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ij.plugin.Slicer Maven / Gradle / Ivy

package ij.plugin;
import ij.*;
import ij.process.*;
import ij.gui.*;
import ij.measure.*;
import ij.util.Tools;
import java.awt.*;
import java.awt.event.*;
import java.util.*;

/** Implements the Image/Stacks/Reslice command. Known shortcomings: 
	for FREELINE or POLYLINE ROI, spatial calibration is ignored: 
	the image is sampled at constant _pixel_ increments (distance 1), so 
	(if y/x aspect ratio != 1 in source image) one dimension in the output is not
	homogeneous (i.e. pixelWidth not the same everywhere).
*/
public class Slicer implements PlugIn, TextListener, ItemListener {

	private static final String[] starts = {"Top", "Left", "Bottom", "Right"};
	private static String startAtS = starts[0];
	private static boolean rotateS;
	private static boolean flipS;
	private static int sliceCountS = 1;
	
	private String startAt = starts[0];
	private boolean rotate;
	private boolean flip;
	private int sliceCount = 1;
	private boolean nointerpolate = Prefs.avoidResliceInterpolation;
	private double inputZSpacing = 1.0;
	private double outputZSpacing = 1.0;
	private int outputSlices = 1;
	private boolean noRoi;
	private boolean rgb, notFloat;
	private Vector fields, checkboxes;
	private Label message;
	private ImagePlus imp;
	private double gx1, gy1, gx2, gy2, gLength;

	// Variables used by getIrregularProfile and doIrregularSetup
	private int n;
	private double[] x;
	private	double[] y;
	private int xbase;
	private int ybase;
	private double length;
	private double[] segmentLengths;
	private double[] dx;
	private double[] dy;

	public void run(String arg) {
		imp = WindowManager.getCurrentImage();
		if (imp==null) {
			IJ.noImage();
			return;
		}
		int stackSize = imp.getStackSize();
		Roi roi = imp.getRoi();
		int roiType = roi!=null?roi.getType():0;
		// stack required except for ROI = none or RECT
		if (stackSize<2 && roi!=null && roiType!=Roi.RECTANGLE) {
			IJ.error("Reslice...", "Stack required");
			return;
		}
		// permissible ROI types: none,RECT,*LINE
		if (roi!=null && roiType!=Roi.RECTANGLE && roiType!=Roi.LINE && roiType!=Roi.POLYLINE && roiType!=Roi.FREELINE) {
			IJ.error("Reslice...", "Line or rectangular selection required");
			return;
		}
		if (!showDialog(imp))
			return;
		long startTime = System.currentTimeMillis();
		ImagePlus imp2 = null;
		rgb = imp.getType()==ImagePlus.COLOR_RGB;
		notFloat = !rgb && imp.getType()!=ImagePlus.GRAY32;
		if (imp.isHyperStack())
			imp2 = resliceHyperstack(imp);
		else
			imp2 = reslice(imp);
		if (imp2==null)
			return;
		ImageProcessor ip = imp.getProcessor();
		double min = ip.getMin();
		double max = ip.getMax();
		if (!rgb) imp2.getProcessor().setMinAndMax(min, max);
		imp2.show();
		if (noRoi)
			imp.deleteRoi();
		else
			imp.draw();
		IJ.showStatus(IJ.d2s(((System.currentTimeMillis()-startTime)/1000.0),2)+" seconds");
	}

	public ImagePlus reslice(ImagePlus imp) {
		 ImagePlus imp2;
		 Roi roi = imp.getRoi();
		 int roiType = roi!=null?roi.getType():0;
		 Calibration origCal = imp.getCalibration();
		 boolean globalCalibration = false;
		 if (nointerpolate) {// temporarily clear spatial calibration
				globalCalibration = imp.getGlobalCalibration()!=null;
				imp.setGlobalCalibration(null);
				Calibration tmpCal = origCal.copy();
				tmpCal.pixelWidth = 1.0;
				tmpCal.pixelHeight = 1.0;
				tmpCal.pixelDepth = 1.0;
				imp.setCalibration(tmpCal);
				inputZSpacing = 1.0;
				if (roiType!=Roi.LINE)
					outputZSpacing = 1.0;
		 }
		double zSpacing = inputZSpacing/imp.getCalibration().pixelWidth;
		 if (roi==null || roiType==Roi.RECTANGLE || roiType==Roi.LINE) {
				imp2 = resliceRectOrLine(imp);
		 } else {// we assert roiType==Roi.POLYLINE || roiType==Roi.FREELINE
				String status = imp.getStack().isVirtual()?"":null;
				IJ.showStatus("Reslice...");
				ImageProcessor ip2 = getSlice(imp, 0.0, 0.0, 0.0, 0.0, status);
				imp2 = new ImagePlus("Reslice of "+imp.getShortTitle(), ip2);
		 }
		 if (nointerpolate) { // restore calibration
		 		if (globalCalibration)
					imp.setGlobalCalibration(origCal);
				imp.setCalibration(origCal);
		 }
		 // create Calibration for new stack
		 // start from previous cal and swap appropriate fields
		 boolean horizontal = false;
		 boolean vertical = false;
		if (roi==null || roiType==Roi.RECTANGLE) {
			if (startAt.equals(starts[0]) || startAt.equals(starts[2]))
				horizontal = true;
			else
				vertical = true;
		} 
		if (roi!=null && roiType==Roi.LINE) {
			Line l = (Line)roi;
			horizontal  = (l.y2-l.y1)==0;
			vertical = (l.x2-l.x1)==0;
		}
		if (imp2==null) return null;
		imp2.setCalibration(imp.getCalibration());
		Calibration cal = imp2.getCalibration();
		if (horizontal) {
			cal.pixelWidth = origCal.pixelWidth;
			cal.pixelHeight = origCal.pixelDepth/zSpacing;
			cal.pixelDepth = origCal.pixelHeight*outputZSpacing;
		} else if (vertical) {
			cal.pixelWidth = origCal.pixelHeight;
			cal.pixelHeight = origCal.pixelDepth/zSpacing;
			//cal.pixelWidth = origCal.pixelDepth/zSpacing;
			//cal.pixelHeight = origCal.pixelHeight;
			cal.pixelDepth = origCal.pixelWidth*outputZSpacing;;
		} else { // oblique line, polyLine or freeline
				if (origCal.pixelHeight==origCal.pixelWidth) {
					cal.pixelWidth = origCal.pixelWidth;
					cal.pixelHeight=origCal.pixelDepth/zSpacing;
					cal.pixelDepth = origCal.pixelWidth*outputZSpacing;
				} else {
					cal.pixelWidth = cal.pixelHeight=cal.pixelDepth=1.0;
					cal.setUnit("pixel");
				}
		 }
		 double tmp;
		 if (rotate) {// if rotated flip X and Y
				tmp = cal.pixelWidth;
				cal.pixelWidth = cal.pixelHeight;
				cal.pixelHeight = tmp;
		 }
		 return imp2;
	}

	ImagePlus resliceHyperstack(ImagePlus imp) {
		int channels = imp.getNChannels();
		int slices = imp.getNSlices();
		int frames = imp.getNFrames();
		if (slices==1)
			return resliceTimeLapseHyperstack(imp);
		int c1 = imp.getChannel();
		int z1 = imp.getSlice();
		int t1 = imp.getFrame();
		int width = imp.getWidth();
		int height = imp.getHeight();
		ImagePlus imp2 = null;
		ImageStack stack2 = null;
		Roi roi = imp.getRoi();
		for (int t=1; t<=frames; t++) {
			for (int c=1; c<=channels; c++) {
				ImageStack tmp1Stack = new ImageStack(width, height);
				for (int z=1; z<=slices; z++) {
					imp.setPositionWithoutUpdate(c, z, t);
					tmp1Stack.addSlice(null, imp.getProcessor());
				}
				ImagePlus tmp1 = new ImagePlus("tmp", tmp1Stack);
				tmp1.setCalibration(imp.getCalibration());
				tmp1.setRoi(roi);
				ImagePlus tmp2 = reslice(tmp1);
				int slices2 = tmp2.getStackSize();
				if (imp2==null) {
					imp2 = tmp2.createHyperStack("Reslice of "+imp.getTitle(), channels, slices2, frames, tmp2.getBitDepth());
					stack2 = imp2.getStack();
				}
				ImageStack tmp2Stack = tmp2.getStack();
				for (int z=1; z<=slices2; z++) {
					imp.setPositionWithoutUpdate(c, z, t);
					int n2 = imp2.getStackIndex(c, z, t);
					stack2.setPixels(tmp2Stack.getPixels(z), n2);
				}
			}
		}
		imp.setPosition(c1, z1, t1);
		if (channels>1 && imp.isComposite()) {
			imp2 = new CompositeImage(imp2, ((CompositeImage)imp).getMode());
			((CompositeImage)imp2).copyLuts(imp);
		}
		return imp2;
	}

	ImagePlus resliceTimeLapseHyperstack(ImagePlus imp) {
		int channels = imp.getNChannels();
		int frames = imp.getNFrames();
		int c1 = imp.getChannel();
		int t1 = imp.getFrame();
		int width = imp.getWidth();
		int height = imp.getHeight();
		ImagePlus imp2 = null;
		ImageStack stack2 = null;
		Roi roi = imp.getRoi();
		int z = 1;
		for (int c=1; c<=channels; c++) {
			ImageStack tmp1Stack = new ImageStack(width, height);
			for (int t=1; t<=frames; t++) {
				imp.setPositionWithoutUpdate(c, z, t);
				tmp1Stack.addSlice(null, imp.getProcessor());
			}
			ImagePlus tmp1 = new ImagePlus("tmp", tmp1Stack);
			tmp1.setCalibration(imp.getCalibration());
			tmp1.setRoi(roi);
			ImagePlus tmp2 = reslice(tmp1);
			int frames2 = tmp2.getStackSize();
			if (imp2==null) {
				imp2 = tmp2.createHyperStack("Reslice of "+imp.getTitle(), channels, 1, frames2, tmp2.getBitDepth());
				stack2 = imp2.getStack();
			}
			ImageStack tmp2Stack = tmp2.getStack();
			for (int t=1; t<=frames2; t++) {
				imp.setPositionWithoutUpdate(c, z, t);
				int n2 = imp2.getStackIndex(c, z, t);
				stack2.setPixels(tmp2Stack.getPixels(z), n2);
			}
		}
		imp.setPosition(c1, 1, t1);
		if (channels>1 && imp.isComposite()) {
			imp2 = new CompositeImage(imp2, ((CompositeImage)imp).getMode());
			((CompositeImage)imp2).copyLuts(imp);
		}
		return imp2;
	}

	boolean showDialog(ImagePlus imp) {
		Calibration cal = imp.getCalibration();
		if (cal.pixelDepth<0.0)
			cal.pixelDepth = -cal.pixelDepth;
		String units = cal.getUnits();
		if (cal.pixelWidth==0.0)
			cal.pixelWidth = 1.0;
		inputZSpacing = cal.pixelDepth;
		double outputSpacing = cal.pixelDepth;
		Roi roi = imp.getRoi();
		boolean line = roi!=null && roi.getType()==Roi.LINE;
		if (line) saveLineInfo(roi);
		String macroOptions = Macro.getOptions();
		boolean macroRunning = macroOptions!=null;
		if (macroRunning) {
			if (macroOptions.indexOf("input=")!=-1)
				macroOptions = macroOptions.replaceAll("slice=", "slice_count=");
			macroOptions = macroOptions.replaceAll("slice=", "output=");
			Macro.setOptions(macroOptions);
			nointerpolate = false;
		} else {
			startAt = startAtS;
			rotate = rotateS;
			flip = flipS;
			sliceCount = sliceCountS;
		}
		GenericDialog gd = new GenericDialog("Reslice");
		gd.addNumericField("Output spacing ("+units+"):", outputSpacing, 3);
		if (line) {
			if (!IJ.isMacro()) outputSlices=sliceCount;
			gd.addNumericField("Slice_count:", outputSlices, 0);
		} else
			gd.addChoice("Start at:", starts, startAt);
		gd.addCheckbox("Flip vertically", flip);
		gd.addCheckbox("Rotate 90 degrees", rotate);
		gd.addCheckbox("Avoid interpolation", nointerpolate);
		gd.setInsets(0, 32, 0);
		gd.addMessage("(use 1 pixel spacing)");
		gd.setInsets(15, 0, 0);
		gd.addMessage("Voxel size: "+d2s(cal.pixelWidth)+"x"+d2s(cal.pixelHeight)
			+"x"+d2s(cal.pixelDepth)+" "+cal.getUnit());
		gd.setInsets(5, 0, 0);
		gd.addMessage("Output size: "+getSize(cal.pixelDepth,outputSpacing,outputSlices)+"				");
		fields = gd.getNumericFields();
		if (!macroRunning) {
			for (int i=0; iProperties correct?.");
				return null;
		 }
		 boolean virtualStack = imp.getStack().isVirtual();
		 String status = null;
		 ImagePlus imp2 = null;
		 ImageStack stack2 = null;
		 boolean isStack = imp.getStackSize()>1;
		 IJ.resetEscape();
		 for (int i=0; i1?(i+1)+"/"+outputSlices+", ":"";
				ImageProcessor ip = getSlice(imp, x1, y1, x2, y2, status);
				//IJ.log(i+" "+x1+" "+y1+" "+x2+" "+y2+"   "+ip);
				if (isStack) drawLine(x1, y1, x2, y2, imp);
				if (stack2==null) {
					stack2 = createOutputStack(imp, ip);
					if (stack2==null || stack2.getSize()0) makePolygon(count, outSpacing);
		 }
		 String size = getSize(inputZSpacing, outSpacing, count);
		 message.setText("Output Size: "+size);
	}

	String getSize(double inSpacing, double outSpacing, int count) {
		 int size = getOutputStackSize(inSpacing, outSpacing, count);
		 int mem = getAvailableMemory();
		 String available = mem!=-1?" ("+mem+"MB free)":"";
		 if (message!=null)
				message.setForeground(mem!=-1&&size>mem?Color.red:Color.black);
		 if (size>0)
				return size+"MB"+available;
		 else
				return "<1MB"+available;
	}

	void makePolygon(int count, double outSpacing) {
		int[] x = new int[4];
		int[] y = new int[4];
		Calibration cal = imp.getCalibration();
		double cx = cal.pixelWidth;	//corrects preview for x calibration
		double cy = cal.pixelHeight;	//corrects preview for y calibration
		x[0] = (int)gx1;
		y[0] = (int)gy1;
		x[1] = (int)gx2;
		y[1] = (int)gy2;
		double dx = gx2 - gx1;
		double dy = gy2 - gy1;
		double nrm = Math.sqrt(dx*dx + dy*dy)/outSpacing;
		double xInc = -(dy/(cx*nrm));	//cx scales the x increment
		double yInc = (dx/(cy*nrm));	//cy scales the y increment
		x[2] = x[1] + (int)(xInc*count);
		y[2] = y[1] + (int)(yInc*count);
		x[3] = x[0] + (int)(xInc*count);
		y[3] = y[0] + (int)(yInc*count);
		imp.setRoi(new PolygonRoi(x, y, 4, PolygonRoi.FREEROI));
	}

	int getOutputStackSize(double inSpacing, double outSpacing, int count) {
		Roi roi = imp.getRoi();
		int width = imp.getWidth();
		int height = imp.getHeight();
		if (roi!=null) {
			Rectangle r = roi.getBounds();
			width = r.width;
			width = r.height;
		}
		int type = roi!=null?roi.getType():0;
		int stackSize = imp.getStackSize();
		double size = 0.0;
		if (type==Roi.RECTANGLE) {
			size = width*height*stackSize;
			if (outSpacing>0&&!nointerpolate) size *= inSpacing/outSpacing;
		} else
			size = gLength*count*stackSize;
		int bits = imp.getBitDepth();
		switch (bits) {
			case 16: size*=2; break;
			case 24: case 32: size*=4; break;
		}
		return (int)Math.round(size/1048576.0);
	}

	int getAvailableMemory() {
		 long max = IJ.maxMemory();
		 if (max==0) return -1;
		 long inUse = IJ.currentMemory();
		 long available = max - inUse;
		 return (int)((available+524288L)/1048576L);
	}
}