fr.amap.amapvox.io.tls.rsp.Rsp.java Source code

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Here is the source code for fr.amap.amapvox.io.tls.rsp.Rsp.java

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/*
 * Copyright (C) 2016 UMR AMAP (botAnique et Modlisation de l'Architecture des Plantes et des vgtations.
 *
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 *
 * This library 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
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with this library; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301  USA
 */
package fr.amap.amapvox.io.tls.rsp;

import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import javax.vecmath.Matrix4d;
import org.jdom2.Document;
import org.jdom2.Element;
import org.jdom2.JDOMException;
import org.jdom2.input.SAXBuilder;

/**
 *
 * @author Julien Heurtebize (julienhtbe@gmail.com)
 */
public class Rsp {

    private String projectName;
    private ArrayList<Scans> rxpList;
    private Matrix4d popMatrix;

    private Document document;
    private SAXBuilder sxb;
    private Element root;

    public Rsp() {
        popMatrix = new Matrix4d();
        popMatrix.setIdentity();
    }

    public RxpScan getRxpScanByName(String name) {

        for (Scans scans : rxpList) {
            for (Entry entry : scans.getScanList().entrySet()) {
                RxpScan scan = (RxpScan) entry.getValue();
                if (scan.getFileName().equals(name)) {
                    return scan;
                }
            }
        }

        return null;
    }

    public Matrix4d getPopMatrix() {
        return popMatrix;
    }

    public String getProjectName() {
        return projectName;
    }

    public ArrayList<Scans> getRxpList() {
        return rxpList;
    }

    private Matrix4d extractMat4D(String matString) {

        String[] matSplit = matString.split(" ");
        Matrix4d matrix = new Matrix4d();

        double[] mat = new double[16];

        int index = 0;
        for (int i = 0; i < matSplit.length; i++) {

            matSplit[i] = matSplit[i].trim();
            if (!matSplit[i].isEmpty() && index < 16) {
                Double matxyx = Double.valueOf(matSplit[i]);
                mat[index] = matxyx;
                index++;
            }
        }

        matrix.set(mat);

        return matrix;
    }

    public void read(final File rspFile) throws JDOMException, IOException {

        sxb = new SAXBuilder();
        rxpList = new ArrayList<>();

        //avoid loading of dtd file
        sxb.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);

        try {
            document = sxb.build(new FileInputStream(rspFile));
            root = document.getRootElement();
            projectName = root.getAttributeValue("name");
            Element scanPositions = root.getChild("scanpositions");
            String folderScanPositions = scanPositions.getAttributeValue("fold");
            List<Element> childrens = scanPositions.getChildren("scanposition");
            popMatrix = extractMat4D(root.getChild("pop").getChildText("matrix"));

            //scan id
            int scanCount = 0;

            for (Element child : childrens) {
                Scans rxp = new Scans();

                rxp.setName(child.getAttributeValue("name"));
                rxp.setFold(child.getAttributeValue("fold"));

                Element registeredElement = child.getChild("registered");

                if (registeredElement != null) {

                    if (Integer.valueOf(registeredElement.getText()) == 1) {

                        Element singlescans = child.getChild("singlescans");
                        String singlescansFold = singlescans.getAttributeValue("fold");
                        Map<Integer, RxpScan> scanList = new HashMap<>();

                        List<Element> scans = singlescans.getChildren("scan");

                        Element sop = child.getChild("sop");
                        Matrix4d sopMatrix = extractMat4D(sop.getChildText("matrix"));
                        rxp.setSopMatrix(sopMatrix);

                        int compteur = 0;
                        for (Element sc : scans) {

                            RxpScan scan = new RxpScan();
                            scan.setName(sc.getAttributeValue("name"));
                            scan.setFileName(sc.getChildText("file"));
                            String rspFilePathOnly = rspFile.getAbsolutePath().substring(0,
                                    rspFile.getAbsolutePath().lastIndexOf(File.separator));

                            scan.setAbsolutePath(rspFilePathOnly + File.separator + folderScanPositions
                                    + File.separator + rxp.getFold() + File.separator + singlescansFold
                                    + File.separator + scan.getFileName());
                            scanList.put(scanCount, scan);

                            if (scan.getName().contains(".mon")) {
                                rxp.setRxpLiteFile(new File(scan.getAbsolutePath()));
                                rxp.setScanLite(scan);
                            } else {
                                rxp.setScanFull(scan);
                            }
                            scan.setFile(new File(scan.getAbsolutePath()));
                            scan.setSopMatrix(sopMatrix);

                            compteur++;
                            scanCount++;
                        }

                        rxp.setScanList(scanList);

                        rxpList.add(rxp);
                    } else {
                        //logger.info("Scan "+ rxp.getName() +" skipped cause unregistered");
                    }
                }

            }

        } catch (JDOMException ex) {
            throw new JDOMException("error parsing or reading rsp: " + rspFile.getAbsolutePath(), ex);
        } catch (IOException ex) {
            throw new IOException("error parsing or reading rsp: " + rspFile.getAbsolutePath(), ex);
        }
    }
}