io.github.mianalysis.mia.process.activecontour.GridInitialiser Maven / Gradle / Ivy
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ModularImageAnalysis (MIA) is an ImageJ plugin which provides a modular framework for assembling image and object analysis workflows. Detected objects can be transformed, filtered, measured and related. Analysis workflows are batch-enabled by default, allowing easy processing of high-content datasets.
package io.github.mianalysis.mia.process.activecontour;
import io.github.mianalysis.mia.process.activecontour.physicalmodel.NodeCollection;
import io.github.mianalysis.mia.process.activecontour.physicalmodel.Vertex;
import io.github.mianalysis.mia.process.math.Indexer;
/**
* Created by Stephen on 07/09/2016.
*/
public class GridInitialiser {
private int n_cols; //Number of columns
private int n_rows; //Number of rows
private double x_min = 0; //Minimum x position
private double y_min = 0; //Minimum y position
private double x_space = 1; //Column spacing
private double y_space = 1; //Row spacing
private boolean fix_edges = false; //Controls if edge nodes are fixed in the corresponding axis
public GridInitialiser(int n_cols, int n_rows) {
this.n_cols = n_cols;
this.n_rows = n_rows;
}
public GridInitialiser() {
this.n_cols = 1;
this.n_rows = 1;
}
public NodeCollection buildGrid(){
Vertex[] node_arr = new Vertex[n_cols*n_rows];
Indexer indexer = new Indexer(n_cols, n_rows);
//Adding Nodes to Vertex array
for (int c = 0;c < n_cols; c++) {
for (int r = 0;r < n_rows; r++) {
double x = x_min+c*x_space;
double y = y_min+r*y_space;
int ind = indexer.getIndex(new int[]{c,r});
node_arr[ind] = new Vertex(x,y);
if (c == 0 & r == 0) {
node_arr[ind].setSpecial(Vertex.TOPLEFT);
} else if (c == n_cols-1 & r == 0) {
node_arr[ind].setSpecial(Vertex.TOPRIGHT);
} else if (c == 0 & r == n_rows-1) {
node_arr[ind].setSpecial(Vertex.BOTTOMLEFT);
} else if (c == n_cols-1 & r == n_rows-1) {
node_arr[ind].setSpecial(Vertex.BOTTOMRIGHT);
}
if (fix_edges) {
if (c == 0 | c == n_cols - 1) {
node_arr[ind].setFixedX(true);
}
if (r == 0 | r == n_rows - 1) {
node_arr[ind].setFixedY(true);
}
}
}
}
//Adding node links
for (int c = 0;c < n_cols; c++) {
for (int r = 0;r < n_rows; r++) {
Vertex top_neighbour = null;
Vertex bottom_neighbour = null;
Vertex left_neighbour = null;
Vertex right_neighbour = null;
if (r > 0) {
int ind_top = indexer.getIndex(new int[]{c, r - 1});
top_neighbour = node_arr[ind_top];
}
if (r < n_rows-1) {
int ind_bottom = indexer.getIndex(new int[]{c, r + 1});
bottom_neighbour = node_arr[ind_bottom];
}
if (c > 0) {
int ind_left = indexer.getIndex(new int[]{c - 1, r});
left_neighbour = node_arr[ind_left];
}
if (c < n_cols-1) {
int ind_right = indexer.getIndex(new int[]{c + 1, r});
right_neighbour = node_arr[ind_right];
}
int ind = indexer.getIndex(new int[]{c,r});
node_arr[ind].setTopNeighbour(top_neighbour);
node_arr[ind].setBottomNeighbour(bottom_neighbour);
node_arr[ind].setLeftNeighbour(left_neighbour);
node_arr[ind].setRightNeighbour(right_neighbour);
}
}
//Adding Nodes to NodeCollection
NodeCollection nodes = new NodeCollection();
for (int i=0;i