Posted by
Gabriel Lapointe on
Nov 21, 2008; 4:11pm
URL: http://imagej.273.s1.nabble.com/doesn-t-recognize-ratio-command-tp3694424p3694428.html
I just started to use the Intensity Correlation Analysis and like some I
had problem if the Display Frequency scatter plot option. Thanks to John
Alexander information that it is simply a lut file that is not present
in the standard ImageJ installation I just changed the source code so
that it uses the fire lut instead, which if I'm not mistaken is in the
ImageJ core.
Here is the fixed source code for those interested.
Gabriel Lapointe
//Version 2.0
//Sept.5.05
//T.J. Collins
[hidden email]
//E.Stanley
[hidden email]
/* Nov.21.2008
Changed the frequency scatter plot lut to allow the use of the
plugin without the need to the Ration.lut file
modification by
[hidden email]
*/
import java.awt.*;
import java.io.*;
import ij.*;
import ij.gui.*;
import ij.process.*;
import ij.text.*;
import ij.plugin.PlugIn;
import java.text.DecimalFormat;
import ij.measure.*;
import ij.measure.ResultsTable.*;
import ij.plugin.filter.*;
public class Intensity_Correlation_Analysis implements PlugIn
{
static boolean headingsSet;
private ImageStack img1, img2;
private static int index1;
private static int index2;
private Roi roi, roi1, roi2;
private ImagePlus imp1, imp2, impmask;
private ImageProcessor ip1, ip2, ipmask;
private static boolean displayCounts =
Prefs.get("ICA_counts.boolean",false);
private boolean displayRGHist = Prefs.get("ICA_RGB.boolean",false);
private boolean displayFreqHist = Prefs.get("ICA_freq.boolean",true);
private boolean displayICQplots =
Prefs.get("ICA_ICQplots.boolean",true);
private boolean displayPositives =
Prefs.get("ICA_positives.boolean",true);
private boolean displayPDMs =Prefs.get("ICA_displayPDMs.boolean",false);
private boolean keepROIimage= Prefs.get("ICA_keepROI.boolean",true);
private boolean useROI ;
private int bitDepth = 255;
private int dualChannelIndex = (int)Prefs.get("ICA_channels.int",0);
private boolean currentSliceOnly= Prefs.get("ICA_current.boolean",true);
private boolean
overlayPositives=Prefs.get("ICA_overlayPositives.boolean",false);
private boolean useThreshold=Prefs.get("ICA_threshold.boolean",false);
private int indexRoi= (int)Prefs.get("ICA_indexRoi.int",0);
private int ch2threshmin=1;
private int ch1threshmin=1;
private int ch2threshmax=255;
private int ch1threshmax=255;
private int xLoc=0;
private int yLoc=0;
private int dot=3;
private int currentSlice ;
private int nslices;
private int width, height, rwidth, rheight, xOffset, yOffset;
private int colIndex1 = 0;
private int colIndex2 = 1;
private int [] color = new int [3];
private ImageWindow winimpROI2,winimpROI1;
public void run(String arg) {
if (showDialog())
correlate(img1, img2);
}
public boolean showDialog()
{
int[] wList = WindowManager.getIDList();
if (wList==null)
{
IJ.noImage();
return false;
}
String[] titles = new String[wList.length];
for (int i=0; i<wList.length; i++)
{
ImagePlus imp = WindowManager.getImage(wList[i]);
if (imp!=null)
titles[i] = imp.getTitle();
else
titles[i] = "";
}
if (wList.length<2)
{
IJ.showMessage("Image Correlator", "Requires at
least two images to be open");
return false;
}
String[] dualChannels= { "Red : Green","Red : Blue", "Green : Blue",};
String[] chooseROI= { "None","Channel 1", "Channel 2",};
if (index1>=titles.length)index1 = 0;
if (index2>=titles.length)index2 = 0;
GenericDialog gd = new GenericDialog("Image Correlation Analysis");
gd.addChoice("Channel_1 ", titles, titles[0]);
gd.addChoice("Channel_2 ", titles, titles[1]);
gd.addChoice("Channel_Combination", dualChannels,
dualChannels[dualChannelIndex]);
gd.addChoice("Use_ROI", chooseROI, chooseROI[indexRoi]);
gd.addCheckbox("Use_Thresholds", useThreshold);
gd.addCheckbox("Keep_merged ROI", keepROIimage);
gd.addCheckbox("Display_Colour Scatter plot", displayRGHist);
gd.addCheckbox("Display_Frequency Scatter plot", displayFreqHist);
gd.addCheckbox("Display_Intensity Counts ", displayCounts);
gd.addCheckbox("Current_Slice only:", currentSliceOnly);
gd.addMessage("Intensity_Correlation Analysis");
gd.addCheckbox("Display_ICA_plots", displayICQplots);
gd.addNumericField("Crosshair_size_(pixels)", dot,0);
gd.addCheckbox("Display_PDM_Image", displayPositives);
gd.addCheckbox("Display_+ve_PDMs_only", overlayPositives);
gd.addCheckbox("List_PDM_values", displayPDMs);
gd.addMessage("For details of Intensity Correlation Analysis (ICA)
"+"\n"+"see and cite: Li, Lau, Morris, Guo & Stanley. "+"\n"+"J
Neurosci. (2004) 24:4070-81. ");
gd.showDialog();
if (gd.wasCanceled())
return false;
index1 = gd.getNextChoiceIndex();
index2 = gd.getNextChoiceIndex();
dualChannelIndex = gd.getNextChoiceIndex();
indexRoi = gd.getNextChoiceIndex();
useThreshold = gd.getNextBoolean();
keepROIimage =gd.getNextBoolean();
displayRGHist = gd.getNextBoolean();
displayFreqHist = gd.getNextBoolean();
displayCounts = gd.getNextBoolean();
currentSliceOnly = gd.getNextBoolean();
displayICQplots =gd.getNextBoolean();
dot = (int)gd.getNextNumber();
displayPositives =gd.getNextBoolean();
overlayPositives =gd.getNextBoolean();
displayPDMs =gd.getNextBoolean();
String title1 = titles[index1];
String title2 = titles[index2];
imp1 = WindowManager.getImage(wList[index1]);
imp2 = WindowManager.getImage(wList[index2]);
ImageStack img1 = imp1.getStack();
ImageStack img2 = imp2.getStack();
width = img1.getWidth();
height = img1.getHeight();
if (imp1.getType()==imp1.COLOR_RGB || imp2.getType()==imp2.COLOR_RGB)
{
IJ.showMessage("Image Correlator", "Both images must
be 8- or 16-bit grayscale.");
return false;
}
currentSlice = imp1.getCurrentSlice();
ImageWindow winimp1= imp1.getWindow();
ImageWindow winimp2= imp2.getWindow();
ImageProcessor ipthresh1 = imp1.getProcessor();
ImageProcessor ipthresh2 = imp2.getProcessor();
if (dualChannelIndex==1) colIndex2 = 2;
if (dualChannelIndex==2) {colIndex1 = 1;colIndex2 =2 ;}
if (imp1.getType()!=imp1.GRAY8)
{bitDepth= 65208;
ch2threshmax=65208;
ch1threshmax=65208;
}
if((useThreshold))
{
if (ipthresh2.getMinThreshold()!=ipthresh2.NO_THRESHOLD)
{
ch2threshmin=(int)ipthresh2.getMinThreshold();
ch2threshmax=(int)ipthresh2.getMaxThreshold();
}
if (ipthresh1.getMinThreshold()!=ipthresh1.NO_THRESHOLD)
{
ch1threshmin=(int)ipthresh1.getMinThreshold();
ch1threshmax=(int)ipthresh1.getMaxThreshold();
}
}
//IJ.showMessage("ch1 "+ch1threshmin+" "+ch1threshmax+"; ch2 "
+ch2threshmin+" "+ ch2threshmax);
nslices = imp1.getStackSize();
if (indexRoi==0) useROI = false;
else useROI=true;
ip1 = imp1.getProcessor();
ip2 = imp2.getProcessor();
roi1 = imp1.getRoi();
roi2 = imp2.getRoi();
Rectangle rect =ip1.getRoi();
if ((indexRoi==1))
{if(roi1==null)
{useROI=false;}
else
{
ipmask = imp1.getMask();
rect = ip1.getRoi();
}
}
if ((indexRoi==2))
{if(roi2==null)
{useROI=false;}
else
{ipmask = imp2.getMask();
rect = ip2.getRoi();
}
}
if (useROI==false)
{
xOffset = 0;yOffset = 0; rwidth=width; rheight =height;
}
else { xOffset = rect.x; yOffset = rect.y; rwidth=rect.width;
rheight =rect.height;
}
//.showMessage(""+useROI);
int g1=0;int g2=0;
return true;
}
public void correlate(ImageStack img1, ImageStack img2)
{
boolean resultsOpen = IJ.isResultsWindow();
if (!resultsOpen) headingsSet = false;
String Ch1fileName = imp1.getTitle();
String Ch2fileName = imp2.getTitle();
String fileName = Ch1fileName + " and " + Ch2fileName;
img1 = imp1.getStack();
img2 = imp2.getStack();
int width2 = img2.getWidth();
int height2 = img2.getHeight();
if ((height!=height2)||(width!=width2))
{
IJ.showMessage("Image Correlator", "Images selected are not the
same size.");
return ;
}
String path = Menus.getPlugInsPath();
ImageProcessor ip1 = imp1.getProcessor();
ImageProcessor ip2 = imp2.getProcessor();
int cdash=0;
ImageProcessor plot = new FloatProcessor(316, 296);
ImageProcessor plot16bit = new ShortProcessor(316, 296);
ImageProcessor plotICQch1 = new ShortProcessor(316, 296);
ImageProcessor plotICQch2 = new ShortProcessor(316, 296);
ImageProcessor plotICQch12 = new ShortProcessor(316, 296);
ImageProcessor plotICQch22 = new ShortProcessor(316, 296);
ImageProcessor ipMerge= new ColorProcessor(rwidth, rheight);
ImageStack mergeStack = new ImageStack (rwidth,rheight);
ImageStack plotStackPDM = new ImageStack (rwidth+35,rheight);
ImageStack plotStackPDMpositives= new ImageStack (rwidth,rheight+15);
ImageStack plotStackPDMnegatives= new ImageStack (rwidth,rheight+15);
StringBuffer sb2 = new StringBuffer();
StringBuffer sb3 = new StringBuffer();
int ch1, z2,ch2;
int sumCh1 = 0;
int sumCh2 = 0;
double sumX = 0;
double sumXY = 0;
double sumXX = 0;
double sumYY = 0;
double sumY = 0;
double sumXtotal = 0;
double sumYtotal = 0;
double colocX = 0;
double colocY = 0;
double countX = 0;
double countY = 0;
int N = 0;
int countnegative = 0;
int countpositive = 0;
int signcountch1=0;
int signcountch2=0;
int countZeroPair=0;
int countNonZeroPair=0;
int ch1max = 0;
int ch2max = 0;
int ch1min = 65208;
int ch2min = 65208;
double ch1Norm = 1;
double ch2Norm = 1;
double ch1normdble =0;
double ch2normdble =0;
DecimalFormat df4 = new DecimalFormat("##0.0000");
DecimalFormat df3 = new DecimalFormat("##0.000");
DecimalFormat df2 = new DecimalFormat("##0.00");
DecimalFormat df1 = new DecimalFormat("##0.0");
DecimalFormat df0 = new DecimalFormat("##0");
double ch2NormMax = 0;
double ch1NormMax=0;
double ch2NormMin = 0;
double ch1NormMin=0;
int PDM2plot=0;
double PDMmax = 0;
double PDMmin = 0;
double PDM=0;
double PDMrange=0;
double PDMnorm=0;
int count=0;
int countTotal=0;
int ch22Plot=128;
int ch12Plot=128;
int numberCh1Pixels = 0;
int numberCh2Pixels=0;
int numberBothNonZero=0;
int mask=1;
int countP=0;
int scaledZ1=0;
int scaledZ2=0;
//run1
int countAll=0;
int countZeroZero=0;
// getting mean ch1
//getting mean ch2
//
//IJ.showMessage("ch1 "+ch1threshmin+" "+ch1threshmax+"; ch2 "
+ch2threshmin+" "+ ch2threshmax);
boolean include = false;
for (int i=1; i<=nslices; i++)
{
if(currentSliceOnly)
{
i = currentSlice;
nslices = currentSlice;
}
IJ.showStatus("Correlating (1/3 steps): "+ i +"/" + nslices);
ip1 = img1.getProcessor(i);
ip2 = img2.getProcessor(i);
for (int y=0; y<rheight; y++)
{
for (int x=0; x<rwidth; x++)
{mask=1;
if((useROI)&&(ipmask!=null)) mask =
(int)ipmask.getPixelValue(x,y);
if (mask!=0)
{
countTotal++;
ch1 = (int)ip1.getPixel(x+xOffset,y+yOffset);
ch2 = (int)ip2.getPixel(x+xOffset,y+yOffset);
if (ch1+ch2==0) countZeroZero++;
countAll++;
if ((ch1>=ch1threshmin)&&(ch2>=ch2threshmin))
include = true;
else include = false;
if(!useThreshold) include = true;
if((ch1>=ch1threshmin))
{sumCh1 = sumCh1 + ch1;
if(ch1>=ch1max) ch1max = ch1;
if(ch1<=ch1min) ch1min = ch1;
numberCh1Pixels++;
}
if((ch2>=ch2threshmin))
{if(ch2>=ch2max) ch2max = ch2;
if(ch2<=ch2min) ch2min = ch2;
numberCh2Pixels++;
sumCh2 = sumCh2 + ch2;
}
if(include)
{
sumX = sumX+ch1;
sumXY = sumXY + (ch1 * ch2);
sumXX = sumXX + (ch1 * ch1);
sumYY = sumYY + (ch2 *ch2);
sumY = sumY + ch2;
countP++;
}
}
}
}
}
countNonZeroPair = countAll-countZeroZero;
double meanCh1= (double)sumCh1/numberCh1Pixels;
double meanCh2 = (double)sumCh2/numberCh2Pixels;
ch1min-=1;
ch1max+=1;
ch2min-=1;
ch2max+=1;
//IJ.showMessage("ch1max: "+ch1max+" ch1min "+ch1min);
// IJ.showMessage("Ch1: "+meanCh1+" Ch2: "+meanCh2+"
Countnon00:"+ countNonZeroPair);
double normMeanCh1 =
((double)meanCh1-(double)ch1min)/((double)ch1max-(double)ch1min);
double
normMeanCh2=((double)meanCh2-(double)ch2min)/((double)ch2max-(double)ch2min);
int ch2Mean2Plot =
(int)((((double)meanCh2-(double)ch2min)/((double)ch2max-(double)ch2min))*(double)256);
int ch1Mean2Plot =
(int)((((double)meanCh1-(double)ch1min)/((double)ch1max-(double)ch1min))*(double)256);
//IJ.showMessage("mean ch1= "+meanCh1+"ch1 min= "+ch1min+" ch1max=
"+ch1max );
if(!useThreshold) countP=countAll-countZeroZero;
double pearsons1 = sumXY - (sumX*sumY/countP);
double pearsons2 = sumXX - (sumX*sumX/countP);
double pearsons3 = sumYY - (sumY*sumY/countP);
//run2 to get PDM extreme
for (int i=1; i<=nslices; i++)
{
IJ.showStatus("Correlating (2/3 steps): "+ i +"/" + nslices);
if(currentSliceOnly)
{
i = currentSlice;
nslices = currentSlice;
}
ip1 = img1.getProcessor(i);
ip2 = img2.getProcessor(i);
for (int y=0; y<rheight; y++)
{
for (int x=0; x<rwidth; x++)
{mask=1;
if((useROI)&&(ipmask!=null)) mask = ipmask.getPixel(x,y);
if (mask!=0)
{
ch1 = (int)ip1.getPixel(x+xOffset,y+yOffset);
ch2 = (int)ip2.getPixel(x+xOffset,y+yOffset);
if ((ch1>=ch1threshmin)&&(ch2>=ch1threshmin))
include = true;
else include = false;
if(!useThreshold) include = true;
if(include)
{
ch1Norm =
(((double)ch1-(double)ch1min)/((double)ch1max-(double)ch1min));
ch2Norm =
(((double)ch2-(double)ch2min)/((double)ch2max-(double)ch2min));
PDM =
((double)ch1Norm-(double)normMeanCh1)*((double)ch2Norm-(double)normMeanCh2);
if (PDM>=PDMmax) PDMmax=PDM;
if (PDM<=PDMmin) PDMmin=PDM;
}
}
}
}
}
if (PDMmax+PDMmin>0) PDMrange = 1.05*(PDMmax);
if (PDMmax+PDMmin<0) PDMrange = -1.05*(PDMmin);
//IJ.showMessage(""+PDMrange);
ImageProcessor ipPDMpositives = new FloatProcessor(width,height+15);
ImageProcessor ipPDMnegatives = new FloatProcessor(width,height+15);
//run 3 to clculate final coefficients and plots
countP=0;
sumX = 0;
sumXY = 0;
sumXX = 0;
sumYY = 0;
sumY = 0;
PDM=0;
int countInclude=0;
countZeroPair=0;
countpositive=0;
for (int i=1; i<=nslices; i++)
{
ImageProcessor ipPDM = new FloatProcessor(rwidth+35,rheight);
ipPDMpositives = new FloatProcessor(rwidth,rheight+15);
ipPDMnegatives = new FloatProcessor(rwidth,rheight+15);
if(currentSliceOnly)
{
i = currentSlice;
nslices = currentSlice;
}
IJ.showStatus("Correlating (3/3 steps): "+ i +"/" + nslices);
ip1 = img1.getProcessor(i);
ip2 = img2.getProcessor(i);
for (int y=0; y<=rheight; y++)
{
for (int x=0; x<=rwidth; x++)
{mask=1;
if((useROI)&&(ipmask!=null)) mask = ipmask.getPixel(x,y);
if (mask!=0)
{
ch1 =
(int)ip1.getPixel(x+xOffset,y+yOffset);
ch2 = (int)ip2.getPixel(x+xOffset,y+yOffset);
if (ch1+ch2==0) countZeroPair++;
//crreate merged image
color[colIndex1]=(int)((ch1*bitDepth)/bitDepth);
color[colIndex2]=(int)((ch2*bitDepth)/bitDepth);
ipMerge.putPixel(x,y,color);
sumXtotal = sumXtotal+ch1;
sumYtotal = sumYtotal+ch2;
if((ch2>=ch2threshmin)&(ch2<=ch2threshmax))
{
colocX = colocX + ch1;
countY = countY + 1;
}
if((ch1threshmin<=ch1)&(ch1<=ch1threshmax))
{
colocY = colocY + ch2;
countX = countX + 1;
}
if ((ch1threshmin<=ch1)&&(ch1<=ch1threshmax))
numberCh1Pixels++;
if ((ch2threshmin<=ch2)&&(ch2<=ch2threshmax))
numberCh2Pixels++;
if(((ch1>=ch1threshmin)&&(ch2>=ch2threshmin))||!useThreshold)
{
countInclude++;
ipPDM.putPixel(x+35,y,0);countP++;
sumX = sumX+ch1;
sumXY = sumXY + (ch1 * ch2);
sumXX = sumXX + (ch1 * ch1);
sumYY = sumYY + (ch2 * ch2);
sumY = sumY + ch2;
ch1Norm = (((double)ch1-ch1min)/(ch1max-ch1min));
ch2Norm =
(((double)ch2-ch2min)/(ch2max-ch2min));
PDMnorm
=((double)ch1Norm-(double)normMeanCh1)*((double)ch2Norm-(double)normMeanCh2);
PDM =
((double)ch1-(double)meanCh1)*((double)ch2-(double)meanCh2);
if ((PDM >0)&&(ch1+ch2!=0)) countpositive++;
//PDM2plot =
127+(int)((((double)PDMnorm/(double)PDMrange))*127);
PDM2plot = (int)(128+(128*(PDMnorm/PDMrange)));
ch12Plot =
(int)((((double)ch1-((double)ch1min))/(((double)ch1max)-((double)ch1min)))*(double)256);
ch22Plot =
(int)((((double)ch2-((double)ch2min))/(((double)ch2max)-((double)ch2min)))*(double)256);
sb2.append(x+"\t"+y+"\t"+df4.format(PDMnorm
)+"\t"+ch1+"\t"+ch2+"\n");
ipPDM.putPixelValue(x+35,y,PDMnorm);
if(PDM>0)
{//ipPDMpositives.putPixelValue(x,y,PDMnorm);
if ((ch1>meanCh1)&&(ch2>meanCh2))
ipPDMpositives.putPixelValue(x,y,PDMnorm);
if ((ch1<meanCh1)&&(ch2<meanCh2))
ipPDMnegatives.putPixelValue(x,y,PDMnorm);
}
signcountch1 = plotICQch12.getPixel(PDM2plot+45,
275-ch12Plot );
signcountch1++;
signcountch2 = plotICQch22.getPixel(PDM2plot
+45,275-ch22Plot );
signcountch2++;
plotICQch1.putPixel(PDM2plot+45,275-ch12Plot
,signcountch1);
plotICQch2.putPixel(PDM2plot+45,275-ch22Plot
,signcountch2);
int dotWidth = (dot-1)/2;
//graph plots
plotICQch12.putPixel(PDM2plot+45,275-ch12Plot
,signcountch1);
plotICQch22.putPixel(PDM2plot+45,275-ch22Plot
,signcountch2);
for (int q=0;q<dot;q++)
{
plotICQch1.putPixel(PDM2plot+45-dotWidth+q,275-ch12Plot ,signcountch1);
plotICQch2.putPixel(PDM2plot+45-dotWidth+q,275-ch22Plot ,signcountch2);
plotICQch1.putPixel(PDM2plot+45,275-dotWidth+q-ch12Plot ,signcountch1);
plotICQch2.putPixel(PDM2plot+45,275-dotWidth+q-ch22Plot ,signcountch2);
}
scaledZ1=
(int)((double)256*(((double)ch1-(double)ch1min)/((double)ch1max-(double)ch1min)));
scaledZ2=
275-(int)((double)256*(((double)ch2-(double)ch2min)/((double)ch2max-(double)ch2min)));
count = plot.getPixel(scaledZ1+45, scaledZ2);
count++;
plot.putPixel(scaledZ1+45, scaledZ2,
count);
if (count<65535) count++;
plot16bit.putPixel(scaledZ1+45, scaledZ2, count);
}
}
}
}
//add ramp
double scale = (rheight/2)/ (2*PDMrange);
for (int y=1; y<(double)(rheight/2); y++)
{for (int x=1; x<25; x++)
{
ipPDM.putPixelValue(5+x, (int)(rheight/4)+y,
(double)(PDMrange-(y/scale)));
}
}
//add text
int fontSize = 12;
int fontDisplacement =(int)((12*0.934211)+1.10526+4);
ipPDM.drawString("+"+df2.format(PDMrange),1,(int)(rheight/4));
ipPDM.drawString(df2.format(-PDMrange),1,
(int)(0.75*rheight)+fontDisplacement);
ipPDMpositives.setColor((int)PDMrange);
ipPDMnegatives.setColor((int)PDMrange);
ipPDM.setMinAndMax(-PDMrange, PDMrange);
ipPDMpositives.setMinAndMax(0, PDMrange/2);
ipPDMnegatives.setMinAndMax(0, PDMrange/2);
ipPDMpositives.drawString("+ve �
+ve",10,(int)rheight-fontDisplacement+30);
ipPDMnegatives.drawString("-ve �
-ve",10,(int)rheight-fontDisplacement+30);
plotStackPDM.addSlice("PDM Stack", ipPDM);
plotStackPDMpositives.addSlice("+vePDMs (+ � +)", ipPDMpositives);
plotStackPDMnegatives.addSlice("+vePDM (- � -)",
ipPDMnegatives);
mergeStack.addSlice("Merged ROI", ipMerge);
}
//collate positives
for (int i=1; i<=nslices;i++)
{if(currentSliceOnly)
{
nslices = 1;
}
ip1 = plotStackPDMnegatives.getProcessor(i);
ip1.setMinAndMax(0, PDMrange);
plotStackPDMpositives.addSlice("+vePDM (- � -)", ip1);
}
double r = pearsons1/(Math.sqrt(pearsons2*pearsons3));
plot.invertLut();
plot.resetMinAndMax();
plot16bit.resetMinAndMax();
String ch1String = " ch1";
String ch2String = " ch2";
if (dualChannelIndex!=0) ch2String = " blue";
if (dualChannelIndex==2) ch1String = " ch2";
Font font;
font = new Font("SansSerif", Font.PLAIN, 12);
int labelx=169;
int labelx2=30;
int labelx3=290;
int labely=295;
String labelCh1Max=df0.format(ch1max);
String labelCh2Max=df0.format(ch2max);
String ch1MeanLabel = df1.format(meanCh1);
String ch2MeanLabel = df1.format(meanCh2);
String ch2MinLabel = df0.format(ch2min);
String ch1MinLabel = df0.format(ch1min);
int ch1AxisOffset = ip1.getStringWidth(labelCh1Max);
int ch2AxisOffset = ip1.getStringWidth(labelCh2Max);
int ch1AxisOffset2 = ip1.getStringWidth(ch1MinLabel );
int ch2AxisOffset2 = ip1.getStringWidth(ch2MinLabel );
int ch1AxisOffset3 = ip1.getStringWidth(ch1MeanLabel );
int ch2AxisOffset3 = ip1.getStringWidth(ch2MeanLabel );
int w=10;
String s="0";
String s1= "-"+df2.format(PDMrange);
String s2 = df2.format(PDMrange);
String s3= "-"+df2.format(PDMrange);
String s4 = df2.format(PDMrange);
if (displayFreqHist)
{
int plotaxis = (int) plot16bit.getMax();
plot16bit.setColor(plotaxis);
plot16bit.drawString(ch1String ,150,295);
plot16bit.drawString(ch2String ,1,150);
plot16bit.drawString(ch1MinLabel ,39-ch1AxisOffset2+w,295);
plot16bit.drawString(ch2MinLabel
,labelx2-ch2AxisOffset2+w,labely-12);
plot16bit.drawString(labelCh1Max,300-ch1AxisOffset+w,295);
plot16bit.drawString(labelCh2Max,labelx2-ch2AxisOffset+w,labely-268);
for (int c=20; c<280; c++)
{
plot16bit.putPixel(45, c,plotaxis );
plot16bit.putPixel(300, c,plotaxis );
}
for (int c=42; c<300; c++)
{
plot16bit.putPixel(c,20,plotaxis );
plot16bit.putPixel(c,275,plotaxis );
}
new ImagePlus("Correlation Plot", plot16bit).show();
ImagePlus imp3 = WindowManager.getCurrentImage();
ImageWindow winimp3 = imp3.getWindow();
imp3.setTitle(fileName + " Freq. CP");
WindowManager.setCurrentWindow(winimp3);
IJ.run("Enhance Contrast", "saturated=0.2 normalize");
IJ.run("Fire");
}
if (displayRGHist)
{
ColorProcessor ipCol = new ColorProcessor(316, 296);
ipCol.setColor(0xffffff);
for (int y=0; y<height; y++)
{
for (int x=0; x<width; x++)
{
ch1 = (int)plot16bit.getPixel(x+45,275-y);
if(ch1>0)
{color[colIndex1]=x;
color[colIndex2]=y;
ipCol.putPixel(x+45,275-y,color);
}
}
}
for (int c=0; c<=2;c++)
{
color [c]= 255;
}
ipCol.drawString(ch1String ,165,295);
ipCol.drawString(ch2String ,10,150);
ipCol.drawString(ch1MinLabel ,39-ch1AxisOffset2+w,295);
ipCol.drawString(ch2MinLabel ,labelx2-ch2AxisOffset2+w,labely-12);
ipCol.drawString(labelCh1Max,300-ch1AxisOffset+w,295);
ipCol.drawString(labelCh2Max,labelx2-ch2AxisOffset+w,labely-268);
for (int c=20; c<280; c++)
{
ipCol.putPixel(45, c,color );
ipCol.putPixel(300, c,color );
}
for (int c=42; c<300; c++)
{
ipCol.putPixel(c,20,color );
ipCol.putPixel(c,275,color );
}
new ImagePlus("Correlation Plot", ipCol).show();
ImagePlus imp4 = WindowManager.getCurrentImage();
ImageWindow winimp4= imp4.getWindow();
IJ.run("Enhance Contrast", "saturated=0.1 normalize");
imp4.setTitle(fileName + " Freq. CP");
}
if (displayICQplots){
plotICQch1.resetMinAndMax();
plotICQch2.resetMinAndMax();
int ch1axis = (int) plotICQch1.getMax();
int ch2axis = (int) plotICQch2.getMax();
for (int c=20; c<280; c++)
{
plotICQch1.putPixel(45, c,ch1axis);
plotICQch2.putPixel(45,c,ch2axis );
plotICQch1.putPixel(173, c,ch1axis);
plotICQch2.putPixel(173,c,ch2axis );
plotICQch1.putPixel(300, c,ch1axis);
plotICQch2.putPixel(300,c,ch2axis );
}
for (int c=42; c<300; c++)
{
plotICQch1.putPixel(c,20,ch1axis);
plotICQch2.putPixel(c,20,ch2axis );
plotICQch1.putPixel(c,275,ch1axis);
plotICQch2.putPixel(c,275,ch2axis );
cdash++;
if (cdash==2)
{
plotICQch1.putPixel(c,275-ch1Mean2Plot,ch1axis);
plotICQch2.putPixel(c,275-ch2Mean2Plot,ch2axis);
cdash=0;
}
}
plotICQch2.setFont(font);
plotICQch1.setFont(font);
plotICQch2.setColor(ch2axis);
plotICQch2.drawString(s ,labelx+1,labely);
plotICQch2.drawString(s1,labelx2,labely);
plotICQch2.drawString(s2,labelx3,labely);
plotICQch1.setColor(ch1axis);
plotICQch1.drawString(s,labelx+1,labely);
plotICQch1.drawString(s3,labelx2,labely);
plotICQch1.drawString(s4,labelx3,labely);
//add titles
plotICQch1.drawString(Ch1fileName ,labelx2-ch1AxisOffset2+w+20,18);
plotICQch2.drawString(Ch2fileName ,labelx2-ch1AxisOffset2+w+20,18);
//add y axis labels
plotICQch1.drawString(ch1MinLabel ,labelx2-ch1AxisOffset2+w,labely-12);
plotICQch2.drawString(ch2MinLabel ,labelx2-ch2AxisOffset2+w,labely-12);
plotICQch1.drawString(labelCh1Max,labelx2-ch1AxisOffset+w,labely-268);
plotICQch2.drawString(labelCh2Max,labelx2-ch2AxisOffset+w,labely-268);
plotICQch2.drawString(ch2MeanLabel,labelx2-ch2AxisOffset3+w,282-ch2Mean2Plot);
plotICQch1.drawString(ch1MeanLabel,labelx2-ch1AxisOffset3+w,282-ch1Mean2Plot);
new ImagePlus("ICA plot -"+Ch1fileName +": "+ ch1String ,
plotICQch1).show();
IJ.run("Enhance Contrast", "saturated=0.0 equalize");
ImagePlus ICQch1 = WindowManager.getCurrentImage();
new ImagePlus("ICA plot -"+Ch2fileName +": "+ ch2String ,
plotICQch2).show();
IJ.run("Enhance Contrast", "saturated=0.0 equalize");
ImagePlus ICQch2 = WindowManager.getCurrentImage();
ImageWindow winICQch1 = ICQch1.getWindow();
ImageWindow winICQch2 = ICQch2.getWindow();
WindowManager.setCurrentWindow(winICQch2);
IJ.run("Cyan");
if (dualChannelIndex==0) IJ.run("Green");
WindowManager.setCurrentWindow(winICQch1);
IJ.run("Red");
if (dualChannelIndex==2) IJ.run("Green");
}
if (displayCounts) displayCounts(plot);
if(overlayPositives ) {new ImagePlus("+vePDM Values - " +fileName ,
plotStackPDMpositives).show();
IJ.run("Fire");
}
if (keepROIimage)new ImagePlus("Merged ROI - "+fileName ,
mergeStack).show();
if (displayPositives)
{ String lutDir =
System.getProperty("user.dir")+File.separator+"lut"+File.separator;
new ImagePlus("PDM Values - "+fileName , plotStackPDM).show();
IJ.run("LUT... ", "open="+"'"+lutDir+"ICA.lut"+"'");
}
if(displayPDMs) new TextWindow( "PDMs", "X-loc\tY-loc\tPDM\tCh1\tCh2",
sb2.toString(),300, 400);
double overlap = sumXY / (Math.sqrt(sumXX*sumYY));
double k1 = sumXY/sumXX;
double k2 = sumXY/sumYY;
double colocM1 = colocX/sumXtotal;
double colocM2 = colocY/sumYtotal;
double pixelratio = (double)countX/(double)countY;
//calculate ICQ
if (!useThreshold) countInclude -=countZeroPair;
//IJ.showMessage("count+ = "+countpositive +" CountNonZeroPair=
"+countNonZeroPair);
double ICQ = ((double)countpositive/(double)countInclude)-0.5;
countnegative = countNonZeroPair-countpositive;
//if (countZeroPair==0) IJ.showMessage("Did you background-correct both
images? \nThere appears to be no zero-zero pixel pairs");
//calculate "percentage overlap"
//int percCh1 = 100*numberBothNonZero/(numberCh1Pixels);
//int percCh2 = 100*numberBothNonZero/(numberCh2Pixels);
String useROIstring = "";
if (useROI) useROIstring = "\nROI used: x "+xLoc+" y"+yLoc+"
w"+width+" h"+height;
StringBuffer ResultsOutput = new StringBuffer();
String Headings =
"Image\tRr\tR\tch1:ch2\tM1\tM2\tN+ve\tNtotal\tICQ\tCh1 Thresh\tCh2
Thresh\n";
if ((!headingsSet)){
IJ.setColumnHeadings(Headings);
headingsSet = true;
IJ.write(Headings);
}
useROIstring ="";
if (currentSliceOnly) useROIstring = " z"+currentSlice;
if(!useThreshold) {ch1threshmin=0;
ch1threshmax=0;ch2threshmin=0;ch2threshmax=0;}
IJ.write(fileName+" x "+xLoc+" y"+yLoc+ useROIstring+" w"+width+"
h"+height+"\t"+df3.format(r)
+"\t" +df3.format(overlap)+
"\t" + df3.format(pixelratio) +
"\t" +df3.format(colocM1)+
"\t" +df3.format(colocM2)+
"\t" +df0.format(countpositive)+
"\t" +df0.format(countNonZeroPair)+
"\t" + df3.format(ICQ)+
"\t" + df0.format(ch1threshmin)+"; "+df0.format(ch1threshmax)+
"\t" + df0.format(ch2threshmin)+"; "+df0.format(ch2threshmax)
);
Prefs.set("ICA_ROI.boolean", useROI);
Prefs.set("ICA_RGB.boolean",displayRGHist );
Prefs.set("ICA_freq.boolean",displayFreqHist );
Prefs.set("ICA_ICQplots.boolean",displayICQplots );
Prefs.set("ICA_positives.boolean",displayPositives );
Prefs.set("ICA_PDMs.boolean",false);
Prefs.set("ICA_channels.int", (int)dualChannelIndex );
Prefs.set("ICA_current.boolean",currentSliceOnly);
Prefs.set("ICA_overlayPositives.boolean",overlayPositives);
Prefs.set("ICA_counts.boolean",displayCounts);
Prefs.set("ICA_displayPDMs.boolean",displayPDMs);
Prefs.set("ICA_threshold.boolean", useThreshold);
Prefs.set("ICA_keepROI.boolean", keepROIimage);
Prefs.set("ICA_indexRoi.int",indexRoi);
imp1.changes = false;
imp2.changes = false;
IJ.setBackgroundColor( 0, 0,0);
IJ.setForegroundColor(255,255,255 );
//imp1.setRoi(roi);
IJ.showStatus("Done");
//new ImagePlus("ICA plot -"+Ch2fileName +": "+ ch2String ,
plotICQch22).show();
System.gc();
}
void displayCounts(ImageProcessor plot) {
StringBuffer sb = new StringBuffer();
int count;
for (int x=0; x<256; x++)
for (int y=255; y>=0; y--) {
count = plot.getPixel(x,y);
if (count>0)
sb.append(x+"\t"+(255-y)+"\t"+count+"\n");
}
new TextWindow( "Pixel intensities and frequencies",
"Ch1\tCh2\tFreq.", sb.toString(), 300, 400);
}
}