public void run(String arg) { if (IJ.versionLessThan("1.49d")) return; if (!showDialog()) return; SaveDialog sd = new SaveDialog("Save as Bricks...", "", ""); basename = sd.getFileName(); directory = sd.getDirectory(); if (basename == null || directory == null) return; build_bricks(); }
public boolean checkBeads() { rmanager = RoiManager.getInstance(); if (IJ.versionLessThan("1.26i")) return false; else if (rmanager == null) { IJ.error("Add bead ROIs to the RoiManager first (select region then press [t])."); return false; } nrois = rmanager.getCount(); if (nrois == 0) { IJ.error("Add bead ROIs to the RoiManager first (select region then press [t])."); return false; } rois = rmanager.getRoisAsArray(); return true; }
public int setup(String arg, ImagePlus imp) { // IJ.register(Average_Oversampled.class); if (IJ.versionLessThan("1.32c")) return DONE; if (this.pre) { // before finding means imp.unlock(); this.imp = imp; this.nslices = imp.getNSlices(); this.width = imp.getWidth(); this.height = imp.getHeight(); this.slicecols = new float[nslices][width]; this.pre = false; return (DOES_ALL + DOES_STACKS + FINAL_PROCESSING); } else { // find SD after finding means of columns float sum; // sum of pixel values column float avg; // average pixel value of a column double devsum; // sum of deviations double devavg; // standard deviation double[] columns = new double[width]; // x-axis of plot double[] sdevs = new double[width]; // y-axis of plot for (int i = 0; i < width; i += 1) { sum = 0; // reset with each column avg = 0; // reset with each column devsum = 0; // reset with each column devavg = 0; // reset with each column columns[i] = i; // building x-axis for (int s = 0; s < nslices; s += 1) { // sum of column means sum = sum + slicecols[s][i]; } avg = sum / nslices; // mean of one column across all slices for (int s = 0; s < nslices; s += 1) { // standard deviation devsum = devsum + Math.pow((slicecols[s][i] - avg), 2); // square diff } devavg = Math.sqrt(devsum / nslices); sdevs[i] = devavg; // building y-axis } Plot plot = new Plot("Average SD by Column", "Columns", "Standard Deviation", columns, sdevs); plot.show(); // calculate CTN double ctn; double sdevssum = 0; for (double sd : sdevs) { sdevssum = sdevssum + sd; } ctn = sdevssum / width; // display CTN on results table ResultsTable rt = ResultsTable.getResultsTable(); // rt.incrementCounter(); rt.addValue("Column Temporal Noise", ctn); rt.show("Results"); this.pre = false; return DONE; } }