SIMcheck.Util_SItoPseudoWidefield Maven / Gradle / Ivy
/* Copyright (c) 2015, Graeme Ball and Micron Oxford,
* University of Oxford, Department of Biochemistry.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see http://www.gnu.org/licenses/ .
*/
package SIMcheck;
import ij.*;
import ij.measure.Calibration;
import ij.plugin.*;
import ij.process.*;
import ij.gui.GenericDialog;
/** This plugin converts a SIM image to a pseudo-wide-field image by averaging
* phases and angles. Assumes OMX V2 CPZAT input channel order.
*
* Note: this plugin has a totally unrelated functionality in that also
* allows a max projection, which is used by the Rec_ModContrastMap to assess
* whether *any* angle is saturated in the raw data (should probably be
* refactored!)
*
* @author Graeme Ball
**/
public class Util_SItoPseudoWidefield implements PlugIn {
public static final String name = "Raw SI to Pseudo-Widefield";
public static final String TLA = "PWF";
// parameter fields
public int phases = 5;
public int angles = 3;
public boolean doNormalize = true;
private static ImagePlus projImg = null; // intermediate & final results
public enum ProjMode { AVG, MAX } // can do average or max projection
// TODO: refactor -- AVG and MAX projection details different / unexpected
@Override
public void run(String arg) {
ImagePlus imp = IJ.getImage();
// TODO: option for padding to reconstructed result size for comparison
GenericDialog gd = new GenericDialog(name);
gd.addMessage("Requires SI raw data in OMX (CPZAT) order.");
gd.addNumericField("Angles", angles, 0);
gd.addNumericField("Phases", phases, 0);
gd.addCheckbox("Intensity normalisation (simple ratio correction)",
doNormalize);
gd.showDialog();
if (gd.wasCanceled()) return;
if(gd.wasOKed()){
angles = (int)gd.getNextNumber();
phases = (int)gd.getNextNumber();
doNormalize = gd.getNextBoolean();
}
if (!I1l.stackDivisibleBy(imp, phases * angles)) {
IJ.showMessage( "SI to Pseudo-Wide-Field",
"Error: stack size not consistent with phases/angles.");
return;
}
if (doNormalize) {
projImg = exec(I1l.normalizeImp(imp), phases, angles, ProjMode.AVG);
} else {
projImg = exec(imp, phases, angles, ProjMode.AVG);
}
IJ.run("Brightness/Contrast...");
projImg.show();
}
/** Execute plugin functionality: raw SI data to pseudo-widefield.
* @param imp input raw SI data ImagePlus
* @param phases number of phases
* @param angles number of angles
* @param m projection mode: AVG or MAX
* @return ImagePlus with all phases and angles averaged
*/
public ImagePlus exec(ImagePlus imp, int phases, int angles, ProjMode m) {
ImagePlus impCopy = imp.duplicate();
this.angles = angles;
this.phases = phases;
int channels = imp.getNChannels();
int Zplanes = imp.getNSlices();
int frames = imp.getNFrames();
Zplanes = Zplanes/(phases*angles); // take phase & angle out of Z
IJ.run("Conversions...", " "); // TODO: reset option state when done..
new StackConverter(impCopy).convertToGray32();
projImg = projectPandA(impCopy, channels, Zplanes, frames, m);
// projectPandA result in projImg; Zplanes reduced by phases*angles
if (m == ProjMode.AVG) {
// AVG projection results 16-bit, resized x2 in XY
new StackConverter(projImg).convertToGray16(); // TODO: was original?
int newWidth = imp.getWidth() * 2;
int newHeight = imp.getHeight() * 2;
String newTitle = I1l.makeTitle(imp, TLA);
if (channels > 1) {
IJ.run(projImg, "Scale...", "x=2 y=2 z=1.0 width=" + newWidth
+ " height=" + newHeight + " depth=" + Zplanes
+ " interpolation=Bicubic average"
+ " create title=" + newTitle);
} else {
// damned "Scale..." command requires "process" to do full stack
// if we have an ordinary stack rather than a hyperstack
IJ.run(projImg, "Scale...", "x=2 y=2 z=1.0 width=" + newWidth
+ " height=" + newHeight + " depth=" + Zplanes
+ " interpolation=Bicubic average process" // "process"
+ " create title=" + newTitle);
}
projImg = ij.WindowManager.getCurrentImage();
I1l.copyCal(imp, projImg);
Calibration cal = projImg.getCalibration();
cal.pixelWidth /= 2;
cal.pixelHeight /= 2;
projImg.hide();
} else {
// MAX proj used in MCM needs 32-bit result, *NOT* resized x2
I1l.copyCal(imp, projImg);
}
if (channels > 1) {
CompositeImage ci = new CompositeImage(projImg);
ci.setMode(IJ.GRAYSCALE);
return (ImagePlus)ci;
} else {
return projImg;
}
}
/** Projection e.g. 5 phases, 3 angles for each CZT. **/
private ImagePlus projectPandA(ImagePlus imp, int nc, int nz, int nt, ProjMode m) {
ImageStack stack = imp.getStack();
ImageStack PAset = new ImageStack(imp.getWidth(), imp.getHeight());
ImageStack avStack = new ImageStack(imp.getWidth(), imp.getHeight());
int sliceIn = 0;
int sliceOut = 0;
// loop through in desired (PA)CZT output order, and project slices when we have a PA set
int PAsetSize = phases * angles;
IJ.showStatus("Averaging over phases and angles");
for (int t = 1; t <= nt; t++) {
for (int z = 1; z <= nz; z++) {
IJ.showProgress(z, nz);
for (int c = 1; c <= nc; c++) {
for (int a = 1; a <= angles; a++) {
for (int p = 1; p <= phases; p++) {
sliceIn = (t - 1) * (nc * phases * nz * angles);
sliceIn += (a - 1) * (nc * phases * nz);
sliceIn += (z - 1) * (nc * phases);
sliceIn += (p - 1) * nc;
sliceIn += c;
sliceOut++;
ImageProcessor ip = stack.getProcessor(sliceIn);
PAset.addSlice(null, stack.getProcessor(sliceIn));
if ((p * a == PAsetSize)) {
switch (m)
{
case AVG:
ip = avSlices(imp, PAset, PAsetSize);
break;
case MAX:
ip = maxSlices(imp, PAset, PAsetSize);
break;
default:
ip = avSlices(imp, PAset, PAsetSize);
}
for (int slice = PAsetSize; slice >= 1; slice--) {
PAset.deleteSlice(slice);
}
sliceOut++;
avStack.addSlice(String.valueOf(sliceOut), ip);
}
}
}
}
}
}
projImg = new ImagePlus("projImg", avStack);
projImg.setDimensions(nc, nz, nt);
int centralZ = nz / 2;
projImg.setZ(centralZ);
projImg.setC(1);
projImg.setT(1);
projImg.setOpenAsHyperStack(true);
return projImg;
}
/** Return FloatProcessor with average of slices in stack. */
private static ImageProcessor avSlices(
ImagePlus imp, ImageStack stack, int slices) {
int width = imp.getWidth();
int height = imp.getHeight();
int len = width * height;
FloatProcessor oip = new FloatProcessor(width, height);
float[] avpixels = (float[])oip.getPixels();
for (int slice = 1; slice <= slices; slice++){
FloatProcessor fp = (FloatProcessor)stack.getProcessor(slice).convertToFloat();
float[] fpixels = (float[])fp.getPixels();
for (int i = 0; i < len; i++) {
avpixels[i] += fpixels[i];
}
}
float fslices = (float)slices;
for (int i = 0; i < len; i++) {
avpixels[i] /= fslices;
}
oip = new FloatProcessor(width, height, avpixels, null);
return oip;
}
/** Return (ImageProcessor)FloatProcessor with max of slices in stack. */
private static ImageProcessor maxSlices(
ImagePlus imp, ImageStack stack, int slices) {
int width = imp.getWidth();
int height = imp.getHeight();
int len = width * height;
FloatProcessor fpOut = new FloatProcessor(width, height);
float[] maxPixels = null;
for (int slice = 1; slice <= slices; slice++){
FloatProcessor fp = (FloatProcessor)stack.getProcessor(slice).convertToFloat();
float[] fpixels = (float[])fp.getPixels();
if (slice == 1) {
maxPixels = fpixels;
}
for (int i = 0; i < len; i++) {
if (fpixels[i] > maxPixels[i]) {
maxPixels[i] = fpixels[i];
}
}
}
fpOut = new FloatProcessor(width, height, maxPixels, null);
return fpOut;
}
/** Interactive test method. */
public static void main(String[] args) {
// TODO: automatic tests for private methods
new ImageJ();
TestData.raw.show();
// interactive tests of exec (AVG and MAX projections)
ImagePlus impTest = ij.WindowManager.getCurrentImage();
// 1. AVG
Util_SItoPseudoWidefield si2wf = new Util_SItoPseudoWidefield();
ImagePlus impAvg = si2wf.exec(impTest, 5, 3, ProjMode.AVG);
impAvg.setTitle("impAvg");
impAvg.show();
// 2. AVG
ImagePlus impMax = si2wf.exec(impTest, 5, 3, ProjMode.MAX);
impMax.setTitle("impMax");
impMax.show();
IJ.runPlugIn(Util_SItoPseudoWidefield.class.getName(), "");
}
}
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