Java Code Examples for ij.process.ImageProcessor#fill()
The following examples show how to use
ij.process.ImageProcessor#fill() .
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Example 1
Source File: GeodesicDistanceMapPluginTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 6 votes |
/** * Test method for {@link inra.ijpb.plugins.GeodesicDistanceMapPlugin#process(ij.ImagePlus, ij.ImagePlus, java.lang.String, short[], boolean)}. */ @Test public void testProcess_Short() { ImagePlus maskPlus = IJ.openImage(getClass().getResource("/files/circles.tif").getFile()); ImageProcessor mask = maskPlus.getProcessor(); ImageProcessor marker = mask.duplicate(); marker.fill(); marker.set(30, 30, 255); ImagePlus markerPlus = new ImagePlus("marker", marker); GeodesicDistanceMapPlugin plugin = new GeodesicDistanceMapPlugin(); short[] weights = new short[]{3, 4}; ImagePlus mapPlus = plugin.process(markerPlus, maskPlus, "map", weights, true); ImageProcessor map = mapPlus.getProcessor(); assertEquals(259, map.get(190, 213)); }
Example 2
Source File: GeodesicDistanceMapPluginTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 6 votes |
/** * Test method for {@link inra.ijpb.plugins.GeodesicDistanceMapPlugin#process(ij.ImagePlus, ij.ImagePlus, java.lang.String, float[], boolean)}. */ @Test public void testProcess_Float() { ImagePlus maskPlus = IJ.openImage(getClass().getResource("/files/circles.tif").getFile()); ImageProcessor mask = maskPlus.getProcessor(); ImageProcessor marker = mask.duplicate(); marker.fill(); marker.set(30, 30, 255); ImagePlus markerPlus = new ImagePlus("marker", marker); GeodesicDistanceMapPlugin plugin = new GeodesicDistanceMapPlugin(); float[] weights = new float[]{3, 4}; ImagePlus mapPlus = plugin.process(markerPlus, maskPlus, "map", weights, true); ImageProcessor map = mapPlus.getProcessor(); assertEquals(259, map.getf(190, 213), .01); }
Example 3
Source File: DiskStrelTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 6 votes |
/** * Dilates a single pixel by a 3x3 disk, and check the shape of the result. * The result should be a 3x3 square (approximation of 3x3 disk) */ @Test public void testDilate_SinglePixel_Radius() { Strel strel = DiskStrel.fromRadius(1); ImageProcessor image = new ByteProcessor(10, 10); image.setValue(0); image.fill(); image.set(5, 5, 255); ImageProcessor result = strel.dilation(image); // Check all values inside square for (int y = 4; y < 7; y++) for (int x = 4; x < 7; x++) assertEquals(255, result.get(x, y)); }
Example 4
Source File: Utils.java From TrakEM2 with GNU General Public License v3.0 | 6 votes |
/** Paints an approximation of the pipe into the set of slices. */ static public void paint(final Pipe pipe, final Map<Layer,ImageProcessor> slices, final int value, final float scale) { final VectorString3D vs = pipe.asVectorString3D(); vs.resample(1); // one pixel final double[] px = vs.getPoints(0); final double[] py = vs.getPoints(1); final double[] pz = vs.getPoints(2); final double[] pr = vs.getDependent(0); // For each point for (int i=0; i<px.length-1; i++) { final ImageProcessor ip = slices.get(pipe.getLayerSet().getNearestLayer(pz[i])); if (null == ip) continue; final OvalRoi ov = new OvalRoi((int)((px[i] - pr[i]) * scale), (int)((py[i] - pr[i]) * scale), (int)(pr[i]*2*scale), (int)(pr[i]*2*scale)); ip.setRoi(ov); ip.setValue(value); ip.fill(ip.getMask()); } }
Example 5
Source File: FloodFillTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
@Test public final void testFloodFill_EmptySquaresC4() { int[] data = new int[]{ 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 20, 20, 20, 10, 10, 10, 30, 30, 30, 10, 10, 20, 20, 20, 10, 10, 10, 30, 30, 30, 10, 10, 20, 20, 20, 10, 10, 10, 30, 30, 30, 10, 10, 10, 10, 10, 40, 40, 40, 10, 10, 10, 10, 10, 10, 10, 10, 40, 40, 40, 10, 10, 10, 10, 10, 10, 10, 10, 40, 40, 40, 10, 10, 10, 10, 10, 20, 20, 20, 10, 10, 10, 30, 30, 30, 10, 10, 20, 20, 20, 10, 10, 10, 30, 30, 30, 10, 10, 20, 20, 20, 10, 10, 10, 30, 30, 30, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 }; ImageProcessor image = new ByteProcessor(11, 11); for (int i = 0; i < 11*11; i++) { image.set(i, data[i]); } // initialize result ImageProcessor result = new ByteProcessor(11, 11); result.setValue(255); result.fill(); // compute flood fill result FloodFill.floodFill(image, 1, 0, result, 50, 4); assertEquals(50, result.get(0, 0)); assertEquals(50, result.get(10, 0)); assertEquals(50, result.get(0, 10)); assertEquals(50, result.get(10, 10)); assertEquals(50, result.get(5, 3)); assertEquals(50, result.get(5, 7)); assertEquals(50, result.get(3, 5)); assertEquals(50, result.get(7, 5)); // printImage(result); }
Example 6
Source File: OctagonStrelTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
private ImageProcessor createImage_Square10x10 () { ImageProcessor image = new ByteProcessor(30, 30); image.setValue(0); image.fill(); for (int y = 10; y < 20; y++) { for (int x = 10; x < 20; x++) { image.set(x, y, 255); } } return image; }
Example 7
Source File: ShiftedCross3x3Strel_RightTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
private ImageProcessor createImage_Square4x4 () { ImageProcessor image = new ByteProcessor(10, 10); image.setValue(0); image.fill(); for (int y = 3; y < 7; y++) { for (int x = 3; x < 7; x++) { image.set(x, y, 255); } } return image; }
Example 8
Source File: SquareStrelTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
/** * Creates a 30-by-30 image with a 10-by-10 square in the middle. */ private ImageProcessor createImage_Square10x10 () { ImageProcessor image = new ByteProcessor(30, 30); image.setValue(0); image.fill(); for (int y = 10; y < 20; y++) { for (int x = 10; x < 20; x++) { image.set(x, y, 255); } } return image; }
Example 9
Source File: LinearDiagUpStrelTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
private ImageProcessor createImage_Square4x4 () { ImageProcessor image = new ByteProcessor(10, 10); image.setValue(0); image.fill(); for (int y = 3; y < 7; y++) { for (int x = 3; x < 7; x++) { image.set(x, y, 255); } } return image; }
Example 10
Source File: DiskStrelTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
/** * Dilates a single pixel by a disk with diameter 4. * The result should be larger than dilation with diameter 3. */ @Test public void testDilate_SinglePixel_EvenDiameter() { Strel disk3 = DiskStrel.fromDiameter(3); Strel disk4 = DiskStrel.fromDiameter(4); ImageProcessor image = new ByteProcessor(10, 10); image.setValue(0); image.fill(); image.set(5, 5, 255); ImageProcessor result3 = disk3.dilation(image); ImageProcessor result4 = disk4.dilation(image); // Check result3 <= result4 boolean different = false; for (int y = 0; y < 10; y++) { for (int x = 0; x < 10; x++) { int res3 = result3.get(x, y); int res4 = result4.get(x, y); assertTrue(res3 <= res4); if (res3 != res4) { different = true; } } } assertTrue(different); }
Example 11
Source File: LinearDiagDownStrelTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
private ImageProcessor createImage_Square10x10 () { ImageProcessor image = new ByteProcessor(30, 30); image.setValue(0); image.fill(); for (int y = 10; y < 20; y++) { for (int x = 10; x < 20; x++) { image.set(x, y, 255); } } return image; }
Example 12
Source File: LinearDiagDownStrelTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
private ImageProcessor createImage_Square4x4 () { ImageProcessor image = new ByteProcessor(10, 10); image.setValue(0); image.fill(); for (int y = 3; y < 7; y++) { for (int x = 3; x < 7; x++) { image.set(x, y, 255); } } return image; }
Example 13
Source File: LinearDiagUpStrelTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 5 votes |
private ImageProcessor createImage10x15_Square4x4 () { ImageProcessor image = new ByteProcessor(10, 15); image.setValue(0); image.fill(); for (int y = 3; y < 7; y++) { for (int x = 3; x < 7; x++) { image.set(x, y, 255); } } return image; }
Example 14
Source File: GeodesicReconstructionScanningTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 4 votes |
/** * Test method for {@link ijt.filter.morphology.GeodesicReconstruction#reconstructByErosion()}. */ @Test public void testReconstructByErosion_FloatC4() { float BG = -42; float FG = 2500; float[][] data = new float[][]{ {BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, FG, FG, FG, FG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, FG, FG, FG, FG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, BG, BG, BG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, BG, BG, BG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, FG, FG, FG, FG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, FG, FG, FG, FG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG}, }; int height = data.length; int width = data[0].length; ImageProcessor mask = new FloatProcessor(width, height); for (int y = 0; y < height; y++) { for (int x = 0; x < width; x++) { if (data[y][x] == FG) mask.setf(x, y, BG); else mask.setf(x, y, FG); } } ImageProcessor marker = new FloatProcessor(width, height); marker.setColor(FG); marker.fill(); marker.setf(2, 3, BG); GeodesicReconstructionScanning algo = new GeodesicReconstructionScanning( GeodesicReconstructionType.BY_EROSION, 4); ImageProcessor result = algo.applyTo(marker, mask); assertEquals(16, result.getWidth()); assertEquals(10, result.getHeight()); assertEquals(BG, result.getf(2, 8), .01); assertEquals(BG, result.getf(8, 8), .01); assertEquals(BG, result.getf(8, 5), .01); assertEquals(BG, result.getf(14, 8), .01); assertEquals(FG, result.getf(15, 9), .01); assertEquals(FG, result.getf(0, 0), .01); assertEquals(FG, result.getf(5, 3), .01); assertEquals(FG, result.getf(11, 5), .01); }
Example 15
Source File: FloodFillTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 4 votes |
@Test public final void testFloodFillC8Marker() { int[][] data = new int[][]{ {10, 10, 10, 20, 20, 20, 10, 10, 10, 10, 20, 20, 10, 10, 10}, {10, 10, 20, 20, 20, 20, 20, 20, 10, 20, 20, 20, 20, 10, 10}, {10, 20, 10, 10, 10, 10, 20, 20, 10, 20, 10, 10, 20, 20, 10}, {20, 20, 10, 20, 10, 10, 10, 20, 10, 20, 20, 10, 10, 20, 20}, {20, 20, 10, 20, 10, 10, 10, 20, 10, 10, 10, 20, 10, 20, 20}, {20, 20, 10, 10, 20, 20, 10, 20, 10, 10, 10, 20, 10, 20, 20}, {10, 20, 10, 10, 10, 20, 10, 20, 20, 10, 10, 10, 10, 20, 10}, {10, 20, 10, 20, 20, 20, 10, 20, 20, 20, 20, 20, 20, 20, 10}, {10, 10, 20, 20, 10, 10, 10, 10, 10, 10, 10, 20, 20, 10, 10}, }; int height = data.length; int width = data[0].length; ImageProcessor image = new ByteProcessor(width, height); for (int y = 0; y < height; y++) { for (int x = 0; x < width; x++) { image.set(x, y, data[y][x]); } } // initialize empty result image fill with 255 ImageProcessor result = new ByteProcessor(width, height); result.setValue(255); result.fill(); // Apply FloodFill.floodFill(image, 7, 4, result, 50, 8); // printImage(result); for (int y = 0; y < height; y++) { for (int x = 0; x < width; x++) { if (image.get(x, y) == 20) assertEquals(50, result.get(x, y)); else assertEquals(255, result.get(x, y)); } } }
Example 16
Source File: ReconstructionTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 4 votes |
/** * Test method for {@link ijt.filter.morphology.Reconstruction#reconstructByErosion()}. */ @Test public void testReconstructByErosion_C8() { int BG = 0; int FG = 255; int[][] data = new int[][]{ {BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG}, {BG, FG, FG, BG, FG, FG, BG, BG, BG, FG, FG, FG, FG, BG, BG, BG}, {BG, FG, FG, BG, FG, FG, BG, BG, BG, FG, FG, FG, FG, BG, BG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, BG, BG, BG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, BG, BG, BG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, BG, BG, FG, FG, FG, FG, BG, BG, BG, FG, FG, BG, FG, FG, BG}, {BG, BG, BG, FG, FG, FG, FG, BG, BG, BG, FG, FG, BG, FG, FG, BG}, {BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG}, }; int height = data.length; int width = data[0].length; ImageProcessor mask = new ByteProcessor(width, height); for (int y = 0; y < height; y++) { for (int x = 0; x < width; x++) { mask.set(x, y, data[y][x]); } } mask.invert(); ImageProcessor marker = new ByteProcessor(width, height); marker.setColor(255); marker.fill(); marker.set(2, 3, 0); ImageProcessor result = Reconstruction.reconstructByErosion(marker, mask, 8); assertEquals(16, result.getWidth()); assertEquals(10, result.getHeight()); assertEquals(0, result.get(2, 6)); assertEquals(0, result.get(4, 8)); assertEquals(0, result.get(8, 5)); assertEquals(0, result.get(14, 8)); }
Example 17
Source File: DirectionalFilter.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 4 votes |
/** * Apply directional filter with current settings to the specified image. * * @param image * a grayscale image * @return the result of directional filter */ public ImageProcessor process(ImageProcessor image) { // determine the sign of min/max computation int sign = this.type == Type.MAX ? 1 : -1; // initialize result ImageProcessor result = image.duplicate(); if (this.type == Type.MAX) { result.setValue(0); } else { result.setValue(Integer.MAX_VALUE); } result.fill(); int sizeX = image.getWidth(); int sizeY = image.getHeight(); fireStatusChanged(this, "Directional Filter..."); // Iterate over the set of directions for (int i = 0; i < nDirections; i++) { fireProgressChanged(this, i, nDirections); // Create the structuring element for current orientation double theta = ((double) i) * 180.0 / nDirections; Strel strel = this.strelFactory.createStrel(theta); // Apply oriented filter ImageProcessor oriented = this.operation.apply(image, strel); // combine current result with global result for (int y = 0; y < sizeY; y++) { for (int x = 0; x < sizeX; x++) { float value = oriented.getf(x, y); if (value * sign > result.getf(x, y) * sign) { result.setf(x, y, value); } } } } fireProgressChanged(this, 1, 1); // return the min or max value computed over all orientations return result; }
Example 18
Source File: GeodesicReconstructionScanningTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 4 votes |
/** * Test method for {@link ijt.filter.morphology.GeodesicReconstruction#reconstructByErosion()}. */ @Test public void testReconstructByErosion_FloatC8() { float BG = -42; float FG = 2500; float[][] data = new float[][]{ {BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, FG, FG, FG, FG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, FG, FG, FG, FG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, BG, BG, BG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, BG, BG, BG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, FG, FG, FG, FG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, FG, FG, FG, FG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG}, }; int height = data.length; int width = data[0].length; ImageProcessor mask = new FloatProcessor(width, height); for (int y = 0; y < height; y++) { for (int x = 0; x < width; x++) { if (data[y][x] == FG) mask.setf(x, y, BG); else mask.setf(x, y, FG); } } ImageProcessor marker = new FloatProcessor(width, height); marker.setColor(FG); marker.fill(); marker.setf(2, 3, BG); GeodesicReconstructionScanning algo = new GeodesicReconstructionScanning( GeodesicReconstructionType.BY_EROSION, 8); ImageProcessor result = algo.applyTo(marker, mask); assertEquals(16, result.getWidth()); assertEquals(10, result.getHeight()); assertEquals(BG, result.getf(2, 8), .01); assertEquals(BG, result.getf(8, 8), .01); assertEquals(BG, result.getf(8, 5), .01); assertEquals(BG, result.getf(14, 8), .01); assertEquals(FG, result.getf(15, 9), .01); assertEquals(FG, result.getf(0, 0), .01); assertEquals(FG, result.getf(5, 3), .01); assertEquals(FG, result.getf(11, 5), .01); }
Example 19
Source File: GeodesicReconstructionHybridTest.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 4 votes |
/** * Test method for {@link ijt.filter.morphology.GeodesicReconstruction#reconstructByErosion()}. */ @Test public void testReconstructByErosion_FloatC8() { float BG = -42; float FG = 2500; float[][] data = new float[][]{ {BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, FG, FG, FG, FG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, FG, FG, FG, FG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, BG, BG, BG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, BG, BG, BG, BG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, FG, FG, FG, FG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, FG, FG, FG, FG, FG, FG, FG, FG, BG, FG, FG, BG, FG, FG, BG}, {BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG, BG}, }; int height = data.length; int width = data[0].length; ImageProcessor mask = new FloatProcessor(width, height); for (int y = 0; y < height; y++) { for (int x = 0; x < width; x++) { if (data[y][x] == FG) mask.setf(x, y, BG); else mask.setf(x, y, FG); } } ImageProcessor marker = new FloatProcessor(width, height); marker.setColor(FG); marker.fill(); marker.setf(2, 3, BG); GeodesicReconstructionHybrid algo = new GeodesicReconstructionHybrid( GeodesicReconstructionType.BY_EROSION, 8); ImageProcessor result = algo.applyTo(marker, mask); assertEquals(16, result.getWidth()); assertEquals(10, result.getHeight()); assertEquals(BG, result.getf(2, 8), .01); assertEquals(BG, result.getf(8, 8), .01); assertEquals(BG, result.getf(8, 5), .01); assertEquals(BG, result.getf(14, 8), .01); assertEquals(FG, result.getf(15, 9), .01); assertEquals(FG, result.getf(0, 0), .01); assertEquals(FG, result.getf(5, 3), .01); assertEquals(FG, result.getf(11, 5), .01); }
Example 20
Source File: RegionalExtremaByFlooding.java From MorphoLibJ with GNU Lesser General Public License v3.0 | 4 votes |
/** * Computes regional extrema in current input image, using * flood-filling-like algorithm with 4 connectivity. * Computations are made with double values. */ private ImageProcessor regionalExtremaC4(ImageProcessor image) { // get image size int sizeX = image.getWidth(); int sizeY = image.getHeight(); // allocate memory for output, and fill with 255 ImageProcessor result = new ByteProcessor(sizeX, sizeY); result.setValue(255); result.fill(); // initialize local data depending on extrema type int sign = 1; if (this.extremaType == ExtremaType.MAXIMA) { sign = -1; } // Iterate over image pixels for (int y = 0; y < sizeY; y++) { for (int x = 0; x < sizeX; x++) { // Check if current pixel was already processed if (result.getf(x, y) == 0) continue; // current value float currentValue = image.getf(x, y); // compute extrema value in 4-neighborhood (computes max value // if sign is -1) float value = currentValue * sign; if (x > 0) value = min(value, image.getf(x-1, y) * sign); if (y > 0) value = min(value, image.getf(x, y-1) * sign); if (x < sizeX - 1) value = min(value, image.getf(x+1, y) * sign); if (y < sizeY - 1) value = min(value, image.getf(x, y+1) * sign); // if one of the neighbors of current pixel has a lower (resp. // greater) value, the the current pixel is not an extremum. // Consequently, the current pixel, and all its connected // neighbors with same value are set to 0 in the output image. if (value < currentValue * sign) { FloodFill.floodFillFloat(image, x, y, result, 0.f, 4); } } } return result; }