package ij.plugin.filter;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.measure.*;
import ij.util.*;
import ij.io.*;
import ij.plugin.TextReader;
import java.awt.*;
import java.util.*;
import java.awt.event.*;
import java.io.*;
/** Implements the Analyze/Calibrate command. */
public class Calibrator implements PlugInFilter, Measurements, ActionListener {
private static final String NONE = "None";
private static final String INVERTER = "Pixel Inverter";
private static final String UNCALIBRATED_OD = "Uncalibrated OD";
private static final String CUSTOM = "Custom";
private static boolean showSettings;
private boolean global1, global2;
private ImagePlus imp;
private int choiceIndex;
private String[] functions;
private int nFits = CurveFitter.fitList.length;
private int spacerIndex = nFits+1;
private int inverterIndex = nFits+2;
private int odIndex = nFits+3;
private int customIndex = nFits+4;
private static String xText = "";
private static String yText = "";
private static boolean importedValues;
private String unit;
private double lx=0.02, ly=0.1;
private int oldFunction;
private String sumResiduals, fitGoodness;
private Button open, save;
private GenericDialog gd;
public int setup(String arg, ImagePlus imp) {
this.imp = imp;
IJ.register(Calibrator.class);
return DOES_ALL-DOES_RGB+NO_CHANGES;
}
public void run(ImageProcessor ip) {
global1 = imp.getGlobalCalibration()!=null;
if (!showDialog(imp))
return;
if (choiceIndex==customIndex) {
showPlot(null, null, imp.getCalibration(), null);
return;
} else if (imp.getType()==ImagePlus.GRAY32) {
if (choiceIndex==0)
imp.getCalibration().setValueUnit(unit);
else
IJ.error("Calibrate", "Function must be \"None\" for 32-bit images,\nbut you can change the Unit.");
} else
calibrate(imp);
}
public boolean showDialog(ImagePlus imp) {
String defaultChoice;
Calibration cal = imp.getCalibration();
functions = getFunctionList(cal.getFunction()==Calibration.CUSTOM);
int function = cal.getFunction();
oldFunction = function;
double[] p = cal.getCoefficients();
unit = cal.getValueUnit();
if (function==Calibration.NONE)
defaultChoice=NONE;
else if (function<nFits&&function==Calibration.STRAIGHT_LINE&&p!=null&& p[0]==255.0&&p[1]==-1.0)
defaultChoice=INVERTER;
else if (function<nFits)
defaultChoice = CurveFitter.fitList[function];
else if (function==Calibration.UNCALIBRATED_OD)
defaultChoice=UNCALIBRATED_OD;
else if (function==Calibration.CUSTOM)
defaultChoice=CUSTOM;
else
defaultChoice=NONE;
String tmpText = getMeans();
if (!importedValues && !tmpText.equals(""))
xText = tmpText;
gd = new GenericDialog("Calibrate...");
gd.addChoice("Function:", functions, defaultChoice);
gd.addStringField("Unit:", unit, 16);
gd.addTextAreas(xText, yText, 20, 14);
//gd.addMessage("Left column contains uncalibrated measured values,\n right column contains known values (e.g., OD).");
gd.addPanel(makeButtonPanel(gd));
gd.addCheckbox("Global calibration", global1);
//gd.addCheckbox("Show Simplex Settings", showSettings);
gd.addHelp(IJ.URL+"/docs/menus/analyze.html#cal");
gd.showDialog();
if (gd.wasCanceled())
return false;
else {
choiceIndex = gd.getNextChoiceIndex();
unit = gd.getNextString();
xText = gd.getNextText();
yText = gd.getNextText();
global2 = gd.getNextBoolean();
//showSettings = gd.getNextBoolean();
return true;
}
}
/** Creates a panel containing "Open..." and "Save..." buttons. */
Panel makeButtonPanel(GenericDialog gd) {
Panel buttons = new Panel();
buttons.setLayout(new FlowLayout(FlowLayout.CENTER, 5, 0));
open = new Button("Open...");
open.addActionListener(this);
buttons.add(open);
save = new Button("Save...");
save.addActionListener(this);
buttons.add(save);
return buttons;
}
public void calibrate(ImagePlus imp) {
Calibration cal = imp.getCalibration();
Calibration calOrig = cal.copy();
int function = Calibration.NONE;
boolean is16Bits = imp.getType()==ImagePlus.GRAY16;
double[] parameters = null;
double[] x=null, y=null;
boolean zeroClip=false;
if (choiceIndex<=0) {
if (oldFunction==Calibration.NONE&&!yText.equals("")&&!xText.equals(""))
IJ.error("Calibrate", "Please select a function");
function = Calibration.NONE;
} else if (choiceIndex<=nFits) {
function = choiceIndex - 1;
x = getData(xText);
y = getData(yText);
if (!cal.calibrated() || y.length!=0 || function!=oldFunction) {
parameters = doCurveFitting(x, y, function);
if (parameters==null)
return;
}
if (!is16Bits && function!=Calibration.STRAIGHT_LINE) {
zeroClip = true;
for (int i=0; i<y.length; i++)
if (y[i]<0.0) zeroClip = false;
}
} else if (choiceIndex==inverterIndex) {
function = Calibration.STRAIGHT_LINE;
parameters = new double[2];
if (is16Bits)
parameters[0] = 65535;
else
parameters[0] = 255;
parameters[1] = -1.0;
unit = "Inverted Gray Value";
} else if (choiceIndex==odIndex) {
if (is16Bits) {
IJ.error("Calibrate", "Uncalibrated OD is not supported on 16-bit images.");
return;
}
function = Calibration.UNCALIBRATED_OD;
unit = "Uncalibrated OD";
}
cal.setFunction(function, parameters, unit, zeroClip);
if (!cal.equals(calOrig))
imp.setCalibration(cal);
imp.setGlobalCalibration(global2?cal:null);
if (global2 || global2!=global1)
WindowManager.repaintImageWindows();
else
imp.repaintWindow();
if (global2 && global2!=global1)
FileOpener.setShowConflictMessage(true);
if (function!=Calibration.NONE)
showPlot(x, y, cal, fitGoodness);
}
double[] doCurveFitting(double[] x, double[] y, int fitType) {
if (x.length!=y.length || y.length==0) {
IJ.error("Calibrate",
"To create a calibration curve, the left column must\n"
+"contain a list of measured mean pixel values and the\n"
+"right column must contain the same number of calibration\n"
+"standard values. Use the Measure command to add mean\n"
+"pixel value measurements to the left column.\n"
+" \n"
+" Left column: "+x.length+" values\n"
+" Right column: "+y.length+" values\n"
);
return null;
}
int n = x.length;
double xmin=0.0,xmax;
if (imp.getType()==ImagePlus.GRAY16)
xmax=65535.0;
else
xmax=255.0;
double[] a = Tools.getMinMax(y);
double ymin=a[0], ymax=a[1];
CurveFitter cf = new CurveFitter(x, y);
cf.doFit(fitType, showSettings);
int np = cf.getNumParams();
double[] p = cf.getParams();
fitGoodness = IJ.d2s(cf.getRSquared(),6);
double[] parameters = new double[np];
for (int i=0; i<np; i++)
parameters[i] = p[i];
return parameters;
}
void showPlot(double[] x, double[] y, Calibration cal, String rSquared) {
if (!cal.calibrated() || (IJ.macroRunning()&&Macro.getOptions()!=null))
return;
int xmin,xmax,range;
float[] ctable = cal.getCTable();
if (ctable.length==256) { //8-bit image
xmin = 0;
xmax = 255;
} else { // 16-bit image
xmin = 0;
xmax = 65535;
}
range = 256;
float[] px = new float[range];
float[] py = new float[range];
for (int i=0; i<range; i++)
px[i]=(float)((i/255.0)*xmax);
for (int i=0; i<range; i++)
py[i]=ctable[(int)px[i]];
double[] a = Tools.getMinMax(py);
double ymin = a[0];
double ymax = a[1];
int fit = cal.getFunction();
String unit = cal.getValueUnit();
Plot plot = new Plot("Calibration Function","pixel value",unit,px,py);
plot.setLimits(xmin,xmax,ymin,ymax);
if (x!=null&&y!=null&&x.length>0&&y.length>0)
plot.addPoints(x, y, PlotWindow.CIRCLE);
double[] p = cal.getCoefficients();
if (fit<=Calibration.LOG2) {
drawLabel(plot, CurveFitter.fList[fit]);
ly += 0.04;
}
if (p!=null) {
int np = p.length;
drawLabel(plot, "a="+IJ.d2s(p[0],6));
drawLabel(plot, "b="+IJ.d2s(p[1],6));
if (np>=3)
drawLabel(plot, "c="+IJ.d2s(p[2],6));
if (np>=4)
drawLabel(plot, "d="+IJ.d2s(p[3],6));
if (np>=5)
drawLabel(plot, "e="+IJ.d2s(p[4],6));
ly += 0.04;
}
if (rSquared!=null)
{drawLabel(plot, "R^2="+rSquared); rSquared=null;}
plot.show();
}
void drawLabel(Plot plot, String label) {
plot.addLabel(lx, ly, label);
ly += 0.08;
}
double sqr(double x) {return x*x;}
String[] getFunctionList(boolean custom) {
int n = nFits+4;
if (custom) n++;
String[] list = new String[n];
list[0] = NONE;
for (int i=0; i<nFits; i++)
list[1+i] = CurveFitter.fitList[i];
list[spacerIndex] = "-";
list[inverterIndex] = INVERTER;
list[odIndex] = UNCALIBRATED_OD;
if (custom)
list[customIndex] = CUSTOM;
return list;
}
String getMeans() {
float[] umeans = Analyzer.getUMeans();
int count = Analyzer.getCounter();
if (umeans==null || count==0)
return "";
if (count>MAX_STANDARDS)
count = MAX_STANDARDS;
String s = "";
for (int i=0; i<count; i++)
s += IJ.d2s(umeans[i],2)+"\n";
importedValues = false;
return s;
}
double[] getData(String xData) {
int len = xData.length();
StringBuffer sb = new StringBuffer(len);
for (int i=0; i<len; i++) {
char c = xData.charAt(i);
if ((c>='0'&&c<='9') || c=='-' || c=='.' || c==',' || c=='\n' || c=='\r' || c==' ')
sb.append(c);
}
xData = sb.toString();
StringTokenizer st = new StringTokenizer(xData);
int nTokens = st.countTokens();
if (nTokens<1)
return new double[0];
int n = nTokens;
double data[] = new double[n];
for (int i=0; i<n; i++) {
data[i] = getNum(st);
}
return data;
}
double getNum(StringTokenizer st) {
Double d;
String token = st.nextToken();
try {d = new Double(token);}
catch (NumberFormatException e){d = null;}
if (d!=null)
return(d.doubleValue());
else
return 0.0;
}
void save() {
TextArea ta1 = gd.getTextArea1();
TextArea ta2 = gd.getTextArea2();
ta1.selectAll();
String text1 = ta1.getText();
ta1.select(0, 0);
ta2.selectAll();
String text2 = ta2.getText();
ta2.select(0, 0);
double[] x = getData(text1);
double[] y = getData(text2);
SaveDialog sd = new SaveDialog("Save as Text...", "calibration", ".txt");
String name = sd.getFileName();
if (name == null)
return;
String directory = sd.getDirectory();
PrintWriter pw = null;
try {
FileOutputStream fos = new FileOutputStream(directory+name);
BufferedOutputStream bos = new BufferedOutputStream(fos);
pw = new PrintWriter(bos);
}
catch (IOException e) {
IJ.error("" + e);
return;
}
IJ.wait(250); // give system time to redraw ImageJ window
int n = Math.max(x.length, y.length);
for (int i=0; i<n; i++) {
String xs = x.length==0?"":i<x.length?""+x[i]:"0";
String ys = y.length==0?"":i<y.length?""+y[i]:"0";
pw.println(xs + "\t"+ ys);
}
pw.close();
}
void open() {
OpenDialog od = new OpenDialog("Open Calibration...", "");
String directory = od.getDirectory();
String name = od.getFileName();
if (name==null)
return;
String path = directory + name;
TextReader tr = new TextReader();
ImageProcessor ip = tr.open(path);
if (ip==null)
return;
int width = ip.getWidth();
int height = ip.getHeight();
if (!((width==1||width==2)&&height>1)) {
IJ.error("Calibrate", "This appears to not be a one or two column text file");
return;
}
StringBuffer sb = new StringBuffer();
for (int i=0; i<height; i++) {
sb.append(""+ip.getPixelValue(0, i));
sb.append("\n");
}
String s1=null, s2=null;
if (width==2) {
s1 = new String(sb);
sb = new StringBuffer();
for (int i=0; i<height; i++) {
sb.append(""+ip.getPixelValue(1, i));
sb.append("\n");
}
s2 = new String(sb);
} else
s2 = new String(sb);
if (s1!=null) {
TextArea ta1 = gd.getTextArea1();
ta1.selectAll();
ta1.setText(s1);
}
TextArea ta2 = gd.getTextArea2();
ta2.selectAll();
ta2.setText(s2);
importedValues = true;
}
public void actionPerformed(ActionEvent e) {
Object source = e.getSource();
if (source==save)
save();
else if (source==open)
open();
}
}