@SuppressWarnings("unchecked")
@Override
public Region<E> close(Region<E> reg) {
// return erode(dilate(reg));
try {
CubeHistogram<E> ch = new CubeHistogram<E>((PixelCube<E, BaseIndex>) reg);
Erosion<E> er = new Erosion<E>((StructureElement<E>) se);
er.initFunction(ch);
Dilation<E> dil = new Dilation<E>((StructureElement<E>) se);
dil.initFunction(ch);
reg.setIterationPattern(IP_DEFAULT);
reg.setIndexing(BASE_INDEXING);
Region<E> out = new Region<E>((PixelCube<E, ?>) reg.clone(), (StructureElement<E>) se);
// out.setIterationPattern(IP_DEFAULT);
// out.setIndexing(BASE_INDEXING);
final ZonalProcessor zp = reg.getProcessor();
final VectorCube<E> ve = reg.getVectorCube();
// System.out.println(ve);
// final double limbodil=0;s
// Pair<Number,Number> p= (Pair<Number, Number>) ch.getMinMax();
// final double limboer=p.second.doubleValue();
Access<E> accessOut = out.getAccess();
BoundaryCondition<int[]> bc = reg.getBoundaryCondition();
final int n = (int) accessOut.length();
int offset = Util.cumprod(se.getDimensions()) + 1; // (int)ve.size();
System.out.println("offset: " + offset);
for (int i = 0; i < n + offset; i++) {
if (i < n) {
final E elem = zp.elementTransformCond(ve, dil, bc, i);
accessOut.putE(i, elem);
}
if (i >= offset) {
final int z = i - offset;
// System.out.println("z: "+ z);
final E elem = zp.elementTransformCond(ve, er, bc, z);
accessOut.putE(z, elem);
}
}
// } // end if
return out;
} catch (UnsupportedTypeException e) {
e.printStackTrace();
}
return null;
}
/** This function is called at this end of the function run(). */
public void done() {
GnwGuiSettings global = GnwGuiSettings.getInstance();
// For each subnet found, a structure or dynamical model item is created
// and place on the desktop
for (int i = 0; i < output_.length; i++) {
if (output_[i] instanceof ImodNetwork) {
StructureElement structure =
new StructureElement(output_[i].getId(), global.getNetworkDesktop());
structure.setNetwork((ImodNetwork) output_[i]);
structure.setFather(item_);
item_.addChild(structure);
} else if (output_[i] instanceof GeneNetwork) {
DynamicalModelElement dynamicNetwork =
new DynamicalModelElement(output_[i].getId(), global.getNetworkDesktop());
dynamicNetwork.setGeneNetwork((GeneNetwork) output_[i]);
dynamicNetwork.setFather(item_);
item_.addChild(dynamicNetwork);
}
}
// Display all the subnets found on the desktop as children of the mother network
// used to generate them.
global.getNetworkDesktop().displayChildrenOf(item_);
snake_.stop();
myCardLayout.show(cards, runButton_.getName());
// close the window
SubnetExtraction.this.escapeAction();
// If some sunet sizes < size_, the user should be informed.
// if (extractor_.getUnderSized()) {
// JOptionPane.showMessageDialog(global.getGnwGui().getFrame(), "<html>At least one network
// generated is under-sized, " +
// "<br>i.e. extraction of a module not linked with the rest of the network.</html>");
// }
log.log(Level.INFO, "Done!");
}
@SuppressWarnings("unchecked")
public MorphoProcessorXD(Region<?> reg) throws UnsupportedTypeException {
se = new StructureElement<E>((VectorCube<E>) reg.getVectorCube());
region = reg;
type = reg.getType();
CubeHistogram<E> ch = new CubeHistogram<E>((PixelCube<E, ?>) region);
// System.out.println(ch);
// System.out.println("min max :"+se.getMinMax());
se.setMinMax(ch);
scaled = true;
// System.out.println("scaling ... \n " +se);
}
public MorphoProcessorXD(StructureElement<?> ase) {
se = ase;
type = se.getType();
}