ij.plugin.CalibrationBar Maven / Gradle / Ivy

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package ij.plugin;
import ij.*;
import java.awt.*;
import java.awt.image.*;
import java.awt.event.*;
import java.io.*;
import java.awt.datatransfer.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.Measurements;
import ij.plugin.filter.Analyzer;
import ij.text.TextWindow;
import ij.measure.*;

/** This plugin implements the Analyze/Tools/Calibration Bar command.
	Bob Dougherty, OptiNav, Inc., 4/14/2002
	Based largely on HistogramWindow.java by Wayne Rasband.
	July 2002: Modified by Daniel Marsh and renamed CalibrationBar.
	January 2013: Displays calibration bar as an overlay.
*/

public class CalibrationBar implements PlugIn {
	final static int BAR_LENGTH = 128;
	final static int BAR_THICKNESS = 12;
	final static int XMARGIN = 10;
	final static int YMARGIN = 10;
	final static int WIN_HEIGHT = BAR_LENGTH;
	final static int BOX_PAD = 0;
	static int nBins = 256;
	static final String[] colors = {"White","Light Gray","Dark Gray","Black","Red","Green","Blue","Yellow","None"};
	static final String[] locations = {"Upper Right","Lower Right","Lower Left", "Upper Left", "At Selection"};
	static final int UPPER_RIGHT=0, LOWER_RIGHT=1, LOWER_LEFT=2, UPPER_LEFT=3, AT_SELECTION=4;

	static String fillColor = colors[0];
	static String textColor = colors[3];
	static String location = locations[UPPER_RIGHT];
	static double zoom = 1;
	static int numLabels = 5;
	static int fontSize = 12;
	static int decimalPlaces = 0;
	ImagePlus imp;
	LiveDialog gd;

	ImageStatistics stats;
	Calibration cal;
	int[] histogram;
	LookUpTable lut;
	Image img;
	Button setup, redraw, insert, unInsert;
	Checkbox ne,nw,se,sw;
	CheckboxGroup locGroup;
	Label value, note;
	int newMaxCount;
	boolean logScale;
	int win_width;
	int userPadding = 0;
	int fontHeight = 0;
	boolean boldText;
	boolean flatten;
	Object backupPixels;
	byte[] byteStorage;
	int[] intStorage;
	short[] shortStorage;
	float[] floatStorage;
	String boxOutlineColor = colors[8];
	String barOutlineColor = colors[3];
	
	ImageProcessor ip;
	String[] fieldNames = null;
	int insetPad;
	boolean decimalPlacesChanged;

	public void run(String arg) {
		imp = IJ.getImage();
		if (imp.getBitDepth()==24 || imp.getCompositeMode()==IJ.COMPOSITE) {
			IJ.error("Calibration Bar", "RGB and composite images are not supported");
			return;
		}
		if (imp.getRoi()!=null)
			location = locations[AT_SELECTION];
		ImageCanvas ic = imp.getCanvas();
		double mag = (ic!=null)?ic.getMagnification():1.0;
		if (zoom<=1 && mag<1)
			zoom = (double) 1.0/mag;
		insetPad = imp.getWidth()/50;
		if (insetPad<4)
			insetPad = 4;
		updateColorBar();
		if (IJ.isMacro()) {
			flatten = true;
			fillColor = colors[0];
			textColor = colors[3];
			location = locations[UPPER_RIGHT];
			zoom = 1;
			numLabels = 5;
			fontSize = 12;
			decimalPlaces = 0;
		}
		if (!showDialog()) {
			imp.setOverlay(null);
			return;
		}
		updateColorBar();
		if (flatten) {
			imp.deleteRoi();
			IJ.wait(100);
			ImagePlus imp2 = imp.flatten();
			imp2.setTitle(imp.getTitle()+" with bar");
			imp.setOverlay(null);
			imp2.show();
		}
	}

	private void updateColorBar() {
		Roi roi = imp.getRoi();
		if (roi!=null &&  location.equals(locations[AT_SELECTION])) {
			Rectangle r = roi.getBounds();
			drawBarAsOverlay(imp, r.x, r.y);
		} else if ( location.equals(locations[UPPER_LEFT]))
			drawBarAsOverlay(imp, insetPad, insetPad);
		else if (location.equals(locations[UPPER_RIGHT])) {
			calculateWidth();
			drawBarAsOverlay(imp, imp.getWidth()-insetPad-win_width, insetPad);
		} else if (location.equals(locations[LOWER_LEFT]) )
			drawBarAsOverlay(imp, insetPad,imp.getHeight() - (int)(WIN_HEIGHT*zoom + 2*(int)(YMARGIN*zoom)) - (int)(insetPad*zoom));
		else if(location.equals(locations[LOWER_RIGHT])) {
			calculateWidth();
			drawBarAsOverlay(imp, imp.getWidth()-win_width-insetPad,
				 imp.getHeight() - (int)(WIN_HEIGHT*zoom + 2*(int)(YMARGIN*zoom)) - insetPad);
		}
		this.imp.updateAndDraw();
	}

	private boolean showDialog() {
		gd = new LiveDialog("Calibration Bar");
		gd.addChoice("Location:", locations, location);
		gd.addChoice("Fill color: ", colors, fillColor);
		gd.addChoice("Label color: ", colors, textColor);
		gd.addNumericField("Number of labels:", numLabels, 0);
		gd.addNumericField("Decimal places:", decimalPlaces, 0);
		gd.addNumericField("Font size:", fontSize, 0);
		gd.addNumericField("Zoom factor:", zoom, 1);
		String[] labels = {"Bold text", "Overlay"};
		boolean[] states = {boldText, !flatten};
		gd.setInsets(10, 30, 0);
		gd.addCheckboxGroup(1, 2, labels, states);
		gd.showDialog();
		if (gd.wasCanceled())
			return false;
		location = gd.getNextChoice();
		fillColor = gd.getNextChoice();
		textColor = gd.getNextChoice();
		numLabels = (int)gd.getNextNumber();
		decimalPlaces = (int)gd.getNextNumber();
		fontSize = (int)gd.getNextNumber();
		zoom = (double)gd.getNextNumber();
		boldText = gd.getNextBoolean();
		flatten = !gd.getNextBoolean();
		return true;
	}

	private void drawBarAsOverlay(ImagePlus imp, int x, int y) {
		Roi roi = imp.getRoi();
		if (roi!=null)
			imp.deleteRoi();
		stats = imp.getStatistics(Measurements.MIN_MAX, nBins);
		if (roi!=null)
			imp.setRoi(roi);
		histogram = stats.histogram;
		lut = imp.createLut();
		cal = imp.getCalibration();
		Overlay overlay = new Overlay();

		int maxTextWidth = addText(null, 0, 0);
		win_width = (int)(XMARGIN*zoom) + 5 + (int)(BAR_THICKNESS*zoom) + maxTextWidth + (int)((XMARGIN/2)*zoom);
		if (x==-1 && y==-1)
			return;	 // return if calculating width

		Color c = getColor(fillColor);
		if (c!=null) {
			Roi r = new Roi(x, y, win_width, (int)(WIN_HEIGHT*zoom + 2*(int)(YMARGIN*zoom)));
			r.setFillColor(c);
			overlay.add(r);
		}
		int xOffset = x;
		int yOffset = y;
		if (decimalPlaces == -1)
			decimalPlaces = Analyzer.getPrecision();
		x = (int)(XMARGIN*zoom) + xOffset;
		y = (int)(YMARGIN*zoom) + yOffset;
		addVerticalColorBar(overlay, x, y, (int)(BAR_THICKNESS*zoom), (int)(BAR_LENGTH*zoom) );
		addText(overlay, x + (int)(BAR_THICKNESS*zoom), y);
		c = getColor(boxOutlineColor);
		/*
		if (c!=null && !fillColor.equals("None")) {
			int xbase = xOffset+BOX_PAD;
			int ybase = yOffset+BOX_PAD;
			int w = win_width-BOX_PAD;
			int h = (int)(WIN_HEIGHT*zoom + 2*(int)(YMARGIN*zoom));
			Roi r = new Roi(xbase, ybase, w, h);
			r.setStrokeColor(c);
			r.setStrokeWidth(1.0);
			overlay.add(r);
		}
		*/
		overlay.setIsCalibrationBar(true);
		if (imp.getCompositeMode()>0) {
			for (int i=0; i255) max = 255;
			colors = max-min+1;
			start = min;
		}
		for (int i = 0; i<(int)(BAR_LENGTH*zoom); i++) {
			int iMap = start + (int)Math.round((i*colors)/(BAR_LENGTH*zoom));
			if (iMap>=mapSize)
				iMap =mapSize - 1;
			int j = (int)(BAR_LENGTH*zoom) - i - 1;
			Line line = new Line(x, j+y, thickness+x, j+y);
			line.setStrokeColor(new Color(rLUT[iMap]&0xff, gLUT[iMap]&0xff, bLUT[iMap]&0xff));
			line.setStrokeWidth(1.0001);
			overlay.add(line);
		}

		Color c = getColor(barOutlineColor);
		if (c!=null) {
			Roi r = new Roi(x, y, width, height);
			r.setStrokeColor(c);
			r.setStrokeWidth(1.0);
			overlay.add(r);
		}
	}

	private int addText(Overlay overlay, int x, int y) {

		Color c = getColor(textColor);
		if (c == null)
			return 0;
		double hmin = cal.getCValue(stats.histMin);
		double hmax = cal.getCValue(stats.histMax);
		double barStep = (double)(BAR_LENGTH*zoom) ;
		if (numLabels > 2)
			barStep /= (numLabels - 1);

		int fontType = boldText?Font.BOLD:Font.PLAIN;
		Font font = null;
		if (fontSize<9)
			font = new Font("SansSerif", fontType, 9);
		else
			font = new Font("SansSerif", fontType, (int)( fontSize*zoom));
		int maxLength = 0;

		//Blank offscreen image for font metrics
		Image img = GUI.createBlankImage(128, 64);
		Graphics g = img.getGraphics();
		FontMetrics metrics = g.getFontMetrics(font);
		fontHeight = metrics.getHeight();

		for (int i = 0; i < numLabels; i++) {
			double yLabelD = (int)(YMARGIN*zoom + BAR_LENGTH*zoom - i*barStep - 1);
			int yLabel = (int)(Math.round( y + BAR_LENGTH*zoom - i*barStep - 1));
			Calibration cal = imp.getCalibration();
			//s = cal.getValueUnit();
			ImageProcessor ipOrig = imp.getProcessor();
			double min = ipOrig.getMin();
			double max = ipOrig.getMax();
			if (ipOrig instanceof ByteProcessor) {
				if (min<0) min = 0;
				if (max>255) max = 255;
			}
			double grayLabel = min + (max-min)/(numLabels-1) * i;
			if (cal.calibrated()) {
				grayLabel = cal.getCValue(grayLabel);
				double cmin = cal.getCValue(min);
				double cmax = cal.getCValue(max);
				if (!decimalPlacesChanged && decimalPlaces==0 && ((int)cmax!=cmax||(int)cmin!=cmin))
					decimalPlaces = 2;
			}
			if (overlay!=null) {
				TextRoi label = new TextRoi(d2s(grayLabel), x + 5, yLabel + fontHeight/2, font);
				label.setStrokeColor(c);
				overlay.add(label);
			}
			int iLength = metrics.stringWidth(d2s(grayLabel));
			if (iLength > maxLength)
				maxLength = iLength;
		}
		return maxLength;
	}

	String d2s(double d) {
			return IJ.d2s(d,decimalPlaces);
	}

	int getFontHeight() {
		Image img = GUI.createBlankImage(64, 64); //dummy version to get fontHeight
		Graphics g = img.getGraphics();
		int fontType = boldText?Font.BOLD:Font.PLAIN;
		Font font = new Font("SansSerif", fontType, (int) (fontSize*zoom) );
		FontMetrics metrics = g.getFontMetrics(font);
		return	metrics.getHeight();
	}

	Color getColor(String color) {
		Color c = Color.white;
		if (color.equals(colors[1]))
			c = Color.lightGray;
		else if (color.equals(colors[2]))
			c = Color.darkGray;
		else if (color.equals(colors[3]))
			c = Color.black;
		else if (color.equals(colors[4]))
			c = Color.red;
		else if (color.equals(colors[5]))
			c = Color.green;
		else if (color.equals(colors[6]))
			c = Color.blue;
		else if (color.equals(colors[7]))
			c = Color.yellow;
		else if (color.equals(colors[8]))
			c = null;
		return c;
	}	 

	void calculateWidth() {
		drawBarAsOverlay(imp, -1, -1);
	}
		
	class LiveDialog extends GenericDialog {

		LiveDialog(String title) {
			super(title);
		}

		public void textValueChanged(TextEvent e) {

			if (fieldNames == null) {
				fieldNames = new String[4];
				for(int i=0;i<4;i++)
					fieldNames[i] = ((TextField)numberField.elementAt(i)).getName();
			}

			TextField tf = (TextField)e.getSource();
			String name = tf.getName();
			String value = tf.getText();

			if (value.equals(""))
				return;

			int i=0;
			boolean needsRefresh = false;

			if (name.equals(fieldNames[0])) {

				i = getValue( value ).intValue() ;
				if(i<1)
					return;
				else {
					needsRefresh = true;
					numLabels = i;
				}
			} else if (name.equals(fieldNames[1])) {
				i = getValue( value ).intValue() ;
				if (i<0)
					return;
				else {
					needsRefresh = true;
					decimalPlaces = i;
					decimalPlacesChanged = true;
				}

			} else if (name.equals(fieldNames[2])) {
				i = getValue( value ).intValue() ;
				if(i<1)
					return;
				else {
					needsRefresh = true;
					fontSize = i;

				}

			} else if (name.equals(fieldNames[3])) {
				double d = 0;
				d = getValue( "0" + value ).doubleValue() ;
				if(d<=0)
					return;
				else {
					needsRefresh = true;
					zoom = d;
				}
			}

			if (needsRefresh)
				updateColorBar();
			return;
		}

		public void itemStateChanged(ItemEvent e) {
			location = ( (Choice)(choice.elementAt(0)) ).getSelectedItem();
			fillColor = ( (Choice)(choice.elementAt(1)) ).getSelectedItem();
			textColor = ( (Choice)(choice.elementAt(2)) ).getSelectedItem();
			boldText = ( (Checkbox)(checkbox.elementAt(0)) ).getState();
			flatten = !( (Checkbox)(checkbox.elementAt(1)) ).getState();
			updateColorBar();
		}

	} //LiveDialog inner class

}