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ijp-biop-run-macro/Algorithms/CalculateMinMax.java
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CalculateMinMax.java
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import ij.IJ;
import mpicbg.imglib.cursor.Cursor;
import mpicbg.imglib.image.Image;
import mpicbg.imglib.type.numeric.RealType;
/**
* A class that calculates the minimum and maximum intensity value of the two source
* images in the data container.
*
* @param <T>
*/
public class CalculateMinMax<T extends RealType<T>> extends Algorithm {
public void execute(DataContainer container) throws MissingPreconditionException {
// check if min and max have already been calculated
boolean ch1MinCalculated = container.get(DataContainer.DataTags.MinCh1) != null;
boolean ch1MaxCalculated = container.get(DataContainer.DataTags.MaxCh1) != null;
boolean ch2MinCalculated = container.get(DataContainer.DataTags.MinCh2) != null;
boolean ch2MaxCalculated = container.get(DataContainer.DataTags.MaxCh2) != null;
if (ch1MinCalculated) {
IJ.log("[Calculate Min] The min of channel 1 seems to be calculated already.");
} else {
double min = getImageMin(container.getSourceImage1());
Result result= new Result.SimpleValueResult("Min of channel 1", min);
container.add(result, DataContainer.DataTags.MinCh1);
}
if (ch1MaxCalculated) {
IJ.log("[Calculate Max] The max of channel 1 seems to be calculated already.");
} else {
double max = getImageMax(container.getSourceImage1());
Result result= new Result.SimpleValueResult("Max of channel 1", max);
container.add(result, DataContainer.DataTags.MaxCh1);
}
if (ch2MinCalculated) {
IJ.log("[Calculate Min] The min of channel 2 seems to be calculated already.");
} else {
double min = getImageMin(container.getSourceImage2());
Result result= new Result.SimpleValueResult("Min of channel 2", min);
container.add(result, DataContainer.DataTags.MinCh2);
}
if (ch2MaxCalculated) {
IJ.log("[Calculate Max] The max of channel 2 seems to be calculated already.");
} else {
double max = getImageMax(container.getSourceImage2());
Result result= new Result.SimpleValueResult("Max of channel 2", max);
container.add(result, DataContainer.DataTags.MaxCh2);
}
}
/**
* Calculates the min of an image.
*
* @param img The image to calculate the min of
* @return The min of the image passed
*/
protected double getImageMin(Image<T> img) {
double min = img.createType().getMaxValue();
Cursor<T> cursor = img.createCursor();
while (cursor.hasNext()) {
cursor.fwd();
T type = cursor.getType();
double currValue = type.getRealDouble();
if (currValue < min)
min = currValue;
}
cursor.close();
return min;
}
/**
* Calculates the max of an image.
*
* @param img The image to calculate the max of
* @return The max of the image passed
*/
protected double getImageMax(Image<T> img) {
double max = img.createType().getMinValue();
Cursor<T> cursor = img.createCursor();
while (cursor.hasNext()) {
cursor.fwd();
T type = cursor.getType();
double currValue = type.getRealDouble();
if (currValue > max)
max = currValue;
}
cursor.close();
return max;
}
}
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