109 lines
4.1 KiB
Java
109 lines
4.1 KiB
Java
import ij.io.OpenDialog;
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import ij.io.SaveDialog;
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import java.util.ArrayList;
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import java.io.IOException;
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import java.io.File;
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import jmatio.types.*;
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import jmatio.io.*;
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import ij.gui.GenericDialog;
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import ij.IJ;
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import ij.Prefs;
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public class ShiftsIO {
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public ShiftsIO () {}
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public double[][] load(String filename, String varname) {
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if (filename==null){
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String analysis_dir = Prefs.get("peem.analysis_dir", "");
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OpenDialog od = new OpenDialog("Open_shifts .mat file:", analysis_dir, "shifts.mat");
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String dir = od.getDirectory();
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if (null == dir) return null; // dialog was canceled
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if (!dir.endsWith(File.separator)) dir += File.separator;
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filename = dir + od.getFileName();
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Prefs.set("peem.analysis_dir", dir);
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}
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return low_load(filename, varname);
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}
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private double[][] low_load(String filename, String varname) {
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MatFileReader mfr = null;
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try {
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mfr = new MatFileReader(filename);
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} catch (IOException e) {
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System.err.println("Caught IOException: "
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+ e.getMessage());
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}
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if (mfr != null) {
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MLDouble array = (MLDouble)mfr.getMLArray(varname);
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if (array != null){
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return array.getArray();
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} else {
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return null;
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}
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} else {
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return null;
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}
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}
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public void save(String filename, double[][] shifts, String varname) {
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boolean update = false;
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if (filename==null){
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String analysis_dir = Prefs.get("peem.analysis_dir", "");
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SaveDialog sd = new SaveDialog("Save_shifts .mat file:", analysis_dir, "shifts.mat", ".mat");
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String dir = sd.getDirectory();
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String fname = sd.getFileName();
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if (null == fname) return; // user canceled dialog
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if (!dir.endsWith(File.separator)) dir += File.separator;
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Prefs.set("peem.analysis_dir", dir);
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if ((new File(dir + fname)).exists()) { // if file exist, overwrite or update shifts ?
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GenericDialog gd = new GenericDialog("Update");
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String[] options = {"overwrite","update"};
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gd.addChoice("Mode of operation with existing file. You want to: ", options, options[0]);
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gd.showDialog();
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if (gd.wasCanceled()) return;
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if (gd.getNextChoiceIndex() == 1) update = true;
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}
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filename = dir + fname;
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}
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double[][] final_shifts;
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if (update) {
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double[][] prev_shifts = low_load(filename, "directshifts");
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if (prev_shifts == null) {
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IJ.error("Can't read the direct shifts in this file");
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return;
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}
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if (prev_shifts.length == shifts.length) {
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for (int j = 0; j < prev_shifts.length; j++) {
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prev_shifts[j][3] += shifts[j][3];
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prev_shifts[j][4] += shifts[j][4];
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}
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} else if (shifts.length == 2) {// 2 shifts, like between two slices of different
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// sequences
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for (int j = 0; j < prev_shifts.length; j++) {
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prev_shifts[j][3] += shifts[1][3];
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prev_shifts[j][4] += shifts[1][4];
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}
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} else {
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IJ.error("Old and new shifts have incompatible length !");
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return;
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}
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final_shifts = prev_shifts;
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} else {
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final_shifts = shifts;
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}
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MLDouble mlDouble = new MLDouble(varname, final_shifts);
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ArrayList<MLArray> list = new ArrayList<MLArray>();
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list.add(mlDouble);
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try {
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new MatFileWriter(filename, list);
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} catch (IOException e) {
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System.err.println("Caught IOException: "
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+ e.getMessage());
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}
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}
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} |