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Adds log checkbox to GUI #22

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Adds log checkbox to GUI #22

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37dd61b
log gui functionality
abrewe Jun 15, 2022
4fbfb69
format, 32bit behavior
abrewe Jun 30, 2022
1017728
formatting
abrewe Jun 30, 2022
3fd6088
more formatting
abrewe Jun 30, 2022
4314d03
final formats
abrewe Jun 30, 2022
92cb99d
increase efficiency
abrewe Jul 11, 2022
630005d
fix compile error (hopefully)
abrewe Jul 13, 2022
87d7be6
Update log-snap behavior
abrewe Jul 15, 2022
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248 changes: 178 additions & 70 deletions ImageJ/EPICS_areaDetector/EPICS_AD_Viewer.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,8 @@ public class EPICS_AD_Viewer implements PlugIn
{
ImagePlus img;
ImageStack imageStack;

Object snapBackup = null;
Object altSnapBackup = null;
int imageSizeX = 0;
int imageSizeY = 0;
int imageSizeZ = 0;
Expand Down Expand Up @@ -70,6 +71,7 @@ public class EPICS_AD_Viewer implements PlugIn
JButton startButton;
JButton stopButton;
JButton snapButton;
JCheckBox logCheckBox;

boolean isDebugMessages;
boolean isDebugFile;
Expand All @@ -78,6 +80,8 @@ public class EPICS_AD_Viewer implements PlugIn
boolean isSaveToStack;
boolean isNewStack;
boolean isConnected;
boolean isLogOn;
boolean firstLog;
volatile boolean isNewImageAvailable;

javax.swing.Timer timer;
Expand All @@ -94,6 +98,8 @@ public void run(String arg)
isNewImageAvailable = false;
isSaveToStack = false;
isNewStack = false;
isLogOn = false;
firstLog=false;
Date date = new Date();
prevTime = date.getTime();
numImageUpdates = 0;
Expand All @@ -102,19 +108,18 @@ public void run(String arg)

if (isDebugFile)
{
debugFile = new FileOutputStream(System.getProperty("user.home") +
System.getProperty("file.separator") + "IJEPICS_debug.txt");
debugFile = new FileOutputStream(System.getProperty("user.home") + System.getProperty("file.separator") + "IJEPICS_debug.txt");
debugPrintStream = new PrintStream(debugFile);
}
javax.swing.SwingUtilities.invokeLater(
new Runnable()
{
public void run()
{
createAndShowGUI();
}
}
);
new Runnable()
{
public void run()
{
createAndShowGUI();
}
}
);

img = new ImagePlus(PVPrefix, new ByteProcessor(100, 100));
img.show();
Expand Down Expand Up @@ -178,8 +183,17 @@ public void makeImageCopy()
{
ImageProcessor ip = img.getProcessor();
if (ip == null) return;
ImagePlus imgcopy = new ImagePlus(PVPrefix + ":" + ArrayCounter, ip.duplicate());
imgcopy.show();
if(isLogOn) {
ImageProcessor ipcopy = ip.duplicate();
ipcopy.setPixels(snapBackup);
ImagePlus imgcopy = new ImagePlus(PVPrefix + ":" + ArrayCounter, ipcopy);
resetContrast(imgcopy);
imgcopy.show();
}
else {
ImagePlus imgcopy = new ImagePlus(PVPrefix + ":" + ArrayCounter, ip.duplicate());
imgcopy.show();
}
}

public void connectPVs()
Expand Down Expand Up @@ -210,9 +224,9 @@ public void connectPVs()
ch_image = createEPICSChannel(PVPrefix + "ArrayData");
ch_image_id = createEPICSChannel(PVPrefix + "ArrayCounter_RBV");
ch_image_id.addMonitor(
Monitor.VALUE,
new newArrayCounterCallback()
);
Monitor.VALUE,
new newArrayCounterCallback()
);
ctxt.flushIO();
checkConnections();
}
Expand Down Expand Up @@ -313,12 +327,12 @@ public void checkConnections()
try
{
connected = (ch_nx != null && ch_nx.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_ny != null && ch_ny.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_nz != null && ch_nz.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_colorMode != null && ch_colorMode.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_dataType != null && ch_dataType.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_image != null && ch_image.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_image_id != null && ch_image_id.getConnectionState() == Channel.ConnectionState.CONNECTED);
ch_ny != null && ch_ny.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_nz != null && ch_nz.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_colorMode != null && ch_colorMode.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_dataType != null && ch_dataType.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_image != null && ch_image.getConnectionState() == Channel.ConnectionState.CONNECTED &&
ch_image_id != null && ch_image_id.getConnectionState() == Channel.ConnectionState.CONNECTED);
if (connected && !isConnected)
{
isConnected = true;
Expand Down Expand Up @@ -402,7 +416,7 @@ public void updateImage()
}
}
catch (Exception ex) {
IJ.log("updateImage got exception: " + ex.getMessage());
IJ.log("updateImage got exception: " + ex.getMessage());
}
makeNewWindow = false;
}
Expand Down Expand Up @@ -445,7 +459,7 @@ else if (ADDataType == 3)
{
imageStack = new ImageStack(img.getWidth(), img.getHeight());
imageStack.addSlice(PVPrefix + ArrayCounter, img.getProcessor());
// Note: we need to add this first slice twice in order to get the slider bar
// Note: we need to add this first slice twice in order to get the slider bar
// on the window - ImageJ won't put it there if there is only 1 slice.
imageStack.addSlice(PVPrefix + ArrayCounter, img.getProcessor());
img.close();
Expand Down Expand Up @@ -487,11 +501,11 @@ else if (colorMode >= 2 && colorMode <= 4)
prevDispMax = dispMax;
double slope = 255/(dispMax - dispMin);
for (i=0; i<256; i++) {
if (i<dispMin)
if (i<dispMin)
colorLUT[i] = 0;
else if (i>dispMax)
colorLUT[i] = (byte)255;
else
else
colorLUT[i] = (byte)((i-dispMin)*slope + 0.5);
}
}
Expand All @@ -502,44 +516,57 @@ else if (i>dispMax)
switch (colorMode)
{
case 2:
{
int in = 0, out = 0;
while (in < getsize)
{
int in = 0, out = 0;
while (in < getsize)
{
pixels[out++] = (inpixels[in++] & 0xFF) << 16 | (inpixels[in++] & 0xFF) << 8 | (inpixels[in++] & 0xFF);
}
pixels[out++] = (inpixels[in++] & 0xFF) << 16 | (inpixels[in++] & 0xFF) << 8 | (inpixels[in++] & 0xFF);
}
break;
}
break;
case 3:
{
int nCols = imageSizeX, nRows = imageSizeZ, row, col;
int redIn, greenIn, blueIn, out = 0;
for (row = 0; row < nRows; row++)
{
int nCols = imageSizeX, nRows = imageSizeZ, row, col;
int redIn, greenIn, blueIn, out = 0;
for (row = 0; row < nRows; row++)
redIn = row * nCols * 3;
greenIn = redIn + nCols;
blueIn = greenIn + nCols;
for (col = 0; col < nCols; col++)
{
redIn = row * nCols * 3;
greenIn = redIn + nCols;
blueIn = greenIn + nCols;
for (col = 0; col < nCols; col++)
{
pixels[out++] = (inpixels[redIn++] & 0xFF) << 16 | (inpixels[greenIn++] & 0xFF) << 8 | (inpixels[blueIn++] & 0xFF);
}
pixels[out++] = (inpixels[redIn++] & 0xFF) << 16 | (inpixels[greenIn++] & 0xFF) << 8 | (inpixels[blueIn++] & 0xFF);
}
}
break;
}
break;
case 4:
{
int imageSize = imageSizeX * imageSizeY;
int redIn = 0, greenIn = imageSize, blueIn = 2 * imageSize, out = 0;
while (redIn < imageSize)
{
int imageSize = imageSizeX * imageSizeY;
int redIn = 0, greenIn = imageSize, blueIn = 2 * imageSize, out = 0;
while (redIn < imageSize)
{
pixels[out++] = (inpixels[redIn++] & 0xFF) << 16 | (inpixels[greenIn++] & 0xFF) << 8 | (inpixels[blueIn++] & 0xFF);
}
pixels[out++] = (inpixels[redIn++] & 0xFF) << 16 | (inpixels[greenIn++] & 0xFF) << 8 | (inpixels[blueIn++] & 0xFF);
}
break;
}
break;
}
img.getProcessor().setPixels(pixels);
}

if (isLogOn)
{
img.getProcessor().snapshot();
snapBackup=img.getProcessor().getSnapshotPixels();
if(ADDataType!=3 && ADDataType!=1)
log(img);
else {
img.getProcessor().log();
}
if (firstLog){
resetContrast(img);
firstLog = false;
}
}
if (isSaveToStack)
{
img.getStack().addSlice(PVPrefix + ArrayCounter, img.getProcessor().duplicate());
Expand Down Expand Up @@ -640,6 +667,7 @@ public void createAndShowGUI()
stopButton.setEnabled(false);
snapButton = new JButton("Snap");
JCheckBox captureCheckBox = new JCheckBox("");
logCheckBox = new JCheckBox("");

frame = new JFrame("Image J EPICS_AD_Viewer Plugin");
JPanel panel = new JPanel(new BorderLayout());
Expand All @@ -666,6 +694,8 @@ public void createAndShowGUI()
panel.add(new JLabel("Frames/s"), c);
c.gridx = 5;
panel.add(new JLabel("Capture to Stack"), c);
c.gridx = 9;
panel.add(new JLabel("Log"), c);

// Middle row
// These widgets should be centered
Expand All @@ -689,6 +719,8 @@ public void createAndShowGUI()
panel.add(startButton, c);
c.gridx = 8;
panel.add(stopButton, c);
c.gridx = 9;
panel.add(logCheckBox, c);

// Bottom row
c.gridy = 2;
Expand All @@ -706,7 +738,7 @@ public void createAndShowGUI()
frame.setVisible(true);


int timerDelay = 2000; // 2 seconds
int timerDelay = 2000; // 2 seconds
timer = new javax.swing.Timer(timerDelay, new ActionListener()
{
public void actionPerformed(ActionEvent event)
Expand Down Expand Up @@ -756,6 +788,64 @@ public void actionPerformed(ActionEvent event)
logMessage("Image display stopped", true, true);
}
});
logCheckBox.addItemListener(new ItemListener() {
public void itemStateChanged(ItemEvent e) {
if (e.getStateChange() == ItemEvent.SELECTED) {
if (colorMode >= 2 && colorMode <= 4) {
logMessage("Log not intended for color images", true, true);
logCheckBox.setSelected(false);
} else {
isLogOn = true;
logMessage("Log display on", true, true);
firstLog = true;
if (!stopButton.isEnabled()) {
if (WindowManager.getCurrentWindow().equals(img.getWindow())) {
snapBackup = takeLog(img);
img.updateAndDraw();
resetContrast(img);
} else {
ImagePlus imgC = WindowManager.getCurrentImage();
altSnapBackup = takeLog(imgC);
imgC.updateAndDraw();
resetContrast(imgC);
}
} else if (!WindowManager.getCurrentWindow().equals(img.getWindow())) {
ImagePlus imgC = WindowManager.getCurrentImage();
altSnapBackup = takeLog(imgC);
imgC.updateAndDraw();
resetContrast(imgC);
isLogOn = false;
}
}
} else {
logMessage("Log display off", true, true);
isLogOn = false;
if (!stopButton.isEnabled()) {
if (WindowManager.getCurrentWindow().equals(img.getWindow())) {
WindowManager.setCurrentWindow(img.getWindow());
img.getProcessor().setSnapshotPixels(snapBackup);
Undo.undo();
resetContrast(img);
}
else{
ImagePlus imgC = WindowManager.getCurrentImage();
imgC.getProcessor().setSnapshotPixels(altSnapBackup);
Undo.undo();
resetContrast(imgC);
}
}
else if (!WindowManager.getCurrentWindow().equals(img.getWindow())){
ImagePlus imgC = WindowManager.getCurrentImage();
imgC.getProcessor().setSnapshotPixels(altSnapBackup);
Undo.undo();
resetContrast(imgC);
}
else{
resetContrast(img);
}
}
}
});

snapButton.addActionListener(new ActionListener()
{
Expand All @@ -766,27 +856,45 @@ public void actionPerformed(ActionEvent event)
});

captureCheckBox.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
if (e.getStateChange() == ItemEvent.SELECTED)
{
isSaveToStack = true;
isNewStack = true;
IJ.log("record on");
}
else
{
isSaveToStack = false;
IJ.log("record off");
}

}
}
{
public void itemStateChanged(ItemEvent e) {
if (e.getStateChange() == ItemEvent.SELECTED) {
isSaveToStack = true;
isNewStack = true;
IJ.log("record on");
} else {
isSaveToStack = false;
IJ.log("record off");
}

}
}
);

}

private Object takeLog(ImagePlus image){
image.getProcessor().snapshot();
image.getProcessor().resetMinAndMax();
image.getProcessor().log();
return image.getProcessor().getSnapshotPixels();
}
private void log(ImagePlus image){
float[] pixelArr = (float[]) image.getProcessor().getPixels();
int i = 0;
for(float x : pixelArr){
if(Math.abs(x - 0) < 1e-9)
pixelArr[i++]=Float.NEGATIVE_INFINITY;
else if(x<0)
pixelArr[i++]=Float.NaN;
else
pixelArr[i++]=(float)Math.log(x);
}
image.getProcessor().setPixels(pixelArr);
}
private void resetContrast(ImagePlus image){
image.getProcessor().resetMinAndMax();
new ContrastEnhancer().stretchHistogram(image, 0.51);
}
public class FrameExitListener extends WindowAdapter
{
public void windowClosing(WindowEvent event)
Expand Down
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