Skip to content

Commit

Permalink
test modules for exponential fitting added, jar update
Browse files Browse the repository at this point in the history
  • Loading branch information
@miura
miura committed Apr 21, 2012
1 parent 009fb24 commit c39c2d7
Show file tree
Hide file tree
Showing 3 changed files with 98 additions and 19 deletions.
Binary file modified CorrectBleach_.jar
View file
Binary file not shown.
21 changes: 18 additions & 3 deletions src/emblcmci/BleachCorrection.java
View file
Expand Up @@ -58,7 +58,12 @@
public class BleachCorrection implements PlugInFilter {
ImagePlus imp;

String[] CorrectionMethods = { "Simple Ratio", "Exponential Fit (Frame-wise)","Exponential Fit (Pixel-wise)", "Histogram Matching" };
String[] CorrectionMethods = {
"Simple Ratio",
"Exponential Fit (Frame-wise)",
"Exponential Fit (Pixel-wise)",
"Exponential Fit (Frame-Wise Double Fit)",
"Histogram Matching" };

/**Correction Method 0: simple ratio 1: exponential fit frame 2: exponential fit pixel 3: histogramMatch
*/
Expand Down Expand Up @@ -117,8 +122,18 @@ else if (CorrectionMethod == 2){ //Exponential Fitting Method
}

BCEF.core2();
}
else if (CorrectionMethod == 3){ //HIstogram Matching Method
}
else if (CorrectionMethod == 3){ //Exponential Fitting Method
BleachCorrection_ExpoFit BCEF;
if (curROI == null) {
BCEF = new BleachCorrection_ExpoFit(impdup);
} else {
BCEF = new BleachCorrection_ExpoFit(impdup, curROI);
}

BCEF.core3();
}
else if (CorrectionMethod == 4){ //HIstogram Matching Method
BleachCorrection_MH BCMH = null;
//if (curROI == null) {
BCMH = new BleachCorrection_MH(impdup);
Expand Down
96 changes: 80 additions & 16 deletions src/emblcmci/BleachCorrection_ExpoFit.java
View file
Expand Up @@ -159,21 +159,19 @@ public double calcExponentialOffset(double a, double b, double c, double x){
}
/** 20120420
* returns a FloatProcessor, ratio at the corresponding time point x
* @param ip
* @param b
* @param ip iprocessor of current frame
* @param b
* @param c
* @param x
* @return
*/
public FloatProcessor calcExponentialOffset(ImageProcessor ip, double b, double c, double x){
public FloatProcessor calcOriginalExponential(ImageProcessor ip, double b, double c, double x){
float[] ipfA = (float[]) ip.toFloat(0, null).getPixels();
FloatProcessor ip2 = ip.duplicate().toFloat(0, null);
float[] destA = (float[]) ip2.getPixels();
for (int i = 0; i < ipfA.length; i++){
float amp = (float) Math.abs(ipfA[i] - c);
destA[i] = (float) (amp * Math.exp(-b*x) + c)/ipfA[i] ;
// if (destA[i]<1.0)
// IJ.log(Float.toString(destA[i]));
// destA[i] = (float) (amp * Math.exp(-b*x) + c)/ipfA[i] ;
destA[i] = (float) ((ipfA[i] - c)/Math.exp(-b*x) + c) ;
}
return ip2;
}
Expand Down Expand Up @@ -265,28 +263,94 @@ public void core2(){
float[] cipA, ratioA;
for (int i = 0; i < imp.getStackSize(); i++){
curip = imp.getImageStack().getProcessor(i+1);
FloatProcessor ratioim = calcExponentialOffset(firstip, res_b, res_c, (double) i+1);
cipA = (float[]) curip.duplicate().toFloat(0, null).getPixels();
ratioA = (float[]) ratioim.getPixels();
for (int j = 0; j < cipA.length; j++)
if (ratioA[j] != 0)
ratioA[j] = (float) Math.round(cipA[j]/ratioA[j]);
FloatProcessor estim = calcOriginalExponential(curip, res_b, res_c, (double) i+1);
// cipA = (float[]) curip.duplicate().toFloat(0, null).getPixels();
// ratioA = (float[]) ratioim.getPixels();
// for (int j = 0; j < cipA.length; j++)
// if (ratioA[j] != 0)
// ratioA[j] = (float) Math.round(cipA[j]/ratioA[j]);
if (imtype == imp.GRAY8)
ratioim.convertToByte(false);
estim.convertToByte(false);
else if (imtype == imp.GRAY16)
ratioim.convertToShort(false);
estim.convertToShort(false);
else if (imtype == imp.GRAY32){

} else {
IJ.error("this image type not implemented");
}
curip.copyBits(ratioim, 0, 0, Blitter.COPY);
curip.copyBits(estim, 0, 0, Blitter.COPY);

}
}
}
}


/** does both DOUBLE decay fitting and bleach correction.
* ... first fit is for baseline estimation, second for the ratio calculation.
*/
public void core3(){
int[] impdimA = imp.getDimensions();
IJ.log("slices"+Integer.toString(impdimA[3])+" -- frames"+Integer.toString(impdimA[4]));
//IJ.log(Integer.toString(imp.getNChannels())+":"+Integer.toString(imp.getNSlices())+":"+ Integer.toString(imp.getNFrames()));
int zframes = impdimA[3];
int tframes = impdimA[4];
if (impdimA[3]>1 && impdimA[4]>1){ // if slices and frames are both more than 1
is3DT =true;
if ((impdimA[3] * impdimA[4]) != imp.getStackSize()){
IJ.showMessage("slice and time frames do not match with the length of the stack. Please correct!");
return;
}
}
CurveFitter cf;
if (is3DT) cf = decayFitting3D(zframes, tframes);
else cf = dcayFitting();
if (cf != null){
double base_c = cf.getParams()[2];
ImageProcessor curip;
System.out.println("baseline level:" + base_c);
//subtract baseline
if (is3DT){
for (int i = 0; i < tframes; i++){
for (int j = 0; j < zframes; j++){
curip = imp.getImageStack().getProcessor(i * zframes + j + 1);
curip.subtract(base_c);
}
}
} else {
for (int i = 0; i < imp.getStackSize(); i++){
curip = imp.getImageStack().getProcessor(i+1);
curip.subtract(base_c);
}
}
}
//second round
if (is3DT) cf = decayFitting3D(zframes, tframes);
else cf = dcayFitting();
if (cf != null) {
double[] respara = cf.getParams();
double res_a = respara[0];
double res_b = respara[1];
double res_c = respara[2];
double ratio = 0.0;
ImageProcessor curip;
System.out.println(res_a + "," + res_b + "," + res_c);
if (is3DT){
for (int i = 0; i < tframes; i++){
for (int j = 0; j < zframes; j++){
curip = imp.getImageStack().getProcessor(i * zframes + j + 1);
ratio = calcExponentialOffset(res_a, res_b, res_c, 0.0) / calcExponentialOffset(res_a, res_b, res_c, (double) (i + 1));
curip.multiply(ratio);
}
}
} else {
for (int i = 0; i < imp.getStackSize(); i++){
curip = imp.getImageStack().getProcessor(i+1);
ratio = calcExponentialOffset(res_a, res_b, res_c, 0.0) / calcExponentialOffset(res_a, res_b, res_c, (double) (i + 1));
curip.multiply(ratio);
}
}
}
}

}

0 comments on commit c39c2d7

Please sign in to comment.