@Override
public boolean run(JEXEntry optionalEntry) {
if (imageData == null || !imageData.getTypeName().getType().equals(JEXData.IMAGE)) {
return false;
}
// Run the function
TreeMap<DimensionMap, String> images = ImageReader.readObjectToImagePathTable(imageData);
TreeMap<DimensionMap, String> outputMap = new TreeMap<DimensionMap, String>();
int count = 0;
int total = images.size();
for (DimensionMap dim : images.keySet()) {
if (this.isCanceled()) {
return false;
}
String path = images.get(dim);
// File f = new File(path);
// get the image
ImagePlus im = new ImagePlus(path);
ij.process.ImageProcessor imProc = im.getProcessor();
if (imProc == null) continue;
FloatProcessor imp =
(FloatProcessor) im.getProcessor().convertToFloat(); // should be a float processor
int newWidth = (int) (imp.getWidth() * scale);
imp.setInterpolationMethod(ImageProcessor.BILINEAR);
imp = (FloatProcessor) imp.resize(newWidth);
ImagePlus toSave = FunctionUtility.makeImageToSave(imp, "false", bitDepth);
String finalPath = JEXWriter.saveImage(toSave);
outputMap.put(dim.copy(), finalPath);
Logs.log("Finished processing " + count + " of " + total + ".", 1, this);
count++;
// Status bar
int percentage = (int) (100 * ((double) count / (double) images.size()));
JEXStatics.statusBar.setProgressPercentage(percentage);
}
// Set the outputs
output = ImageWriter.makeImageStackFromPaths("temp", outputMap);
output.setDataObjectInfo("Stack binned using binning function");
// Return status
return true;
}
private void adjustImage() {
FunctionUtility.imAdjust(imp, oldMin, oldMax, newMin, newMax, gamma);
}
/** Apply the roi to all other images */
public void finishIT() {
auto = Boolean.parseBoolean(params.getValueOfParameter("Automatic"));
oldMin = Double.parseDouble(params.getValueOfParameter("Old Min"));
oldMax = Double.parseDouble(params.getValueOfParameter("Old Max"));
newMin = Double.parseDouble(params.getValueOfParameter("New Min"));
newMax = Double.parseDouble(params.getValueOfParameter("New Max"));
gamma = Double.parseDouble(params.getValueOfParameter("Gamma"));
depth = Integer.parseInt(params.getValueOfParameter("Output Bit Depth"));
output = new JEXData(JEXData.IMAGE, outputNames[0].getName(), "Adjusted image");
// Run the function
// TreeMap<DimensionMap,JEXDataSingle> map = imset.getDataMap();
TreeMap<DimensionMap, String> pathMap = ImageReader.readObjectToImagePathTable(imset);
int count = 0;
int total = pathMap.size();
JEXStatics.statusBar.setProgressPercentage(0);
TreeMap<DimensionMap, String> imMap = new TreeMap<DimensionMap, String>();
for (DimensionMap dim : pathMap.keySet()) {
// JEXDataSingle ds = map.get(dim);
// String imagePath = ds.get(JEXDataSingle.FOLDERNAME) +
// File.separator + ds.get(JEXDataSingle.FILENAME);
String imagePath = pathMap.get(dim);
// File imageFile = new File(imagePath);
// String imageName = imageFile.getName();
// get the image
im = new ImagePlus(imagePath);
imp = (FloatProcessor) im.getProcessor().convertToFloat(); // should
// be a
// float
// processor
// //// Begin Actual Function
adjustImage();
// //// End Actual Function
// //// Save the results
ImagePlus toSave = FunctionUtility.makeImageToSave(imp, "false", depth);
String imPath = JEXWriter.saveImage(toSave);
// Put into imMap
imMap.put(dim, imPath);
// String localDir = JEXWriter.getEntryFolder(entry);
// String newFileName = FunctionUtility.getNextName(localDir,
// imageName, "A");
// String newImagePath = localDir + File.separator + newFileName;
// FunctionUtility.imSave(imp, "false", depth, newImagePath);
//
// // Put into imMap
// imMap.put(dim, localDir + File.separator + newFileName) ;
// JEXDataSingle outputds = new DefaultJEXDataSingle();
// outputds.put(JEXDataSingle.FOLDERNAME, localDir);
// outputds.put(JEXDataSingle.FILENAME, newFileName);
// output.addData(dim,outputds);
// Increment count
Logs.log("Finished processing " + count + " of " + total + ".", 1, this);
count++;
// Status bar
int percentage = (int) (100 * ((double) count / (double) pathMap.size()));
JEXStatics.statusBar.setProgressPercentage(percentage);
}
output = ImageWriter.makeImageStackFromPaths(outputNames[0].getName(), imMap);
}