/** Opens all the images in the specified directory as a stack, using the format specified by 'fi'. */ public static ImagePlus openAll(String directory, FileInfo fi) { ImagePlus imp = openAllVirtual(directory,fi); if (imp!=null) return imp.duplicate(); else return null; }
/** Opens all the images in the specified directory as a stack, using the format specified by 'fi'. */ public static ImagePlus openAll(String directory, FileInfo fi) { ImagePlus imp = openAllVirtual(directory,fi); if (imp!=null) return imp.duplicate(); else return null; }
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.MAX, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ MAXIMUM ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.MEAN, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ MEAN ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.MAX, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ MAXIMUM ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.VAR, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ VARIANCE ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.MEAN, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ MEAN ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.MIN, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ MINIMUM ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.MEDIAN, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ MEDIAN ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.VAR, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ VARIANCE ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.MIN, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ MINIMUM ] +"_" + sigma, is ); result.add( ip ); return result; } };
public ArrayList< ImagePlus > call() { final ImagePlus im = originalImage.duplicate(); if( originalImage.getType() != ImagePlus.COLOR_RGB ) { ImageConverter ic = new ImageConverter( im ); ic.convertToGray32(); } ArrayList<ImagePlus> result = new ArrayList<ImagePlus>(); final ImageStack is = Filters3D.filter(im.getImageStack(), Filters3D.MEDIAN, (float) (sigma * scaleFactor[0]), (float) (sigma * scaleFactor[1]), (float) (sigma * scaleFactor[2])); final ImagePlus ip = new ImagePlus( availableFeatures[ MEDIAN ] +"_" + sigma, is ); result.add( ip ); return result; } };
public static void save( final Img< FloatType > img, final String file ) { final ImagePlus imp = ImageJFunctions.wrap( img, "" ).duplicate(); final FileSaver s = new FileSaver( imp ); if ( img.numDimensions() == 3 ) { imp.setDimensions( 1, (int)img.dimension( 2 ), 1 ); s.saveAsTiffStack( file ); } else { s.saveAsTiff( file ); } imp.close(); }
/** * Add HSB features */ public void addHSB() { final ImagePlus hsb = originalImage.duplicate(); ImageConverter ic = new ImageConverter( hsb ); ic.convertToHSB(); for(int n=1; n<=hsb.getImageStackSize(); n++) wholeStack.addSlice(hsb.getImageStack().getSliceLabel(n), hsb.getImageStack().getProcessor(n).convertToRGB()); }
/** * Add HSB features */ public void addHSB() { final ImagePlus hsb = originalImage.duplicate(); ImageConverter ic = new ImageConverter( hsb ); ic.convertToHSB(); for(int n=1; n<=hsb.getImageStackSize(); n++) wholeStack.addSlice(hsb.getImageStack().getSliceLabel(n), hsb.getImageStack().getProcessor(n).convertToRGB()); }
@Override public void run(String arg0) { ImagePlus imagePlus = IJ.getImage(); ImagePlus resultPlus = imagePlus.duplicate(); LabelImages.removeLargestLabel(resultPlus); String newName = imagePlus.getShortTitle() + "-killLargest"; resultPlus.setTitle(newName); // Display with same settings as original image resultPlus.show(); if (imagePlus.getStackSize() > 1) { resultPlus.setZ(imagePlus.getZ()); resultPlus.setSlice(imagePlus.getCurrentSlice()); } } }
@Override public void run(String arg0) { ImagePlus imagePlus = IJ.getImage(); ImagePlus resultPlus = imagePlus.duplicate(); BinaryImages.removeLargestRegion(resultPlus); String newName = imagePlus.getShortTitle() + "-killLargest"; resultPlus.setTitle(newName); // Display with same settings as original image resultPlus.show(); if (imagePlus.getStackSize() > 1) { resultPlus.setZ(imagePlus.getZ()); resultPlus.setSlice(imagePlus.getCurrentSlice()); } } }
public ImagePlus call(){ final ImagePlus hsb = originalImage.duplicate(); ImageConverter ic = new ImageConverter( hsb ); ic.convertToHSB(); ImageStack is = new ImageStack(originalImage.getWidth(), originalImage.getHeight()); for(int n=1; n<=hsb.getImageStackSize(); n++) is.addSlice(hsb.getImageStack().getSliceLabel(n), hsb.getImageStack().getProcessor(n).convertToRGB()); return new ImagePlus ("HSB", is); } };
public ImagePlus call(){ final ImagePlus hsb = originalImage.duplicate(); ImageConverter ic = new ImageConverter( hsb ); ic.convertToHSB(); ImageStack is = new ImageStack(originalImage.getWidth(), originalImage.getHeight()); for(int n=1; n<=hsb.getImageStackSize(); n++) is.addSlice(hsb.getImageStack().getSliceLabel(n), hsb.getImageStack().getProcessor(n).convertToRGB()); return new ImagePlus ("HSB", is); } };
/** * Display the whole image after classification */ void showClassificationImage() { if( null == classifiedImage ) { // if not result image is there yet, calculate it win.setButtonsEnabled( false ); wekaSegmentation.applyClassifier( false ); classifiedImage = wekaSegmentation.getClassifiedImage(); win.updateButtonsEnabling(); } final ImagePlus resultImage = classifiedImage.duplicate(); resultImage.setTitle( "Classified image" ); convertTo8bitNoScaling( resultImage ); resultImage.getProcessor().setColorModel( overlayLUT ); resultImage.getImageStack().setColorModel( overlayLUT ); resultImage.updateAndDraw(); resultImage.show(); }