Shift calculation tests

2021-06-30 16:15:12 +02:00
parent fee5f5ffba
commit 163c0ff09b
83 changed files with 4434 additions and 318 deletions
@@ -0,0 +1,109 @@
+import ij.io.OpenDialog;
+import ij.io.SaveDialog;
+import java.util.ArrayList;
+import java.io.IOException;
+import java.io.File;
+import jmatio.types.*;
+import jmatio.io.*;
+import ij.gui.GenericDialog;
+import ij.IJ;
+import ij.Prefs;
+
+public class ShiftsIO {
+    
+    public ShiftsIO () {}
+
+    public double[][] load(String filename, String varname) {
+        if (filename==null){
+                String analysis_dir =  Prefs.get("peem.analysis_dir", "");
+                OpenDialog od = new OpenDialog("Open_shifts .mat file:", analysis_dir, "shifts.mat");
+                String dir = od.getDirectory();
+                if (null == dir) return null; // dialog was canceled
+                if (!dir.endsWith(File.separator)) dir += File.separator;
+                filename = dir + od.getFileName();
+                Prefs.set("peem.analysis_dir", dir);
+            }
+            return low_load(filename, varname);
+    }
+
+       private double[][] low_load(String filename, String varname) {
+        MatFileReader mfr = null;
+        try {
+            mfr = new MatFileReader(filename);
+        } catch (IOException e) {
+                System.err.println("Caught IOException: "
+                    + e.getMessage());
+        }
+
+        if (mfr != null) {
+            MLDouble array = (MLDouble)mfr.getMLArray(varname);
+            if (array != null){
+                return array.getArray();
+            } else {
+                return null;
+            }
+        } else {
+            return null;
+        }
+    }
+
+    public void save(String filename, double[][] shifts, String varname) {
+        boolean update = false;
+        if (filename==null){
+        String analysis_dir =  Prefs.get("peem.analysis_dir", "");
+        SaveDialog sd = new SaveDialog("Save_shifts .mat file:", analysis_dir, "shifts.mat", ".mat");
+            String dir = sd.getDirectory();
+            String fname = sd.getFileName();
+            if (null == fname) return; // user canceled dialog
+            if (!dir.endsWith(File.separator)) dir += File.separator;
+            Prefs.set("peem.analysis_dir", dir);       
+        
+            if ((new File(dir + fname)).exists()) { // if file exist, overwrite or update shifts ?
+                GenericDialog gd = new GenericDialog("Update");
+                String[] options = {"overwrite","update"};
+            gd.addChoice("Mode of operation with existing file. You want to: ", options, options[0]);
+            gd.showDialog();
+            if (gd.wasCanceled()) return;
+            if (gd.getNextChoiceIndex() == 1) update = true;
+            }
+            filename = dir + fname;
+        } 
+        double[][] final_shifts;
+            if (update) {
+                double[][] prev_shifts = low_load(filename, "directshifts");
+                if (prev_shifts == null) {
+                    IJ.error("Can't read the direct shifts in this file");
+                    return;
+                }
+
+            if (prev_shifts.length == shifts.length) {
+                    for (int j = 0; j < prev_shifts.length; j++) {
+                        prev_shifts[j][3] += shifts[j][3];
+                        prev_shifts[j][4] += shifts[j][4];
+                    }
+            } else if (shifts.length == 2) {// 2 shifts, like between two slices of different
+                            // sequences
+                 for (int j = 0; j < prev_shifts.length; j++) {
+                        prev_shifts[j][3] += shifts[1][3];
+                        prev_shifts[j][4] += shifts[1][4];
+                    }
+            } else {
+                IJ.error("Old and new shifts have incompatible length !");
+                return;
+            }
+            final_shifts = prev_shifts;
+            } else {
+            final_shifts = shifts;
+            }
+            
+            MLDouble mlDouble = new MLDouble(varname, final_shifts);
+            ArrayList<MLArray> list = new ArrayList<MLArray>();
+        list.add(mlDouble);
+        try {
+            new MatFileWriter(filename, list);
+        } catch (IOException e) {
+                System.err.println("Caught IOException: "
+                            + e.getMessage());
+        }       
+    }
+}