<commit_before>//
// FEIReader.java
//

/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program 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 this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

package loci.formats.in;

import java.io.IOException;

import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;

/**
 * FEIReader is the file format reader for FEI and Philips .img files.
 *
 * <dl><dt><b>Source code:</b></dt>
 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/bio-formats/src/loci/formats/in/FEIReader.java">Trac</a>,
 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/bio-formats/src/loci/formats/in/FEIReader.java">SVN</a></dd></dl>
 */
public class FEIReader extends FormatReader {

  // -- Constants --

  public static final String FEI_MAGIC_STRING = "XL";
  private static final int INVALID_PIXELS = 112;

  // -- Fields --

  private int headerSize;

  // -- Constructor --

  /** Constructs a new FEI reader. */
  public FEIReader() {
    super("FEI/Philips", "img");
    suffixSufficient = false;
    domains = new String[] {FormatTools.SEM_DOMAIN};
  }

  // -- IFormatReader API methods --

  /* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
  public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    final int blockLen = 2;
    if (!FormatTools.validStream(stream, blockLen, false)) return false;
    return stream.readString(blockLen).startsWith(FEI_MAGIC_STRING);
  }

  /**
   * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
   */
  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
    throws FormatException, IOException
  {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);

    in.seek(headerSize);

    byte[] segment = new byte[getSizeX() / 2];
    // interlace frames - there are four rows of two columns
    int halfRow = getSizeX() / 2;
    for (int q=0; q<4; q++) {
      for (int row=q; row<h; row+=4) {
        for (int s=0; s<2; s++) {
          in.read(segment);
          in.skipBytes(INVALID_PIXELS / 2);
          for (int col=s; col<w; col+=2) {
            buf[row*w + col] = segment[col / 2];
          }
        }
      }
    }

    return buf;
  }

  /* @see loci.formats.IFormatReader#close(boolean) */
  public void close(boolean fileOnly) throws IOException {
    super.close(fileOnly);
    if (!fileOnly) {
      headerSize = 0;
    }
  }<commit_msg>Updated FEI reader to properly support sub-image reading.<commit_after>//
// FEIReader.java
//

/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program 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 this program; if not, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
*/

package loci.formats.in;

import java.io.IOException;

import loci.common.RandomAccessInputStream;
import loci.formats.FormatException;
import loci.formats.FormatReader;
import loci.formats.FormatTools;
import loci.formats.MetadataTools;
import loci.formats.meta.MetadataStore;

/**
 * FEIReader is the file format reader for FEI and Philips .img files.
 *
 * <dl><dt><b>Source code:</b></dt>
 * <dd><a href="http://dev.loci.wisc.edu/trac/java/browser/trunk/components/bio-formats/src/loci/formats/in/FEIReader.java">Trac</a>,
 * <a href="http://dev.loci.wisc.edu/svn/java/trunk/components/bio-formats/src/loci/formats/in/FEIReader.java">SVN</a></dd></dl>
 */
public class FEIReader extends FormatReader {

  // -- Constants --

  public static final String FEI_MAGIC_STRING = "XL";
  private static final int INVALID_PIXELS = 112;

  // -- Fields --

  private int headerSize;

  // -- Constructor --

  /** Constructs a new FEI reader. */
  public FEIReader() {
    super("FEI/Philips", "img");
    suffixSufficient = false;
    domains = new String[] {FormatTools.SEM_DOMAIN};
  }

  // -- IFormatReader API methods --

  /* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
  public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    final int blockLen = 2;
    if (!FormatTools.validStream(stream, blockLen, false)) return false;
    return stream.readString(blockLen).startsWith(FEI_MAGIC_STRING);
  }

  /**
   * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
   */
  public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
    throws FormatException, IOException
  {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);

    in.seek(headerSize);

    byte[] segment = new byte[getSizeX() / 2];
    byte[] plane = new byte[FormatTools.getPlaneSize(this)];
    // interlace frames - there are four rows of two columns
    int halfRow = getSizeX() / 2;
    for (int q=0; q<4; q++) {
      for (int row=q; row<getSizeY(); row+=4) {
        for (int s=0; s<2; s++) {
          in.read(segment);
          in.skipBytes(INVALID_PIXELS / 2);
          for (int col=s; col<getSizeX(); col+=2) {
            plane[row*getSizeX() + col] = segment[col / 2];
          }
        }
      }
    }

    RandomAccessInputStream pixels = new RandomAccessInputStream(plane);
    readPlane(pixels, x, y, w, h, buf);
    pixels.close();

    return buf;
  }

  /* @see loci.formats.IFormatReader#close(boolean) */
  public void close(boolean fileOnly) throws IOException {
    super.close(fileOnly);
    if (!fileOnly) {
      headerSize = 0;
    }
  }
{'fraction_non_alphanumeric': 0.12023844140738586, 'fraction_numerical': 0.009886594940389648, 'mean_word_length': 3.39272030651341, 'pattern_counts': {'":': 0, '<': 35, '<?xml version=': 0, '>': 27, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1459447', 'n_tokens_mistral': 2250, 'n_tokens_neox': 2159, 'n_words': 664}