public void run(ImageProcessor ip) { if (enlarge && gd.wasOKed()) synchronized (this) { if (!isEnlarged) { enlargeCanvas(); isEnlarged = true; } } if (isEnlarged) { // enlarging may have made the ImageProcessor invalid, also for the parallel // threads int slice = pfr.getSliceNumber(); if (imp.getStackSize() == 1) ip = imp.getProcessor(); else ip = imp.getStack().getProcessor(slice); } ip.setInterpolationMethod(interpolationMethod); if (fillWithBackground) { Color bgc = Toolbar.getBackgroundColor(); if (bitDepth == 8) ip.setBackgroundValue(ip.getBestIndex(bgc)); else if (bitDepth == 24) ip.setBackgroundValue(bgc.getRGB()); } else ip.setBackgroundValue(0); ip.rotate(angle); if (!gd.wasOKed()) drawGridLines(gridLines); if (isEnlarged && imp.getStackSize() == 1) { imp.changes = true; imp.updateAndDraw(); Undo.setup(Undo.COMPOUND_FILTER_DONE, imp); } }
/** * Builds dialog to query users for projection parameters. * * @param start starting slice to display * @param stop last slice */ protected GenericDialog buildControlDialog(int start, int stop) { GenericDialog gd = new GenericDialog("ZProjection", IJ.getInstance()); gd.addNumericField("Start slice:", startSlice, 0 /*digits*/); gd.addNumericField("Stop slice:", stopSlice, 0 /*digits*/); gd.addChoice("Projection type", METHODS, METHODS[method]); if (isHyperstack && imp.getNFrames() > 1 && imp.getNSlices() > 1) gd.addCheckbox("All time frames", allTimeFrames); return gd; }
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) { this.pfr = pfr; String macroOptions = Macro.getOptions(); if (macroOptions != null) { if (macroOptions.indexOf(" interpolate") != -1) macroOptions.replaceAll(" interpolate", " interpolation=Bilinear"); else if (macroOptions.indexOf(" interpolation=") == -1) macroOptions = macroOptions + " interpolation=None"; Macro.setOptions(macroOptions); } gd = new GenericDialog("Rotate", IJ.getInstance()); gd.addNumericField("Angle (degrees):", angle, (int) angle == angle ? 1 : 2); gd.addNumericField("Grid Lines:", gridLines, 0); gd.addChoice("Interpolation:", methods, methods[interpolationMethod]); if (bitDepth == 8 || bitDepth == 24) gd.addCheckbox("Fill with Background Color", fillWithBackground); if (canEnlarge) gd.addCheckbox("Enlarge Image to Fit Result", enlarge); else enlarge = false; gd.addPreviewCheckbox(pfr); gd.addDialogListener(this); gd.showDialog(); drawGridLines(0); if (gd.wasCanceled()) { return DONE; } if (!enlarge) flags |= KEEP_PREVIEW; // standard filter without enlarge else if (imp.getStackSize() == 1) flags |= NO_CHANGES; // undoable as a "compound filter" return IJ.setupDialog(imp, flags); }
void showDialog() { int width = imp.getWidth(); int height = imp.getHeight(); Calibration cal = imp.getCalibration(); int places; if (cal.scaled()) { pixelWidth = cal.pixelWidth; pixelHeight = cal.pixelHeight; units = cal.getUnits(); places = 2; } else { pixelWidth = 1.0; pixelHeight = 1.0; units = "pixels"; places = 0; } if (areaPerPoint == 0.0) areaPerPoint = (width * cal.pixelWidth * height * cal.pixelHeight) / 81.0; // default to 9x9 grid ImageWindow win = imp.getWindow(); GenericDialog gd = new GenericDialog("Grid..."); gd.addChoice("Grid Type:", types, type); gd.addNumericField("Area per Point:", areaPerPoint, places, 6, units + "^2"); gd.addChoice("Color:", colors, color); gd.addCheckbox("Random Offset", randomOffset); gd.addDialogListener(this); gd.showDialog(); if (gd.wasCanceled()) showGrid(null); }
public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) { iterations = (int) gd.getNextNumber(); count = (int) gd.getNextNumber(); boolean bb = Prefs.blackBackground; Prefs.blackBackground = gd.getNextBoolean(); if (Prefs.blackBackground != bb) ThresholdAdjuster.update(); Prefs.padEdges = gd.getNextBoolean(); EDM.setOutputType(gd.getNextChoiceIndex()); boolean isInvalid = gd.invalidNumber(); if (iterations < 1) { iterations = 1; isInvalid = true; } if (iterations > MAX_ITERATIONS) { iterations = MAX_ITERATIONS; isInvalid = true; } if (count < 1) { count = 1; isInvalid = true; } if (count > 8) { count = 8; isInvalid = true; } if (isInvalid) return false; if (imp != null) { operation = gd.getNextChoice(); arg = operation.toLowerCase(); } return true; }
void interpolate() { Roi roi = imp.getRoi(); if (roi == null) { noRoi("Interpolate"); return; } if (roi.getType() == Roi.POINT) return; if (IJ.isMacro() && Macro.getOptions() == null) Macro.setOptions("interval=1"); GenericDialog gd = new GenericDialog("Interpolate"); gd.addNumericField("Interval:", 1.0, 1, 4, "pixel"); gd.addCheckbox("Smooth", IJ.isMacro() ? false : smooth); gd.showDialog(); if (gd.wasCanceled()) return; double interval = gd.getNextNumber(); smooth = gd.getNextBoolean(); Undo.setup(Undo.ROI, imp); FloatPolygon poly = roi.getInterpolatedPolygon(interval, smooth); int t = roi.getType(); int type = roi.isLine() ? Roi.FREELINE : Roi.FREEROI; if (t == Roi.POLYGON && interval > 1.0) type = Roi.POLYGON; if ((t == Roi.RECTANGLE || t == Roi.OVAL || t == Roi.FREEROI) && interval >= 5.0) type = Roi.POLYGON; if ((t == Roi.LINE || t == Roi.FREELINE) && interval >= 5.0) type = Roi.POLYLINE; if (t == Roi.POLYLINE && interval >= 1.0) type = Roi.POLYLINE; ImageCanvas ic = imp.getCanvas(); if (poly.npoints <= 150 && ic != null && ic.getMagnification() >= 12.0) type = roi.isLine() ? Roi.POLYLINE : Roi.POLYGON; Roi p = new PolygonRoi(poly, type); if (roi.getStroke() != null) p.setStrokeWidth(roi.getStrokeWidth()); p.setStrokeColor(roi.getStrokeColor()); p.setName(roi.getName()); transferProperties(roi, p); imp.setRoi(p); }
public void run(String arg) { int[] wList = WindowManager.getIDList(); if (wList == null) { IJ.error("No images are open."); return; } double thalf = 0.5; boolean keep; GenericDialog gd = new GenericDialog("Bleach correction"); gd.addNumericField("t½:", thalf, 1); gd.addCheckbox("Keep source stack:", true); gd.showDialog(); if (gd.wasCanceled()) return; long start = System.currentTimeMillis(); thalf = gd.getNextNumber(); keep = gd.getNextBoolean(); if (keep) IJ.run("Duplicate...", "title='Bleach corrected' duplicate"); ImagePlus imp1 = WindowManager.getCurrentImage(); int d1 = imp1.getStackSize(); double v1, v2; int width = imp1.getWidth(); int height = imp1.getHeight(); ImageProcessor ip1, ip2, ip3; int slices = imp1.getStackSize(); ImageStack stack1 = imp1.getStack(); ImageStack stack2 = imp1.getStack(); int currentSlice = imp1.getCurrentSlice(); for (int n = 1; n <= slices; n++) { ip1 = stack1.getProcessor(n); ip3 = stack1.getProcessor(1); ip2 = stack2.getProcessor(n); for (int x = 0; x < width; x++) { for (int y = 0; y < height; y++) { v1 = ip1.getPixelValue(x, y); v2 = ip3.getPixelValue(x, y); // =B8/(EXP(-C$7*A8)) v1 = (v1 / Math.exp(-n * thalf)); ip2.putPixelValue(x, y, v1); } } IJ.showProgress((double) n / slices); IJ.showStatus(n + "/" + slices); } // stack2.show(); imp1.updateAndDraw(); }
public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) { checkc2 = gd.getNextBoolean(); double[] params = new double[10]; int[] fixes = new int[10]; for (int i = 0; i < params.length; i++) { params[i] = gd.getNextNumber(); if (gd.getNextBoolean()) { fixes[i] = 1; } else { fixes[i] = 0; } } gd.getNextBoolean(); gd.getNextNumber(); gd.getNextNumber(); NLLSfit_v2 fitclass = new NLLSfit_v2(this, 0); double[] stats = new double[2]; float[] fit = fitclass.fitdata(params, fixes, null, tempdata, null, stats, true); pw.updateSeries(fit, series, false); c2 = (float) stats[1]; return true; }
public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) { angle = gd.getNextNumber(); // only check for invalid input to "angle", don't care about gridLines if (gd.invalidNumber()) { if (gd.wasOKed()) IJ.error("Angle is invalid."); return false; } gridLines = (int) gd.getNextNumber(); interpolationMethod = gd.getNextChoiceIndex(); if (bitDepth == 8 || bitDepth == 24) fillWithBackground = gd.getNextBoolean(); if (canEnlarge) enlarge = gd.getNextBoolean(); return true; }
void addSelection() { ImagePlus imp = IJ.getImage(); String macroOptions = Macro.getOptions(); if (macroOptions != null && IJ.macroRunning() && macroOptions.indexOf("remove") != -1) { imp.setOverlay(null); return; } Roi roi = imp.getRoi(); if (roi == null && imp.getOverlay() != null) { GenericDialog gd = new GenericDialog("No Selection"); gd.addMessage("\"Overlay>Add\" requires a selection."); gd.setInsets(15, 40, 0); gd.addCheckbox("Remove existing overlay", false); gd.showDialog(); if (gd.wasCanceled()) return; if (gd.getNextBoolean()) imp.setOverlay(null); return; } if (roi == null) { IJ.error("This command requires a selection."); return; } roi = (Roi) roi.clone(); if (roi.getStrokeColor() == null) roi.setStrokeColor(Toolbar.getForegroundColor()); int width = Line.getWidth(); Rectangle bounds = roi.getBounds(); boolean tooWide = width > Math.max(bounds.width, bounds.height) / 3.0; if (roi.getStroke() == null && width > 1 && !tooWide) roi.setStrokeWidth(Line.getWidth()); Overlay overlay = imp.getOverlay(); if (overlay != null && overlay.size() > 0 && !roi.isDrawingTool()) { Roi roi2 = overlay.get(overlay.size() - 1); if (roi.getStroke() == null) roi.setStrokeWidth(roi2.getStrokeWidth()); if (roi.getFillColor() == null) roi.setFillColor(roi2.getFillColor()); } boolean points = roi instanceof PointRoi && ((PolygonRoi) roi).getNCoordinates() > 1; if (points) roi.setStrokeColor(Color.red); if (!IJ.altKeyDown() && !(roi instanceof Arrow)) { RoiProperties rp = new RoiProperties("Add to Overlay", roi); if (!rp.showDialog()) return; } String name = roi.getName(); boolean newOverlay = name != null && name.equals("new-overlay"); if (overlay == null || newOverlay) overlay = new Overlay(); overlay.add(roi); imp.setOverlay(overlay); overlay2 = overlay; if (points || (roi instanceof ImageRoi) || (roi instanceof Arrow)) imp.killRoi(); Undo.setup(Undo.OVERLAY_ADDITION, imp); }
public boolean showDialog(ImageStack stack) { hyperstack = imp.isHyperStack(); boolean showCheckbox = false; if (hyperstack && imp.getNSlices() > 1 && imp.getNFrames() > 1) showCheckbox = true; else if (hyperstack && imp.getNSlices() > 1) reduceSlices = true; int n = stack.getSize(); GenericDialog gd = new GenericDialog("Reduce Size"); gd.addNumericField("Reduction Factor:", factor, 0); if (showCheckbox) gd.addCheckbox("Reduce in Z-Dimension", false); gd.showDialog(); if (gd.wasCanceled()) return false; factor = (int) gd.getNextNumber(); if (showCheckbox) reduceSlices = gd.getNextBoolean(); return true; }
void checkForCalibrationConflict(ImagePlus imp, Calibration cal) { Calibration gcal = imp.getGlobalCalibration(); if (gcal == null || !showConflictMessage || IJ.isMacro()) return; if (cal.pixelWidth == gcal.pixelWidth && cal.getUnit().equals(gcal.getUnit())) return; GenericDialog gd = new GenericDialog(imp.getTitle()); gd.addMessage("The calibration of this image conflicts\nwith the current global calibration."); gd.addCheckbox("Disable_Global Calibration", true); gd.addCheckbox("Disable_these Messages", false); gd.showDialog(); if (gd.wasCanceled()) return; boolean disable = gd.getNextBoolean(); if (disable) { imp.setGlobalCalibration(null); imp.setCalibration(cal); WindowManager.repaintImageWindows(); } boolean dontShow = gd.getNextBoolean(); if (dontShow) showConflictMessage = false; }
public void run(String arg) { GenericDialog gd = new GenericDialog("Options"); gd.addCheckbox("Add_Titles", true); gd.addCheckbox("Close Original", false); gd.showDialog(); if (gd.wasCanceled()) { return; } boolean addtitles = gd.getNextBoolean(); boolean closeorig = gd.getNextBoolean(); // first get the table window Frame[] niframes = WindowManager.getNonImageWindows(); boolean first = true; TextWindow tw2 = null; int ncols = 0; String[] col_labels = null; for (int i = 0; i < niframes.length; i++) { if (niframes[i] instanceof TextWindow && !niframes[i].getTitle().equals("Log")) { TextWindow tw = (TextWindow) niframes[i]; TextPanel tp = tw.getTextPanel(); List<List<String>> listtable = table_tools.table2listtable(tp); if (listtable.size() == 0) { col_labels = table_tools.getcollabels(tp); ncols = col_labels.length; ArrayList<String> temp = new ArrayList<String>(); for (int j = 0; j < ncols; j++) temp.add(""); listtable.add(temp); } if (first) { col_labels = table_tools.getcollabels(tp); ncols = col_labels.length; String headings = tp.getColumnHeadings(); if (addtitles) { String[] titles = repeated(tw.getTitle(), listtable.size()); table_tools.add_listtable_column(listtable, titles, 0); headings = "name\t" + headings; } tw2 = new TextWindow( "Combined Table", headings, table_tools.print_listtable(listtable), 400, 200); first = false; } else { if (addtitles) { String[] titles = repeated(tw.getTitle(), listtable.size()); table_tools.add_listtable_column(listtable, titles, 0); } tw2.append(table_tools.print_listtable(listtable)); } if (closeorig) tw.close(); } } }
public void run(String arg) { ImagePlus imp = WindowManager.getCurrentImage(); if (imp == null) { IJ.noImage(); return; } if (imp.getStackSize() > 1) { IJ.error("This command requires a montage"); return; } GenericDialog gd = new GenericDialog("Stack Maker"); gd.addNumericField("Images_per_row: ", w, 0); gd.addNumericField("Images_per_column: ", h, 0); gd.addNumericField("Border width: ", b, 0); gd.showDialog(); if (gd.wasCanceled()) return; w = (int) gd.getNextNumber(); h = (int) gd.getNextNumber(); b = (int) gd.getNextNumber(); ImageStack stack = makeStack(imp.getProcessor(), w, h, b); new ImagePlus("Stack", stack).show(); }
int showDialog(String[] versions) { GenericDialog gd = new GenericDialog("ImageJ Updater"); gd.addChoice("Upgrade To:", versions, versions[0]); String msg = "You are currently running v" + version() + ".\n" + " \n" + "If you click \"OK\", ImageJ will quit\n" + "and you will be running the upgraded\n" + "version after you restart ImageJ.\n"; gd.addMessage(msg); gd.showDialog(); if (gd.wasCanceled()) return -1; else return gd.getNextChoiceIndex(); }
// Conversion Options void conversions() { double[] weights = ColorProcessor.getWeightingFactors(); boolean weighted = !(weights[0] == 1d / 3d && weights[1] == 1d / 3d && weights[2] == 1d / 3d); // boolean weighted = !(Math.abs(weights[0]-1d/3d)<0.0001 && Math.abs(weights[1]-1d/3d)<0.0001 // && Math.abs(weights[2]-1d/3d)<0.0001); GenericDialog gd = new GenericDialog("Conversion Options"); gd.addCheckbox("Scale when converting", ImageConverter.getDoScaling()); String prompt = "Weighted RGB conversions"; if (weighted) prompt += " (" + IJ.d2s(weights[0]) + "," + IJ.d2s(weights[1]) + "," + IJ.d2s(weights[2]) + ")"; gd.addCheckbox(prompt, weighted); gd.showDialog(); if (gd.wasCanceled()) return; ImageConverter.setDoScaling(gd.getNextBoolean()); Prefs.weightedColor = gd.getNextBoolean(); if (!Prefs.weightedColor) ColorProcessor.setWeightingFactors(1d / 3d, 1d / 3d, 1d / 3d); else if (Prefs.weightedColor && !weighted) ColorProcessor.setWeightingFactors(0.299, 0.587, 0.114); return; }
public double[][] get_constraints(double[] params) { // here we populate the constraints GenericDialog gd = new GenericDialog("Constraints"); for (int i = 0; i < 10; i++) { if (constraints == null) { gd.addNumericField("P" + (i + 1) + "_upper", params[i], 5, 10, null); gd.addNumericField("P" + (i + 1) + "_lower", params[i], 5, 10, null); } else { gd.addNumericField("P" + (i + 1) + "_upper", constraints[1][i], 5, 10, null); gd.addNumericField("P" + (i + 1) + "_lower", constraints[0][i], 5, 10, null); } } gd.showDialog(); if (gd.wasCanceled()) { return null; } double[][] constraints = new double[2][10]; for (int i = 0; i < 10; i++) { constraints[1][i] = gd.getNextNumber(); constraints[0][i] = gd.getNextNumber(); } return constraints; }
public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) { int width = imp.getWidth(); int height = imp.getHeight(); type = gd.getNextChoice(); areaPerPoint = gd.getNextNumber(); color = gd.getNextChoice(); randomOffset = gd.getNextBoolean(); double minArea = (width * height) / 50000.0; if (type.equals(types[1]) && minArea < 144.0) minArea = 144.0; else if (minArea < 16) minArea = 16.0; if (areaPerPoint / (pixelWidth * pixelHeight) < minArea) { String err = "\"Area per Point\" too small"; if (gd.wasOKed()) IJ.error("Grid", err); else IJ.showStatus(err); return true; } double tileSize = Math.sqrt(areaPerPoint); tileWidth = tileSize / pixelWidth; tileHeight = tileSize / pixelHeight; if (randomOffset) { xstart = (int) (random.nextDouble() * tileWidth); ystart = (int) (random.nextDouble() * tileHeight); } else { xstart = (int) (tileWidth / 2.0 + 0.5); ystart = (int) (tileHeight / 2.0 + 0.5); } linesV = (int) ((width - xstart) / tileWidth) + 1; linesH = (int) ((height - ystart) / tileHeight) + 1; if (gd.invalidNumber()) return true; if (type.equals(types[0])) drawLines(); else if (type.equals(types[1])) drawCrosses(); else if (type.equals(types[2])) drawPoints(); else showGrid(null); return true; }
private void makeBand(ImagePlus imp) { Roi roi = imp.getRoi(); if (roi == null) { noRoi("Make Band"); return; } if (!roi.isArea()) { IJ.error("Make Band", "Area selection required"); return; } Calibration cal = imp.getCalibration(); double pixels = bandSize; double size = pixels * cal.pixelWidth; int decimalPlaces = 0; if ((int) size != size) decimalPlaces = 2; GenericDialog gd = new GenericDialog("Make Band"); gd.addNumericField("Band Size:", size, decimalPlaces, 4, cal.getUnits()); gd.showDialog(); if (gd.wasCanceled()) return; size = gd.getNextNumber(); if (Double.isNaN(size)) { IJ.error("Make Band", "invalid number"); return; } int n = (int) Math.round(size / cal.pixelWidth); if (n > 255) { IJ.error("Make Band", "Cannot make bands wider that 255 pixels"); return; } int width = imp.getWidth(); int height = imp.getHeight(); Rectangle r = roi.getBounds(); ImageProcessor ip = roi.getMask(); if (ip == null) { ip = new ByteProcessor(r.width, r.height); ip.invert(); } ImageProcessor mask = new ByteProcessor(width, height); mask.insert(ip, r.x, r.y); ImagePlus edm = new ImagePlus("mask", mask); boolean saveBlackBackground = Prefs.blackBackground; Prefs.blackBackground = false; IJ.run(edm, "Distance Map", ""); Prefs.blackBackground = saveBlackBackground; ip = edm.getProcessor(); ip.setThreshold(0, n, ImageProcessor.NO_LUT_UPDATE); int xx = -1, yy = -1; for (int x = r.x; x < r.x + r.width; x++) { for (int y = r.y; y < r.y + r.height; y++) { if (ip.getPixel(x, y) < n) { xx = x; yy = y; break; } } if (xx >= 0 || yy >= 0) break; } int count = IJ.doWand(edm, xx, yy, 0, null); if (count <= 0) { IJ.error("Make Band", "Unable to make band"); return; } ShapeRoi roi2 = new ShapeRoi(edm.getRoi()); if (!(roi instanceof ShapeRoi)) roi = new ShapeRoi(roi); ShapeRoi roi1 = (ShapeRoi) roi; roi2 = roi2.not(roi1); imp.setRoi(roi2); bandSize = n; }
void addImage() { ImagePlus imp = IJ.getImage(); int[] wList = WindowManager.getIDList(); if (wList == null || wList.length < 2) { IJ.error("Add Image...", "The command requires at least two open images."); return; } String[] titles = new String[wList.length]; for (int i = 0; i < wList.length; i++) { ImagePlus imp2 = WindowManager.getImage(wList[i]); titles[i] = imp2 != null ? imp2.getTitle() : ""; } int x = 0, y = 0; Roi roi = imp.getRoi(); if (roi != null && roi.isArea()) { Rectangle r = roi.getBounds(); x = r.x; y = r.y; } int index = 0; if (wList.length == 2) { ImagePlus i1 = WindowManager.getImage(wList[0]); ImagePlus i2 = WindowManager.getImage(wList[1]); if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) index = 1; } else if (imp.getID() == wList[0]) index = 1; GenericDialog gd = new GenericDialog("Add Image..."); gd.addChoice("Image to add:", titles, titles[index]); gd.addNumericField("X location:", x, 0); gd.addNumericField("Y location:", y, 0); gd.addNumericField("Opacity (0-100%):", 100, 0); gd.addCheckbox("Create image selection", createImageRoi); gd.showDialog(); if (gd.wasCanceled()) return; index = gd.getNextChoiceIndex(); x = (int) gd.getNextNumber(); y = (int) gd.getNextNumber(); double opacity = gd.getNextNumber() / 100.0; createImageRoi = gd.getNextBoolean(); ImagePlus overlay = WindowManager.getImage(wList[index]); if (wList.length == 2) { ImagePlus i1 = WindowManager.getImage(wList[0]); ImagePlus i2 = WindowManager.getImage(wList[1]); if (i2.getWidth() < i1.getWidth() && i2.getHeight() < i1.getHeight()) { imp = i1; overlay = i2; } } if (overlay == imp) { IJ.error( "Add Image...", "Image to be added cannot be the same as\n\"" + imp.getTitle() + "\"."); return; } if (overlay.getWidth() > imp.getWidth() && overlay.getHeight() > imp.getHeight()) { IJ.error( "Add Image...", "Image to be added cannnot be larger than\n\"" + imp.getTitle() + "\"."); return; } if (createImageRoi && x == 0 && y == 0) { x = imp.getWidth() / 2 - overlay.getWidth() / 2; y = imp.getHeight() / 2 - overlay.getHeight() / 2; } roi = new ImageRoi(x, y, overlay.getProcessor()); roi.setName(overlay.getShortTitle()); if (opacity != 1.0) ((ImageRoi) roi).setOpacity(opacity); if (createImageRoi) imp.setRoi(roi); else { Overlay overlayList = imp.getOverlay(); if (overlayList == null) overlayList = new Overlay(); overlayList.add(roi); imp.setOverlay(overlayList); overlay2 = overlayList; Undo.setup(Undo.OVERLAY_ADDITION, imp); } }
public void run(String arg) { GenericDialog gd = new GenericDialog("Options"); double sfreq = 20000.0; gd.addNumericField("Sampling Frequency?", sfreq, 1, 10, null); String[] psfchoice = {"3D Gaussian", "Gaus-Lorentz^2", "2D Gaussian"}; gd.addChoice("PSF Type?", psfchoice, psfchoice[0]); String[] filetypechoice = { "Confocor 3 raw", "Short binary trajectory", "PlotWindow trajectory", "Ascii Text File" }; gd.addChoice("File Type?", filetypechoice, filetypechoice[0]); boolean ch2green = true; gd.addCheckbox("Ch2 is green?", ch2green); gd.showDialog(); if (gd.wasCanceled()) { return; } sfreq = gd.getNextNumber(); int psfflag = gd.getNextChoiceIndex(); int fileflag = gd.getNextChoiceIndex(); ch2green = gd.getNextBoolean(); int nfiles = 0; Object[] histograms = null; int xmax = 0; int ymax = 0; String[] names = null; if (fileflag < 2) { jdataio ioclass = new jdataio(); File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance()); if (filearray.length == 0) { return; } String dir = filearray[0].getAbsolutePath(); int sepindex = dir.lastIndexOf(File.separator); String newdir = dir.substring(0, sepindex + 1); OpenDialog.setDefaultDirectory(newdir); nfiles = filearray.length / 2; if (nfiles > 25) { nfiles = 25; } histograms = new Object[nfiles]; names = organize_c3_files(filearray); for (int i = 0; i < nfiles; i++) { try { int length1 = (int) (((double) filearray[2 * i].length() - 128.0) / 4.0); int length2 = (int) (((double) filearray[2 * i + 1].length() - 128.0) / 4.0); int length3 = (int) (((double) filearray[2 * i].length()) / 2.0); int length4 = (int) (((double) filearray[2 * i + 1].length()) / 2.0); InputStream instream = new BufferedInputStream(new FileInputStream(filearray[2 * i])); InputStream instream2 = new BufferedInputStream(new FileInputStream(filearray[2 * i + 1])); if (fileflag == 0) { int[] pmdata = new int[length1]; int[] pmdata2 = new int[length2]; if (!ioclass.skipstreambytes(instream, 128)) { showioerror(); instream.close(); return; } if (!ioclass.skipstreambytes(instream2, 128)) { showioerror(); instream2.close(); return; } if (!ioclass.readintelintfile(instream, length1, pmdata)) { showioerror(); instream.close(); return; } if (!ioclass.readintelintfile(instream2, length2, pmdata2)) { showioerror(); instream2.close(); return; } if (ch2green) { histograms[i] = (new pmodeconvert()).pm2pch(pmdata2, pmdata, sfreq, 20000000); } else { histograms[i] = (new pmodeconvert()).pm2pch(pmdata, pmdata2, sfreq, 20000000); } } else { float[] tmdata = new float[length3]; float[] tmdata2 = new float[length4]; if (!ioclass.readintelshortfile(instream, length3, tmdata)) { showioerror(); instream.close(); return; } if (!ioclass.readintelshortfile(instream2, length4, tmdata2)) { showioerror(); instream2.close(); return; } if (ch2green) { histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata2, tmdata); } else { histograms[i] = (new pmodeconvert()).create_2Dhistogram(tmdata, tmdata2); } } if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } instream.close(); instream2.close(); } catch (IOException e) { showioerror(); return; } } } else { if (fileflag == 2) { ImageWindow iw = WindowManager.getCurrentWindow(); float[][] trajectories = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues"); float[][] tempxvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues"); sfreq = 1.0 / ((double) tempxvals[0][1]); nfiles = trajectories.length / 2; if (nfiles > 25) { nfiles = 25; } names = new String[nfiles + 1]; names[nfiles] = "avg"; histograms = new Object[nfiles]; for (int i = 0; i < nfiles; i++) { names[i] = "trajectory " + (i + 1); if (ch2green) { histograms[i] = (new pmodeconvert()) .create_2Dhistogram(trajectories[2 * i + 1], trajectories[2 * i]); } else { histograms[i] = (new pmodeconvert()) .create_2Dhistogram(trajectories[2 * i], trajectories[2 * i + 1]); } if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } } } else { // here we read tab delimited lines from files jdataio ioclass = new jdataio(); File[] filearray = ioclass.openfiles(OpenDialog.getDefaultDirectory(), IJ.getInstance()); if (filearray.length == 0) { return; } String dir = filearray[0].getAbsolutePath(); int sepindex = dir.lastIndexOf(File.separator); String newdir = dir.substring(0, sepindex + 1); OpenDialog.setDefaultDirectory(newdir); nfiles = filearray.length; if (nfiles > 25) { nfiles = 25; } histograms = new Object[nfiles]; names = new String[nfiles + 1]; names[nfiles] = "avg"; for (int i = 0; i < nfiles; i++) { try { names[i] = filearray[i].getName(); BufferedReader d = new BufferedReader(new FileReader(filearray[i])); String[] lines = new String[256]; int counter = 0; do { lines[counter] = d.readLine(); counter++; } while ((lines[counter - 1] != null && lines[counter - 1] != "") && counter < 256); int numcolumns = 0; for (int j = 0; j < counter - 1; j++) { int temp = getncolumns(lines[j]); if (temp > numcolumns) { numcolumns = temp; } } float[][] temphist2 = null; if (ch2green) { temphist2 = new float[numcolumns][counter - 1]; } else { temphist2 = new float[counter - 1][numcolumns]; } for (int k = 0; k < counter - 1; k++) { float[] temp = tab_delim2float(lines[k]); for (int j = 0; j < numcolumns; j++) { if (ch2green) { temphist2[j][k] = temp[j]; } else { temphist2[k][j] = temp[j]; } } } histograms[i] = temphist2; d.close(); } catch (IOException e) { showioerror(); return; } } for (int i = 0; i < nfiles; i++) { if (((float[][]) histograms[i]).length > xmax) { xmax = ((float[][]) histograms[i]).length; } if (((float[][]) histograms[i])[0].length > ymax) { ymax = ((float[][]) histograms[i])[0].length; } } } } // note that here x is green and y is red float[][][] pch = new float[nfiles][xmax][ymax]; for (int i = 0; i < nfiles; i++) { for (int j = 0; j < ((float[][]) histograms[i]).length; j++) { for (int k = 0; k < ((float[][]) histograms[i])[j].length; k++) { pch[i][j][k] = ((float[][]) histograms[i])[j][k]; } } } final PCH2DFitWindow cw = new PCH2DFitWindow(); cw.init(names, pch, psfflag); final Frame f = new Frame("PCH 2D Analysis"); f.setLocation(10, 10); f.addWindowListener( new WindowAdapter() { public void windowClosing(WindowEvent e) { f.dispose(); } }); f.add(cw); f.pack(); f.setResizable(false); Insets ins = f.getInsets(); cw.totalSize.height = PCH2DFitWindow.H + ins.bottom + ins.top + 65; cw.totalSize.width = PCH2DFitWindow.WR + ins.left + ins.right; f.setSize(cw.totalSize); f.setVisible(true); cw.requestFocus(); }
public boolean get_errors(double[] params, int[] fixes) { GenericDialog gd = new GenericDialog("Error Options"); String[] methods = {"Support Plane", "Monte Carlo"}; gd.addChoice("Method", methods, methods[0]); float conf = 0.67f; gd.addNumericField("SP_Confidence Limit (%)", (int) (conf * 100.0f), 5, 10, null); String[] labels = {"P1", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", "P10"}; gd.addChoice("SP_Parameter", labels, labels[0]); double spacing = 0.01; gd.addNumericField("SP_Chi^2_plot_spacing (% of value)?", spacing * 100.0, 2, 10, null); int ntrials = 100; gd.addNumericField("MC_#_Trials", ntrials, 0); gd.showDialog(); if (gd.wasCanceled()) { return false; } int methodindex = gd.getNextChoiceIndex(); conf = 0.01f * (float) gd.getNextNumber(); int paramindex = gd.getNextChoiceIndex(); spacing = 0.01 * gd.getNextNumber(); ntrials = (int) gd.getNextNumber(); if (methodindex == 0) { support_plane_errors_v2 erclass = new support_plane_errors_v2(this, 0.0001, 50, false, 0.1); int errindex = paramindex; int nfit = 0; for (int i = 0; i < labels.length; i++) { if (fixes[i] == 0) { nfit++; } } int npts = tempdata.length; int dofnum = npts - (nfit - 1) - 1; int dofden = npts - nfit - 1; double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf); IJ.log("FLimit = " + (float) flim); if (flim == Double.NaN && flim < 1.0) { IJ.showMessage("Invalid Limiting F Value"); return false; } double truespacing = Math.abs(params[errindex] * spacing); double[][] c2plot = erclass.geterrors( params, fixes, constraints, tempdata, weights, flim, truespacing, errindex); IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]); IJ.log( "upper error = " + (c2plot[1][0] - params[errindex]) + " lower error = " + (params[errindex] - c2plot[0][0])); int templength = c2plot[0].length; float[][] c2plotf = new float[2][templength - 1]; for (int i = 0; i < (templength - 1); i++) { c2plotf[0][i] = (float) c2plot[0][i + 1]; c2plotf[1][i] = (float) c2plot[1][i + 1]; } new PlotWindow4("c2 plot", labels[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw(); } else { StringBuffer sb = new StringBuffer(); sb.append("Trial\t"); for (int i = 0; i < labels.length; i++) { if (fixes[i] == 0) sb.append(labels[i] + "\t"); } sb.append("chi^2"); tw = new TextWindow("Monte Carlo Results", sb.toString(), "", 400, 400); redirect = true; monte_carlo_errors_v2 erclass = new monte_carlo_errors_v2(this, 0.0001, 50, false, 0.1); double[][] errors = erclass.geterrors(params, fixes, constraints, tempdata, weights, ntrials); sb = new StringBuffer(); sb.append("StDev\t"); for (int i = 0; i < errors.length; i++) { float[] ferr = new float[errors[0].length]; for (int j = 0; j < ferr.length; j++) ferr[j] = (float) errors[i][j]; float stdev = jstatistics.getstatistic("StDev", ferr, null); sb.append("" + stdev); if (i < (errors.length - 1)) sb.append("\t"); } tw.append(sb.toString()); redirect = false; } return true; }
// Input/Output options void io() { GenericDialog gd = new GenericDialog("I/O Options"); gd.addNumericField("JPEG quality (0-100):", FileSaver.getJpegQuality(), 0, 3, ""); gd.addNumericField("GIF and PNG transparent index:", Prefs.getTransparentIndex(), 0, 3, ""); gd.addStringField( "File extension for tables (.txt, .xls or .csv):", Prefs.get("options.ext", ".csv"), 4); gd.addCheckbox("Use JFileChooser to open/save", Prefs.useJFileChooser); if (!IJ.isMacOSX()) gd.addCheckbox("Use_file chooser to import sequences", Prefs.useFileChooser); gd.addCheckbox("Save TIFF and raw in Intel byte order", Prefs.intelByteOrder); gd.addCheckbox("Skip dialog when opening .raw files", Prefs.skipRawDialog); gd.setInsets(15, 20, 0); gd.addMessage("Results Table Options"); gd.setInsets(3, 40, 0); gd.addCheckbox("Copy_column headers", Prefs.copyColumnHeaders); gd.setInsets(0, 40, 0); gd.addCheckbox("Copy_row numbers", !Prefs.noRowNumbers); gd.setInsets(0, 40, 0); gd.addCheckbox("Save_column headers", !Prefs.dontSaveHeaders); gd.setInsets(0, 40, 0); gd.addCheckbox("Save_row numbers", !Prefs.dontSaveRowNumbers); gd.showDialog(); if (gd.wasCanceled()) return; int quality = (int) gd.getNextNumber(); if (quality < 0) quality = 0; if (quality > 100) quality = 100; FileSaver.setJpegQuality(quality); int transparentIndex = (int) gd.getNextNumber(); Prefs.setTransparentIndex(transparentIndex); String extension = gd.getNextString(); if (!extension.startsWith(".")) extension = "." + extension; Prefs.set("options.ext", extension); Prefs.useJFileChooser = gd.getNextBoolean(); if (!IJ.isMacOSX()) Prefs.useFileChooser = gd.getNextBoolean(); Prefs.intelByteOrder = gd.getNextBoolean(); Prefs.skipRawDialog = gd.getNextBoolean(); Prefs.copyColumnHeaders = gd.getNextBoolean(); Prefs.noRowNumbers = !gd.getNextBoolean(); Prefs.dontSaveHeaders = !gd.getNextBoolean(); Prefs.dontSaveRowNumbers = !gd.getNextBoolean(); return; }
// Miscellaneous Options void miscOptions() { String key = IJ.isMacintosh() ? "command" : "control"; GenericDialog gd = new GenericDialog("Miscellaneous Options", IJ.getInstance()); gd.addStringField("Divide by zero value:", "" + FloatBlitter.divideByZeroValue, 10); gd.addCheckbox("Use pointer cursor", Prefs.usePointerCursor); gd.addCheckbox("Hide \"Process Stack?\" dialog", IJ.hideProcessStackDialog); gd.addCheckbox("Require " + key + " key for shortcuts", Prefs.requireControlKey); gd.addCheckbox("Move isolated plugins to Misc. menu", Prefs.moveToMisc); if (!IJ.isMacOSX()) gd.addCheckbox("Run single instance listener", Prefs.runSocketListener); gd.addCheckbox("Enhanced line tool", Prefs.enhancedLineTool); gd.addCheckbox("Reverse CZT order of \">\" and \"<\"", Prefs.reverseNextPreviousOrder); gd.addCheckbox("Debug mode", IJ.debugMode); gd.addHelp(IJ.URL + "/docs/menus/edit.html#misc"); gd.showDialog(); if (gd.wasCanceled()) return; String divValue = gd.getNextString(); if (divValue.equalsIgnoreCase("infinity") || divValue.equalsIgnoreCase("infinite")) FloatBlitter.divideByZeroValue = Float.POSITIVE_INFINITY; else if (divValue.equalsIgnoreCase("NaN")) FloatBlitter.divideByZeroValue = Float.NaN; else if (divValue.equalsIgnoreCase("max")) FloatBlitter.divideByZeroValue = Float.MAX_VALUE; else { Float f; try { f = new Float(divValue); } catch (NumberFormatException e) { f = null; } if (f != null) FloatBlitter.divideByZeroValue = f.floatValue(); } IJ.register(FloatBlitter.class); Prefs.usePointerCursor = gd.getNextBoolean(); IJ.hideProcessStackDialog = gd.getNextBoolean(); Prefs.requireControlKey = gd.getNextBoolean(); Prefs.moveToMisc = gd.getNextBoolean(); if (!IJ.isMacOSX()) Prefs.runSocketListener = gd.getNextBoolean(); Prefs.enhancedLineTool = gd.getNextBoolean(); Prefs.reverseNextPreviousOrder = gd.getNextBoolean(); IJ.setDebugMode(gd.getNextBoolean()); }
// DICOM options void dicom() { GenericDialog gd = new GenericDialog("DICOM Options"); gd.addCheckbox("Open as 32-bit float", Prefs.openDicomsAsFloat); // gd.addCheckbox("Calculate voxel depth", Prefs.calculateDicomVoxelDepth); gd.addMessage("Orthogonal Views"); gd.setInsets(5, 40, 0); gd.addCheckbox("Rotate YZ", Prefs.rotateYZ); gd.setInsets(0, 40, 0); gd.addCheckbox("Flip XZ", Prefs.flipXZ); gd.showDialog(); if (gd.wasCanceled()) return; Prefs.openDicomsAsFloat = gd.getNextBoolean(); // Prefs.calculateDicomVoxelDepth = gd.getNextBoolean(); Prefs.rotateYZ = gd.getNextBoolean(); Prefs.flipXZ = gd.getNextBoolean(); }
private boolean showDialog() { String[] types = {"RAW", "JPEG", "ZLIB"}; GenericDialog gd = new GenericDialog("Generate Bricks"); gd.addChoice("FileType", types, filetype); gd.addNumericField("JPEG quality", jpeg_quality, 0); gd.addNumericField("Max file size (MB)", bdsizelimit, 0); int[] wlist = WindowManager.getIDList(); if (wlist == null) return false; String[] titles = new String[wlist.length]; for (int i = 0; i < wlist.length; i++) titles[i] = ""; int tnum = 0; for (int i = 0; i < wlist.length; i++) { ImagePlus imp = WindowManager.getImage(wlist[i]); if (imp != null) { titles[tnum] = imp.getTitle(); tnum++; } } gd.addChoice("Source image: ", titles, titles[0]); gd.showDialog(); if (gd.wasCanceled()) return false; filetype = types[gd.getNextChoiceIndex()]; jpeg_quality = (int) gd.getNextNumber(); if (jpeg_quality > 100) jpeg_quality = 100; if (jpeg_quality < 0) jpeg_quality = 0; bdsizelimit = (int) gd.getNextNumber(); int id = gd.getNextChoiceIndex(); lvImgTitle = new ArrayList<String>(); lvImgTitle.add(titles[id]); Prefs.set("filetype.string", filetype); Prefs.set("jpeg_quality.int", jpeg_quality); Prefs.set("bdsizelimit.int", bdsizelimit); return true; }
public void run(String arg) { GenericDialog gd = new GenericDialog("Options"); gd.addCheckbox("Acceptor_First", true); gd.showDialog(); if (gd.wasCanceled()) return; boolean a1 = gd.getNextBoolean(); int asp = 0; int dsp = 1; int aop = 2; int dop = 3; int atp = 4; int dtp = 5; if (!a1) { asp = 1; dsp = 0; aop = 3; dop = 2; atp = 5; dtp = 4; } ImageWindow iw = WindowManager.getCurrentWindow(); float[][] xvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues"); float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues"); int[] npts = (int[]) jutils.runPW4VoidMethod(iw, "getNpts"); int maxpts = (int) jstatistics.getstatistic("Max", npts, null); int nsets = npts.length / 6; float[][] rtxvals = new float[nsets][maxpts]; float[][] rtavals = new float[nsets][maxpts]; float[][] rtdvals = new float[nsets][maxpts]; int[] rtnpts = new int[nsets]; int fretlength = 10; float[][] stfretvals = new float[nsets][fretlength]; float[][] offfretvals = new float[nsets][fretlength]; TextWindow tw = jutils.selectTable("DNA Damage FRET"); if (tw == null) tw = new TextWindow( "DNA Damage FRET", "title\tacceptor\tdonor\testripe\teoff\tmaxart\tmaxdrt", "", 400, 200); // note that st stands for stripe and off is for areas off the damage stripe for (int i = 0; i < npts.length / 6; i++) { int len = npts[i * 6]; int damageindex = findbleach(yvals[i * 6 + dsp], len); int fretindex = findbleach(yvals[i * 6 + atp], len); IJ.log("set " + i + " damage pos = " + damageindex + " , fret pos = " + fretindex); int predamagestart = damageindex - 4; int prefretstart = fretindex - 5; float staccpredam = getavg(yvals[i * 6 + asp], len, predamagestart, damageindex - 1); float stdonpredam = getavg(yvals[i * 6 + dsp], len, predamagestart, damageindex - 1); float nucaccpredam = getavg(yvals[i * 6 + atp], len, predamagestart, damageindex - 1); float nucdonpredam = getavg(yvals[i * 6 + dtp], len, predamagestart, damageindex - 1); float stdonprefret = getavg(yvals[i * 6 + dsp], len, prefretstart, fretindex - 2); float stdonafret = getavg(yvals[i * 6 + dsp], len, fretindex, fretindex + 3); float offdonprefret = getavg(yvals[i * 6 + dop], len, prefretstart, fretindex - 2); float offdonafret = getavg(yvals[i * 6 + dop], len, fretindex, fretindex + 3); float estripe = 1.0f - stdonprefret / stdonafret; float eoff = 1.0f - offdonprefret / offdonafret; rtnpts[i] = len; for (int j = 0; j < len; j++) { rtxvals[i][j] = j - damageindex - 1; rtavals[i][j] = (yvals[i * 6 + asp][j] / staccpredam) / (yvals[i * 6 + atp][j] / nucaccpredam); rtdvals[i][j] = (yvals[i * 6 + dsp][j] / stdonpredam) / (yvals[i * 6 + dtp][j] / nucdonpredam); } float[] smart = (float[]) algutils.get_subarray(rtavals[i], 0, fretindex); float[] smdrt = (float[]) algutils.get_subarray(rtdvals[i], 0, fretindex); jsmooth.blur1D(smart, 2.0f); jsmooth.blur1D(smdrt, 2.0f); float maxart = 0.0f; float maxdrt = 0.0f; for (int j = 0; j < fretindex - 2; j++) { if (smart[j] > maxart) maxart = smart[j]; if (smdrt[j] > maxdrt) maxdrt = smdrt[j]; } stfretvals[i] = getregion(yvals[i * 6 + dsp], len, prefretstart, fretlength); offfretvals[i] = getregion(yvals[i * 6 + dop], len, prefretstart, fretlength); tw.append( iw.getTitle() + "-" + (i + 1) + "\t" + staccpredam + "\t" + stdonpredam + "\t" + estripe + "\t" + eoff + "\t" + maxart + "\t" + maxdrt); } new PlotWindow4("Stripe_FRET_profiles", "time", "intensity", stfretvals, null).draw(); new PlotWindow4("OffStripe_FRET_profiles", "time", "intensity", offfretvals, null).draw(); new PlotWindow4("Acc_Rt_profiles", "time", "intensity", rtxvals, rtavals, rtnpts).draw(); new PlotWindow4("Don_Rt_profiles", "time", "intensity", rtxvals, rtdvals, rtnpts).draw(); }
private void geterrors() { GenericDialog gd = new GenericDialog("Options"); float conf = 0.67f; gd.addNumericField("Confidence Limit", (int) (conf * 100.0f), 5, 10, null); gd.addChoice("Error Parameter", paramsnames, paramsnames[0]); double spacing = 0.01; gd.addNumericField("Chi^2 plot spacing (% of value)?", spacing * 100.0, 2, 10, null); boolean globalerror = false; gd.addCheckbox("Global Fit Error?", globalerror); int dataset = 0; gd.addNumericField("Data Set (for Global Error)", dataset, 0); gd.showDialog(); if (gd.wasCanceled()) { return; } conf = 0.01f * (float) gd.getNextNumber(); int paramindex = (int) gd.getNextChoiceIndex(); spacing = 0.01 * gd.getNextNumber(); globalerror = gd.getNextBoolean(); dataset = (int) gd.getNextNumber(); if (globalerror) { support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, true, 0.1); int[] erindeces = {paramindex, dataset}; // need to set up all the matrices int nsel = 0; int nparams = 11; for (int i = 0; i < ncurves; i++) { if (include[i]) { nsel++; } } double[][] params = new double[nsel][nparams]; String[][] tempformulas = new String[nsel][nparams]; double[][][] constraints = new double[2][nsel][nparams]; int[][] vflmatrix = new int[nsel][nparams]; float[][] tempdata = new float[nsel][xpts * ypts]; float[][] tempweights = new float[nsel][xpts * ypts]; int nfit = 0; int counter = 0; for (int i = 0; i < ncurves; i++) { if (include[i]) { for (int j = 0; j < nparams; j++) { params[counter][j] = globalparams[i][j]; tempformulas[counter][j] = globalformulas[i][j]; constraints[0][counter][j] = globalconstraints[0][i][j]; constraints[1][counter][j] = globalconstraints[1][i][j]; vflmatrix[counter][j] = globalvflmatrix[i][j]; if (vflmatrix[counter][j] == 0 || (j == 0 && vflmatrix[counter][j] == 2)) { nfit++; } } for (int j = 0; j < xpts; j++) { for (int k = 0; k < ypts; k++) { tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]); tempweights[counter][j + k * xpts] = weights[i][j][k]; } } counter++; } } int dofnum = xpts * ypts * nsel - (nfit - 1) - 1; int dofden = xpts * ypts * nsel - nfit - 1; // double flim=FLimit(dofnum,dofden,(double)conf); double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf); IJ.log("FLimit = " + (float) flim); if (flim == Double.NaN && flim < 1.0) { IJ.showMessage("Invalid Limiting F Value"); return; } double truespacing = Math.abs(params[erindeces[1]][erindeces[0]] * spacing); double[][] c2plot = erclass.geterrorsglobal( params, vflmatrix, tempformulas, paramsnames, constraints, tempdata, tempweights, flim, truespacing, erindeces); IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]); int templength = c2plot[0].length; float[][] c2plotf = new float[2][templength - 1]; for (int i = 0; i < (templength - 1); i++) { c2plotf[0][i] = (float) c2plot[0][i + 1]; c2plotf[1][i] = (float) c2plot[1][i + 1]; } new PlotWindow4( "c2 plot", paramsnames[paramindex] + "[" + dataset + "]", "Chi^2", c2plotf[0], c2plotf[1]) .draw(); } else { support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, false, 0.1); int errindex = paramindex; float[] tempdata = new float[xpts * ypts]; float[] tempweights = new float[xpts * ypts]; for (int i = 0; i < xpts; i++) { for (int j = 0; j < ypts; j++) { tempdata[i + j * xpts] = (float) ((double) avg[i][j] / (double) nmeas[ncurves]); tempweights[i + j * xpts] = avgweights[i][j]; } } int nfit = 0; for (int i = 0; i < 7; i++) { if (avgfixes[i] == 0) { nfit++; } } int dofnum = xpts * ypts - (nfit - 1) - 1; int dofden = xpts * ypts - nfit - 1; double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf); IJ.log("FLimit = " + (float) flim); if (flim == Double.NaN && flim < 1.0) { IJ.showMessage("Invalid Limiting F Value"); return; } double truespacing = Math.abs(avgparams[errindex] * spacing); double[][] c2plot = erclass.geterrors( avgparams, avgfixes, avgconstraints, tempdata, tempweights, flim, truespacing, errindex); IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]); int templength = c2plot[0].length; float[][] c2plotf = new float[2][templength - 1]; for (int i = 0; i < (templength - 1); i++) { c2plotf[0][i] = (float) c2plot[0][i + 1]; c2plotf[1][i] = (float) c2plot[1][i + 1]; } new PlotWindow4("c2 plot", paramsnames[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw(); } }
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; }
boolean showoptions(double[] params, int[] fixes) { // GenericDialog gd=new NonBlockingGenericDialog("Options"); GenericDialog gd = new GenericDialog("Options"); gd.addCheckbox("Check Chi Squared", checkc2); for (int i = 0; i < 10; i++) { gd.addNumericField("P" + (i + 1), params[i], 5, 10, null); gd.addCheckbox("Fix?", (fixes[i] == 1)); } gd.addCheckbox("Get_Errors", false); gd.addCheckbox("Set_Constraints", false); gd.addNumericField("Iterations", iterations, 0, 10, null); gd.addNumericField("chi squared", c2, 5, 10, null); gd.addDialogListener(this); gd.showDialog(); if (gd.wasCanceled()) { return false; } checkc2 = gd.getNextBoolean(); for (int i = 0; i < 10; i++) { params[i] = gd.getNextNumber(); if (gd.getNextBoolean()) { fixes[i] = 1; } else { fixes[i] = 0; } } boolean geterrors = gd.getNextBoolean(); boolean setconstraints = gd.getNextBoolean(); for (int i = 0; i < 10; i++) { if (function.indexOf("P" + (i + 1)) < 0) { fixes[i] = 1; } } if (geterrors) { if (!get_errors(params, fixes)) { return false; } } if (setconstraints) constraints = get_constraints(params); return true; }