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OrientationJ/src/imageware/ByteAccess.java
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ByteAccess.java
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package imageware; import ij.ImageStack; import java.awt.Image; /** * Class ByteAccess. * * @author Daniel Sage Biomedical Imaging Group Ecole Polytechnique Federale de * Lausanne, Lausanne, Switzerland */ public class ByteAccess extends ByteBuffer implements Access { // ------------------------------------------------------------------ // // Constructors section // // ------------------------------------------------------------------ protected ByteAccess(int nx, int ny, int nz) { super(nx, ny, nz); } protected ByteAccess(Image image, int mode) { super(image, mode); } protected ByteAccess(ImageStack stack, int mode) { super(stack, mode); } protected ByteAccess(ImageStack stack, byte chan) { super(stack, chan); } protected ByteAccess(byte[] array, int mode) { super(array, mode); } protected ByteAccess(byte[][] array, int mode) { super(array, mode); } protected ByteAccess(byte[][][] array, int mode) { super(array, mode); } protected ByteAccess(short[] array, int mode) { super(array, mode); } protected ByteAccess(short[][] array, int mode) { super(array, mode); } protected ByteAccess(short[][][] array, int mode) { super(array, mode); } protected ByteAccess(float[] array, int mode) { super(array, mode); } protected ByteAccess(float[][] array, int mode) { super(array, mode); } protected ByteAccess(float[][][] array, int mode) { super(array, mode); } protected ByteAccess(double[] array, int mode) { super(array, mode); } protected ByteAccess(double[][] array, int mode) { super(array, mode); } protected ByteAccess(double[][][] array, int mode) { super(array, mode); } // ------------------------------------------------------------------ // // getPixel section // // ------------------------------------------------------------------ /** * Get a pixel at specific position without specific boundary conditions * * If the positions is outside of this imageware, the method return 0.0. * * @param x * position in the X axis * @param y * position in the Y axis * @param z * position in the Z axis * @return a pixel value */ public double getPixel(int x, int y, int z) { if (x >= nx) return 0.0; if (y >= ny) return 0.0; if (z >= nz) return 0.0; if (x < 0) return 0.0; if (y < 0) return 0.0; if (z < 0) return 0.0; return ((byte[]) data[z])[x + y * nx] & 0xFF; } /** * Get a pixel at specific position with specific boundary conditions * * If the positions is outside of this imageware, the method apply the * boundary conditions to return a value. * * @param x * position in the X axis * @param y * position in the Y axis * @param z * position in the Z axis * @return a pixel value */ public double getPixel(int x, int y, int z, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw new ArrayStoreException("\n-------------------------------------------------------\n" + "Error in imageware package\n" + "Unable to put a pixel \n" + "at the position (" + x + "," + y + "," + z + ".\n" + "-------------------------------------------------------\n"); } int xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } return ((byte[]) data[zp])[xp + yp * nx] & 0xFF; } /** * Get a interpolated pixel value at specific position without specific * boundary conditions. * * If the positions is not on the pixel grid, the method return a * interpolated value of the pixel (linear interpolation). If the positions * is outside of this imageware, the method return 0.0. * * @param x * position in the X axis * @param y * position in the Y axis * @param z * position in the Z axis * @return a interpolated value */ public double getInterpolatedPixel(double x, double y, double z) { if (x > nx - 1) return 0.0; if (y > ny - 1) return 0.0; if (z > nz - 1) return 0.0; if (x < 0) return 0.0; if (y < 0) return 0.0; if (z < 0) return 0.0; double output = 0.0; /* * int i = (x >= 0.0 ? ((int)x) : ((int)x - 1)); int j = (y >= 0.0 ? * ((int)y) : ((int)y - 1)); int k = (z >= 0.0 ? ((int)z) : ((int)z - * 1)); */ int i = (x >= 0.0 ? ((int) x) : ((int) x - 1)); int j = (y >= 0.0 ? ((int) y) : ((int) y - 1)); int k = (z >= 0.0 ? ((int) z) : ((int) z - 1)); boolean fi = (i == nx - 1); boolean fj = (j == ny - 1); boolean fk = (k == nz - 1); int index = i + j * nx; switch (getDimension()) { case 1: double v1_0 = (double) (((byte[]) data[k])[index] & 0xFF); double v1_1 = (fi ? v1_0 : (double) (((byte[]) data[k])[index + 1] & 0xFF)); double dx1 = x - (double) i; return v1_1 * dx1 - v1_0 * (dx1 - 1.0); case 2: double v2_00 = (double) (((byte[]) data[k])[index] & 0xFF); double v2_10 = (fi ? v2_00 : (double) (((byte[]) data[k])[index + 1] & 0xFF)); double v2_01 = (fj ? v2_00 : (double) (((byte[]) data[k])[index + nx] & 0xFF)); double v2_11 = (fi ? (fj ? v2_00 : v2_01) : (double) (((byte[]) data[k])[index + 1 + nx] & 0xFF)); double dx2 = x - (double) i; double dy2 = y - (double) j; return (dx2 * (v2_11 * dy2 - v2_10 * (dy2 - 1.0)) - (dx2 - 1.0) * (v2_01 * dy2 - v2_00 * (dy2 - 1.0))); case 3: double v3_000 = (double) (((byte[]) data[k])[index] & 0xFF); double v3_100 = (fi ? v3_000 : (double) (((byte[]) data[k])[index + 1] & 0xFF)); double v3_010 = (fj ? v3_000 : (double) (((byte[]) data[k])[index + nx] & 0xFF)); double v3_110 = (fi ? (fj ? v3_000 : v3_010) : (double) (((byte[]) data[k])[index + 1 + nx] & 0xFF)); double v3_001 = (fk ? v3_000 : (double) (((byte[]) data[k + 1])[index] & 0xFF)); double v3_011 = (fk ? (fj ? v3_000 : v3_010) : (double) (((byte[]) data[k + 1])[index + 1] & 0xFF)); double v3_101 = (fk ? (fi ? v3_000 : v3_100) : (double) (((byte[]) data[k + 1])[index + nx] & 0xFF)); double v3_111 = (fk ? (fj ? (fi ? v3_000 : v3_100) : v3_110) : (double) (((byte[]) data[k + 1])[index + 1 + nx] & 0xFF)); double dx3 = x - (double) i; double dy3 = y - (double) j; double dz3 = z - (double) k; double z1 = (dx3 * (v3_110 * dy3 - v3_100 * (dy3 - 1.0)) - (dx3 - 1.0) * (v3_010 * dy3 - v3_000 * (dy3 - 1.0))); double z2 = (dx3 * (v3_111 * dy3 - v3_101 * (dy3 - 1.0)) - (dx3 - 1.0) * (v3_011 * dy3 - v3_001 * (dy3 - 1.0))); return z2 * dz3 - z1 * (dz3 - 1.0); } return output; } /** * Get a interpolated pixel value at specific position with specific * boundary conditions. * * If the positions is not on the pixel grid, the method return a * interpolated value of the pixel (linear interpolation). If the positions * is outside of this imageware, the method apply the boundary conditions to * return a value. * * @param x * position in the X axis * @param y * position in the Y axis * @param z * position in the Z axis * @param boundaryConditions * MIRROR or PERIODIC boundary conditions * @return a interpolated value */ public double getInterpolatedPixel(double x, double y, double z, byte boundaryConditions) { double output = 0.0; int i = (x >= 0.0 ? ((int) x) : ((int) x - 1)); int j = (y >= 0.0 ? ((int) y) : ((int) y - 1)); int k = (z >= 0.0 ? ((int) z) : ((int) z - 1)); switch (getDimension()) { case 1: double v1_0 = getPixel(i, j, k, boundaryConditions); double v1_1 = getPixel(i + 1, j, k, boundaryConditions); double dx1 = x - (double) i; return v1_1 * dx1 - v1_0 * (dx1 - 1.0); case 2: double v2_00 = getPixel(i, j, k, boundaryConditions); double v2_10 = getPixel(i + 1, j, k, boundaryConditions); double v2_01 = getPixel(i, j + 1, k, boundaryConditions); double v2_11 = getPixel(i + 1, j + 1, k, boundaryConditions); double dx2 = x - (double) i; double dy2 = y - (double) j; return (dx2 * (v2_11 * dy2 - v2_10 * (dy2 - 1.0)) - (dx2 - 1.0) * (v2_01 * dy2 - v2_00 * (dy2 - 1.0))); case 3: double v3_000 = getPixel(i, j, k, boundaryConditions); double v3_100 = getPixel(i + 1, j, k, boundaryConditions); double v3_010 = getPixel(i, j + 1, k, boundaryConditions); double v3_110 = getPixel(i + 1, j + 1, k, boundaryConditions); double v3_001 = getPixel(i, j, k + 1, boundaryConditions); double v3_011 = getPixel(i + 1, j, k + 1, boundaryConditions); double v3_101 = getPixel(i, j + 1, k + 1, boundaryConditions); double v3_111 = getPixel(i + 1, j + 1, k + 1, boundaryConditions); double dx3 = x - (double) i; double dy3 = y - (double) j; double dz3 = z - (double) k; double z1 = (dx3 * (v3_110 * dy3 - v3_100 * (dy3 - 1.0)) - (dx3 - 1.0) * (v3_010 * dy3 - v3_000 * (dy3 - 1.0))); double z2 = (dx3 * (v3_111 * dy3 - v3_101 * (dy3 - 1.0)) - (dx3 - 1.0) * (v3_011 * dy3 - v3_001 * (dy3 - 1.0))); return z2 * dz3 - z1 * (dz3 - 1.0); } return output; } // ------------------------------------------------------------------ // // putPixel section // // ------------------------------------------------------------------ /** * Put a pixel at specific position * * If the positions is outside of this imageware, the method does nothing. * * @param x * position in the X axis * @param y * position in the Y axis * @param z * position in the Z axis */ public void putPixel(int x, int y, int z, double value) { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; if (x < 0) return; if (y < 0) return; if (z < 0) return; ((byte[]) data[z])[x + y * nx] = (byte) value; } // ------------------------------------------------------------------ // // getBounded section // // ------------------------------------------------------------------ /** * Get an array from the imageware at the position (x,y,z) in X axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 1D array to get into the imageware */ public void getBoundedX(int x, int y, int z, byte[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int offset = (x + iinf) + (y) * nx; int leni = buffer.length; if (x + leni < 0) return; if (y < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { buffer[i] = (byte) (tmp[offset] & 0xFF); offset++; } } catch (Exception e) { throw_get("X", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in X axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 1D array to get into the imageware */ public void getBoundedX(int x, int y, int z, short[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int offset = (x + iinf) + (y) * nx; int leni = buffer.length; if (x + leni < 0) return; if (y < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { buffer[i] = (short) (tmp[offset] & 0xFF); offset++; } } catch (Exception e) { throw_get("X", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in X axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 1D array to get into the imageware */ public void getBoundedX(int x, int y, int z, float[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int offset = (x + iinf) + (y) * nx; int leni = buffer.length; if (x + leni < 0) return; if (y < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { buffer[i] = (float) (tmp[offset] & 0xFF); offset++; } } catch (Exception e) { throw_get("X", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in X axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 1D array to get into the imageware */ public void getBoundedX(int x, int y, int z, double[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int offset = (x + iinf) + (y) * nx; int leni = buffer.length; if (x + leni < 0) return; if (y < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { buffer[i] = (double) (tmp[offset] & 0xFF); offset++; } } catch (Exception e) { throw_get("X", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in Y axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 1D array to get into the imageware */ public void getBoundedY(int x, int y, int z, byte[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int offset = (x) + (y + iinf) * nx; int leni = buffer.length; if (x < 0) return; if (y + leni < 0) return; if (z < 0) return; int isup = (y + leni >= ny ? ny - y : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { buffer[i] = (byte) (tmp[offset] & 0xFF); offset += nx; } } catch (Exception e) { throw_get("Y", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in Y axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 1D array to get into the imageware */ public void getBoundedY(int x, int y, int z, short[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int offset = (x) + (y + iinf) * nx; int leni = buffer.length; if (x < 0) return; if (y + leni < 0) return; if (z < 0) return; int isup = (y + leni >= ny ? ny - y : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { buffer[i] = (short) (tmp[offset] & 0xFF); offset += nx; } } catch (Exception e) { throw_get("Y", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in Y axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 1D array to get into the imageware */ public void getBoundedY(int x, int y, int z, float[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int offset = (x) + (y + iinf) * nx; int leni = buffer.length; if (x < 0) return; if (y + leni < 0) return; if (z < 0) return; int isup = (y + leni >= ny ? ny - y : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { buffer[i] = (float) (tmp[offset] & 0xFF); offset += nx; } } catch (Exception e) { throw_get("Y", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in Y axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 1D array to get into the imageware */ public void getBoundedY(int x, int y, int z, double[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int offset = (x) + (y + iinf) * nx; int leni = buffer.length; if (x < 0) return; if (y + leni < 0) return; if (z < 0) return; int isup = (y + leni >= ny ? ny - y : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { buffer[i] = (double) (tmp[offset] & 0xFF); offset += nx; } } catch (Exception e) { throw_get("Y", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in Z axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 1D array to get into the imageware */ public void getBoundedZ(int x, int y, int z, byte[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (z < 0 ? -z : 0); int k = z + iinf; int offset = (x) + (y) * nx; int leni = buffer.length; if (x < 0) return; if (y < 0) return; if (z + leni < 0) return; int isup = (z + leni >= nz ? nz - z : leni); for (int i = iinf; i < isup; i++) { buffer[i] = (byte) (((byte[]) data[k])[offset] & 0xFF); k++; } } catch (Exception e) { throw_get("Z", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in Z axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 1D array to get into the imageware */ public void getBoundedZ(int x, int y, int z, short[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (z < 0 ? -z : 0); int k = z + iinf; int offset = (x) + (y) * nx; int leni = buffer.length; if (x < 0) return; if (y < 0) return; if (z + leni < 0) return; int isup = (z + leni >= nz ? nz - z : leni); for (int i = iinf; i < isup; i++) { buffer[i] = (short) (((byte[]) data[k])[offset] & 0xFF); k++; } } catch (Exception e) { throw_get("Z", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in Z axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 1D array to get into the imageware */ public void getBoundedZ(int x, int y, int z, float[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (z < 0 ? -z : 0); int k = z + iinf; int offset = (x) + (y) * nx; int leni = buffer.length; if (x < 0) return; if (y < 0) return; if (z + leni < 0) return; int isup = (z + leni >= nz ? nz - z : leni); for (int i = iinf; i < isup; i++) { buffer[i] = (float) (((byte[]) data[k])[offset] & 0xFF); k++; } } catch (Exception e) { throw_get("Z", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in Z axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 1D array to get into the imageware */ public void getBoundedZ(int x, int y, int z, double[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (z < 0 ? -z : 0); int k = z + iinf; int offset = (x) + (y) * nx; int leni = buffer.length; if (x < 0) return; if (y < 0) return; if (z + leni < 0) return; int isup = (z + leni >= nz ? nz - z : leni); for (int i = iinf; i < isup; i++) { buffer[i] = (double) (((byte[]) data[k])[offset] & 0xFF); k++; } } catch (Exception e) { throw_get("Z", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XY axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 2D array to get into the imageware */ public void getBoundedXY(int x, int y, int z, byte[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); byte[] tmp = (byte[]) data[z]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (byte) (tmp[offset] & 0xFF); offset++; } } } catch (Exception e) { throw_get("XY", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XY axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 2D array to get into the imageware */ public void getBoundedXY(int x, int y, int z, short[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); byte[] tmp = (byte[]) data[z]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (short) (tmp[offset] & 0xFF); offset++; } } } catch (Exception e) { throw_get("XY", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XY axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 2D array to get into the imageware */ public void getBoundedXY(int x, int y, int z, float[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); byte[] tmp = (byte[]) data[z]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (float) (tmp[offset] & 0xFF); offset++; } } } catch (Exception e) { throw_get("XY", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XY axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 2D array to get into the imageware */ public void getBoundedXY(int x, int y, int z, double[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); byte[] tmp = (byte[]) data[z]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (double) (tmp[offset] & 0xFF); offset++; } } } catch (Exception e) { throw_get("XY", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 2D array to get into the imageware */ public void getBoundedXZ(int x, int y, int z, byte[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y < 0) return; if (z + lenj < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (byte) (((byte[]) data[z])[offset] & 0xFF); offset++; } k++; } } catch (Exception e) { throw_get("YZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 2D array to get into the imageware */ public void getBoundedXZ(int x, int y, int z, short[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y < 0) return; if (z + lenj < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (short) (((byte[]) data[z])[offset] & 0xFF); offset++; } k++; } } catch (Exception e) { throw_get("YZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 2D array to get into the imageware */ public void getBoundedXZ(int x, int y, int z, float[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y < 0) return; if (z + lenj < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (float) (((byte[]) data[z])[offset] & 0xFF); offset++; } k++; } } catch (Exception e) { throw_get("YZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 2D array to get into the imageware */ public void getBoundedXZ(int x, int y, int z, double[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y < 0) return; if (z + lenj < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (double) (((byte[]) data[z])[offset] & 0xFF); offset++; } k++; } } catch (Exception e) { throw_get("YZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in YZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 2D array to get into the imageware */ public void getBoundedYZ(int x, int y, int z, byte[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x < 0) return; if (y + leni < 0) return; if (z + lenj < 0) return; int isup = (y + leni >= ny ? ny - y : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = x + (y + iinf) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (byte) (((byte[]) data[z])[offset] & 0xFF); offset += nx; } k++; } } catch (Exception e) { throw_get("XZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in YZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 2D array to get into the imageware */ public void getBoundedYZ(int x, int y, int z, short[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x < 0) return; if (y + leni < 0) return; if (z + lenj < 0) return; int isup = (y + leni >= ny ? ny - y : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = x + (y + iinf) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (short) (((byte[]) data[z])[offset] & 0xFF); offset += nx; } k++; } } catch (Exception e) { throw_get("XZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in YZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 2D array to get into the imageware */ public void getBoundedYZ(int x, int y, int z, float[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x < 0) return; if (y + leni < 0) return; if (z + lenj < 0) return; int isup = (y + leni >= ny ? ny - y : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = x + (y + iinf) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (float) (((byte[]) data[z])[offset] & 0xFF); offset += nx; } k++; } } catch (Exception e) { throw_get("XZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in YZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 2D array to get into the imageware */ public void getBoundedYZ(int x, int y, int z, double[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x < 0) return; if (y + leni < 0) return; if (z + lenj < 0) return; int isup = (y + leni >= ny ? ny - y : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = x + (y + iinf) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j] = (double) (((byte[]) data[z])[offset] & 0xFF); offset += nx; } k++; } } catch (Exception e) { throw_get("XZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XYZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 3D array to get into the imageware */ public void getBoundedXYZ(int x, int y, int z, byte[][][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int kinf = (z < 0 ? -z : 0); int ko = z + kinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z + lenk < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); int ksup = (z + lenk >= nz ? nz - z : lenk); for (int k = kinf; k < ksup; k++) { byte[] tmp = (byte[]) data[ko]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j][k] = (byte) (tmp[offset] & 0xFF); offset++; } } ko++; } } catch (Exception e) { throw_get("XYZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XYZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 3D array to get into the imageware */ public void getBoundedXYZ(int x, int y, int z, short[][][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int kinf = (z < 0 ? -z : 0); int ko = z + kinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z + lenk < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); int ksup = (z + lenk >= nz ? nz - z : lenk); for (int k = kinf; k < ksup; k++) { byte[] tmp = (byte[]) data[ko]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j][k] = (short) (tmp[offset] & 0xFF); offset++; } } ko++; } } catch (Exception e) { throw_get("XYZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XYZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 3D array to get into the imageware */ public void getBoundedXYZ(int x, int y, int z, float[][][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int kinf = (z < 0 ? -z : 0); int ko = z + kinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z + lenk < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); int ksup = (z + lenk >= nz ? nz - z : lenk); for (int k = kinf; k < ksup; k++) { byte[] tmp = (byte[]) data[ko]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j][k] = (float) (tmp[offset] & 0xFF); offset++; } } ko++; } } catch (Exception e) { throw_get("XYZ", "Bounded check", buffer, x, y, z); } } /** * Get an array from the imageware at the position (x,y,z) in XYZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 3D array to get into the imageware */ public void getBoundedXYZ(int x, int y, int z, double[][][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int kinf = (z < 0 ? -z : 0); int ko = z + kinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z + lenk < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); int ksup = (z + lenk >= nz ? nz - z : lenk); for (int k = kinf; k < ksup; k++) { byte[] tmp = (byte[]) data[ko]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { buffer[i][j][k] = (double) (tmp[offset] & 0xFF); offset++; } } ko++; } } catch (Exception e) { throw_get("XYZ", "Bounded check", buffer, x, y, z); } } // ------------------------------------------------------------------ // // getBlock section // // ------------------------------------------------------------------ /** * Get an array from the imageware at the start position (x,y,z) in X axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockX(int x, int y, int z, byte[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; byte[] tmp = (byte[]) data[zp]; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i] = (byte) (tmp[xp + yp] & 0xFF); } } catch (Exception e) { throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in X axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockX(int x, int y, int z, short[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; byte[] tmp = (byte[]) data[zp]; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i] = (short) (tmp[xp + yp] & 0xFF); } } catch (Exception e) { throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in X axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockX(int x, int y, int z, float[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; byte[] tmp = (byte[]) data[zp]; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i] = (float) (tmp[xp + yp] & 0xFF); } } catch (Exception e) { throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in X axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockX(int x, int y, int z, double[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; byte[] tmp = (byte[]) data[zp]; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i] = (double) (tmp[xp + yp] & 0xFF); } } catch (Exception e) { throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in Y axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockY(int x, int y, int z, byte[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } byte[] tmp = (byte[]) data[zp]; for (int i = 0; i < leni; i++) { yp = y + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i] = (byte) (tmp[xp + yp * nx] & 0xFF); } } catch (Exception e) { throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in Y axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockY(int x, int y, int z, short[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } byte[] tmp = (byte[]) data[zp]; for (int i = 0; i < leni; i++) { yp = y + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i] = (short) (tmp[xp + yp * nx] & 0xFF); } } catch (Exception e) { throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in Y axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockY(int x, int y, int z, float[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } byte[] tmp = (byte[]) data[zp]; for (int i = 0; i < leni; i++) { yp = y + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i] = (float) (tmp[xp + yp * nx] & 0xFF); } } catch (Exception e) { throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in Y axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockY(int x, int y, int z, double[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } byte[] tmp = (byte[]) data[zp]; for (int i = 0; i < leni; i++) { yp = y + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i] = (double) (tmp[xp + yp * nx] & 0xFF); } } catch (Exception e) { throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in Z axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockZ(int x, int y, int z, byte[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int xyp = xp + yp * nx; for (int i = 0; i < leni; i++) { zp = z + i; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } buffer[i] = (byte) (((byte[]) data[zp])[xyp] & 0xFF); } } catch (Exception e) { throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in Z axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockZ(int x, int y, int z, short[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int xyp = xp + yp * nx; for (int i = 0; i < leni; i++) { zp = z + i; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } buffer[i] = (short) (((byte[]) data[zp])[xyp] & 0xFF); } } catch (Exception e) { throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in Z axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockZ(int x, int y, int z, float[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int xyp = xp + yp * nx; for (int i = 0; i < leni; i++) { zp = z + i; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } buffer[i] = (float) (((byte[]) data[zp])[xyp] & 0xFF); } } catch (Exception e) { throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in Z axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockZ(int x, int y, int z, double[] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int xyp = xp + yp * nx; for (int i = 0; i < leni; i++) { zp = z + i; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } buffer[i] = (double) (((byte[]) data[zp])[xyp] & 0xFF); } } catch (Exception e) { throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * get an array into the imageware at the start position (x,y,z) in XY axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXY(int x, int y, int z, byte[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = (byte[]) data[zp]; for (int j = 0; j < lenj; j++) { yp = y + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (byte) (tmp[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * get an array into the imageware at the start position (x,y,z) in XY axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXY(int x, int y, int z, short[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = (byte[]) data[zp]; for (int j = 0; j < lenj; j++) { yp = y + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (short) (tmp[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * get an array into the imageware at the start position (x,y,z) in XY axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXY(int x, int y, int z, float[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = (byte[]) data[zp]; for (int j = 0; j < lenj; j++) { yp = y + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (float) (tmp[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * get an array into the imageware at the start position (x,y,z) in XY axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXY(int x, int y, int z, double[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = (byte[]) data[zp]; for (int j = 0; j < lenj; j++) { yp = y + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (double) (tmp[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in XZ axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXZ(int x, int y, int z, byte[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int j = 0; j < lenj; j++) { zp = z + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - yp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (byte) (((byte[]) data[zp])[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in XZ axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXZ(int x, int y, int z, short[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int j = 0; j < lenj; j++) { zp = z + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - yp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (short) (((byte[]) data[zp])[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in XZ axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXZ(int x, int y, int z, float[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int j = 0; j < lenj; j++) { zp = z + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - yp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (float) (((byte[]) data[zp])[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in XZ axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXZ(int x, int y, int z, double[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int j = 0; j < lenj; j++) { zp = z + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - yp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (double) (((byte[]) data[zp])[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in YZ axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockYZ(int x, int y, int z, byte[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } for (int j = 0; j < lenj; j++) { zp = z + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { yp = y + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i][j] = (byte) (((byte[]) data[zp])[xp + yp * nx] & 0xFF); } } } catch (Exception e) { throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in YZ axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockYZ(int x, int y, int z, short[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } for (int j = 0; j < lenj; j++) { zp = z + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { yp = y + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i][j] = (short) (((byte[]) data[zp])[xp + yp * nx] & 0xFF); } } } catch (Exception e) { throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in YZ axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockYZ(int x, int y, int z, float[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } for (int j = 0; j < lenj; j++) { zp = z + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { yp = y + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i][j] = (float) (((byte[]) data[zp])[xp + yp * nx] & 0xFF); } } } catch (Exception e) { throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in YZ axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockYZ(int x, int y, int z, double[][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } for (int j = 0; j < lenj; j++) { zp = z + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { yp = y + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i][j] = (double) (((byte[]) data[zp])[xp + yp * nx] & 0xFF); } } } catch (Exception e) { throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in XYZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 3D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXYZ(int x, int y, int z, byte[][][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; for (int k = 0; k < lenk; k++) { zp = z + k; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = (byte[]) data[zp]; for (int j = 0; j < lenj; j++) { yp = y + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j][k] = (byte) (tmp[xp + yp] & 0xFF); } } } } catch (Exception e) { throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in XYZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 3D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXYZ(int x, int y, int z, short[][][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; for (int k = 0; k < lenk; k++) { zp = z + k; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = (byte[]) data[zp]; for (int j = 0; j < lenj; j++) { yp = y + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j][k] = (short) (tmp[xp + yp] & 0xFF); } } } } catch (Exception e) { throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in XYZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 3D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXYZ(int x, int y, int z, float[][][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; for (int k = 0; k < lenk; k++) { zp = z + k; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = (byte[]) data[zp]; for (int j = 0; j < lenj; j++) { yp = y + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j][k] = (float) (tmp[xp + yp] & 0xFF); } } } } catch (Exception e) { throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the start position (x,y,z) in XYZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 3D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getBlockXYZ(int x, int y, int z, double[][][] buffer, byte boundaryConditions) { int xperiod = 0; int yperiod = 0; int zperiod = 0; switch (boundaryConditions) { case ImageWare.MIRROR: xperiod = (nx <= 1 ? 1 : 2 * nx - 2); yperiod = (ny <= 1 ? 1 : 2 * ny - 2); zperiod = (nz <= 1 ? 1 : 2 * nz - 2); break; case ImageWare.PERIODIC: xperiod = nx; yperiod = ny; zperiod = nz; break; default: throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; for (int k = 0; k < lenk; k++) { zp = z + k; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = (byte[]) data[zp]; for (int j = 0; j < lenj; j++) { yp = y + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = x + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j][k] = (double) (tmp[xp + yp] & 0xFF); } } } } catch (Exception e) { throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } // ------------------------------------------------------------------ // // getBlock section // // ------------------------------------------------------------------ /** * Get an array from the imageware at the center position (x,y,z) in X axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodX(int x, int y, int z, byte[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; int xs = x - leni / 2; byte[] tmp = ((byte[]) data[zp]); for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i] = (byte) (tmp[xp + yp] & 0xFF); } } catch (Exception e) { throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in X axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodX(int x, int y, int z, short[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; int xs = x - leni / 2; byte[] tmp = ((byte[]) data[zp]); for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i] = (short) (tmp[xp + yp] & 0xFF); } } catch (Exception e) { throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in X axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodX(int x, int y, int z, float[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; int xs = x - leni / 2; byte[] tmp = ((byte[]) data[zp]); for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i] = (float) (tmp[xp + yp] & 0xFF); } } catch (Exception e) { throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in X axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodX(int x, int y, int z, double[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; int xs = x - leni / 2; byte[] tmp = ((byte[]) data[zp]); for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i] = (double) (tmp[xp + yp] & 0xFF); } } catch (Exception e) { throw_get("X", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in Y axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodY(int x, int y, int z, byte[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int ys = y - leni / 2; byte[] tmp = ((byte[]) data[zp]); for (int i = 0; i < leni; i++) { yp = ys + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i] = (byte) (tmp[xp + yp * nx] & 0xFF); } } catch (Exception e) { throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in Y axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodY(int x, int y, int z, short[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int ys = y - leni / 2; byte[] tmp = ((byte[]) data[zp]); for (int i = 0; i < leni; i++) { yp = ys + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i] = (short) (tmp[xp + yp * nx] & 0xFF); } } catch (Exception e) { throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in Y axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodY(int x, int y, int z, float[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int ys = y - leni / 2; byte[] tmp = ((byte[]) data[zp]); for (int i = 0; i < leni; i++) { yp = ys + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i] = (float) (tmp[xp + yp * nx] & 0xFF); } } catch (Exception e) { throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in Y axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodY(int x, int y, int z, double[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int ys = y - leni / 2; byte[] tmp = ((byte[]) data[zp]); for (int i = 0; i < leni; i++) { yp = ys + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i] = (double) (tmp[xp + yp * nx] & 0xFF); } } catch (Exception e) { throw_get("Y", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in Z axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodZ(int x, int y, int z, byte[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int xyp = xp + yp * nx; int zs = z - leni / 2; for (int i = 0; i < leni; i++) { zp = zs + i; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } buffer[i] = (byte) (((byte[]) data[zp])[xyp] & 0xFF); } } catch (Exception e) { throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in Z axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodZ(int x, int y, int z, short[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int xyp = xp + yp * nx; int zs = z - leni / 2; for (int i = 0; i < leni; i++) { zp = zs + i; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } buffer[i] = (short) (((byte[]) data[zp])[xyp] & 0xFF); } } catch (Exception e) { throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in Z axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodZ(int x, int y, int z, float[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int xyp = xp + yp * nx; int zs = z - leni / 2; for (int i = 0; i < leni; i++) { zp = zs + i; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } buffer[i] = (float) (((byte[]) data[zp])[xyp] & 0xFF); } } catch (Exception e) { throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in Z axis. * Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 1D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodZ(int x, int y, int z, double[] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } int xyp = xp + yp * nx; int zs = z - leni / 2; for (int i = 0; i < leni; i++) { zp = zs + i; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } buffer[i] = (double) (((byte[]) data[zp])[xyp] & 0xFF); } } catch (Exception e) { throw_get("Z", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * get an array into the imageware at the center position (x,y,z) in XY * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXY(int x, int y, int z, byte[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } int xs = x - leni / 2; int ys = y - lenj / 2; byte[] tmp = ((byte[]) data[zp]); for (int j = 0; j < lenj; j++) { yp = ys + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (byte) (tmp[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * get an array into the imageware at the center position (x,y,z) in XY * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXY(int x, int y, int z, short[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } int xs = x - leni / 2; int ys = y - lenj / 2; byte[] tmp = ((byte[]) data[zp]); for (int j = 0; j < lenj; j++) { yp = ys + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (short) (tmp[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * get an array into the imageware at the center position (x,y,z) in XY * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXY(int x, int y, int z, float[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } int xs = x - leni / 2; int ys = y - lenj / 2; byte[] tmp = ((byte[]) data[zp]); for (int j = 0; j < lenj; j++) { yp = ys + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (float) (tmp[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * get an array into the imageware at the center position (x,y,z) in XY * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXY(int x, int y, int z, double[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; zp = z; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } int xs = x - leni / 2; int ys = y - lenj / 2; byte[] tmp = ((byte[]) data[zp]); for (int j = 0; j < lenj; j++) { yp = ys + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (double) (tmp[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XY", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in XZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXZ(int x, int y, int z, byte[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; int xs = x - leni / 2; int zs = z - lenj / 2; for (int j = 0; j < lenj; j++) { zp = zs + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - yp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (byte) (((byte[]) data[zp])[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in XZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXZ(int x, int y, int z, short[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; int xs = x - leni / 2; int zs = z - lenj / 2; for (int j = 0; j < lenj; j++) { zp = zs + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - yp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (short) (((byte[]) data[zp])[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in XZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXZ(int x, int y, int z, float[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; int xs = x - leni / 2; int zs = z - lenj / 2; for (int j = 0; j < lenj; j++) { zp = zs + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - yp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (float) (((byte[]) data[zp])[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in XZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXZ(int x, int y, int z, double[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; yp = y; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; int xs = x - leni / 2; int zs = z - lenj / 2; for (int j = 0; j < lenj; j++) { zp = zs + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - yp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j] = (double) (((byte[]) data[zp])[xp + yp] & 0xFF); } } } catch (Exception e) { throw_get("XZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in YZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodYZ(int x, int y, int z, byte[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int ys = y - leni / 2; int zs = z - lenj / 2; for (int j = 0; j < lenj; j++) { zp = zs + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { yp = ys + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i][j] = (byte) (((byte[]) data[zp])[xp + yp * nx] & 0xFF); } } } catch (Exception e) { throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in YZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodYZ(int x, int y, int z, short[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int ys = y - leni / 2; int zs = z - lenj / 2; for (int j = 0; j < lenj; j++) { zp = zs + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { yp = ys + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i][j] = (short) (((byte[]) data[zp])[xp + yp * nx] & 0xFF); } } } catch (Exception e) { throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in YZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodYZ(int x, int y, int z, float[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int ys = y - leni / 2; int zs = z - lenj / 2; for (int j = 0; j < lenj; j++) { zp = zs + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { yp = ys + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i][j] = (float) (((byte[]) data[zp])[xp + yp * nx] & 0xFF); } } } catch (Exception e) { throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in YZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 2D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodYZ(int x, int y, int z, double[][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; xp = x; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } int ys = y - leni / 2; int zs = z - lenj / 2; for (int j = 0; j < lenj; j++) { zp = zs + j; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } for (int i = 0; i < leni; i++) { yp = ys + i; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } buffer[i][j] = (double) (((byte[]) data[zp])[xp + yp * nx] & 0xFF); } } } catch (Exception e) { throw_get("YZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in XYZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * byte 3D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXYZ(int x, int y, int z, byte[][][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; int xs = x - leni / 2; int ys = y - lenj / 2; int zs = z - lenk / 2; for (int k = 0; k < lenk; k++) { zp = zs + k; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = ((byte[]) data[zp]); for (int j = 0; j < lenj; j++) { yp = ys + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j][k] = (byte) (tmp[xp + yp] & 0xFF); } } } } catch (Exception e) { throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in XYZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * short 3D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXYZ(int x, int y, int z, short[][][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; int xs = x - leni / 2; int ys = y - lenj / 2; int zs = z - lenk / 2; for (int k = 0; k < lenk; k++) { zp = zs + k; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = ((byte[]) data[zp]); for (int j = 0; j < lenj; j++) { yp = ys + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j][k] = (short) (tmp[xp + yp] & 0xFF); } } } } catch (Exception e) { throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in XYZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * float 3D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXYZ(int x, int y, int z, float[][][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; int xs = x - leni / 2; int ys = y - lenj / 2; int zs = z - lenk / 2; for (int k = 0; k < lenk; k++) { zp = zs + k; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = ((byte[]) data[zp]); for (int j = 0; j < lenj; j++) { yp = ys + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j][k] = (float) (tmp[xp + yp] & 0xFF); } } } } catch (Exception e) { throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } /** * Get an array from the imageware at the center position (x,y,z) in XYZ * axis. Apply boundary conditions to get the outside area. * * @param x * X starting position to get the buffer * @param y * Y starting position to get the buffer * @param z * Z starting position to get the buffer * @param buffer * double 3D array to get into the imageware * @param boundaryConditions * mirror or periodic boundary conditions */ public void getNeighborhoodXYZ(int x, int y, int z, double[][][] buffer, byte boundaryConditions) { int xperiod = (boundaryConditions == ImageWare.MIRROR ? (nx <= 1 ? 1 : 2 * nx - 2) : nx); int yperiod = (boundaryConditions == ImageWare.MIRROR ? (ny <= 1 ? 1 : 2 * ny - 2) : ny); int zperiod = (boundaryConditions == ImageWare.MIRROR ? (nz <= 1 ? 1 : 2 * nz - 2) : nz); int xp, yp, zp; try { int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; int xs = x - leni / 2; int ys = y - lenj / 2; int zs = z - lenk / 2; for (int k = 0; k < lenk; k++) { zp = zs + k; while (zp < 0) zp += zperiod; while (zp >= nz) { zp = zperiod - zp; zp = (zp < 0 ? -zp : zp); } byte[] tmp = ((byte[]) data[zp]); for (int j = 0; j < lenj; j++) { yp = ys + j; while (yp < 0) yp += yperiod; while (yp >= ny) { yp = yperiod - yp; yp = (yp < 0 ? -yp : yp); } yp *= nx; for (int i = 0; i < leni; i++) { xp = xs + i; while (xp < 0) xp += xperiod; while (xp >= nx) { xp = xperiod - xp; xp = (xp < 0 ? -xp : xp); } buffer[i][j][k] = (double) (tmp[xp + yp] & 0xFF); } } } } catch (Exception e) { throw_get("XYZ", "Mirror or periodic boundaray conditions", buffer, x, y, z); } } // ------------------------------------------------------------------ // // putBounded section // // ------------------------------------------------------------------ /** * Put an array into the imageware at the position (x,y,z) in X axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 1D array to put into the imageware */ public void putBoundedX(int x, int y, int z, byte[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int offset = (x + iinf) + (y) * nx; int leni = buffer.length; if (x + leni < 0) return; if (y < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i] & 0xFF); offset++; } } catch (Exception e) { throw_put("X", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in X axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 1D array to put into the imageware */ public void putBoundedX(int x, int y, int z, short[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int offset = (x + iinf) + (y) * nx; int leni = buffer.length; if (x + leni < 0) return; if (y < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i] & 0xFFFF); offset++; } } catch (Exception e) { throw_put("X", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in X axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 1D array to put into the imageware */ public void putBoundedX(int x, int y, int z, float[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int offset = (x + iinf) + (y) * nx; int leni = buffer.length; if (x + leni < 0) return; if (y < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i]); offset++; } } catch (Exception e) { throw_put("X", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in X axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 1D array to put into the imageware */ public void putBoundedX(int x, int y, int z, double[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int offset = (x + iinf) + (y) * nx; int leni = buffer.length; if (x + leni < 0) return; if (y < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i]); offset++; } } catch (Exception e) { throw_put("X", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in Y axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 1D array to put into the imageware */ public void putBoundedY(int x, int y, int z, byte[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int offset = (x) + (y + iinf) * nx; int leni = buffer.length; if (x < 0) return; if (y + leni < 0) return; if (z < 0) return; int isup = (y + leni >= ny ? ny - y : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i] & 0xFF); offset += nx; } } catch (Exception e) { throw_put("Y", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in Y axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 1D array to put into the imageware */ public void putBoundedY(int x, int y, int z, short[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int offset = (x) + (y + iinf) * nx; int leni = buffer.length; if (x < 0) return; if (y + leni < 0) return; if (z < 0) return; int isup = (y + leni >= ny ? ny - y : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i] & 0xFFFF); offset += nx; } } catch (Exception e) { throw_put("Y", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in Y axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 1D array to put into the imageware */ public void putBoundedY(int x, int y, int z, float[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int offset = (x) + (y + iinf) * nx; int leni = buffer.length; if (x < 0) return; if (y + leni < 0) return; if (z < 0) return; int isup = (y + leni >= ny ? ny - y : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i]); offset += nx; } } catch (Exception e) { throw_put("Y", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in Y axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 1D array to put into the imageware */ public void putBoundedY(int x, int y, int z, double[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int offset = (x) + (y + iinf) * nx; int leni = buffer.length; if (x < 0) return; if (y + leni < 0) return; if (z < 0) return; int isup = (y + leni >= ny ? ny - y : leni); byte[] tmp = (byte[]) data[z]; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i]); offset += nx; } } catch (Exception e) { throw_put("Y", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in Z axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 1D array to put into the imageware */ public void putBoundedZ(int x, int y, int z, byte[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (z < 0 ? -z : 0); int k = z + iinf; int offset = (x) + (y) * nx; int leni = buffer.length; if (x < 0) return; if (y < 0) return; if (z + leni < 0) return; int isup = (z + leni >= nz ? nz - z : leni); for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i] & 0xFF); k++; } } catch (Exception e) { throw_put("Z", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in Z axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 1D array to put into the imageware */ public void putBoundedZ(int x, int y, int z, short[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (z < 0 ? -z : 0); int k = z + iinf; int offset = (x) + (y) * nx; int leni = buffer.length; if (x < 0) return; if (y < 0) return; if (z + leni < 0) return; int isup = (z + leni >= nz ? nz - z : leni); for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i] & 0xFFFF); k++; } } catch (Exception e) { throw_put("Z", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in Z axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 1D array to put into the imageware */ public void putBoundedZ(int x, int y, int z, float[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (z < 0 ? -z : 0); int k = z + iinf; int offset = (x) + (y) * nx; int leni = buffer.length; if (x < 0) return; if (y < 0) return; if (z + leni < 0) return; int isup = (z + leni >= nz ? nz - z : leni); for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i]); k++; } } catch (Exception e) { throw_put("Z", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in Z axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 1D array to put into the imageware */ public void putBoundedZ(int x, int y, int z, double[] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (z < 0 ? -z : 0); int k = z + iinf; int offset = (x) + (y) * nx; int leni = buffer.length; if (x < 0) return; if (y < 0) return; if (z + leni < 0) return; int isup = (z + leni >= nz ? nz - z : leni); for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i]); k++; } } catch (Exception e) { throw_put("Z", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XY axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 2D array to put into the imageware */ public void putBoundedXY(int x, int y, int z, byte[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); byte[] tmp = (byte[]) data[z]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i][j] & 0xFF); offset++; } } } catch (Exception e) { throw_put("XY", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XY axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 2D array to put into the imageware */ public void putBoundedXY(int x, int y, int z, short[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); byte[] tmp = (byte[]) data[z]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i][j] & 0xFFFF); offset++; } } } catch (Exception e) { throw_put("XY", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XY axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 2D array to put into the imageware */ public void putBoundedXY(int x, int y, int z, float[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); byte[] tmp = (byte[]) data[z]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i][j]); offset++; } } } catch (Exception e) { throw_put("XY", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XY axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 2D array to put into the imageware */ public void putBoundedXY(int x, int y, int z, double[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); byte[] tmp = (byte[]) data[z]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i][j]); offset++; } } } catch (Exception e) { throw_put("XY", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 2D array to put into the imageware */ public void putBoundedXZ(int x, int y, int z, byte[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y < 0) return; if (z + lenj < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y) * nx; for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i][j] & 0xFF); offset++; } k++; } } catch (Exception e) { throw_put("YZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 2D array to put into the imageware */ public void putBoundedXZ(int x, int y, int z, short[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y < 0) return; if (z + lenj < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y) * nx; for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i][j] & 0xFFFF); offset++; } k++; } } catch (Exception e) { throw_put("YZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 2D array to put into the imageware */ public void putBoundedXZ(int x, int y, int z, float[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y < 0) return; if (z + lenj < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y) * nx; for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i][j]); offset++; } k++; } } catch (Exception e) { throw_put("YZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 2D array to put into the imageware */ public void putBoundedXZ(int x, int y, int z, double[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x + leni < 0) return; if (y < 0) return; if (z + lenj < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y) * nx; for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i][j]); offset++; } k++; } } catch (Exception e) { throw_put("YZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in YZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 2D array to put into the imageware */ public void putBoundedYZ(int x, int y, int z, byte[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x < 0) return; if (y + leni < 0) return; if (z + lenj < 0) return; int isup = (y + leni >= ny ? ny - y : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = x + (y + iinf) * nx; for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i][j] & 0xFF); offset += nx; } k++; } } catch (Exception e) { throw_put("XZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in YZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 2D array to put into the imageware */ public void putBoundedYZ(int x, int y, int z, short[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x < 0) return; if (y + leni < 0) return; if (z + lenj < 0) return; int isup = (y + leni >= ny ? ny - y : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = x + (y + iinf) * nx; for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i][j] & 0xFFFF); offset += nx; } k++; } } catch (Exception e) { throw_put("XZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in YZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 2D array to put into the imageware */ public void putBoundedYZ(int x, int y, int z, float[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x < 0) return; if (y + leni < 0) return; if (z + lenj < 0) return; int isup = (y + leni >= ny ? ny - y : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = x + (y + iinf) * nx; for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i][j]); offset += nx; } k++; } } catch (Exception e) { throw_put("XZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in YZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 2D array to put into the imageware */ public void putBoundedYZ(int x, int y, int z, double[][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (y < 0 ? -y : 0); int jinf = (z < 0 ? -z : 0); int k = z + jinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; if (x < 0) return; if (y + leni < 0) return; if (z + lenj < 0) return; int isup = (y + leni >= ny ? ny - y : leni); int jsup = (z + lenj >= nz ? nz - z : lenj); for (int j = jinf; j < jsup; j++) { offset = x + (y + iinf) * nx; for (int i = iinf; i < isup; i++) { ((byte[]) data[k])[offset] = (byte) (buffer[i][j]); offset += nx; } k++; } } catch (Exception e) { throw_put("XZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XYZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * byte 3D array to put into the imageware */ public void putBoundedXYZ(int x, int y, int z, byte[][][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int kinf = (z < 0 ? -z : 0); int ko = z + kinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z + lenk < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); int ksup = (z + lenk >= nz ? nz - z : lenk); for (int k = kinf; k < ksup; k++) { byte[] tmp = (byte[]) data[ko]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i][j][k] & 0xFF); offset++; } } ko++; } } catch (Exception e) { throw_put("XYZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XYZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * short 3D array to put into the imageware */ public void putBoundedXYZ(int x, int y, int z, short[][][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int kinf = (z < 0 ? -z : 0); int ko = z + kinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z + lenk < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); int ksup = (z + lenk >= nz ? nz - z : lenk); for (int k = kinf; k < ksup; k++) { byte[] tmp = (byte[]) data[ko]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i][j][k] & 0xFFFF); offset++; } } ko++; } } catch (Exception e) { throw_put("XYZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XYZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * float 3D array to put into the imageware */ public void putBoundedXYZ(int x, int y, int z, float[][][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int kinf = (z < 0 ? -z : 0); int ko = z + kinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z + lenk < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); int ksup = (z + lenk >= nz ? nz - z : lenk); for (int k = kinf; k < ksup; k++) { byte[] tmp = (byte[]) data[ko]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i][j][k]); offset++; } } ko++; } } catch (Exception e) { throw_put("XYZ", "Bounded check", buffer, x, y, z); } } /** * Put an array into the imageware at the position (x,y,z) in XYZ axis. Copy * only the bounded area, intersection between the array and the imageware. * * @param x * X starting position to put the buffer * @param y * Y starting position to put the buffer * @param z * Z starting position to put the buffer * @param buffer * double 3D array to put into the imageware */ public void putBoundedXYZ(int x, int y, int z, double[][][] buffer) { try { if (x >= nx) return; if (y >= ny) return; if (z >= nz) return; int iinf = (x < 0 ? -x : 0); int jinf = (y < 0 ? -y : 0); int kinf = (z < 0 ? -z : 0); int ko = z + kinf; int offset = 0; int leni = buffer.length; int lenj = buffer[0].length; int lenk = buffer[0][0].length; if (x + leni < 0) return; if (y + lenj < 0) return; if (z + lenk < 0) return; int isup = (x + leni >= nx ? nx - x : leni); int jsup = (y + lenj >= ny ? ny - y : lenj); int ksup = (z + lenk >= nz ? nz - z : lenk); for (int k = kinf; k < ksup; k++) { byte[] tmp = (byte[]) data[ko]; for (int j = jinf; j < jsup; j++) { offset = (x + iinf) + (y + j) * nx; for (int i = iinf; i < isup; i++) { tmp[offset] = (byte) (buffer[i][j][k]); offset++; } } ko++; } } catch (Exception e) { throw_put("XYZ", "Bounded check", buffer, x, y, z); } } } // end of class
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