/**
* Class constructor alloowing specification of the heading text.
*
* @param properties the Properties object containing the initial values of the extensions list
* and the path to be displayed. This object is updated tin response to root changes,
* extension changes, and file selections. If any property is missing, a suitable one is
* supplied by default.
* @param heading the text to appear in the heading of the JPanel.
* @param background the background color or null if the default is to be used.
*/
public SourcePanel(ApplicationProperties properties, String heading, Color background) {
super();
this.properties = properties;
if (background == null) this.background = Color.getHSBColor(0.58f, 0.17f, 0.95f);
else this.background = background;
// Make the file filter
filter = new GeneralFileFilter();
String extensions = properties.getProperty("extensions");
if (extensions != null) filter.setExtensions(extensions);
else {
filter.addExtension(".dcm");
properties.setProperty("extensions", filter.getExtensionString());
}
// Get the starting directory path from the properties.
// If it is missing, start in the directory containing the program.
String currentDirectoryPath = properties.getProperty("directory");
if (currentDirectoryPath == null) currentDirectoryPath = System.getProperty("user.dir");
// Create the UI components
this.setLayout(new BorderLayout());
directoryPane = new DirectoryPane(filter, currentDirectoryPath);
directoryPane.addFileListener(this);
headerPanel = new HeaderPanel(heading);
footerPanel = new FooterPanel();
this.add(headerPanel, BorderLayout.NORTH);
this.add(directoryPane, BorderLayout.CENTER);
this.add(footerPanel, BorderLayout.SOUTH);
}
/* Wraps everything into a Cell Manager Class*/
private CellManager toCellManager(ImagePlus imp, ArrayList<PolygonRoi> rois, ImagePlus av_imp) {
CellManager cm = new CellManager(av_imp, imp, this.ovr);
Iterator itr = rois.iterator();
ArrayList<Double> av_sig = new ArrayList<>();
PolygonRoi roi;
while (itr.hasNext()) {
roi = (PolygonRoi) itr.next();
av_sig = Activity_Analysis.getAverageSignal(imp, roi);
CalciumSignal ca_sig = new CalciumSignal(av_sig, this.dt_r);
ovr.add(roi);
ca_sig.DeltaF();
cm.addCell(ca_sig, roi);
}
// catch(Exception e){
// IJ.showMessage(e.getMessage());
// }
// }
ovr.setLabelColor(Color.WHITE);
// ovr.setFillColor(Color.GREEN);
ovr.setStrokeColor(Color.getHSBColor(100, 30, 87));
av_imp.setOverlay(ovr);
av_imp.show();
IJ.run("In [+]", "");
IJ.run("In [+]", "");
return cm;
}
void initComponents() {
JPanel mainPanel = new JPanel(new BorderLayout());
JPanel buttonPanel = new JPanel();
buttonPanel.setLayout(new BoxLayout(buttonPanel, BoxLayout.X_AXIS));
Color bgColor = Color.getHSBColor(0.58f, 0.17f, 0.95f);
buttonPanel.setBackground(bgColor);
Border empty = BorderFactory.createEmptyBorder(5, 5, 5, 5);
buttonPanel.setBorder(empty);
textField = new JTextField(75);
buttonPanel.add(textField);
buttonPanel.add(Box.createHorizontalStrut(10));
searchPHI = new JButton("Search PHI");
searchPHI.addActionListener(this);
buttonPanel.add(searchPHI);
buttonPanel.add(Box.createHorizontalStrut(10));
searchTrial = new JButton("Search Trial IDs");
searchTrial.addActionListener(this);
buttonPanel.add(searchTrial);
buttonPanel.add(Box.createHorizontalStrut(20));
buttonPanel.add(Box.createHorizontalGlue());
saveAs = new JCheckBox("Save As...");
saveAs.setBackground(bgColor);
buttonPanel.add(saveAs);
mainPanel.add(buttonPanel, BorderLayout.NORTH);
JScrollPane scrollPane = new JScrollPane();
textPane = new ColorPane();
// textPane.setEditable(false);
scrollPane.setViewportView(textPane);
mainPanel.add(scrollPane, BorderLayout.CENTER);
JPanel footerPanel = new JPanel();
footerPanel.setLayout(new BoxLayout(footerPanel, BoxLayout.X_AXIS));
footerPanel.setBackground(bgColor);
message = new JLabel("Ready...");
footerPanel.add(message);
mainPanel.add(footerPanel, BorderLayout.SOUTH);
setTitle(windowTitle);
addWindowListener(
new WindowAdapter() {
public void windowClosing(WindowEvent evt) {
System.exit(0);
}
});
getContentPane().add(mainPanel, BorderLayout.CENTER);
pack();
centerFrame();
}
public FooterPanel() {
super();
this.setLayout(new BoxLayout(this, BoxLayout.X_AXIS));
this.setBackground(Color.getHSBColor(0.58f, 0.17f, 0.95f));
subdirectories = new JCheckBox("Include subdirectories");
subdirectories.setBackground(background);
this.add(subdirectories);
this.add(Box.createHorizontalGlue());
extensionButton = new JButton(filter.getDescription());
this.add(extensionButton);
this.add(Box.createHorizontalStrut(17));
extensionButton.addActionListener(this);
}
protected Color colorForValue(double value, double brightness) {
return Color.getHSBColor((float) value, 1.0f, (float) brightness); // use array value as hue
}
ImageProcessor setup(ImagePlus imp) {
ImageProcessor ip;
int type = imp.getType();
if (type != ImagePlus.COLOR_RGB) return null;
ip = imp.getProcessor();
int id = imp.getID();
int slice = imp.getCurrentSlice();
if ((id != previousImageID) | (slice != previousSlice) | (flag)) {
flag = false; // if true, flags a change from HSB to RGB or viceversa
numSlices = imp.getStackSize();
stack = imp.getStack();
width = stack.getWidth();
height = stack.getHeight();
numPixels = width * height;
hSource = new byte[numPixels];
sSource = new byte[numPixels];
bSource = new byte[numPixels];
// restore = (int[])ip.getPixelsCopy(); //This runs into trouble sometimes, so do it the
// long way:
int[] temp = (int[]) ip.getPixels();
restore = new int[numPixels];
for (int i = 0; i < numPixels; i++) restore[i] = temp[i];
fillMask = new int[numPixels];
// Get hsb or rgb from image.
ColorProcessor cp = (ColorProcessor) ip;
IJ.showStatus("Gathering data");
if (isRGB) cp.getRGB(hSource, sSource, bSource);
else cp.getHSB(hSource, sSource, bSource);
IJ.showStatus("done");
// Create a spectrum ColorModel for the Hue histogram plot.
Color c;
byte[] reds = new byte[256];
byte[] greens = new byte[256];
byte[] blues = new byte[256];
for (int i = 0; i < 256; i++) {
c = Color.getHSBColor(i / 255f, 1f, 1f);
reds[i] = (byte) c.getRed();
greens[i] = (byte) c.getGreen();
blues[i] = (byte) c.getBlue();
}
ColorModel cm = new IndexColorModel(8, 256, reds, greens, blues);
// Make an image with just the hue from the RGB image and the spectrum LUT.
// This is just for a hue histogram for the plot. Do not show it.
// ByteProcessor bpHue = new ByteProcessor(width,height,h,cm);
ByteProcessor bpHue = new ByteProcessor(width, height, hSource, cm);
ImagePlus impHue = new ImagePlus("Hue", bpHue);
// impHue.show();
ByteProcessor bpSat = new ByteProcessor(width, height, sSource, cm);
ImagePlus impSat = new ImagePlus("Sat", bpSat);
// impSat.show();
ByteProcessor bpBri = new ByteProcessor(width, height, bSource, cm);
ImagePlus impBri = new ImagePlus("Bri", bpBri);
// impBri.show();
plot.setHistogram(impHue, 0);
splot.setHistogram(impSat, 1);
bplot.setHistogram(impBri, 2);
updateLabels();
updatePlot();
updateScrollBars();
imp.updateAndDraw();
}
previousImageID = id;
previousSlice = slice;
return ip;
}