/**
* Creates a new FloatProcessor using the specified FloatProcessor. Set 'cm' to null to use the
* default grayscale LUT.
*/
public SerializableFloatProcessor(FloatProcessor floatProcessor) {
floatProcessor = (FloatProcessor) floatProcessor.duplicate();
this.width = floatProcessor.getWidth();
this.height = floatProcessor.getHeight();
this.pixels = (float[]) floatProcessor.getPixels();
this.cm = floatProcessor.getColorModel();
resetRoi();
if (pixels != null) findMinAndMax();
}
@Override
public boolean run(JEXEntry optionalEntry) {
if (imageData == null || !imageData.getTypeName().getType().equals(JEXData.IMAGE)) {
return false;
}
// Run the function
TreeMap<DimensionMap, String> images = ImageReader.readObjectToImagePathTable(imageData);
TreeMap<DimensionMap, String> outputMap = new TreeMap<DimensionMap, String>();
int count = 0;
int total = images.size();
for (DimensionMap dim : images.keySet()) {
if (this.isCanceled()) {
return false;
}
String path = images.get(dim);
// File f = new File(path);
// get the image
ImagePlus im = new ImagePlus(path);
ij.process.ImageProcessor imProc = im.getProcessor();
if (imProc == null) continue;
FloatProcessor imp =
(FloatProcessor) im.getProcessor().convertToFloat(); // should be a float processor
int newWidth = (int) (imp.getWidth() * scale);
imp.setInterpolationMethod(ImageProcessor.BILINEAR);
imp = (FloatProcessor) imp.resize(newWidth);
ImagePlus toSave = FunctionUtility.makeImageToSave(imp, "false", bitDepth);
String finalPath = JEXWriter.saveImage(toSave);
outputMap.put(dim.copy(), finalPath);
Logs.log("Finished processing " + count + " of " + total + ".", 1, this);
count++;
// Status bar
int percentage = (int) (100 * ((double) count / (double) images.size()));
JEXStatics.statusBar.setProgressPercentage(percentage);
}
// Set the outputs
output = ImageWriter.makeImageStackFromPaths("temp", outputMap);
output.setDataObjectInfo("Stack binned using binning function");
// Return status
return true;
}
void SMLblur1Direction(
final FloatProcessor ippp,
final double sigma,
final double accuracy,
final boolean xDirection,
final int extraLines) {
final float[] pixels = (float[]) ippp.getPixels();
final int width = ippp.getWidth();
final int height = ippp.getHeight();
final int length =
xDirection ? width : height; // number of points per line (line can be a row or column)
final int pointInc =
xDirection ? 1 : width; // increment of the pixels array index to the next poin a line
final int lineInc =
xDirection ? width : 1; // increment of the pixels array index to the next line
final int lineFromA = 0 - extraLines; // the first line to process
final int lineFrom;
if (lineFromA < 0) lineFrom = 0;
else lineFrom = lineFromA;
final int lineToA = (xDirection ? height : width) + extraLines; // the last line+1 to process
final int lineTo;
if (lineToA > (xDirection ? height : width)) lineTo = (xDirection ? height : width);
else lineTo = lineToA;
final int writeFrom = 0; // first point of a line that needs to be written
final int writeTo = xDirection ? width : height;
final float[][] gaussKernel = lowpassGauss.makeGaussianKernel(sigma, accuracy, length);
final int kRadius = gaussKernel[0].length; // Gaussian kernel radius after upscaling
final int readFrom =
(writeFrom - kRadius < 0)
? 0
: writeFrom - kRadius; // not including broadening by downscale&upscale
final int readTo = (writeTo + kRadius > length) ? length : writeTo + kRadius;
final int newLength = length;
final float[] cache1 =
new float[newLength]; // holds data before convolution (after downscaling, if any)
int pixel0 = 0;
for (int line = lineFrom; line < lineTo; line++, pixel0 += lineInc) {
int p = pixel0 + readFrom * pointInc;
for (int i = readFrom; i < readTo; i++, p += pointInc) cache1[i] = pixels[p];
SMLconvolveLine(
cache1, pixels, gaussKernel, readFrom, readTo, writeFrom, writeTo, pixel0, pointInc);
}
return;
}
public void run(String arg) {
ImagePlus imp = WindowManager.getCurrentImage();
Calibration cal = imp.getCalibration();
GenericDialog gd = new GenericDialog("Options");
int subsize = 32;
gd.addNumericField("Subregion Size (pixels)?", subsize, 0);
int stepsize = 16;
gd.addNumericField("Step Size?", stepsize, 0);
int shift = 3;
gd.addNumericField("STICS temporal Shift?", shift, 0);
float xoffset = 0.0f;
gd.addNumericField("X_Offset", xoffset, 5, 15, null);
float yoffset = 0.0f;
gd.addNumericField("Y_Offset", yoffset, 5, 15, null);
float multiplier = 8.0f;
gd.addNumericField("Velocity Multiplier", multiplier, 5, 15, null);
float ftime = 1.0f;
gd.addNumericField("Frame_Time(min)", ftime, 5, 15, null);
float scaling = (float) cal.pixelWidth;
gd.addNumericField("Pixel_Size(um)", scaling, 5, 15, null);
boolean norm = true;
gd.addCheckbox("Normalize_Vector_lengths?", norm);
boolean centered = true;
gd.addCheckbox("Center_Vectors?", centered);
float magthresh = 0.0f;
gd.addNumericField("Magnitude_Threshhold?", magthresh, 5, 15, null);
int rlength = 10;
gd.addNumericField("Running_avg_length", rlength, 0);
int inc = 5;
gd.addNumericField("Start_frame_increment", inc, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
subsize = (int) gd.getNextNumber();
stepsize = (int) gd.getNextNumber();
shift = (int) gd.getNextNumber();
xoffset = (float) gd.getNextNumber();
yoffset = (float) gd.getNextNumber();
multiplier = (float) gd.getNextNumber();
ftime = (float) gd.getNextNumber();
scaling = (float) gd.getNextNumber();
norm = gd.getNextBoolean();
centered = gd.getNextBoolean();
magthresh = (float) gd.getNextNumber();
rlength = (int) gd.getNextNumber();
inc = (int) gd.getNextNumber();
int width = imp.getWidth();
int xregions = 1 + (int) (((float) width - (float) subsize) / (float) stepsize);
int newwidth = xregions * subsize;
int height = imp.getHeight();
int yregions = 1 + (int) (((float) height - (float) subsize) / (float) stepsize);
int newheight = yregions * subsize;
ImageStack stack = imp.getStack();
int slices = imp.getNSlices();
int channels = imp.getNChannels();
int frames = imp.getNFrames();
if (frames == 1) {
frames = slices;
slices = 1;
}
Roi roi = imp.getRoi();
if (roi == null) {
roi = new Roi(0, 0, width, height);
}
STICS_map map = new STICS_map(subsize, stepsize);
Object[] tseries = jutils.get3DTSeries(stack, 0, 0, frames, slices, channels);
map.update_STICS_map(tseries, width, height, 0, rlength, roi.getPolygon(), shift);
FloatProcessor fp =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
ImageStack vector_stack = new ImageStack(fp.getWidth(), fp.getHeight());
vector_stack.addSlice("", fp);
float[][] vel = map.get_scaled_velocities(scaling, ftime, stepsize);
ImageStack velstack = new ImageStack(map.xregions, map.yregions);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
int velframes = 2;
IJ.showStatus("frame " + 0 + " calculated");
for (int i = inc; i < (frames - rlength); i += inc) {
map.update_STICS_map(tseries, width, height, i, rlength, roi.getPolygon(), shift);
FloatProcessor fp2 =
map.get_map(scaling, ftime, stepsize, centered, norm, multiplier, stepsize, magthresh);
vector_stack.addSlice("", fp2);
vel = map.get_scaled_velocities(scaling, ftime, stepsize);
velstack.addSlice("", vel[0]);
velstack.addSlice("", vel[1]);
velframes += 2;
IJ.showStatus("frame " + i + " calculated");
}
(new ImagePlus("STICS Vectors", vector_stack)).show();
ImagePlus imp3 = new ImagePlus("Velocities", velstack);
imp3.setOpenAsHyperStack(true);
imp3.setDimensions(2, 1, velframes / 2);
new CompositeImage(imp3, CompositeImage.COLOR).show();
}