void setStackDisplayRange(ImagePlus imp) {
ImageStack stack = imp.getStack();
double min = Double.MAX_VALUE;
double max = -Double.MAX_VALUE;
int n = stack.getSize();
for (int i = 1; i <= n; i++) {
if (!silentMode) IJ.showStatus("Calculating stack min and max: " + i + "/" + n);
ImageProcessor ip = stack.getProcessor(i);
ip.resetMinAndMax();
if (ip.getMin() < min) min = ip.getMin();
if (ip.getMax() > max) max = ip.getMax();
}
imp.getProcessor().setMinAndMax(min, max);
imp.updateAndDraw();
}
/**
* Updates this stack so its attributes, such as min, max, calibration table and color model, are
* the same as 'ip'.
*/
public void update(ImageProcessor ip) {
if (ip != null) {
min = ip.getMin();
max = ip.getMax();
cTable = ip.getCalibrationTable();
cm = ip.getColorModel();
}
}
/** Adds the image in 'ip' to the end of the stack. */
public void addSlice(String sliceLabel, ImageProcessor ip) {
if (ip.getWidth() != width || ip.getHeight() != height)
throw new IllegalArgumentException("Dimensions do not match");
if (nSlices == 0) {
cm = ip.getColorModel();
min = ip.getMin();
max = ip.getMax();
}
addSlice(sliceLabel, ip.getPixels());
}
public void resetDisplayRanges() {
int channels = getNChannels();
if (lut == null) setupLuts(channels);
ImageStack stack2 = getImageStack();
if (lut == null
|| channels != lut.length
|| channels > stack2.getSize()
|| channels > MAX_CHANNELS) return;
for (int i = 0; i < channels; ++i) {
ImageProcessor ip2 = stack2.getProcessor(i + 1);
ip2.resetMinAndMax();
lut[i].min = ip2.getMin();
lut[i].max = ip2.getMax();
}
}
/** 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;
}
/**
* Read VoxelMatrix file
*
* @param path input file name with path
* @return read image or null if error
*/
public static ImagePlus read(String path) {
if (null == path) return null;
ImagePlus imp = new ImagePlus();
try {
// create file input & data input stream
FileInputStream fis = new FileInputStream(path);
DataInputStream dis = new DataInputStream(fis);
int size1, size2, size3;
size1 = reverse(dis.readInt()); // 0
size2 = reverse(dis.readInt()); // 0
size3 = reverse(dis.readInt()); // 0
// Distinguish between versions: previous versions of VM files used 3 values
if (size1 > 0 && size2 > 0 && size3 > 0) {
// old version type = int;
imp = readOldFormat(path, dis, size1, size2, size3);
fis.close();
dis.close();
if (size3 > 1) {
imp.setSlice(size3 / 2);
ImageProcessor ip = imp.getProcessor();
ip.resetMinAndMax();
imp.setDisplayRange(ip.getMin(), ip.getMax());
}
} else {
imp = openNewFormat(path, dis);
fis.close();
dis.close();
}
} catch (Exception e) {
e.printStackTrace();
return null;
}
return imp;
}
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);
}
}
}
String getInfo(ImagePlus imp, ImageProcessor ip) {
String s = new String("\n");
s += "Title: " + imp.getTitle() + "\n";
Calibration cal = imp.getCalibration();
int stackSize = imp.getStackSize();
int channels = imp.getNChannels();
int slices = imp.getNSlices();
int frames = imp.getNFrames();
int digits = imp.getBitDepth() == 32 ? 4 : 0;
if (cal.scaled()) {
String unit = cal.getUnit();
String units = cal.getUnits();
s +=
"Width: "
+ IJ.d2s(imp.getWidth() * cal.pixelWidth, 2)
+ " "
+ units
+ " ("
+ imp.getWidth()
+ ")\n";
s +=
"Height: "
+ IJ.d2s(imp.getHeight() * cal.pixelHeight, 2)
+ " "
+ units
+ " ("
+ imp.getHeight()
+ ")\n";
if (slices > 1)
s += "Depth: " + IJ.d2s(slices * cal.pixelDepth, 2) + " " + units + " (" + slices + ")\n";
double xResolution = 1.0 / cal.pixelWidth;
double yResolution = 1.0 / cal.pixelHeight;
int places = Tools.getDecimalPlaces(xResolution, yResolution);
if (xResolution == yResolution)
s += "Resolution: " + IJ.d2s(xResolution, places) + " pixels per " + unit + "\n";
else {
s += "X Resolution: " + IJ.d2s(xResolution, places) + " pixels per " + unit + "\n";
s += "Y Resolution: " + IJ.d2s(yResolution, places) + " pixels per " + unit + "\n";
}
} else {
s += "Width: " + imp.getWidth() + " pixels\n";
s += "Height: " + imp.getHeight() + " pixels\n";
if (stackSize > 1) s += "Depth: " + slices + " pixels\n";
}
if (stackSize > 1)
s +=
"Voxel size: "
+ d2s(cal.pixelWidth)
+ "x"
+ d2s(cal.pixelHeight)
+ "x"
+ d2s(cal.pixelDepth)
+ " "
+ cal.getUnit()
+ "\n";
else
s +=
"Pixel size: "
+ d2s(cal.pixelWidth)
+ "x"
+ d2s(cal.pixelHeight)
+ " "
+ cal.getUnit()
+ "\n";
s += "ID: " + imp.getID() + "\n";
String zOrigin = stackSize > 1 || cal.zOrigin != 0.0 ? "," + d2s(cal.zOrigin) : "";
s += "Coordinate origin: " + d2s(cal.xOrigin) + "," + d2s(cal.yOrigin) + zOrigin + "\n";
int type = imp.getType();
switch (type) {
case ImagePlus.GRAY8:
s += "Bits per pixel: 8 ";
String lut = "LUT";
if (imp.getProcessor().isColorLut()) lut = "color " + lut;
else lut = "grayscale " + lut;
if (imp.isInvertedLut()) lut = "inverting " + lut;
s += "(" + lut + ")\n";
if (imp.getNChannels() > 1) s += displayRanges(imp);
else s += "Display range: " + (int) ip.getMin() + "-" + (int) ip.getMax() + "\n";
break;
case ImagePlus.GRAY16:
case ImagePlus.GRAY32:
if (type == ImagePlus.GRAY16) {
String sign = cal.isSigned16Bit() ? "signed" : "unsigned";
s += "Bits per pixel: 16 (" + sign + ")\n";
} else s += "Bits per pixel: 32 (float)\n";
if (imp.getNChannels() > 1) s += displayRanges(imp);
else {
s += "Display range: ";
double min = ip.getMin();
double max = ip.getMax();
if (cal.calibrated()) {
min = cal.getCValue((int) min);
max = cal.getCValue((int) max);
}
s += IJ.d2s(min, digits) + " - " + IJ.d2s(max, digits) + "\n";
}
break;
case ImagePlus.COLOR_256:
s += "Bits per pixel: 8 (color LUT)\n";
break;
case ImagePlus.COLOR_RGB:
s += "Bits per pixel: 32 (RGB)\n";
break;
}
double interval = cal.frameInterval;
double fps = cal.fps;
if (stackSize > 1) {
ImageStack stack = imp.getStack();
int slice = imp.getCurrentSlice();
String number = slice + "/" + stackSize;
String label = stack.getShortSliceLabel(slice);
if (label != null && label.length() > 0) label = " (" + label + ")";
else label = "";
if (interval > 0.0 || fps != 0.0) {
s += "Frame: " + number + label + "\n";
if (fps != 0.0) {
String sRate =
Math.abs(fps - Math.round(fps)) < 0.00001 ? IJ.d2s(fps, 0) : IJ.d2s(fps, 5);
s += "Frame rate: " + sRate + " fps\n";
}
if (interval != 0.0)
s +=
"Frame interval: "
+ ((int) interval == interval ? IJ.d2s(interval, 0) : IJ.d2s(interval, 5))
+ " "
+ cal.getTimeUnit()
+ "\n";
} else s += "Image: " + number + label + "\n";
if (imp.isHyperStack()) {
if (channels > 1) s += " Channel: " + imp.getChannel() + "/" + channels + "\n";
if (slices > 1) s += " Slice: " + imp.getSlice() + "/" + slices + "\n";
if (frames > 1) s += " Frame: " + imp.getFrame() + "/" + frames + "\n";
}
if (imp.isComposite()) {
if (!imp.isHyperStack() && channels > 1) s += " Channels: " + channels + "\n";
String mode = ((CompositeImage) imp).getModeAsString();
s += " Composite mode: \"" + mode + "\"\n";
}
}
if (ip.getMinThreshold() == ImageProcessor.NO_THRESHOLD) s += "No Threshold\n";
else {
double lower = ip.getMinThreshold();
double upper = ip.getMaxThreshold();
int dp = digits;
if (cal.calibrated()) {
lower = cal.getCValue((int) lower);
upper = cal.getCValue((int) upper);
dp = cal.isSigned16Bit() ? 0 : 4;
}
s += "Threshold: " + IJ.d2s(lower, dp) + "-" + IJ.d2s(upper, dp) + "\n";
}
ImageCanvas ic = imp.getCanvas();
double mag = ic != null ? ic.getMagnification() : 1.0;
if (mag != 1.0) s += "Magnification: " + IJ.d2s(mag, 2) + "\n";
if (cal.calibrated()) {
s += " \n";
int curveFit = cal.getFunction();
s += "Calibration Function: ";
if (curveFit == Calibration.UNCALIBRATED_OD) s += "Uncalibrated OD\n";
else if (curveFit == Calibration.CUSTOM) s += "Custom lookup table\n";
else s += CurveFitter.fList[curveFit] + "\n";
double[] c = cal.getCoefficients();
if (c != null) {
s += " a: " + IJ.d2s(c[0], 6) + "\n";
s += " b: " + IJ.d2s(c[1], 6) + "\n";
if (c.length >= 3) s += " c: " + IJ.d2s(c[2], 6) + "\n";
if (c.length >= 4) s += " c: " + IJ.d2s(c[3], 6) + "\n";
if (c.length >= 5) s += " c: " + IJ.d2s(c[4], 6) + "\n";
}
s += " Unit: \"" + cal.getValueUnit() + "\"\n";
} else s += "Uncalibrated\n";
FileInfo fi = imp.getOriginalFileInfo();
if (fi != null) {
if (fi.url != null && !fi.url.equals("")) s += "URL: " + fi.url + "\n";
else if (fi.directory != null && fi.fileName != null)
s += "Path: " + fi.directory + fi.fileName + "\n";
}
ImageWindow win = imp.getWindow();
if (win != null) {
Point loc = win.getLocation();
Dimension screen = IJ.getScreenSize();
s +=
"Screen location: "
+ loc.x
+ ","
+ loc.y
+ " ("
+ screen.width
+ "x"
+ screen.height
+ ")\n";
}
Overlay overlay = imp.getOverlay();
if (overlay != null) {
String hidden = imp.getHideOverlay() ? " (hidden)" : " ";
int n = overlay.size();
String elements = n == 1 ? " element" : " elements";
s += "Overlay: " + n + elements + (imp.getHideOverlay() ? " (hidden)" : "") + "\n";
} else s += "No Overlay\n";
Roi roi = imp.getRoi();
if (roi == null) {
if (cal.calibrated()) s += " \n";
s += "No Selection\n";
} else if (roi instanceof EllipseRoi) {
s += "\nElliptical Selection\n";
double[] p = ((EllipseRoi) roi).getParams();
double dx = p[2] - p[0];
double dy = p[3] - p[1];
double major = Math.sqrt(dx * dx + dy * dy);
s += " Major: " + IJ.d2s(major, 2) + "\n";
s += " Minor: " + IJ.d2s(major * p[4], 2) + "\n";
s += " X1: " + IJ.d2s(p[0], 2) + "\n";
s += " Y1: " + IJ.d2s(p[1], 2) + "\n";
s += " X2: " + IJ.d2s(p[2], 2) + "\n";
s += " Y2: " + IJ.d2s(p[3], 2) + "\n";
s += " Aspect ratio: " + IJ.d2s(p[4], 2) + "\n";
} else {
s += " \n";
s += roi.getTypeAsString() + " Selection";
String points = null;
if (roi instanceof PointRoi) {
int npoints = ((PolygonRoi) roi).getNCoordinates();
String suffix = npoints > 1 ? "s)" : ")";
points = " (" + npoints + " point" + suffix;
}
String name = roi.getName();
if (name != null) {
s += " (\"" + name + "\")";
if (points != null) s += "\n " + points;
} else if (points != null) s += points;
s += "\n";
Rectangle r = roi.getBounds();
if (roi instanceof Line) {
Line line = (Line) roi;
s += " X1: " + IJ.d2s(line.x1d * cal.pixelWidth) + "\n";
s += " Y1: " + IJ.d2s(yy(line.y1d, imp) * cal.pixelHeight) + "\n";
s += " X2: " + IJ.d2s(line.x2d * cal.pixelWidth) + "\n";
s += " Y2: " + IJ.d2s(yy(line.y2d, imp) * cal.pixelHeight) + "\n";
} else if (cal.scaled()) {
s += " X: " + IJ.d2s(cal.getX(r.x)) + " (" + r.x + ")\n";
s += " Y: " + IJ.d2s(cal.getY(r.y, imp.getHeight())) + " (" + r.y + ")\n";
s += " Width: " + IJ.d2s(r.width * cal.pixelWidth) + " (" + r.width + ")\n";
s += " Height: " + IJ.d2s(r.height * cal.pixelHeight) + " (" + r.height + ")\n";
} else {
s += " X: " + r.x + "\n";
s += " Y: " + yy(r.y, imp) + "\n";
s += " Width: " + r.width + "\n";
s += " Height: " + r.height + "\n";
}
}
return s;
}
static ImagePlus openNewFormat(String path, DataInputStream dis) throws IOException {
// ImagePlus imp;
// New version of VM using 12 parameter fields
int version = reverse(dis.readInt());
int type = reverse(dis.readInt());
int size1 = reverse(dis.readInt());
int size2 = reverse(dis.readInt());
int size3 = reverse(dis.readInt());
ImageStack stack = new ImageStack(size1, size2);
int voxelUnit = reverse(dis.readInt());
float voxelWidth = Float.intBitsToFloat(reverse(dis.readInt()));
float voxelHeight = Float.intBitsToFloat(reverse(dis.readInt()));
float voxelDepth = Float.intBitsToFloat(reverse(dis.readInt()));
final int numPixels = size1 * size2;
final int bufferSize = 4 * numPixels;
final byte[] buffer = new byte[bufferSize];
// write pixels
for (int z = 0; z < size3; ++z) {
final float[][] pixels = new float[size1][size2];
int n = dis.read(buffer, 0, bufferSize);
for (int j = 0; j < bufferSize; j += 4) {
int tmp =
(int)
(((buffer[j + 3] & 0xff) << 24)
| ((buffer[j + 2] & 0xff) << 16)
| ((buffer[j + 1] & 0xff) << 8)
| (buffer[j] & 0xff));
int currentPos = j / 4;
int y = currentPos / size2;
int x = currentPos % size2;
if (type == 5) pixels[y][x] = Float.intBitsToFloat(tmp); // float type
else if (type == 2) pixels[y][x] = (float) tmp; // int type
}
final FloatProcessor fp = new FloatProcessor(pixels);
stack.addSlice(fp);
}
ImagePlus imp = new ImagePlus(path, stack);
if (size3 > 1) {
imp.setSlice(size3 / 2);
ImageProcessor ip = imp.getProcessor();
ip.resetMinAndMax();
imp.setDisplayRange(ip.getMin(), ip.getMax());
}
Calibration calibration = new Calibration();
String unit = intToUnitString(voxelUnit);
calibration.setXUnit(unit);
calibration.setYUnit(unit);
calibration.setZUnit(unit);
calibration.pixelWidth = voxelWidth;
calibration.pixelHeight = voxelHeight;
calibration.pixelDepth = voxelDepth;
imp.setCalibration(calibration);
return imp;
}
public synchronized void updateImage() {
int imageSize = width * height;
int nChannels = getNChannels();
int redValue, greenValue, blueValue;
int ch = getChannel();
// IJ.log("updateImage: "+ch+"/"+nChannels+" "+currentSlice+" "+currentFrame);
if (ch > nChannels) ch = nChannels;
boolean newChannel = false;
if (ch - 1 != currentChannel) {
previousChannel = currentChannel;
currentChannel = ch - 1;
newChannel = true;
}
ImageProcessor ip = getProcessor();
if (mode != COMPOSITE) {
if (newChannel) {
setupLuts(nChannels);
LUT cm = lut[currentChannel];
if (mode == COLOR) ip.setColorModel(cm);
if (!(cm.min == 0.0 && cm.max == 0.0)) ip.setMinAndMax(cm.min, cm.max);
if (!IJ.isMacro()) ContrastAdjuster.update();
for (int i = 0; i < MAX_CHANNELS; i++) active[i] = i == currentChannel ? true : false;
Channels.updateChannels();
}
if (ip != null) img = ip.createImage();
return;
}
if (nChannels == 1) {
cip = null;
rgbPixels = null;
awtImage = null;
if (ip != null) img = ip.createImage();
return;
}
if (cip == null
|| cip[0].getWidth() != width
|| cip[0].getHeight() != height
|| getBitDepth() != bitDepth) {
setup(nChannels, getImageStack());
rgbPixels = null;
rgbSampleModel = null;
if (currentChannel >= nChannels) {
setSlice(1);
currentChannel = 0;
newChannel = true;
}
bitDepth = getBitDepth();
}
if (newChannel) {
getProcessor().setMinAndMax(cip[currentChannel].getMin(), cip[currentChannel].getMax());
if (!IJ.isMacro()) ContrastAdjuster.update();
}
// IJ.log(nChannels+" "+ch+" "+currentChannel+" "+newChannel);
if (getSlice() != currentSlice || getFrame() != currentFrame) {
currentSlice = getSlice();
currentFrame = getFrame();
int position = getStackIndex(1, currentSlice, currentFrame);
if (cip == null) return;
for (int i = 0; i < nChannels; ++i)
cip[i].setPixels(getImageStack().getProcessor(position + i).getPixels());
}
if (rgbPixels == null) {
rgbPixels = new int[imageSize];
newPixels = true;
imageSource = null;
rgbRaster = null;
rgbImage = null;
}
cip[currentChannel].setMinAndMax(ip.getMin(), ip.getMax());
if (singleChannel && nChannels <= 3) {
switch (currentChannel) {
case 0:
cip[0].updateComposite(rgbPixels, 1);
break;
case 1:
cip[1].updateComposite(rgbPixels, 2);
break;
case 2:
cip[2].updateComposite(rgbPixels, 3);
break;
}
} else {
if (cip == null) return;
if (syncChannels) {
ImageProcessor ip2 = getProcessor();
double min = ip2.getMin(), max = ip2.getMax();
for (int i = 0; i < nChannels; i++) {
cip[i].setMinAndMax(min, max);
lut[i].min = min;
lut[i].max = max;
}
syncChannels = false;
}
if (active[0]) cip[0].updateComposite(rgbPixels, 4);
else {
for (int i = 1; i < imageSize; i++) rgbPixels[i] = 0;
}
if (cip == null || nChannels > cip.length) return;
for (int i = 1; i < nChannels; i++) if (active[i]) cip[i].updateComposite(rgbPixels, 5);
}
if (IJ.isJava16()) createBufferedImage();
else createImage();
if (img == null && awtImage != null) img = awtImage;
singleChannel = false;
}