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v.0.0.7
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@ekatrukha
ekatrukha committed Mar 25, 2024
1 parent a32b25f commit 1e0e063
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Showing 3 changed files with 153 additions and 57 deletions.
2 changes: 0 additions & 2 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,4 +1,2 @@
bin
/bin/
/target/
/.settings/
192 changes: 137 additions & 55 deletions src/main/java/correlescence/Temporal_ICS.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,7 +31,7 @@ public class Temporal_ICS implements PlugIn {
/** correlation normalization method
* 0 = overlap area
* 1 = full area **/
int nNormMethod=1;
int nNormMethod = 0;

/** object calculating correlation **/
imCC1D x1D = new imCC1D();
Expand All @@ -56,9 +56,14 @@ public class Temporal_ICS implements PlugIn {

/** stack projection to subtract **/
int nProjMethod;

/** find first/highest maximum or all of them**/
int nMaxFindingMethod;

public static final int MAX_First=0, MAX_max=1, MAX_all=2;

/** find first maximum **/
boolean bFindFirstMax;
/** find CC maximum **/
boolean bFindCCMax;

/** estimate the period/frequency more precisely **/
boolean bSubFramePeak;
Expand All @@ -72,6 +77,9 @@ public class Temporal_ICS implements PlugIn {
/** rotated stack containing TICS **/
ImageStack ipICSRotated;

/** stack containing all CC maxima **/
ImageStack isMaxLocations;

/** rescale CC image? **/
boolean bRescaleCC;

Expand All @@ -93,6 +101,9 @@ public class Temporal_ICS implements PlugIn {
String[] projMethods =
{"Average Intensity", "Max Intensity", "Min Intensity", "Sum Slices", "Standard Deviation", "Median"};

String[] maxMethods =
{"First maximum", "Highest Maximum", "All maxima"};

String [] sOutput = new String [] {
"Frequency","Period"};
String [] sOutputUnits = new String [] {
Expand All @@ -111,7 +122,6 @@ public void run(String arg)
ImagePlus finalImpMax=null;
String sTitle;

// TODO Auto-generated method stub
imp = IJ.getImage();

if (imp==null)
Expand Down Expand Up @@ -235,7 +245,7 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
}

//if we want to calculate maximum
if(bFindFirstMax)
if(bFindCCMax)
{
String sTitleMax = "TICS_";
if(nOutput==0)
Expand All @@ -248,6 +258,18 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
sTitleMax = sTitleMax+"period_";
IJ.log("Reported TICS results represent period.");
}
switch (nMaxFindingMethod)
{
case MAX_First:
IJ.log("Finding the first peak of auto-CC.");
break;
case MAX_max:
IJ.log("Finding the highest peak of auto-CC.");
break;
case MAX_all:
IJ.log("Finding all peaks of auto-CC.");
break;
}
if(nOutputUnits==0)
{
IJ.log("Time units: frames.");
Expand All @@ -256,11 +278,19 @@ else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16 &
{
IJ.log("Frame interval "+Double.toString(dTimeUnits)+ " "+outCal.getTimeUnit());
}

finalImpMax = new ImagePlus(sTitleMax+sTitle,findMax(ipICSRotated,dMaxTol));
finalImpMax.setCalibration(outCal);
finalImpMax.show();
IJ.run(finalImpMax,"Fire","");

finalImpMax = findMax(ipICSRotated,dMaxTol,nMaxFindingMethod ,sTitleMax+sTitle);

if(nMaxFindingMethod == MAX_all)
{
new ImagePlus("CC_max_pos_" + sTitle, resliceRotateStack(new ImagePlus("looped",isMaxLocations))).show();
}
else
{
finalImpMax.setCalibration(outCal);
finalImpMax.show();
IJ.run(finalImpMax,"Fire","");
}
}
if(bICSfreqphase)
{
Expand Down Expand Up @@ -321,11 +351,18 @@ public void ICS_pixel()

IJ.showStatus("Calculating temporal correlation...");
ipICSRotated = new ImageStack(nMaxUserDelayICS+1,origH);
if(nMaxFindingMethod == MAX_all)
{
isMaxLocations = new ImageStack(nMaxUserDelayICS+1,origH);
}
for (nindW=0;nindW<origW;nindW++)
{
ipRotatedSlice=getResliceRotatedSlice(imp, nindW);
ipRotatedSlice = getResliceRotatedSlice(imp, nindW);
ipICSRotated.addSlice(xCorrSpace(ipRotatedSlice, nMaxUserDelayICS,nCalcMethod,nNormMethod));

if(nMaxFindingMethod == MAX_all)
{
isMaxLocations.addSlice(new FloatProcessor(nMaxUserDelayICS+1,origH));
}
IJ.showProgress(nindW, origW-1);
}

Expand Down Expand Up @@ -359,6 +396,7 @@ public boolean xDialogTICS()
xTICSDial.addNumericField("Height resized:", Prefs.get("Correlescence.ICSrescaleH", 200), 0,5," ");
xTICSDial.addCheckbox("Estimate period/frequency?", Prefs.get("Correlescence.ICSfindfirstmax", false));
xTICSDial.addNumericField("Tolerance of first CC maximum >", Prefs.get("Correlescence.dMaxTolICS", 0.25), 1,7," ");
xTICSDial.addChoice("Analyze CC and find:", maxMethods, Prefs.get("Correlescence.ICSmaxmethod", "First maximum"));
xTICSDial.addCheckbox("Subframe precision?", Prefs.get("Correlescence.ICSsubframepeak", true));
xTICSDial.addCheckbox("Show TICS stack?", Prefs.get("Correlescence.ICSshowTICSstack", false));
xTICSDial.addMessage("~~~~~~~ FFT ~~~~~~~");
Expand Down Expand Up @@ -389,12 +427,15 @@ public boolean xDialogTICS()
nScaledH=(int)xTICSDial.getNextNumber();
Prefs.set("Correlescence.ICSrescaleH", nScaledH);

bFindFirstMax = xTICSDial.getNextBoolean();
Prefs.set("Correlescence.ICSfindfirstmax", bFindFirstMax);
bFindCCMax = xTICSDial.getNextBoolean();
Prefs.set("Correlescence.ICSfindfirstmax", bFindCCMax);

dMaxTol=xTICSDial.getNextNumber();
Prefs.set("Correlescence.dMaxTolICS", dMaxTol);

nMaxFindingMethod = xTICSDial.getNextChoiceIndex();
Prefs.set("Correlescence.ICSmaxmethod", maxMethods[nMaxFindingMethod]);

bSubFramePeak = xTICSDial.getNextBoolean();
Prefs.set("Correlescence.ICSsubframepeak", bSubFramePeak);

Expand Down Expand Up @@ -448,7 +489,7 @@ public ImageProcessor getResliceRotatedSlice(ImagePlus imp_in, int nWidthPos)

/** Function reslices (rotates) stack, so time becomes x and height becomes y)
* **/
public ImageStack resliceRotateStack(ImagePlus imp_in)
static public ImageStack resliceRotateStack(ImagePlus imp_in)
{

ImageStack rotatedIm;
Expand Down Expand Up @@ -484,14 +525,16 @@ public ImageStack resliceRotateStack(ImagePlus imp_in)
}
/** function to find first maximum with given tolerance
* in the (rotated) stack of TICS **/
public FloatProcessor findMax(ImageStack imp_in, double tolerance)
public ImagePlus findMax(final ImageStack imp_in, final double tolerance, final int nMaxMethod, String sTitle)
//public FloatProcessor findMax(ImageStack imp_in, double tolerance)
{
int stackSize, inWidth, inHeight;
int j,k;

FloatProcessor ipFin;

ImageProcessor ip;
ImageProcessor ipMaxLoc = null;

double[] line = null;

Expand All @@ -507,19 +550,30 @@ public FloatProcessor findMax(ImageStack imp_in, double tolerance)
inWidth = imp_in.getWidth();
inHeight = imp_in.getHeight();
stackSize = imp_in.getSize();
ipFin = new FloatProcessor(stackSize,inHeight);

if(nMaxFindingMethod != MAX_all)
{
ipFin = new FloatProcessor(stackSize,inHeight);
}
else
{
ipFin = null;
}
IJ.showStatus("Estimating frequency/period..");

for (k=0;k<stackSize;k++)
{
ip = imp_in.getProcessor(k+1);
IJ.showProgress(k, stackSize-1);
if(nMaxFindingMethod == MAX_all)
{
ipMaxLoc = isMaxLocations.getProcessor(k+1);
}

for (j=0;j<inHeight;j++)
{
line = getImageRowD(ip,j,inWidth);

//find maxima
maxpos = MaximumFinder.findMaxima(line, tolerance, true);

Arrays.sort(maxpos);
Expand All @@ -532,57 +586,85 @@ public FloatProcessor findMax(ImageStack imp_in, double tolerance)
}
else
{
//if(nMaxMethod == MAX_First)
//first maximum
maxInd = maxpos[0];
//highest maximum
if(nMaxMethod == MAX_max)
{
double maxV = line[maxInd];
for (int i=1;i<arrlength;i++)
{
if(line[maxpos[i]]>maxV)
{
maxInd = i;
maxV=line[maxInd];
}
}
}
//all maxima, store it in imageprocessor
if(nMaxMethod == MAX_all)
{
for (int i=0;i<arrlength;i++)
{
ipMaxLoc.putPixelValue(maxpos[i], j, 1.0);
}
}
}


if(maxInd > 1 && maxInd <line.length-1 && bSubFramePeak)
{
//centroid estimate
//according to https://iopscience.iop.org/article/10.3847/2515-5172/aae265
// A Robust Method to Measure Centroids of Spectral Lines
// Richard Teague and Daniel Foreman-Mackey
// DOI 10.3847/2515-5172/aae265
finVal= maxInd - 0.5*(line[maxInd+1]-line[maxInd-1])/(line[maxInd+1]+line[maxInd-1]-2*line[maxInd]);
}
else
{
finVal = maxInd;
}
//convert to time units (1 if frames)
finVal *= dTimeUnits;

//in case frequency needs to be reported
if(nOutput == 0)
{
finVal = 1./finVal;
}

//special case
if(maxInd == 0)
if(nMaxMethod != MAX_all)
{
//frequency
if(nOutput == 0)
if(maxInd > 1 && maxInd <line.length-1 && bSubFramePeak)
{
finVal = 0.0;
//centroid estimate
//according to https://iopscience.iop.org/article/10.3847/2515-5172/aae265
// A Robust Method to Measure Centroids of Spectral Lines
// Richard Teague and Daniel Foreman-Mackey
// DOI 10.3847/2515-5172/aae265
finVal= maxInd - 0.5*(line[maxInd+1]-line[maxInd-1])/(line[maxInd+1]+line[maxInd-1]-2*line[maxInd]);
}
//period
else
{
finVal = Double.POSITIVE_INFINITY;
finVal = maxInd;
}
}


//store result
ipFin.putPixelValue(k, j, finVal);


//convert to time units (1 if frames)
finVal *= dTimeUnits;

//in case frequency needs to be reported
if(nOutput == 0)
{
finVal = 1./finVal;
}

//special case
if(maxInd == 0)
{
//frequency
if(nOutput == 0)
{
finVal = 0.0;
}
//period
else
{
finVal = Double.POSITIVE_INFINITY;
}
}

//store result
ipFin.putPixelValue(k, j, finVal);
}
}

}
IJ.showProgress(3, 3);
IJ.showStatus("Estimating frequency/period..done");
return ipFin;
if(nMaxMethod == MAX_all)
return null;
else

return new ImagePlus(sTitle,ipFin);
}

/** given input image it treats x coordinates as time,
Expand Down
16 changes: 16 additions & 0 deletions src/test/java/tests/TICSTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,16 @@
package tests;

import correlescence.Correlescence2D;
import correlescence.Temporal_ICS;
import ij.IJ;
import ij.ImageJ;

public class TICSTest {
public static void main( final String[] args )
{
new ImageJ();
IJ.open("/home/eugene/Desktop/cc_test.tif");
Temporal_ICS tics = new Temporal_ICS();
tics.run(null);
}
}

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