void loadParticleResults(String filename, ResultsTable res) {
try {
String line;
FileReader fr = new FileReader(filename);
BufferedReader br = new BufferedReader(fr);
java.lang.String header =
" Intensity X (px) Y (px) X (nm) Y (nm) Z (nm) Left-Width(px) Right-Width (px) Up-Height (px) Down-Height (px) X Symmetry (%) Y Symmetry (%) Width minus Height (px) Frame Number";
java.lang.String firstline = br.readLine();
if (!firstline.contains("X (px) Y (px) X (nm) Y (nm) Z (nm)")) {
IJ.error("File does not seam to be a Particles Table file");
IJ.log("Found header: " + firstline);
IJ.log("Expecting: " + header);
return;
}
res.reset();
int counter = 1;
java.util.concurrent.locks.Lock lock = new java.util.concurrent.locks.ReentrantLock();
ThreadedLoader tloader = new ThreadedLoader();
// java.lang.String txt = fr.read();
while ((line = br.readLine()) != null) {
tloader = new ThreadedLoader();
tloader.mysetup(res, lock, line);
tloader.start();
IJ.showStatus("Loading particle " + counter + "... sit back and relax.");
counter++;
}
try {
tloader.join();
} catch (Exception e) {
IJ.error("" + e);
}
if (res.getCounter() < 5000000) {
IJ.showStatus("Creating particle table, this should take a few seconds...");
res.show("Results");
} else
IJ.showMessage(
"Warning",
"Results table has too many particles, they will not be shown but the data still exists within it\nyou can still use all the plugin functionality or save table changes though the 'Save Particle Table' command.");
fr.close();
IJ.showStatus("Done loading table...");
} catch (FileNotFoundException e) {
IJ.error("File not found exception" + e);
return;
} catch (IOException e) {
IJ.error("IOException exception" + e);
return;
} catch (NumberFormatException e) {
IJ.error("Number format exception" + e);
return;
}
}
void enlargeArrays() {
if (xp != null) {
int[] xptemp = new int[maxPoints * 2];
int[] yptemp = new int[maxPoints * 2];
System.arraycopy(xp, 0, xptemp, 0, maxPoints);
System.arraycopy(yp, 0, yptemp, 0, maxPoints);
xp = xptemp;
yp = yptemp;
}
if (xpf != null) {
float[] xpftemp = new float[maxPoints * 2];
float[] ypftemp = new float[maxPoints * 2];
System.arraycopy(xpf, 0, xpftemp, 0, maxPoints);
System.arraycopy(ypf, 0, ypftemp, 0, maxPoints);
xpf = xpftemp;
ypf = ypftemp;
}
int[] xp2temp = new int[maxPoints * 2];
int[] yp2temp = new int[maxPoints * 2];
System.arraycopy(xp2, 0, xp2temp, 0, maxPoints);
System.arraycopy(yp2, 0, yp2temp, 0, maxPoints);
xp2 = xp2temp;
yp2 = yp2temp;
if (IJ.debugMode) IJ.log("PolygonRoi: " + maxPoints + " points");
maxPoints *= 2;
}
public FileOpener(FileInfo fi) {
this.fi = fi;
if (fi != null) {
width = fi.width;
height = fi.height;
}
if (IJ.debugMode) IJ.log("FileInfo: " + fi);
}
void drawAllROIs(Graphics g) {
RoiManager rm = RoiManager.getInstance();
if (rm == null) {
rm = Interpreter.getBatchModeRoiManager();
if (rm != null && rm.getList().getItemCount() == 0) rm = null;
}
if (rm == null) {
// if (showAllList!=null)
// overlay = showAllList;
showAllROIs = false;
repaint();
return;
}
initGraphics(g, null, showAllColor);
Hashtable rois = rm.getROIs();
java.awt.List list = rm.getList();
boolean drawLabels = rm.getDrawLabels();
currentRoi = null;
int n = list.getItemCount();
if (IJ.debugMode) IJ.log("paint: drawing " + n + " \"Show All\" ROIs");
if (labelRects == null || labelRects.length != n) labelRects = new Rectangle[n];
if (!drawLabels) showAllList = new Overlay();
else showAllList = null;
if (imp == null) return;
int currentImage = imp.getCurrentSlice();
int channel = 0, slice = 0, frame = 0;
boolean hyperstack = imp.isHyperStack();
if (hyperstack) {
channel = imp.getChannel();
slice = imp.getSlice();
frame = imp.getFrame();
}
drawNames = Prefs.useNamesAsLabels;
for (int i = 0; i < n; i++) {
String label = list.getItem(i);
Roi roi = (Roi) rois.get(label);
if (roi == null) continue;
if (showAllList != null) showAllList.add(roi);
if (i < 200 && drawLabels && roi == imp.getRoi()) currentRoi = roi;
if (Prefs.showAllSliceOnly && imp.getStackSize() > 1) {
if (hyperstack && roi.getPosition() == 0) {
int c = roi.getCPosition();
int z = roi.getZPosition();
int t = roi.getTPosition();
if ((c == 0 || c == channel) && (z == 0 || z == slice) && (t == 0 || t == frame))
drawRoi(g, roi, drawLabels ? i : -1);
} else {
int position = roi.getPosition();
if (position == 0) position = getSliceNumber(roi.getName());
if (position == 0 || position == currentImage) drawRoi(g, roi, drawLabels ? i : -1);
}
} else drawRoi(g, roi, drawLabels ? i : -1);
}
((Graphics2D) g).setStroke(Roi.onePixelWide);
drawNames = false;
}
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);
boolean ok = rp.showDialog();
if (IJ.debugMode) IJ.log(roi.getDebugInfo());
return ok;
}
/** Opens a stack of images. */
ImagePlus openStack(ColorModel cm, boolean show) {
ImageStack stack = new ImageStack(fi.width, fi.height, cm);
long skip = fi.getOffset();
Object pixels;
try {
ImageReader reader = new ImageReader(fi);
InputStream is = createInputStream(fi);
if (is == null) return null;
IJ.resetEscape();
for (int i = 1; i <= fi.nImages; i++) {
if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
if (IJ.escapePressed()) {
IJ.beep();
IJ.showProgress(1.0);
silentMode = false;
return null;
}
pixels = reader.readPixels(is, skip);
if (pixels == null) break;
stack.addSlice(null, pixels);
skip = fi.gapBetweenImages;
if (!silentMode) IJ.showProgress(i, fi.nImages);
}
is.close();
} catch (Exception e) {
IJ.log("" + e);
} catch (OutOfMemoryError e) {
IJ.outOfMemory(fi.fileName);
stack.trim();
}
if (!silentMode) IJ.showProgress(1.0);
if (stack.getSize() == 0) return null;
if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
}
ImagePlus imp = new ImagePlus(fi.fileName, stack);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (show) imp.show();
imp.setFileInfo(fi);
setCalibration(imp);
ImageProcessor ip = imp.getProcessor();
if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
setStackDisplayRange(imp);
if (!silentMode) IJ.showProgress(1.0);
silentMode = false;
return imp;
}
public Properties decodeDescriptionString(FileInfo fi) {
if (fi.description == null || fi.description.length() < 7) return null;
if (IJ.debugMode) IJ.log("Image Description: " + new String(fi.description).replace('\n', ' '));
if (!fi.description.startsWith("ImageJ")) return null;
Properties props = new Properties();
InputStream is = new ByteArrayInputStream(fi.description.getBytes());
try {
props.load(is);
is.close();
} catch (IOException e) {
return null;
}
fi.unit = props.getProperty("unit", "");
Double n = getNumber(props, "cf");
if (n != null) fi.calibrationFunction = n.intValue();
double c[] = new double[5];
int count = 0;
for (int i = 0; i < 5; i++) {
n = getNumber(props, "c" + i);
if (n == null) break;
c[i] = n.doubleValue();
count++;
}
if (count >= 2) {
fi.coefficients = new double[count];
for (int i = 0; i < count; i++) fi.coefficients[i] = c[i];
}
fi.valueUnit = props.getProperty("vunit");
n = getNumber(props, "images");
if (n != null && n.doubleValue() > 1.0) fi.nImages = (int) n.doubleValue();
if (fi.nImages > 1) {
double spacing = getDouble(props, "spacing");
if (spacing != 0.0) {
if (spacing < 0) spacing = -spacing;
fi.pixelDepth = spacing;
}
}
return props;
}
protected void handlePopupMenu(MouseEvent e) {
if (disablePopupMenu) return;
if (IJ.debugMode) IJ.log("show popup: " + (e.isPopupTrigger() ? "true" : "false"));
int x = e.getX();
int y = e.getY();
Roi roi = imp.getRoi();
if (roi != null
&& (roi.getType() == Roi.POLYGON
|| roi.getType() == Roi.POLYLINE
|| roi.getType() == Roi.ANGLE)
&& roi.getState() == roi.CONSTRUCTING) {
roi.handleMouseUp(x, y); // simulate double-click to finalize
roi.handleMouseUp(x, y); // polygon or polyline selection
return;
}
PopupMenu popup = Menus.getPopupMenu();
if (popup != null) {
add(popup);
if (IJ.isMacOSX()) IJ.wait(10);
popup.show(this, x, y);
}
}
void drawOverlay(Graphics g) {
if (imp != null && imp.getHideOverlay()) return;
Color labelColor = overlay.getLabelColor();
if (labelColor == null) labelColor = Color.white;
initGraphics(g, labelColor, Roi.getColor());
int n = overlay.size();
if (IJ.debugMode) IJ.log("paint: drawing " + n + " ROI display list");
int currentImage = imp != null ? imp.getCurrentSlice() : -1;
if (imp.getStackSize() == 1) currentImage = -1;
int channel = 0, slice = 0, frame = 0;
boolean hyperstack = imp.isHyperStack();
if (hyperstack) {
channel = imp.getChannel();
slice = imp.getSlice();
frame = imp.getFrame();
}
drawNames = overlay.getDrawNames();
boolean drawLabels = drawNames || overlay.getDrawLabels();
for (int i = 0; i < n; i++) {
if (overlay == null) break;
Roi roi = overlay.get(i);
if (hyperstack && roi.getPosition() == 0) {
int c = roi.getCPosition();
int z = roi.getZPosition();
int t = roi.getTPosition();
if ((c == 0 || c == channel) && (z == 0 || z == slice) && (t == 0 || t == frame))
drawRoi(g, roi, drawLabels ? i + LIST_OFFSET : -1);
} else {
int position = roi.getPosition();
if (position == 0 || position == currentImage)
drawRoi(g, roi, drawLabels ? i + LIST_OFFSET : -1);
}
}
((Graphics2D) g).setStroke(Roi.onePixelWide);
drawNames = false;
}
void setCalibration(ImagePlus imp) {
if (fi.fileType == FileInfo.GRAY16_SIGNED) {
if (IJ.debugMode) IJ.log("16-bit signed");
double[] coeff = new double[2];
coeff[0] = -32768.0;
coeff[1] = 1.0;
imp.getLocalCalibration().setFunction(Calibration.STRAIGHT_LINE, coeff, "gray value");
}
Properties props = decodeDescriptionString(fi);
Calibration cal = imp.getCalibration();
boolean calibrated = false;
if (fi.pixelWidth > 0.0 && fi.unit != null) {
cal.pixelWidth = fi.pixelWidth;
cal.pixelHeight = fi.pixelHeight;
cal.pixelDepth = fi.pixelDepth;
cal.setUnit(fi.unit);
calibrated = true;
}
if (fi.valueUnit != null) {
int f = fi.calibrationFunction;
if ((f >= Calibration.STRAIGHT_LINE && f <= Calibration.RODBARD2 && fi.coefficients != null)
|| f == Calibration.UNCALIBRATED_OD) {
boolean zeroClip = props != null && props.getProperty("zeroclip", "false").equals("true");
cal.setFunction(f, fi.coefficients, fi.valueUnit, zeroClip);
calibrated = true;
}
}
if (calibrated) checkForCalibrationConflict(imp, cal);
if (fi.frameInterval != 0.0) cal.frameInterval = fi.frameInterval;
if (props == null) return;
cal.xOrigin = getDouble(props, "xorigin");
cal.yOrigin = getDouble(props, "yorigin");
cal.zOrigin = getDouble(props, "zorigin");
cal.info = props.getProperty("info");
cal.fps = getDouble(props, "fps");
cal.loop = getBoolean(props, "loop");
cal.frameInterval = getDouble(props, "finterval");
cal.setTimeUnit(props.getProperty("tunit", "sec"));
double displayMin = getDouble(props, "min");
double displayMax = getDouble(props, "max");
if (!(displayMin == 0.0 && displayMax == 0.0)) {
int type = imp.getType();
ImageProcessor ip = imp.getProcessor();
if (type == ImagePlus.GRAY8 || type == ImagePlus.COLOR_256)
ip.setMinAndMax(displayMin, displayMax);
else if (type == ImagePlus.GRAY16 || type == ImagePlus.GRAY32) {
if (ip.getMin() != displayMin || ip.getMax() != displayMax)
ip.setMinAndMax(displayMin, displayMax);
}
}
int stackSize = imp.getStackSize();
if (stackSize > 1) {
int channels = (int) getDouble(props, "channels");
int slices = (int) getDouble(props, "slices");
int frames = (int) getDouble(props, "frames");
if (channels == 0) channels = 1;
if (slices == 0) slices = 1;
if (frames == 0) frames = 1;
// IJ.log("setCalibration: "+channels+" "+slices+" "+frames);
if (channels * slices * frames == stackSize) {
imp.setDimensions(channels, slices, frames);
if (getBoolean(props, "hyperstack")) imp.setOpenAsHyperStack(true);
}
}
}
/*
if selection is closed shape, create a circle with the same area and centroid, otherwise use<br>
the Pratt method to fit a circle to the points that define the line or multi-point selection.<br>
Reference: Pratt V., Direct least-squares fitting of algebraic surfaces", Computer Graphics, Vol. 21, pages 145-152 (1987).<br>
Original code: Nikolai Chernov's MATLAB script for Newton-based Pratt fit.<br>
(http://www.math.uab.edu/~chernov/cl/MATLABcircle.html)<br>
Java version: https://github.com/mdoube/BoneJ/blob/master/src/org/doube/geometry/FitCircle.java<br>
@authors Nikolai Chernov, Michael Doube, Ved Sharma
*/
void fitCircle(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Fit Circle");
return;
}
if (roi.isArea()) { // create circle with the same area and centroid
ImageProcessor ip = imp.getProcessor();
ip.setRoi(roi);
ImageStatistics stats =
ImageStatistics.getStatistics(ip, Measurements.AREA + Measurements.CENTROID, null);
double r = Math.sqrt(stats.pixelCount / Math.PI);
imp.killRoi();
int d = (int) Math.round(2.0 * r);
IJ.makeOval(
(int) Math.round(stats.xCentroid - r), (int) Math.round(stats.yCentroid - r), d, d);
return;
}
Polygon poly = roi.getPolygon();
int n = poly.npoints;
int[] x = poly.xpoints;
int[] y = poly.ypoints;
if (n < 3) {
IJ.error("Fit Circle", "At least 3 points are required to fit a circle.");
return;
}
// calculate point centroid
double sumx = 0, sumy = 0;
for (int i = 0; i < n; i++) {
sumx = sumx + poly.xpoints[i];
sumy = sumy + poly.ypoints[i];
}
double meanx = sumx / n;
double meany = sumy / n;
// calculate moments
double[] X = new double[n], Y = new double[n];
double Mxx = 0, Myy = 0, Mxy = 0, Mxz = 0, Myz = 0, Mzz = 0;
for (int i = 0; i < n; i++) {
X[i] = x[i] - meanx;
Y[i] = y[i] - meany;
double Zi = X[i] * X[i] + Y[i] * Y[i];
Mxy = Mxy + X[i] * Y[i];
Mxx = Mxx + X[i] * X[i];
Myy = Myy + Y[i] * Y[i];
Mxz = Mxz + X[i] * Zi;
Myz = Myz + Y[i] * Zi;
Mzz = Mzz + Zi * Zi;
}
Mxx = Mxx / n;
Myy = Myy / n;
Mxy = Mxy / n;
Mxz = Mxz / n;
Myz = Myz / n;
Mzz = Mzz / n;
// calculate the coefficients of the characteristic polynomial
double Mz = Mxx + Myy;
double Cov_xy = Mxx * Myy - Mxy * Mxy;
double Mxz2 = Mxz * Mxz;
double Myz2 = Myz * Myz;
double A2 = 4 * Cov_xy - 3 * Mz * Mz - Mzz;
double A1 = Mzz * Mz + 4 * Cov_xy * Mz - Mxz2 - Myz2 - Mz * Mz * Mz;
double A0 = Mxz2 * Myy + Myz2 * Mxx - Mzz * Cov_xy - 2 * Mxz * Myz * Mxy + Mz * Mz * Cov_xy;
double A22 = A2 + A2;
double epsilon = 1e-12;
double ynew = 1e+20;
int IterMax = 20;
double xnew = 0;
int iterations = 0;
// Newton's method starting at x=0
for (int iter = 1; iter <= IterMax; iter++) {
iterations = iter;
double yold = ynew;
ynew = A0 + xnew * (A1 + xnew * (A2 + 4. * xnew * xnew));
if (Math.abs(ynew) > Math.abs(yold)) {
if (IJ.debugMode) IJ.log("Fit Circle: wrong direction: |ynew| > |yold|");
xnew = 0;
break;
}
double Dy = A1 + xnew * (A22 + 16 * xnew * xnew);
double xold = xnew;
xnew = xold - ynew / Dy;
if (Math.abs((xnew - xold) / xnew) < epsilon) break;
if (iter >= IterMax) {
if (IJ.debugMode) IJ.log("Fit Circle: will not converge");
xnew = 0;
}
if (xnew < 0) {
if (IJ.debugMode) IJ.log("Fit Circle: negative root: x = " + xnew);
xnew = 0;
}
}
if (IJ.debugMode)
IJ.log("Fit Circle: n=" + n + ", xnew=" + IJ.d2s(xnew, 2) + ", iterations=" + iterations);
// calculate the circle parameters
double DET = xnew * xnew - xnew * Mz + Cov_xy;
double CenterX = (Mxz * (Myy - xnew) - Myz * Mxy) / (2 * DET);
double CenterY = (Myz * (Mxx - xnew) - Mxz * Mxy) / (2 * DET);
double radius = Math.sqrt(CenterX * CenterX + CenterY * CenterY + Mz + 2 * xnew);
if (Double.isNaN(radius)) {
IJ.error("Fit Circle", "Points are collinear.");
return;
}
CenterX = CenterX + meanx;
CenterY = CenterY + meany;
imp.killRoi();
IJ.makeOval(
(int) Math.round(CenterX - radius),
(int) Math.round(CenterY - radius),
(int) Math.round(2 * radius),
(int) Math.round(2 * radius));
}
void analyzeParticle(int x, int y, ImagePlus imp, ImageProcessor ip) {
// Wand wand = new Wand(ip);
ImageProcessor ip2 = redirectIP != null ? redirectIP : ip;
wand.autoOutline(x, y, level1, level2, wandMode);
if (wand.npoints == 0) {
IJ.log("wand error: " + x + " " + y);
return;
}
Roi roi = new PolygonRoi(wand.xpoints, wand.ypoints, wand.npoints, roiType);
Rectangle r = roi.getBounds();
if (r.width > 1 && r.height > 1) {
PolygonRoi proi = (PolygonRoi) roi;
pf.setPolygon(proi.getXCoordinates(), proi.getYCoordinates(), proi.getNCoordinates());
ip2.setMask(pf.getMask(r.width, r.height));
if (floodFill) ff.particleAnalyzerFill(x, y, level1, level2, ip2.getMask(), r);
}
ip2.setRoi(r);
ip.setValue(fillColor);
ImageStatistics stats = getStatistics(ip2, measurements, calibration);
boolean include = true;
if (excludeEdgeParticles) {
if (r.x == minX || r.y == minY || r.x + r.width == maxX || r.y + r.height == maxY)
include = false;
if (polygon != null) {
Rectangle bounds = roi.getBounds();
int x1 = bounds.x + wand.xpoints[wand.npoints - 1];
int y1 = bounds.y + wand.ypoints[wand.npoints - 1];
int x2, y2;
for (int i = 0; i < wand.npoints; i++) {
x2 = bounds.x + wand.xpoints[i];
y2 = bounds.y + wand.ypoints[i];
if (!polygon.contains(x2, y2)) {
include = false;
break;
}
if ((x1 == x2 && ip.getPixel(x1, y1 - 1) == fillColor)
|| (y1 == y2 && ip.getPixel(x1 - 1, y1) == fillColor)) {
include = false;
break;
}
x1 = x2;
y1 = y2;
}
}
}
ImageProcessor mask = ip2.getMask();
if (minCircularity > 0.0 || maxCircularity < 1.0) {
double perimeter = roi.getLength();
double circularity =
perimeter == 0.0 ? 0.0 : 4.0 * Math.PI * (stats.pixelCount / (perimeter * perimeter));
if (circularity > 1.0) circularity = 1.0;
// IJ.log(circularity+" "+perimeter+" "+stats.area);
if (circularity < minCircularity || circularity > maxCircularity) include = false;
}
if (stats.pixelCount >= minSize && stats.pixelCount <= maxSize && include) {
particleCount++;
if (roiNeedsImage) roi.setImage(imp);
stats.xstart = x;
stats.ystart = y;
saveResults(stats, roi);
if (showChoice != NOTHING) drawParticle(drawIP, roi, stats, mask);
}
if (redirectIP != null) ip.setRoi(r);
ip.fill(mask);
}
