// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2024.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.xray.parsers;
  
  import ffx.crystal.Crystal;
  
  import static ffx.utilities.TinkerUtils.version;
  import static java.lang.String.format;
  import static org.apache.commons.math3.util.FastMath.pow;
  import static org.apache.commons.math3.util.FastMath.sqrt;
  
  import java.io.DataOutputStream;
  import java.io.File;
  import java.io.FileOutputStream;
  import java.nio.ByteBuffer;
  import java.nio.ByteOrder;
  import java.util.logging.Level;
  import java.util.logging.Logger;
  
  /**
   * CCP4MapWriter class.
   *
   * @author Timothy D. Fenn
   * @see <ul>
   *     <li><a href="http://www.ccp4.ac.uk/html/maplib.html" target="_blank">CCP4 map format</a>
   *     <li><a href="http://www.ccp4.ac.uk/dist/html/library.html" target="_blank">CCP4 library
   *     documentation </a>
   *     <li><a href="http://www.ccp4.ac.uk/html/maplib.html" target="_blank">CCP4 map format </a>
   *     <li><a href="http://www.ccp4.ac.uk/dist/html/library.html" target="_blank">CCP4 library
   *     documentation </a>
   *     </ul>
   * @since 1.0
   */
  public class CCP4MapWriter {
  
    private static final Logger logger = Logger.getLogger(CCP4MapWriter.class.getName());
    private final String filename;
    private final Crystal crystal;
    private final int extx, exty, extz;
    private final int orix, oriy, oriz, nx, ny, nz;
    private int stride;
  
    /**
     * construct mapwriter object
     *
     * @param extx slices in x
     * @param exty slices in y
     * @param extz slices in z
     * @param crystal {@link Crystal} object
     * @param filename output filename
     */
    public CCP4MapWriter(int extx, int exty, int extz, Crystal crystal, String filename) {
      this.orix = 0;
      this.oriy = 0;
      this.oriz = 0;
      this.extx = extx;
      this.exty = exty;
      this.extz = extz;
      this.nx = extx;
      this.ny = exty;
      this.nz = extz;
      this.crystal = crystal;
      this.filename = filename;
      this.stride = 2;
   }
 
   /**
    * Constructor for CCP4MapWriter.
    *
    * @param orix an int.
    * @param oriy an int.
    * @param oriz an int.
    * @param extx an int.
    * @param exty an int.
    * @param extz an int.
    * @param nx an int.
    * @param ny an int.
    * @param nz an int.
    * @param crystal a {@link ffx.crystal.Crystal} object.
    * @param filename a {@link java.lang.String} object.
    */
   public CCP4MapWriter(
       int orix, int oriy, int oriz,
       int extx, int exty, int extz,
       int nx, int ny, int nz,
       Crystal crystal, String filename) {
     this.orix = orix;
     this.oriy = oriy;
     this.oriz = oriz;
     this.extx = extx;
     this.exty = exty;
     this.extz = extz;
     this.nx = nx;
     this.ny = ny;
     this.nz = nz;
     this.crystal = crystal;
     this.filename = filename;
     this.stride = 2;
   }
 
   /**
    * Set the stepping across the array (e.g. 2 if data is separated by 1 space)
    *
    * @param stride the step size desired
    */
   public void setStride(int stride) {
     this.stride = stride;
   }
 
   /**
    * Write data to file (does not normalize).
    *
    * @param data map data to write out
    */
   public void write(double[] data) {
     write(data, false);
   }
 
   /**
    * write data to file, does not normalize
    *
    * @param data map data to write out
    * @param norm should the data be normalized by mean/sd?
    */
   public void write(double[] data, boolean norm) {
     ByteOrder b = ByteOrder.nativeOrder();
     FileOutputStream fos;
     DataOutputStream dos;
 
     double min = Double.POSITIVE_INFINITY;
     double max = Double.NEGATIVE_INFINITY;
     double mean = 0.0;
     double sd = 0.0;
 
     int n = 0;
     for (int k = 0; k < extz; k++) {
       for (int j = 0; j < exty; j++) {
         for (int i = 0; i < extx; i++) {
           int index = stride * (i + extx * (j + exty * k));
           n++;
           if (data[index] < min) {
             min = data[index];
           }
           if (data[index] > max) {
             max = data[index];
           }
           mean += (data[index] - mean) / n;
         }
       }
     }
 
     n = 0;
     for (int k = 0; k < extz; k++) {
       for (int j = 0; j < exty; j++) {
         for (int i = 0; i < extx; i++) {
           int index = stride * (i + extx * (j + exty * k));
           sd += pow(data[index] - mean, 2.0);
           n++;
         }
       }
     }
     sd = sqrt(sd / n);
 
     if (norm) {
       for (int k = 0; k < extz; k++) {
         for (int j = 0; j < exty; j++) {
           for (int i = 0; i < extx; i++) {
             int index = stride * (i + extx * (j + exty * k));
             data[index] = (data[index] - mean) / sd;
           }
         }
       }
       // recurse
       write(data, false);
     }
 
     File file = version(new File(filename));
     String name = file.getName();
 
     try {
       if (logger.isLoggable(Level.INFO)) {
         StringBuilder sb = new StringBuilder();
         sb.append(format("\n Writing CCP4 map file: \"%s\"", name));
         sb.append(format("\n  Map min: %g max: %g mean: %g standard dev.: %g", min, max, mean, sd));
         logger.info(sb.toString());
       }
 
       fos = new FileOutputStream(file);
       dos = new DataOutputStream(fos);
 
       byte[] bytes = new byte[2048];
       int offset = 0;
 
       int imapdata;
       float fmapdata;
       String mapstr;
 
       // header
       ByteBuffer bb = ByteBuffer.wrap(bytes);
       bb.order(b).putInt(extx);
       bb.order(b).putInt(exty);
       bb.order(b).putInt(extz);
 
       // mode (2 = reals, only one we accept)
       bb.order(b).putInt(2);
 
       bb.order(b).putInt(orix);
       bb.order(b).putInt(oriy);
       bb.order(b).putInt(oriz);
       bb.order(b).putInt(nx);
       bb.order(b).putInt(ny);
       bb.order(b).putInt(nz);
 
       bb.order(b).putFloat((float) crystal.a);
       bb.order(b).putFloat((float) crystal.b);
       bb.order(b).putFloat((float) crystal.c);
       bb.order(b).putFloat((float) crystal.alpha);
       bb.order(b).putFloat((float) crystal.beta);
       bb.order(b).putFloat((float) crystal.gamma);
 
       bb.order(b).putInt(1);
       bb.order(b).putInt(2);
       bb.order(b).putInt(3);
 
       bb.order(b).putFloat((float) min);
       bb.order(b).putFloat((float) max);
       bb.order(b).putFloat((float) mean);
 
       bb.order(b).putInt(crystal.spaceGroup.number);
       // bb.order(b).putInt(1);
 
       // symmetry bytes - should set this up at some point
       // imapdata = swap ? ByteSwap.swap(320) : 320;
       bb.order(b).putInt(80);
 
       bb.order(b).putInt(0);
 
       for (int i = 0; i < 12; i++) {
         bb.order(b).putFloat(0.0f);
       }
 
       for (int i = 0; i < 15; i++) {
         bb.order(b).putInt(0);
       }
       dos.write(bytes, offset, 208);
       bb.rewind();
 
       mapstr = "MAP ";
       dos.writeBytes(mapstr);
 
       // machine code: double, float, int, uchar
       // 0x4441 for LE, 0x1111 for BE
       if (ByteOrder.nativeOrder().equals(ByteOrder.LITTLE_ENDIAN)) {
         imapdata = 0x4441;
       } else {
         imapdata = 0x1111;
       }
       bb.order(b).putInt(imapdata);
 
       bb.order(b).putFloat((float) sd);
 
       bb.order(b).putInt(1);
       dos.write(bytes, offset, 12);
 
       StringBuilder sb = new StringBuilder();
       sb.append("map data from ffx");
       while (sb.length() < 80) {
         sb.append(" ");
       }
       dos.writeBytes(sb.toString());
 
       sb = new StringBuilder();
       while (sb.length() < 80) {
         sb.append(" ");
       }
       for (int i = 0; i < 9; i++) {
         dos.writeBytes(sb.toString());
       }
 
       sb = new StringBuilder();
       sb.append("x,y,z");
       while (sb.length() < 80) {
         sb.append(" ");
       }
       dos.writeBytes(sb.toString());
 
       bb.rewind();
       for (int k = 0; k < extz; k++) {
         for (int j = 0; j < exty; j++) {
           for (int i = 0; i < extx; i++) {
             int index = stride * (i + extx * (j + exty * k));
             fmapdata = (float) data[index];
             bb.order(b).putFloat(fmapdata);
             if (!bb.hasRemaining()) {
               dos.write(bytes);
               bb.rewind();
             }
           }
         }
       }
       if (bb.position() > 0) {
         dos.write(bytes);
         bb.rewind();
       }
 
       dos.close();
     } catch (Exception e) {
       String message = "Fatal exception evaluating structure factors.\n";
       logger.log(Level.SEVERE, message, e);
     }
   }
 }