/**
* Returns a list of parameters necessary for this function to run... Every parameter is defined
* as a line in a form that provides the ability to set how it will be displayed to the user and
* what options are available to choose from The simplest FormLine can be written as: FormLine p =
* new FormLine(parameterName); This will provide a text field for the user to input the value of
* the parameter named parameterName More complex displaying options can be set by consulting the
* FormLine API
*
* @return list of FormLine to create a parameter panel
*/
@Override
public ParameterSet requiredParameters() {
Parameter p0 =
new Parameter(
"Automatic",
"Enable visual interface",
Parameter.DROPDOWN,
new String[] {"true", "false"},
0);
Parameter p1 = new Parameter("Old Min", "Image Intensity Value", "0.0");
Parameter p2 = new Parameter("Old Max", "Image Intensity Value", "4095.0");
Parameter p3 = new Parameter("New Min", "Image Intensity Value", "0.0");
Parameter p4 = new Parameter("New Max", "Image Intensity Value", "65535.0");
Parameter p5 = new Parameter("Gamma", "0.1-5.0, value of 1 results in no change", "1.0");
Parameter p6 =
new Parameter(
"Output Bit Depth",
"Depth of the outputted image",
Parameter.DROPDOWN,
new String[] {"8", "16", "32"},
1);
// Make an array of the parameters and return it
ParameterSet parameterArray = new ParameterSet();
parameterArray.addParameter(p0);
parameterArray.addParameter(p1);
parameterArray.addParameter(p2);
parameterArray.addParameter(p3);
parameterArray.addParameter(p4);
parameterArray.addParameter(p5);
parameterArray.addParameter(p6);
return parameterArray;
}
AdjustImageHelperFunction(
JEXData imset, JEXEntry entry, TypeName[] outputNames, ParameterSet parameters) {
// Pass the variables
this.imset = imset;
this.params = parameters;
this.entry = entry;
this.outputNames = outputNames;
// //// Get params
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"));
TreeMap<DimensionMap, JEXDataSingle> map = imset.getDataMap();
int length = map.size();
images = new String[length];
dimensions = new DimensionMap[length];
int i = 0;
TreeMap<DimensionMap, String> pathMap = ImageReader.readObjectToImagePathTable(imset);
for (DimensionMap dim : pathMap.keySet()) {
String path = pathMap.get(dim);
dimensions[i] = dim;
images[i] = path;
i++;
}
// Prepare the graphics
imagepanel = new ImagePanel(this, "Adjust image");
displayImage(index);
wrap = new GraphicalFunctionWrap(this, params);
wrap.addStep(
0,
"Select roi",
new String[] {"Automatic", "Old Min", "Old Max", "New Min", "New Max", "Output Bit Depth"});
wrap.setInCentralPanel(imagepanel);
wrap.setDisplayLoopPanel(true);
}
public void runStep(int index) {
// Get the new parameters
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"));
// prepare the images for calculation
ImagePlus im = new ImagePlus(images[index]);
imagepanel.setImage(im);
imp = (FloatProcessor) im.getProcessor().convertToFloat(); // should be
// a float
// processor
adjustImage();
imagepanel.setImage(new ImagePlus("", imp));
}
/** 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);
}