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OrientationJ/src/imageware/DoubleProcess.java
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DoubleProcess.java
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package imageware; import ij.ImageStack; import java.awt.Image; /** * Class DoubleProcess. * * @author Daniel Sage Biomedical Imaging Group Ecole Polytechnique Federale de * Lausanne, Lausanne, Switzerland */ public class DoubleProcess extends DoublePointwise implements Process { // ------------------------------------------------------------------ // // Constructors section // // ------------------------------------------------------------------ protected DoubleProcess(int nx, int ny, int nz) { super(nx, ny, nz); } protected DoubleProcess(Image image, int mode) { super(image, mode); } protected DoubleProcess(ImageStack stack, int mode) { super(stack, mode); } protected DoubleProcess(ImageStack stack, byte chan) { super(stack, chan); } protected DoubleProcess(byte[] array, int mode) { super(array, mode); } protected DoubleProcess(byte[][] array, int mode) { super(array, mode); } protected DoubleProcess(byte[][][] array, int mode) { super(array, mode); } protected DoubleProcess(short[] array, int mode) { super(array, mode); } protected DoubleProcess(short[][] array, int mode) { super(array, mode); } protected DoubleProcess(short[][][] array, int mode) { super(array, mode); } protected DoubleProcess(float[] array, int mode) { super(array, mode); } protected DoubleProcess(float[][] array, int mode) { super(array, mode); } protected DoubleProcess(float[][][] array, int mode) { super(array, mode); } protected DoubleProcess(double[] array, int mode) { super(array, mode); } protected DoubleProcess(double[][] array, int mode) { super(array, mode); } protected DoubleProcess(double[][][] array, int mode) { super(array, mode); } /** * Apply a separable gaussian smoothing over the image with the same * strengthness in all directions. To have a smmothing effect the * strengthness should be strictly greater than 0 and the size in the * considered directions should be greater strictly than 1. * * @param sigma * Strengthness of the smoothing */ public void smoothGaussian(double sigma) { smoothGaussian(sigma, sigma, sigma); } /** * Apply a separablegaussian smoothing over the image with an independant * strengthness in the different directions. To have a smmothing effect the * strengthness should be strictly greater than 0 and the size in the * considered directions should be greater strictly than 1. * * @param sigmaX * Strengthness of the smoothing in X axis * @param sigmaY * Strengthness of the smoothing in X axis * @param sigmaZ * Strengthness of the smoothing in X axis */ public void smoothGaussian(double sigmaX, double sigmaY, double sigmaZ) { int n = 3; double N = (double) n; double poles[] = new double[n]; if (nx > 1 && sigmaX > 0.0) { double s2 = sigmaX * sigmaX; double alpha = 1.0 + (N / s2) - (Math.sqrt(N * N + 2 * N * s2) / s2); poles[0] = poles[1] = poles[2] = alpha; double line[] = new double[nx]; for (int z = 0; z < nz; z++) { for (int y = 0; y < ny; y++) { getX(0, y, z, line); putX(0, y, z, Convolver.convolveIIR(line, poles)); } } } if (ny > 1 && sigmaY > 0.0) { double s2 = sigmaY * sigmaY; double alpha = 1.0 + (N / s2) - (Math.sqrt(N * N + 2 * N * s2) / s2); poles[0] = poles[1] = poles[2] = alpha; double line[] = new double[ny]; for (int x = 0; x < nx; x++) { for (int z = 0; z < nz; z++) { getY(x, 0, z, line); putY(x, 0, z, Convolver.convolveIIR(line, poles)); } } } if (nz > 1 && sigmaZ > 0.0) { double s2 = sigmaZ * sigmaZ; double alpha = 1.0 + (N / s2) - (Math.sqrt(N * N + 2 * N * s2) / s2); poles[0] = poles[1] = poles[2] = alpha; double line[] = new double[nz]; for (int y = 0; y < ny; y++) { for (int x = 0; x < nx; x++) { getZ(x, y, 0, line); putZ(x, y, 0, Convolver.convolveIIR(line, poles)); } } } } /** * Get the maximum of this imageware and a imageware. * * @param imageware * imageware to max */ public void max(ImageWare imageware) { if (!isSameSize(imageware)) { throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unable to get the maximum because the two operands are not the same size.\n" + "[" + nx + "," + ny + "," + "," + nz + "] != " + "[" + imageware.getSizeX() + "," + imageware.getSizeY() + "," + imageware.getSizeZ() + "].\n" + "-------------------------------------------------------\n"); } switch (imageware.getType()) { case ImageWare.BYTE: for (int z = 0; z < nz; z++) { byte[] tmp = ((ByteSet) imageware).getSliceByte(z); for (int k = 0; k < nxy; k++) { if (((double[]) data[z])[k] < (double) tmp[k]) ((double[]) data[z])[k] = (double) tmp[k]; } } break; case ImageWare.SHORT: for (int z = 0; z < nz; z++) { short[] tmp = ((ShortSet) imageware).getSliceShort(z); for (int k = 0; k < nxy; k++) { if (((double[]) data[z])[k] < (double) tmp[k]) ((double[]) data[z])[k] = (double) tmp[k]; } } break; case ImageWare.FLOAT: for (int z = 0; z < nz; z++) { float[] tmp = ((FloatSet) imageware).getSliceFloat(z); for (int k = 0; k < nxy; k++) { if (((double[]) data[z])[k] < (double) tmp[k]) ((double[]) data[z])[k] = (double) tmp[k]; } } break; case ImageWare.DOUBLE: for (int z = 0; z < nz; z++) { double[] tmp = ((DoubleSet) imageware).getSliceDouble(z); for (int k = 0; k < nxy; k++) { if (((double[]) data[z])[k] < (double) tmp[k]) ((double[]) data[z])[k] = (double) tmp[k]; } } break; default: throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unknown type " + imageware.getType() + "].\n" + "-------------------------------------------------------\n"); } } /** * Get the minimum of this imageware and a imageware. * * @param imageware * imageware to min */ public void min(ImageWare imageware) { if (!isSameSize(imageware)) { throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unable to get the minimum because the two operands are not the same size.\n" + "[" + nx + "," + ny + "," + "," + nz + "] != " + "[" + imageware.getSizeX() + "," + imageware.getSizeY() + "," + imageware.getSizeZ() + "].\n" + "-------------------------------------------------------\n"); } switch (imageware.getType()) { case ImageWare.BYTE: for (int z = 0; z < nz; z++) { byte[] tmp = ((ByteSet) imageware).getSliceByte(z); for (int k = 0; k < nxy; k++) { if (((double[]) data[z])[k] > (double) tmp[k]) ((double[]) data[z])[k] = (double) tmp[k]; } } break; case ImageWare.SHORT: for (int z = 0; z < nz; z++) { short[] tmp = ((ShortSet) imageware).getSliceShort(z); for (int k = 0; k < nxy; k++) { if (((double[]) data[z])[k] > (double) tmp[k]) ((double[]) data[z])[k] = (double) tmp[k]; } } break; case ImageWare.FLOAT: for (int z = 0; z < nz; z++) { float[] tmp = ((FloatSet) imageware).getSliceFloat(z); for (int k = 0; k < nxy; k++) { if (((double[]) data[z])[k] > (double) tmp[k]) ((double[]) data[z])[k] = (double) tmp[k]; } } break; case ImageWare.DOUBLE: for (int z = 0; z < nz; z++) { double[] tmp = ((DoubleSet) imageware).getSliceDouble(z); for (int k = 0; k < nxy; k++) { if (((double[]) data[z])[k] > (double) tmp[k]) ((double[]) data[z])[k] = (double) tmp[k]; } } break; default: throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unknown type " + imageware.getType() + "].\n" + "-------------------------------------------------------\n"); } } /** * Add a imageware to the current imageware. * * @param imageware * imageware to add */ public void add(ImageWare imageware) { if (!isSameSize(imageware)) { throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unable to add because the two operands are not the same size.\n" + "[" + nx + "," + ny + "," + "," + nz + "] != " + "[" + imageware.getSizeX() + "," + imageware.getSizeY() + "," + imageware.getSizeZ() + "].\n" + "-------------------------------------------------------\n"); } switch (imageware.getType()) { case ImageWare.BYTE: for (int z = 0; z < nz; z++) { byte[] tmp = ((ByteSet) imageware).getSliceByte(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] += (double) tmp[k]; } } break; case ImageWare.SHORT: for (int z = 0; z < nz; z++) { short[] tmp = ((ShortSet) imageware).getSliceShort(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] += (double) tmp[k]; } } break; case ImageWare.FLOAT: for (int z = 0; z < nz; z++) { float[] tmp = ((FloatSet) imageware).getSliceFloat(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] += (double) tmp[k]; } } break; case ImageWare.DOUBLE: for (int z = 0; z < nz; z++) { double[] tmp = ((DoubleSet) imageware).getSliceDouble(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] += (double) tmp[k]; } } break; default: throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unknown type " + imageware.getType() + "].\n" + "-------------------------------------------------------\n"); } } /** * Multiply a imageware to the current imageware. * * @param imageware * imageware to multiply */ public void multiply(ImageWare imageware) { if (!isSameSize(imageware)) { throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unable to multiply because the two operands are not the same size.\n" + "[" + nx + "," + ny + "," + "," + nz + "] != " + "[" + imageware.getSizeX() + "," + imageware.getSizeY() + "," + imageware.getSizeZ() + "].\n" + "-------------------------------------------------------\n"); } switch (imageware.getType()) { case ImageWare.BYTE: for (int z = 0; z < nz; z++) { byte[] tmp = ((ByteSet) imageware).getSliceByte(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] *= (double) tmp[k]; } } break; case ImageWare.SHORT: for (int z = 0; z < nz; z++) { short[] tmp = ((ShortSet) imageware).getSliceShort(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] *= (double) tmp[k]; } } break; case ImageWare.FLOAT: for (int z = 0; z < nz; z++) { float[] tmp = ((FloatSet) imageware).getSliceFloat(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] *= (double) tmp[k]; } } break; case ImageWare.DOUBLE: for (int z = 0; z < nz; z++) { double[] tmp = ((DoubleSet) imageware).getSliceDouble(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] *= (double) tmp[k]; } } break; default: throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unknown type " + imageware.getType() + "].\n" + "-------------------------------------------------------\n"); } } /** * Subtract a imageware to the current imageware. * * @param imageware * imageware to subtract */ public void subtract(ImageWare imageware) { if (!isSameSize(imageware)) { throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unable to subtract because the two operands are not the same size.\n" + "[" + nx + "," + ny + "," + "," + nz + "] != " + "[" + imageware.getSizeX() + "," + imageware.getSizeY() + "," + imageware.getSizeZ() + "].\n" + "-------------------------------------------------------\n"); } switch (imageware.getType()) { case ImageWare.BYTE: for (int z = 0; z < nz; z++) { byte[] tmp = ((ByteSet) imageware).getSliceByte(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] -= (double) tmp[k]; } } break; case ImageWare.SHORT: for (int z = 0; z < nz; z++) { short[] tmp = ((ShortSet) imageware).getSliceShort(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] -= (double) tmp[k]; } } break; case ImageWare.FLOAT: for (int z = 0; z < nz; z++) { float[] tmp = ((FloatSet) imageware).getSliceFloat(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] -= (double) tmp[k]; } } break; case ImageWare.DOUBLE: for (int z = 0; z < nz; z++) { double[] tmp = ((DoubleSet) imageware).getSliceDouble(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] -= (double) tmp[k]; } } break; default: throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unknown type " + imageware.getType() + "].\n" + "-------------------------------------------------------\n"); } } /** * Divide a imageware to the current imageware. * * @param imageware * imageware to divide */ public void divide(ImageWare imageware) { if (!isSameSize(imageware)) { throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unable to divide because the two operands are not the same size.\n" + "[" + nx + "," + ny + "," + "," + nz + "] != " + "[" + imageware.getSizeX() + "," + imageware.getSizeY() + "," + imageware.getSizeZ() + "].\n" + "-------------------------------------------------------\n"); } switch (imageware.getType()) { case ImageWare.BYTE: for (int z = 0; z < nz; z++) { byte[] tmp = ((ByteSet) imageware).getSliceByte(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] /= (double) tmp[k]; } } break; case ImageWare.SHORT: for (int z = 0; z < nz; z++) { short[] tmp = ((ShortSet) imageware).getSliceShort(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] /= (double) tmp[k]; } } break; case ImageWare.FLOAT: for (int z = 0; z < nz; z++) { float[] tmp = ((FloatSet) imageware).getSliceFloat(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] /= (double) tmp[k]; } } break; case ImageWare.DOUBLE: for (int z = 0; z < nz; z++) { double[] tmp = ((DoubleSet) imageware).getSliceDouble(z); for (int k = 0; k < nxy; k++) { ((double[]) data[z])[k] /= (double) tmp[k]; } } break; default: throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unknown type " + imageware.getType() + "].\n" + "-------------------------------------------------------\n"); } } } // end of class
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