std::vector<rsgis::img::PxlLoc>::iterator iterPxls = cClump->pxls->begin(); iterPxls != cClump->pxls->end(); ++iterPxls)
{
// Above
if(((long)(*iterPxls).yPos)-1 >= 0)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos, (*iterPxls).yPos-1, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Below
if(((long)(*iterPxls).yPos)+1 < height)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos, (*iterPxls).yPos+1, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Left
if(((long)(*iterPxls).xPos-1) >= 0)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos-1, (*iterPxls).yPos, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Right
if(((long)(*iterPxls).xPos+1) < width)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos+1, (*iterPxls).yPos, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
}
neighbours.sort();
neighbours.unique();
// Decide on which neighbour to measure with.
firstNeighbourTested = true;
for(std::list<unsigned long>::iterator iterClumps = neighbours.begin(); iterClumps != neighbours.end(); ++iterClumps)
{
if(clumpTable->at((*iterClumps)-1)->pxls->size() > cClump->pxls->size())
{
for(unsigned int b = 0; b < numSpecBands; ++b)
{
if(b == 0)
{
distance = (cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b])*(cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b]);
}
else
{
distance += (cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b])*(cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b]);
}
}
distance = sqrt(distance);
if(firstNeighbourTested)
{
closestNeighbour = *iterClumps;
closestNeighbourDist = distance;
firstNeighbourTested = false;
}
else if(distance < closestNeighbourDist)
{
closestNeighbour = *iterClumps;
closestNeighbourDist = distance;
}
}
}
// Perform Merge
if(!firstNeighbourTested)
{
if(bandStatsAvail)
{
for(unsigned int b = 0; b < numSpecBands; ++b)
{
if(b == 0)
{
distance = ((stretch2reflOffs[b]+(cClump->meanVals[b]*stretch2reflGains[b])) - (stretch2reflOffs[b]+(clumpTable->at(closestNeighbour-1)->meanVals[b]*stretch2reflGains[b])))*((stretch2reflOffs[b]+(cClump->meanVals[b]*stretch2reflGains[b])) - (stretch2reflOffs[b]+(clumpTable->at(closestNeighbour-1)->meanVals[b]*stretch2reflGains[b])));
}
else
{
distance += ((stretch2reflOffs[b]+(cClump->meanVals[b]*stretch2reflGains[b])) - (stretch2reflOffs[b]+(clumpTable->at(closestNeighbour-1)->meanVals[b]*stretch2reflGains[b])))*((stretch2reflOffs[b]+(cClump->meanVals[b]*stretch2reflGains[b])) - (stretch2reflOffs[b]+(clumpTable->at(closestNeighbour-1)->meanVals[b]*stretch2reflGains[b])));
}
}
closestNeighbourDist = sqrt(distance);
}
if(closestNeighbourDist < specThreshold)
{
// PUT INTO LOOK UP TABLE TO BE APPLIED AFTERWARDS.
tClump = clumpTable->at(closestNeighbour-1);
std::pair<rsgis::img::ImgClump*, rsgis::img::ImgClump*> pair2Merge = std::pair<rsgis::img::ImgClump*, rsgis::img::ImgClump*>(cClump, tClump);
mergeLookupTab.push_back(pair2Merge);
++smallClumpsCounter;
}
}
}
}
// Update Clump Table
std::pair<rsgis::img::ImgClump*, rsgis::img::ImgClump*> pair2Merge;
for(size_t idx = 0; idx < mergeLookupTab.size(); ++idx)
{
pair2Merge = mergeLookupTab.at(idx);
closestNeighbour = pair2Merge.second->clumpID;
for(size_t n = 0; n < pair2Merge.first->pxls->size(); ++n)
{
tLoc = pair2Merge.first->pxls->at(n);
pair2Merge.second->pxls->push_back(tLoc);
// Update Pixel Values - in clump image.
clumpBand->RasterIO(GF_Write, tLoc.xPos, tLoc.yPos, 1, 1, &closestNeighbour, 1, 1, GDT_UInt32, 0, 0);
}
for(unsigned int b = 0; b < numSpecBands; ++b)
{
pair2Merge.second->sumVals[b] += pair2Merge.first->sumVals[b];
pair2Merge.second->meanVals[b] = pair2Merge.second->sumVals[b]/pair2Merge.second->pxls->size();
}
delete[] pair2Merge.first->sumVals;
delete[] pair2Merge.first->meanVals;
delete pair2Merge.first->pxls;
pair2Merge.first->active = false;
}
std::cout << "Eliminated " << smallClumpsCounter << " small clumps\n\n";
smallClumps.clear();
smallClumpsCounter = 0;
}
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
if((*iterClumps) != NULL)
{
if((*iterClumps)->active)
{
delete[] (*iterClumps)->sumVals;
delete[] (*iterClumps)->meanVals;
delete (*iterClumps)->pxls;
}
delete (*iterClumps);
}
}
delete clumpTable;
if(bandStatsAvail)
{
delete[] stretch2reflOffs;
delete[] stretch2reflGains;
}
}
void RSGISEliminateSmallClumps::stepwiseIterativeEliminateSmallClumps(GDALDataset *spectral, GDALDataset *clumps, unsigned int minClumpSize, float specThreshold, std::vector<rsgis::img::BandSpecThresholdStats> *bandStretchStats, bool bandStatsAvail)
{
if(spectral->GetRasterXSize() != clumps->GetRasterXSize())
{
throw rsgis::img::RSGISImageCalcException("Widths are not the same");
}
if(spectral->GetRasterYSize() != clumps->GetRasterYSize())
{
throw rsgis::img::RSGISImageCalcException("Heights are not the same");
}
unsigned int width = spectral->GetRasterXSize();
unsigned int height = spectral->GetRasterYSize();
unsigned int numSpecBands = spectral->GetRasterCount();
double *stretch2reflOffs = NULL;
double *stretch2reflGains = NULL;
if(bandStatsAvail && (numSpecBands != bandStretchStats->size()))
{
throw rsgis::img::RSGISImageCalcException("The number of image bands and the number band statistics are not the same.");
}
else if(bandStatsAvail)
{
stretch2reflOffs = new double[numSpecBands];
stretch2reflGains = new double[numSpecBands];
for(unsigned int i = 0; i < numSpecBands; ++i)
{
stretch2reflOffs[i] = bandStretchStats->at(i).origMin;
stretch2reflGains[i] = (bandStretchStats->at(i).origMax - bandStretchStats->at(i).origMin) / (bandStretchStats->at(i).imgMax - bandStretchStats->at(i).imgMin);
}
}
GDALRasterBand *clumpBand = clumps->GetRasterBand(1);
unsigned int uiPxlVal = 0;
std::cout << "Calc Number of clumps\n";
rsgis::rastergis::RSGISRasterAttUtils ratUtils;
long minVal = 0;
long maxVal = 0;
ratUtils.getImageBandMinMax(clumps, 1, &minVal, &maxVal);
unsigned long maxClumpIdx = boost::lexical_cast<unsigned long>(maxVal);
std::cout << "There are " << maxClumpIdx << " initial clumps." << std::endl;
std::vector<rsgis::img::ImgClump*> *clumpTable = new std::vector<rsgis::img::ImgClump*>();
clumpTable->reserve(maxClumpIdx);
std::cout << "Build clump table\n";
rsgis::img::ImgClump *cClump = NULL;
rsgis::img::ImgClump *tClump = NULL;
for(unsigned int i = 0; i < maxClumpIdx; ++i)
{
cClump = new rsgis::img::ImgClump(i+1);
cClump->sumVals = new float[numSpecBands];
cClump->meanVals = new float[numSpecBands];
cClump->pxls = new std::vector<rsgis::img::PxlLoc>();
cClump->active = true;
for(unsigned int n = 0; n < numSpecBands; ++n)
{
cClump->sumVals[n] = 0;
cClump->meanVals[n] = 0;
}
clumpTable->push_back(cClump);
}
std::deque<rsgis::img::ImgClump*> smallClumps;
std::vector< std::pair<rsgis::img::ImgClump*, rsgis::img::ImgClump*> > mergeLookupTab;
std::cout << "Calculate Initial Clump Means\n";
RSGISPopulateMeansPxlLocs *calcMeans = new RSGISPopulateMeansPxlLocs(clumpTable, numSpecBands);
rsgis::img::RSGISCalcImage calcImg = rsgis::img::RSGISCalcImage(calcMeans);
GDALDataset **datasets = new GDALDataset*[2];
datasets[0] = clumps;
datasets[1] = spectral;
calcImg.calcImagePosPxl(datasets, 2);
delete[] datasets;
delete calcMeans;
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
for(unsigned int n = 0; n < numSpecBands; ++n)
{
(*iterClumps)->meanVals[n] = (*iterClumps)->sumVals[n] / (*iterClumps)->pxls->size();
}
}
std::cout << "There are " << clumpTable->size() << " clumps.\n";
rsgis::img::PxlLoc tLoc;
std::list<unsigned long> neighbours;
unsigned long closestNeighbour = 0;
bool firstNeighbourTested = true;
float closestNeighbourDist = 0;
float distance = 0;
std::cout << "Eliminating Small Clumps." << std::endl;
unsigned long smallClumpsCounter = 0;
unsigned long clumpsBelowThresCounter = 0;
unsigned long initClumpsBelowThresCounter = 0;
bool continueElim = true;
for(unsigned int clumpArea = 1; clumpArea <= minClumpSize; ++clumpArea)
{
continueElim = true;
while(continueElim)
{
std::cout << "Eliminating clumps of size " << clumpArea << std::endl;
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
if(((*iterClumps) != NULL) && ((*iterClumps)->active))
{
if((*iterClumps)->pxls->size() <= clumpArea)
{
smallClumps.push_back(*iterClumps);
}
}
}
initClumpsBelowThresCounter = smallClumps.size();
std::cout << "Found " << initClumpsBelowThresCounter << " small clumps to be eliminated." << std::endl;
mergeLookupTab.clear();
while(smallClumps.size() > 0)
{
cClump = smallClumps.front();
smallClumps.pop_front();
// Check that the clump was not selected for a merging already and therefore over minimum size...
if((cClump->active) & (cClump->pxls->size() < minClumpSize))
{
// Get std::list of neighbours.
neighbours.clear();
for(std::vector<rsgis::img::PxlLoc>::iterator iterPxls = cClump->pxls->begin(); iterPxls != cClump->pxls->end(); ++iterPxls)
{
// Above
if(((long)(*iterPxls).yPos)-1 >= 0)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos, (*iterPxls).yPos-1, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Below
if(((long)(*iterPxls).yPos)+1 < height)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos, (*iterPxls).yPos+1, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Left
if(((long)(*iterPxls).xPos-1) >= 0)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos-1, (*iterPxls).yPos, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
// Right
if(((long)(*iterPxls).xPos+1) < width)
{
clumpBand->RasterIO(GF_Read, (*iterPxls).xPos+1, (*iterPxls).yPos, 1, 1, &uiPxlVal, 1, 1, GDT_UInt32, 0, 0);
if((uiPxlVal != cClump->clumpID) & (uiPxlVal != 0))
{
neighbours.push_back(uiPxlVal);
}
}
}
neighbours.sort();
neighbours.unique();
// Decide on which neighbour to measure with.
firstNeighbourTested = true;
for(std::list<unsigned long>::iterator iterClumps = neighbours.begin(); iterClumps != neighbours.end(); ++iterClumps)
{
if(clumpTable->at((*iterClumps)-1)->pxls->size() > cClump->pxls->size())
{
for(unsigned int b = 0; b < numSpecBands; ++b)
{
if(b == 0)
{
distance = (cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b])*(cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b]);
}
else
{
distance += (cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b])*(cClump->meanVals[b] - clumpTable->at((*iterClumps)-1)->meanVals[b]);
}
}
distance = sqrt(distance);
if(firstNeighbourTested)
{
closestNeighbour = *iterClumps;
closestNeighbourDist = distance;
firstNeighbourTested = false;
}
else if(distance < closestNeighbourDist)
{
closestNeighbour = *iterClumps;
closestNeighbourDist = distance;
}
}
}
// Perform Merge
if(!firstNeighbourTested)
{
if(bandStatsAvail)
{
for(unsigned int b = 0; b < numSpecBands; ++b)
{
if(b == 0)
{
distance = ((stretch2reflOffs[b]+(cClump->meanVals[b]*stretch2reflGains[b])) - (stretch2reflOffs[b]+(clumpTable->at(closestNeighbour-1)->meanVals[b]*stretch2reflGains[b])))*((stretch2reflOffs[b]+(cClump->meanVals[b]*stretch2reflGains[b])) - (stretch2reflOffs[b]+(clumpTable->at(closestNeighbour-1)->meanVals[b]*stretch2reflGains[b])));
}
else
{
distance += ((stretch2reflOffs[b]+(cClump->meanVals[b]*stretch2reflGains[b])) - (stretch2reflOffs[b]+(clumpTable->at(closestNeighbour-1)->meanVals[b]*stretch2reflGains[b])))*((stretch2reflOffs[b]+(cClump->meanVals[b]*stretch2reflGains[b])) - (stretch2reflOffs[b]+(clumpTable->at(closestNeighbour-1)->meanVals[b]*stretch2reflGains[b])));
}
}
closestNeighbourDist = sqrt(distance);
}
if(closestNeighbourDist < specThreshold)
{
// PUT INTO LOOK UP TABLE TO BE APPLIED AFTERWARDS.
tClump = clumpTable->at(closestNeighbour-1);
std::pair<rsgis::img::ImgClump*, rsgis::img::ImgClump*> pair2Merge = std::pair<rsgis::img::ImgClump*, rsgis::img::ImgClump*>(cClump, tClump);
mergeLookupTab.push_back(pair2Merge);
++smallClumpsCounter;
}
}
}
}
// Update Clump Table
std::pair<rsgis::img::ImgClump*, rsgis::img::ImgClump*> pair2Merge;
for(size_t idx = 0; idx < mergeLookupTab.size(); ++idx)
{
pair2Merge = mergeLookupTab.at(idx);
closestNeighbour = pair2Merge.second->clumpID;
for(size_t n = 0; n < pair2Merge.first->pxls->size(); ++n)
{
tLoc = pair2Merge.first->pxls->at(n);
pair2Merge.second->pxls->push_back(tLoc);
// Update Pixel Values - in clump image.
clumpBand->RasterIO(GF_Write, tLoc.xPos, tLoc.yPos, 1, 1, &closestNeighbour, 1, 1, GDT_UInt32, 0, 0);
}
for(unsigned int b = 0; b < numSpecBands; ++b)
{
pair2Merge.second->sumVals[b] += pair2Merge.first->sumVals[b];
pair2Merge.second->meanVals[b] = pair2Merge.second->sumVals[b]/pair2Merge.second->pxls->size();
}
delete[] pair2Merge.first->sumVals;
delete[] pair2Merge.first->meanVals;
delete pair2Merge.first->pxls;
pair2Merge.first->active = false;
}
std::cout << "Eliminated " << smallClumpsCounter << " small clumps\n";
smallClumps.clear();
smallClumpsCounter = 0;
clumpsBelowThresCounter = 0;
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
if(((*iterClumps) != NULL) && ((*iterClumps)->active))
{
if((*iterClumps)->pxls->size() <= clumpArea)
{
++clumpsBelowThresCounter;
}
}
}
std::cout << "There are " << clumpsBelowThresCounter << " small clumps below " << clumpArea << " still to be eliminated\n";
if((clumpsBelowThresCounter > 0) && (clumpsBelowThresCounter != initClumpsBelowThresCounter))
{
continueElim = true;
}
else
{
continueElim = false;
}
}
std::cout << std::endl;
}
for(std::vector<rsgis::img::ImgClump*>::iterator iterClumps = clumpTable->begin(); iterClumps != clumpTable->end(); ++iterClumps)
{
if((*iterClumps) != NULL)
{
if((*iterClumps)->active)
{
delete[] (*iterClumps)->sumVals;
delete[] (*iterClumps)->meanVals;
delete (*iterClumps)->pxls;
}
delete (*iterClumps);
}
}
delete clumpTable;
if(bandStatsAvail)
{
delete[] stretch2reflOffs;
delete[] stretch2reflGains;
}
}
void RSGISEliminateSmallClumps::stepwiseEliminateSmallClumpsNoMean(GDALDataset *spectral, GDALDataset *clumps, unsigned int minClumpSize, float specThreshold, std::vector<rsgis::img::BandSpecThresholdStats> *bandStretchStats, bool bandStatsAvail)
{
if(spectral->GetRasterXSize() != clumps->GetRasterXSize())
{
throw rsgis::img::RSGISImageCalcException("Widths are not the same");
}
if(spectral->GetRasterYSize() != clumps->GetRasterYSize())
{
throw rsgis::img::RSGISImageCalcException("Heights are not the same");
}
unsigned int width = spectral->GetRasterXSize();
unsigned int height = spectral->GetRasterYSize();
unsigned int numSpecBands = spectral->GetRasterCount();
unsigned int *clumpIdxs = new unsigned int[width];
float **spectralVals = new float*[numSpecBands];
GDALRasterBand **spectralBands = new GDALRasterBand*[numSpecBands];
for(unsigned int n = 0; n < numSpecBands; ++n)
{
spectralBands[n] = spectral->GetRasterBand(n+1);
spectralVals[n] = new float[width];
}
GDALRasterBand *clumpBand = clumps->GetRasterBand(1);
unsigned int uiPxlVal = 0;
std::cout << "Calc Number of clumps\n";
rsgis::rastergis::RSGISRasterAttUtils ratUtils;
long minVal = 0;
long maxVal = 0;
ratUtils.getImageBandMinMax(clumps, 1, &minVal, &maxVal);
unsigned long maxClumpIdx = boost::lexical_cast<unsigned long>(maxVal);
rsgis::img::ImgClumpSum **clumpTable = new rsgis::img::ImgClumpSum*[maxClumpIdx];
std::cout << "Build clump table\n";
rsgis::img::ImgClumpSum *tClump = NULL;
unsigned int cClumpIdx = 0;
for(unsigned int i = 0; i < maxClumpIdx; ++i)
{
clumpTable[i] = new rsgis::img::ImgClumpSum(i+1);
clumpTable[i]->sumVals = new float[numSpecBands];
clumpTable[i]->pxls = new std::vector<rsgis::img::PxlLoc>();
clumpTable[i]->active = true;
for(unsigned int n = 0; n < numSpecBands; ++n)
{
clumpTable[i]->sumVals[n] = 0;
}
}
std::deque<unsigned int> smallClumps;
std::vector< std::pair<unsigned int, unsigned int> > mergeLookupTab;
std::cout << "Calculate Initial Clump Means\n";
for(unsigned int i = 0; i < height; ++i)
{
clumpBand->RasterIO(GF_Read, 0, i, width, 1, clumpIdxs, width, 1, GDT_UInt32, 0, 0);
for(unsigned int n = 0; n < numSpecBands; ++n)
{
spectralBands[n]->RasterIO(GF_Read, 0, i, width, 1, spectralVals[n], width, 1, GDT_Float32, 0, 0);
}
for(unsigned int j = 0; j < width; ++j)
{
if(clumpIdxs[j] != 0)
{
cClumpIdx = clumpIdxs[j] - 1;
for(unsigned int n = 0; n < numSpecBands; ++n)
{
clumpTable[cClumpIdx]->sumVals[n] += spectralVals[n][j];
}
clumpTable[cClumpIdx]->pxls->push_back(rsgis::img::PxlLoc(j, i));
}
}
}
std::cout << "There are " << maxClumpIdx << " clumps.\n";
rsgis::img::PxlLoc tLoc;
std::list<unsigned int> neighbours;
unsigned int closestNeighbour = 0;
bool firstNeighbourTested = true;
float closestNeighbourDist = 0;
float distance = 0;
float cMean = 0;
float tMean = 0;
std::cout << "Eliminating Small Clumps." << std::endl;
long smallClumpsCounter = 0;
for(unsigned int clumpArea = 1; clumpArea <= minClumpSize; ++clumpArea)
{
std::cout << "Eliminating clumps of size " << clumpArea << std::endl;
for(unsigned int i = 0; i < maxClumpIdx; ++i)
{
if((clumpTable[i] != NULL) && (clumpTable[i]->active))
{
if(clumpTable[i]->pxls->size() <= clumpArea)
{
smallClumps.push_back(i);
}
}
}
std::cout << "Found " << smallClumps.size() << " small clumps to be eliminated." << std::endl;
mergeLookupTab.clear();
while(smallClumps.size() > 0)
{
cClumpIdx = smallClumps.front();
smallClumps.pop_front();
// Check that the clump was not selected for a merging already and therefore over minimum size...
if((clumpTable[cClumpIdx]->active) & (clumpTable[cClumpIdx]->pxls->size() < minClumpSize))
{
// Get std::list of neighbours.
neighbours.clear();
for(std::vector<rsgis::img::PxlLoc>::iterator iterPxls = clumpTable[cClumpIdx]->pxls->begin(); iterPxls != clumpTable[cClumpIdx]->pxls->end(); ++iterPxls)
{
// Above
if(((long)(*iterPxls).yPos)-1 >= 0)