/**
* Saves statistics for one particle in a results table. This is a method subclasses may want to
* override.
*/
protected void saveResults(ImageStatistics stats, Roi roi) {
analyzer.saveResults(stats, roi);
if (recordStarts) {
rt.addValue("XStart", stats.xstart);
rt.addValue("YStart", stats.ystart);
}
if (addToManager) {
if (roiManager == null) {
if (Macro.getOptions() != null && Interpreter.isBatchMode())
roiManager = Interpreter.getBatchModeRoiManager();
if (roiManager == null) {
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) {
addToManager = false;
return;
}
roiManager = (RoiManager) frame;
}
if (resetCounter) roiManager.runCommand("reset");
}
if (imp.getStackSize() > 1) roi.setPosition(imp.getCurrentSlice());
if (lineWidth != 1) roi.setStrokeWidth(lineWidth);
roiManager.add(imp, roi, rt.getCounter());
}
if (showResults) rt.addResults();
}
/**
* Creates a new GenericDialog with the specified title. Uses the current image image window as
* the parent frame or the ImageJ frame if no image windows are open. Dialog parameters are
* recorded by ImageJ's command recorder but this requires that the first word of each label be
* unique.
*/
public GenericDialog(String title) {
this(
title,
WindowManager.getCurrentImage() != null
? (Frame) WindowManager.getCurrentImage().getWindow()
: IJ.getInstance() != null ? IJ.getInstance() : new Frame());
}
void addToRoiManager(ImagePlus imp) {
if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
if (imp == null) return;
Roi roi = imp.getRoi();
if (roi == null) return;
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
RoiManager rm = (RoiManager) frame;
boolean altDown = IJ.altKeyDown();
IJ.setKeyUp(IJ.ALL_KEYS);
if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
if (roi.getState() == Roi.CONSTRUCTING) { // wait (up to 2 sec.) until ROI finished
long start = System.currentTimeMillis();
while (true) {
IJ.wait(10);
if (roi.getState() != Roi.CONSTRUCTING) break;
if ((System.currentTimeMillis() - start) > 2000) {
IJ.beep();
IJ.error("Add to Manager", "Selection is not complete");
return;
}
}
}
rm.runCommand("add");
IJ.setKeyUp(IJ.ALL_KEYS);
}
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 void run(String arg) {
int[] wList = WindowManager.getIDList();
if (wList == null) {
IJ.error("No images are open.");
return;
}
double thalf = 0.5;
boolean keep;
GenericDialog gd = new GenericDialog("Bleach correction");
gd.addNumericField("t½:", thalf, 1);
gd.addCheckbox("Keep source stack:", true);
gd.showDialog();
if (gd.wasCanceled()) return;
long start = System.currentTimeMillis();
thalf = gd.getNextNumber();
keep = gd.getNextBoolean();
if (keep) IJ.run("Duplicate...", "title='Bleach corrected' duplicate");
ImagePlus imp1 = WindowManager.getCurrentImage();
int d1 = imp1.getStackSize();
double v1, v2;
int width = imp1.getWidth();
int height = imp1.getHeight();
ImageProcessor ip1, ip2, ip3;
int slices = imp1.getStackSize();
ImageStack stack1 = imp1.getStack();
ImageStack stack2 = imp1.getStack();
int currentSlice = imp1.getCurrentSlice();
for (int n = 1; n <= slices; n++) {
ip1 = stack1.getProcessor(n);
ip3 = stack1.getProcessor(1);
ip2 = stack2.getProcessor(n);
for (int x = 0; x < width; x++) {
for (int y = 0; y < height; y++) {
v1 = ip1.getPixelValue(x, y);
v2 = ip3.getPixelValue(x, y);
// =B8/(EXP(-C$7*A8))
v1 = (v1 / Math.exp(-n * thalf));
ip2.putPixelValue(x, y, v1);
}
}
IJ.showProgress((double) n / slices);
IJ.showStatus(n + "/" + slices);
}
// stack2.show();
imp1.updateAndDraw();
}
private static CustomStackWindow getInstance() {
if (cached != null) return cached;
// check if there's an existing SegmentationEditor
int[] ids = WindowManager.getIDList();
for (int id : ids) {
ImageWindow iw = WindowManager.getImage(id).getWindow();
if (iw instanceof CustomStackWindow) return (CustomStackWindow) iw;
}
newSegmentationEditor();
return cached;
}
private static Frame getParentFrame() {
Frame parent =
WindowManager.getCurrentImage() != null
? (Frame) WindowManager.getCurrentImage().getWindow()
: IJ.getInstance() != null ? IJ.getInstance() : new Frame();
if (IJ.isMacOSX() && IJ.isJava18()) {
ImageJ ij = IJ.getInstance();
if (ij != null && ij.isActive()) parent = ij;
else parent = null;
}
return parent;
}
/** Builds the list of currently opened {@link ImagePlus} in ImageJ. */
private void initImageList() {
int[] IDs = WindowManager.getIDList();
if (null == IDs) {
image_names = new String[] {MESSAGES[1]};
images = new ArrayList<ImagePlus>();
return;
}
ImagePlus imp;
images = new ArrayList<ImagePlus>(IDs.length);
for (int i = 0; i < IDs.length; i++) {
imp = WindowManager.getImage(IDs[i]);
images.add(imp);
}
refreshImageNames();
}
public void run(ImageProcessor ip) {
IndexColorModel icm = (IndexColorModel) ip.getColorModel();
// IJ.write("Color Model=" + ip.getColorModel() + " " + ip.isColorLut());
int pixBits = icm.getPixelSize();
int mapSize = icm.getMapSize();
// retrieve the current lookup tables (maps) for R,G,B
byte[] Rmap = new byte[mapSize];
icm.getReds(Rmap);
byte[] Gmap = new byte[mapSize];
icm.getGreens(Gmap);
byte[] Bmap = new byte[mapSize];
icm.getBlues(Bmap);
// modify the lookup tables
for (int idx = 0; idx < mapSize; idx++) {
int r = 0xff & Rmap[idx]; // mask to treat as unsigned byte
int g = 0xff & Gmap[idx];
int b = 0xff & Bmap[idx];
Rmap[idx] = (byte) Math.min(r + 10, 255);
Gmap[idx] = (byte) Math.min(g + 10, 255);
Bmap[idx] = (byte) Math.min(b + 10, 255);
}
// create a new color model and apply to the image
IndexColorModel icm2 = new IndexColorModel(pixBits, mapSize, Rmap, Gmap, Bmap);
ip.setColorModel(icm2);
WindowManager.getCurrentImage().updateAndDraw();
}
public void render(int w, int h, Graphics2D g2) {
if (WindowManager.getImageCount() > 0) {
imp = WindowManager.getCurrentWindow().getImagePlus();
if (imp != null) {
Image img = imp.getImage();
g2.drawImage(img, 0, 0, imp.getWidth(), imp.getHeight(), null);
}
if (buff != null) {
g2.drawImage(buff, 0, 0, imp.getWidth(), imp.getHeight(), null);
}
}
}
public Zipper<Map<Integer, MZipper<RoiContainer>>> exec(
Zipper<Map<Integer, MZipper<RoiContainer>>> z, int frame) {
JFileChooser fc = new JFileChooser();
int returnVal = fc.showOpenDialog(WindowManager.getCurrentWindow().getCanvas());
Map<Integer, MZipper<RoiContainer>> newRois;
if (returnVal == JFileChooser.APPROVE_OPTION) {
try {
FileInputStream f = new FileInputStream(fc.getSelectedFile().getCanonicalPath());
MroiLisp parser = new MroiLisp(f);
parser.ReInit(f);
newRois = parser.roiFile();
// z.rights.clear();
// z.rights.add(newRois);
// z = z.right();
// return z;
return z.insertAndStep(newRois);
} catch (IOException e) {
IJ.error("Couldn't open from " + fc.getSelectedFile().getName() + ": " + e.getMessage());
} catch (mroi.ParseException e) {
IJ.error("Failed in parsing: " + e.getMessage());
} catch (Exception e) {
IJ.error("Malformed input file: " + e.getMessage());
}
}
return z;
}
public String[] getOpenImageNames() {
int[] imageIDList = WindowManager.getIDList();
String[] imageNames = new String[imageIDList.length];
// imageNames[0] = "None";
if (!imageIDList.equals(null) && imageIDList.length > 1) {
for (int i = 0; i < imageIDList.length; i++) {
ImagePlus tempIMP = WindowManager.getImage(imageIDList[i]);
imageNames[i] = tempIMP.getTitle();
}
return imageNames;
} else {
imageNames[0] = "None";
return imageNames;
}
}
/**
* Execute plugin functionality: stack FFT with window function, max projection over all slices
* (phase, Z angle), blank out central 1/8 circle (set to min value), display min-max.
*/
public ResultSet exec(ImagePlus... imps) {
ImagePlus imp = imps[0];
Util_StackFFT2D stackFFT2D = new Util_StackFFT2D();
stackFFT2D.resultTypeChoice = Util_StackFFT2D.resultType[1];
ImagePlus impF = stackFFT2D.exec(imp);
IJ.run(impF, "Z Project...", "projection=[Max Intensity]");
ImagePlus impProjF = ij.WindowManager.getCurrentImage();
maskCentralRegion(impProjF);
if (impProjF.isComposite()) {
// display grayscale, not colored composite
CompositeImage ci = (CompositeImage) impProjF;
ci.setMode(IJ.GRAYSCALE);
impProjF.updateAndDraw();
}
displayMinToMax(impProjF);
impProjF.setTitle(I1l.makeTitle(imps[0], TLA));
String shortInfo =
"Maximum intensity projection of log"
+ " (amplitude^2) 2D FFT stack, central region masked,"
+ " rescaled (min-max) to improve contrast of the relevant"
+ " frequency range.";
results.addImp(shortInfo, impProjF);
results.addInfo(
"How to interpret",
"look for clean 1st & 2nd"
+ " order spots, similar across angles. Note that spot"
+ " intensity depends on image content.");
return results;
}
public void run(String arg) {
imp = WindowManager.getCurrentImage();
if (arg.equals("add")) {
addToRoiManager(imp);
return;
}
if (imp == null) {
IJ.noImage();
return;
}
if (arg.equals("all")) imp.setRoi(0, 0, imp.getWidth(), imp.getHeight());
else if (arg.equals("none")) imp.killRoi();
else if (arg.equals("restore")) imp.restoreRoi();
else if (arg.equals("spline")) fitSpline();
else if (arg.equals("circle")) fitCircle(imp);
else if (arg.equals("ellipse")) createEllipse(imp);
else if (arg.equals("hull")) convexHull(imp);
else if (arg.equals("mask")) createMask(imp);
else if (arg.equals("from")) createSelectionFromMask(imp);
else if (arg.equals("inverse")) invert(imp);
else if (arg.equals("toarea")) lineToArea(imp);
else if (arg.equals("toline")) areaToLine(imp);
else if (arg.equals("properties")) {
setProperties("Properties ", imp.getRoi());
imp.draw();
} else if (arg.equals("band")) makeBand(imp);
else if (arg.equals("tobox")) toBoundingBox(imp);
else runMacro(arg);
}
void createMask(ImagePlus imp) {
Roi roi = imp.getRoi();
boolean useInvertingLut = Prefs.useInvertingLut;
Prefs.useInvertingLut = false;
if (roi == null || !(roi.isArea() || roi.getType() == Roi.POINT)) {
createMaskFromThreshold(imp);
Prefs.useInvertingLut = useInvertingLut;
return;
}
ImagePlus maskImp = null;
Frame frame = WindowManager.getFrame("Mask");
if (frame != null && (frame instanceof ImageWindow))
maskImp = ((ImageWindow) frame).getImagePlus();
if (maskImp == null) {
ImageProcessor ip = new ByteProcessor(imp.getWidth(), imp.getHeight());
if (!Prefs.blackBackground) ip.invertLut();
maskImp = new ImagePlus("Mask", ip);
maskImp.show();
}
ImageProcessor ip = maskImp.getProcessor();
ip.setRoi(roi);
ip.setValue(255);
ip.fill(ip.getMask());
maskImp.updateAndDraw();
Prefs.useInvertingLut = useInvertingLut;
}
void updateSliceSummary() {
int slices = imp.getStackSize();
float[] areas = rt.getColumn(ResultsTable.AREA);
if (areas == null) areas = new float[0];
String label = imp.getTitle();
if (slices > 1) {
label = imp.getStack().getShortSliceLabel(slice);
label = label != null && !label.equals("") ? label : "" + slice;
}
String aLine = null;
double sum = 0.0;
int start = areas.length - particleCount;
if (start < 0) return;
for (int i = start; i < areas.length; i++) sum += areas[i];
int places = Analyzer.getPrecision();
Calibration cal = imp.getCalibration();
String total = "\t" + ResultsTable.d2s(sum, places);
String average = "\t" + ResultsTable.d2s(sum / particleCount, places);
String fraction = "\t" + ResultsTable.d2s(sum * 100.0 / totalArea, 1);
aLine = label + "\t" + particleCount + total + average + fraction;
aLine = addMeans(aLine, areas.length > 0 ? start : -1);
if (slices == 1) {
Frame frame = WindowManager.getFrame("Summary");
if (frame != null && (frame instanceof TextWindow) && summaryHdr.equals(prevHdr))
tw = (TextWindow) frame;
}
if (tw == null) {
String title = slices == 1 ? "Summary" : "Summary of " + imp.getTitle();
tw = new TextWindow(title, summaryHdr, aLine, 450, 300);
prevHdr = summaryHdr;
} else tw.append(aLine);
}
void remove() {
ImagePlus imp = WindowManager.getCurrentImage();
if (imp != null) imp.setOverlay(null);
overlay2 = null;
RoiManager rm = RoiManager.getInstance();
if (rm != null) rm.runCommand("show none");
}
public void run(String arg) {
ImagePlus image = WindowManager.getCurrentImage();
try {
Image3DUniverse univ = new Image3DUniverse();
univ.show();
GUI.center(univ.getWindow());
// only when there is an image and we are not called
// from a macro
if (image != null && !IJ.isMacro()) univ.getExecuter().addContent(image, null);
} catch (Exception e) {
StringBuffer buf = new StringBuffer();
StackTraceElement[] st = e.getStackTrace();
buf.append(
"An unexpected exception occurred. \n"
+ "Please mail me the following lines if you \n"
+ "need help.\n"
+ "[email protected]\n \n");
buf.append(e.getClass().getName() + ":" + e.getMessage() + "\n");
for (int i = 0; i < st.length; i++) {
buf.append(
" at "
+ st[i].getClassName()
+ "."
+ st[i].getMethodName()
+ "("
+ st[i].getFileName()
+ ":"
+ st[i].getLineNumber()
+ ")\n");
}
new ij.text.TextWindow("Error", buf.toString(), 500, 400);
}
}
public Channels() {
super("Channels");
if (instance != null) {
instance.toFront();
return;
}
WindowManager.addWindow(this);
instance = this;
GridBagLayout gridbag = new GridBagLayout();
GridBagConstraints c = new GridBagConstraints();
setLayout(gridbag);
int y = 0;
c.gridx = 0;
c.gridy = y++;
c.gridwidth = 1;
c.fill = GridBagConstraints.BOTH;
c.anchor = GridBagConstraints.CENTER;
int margin = 32;
if (IJ.isMacOSX()) margin = 20;
c.insets = new Insets(10, margin, 10, margin);
choice = new Choice();
for (int i = 0; i < modes.length; i++) choice.addItem(modes[i]);
choice.select(0);
choice.addItemListener(this);
add(choice, c);
CompositeImage ci = getImage();
int nCheckBoxes = ci != null ? ci.getNChannels() : 3;
if (nCheckBoxes > CompositeImage.MAX_CHANNELS) nCheckBoxes = CompositeImage.MAX_CHANNELS;
checkbox = new Checkbox[nCheckBoxes];
for (int i = 0; i < nCheckBoxes; i++) {
checkbox[i] = new Checkbox("Channel " + (i + 1), true);
c.insets = new Insets(0, 25, i < nCheckBoxes - 1 ? 0 : 10, 5);
c.gridy = y++;
add(checkbox[i], c);
checkbox[i].addItemListener(this);
}
c.insets = new Insets(0, 15, 10, 15);
c.fill = GridBagConstraints.NONE;
c.gridy = y++;
moreButton = new Button(moreLabel);
moreButton.addActionListener(this);
add(moreButton, c);
update();
pm = new PopupMenu();
for (int i = 0; i < menuItems.length; i++) addPopupItem(menuItems[i]);
add(pm);
addKeyListener(IJ.getInstance()); // ImageJ handles keyboard shortcuts
setResizable(false);
pack();
if (location == null) {
GUI.center(this);
location = getLocation();
} else setLocation(location);
show();
}
/**
* Adds a checkbox labelled "Preview" for "automatic" preview. The reference to this checkbox can
* be retrieved by getPreviewCheckbox() and it provides the additional method previewRunning for
* optical feedback while preview is prepared. PlugInFilters can have their "run" method
* automatically called for preview under the following conditions: - the PlugInFilter must pass a
* reference to itself (i.e., "this") as an argument to the AddPreviewCheckbox - it must implement
* the DialogListener interface and set the filter parameters in the dialogItemChanged method. -
* it must have DIALOG and PREVIEW set in its flags. A previewCheckbox is always off when the
* filter is started and does not get recorded by the Macro Recorder.
*
* @param pfr A reference to the PlugInFilterRunner calling the PlugInFilter if automatic preview
* is desired, null otherwise.
*/
public void addPreviewCheckbox(PlugInFilterRunner pfr) {
if (previewCheckbox != null) return;
ImagePlus imp = WindowManager.getCurrentImage();
if (imp != null && imp.isComposite() && ((CompositeImage) imp).getMode() == IJ.COMPOSITE)
return;
this.pfr = pfr;
addCheckbox(previewLabel, false, true);
}
void addToRoiManager(ImagePlus imp) {
if (IJ.macroRunning() && Interpreter.isBatchModeRoiManager())
IJ.error("run(\"Add to Manager\") may not work in batch mode macros");
Frame frame = WindowManager.getFrame("ROI Manager");
if (frame == null) IJ.run("ROI Manager...");
if (imp == null) return;
Roi roi = imp.getRoi();
if (roi == null) return;
frame = WindowManager.getFrame("ROI Manager");
if (frame == null || !(frame instanceof RoiManager)) IJ.error("ROI Manager not found");
RoiManager rm = (RoiManager) frame;
boolean altDown = IJ.altKeyDown();
IJ.setKeyUp(IJ.ALL_KEYS);
if (altDown && !IJ.macroRunning()) IJ.setKeyDown(KeyEvent.VK_SHIFT);
rm.runCommand("add");
IJ.setKeyUp(IJ.ALL_KEYS);
}
/** @param args */
public static void main(String[] args) {
// Set params
int[][] pairs = new int[][] {new int[] {1, 2}};
PIV_analyser.WINDOW_SIZE blocksize = PIV_analyser.WINDOW_SIZE._64x64;
// Load the test image
System.out.println("Loading the image...");
FileInfo fi = new FileInfo();
fi.width = 256;
fi.height = 64;
fi.offset = 177;
fi.nImages = 2;
fi.fileName = TESTPIV;
fi.directory = ".";
new FileOpener(fi).open();
// Get a reference to it
ImagePlus imp = WindowManager.getCurrentImage();
// Initialize the plugin
System.out.println("Initializing the plugin...");
PIV_analyser piv = new PIV_analyser();
// give it a ref to the ImageProcessor
piv.setup("", imp);
// setup image pair
piv.setImagePairs(pairs);
// setup window size
piv.setWinsize(blocksize);
// run it and time it
System.out.println("Running the plugin...");
Stopwatch stopwatch = new Stopwatch();
stopwatch.start();
piv.exec(false);
stopwatch.stop();
System.out.println("Done in: " + stopwatch);
System.out.println("Exiting.");
if (LOG) {
File log = new File("log.txt");
Writer output;
try {
output = new BufferedWriter(new FileWriter(log, true));
output.append("[+] Test - " + DateUtils.now() + "\n");
output.append("\t Image: " + TESTPIV + "\n");
output.append("\t Image pairs: " + pairs.length + " pair(s).\n");
output.append("\t Image size: " + imp.getWidth() + " x " + imp.getHeight() + ".\n");
output.append("\t Block size: " + blocksize.toString() + ".\n");
output.append("\t Exec time: " + stopwatch + "\n\n");
output.close();
} catch (IOException e) {
e.printStackTrace();
}
}
imp.changes = false;
imp.close();
if (DISPLAY_COLOR_WHEEL) {
ColorProcessor cp = new ColorProcessor(256, 256);
PIV_analyser.colorCircle(cp);
new ImagePlus("Color coded orientation", cp).show();
}
}
boolean setProperties(String title, Roi roi) {
Frame f = WindowManager.getFrontWindow();
if (f != null && f.getTitle().indexOf("3D Viewer") != -1) return false;
if (roi == null) {
IJ.error("This command requires a selection.");
return false;
}
RoiProperties rp = new RoiProperties(title, roi);
return rp.showDialog();
}
@Override
public void run(String arg0) {
GenericDialog gd = new GenericDialog("Save JPEG");
gd.addStringField("Title", "A");
gd.addStringField("Directory", "/");
gd.showDialog();
String base_name = gd.getNextString();
String direc = gd.getNextString();
save(WindowManager.getCurrentImage(), base_name, direc);
}
/** Sets the color used used for the ROI Manager "Show All" mode. */
public static void setShowAllColor(Color c) {
if (c == null) return;
showAllColor = c;
labelColor = null;
ImagePlus img = WindowManager.getCurrentImage();
if (img != null) {
ImageCanvas ic = img.getCanvas();
if (ic != null && ic.getShowAllROIs()) img.draw();
}
}
public void run(String arg) {
ImageWindow iw = WindowManager.getCurrentWindow();
pw = jutils.getPW4SelCopy(iw);
String title = pw.getTitle();
float[][] yvals = pw.getYValues();
float[][] xvals = pw.getXValues();
int length = yvals[0].length;
if (pw.getShowErrors()) errs = pw.getErrors(0, false);
int[] colors = pw.getColors();
colors[0] = 0;
ScriptEngineManager manager = new ScriptEngineManager();
engine = manager.getEngineByName("js");
ce = (Compilable) engine;
// hitcounter=0;
c2 = 0.0f;
iterations = 0;
checkc2 = false;
double[] stats = new double[3];
tempx = new float[length];
tempdata = new float[length];
System.arraycopy(xvals[0], 0, tempx, 0, length);
System.arraycopy(yvals[0], 0, tempdata, 0, length);
pw.addPoints(tempx, new float[tempx.length], false);
series = pw.getNpts().length - 1;
double[] params = new double[10];
int[] fixes = {0, 0, 0, 1, 1, 1, 1, 1, 1, 1};
init_options(params, fixes);
if (!init_functions()) {
return;
}
while (showoptions(params, fixes)) {
NLLSfit_v2 fitclass;
if (checkc2) {
fitclass = new NLLSfit_v2(this, 0);
} else {
fitclass = new NLLSfit_v2(this, 0.0001, 50, 0.1);
}
float[] fit = fitclass.fitdata(params, fixes, constraints, yvals[0], weights, stats, true);
pw.updateSeries(fit, series, false);
c2 = (float) stats[1];
iterations = (int) stats[0];
}
IJ.log("Chi Squared = " + (float) stats[1]);
IJ.log("Iterations = " + (int) stats[0]);
for (int i = 0; i < 10; i++) {
IJ.log("P" + (i + 1) + " = " + (float) params[i] + " fixed = " + fixes[i]);
}
IJ.log("AIC = " + (float) stats[2]);
// IJ.log("hits = "+hitcounter);
set_options(params, fixes);
}
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 static void addOrthoslice(
String image, String c, String name, String r, String g, String b, String resamplingF) {
Image3DUniverse univ = getUniv();
ImagePlus grey = WindowManager.getImage(image);
Color3f color = ColorTable.getColor(c);
int factor = getInt(resamplingF);
boolean[] channels = new boolean[] {getBoolean(r), getBoolean(g), getBoolean(b)};
univ.addOrthoslice(grey, color, name, 0, channels, factor);
}
private boolean checkImage() {
imp = WindowManager.getCurrentImage();
if (imp == null) {
IJ.beep();
IJ.showStatus("No image");
return false;
}
ip = setup(imp);
if (ip == null) return false;
return true;
}
public void run(String arg) {
if (imp == null) imp = WindowManager.getCurrentImage();
if (imp == null) {
return;
}
CustomCanvas cc = new CustomCanvas(imp);
storePixelValues(imp.getProcessor());
new CustomWindow(imp, cc);
}