public double[] fitfunc(double[] fitparams) { Bindings b = engine.createBindings(); for (int i = 0; i < 10; i++) b.put("P" + (i + 1), fitparams[i]); /*String script1="P1="+fitparams[0]+"; "+ "P2="+fitparams[1]+"; "+ "P3="+fitparams[2]+"; "+ "P4="+fitparams[3]+"; "+ "P5="+fitparams[4]+"; "+ "P6="+fitparams[5]+"; "+ "P7="+fitparams[6]+"; "+ "P8="+fitparams[7]+"; "+ "P9="+fitparams[8]+"; "+ "P10="+fitparams[9]+"; "+ exdef+"; x="; String script2="; retval="+function+";";*/ try { double[] temp = new double[tempx.length]; for (int i = 0; i < tempx.length; i++) { // temp[i]=((Double)engine.eval(script1+(double)tempx[i]+script2)).doubleValue(); b.put("x", tempx[i]); b.put("y", tempdata[i]); temp[i] = (Double) cs.eval(b); } return temp; } catch (Exception e) { IJ.log(e.getMessage()); return null; } }
/** * Notify any DialogListeners of changes having occurred If a listener returns false, do not call * further listeners and disable the OK button and preview Checkbox (if it exists). For * PlugInFilters, this ensures that the PlugInFilterRunner, which listens as the last one, is not * called if the PlugInFilter has detected invalid parameters. Thus, unnecessary calling the * run(ip) method of the PlugInFilter for preview is avoided in that case. */ private void notifyListeners(AWTEvent e) { if (dialogListeners == null) return; boolean everythingOk = true; for (int i = 0; everythingOk && i < dialogListeners.size(); i++) try { resetCounters(); if (!((DialogListener) dialogListeners.elementAt(i)).dialogItemChanged(this, e)) everythingOk = false; } // disable further listeners if false (invalid parameters) returned catch (Exception err) { // for exceptions, don't cover the input by a window but IJ.beep(); // show them at in the "Log" IJ.log( "ERROR: " + err + "\nin DialogListener of " + dialogListeners.elementAt(i) + "\nat " + (err.getStackTrace()[0]) + "\nfrom " + (err.getStackTrace()[1])); // requires Java 1.4 } boolean workaroundOSXbug = IJ.isMacOSX() && okay != null && !okay.isEnabled() && everythingOk; if (previewCheckbox != null) previewCheckbox.setEnabled(everythingOk); if (okay != null) okay.setEnabled(everythingOk); if (workaroundOSXbug) repaint(); // OSX 10.4 bug delays update of enabled until the next input }
public Zipper<Map<Integer, MZipper<RoiContainer>>> exec( Zipper<Map<Integer, MZipper<RoiContainer>>> z, int frame) { JFileChooser fc = new JFileChooser(); int returnVal = fc.showOpenDialog(WindowManager.getCurrentWindow().getCanvas()); Map<Integer, MZipper<RoiContainer>> newRois; if (returnVal == JFileChooser.APPROVE_OPTION) { try { FileInputStream f = new FileInputStream(fc.getSelectedFile().getCanonicalPath()); MroiLisp parser = new MroiLisp(f); parser.ReInit(f); newRois = parser.roiFile(); // z.rights.clear(); // z.rights.add(newRois); // z = z.right(); // return z; return z.insertAndStep(newRois); } catch (IOException e) { IJ.error("Couldn't open from " + fc.getSelectedFile().getName() + ": " + e.getMessage()); } catch (mroi.ParseException e) { IJ.error("Failed in parsing: " + e.getMessage()); } catch (Exception e) { IJ.error("Malformed input file: " + e.getMessage()); } } return z; }
boolean init_functions() { GenericDialog gd = new GenericDialog("Fitting Options"); gd.addStringField("Extra Definitions", exdef, 50); gd.addCheckbox("Weight Using Plot Errors", false); gd.addStringField("Weighting Equation (y is for data)", weightfunction, 50); gd.addStringField("Fit_Equation", function, 50); gd.showDialog(); if (gd.wasCanceled()) { return false; } exdef = gd.getNextString(); boolean errweights = gd.getNextBoolean(); weightfunction = gd.getNextString(); function = gd.getNextString(); // first initialize the weights weights = new float[tempdata.length]; if (errweights || weightfunction.equals("") || weightfunction == null || weightfunction == "1.0") { if (errweights) { for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f / (errs[i] * errs[i]); } else { for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f; } } else { for (int i = 0; i < tempdata.length; i++) { String script = "y =" + tempdata[i] + "; " + "x =" + tempx[i] + "; " + "retval=" + weightfunction + ";"; Double temp = new Double(0.0); try { temp = (Double) engine.eval(script); } catch (Exception e) { IJ.log(e.getMessage()); } if (!(temp.isInfinite() || temp.isNaN())) { weights[i] = temp.floatValue(); } } } // now compile the function script try { String script1 = exdef + "; retval=" + function + ";"; cs = ce.compile(script1); } catch (Exception e) { IJ.log(e.toString()); return false; } return true; }
/** Reads the pixel data from an image described by a FileInfo object. */ Object readPixels(FileInfo fi) { Object pixels = null; try { InputStream is = createInputStream(fi); if (is == null) return null; ImageReader reader = new ImageReader(fi); pixels = reader.readPixels(is); minValue = reader.min; maxValue = reader.max; is.close(); } catch (Exception e) { if (!Macro.MACRO_CANCELED.equals(e.getMessage())) IJ.handleException(e); } return pixels; }
String open(String path) { if (path == null) return null; try { StringBuffer sb = new StringBuffer(5000); BufferedReader r = new BufferedReader(new FileReader(path)); while (true) { String s = r.readLine(); if (s == null) break; else sb.append(s + "\n"); } r.close(); return new String(sb); } catch (Exception e) { IJ.error(e.getMessage()); return null; } }
public void run(String arg) { boolean display = false; File test = new File(arg); display = !test.exists(); OpenDialog od = new OpenDialog("Open mkt file...", arg); if (od != null) { String file = od.getFileName(); if (file == null) return; String directory = od.getDirectory(); directory = directory.replace('\\', '/'); // Windows safe if (!directory.endsWith("/")) directory += "/"; arg = directory + file; } try { FileProjectionSource fileSource = new MKTProjectionSource(); fileSource.initStream(arg); ImagePlusDataSink sink = new ImagePlusDataSink(); Grid2D imp = fileSource.getNextProjection(); int i = 0; while (imp != null) { sink.process(imp, i); i++; imp = fileSource.getNextProjection(); } sink.close(); setStack(ImageUtil.wrapGrid3D(sink.getResult(), "").getStack()); setTitle(new File(arg).getName()); fileSource.close(); if (display) show(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } }