//! write your image processing algorithms in this method
void RegionDistanceTransformation::_processImages() {
Box extent = _getBox();
if (_globalDistanceField) delete _globalDistanceField;
_globalDistanceField = new labField((extent.x1-extent.x0),(extent.y1-extent.y0));
_globalDistanceField->fillWith(32000);
_componentIDs = new labField((extent.x1-extent.x0),(extent.y1-extent.y0));
_componentIDs->fillWith(-1.0);
calcConnectedComp();
calcGlobalDistanceField();
int min,max;
min=320000;
max=-320000;
double pixel;
int x, y;
for (y = extent.y0+1; y < extent.y1-1; y++) {
for (x = extent.x0+1; x < extent.x1-1; x++) {
pixel = _globalDistanceField->getValueAt(x, y);
if (pixel>max) max=pixel;
if (pixel<min) min=pixel;
_setPixelOut(0,x, y, 0, pixel);
pixel = _componentIDs->getValueAt(x, y);
_setPixelOut(1,x, y, 0, pixel);
}
}
std::cout << "min=" << min << " max=" << max << std::endl;
}
void RegionDistanceTransformation::calcGlobalDistanceField()
{
ML_TRACE_IN("void RegionDistanceTransformation::calcGlobalDistanceField()");
//Create distance field
//First only for background or not
unsigned long int pos;
float a,b,c,d;
int currentDistance = 0;
float currentComponentID;
Box extent = _getBox();
for (int i=extent.x0+1; i<extent.x1-1; i++) //Rand lassen
{
for (int j=extent.y0+1; j<extent.y1-1; j++) //Rand lassen
{
pos = j*(extent.x1-extent.x0)+i;
currentDistance = _globalDistanceField->getValueAt(pos);
a=_globalDistanceField->getValueAt(pos-1);
b=_globalDistanceField->getValueAt(pos+1);
c=_globalDistanceField->getValueAt(pos-(extent.x1-extent.x0));
d=_globalDistanceField->getValueAt(pos+(extent.x1-extent.x0));
currentComponentID = _componentIDs->getValueAt(i,j);
if (currentComponentID==0.0) //is pixel a background pixel
{
currentDistance = min(static_cast<float>(currentDistance),min(a+1,min(b+1,min(c+1,d+1))));
}
else
{
//Is there a background pixel in the 4-nei. then its a border pixel with distance=0
//better: pixel that not belongs to component
if (_componentIDs->getValueAt(i-1,j)!=currentComponentID ||
_componentIDs->getValueAt(i+1,j)!=currentComponentID ||
_componentIDs->getValueAt(i,j-1)!=currentComponentID ||
_componentIDs->getValueAt(i,j+1)!=currentComponentID)
{
currentDistance = 0;
}
else
{
currentDistance = min(static_cast<float>(currentDistance),min(a+1,min(b+1,min(c+1,d+1))));
}
}
_globalDistanceField->setValueAt(pos,currentDistance);
}
}
//And reverse
for (int i=extent.x1-2; i>extent.x0; i--) //Rand lassen
{
for (int j=extent.y1-2; j>extent.y0; j--) //Rand lassen
{
pos = j*(extent.x1-extent.x0)+i;
currentDistance = _globalDistanceField->getValueAt(pos);
a=_globalDistanceField->getValueAt(pos-1);
b=_globalDistanceField->getValueAt(pos+1);
c=_globalDistanceField->getValueAt(pos-(extent.x1-extent.x0));
d=_globalDistanceField->getValueAt(pos+(extent.x1-extent.x0));
currentComponentID = _componentIDs->getValueAt(i,j);
if (currentComponentID==0.0) //is pixel a background pixel
{
currentDistance = min(static_cast<float>(currentDistance),min(a+1,min(b+1,min(c+1,d+1))));
}
else
{
//Is there a background pixel in the 4-nei. then its a border pixel with distance=0
if (_componentIDs->getValueAt(i-1,j)!=currentComponentID ||
_componentIDs->getValueAt(i+1,j)!=currentComponentID ||
_componentIDs->getValueAt(i,j-1)!=currentComponentID ||
_componentIDs->getValueAt(i,j+1)!=currentComponentID)
{
currentDistance = 0;
}
else
{
currentDistance = min(static_cast<float>(currentDistance),min(a+1,min(b+1,min(c+1,d+1))));
}
}
_globalDistanceField->setValueAt(pos,currentDistance);
}
}
}
int RegionDistanceTransformation::calcConnectedComp()
{
ML_TRACE_IN("int RegionDistanceTransformation::calcConnectedComp()");
//Calculate the connected components
multimap<int,int> voxelToWatch;
unsigned long int pos;
multimap<int,int>::iterator tempVoxel;
int currentCompID=0;
int tempX,tempY;
float currentObjID;
Box extent = _getBox();
for (int i=extent.x0; i<extent.x1; i++)
{
for (int j=extent.y0; j<extent.y1; j++)
{
pos = j*(extent.x1-extent.x0)+i;
if (_componentIDs->getValueAt(pos)==-1.0)
{
currentCompID++;
currentObjID = _getPixel(i,j,0);
//Find neigbourhs
voxelToWatch.clear();
voxelToWatch.insert(pair<int,int>(i,j));
while (voxelToWatch.size()>0)
{
//pop first voxel
tempVoxel = voxelToWatch.begin();
tempX=(int)tempVoxel->first;
tempY=(int)tempVoxel->second;
pos = tempY*(extent.x1-extent.x0)+tempX;
voxelToWatch.erase(voxelToWatch.begin());
if (_componentIDs->getValueAt(pos)==-1.0)
{
if (tempX<extent.x1-1)
if (_getPixel(tempX+1,tempY,0)==currentObjID
&& _componentIDs->getValueAt(pos+1)==-1.0)
voxelToWatch.insert(pair<int,int>(tempX+1,tempY));
if (tempX>0)
if (_getPixel(tempX-1,tempY,0)==currentObjID
&& _componentIDs->getValueAt(pos-1)==-1.0)
voxelToWatch.insert(pair<int,int>(tempX-1,tempY));
if (tempY<extent.y1-1)
if (_getPixel(tempX,tempY+1,0)==currentObjID
&& _componentIDs->getValueAt(pos+(extent.x1-extent.x0))==-1.0)
voxelToWatch.insert(pair<int,int>(tempX,tempY+1));
if (tempY>0)
if (_getPixel(tempX,tempY-1,0)==currentObjID
&& _componentIDs->getValueAt(pos-(extent.x1-extent.x0))==-1.0)
voxelToWatch.insert(pair<int,int>(tempX,tempY-1));
}
if (currentObjID==0)
{
_componentIDs->setValueAt(pos,0);
}
else
{
int oldValue = _componentIDs->getValueAt(pos);
if (oldValue!=currentCompID)
{
_componentIDs->setValueAt(pos,currentCompID);
}
}
}
}
}
}
return currentCompID;
}
std::vector<double>
OBSpectrophore::GetSpectrophore(OpenBabel::OBMol* mol)
{
// Clear the return variable
_spectro.clear();
// Atoms
_nAtoms = mol->NumAtoms();
if (_nAtoms < 3)
{
std::cerr << "OBSpectrophore::GetSpectrophore() error: not enough atoms in molecule" << std::endl;;
return _spectro;
}
// Coordinate and property arrays
_oricoor = new double*[_nAtoms];
_coor = new double*[_nAtoms];
double** REF1 = new double*[_nAtoms];
double** REF2 = new double*[_nAtoms];
_property = new double*[_nAtoms];
for (unsigned int i = 0; i < _nAtoms; ++i)
{
_oricoor[i] = new double[3];
_coor[i] = new double[3];
REF1[i] = new double[3];
REF2[i] = new double[3];
_property[i] = new double[N_PROPERTIES];
}
// Atom radii and coordinates
_radii = new double[_nAtoms];
_getMoleculeData(mol);
// Atom properties
_calculateProperties(mol);
// Shift molecule to its center of gravity and orient it in a standard way
_orient();
// Calculate the first spectrum to initiate values
unsigned int sphoreSize(N_PROPERTIES * _numberOfProbes);
std::vector<double> ENERGY(sphoreSize);
std::vector<double> SPHORE(sphoreSize);
// Properties
_getBox(_oricoor);
_getEnergies(_oricoor, &(ENERGY[0]));
_initiateSpectrophore(&(ENERGY[0]), &(SPHORE[0]));
// Rotate
double psi;
double cos_psi;
double sin_psi;
double theta;
double cos_theta;
double sin_theta;
double phi;
double cos_phi;
double sin_phi;
for (unsigned int i = 0; i < _rotationStepList.size(); ++i)
{
int rotationStep(_rotationStepList[i]);
for (int iTheta = 0; iTheta < 180; iTheta += rotationStep)
{
theta = 0.017453292519943 * iTheta;
cos_theta = cos(theta);
sin_theta = sin(theta);
_rotateY(_oricoor, REF1, cos_theta, sin_theta);
for (int iPsi = 0; iPsi < 360; iPsi += rotationStep)
{
psi = 0.017453292519943 * iPsi;
cos_psi = cos(psi);
sin_psi = sin(psi);
_rotateZ(REF1, REF2, cos_psi, sin_psi);
for (int iPhi = 0; iPhi < 360; iPhi += rotationStep)
{
phi = 0.017453292519943 * iPhi;
cos_phi = cos(phi);
sin_phi = sin(phi);
_rotateX(REF2, _coor, cos_phi, sin_phi);
// Calculate energies
_getBox(_coor);
_getEnergies(_coor, &(ENERGY[0]));
_updateSpectrophore(&(ENERGY[0]), &(SPHORE[0]));
}
}
}
}
// Cleanup
for (unsigned int i = 0; i < _nAtoms; ++i)
{
delete[] _property[i];
delete[] _oricoor[i];
delete[] REF1[i];
delete[] REF2[i];
delete[] _coor[i];
_property[i] = NULL;
_oricoor[i] = NULL;
REF1[i] = NULL;
REF2[i] = NULL;
_coor[i] = NULL;
}
delete[] _radii;
_radii = NULL;
// Modify the actual sphore data
_spectro.resize(sphoreSize);
for (unsigned int i = 0; i < sphoreSize; ++i)
{
_spectro[i] = -100 * SPHORE[i];
}
// Normalisation
double mean[N_PROPERTIES];
double std[N_PROPERTIES];
unsigned int m;
for (unsigned int i(0); i < N_PROPERTIES; ++i)
{
mean[i] = 0.0;
for (unsigned int n(0); n < 12; ++n)
{
m = (i * 12) + n;
mean[i] += _spectro[m];
}
mean[i] /= 12.0;
std[i] = 0.0;
for (unsigned int n(0); n < 12; ++n)
{
m = (i * 12) + n;
std[i] += (_spectro[m] - mean[i]) * (_spectro[m] - mean[i]);
}
std[i] /= 11.0;
std[i] = sqrt(std[i]);
}
if ((_normalization == OBSpectrophore::NormalizationTowardsZeroMean) ||
(_normalization == OBSpectrophore::NormalizationTowardsZeroMeanAndUnitStd))
{
for (unsigned int i(0); i < N_PROPERTIES; ++i)
{
for (unsigned int n(0); n < 12; ++n)
{
m = (i * 12) + n;
_spectro[m] -= mean[i];
}
}
}
if ((_normalization == OBSpectrophore::NormalizationTowardsUnitStd) ||
(_normalization == OBSpectrophore::NormalizationTowardsZeroMeanAndUnitStd))
{
for (unsigned int i(0); i < N_PROPERTIES; ++i)
{
for (unsigned int n(0); n < 12; ++n)
{
m = (i * 12) + n;
_spectro[m] /= std[i];
}
}
}
// Return
return _spectro;
}
