/** Called from io/Opener.java. */
public void run(String path) {
if (path.equals("")) return;
File theFile = new File(path);
String directory = theFile.getParent();
String fileName = theFile.getName();
if (directory == null) directory = "";
// Try and recognise file type and load the file if recognised
ImagePlus imp = openImage(directory, fileName, path);
if (imp == null) {
IJ.showStatus("");
return; // failed to load file or plugin has opened and displayed it
}
ImageStack stack = imp.getStack();
// get the title from the stack (falling back to the fileName)
String title = imp.getTitle().equals("") ? fileName : imp.getTitle();
// set the stack of this HandleExtraFileTypes object
// to that attached to the ImagePlus object returned by openImage()
setStack(title, stack);
// copy over the calibration info since it doesn't come with the ImageProcessor
setCalibration(imp.getCalibration());
// also copy the Show Info field over if it exists
if (imp.getProperty("Info") != null) setProperty("Info", imp.getProperty("Info"));
// copy the FileInfo
setFileInfo(imp.getOriginalFileInfo());
// copy dimensions
if (IJ.getVersion().compareTo("1.38s") >= 0)
setDimensions(imp.getNChannels(), imp.getNSlices(), imp.getNFrames());
if (IJ.getVersion().compareTo("1.41o") >= 0) setOpenAsHyperStack(imp.getOpenAsHyperStack());
}
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.noImage();
return;
}
ImageStack stack1 = imp.getStack();
String fileName = imp.getTitle();
int endslice = stack1.getSize();
ImagePlus imp2 = duplicateStack(imp);
imp2.show();
String duplicateName = imp2.getTitle();
// IJ.showMessage("Box",fileName);
ImageStack stack2 = imp2.getStack();
stack1.deleteSlice(1);
stack2.deleteSlice(endslice);
String calculatorstring =
("image1='"
+ fileName
+ "' operation=Subtract image2="
+ imp2.getTitle()
+ " create stack");
IJ.run("Image Calculator...", calculatorstring);
ImagePlus imp3 = WindowManager.getCurrentImage();
imp3.setTitle(fileName + " DeltaF up");
imp2.getWindow().close();
imp.getWindow().close();
}
public boolean beadCalibration3d() {
imp = IJ.getImage();
if (imp == null) {
IJ.noImage();
return false;
} else if (imp.getStackSize() == 1) {
IJ.error("Stack required");
return false;
} else if (imp.getType() != ImagePlus.GRAY8 && imp.getType() != ImagePlus.GRAY16) {
// In order to support 32bit images, pict[] must be changed to float[], and getPixel(x, y);
// requires a Float.intBitsToFloat() conversion
IJ.error("8 or 16 bit greyscale image required");
return false;
}
width = imp.getWidth();
height = imp.getHeight();
nslices = imp.getStackSize();
imtitle = imp.getTitle();
models[0] = "*None*";
models[1] = "line";
models[2] = "2nd degree polynomial";
models[3] = "3rd degree polynomial";
models[4] = "4th degree polynomial";
GenericDialog gd = new GenericDialog("3D PALM calibration");
gd.addNumericField("Maximum FWHM (in px)", prefs.get("QuickPALM.3Dcal_fwhm", 20), 0);
gd.addNumericField(
"Particle local threshold (% maximum intensity)", prefs.get("QuickPALM.pthrsh", 20), 0);
gd.addNumericField("Z-spacing (nm)", prefs.get("QuickPALM.z-step", 10), 2);
gd.addNumericField("Calibration Z-smoothing (radius)", prefs.get("QuickPALM.window", 1), 0);
gd.addChoice("Model", models, prefs.get("QuickPALM.model", models[3]));
gd.addCheckbox(
"Show divergence of bead positions against model",
prefs.get("QuickPALM.3Dcal_showDivergence", false));
gd.addCheckbox("Show extra particle info", prefs.get("QuickPALM.3Dcal_showExtraInfo", false));
gd.addMessage("\n\nDon't forget to save the table in the end...");
gd.showDialog();
if (gd.wasCanceled()) return false;
fwhm = gd.getNextNumber();
prefs.set("QuickPALM.QuickPALM.3Dcal_fwhm", fwhm);
pthrsh = gd.getNextNumber() / 100;
prefs.set("QuickPALM.pthrsh", pthrsh * 100);
cal_z = gd.getNextNumber();
prefs.set("QuickPALM.z-step", cal_z);
window = (int) gd.getNextNumber();
prefs.set("QuickPALM.window", window);
model = gd.getNextChoice();
prefs.set("QuickPALM.model", model);
part_divergence = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showDivergence", part_divergence);
part_extrainfo = gd.getNextBoolean();
prefs.set("QuickPALM.3Dcal_showExtraInfo", part_extrainfo);
return true;
}
private boolean showDialog() {
String[] types = {"RAW", "JPEG", "ZLIB"};
GenericDialog gd = new GenericDialog("Generate Bricks");
gd.addChoice("FileType", types, filetype);
gd.addNumericField("JPEG quality", jpeg_quality, 0);
gd.addNumericField("Max file size (MB)", bdsizelimit, 0);
int[] wlist = WindowManager.getIDList();
if (wlist == null) return false;
String[] titles = new String[wlist.length];
for (int i = 0; i < wlist.length; i++) titles[i] = "";
int tnum = 0;
for (int i = 0; i < wlist.length; i++) {
ImagePlus imp = WindowManager.getImage(wlist[i]);
if (imp != null) {
titles[tnum] = imp.getTitle();
tnum++;
}
}
gd.addChoice("Source image: ", titles, titles[0]);
gd.showDialog();
if (gd.wasCanceled()) return false;
filetype = types[gd.getNextChoiceIndex()];
jpeg_quality = (int) gd.getNextNumber();
if (jpeg_quality > 100) jpeg_quality = 100;
if (jpeg_quality < 0) jpeg_quality = 0;
bdsizelimit = (int) gd.getNextNumber();
int id = gd.getNextChoiceIndex();
lvImgTitle = new ArrayList<String>();
lvImgTitle.add(titles[id]);
Prefs.set("filetype.string", filetype);
Prefs.set("jpeg_quality.int", jpeg_quality);
Prefs.set("bdsizelimit.int", bdsizelimit);
return true;
}
public void Calc_5Fr(ImagePlus imp1, ImagePlus imp2) {
if (imp1.getType() != imp2.getType()) {
error();
return;
}
if (imp1.getType() == 0) { // getType returns 0 for 8-bit, 1 for 16-bit
bitDepth = "8-bit";
Prefs.set("ps.bitDepth", bitDepth);
} else {
bitDepth = "16-bit";
Prefs.set("ps.bitDepth", bitDepth);
}
int width = imp1.getWidth();
int height = imp1.getHeight();
if (width != imp2.getWidth() || height != imp2.getHeight()) {
error();
return;
}
ImageStack stack1 = imp1.getStack();
// if (bgStackTitle != "NoBg") ImageStack stack2 = imp2.getStack();
ImageStack stack2 = imp2.getStack();
ImageProcessor ip = imp1.getProcessor();
int dimension = width * height;
byte[] pixB;
short[] pixS;
float[][] pixF = new float[5][dimension];
float[][] pixFBg = new float[5][dimension];
float a;
float b;
float den;
float aSmp;
float bSmp;
float denSmp;
float aBg;
float bBg;
float denBg;
float retF;
float azimF;
byte[] retB = new byte[dimension];
short[] retS = new short[dimension];
byte[] azimB = new byte[dimension];
short[] azimS = new short[dimension];
// Derived Variables:
float swingAngle = 2f * (float) Math.PI * swing;
float tanSwingAngleDiv2 = (float) Math.tan(swingAngle / 2.f);
float tanSwingAngleDiv2DivSqrt2 = (float) (Math.tan(swingAngle / 2.f) / Math.sqrt(2));
float wavelengthDiv2Pi = wavelength / (2f * (float) Math.PI);
// get the pixels of each slice in the stack and convert to float
for (int i = 0; i < 5; i++) {
if (bitDepth == "8-bit") {
pixB = (byte[]) stack1.getPixels(i + 3);
for (int j = 0; j < dimension; j++) pixF[i][j] = 0xff & pixB[j];
if (bgStackTitle != "NoBg") {
pixB = (byte[]) stack2.getPixels(i + 3);
for (int j = 0; j < dimension; j++) pixFBg[i][j] = 0xff & pixB[j];
}
} else {
pixS = (short[]) stack1.getPixels(i + 3);
for (int j = 0; j < dimension; j++) pixF[i][j] = (float) pixS[j];
if (bgStackTitle != "NoBg") {
pixS = (short[]) stack2.getPixels(i + 3);
for (int j = 0; j < dimension; j++) pixFBg[i][j] = (float) pixS[j];
}
}
}
// Algorithm
// terms a and b
for (int j = 0; j < dimension; j++) {
denSmp = (pixF[1][j] + pixF[2][j] + pixF[3][j] + pixF[4][j] - 4 * pixF[0][j]) / 2;
denBg = denSmp;
a = (pixF[4][j] - pixF[1][j]);
aSmp = a;
aBg = a;
b = (pixF[2][j] - pixF[3][j]);
bSmp = b;
bBg = b;
if (bgStackTitle != "NoBg") {
denBg = (pixFBg[1][j] + pixFBg[2][j] + pixFBg[3][j] + pixFBg[4][j] - 4 * pixFBg[0][j]) / 2;
aBg = pixFBg[4][j] - pixFBg[1][j];
bBg = pixFBg[2][j] - pixFBg[3][j];
}
// Special case of sample retardance half wave, denSmp = 0
if (denSmp == 0) {
retF = (float) wavelength / 4;
azimF =
(float) (a == 0 & b == 0 ? 0 : (azimRef + 90 + 90 * Math.atan2(a, b) / Math.PI) % 180);
} else {
// Retardance, the background correction can be improved by separately considering sample
// retardance values larger than a quarter wave
if (bgStackTitle != "NoBg") {
a = aSmp / denSmp - aBg / denBg;
b = bSmp / denSmp - bBg / denBg;
} else {
a = aSmp / denSmp;
b = bSmp / denSmp;
}
retF = (float) Math.atan(tanSwingAngleDiv2 * Math.sqrt(a * a + b * b));
if (denSmp < 0) retF = (float) Math.PI - retF;
retF = retF * wavelengthDiv2Pi; // convert to nm
if (retF > retCeiling) retF = retCeiling;
// Orientation
if ((bgStackTitle == "NoBg") || ((bgStackTitle != "NoBg") && (Math.abs(denSmp) < 1))) {
a = aSmp;
b = bSmp;
}
azimF =
(float) (a == 0 & b == 0 ? 0 : (azimRef + 90 + 90 * Math.atan2(a, b) / Math.PI) % 180);
}
if (bitDepth == "8-bit") retB[j] = (byte) (((int) (255 * retF / retCeiling)) & 0xff);
else retS[j] = (short) (4095 * retF / retCeiling);
if (mirror == "Yes") azimF = 180 - azimF;
if (bitDepth == "8-bit") azimB[j] = (byte) (((int) azimF) & 0xff);
else azimS[j] = (short) (azimF * 10f);
}
// show the resulting images in slice 1 and 2
imp1.setSlice(3);
if (bitDepth == "8-bit") {
stack1.setPixels(retB, 1);
stack1.setPixels(azimB, 2);
} else {
stack1.setPixels(retS, 1);
stack1.setPixels(azimS, 2);
}
imp1.setSlice(1);
IJ.selectWindow(imp1.getTitle());
Prefs.set("ps.sampleStackTitle", sampleStackTitle);
Prefs.set("ps.bgStackTitle", bgStackTitle);
Prefs.set("ps.mirror", mirror);
Prefs.set("ps.wavelength", wavelength);
Prefs.set("ps.swing", swing);
Prefs.set("ps.retCeiling", retCeiling);
Prefs.set("ps.azimRef", azimRef);
Prefs.savePreferences();
}
public boolean showDialog() {
String bgChoice = "NoBg";
int[] wList = WindowManager.getIDList();
if (wList == null) {
IJ.noImage();
return false;
}
String[] sampleTitles = new String[wList.length];
for (int i = 0; i < wList.length; i++) {
ImagePlus imp = WindowManager.getImage(wList[i]);
sampleTitles[i] = imp != null ? imp.getTitle() : "";
}
String[] bgTitles = new String[wList.length + 1];
bgTitles[0] = "NoBg";
for (int i = 1; i < wList.length + 1; i++) {
bgTitles[i] = sampleTitles[i - 1];
}
for (int i = 1; i < (wList.length + 1); i++) {
if (bgTitles[i] == bgStackTitle) bgChoice = bgStackTitle;
}
String sampleChoice = sampleTitles[0];
for (int i = 1; i < (wList.length); i++) {
if (sampleTitles[i] == sampleStackTitle) sampleChoice = sampleStackTitle;
}
String[] mirrors = new String[2];
mirrors[0] = "No";
mirrors[1] = "Yes";
GenericDialog gd = new GenericDialog("PolScope 5Frame Calc");
gd.addChoice("Sample:", sampleTitles, sampleChoice);
gd.addChoice("Background:", bgTitles, bgChoice);
gd.addChoice("Mirror:", mirrors, mirror);
gd.addNumericField("Wavelength: ", wavelength, 1, 8, " nm");
gd.addNumericField("Swing: ", swing, 3, 8, " wavelength");
gd.addNumericField("Ret. Ceiling: ", retCeiling, 1, 8, " nm");
gd.addNumericField("Orient. Ref.: ", azimRef, 1, 8, " degree");
gd.showDialog();
if (gd.wasCanceled()) return false;
int index1 = gd.getNextChoiceIndex();
int index2 = gd.getNextChoiceIndex();
int index3 = gd.getNextChoiceIndex();
wavelength = (float) gd.getNextNumber();
swing = (float) gd.getNextNumber();
retCeiling = (float) gd.getNextNumber();
azimRef = (float) gd.getNextNumber();
imp1 = WindowManager.getImage(wList[index1]);
sampleStackTitle = sampleTitles[index1];
bgStackTitle = bgTitles[index2];
if (bgStackTitle == "NoBg") {
imp2 =
WindowManager.getImage(
wList[
index1]); // only to assign a valid ImagePlus to imp2 which is not used when NoBg
} else {
imp2 = WindowManager.getImage(wList[index2 - 1]);
}
mirror = mirrors[index3];
return true;
}
public void itemStateChanged(ItemEvent e) {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp == null) return;
if (!imp.isComposite()) {
int channels = imp.getNChannels();
if (channels == 1 && imp.getStackSize() <= 4) channels = imp.getStackSize();
if (imp.getBitDepth() == 24 || (channels > 1 && channels < CompositeImage.MAX_CHANNELS)) {
GenericDialog gd = new GenericDialog(imp.getTitle());
gd.addMessage("Convert to multi-channel composite image?");
gd.showDialog();
if (gd.wasCanceled()) return;
else IJ.doCommand("Make Composite");
} else {
IJ.error(
"Channels",
"A composite image is required (e.g., "
+ moreLabel
+ " Open HeLa Cells),\nor create one using "
+ moreLabel
+ " Make Composite.");
return;
}
}
if (!imp.isComposite()) return;
CompositeImage ci = (CompositeImage) imp;
Object source = e.getSource();
if (source == choice) {
int index = ((Choice) source).getSelectedIndex();
switch (index) {
case 0:
ci.setMode(IJ.COMPOSITE);
break;
case 1:
ci.setMode(IJ.COLOR);
break;
case 2:
ci.setMode(IJ.GRAYSCALE);
break;
}
ci.updateAndDraw();
if (Recorder.record) {
String mode = null;
switch (index) {
case 0:
mode = "composite";
break;
case 1:
mode = "color";
break;
case 2:
mode = "grayscale";
break;
}
Recorder.record("Stack.setDisplayMode", mode);
}
} else if (source instanceof Checkbox) {
for (int i = 0; i < checkbox.length; i++) {
Checkbox cb = (Checkbox) source;
if (cb == checkbox[i]) {
if (ci.getMode() == IJ.COMPOSITE) {
boolean[] active = ci.getActiveChannels();
active[i] = cb.getState();
if (Recorder.record) {
String str = "";
for (int c = 0; c < ci.getNChannels(); c++) str += active[c] ? "1" : "0";
Recorder.record("Stack.setActiveChannels", str);
Recorder.record("//Stack.toggleChannel", imp.getChannel());
}
} else {
imp.setPosition(i + 1, imp.getSlice(), imp.getFrame());
if (Recorder.record) Recorder.record("Stack.setChannel", i + 1);
}
ci.updateAndDraw();
return;
}
}
}
}