//
// EPSReader.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;
import loci.formats.tiff.IFD;
import loci.formats.tiff.IFDList;
import loci.formats.tiff.TiffParser;
/**
* Reader is the file format reader for Encapsulated PostScript (EPS) files.
* Some regular PostScript files are also supported.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/EPSReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/EPSReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class EPSReader extends FormatReader {
// -- Fields --
/** Starting line of pixel data. */
private int start;
/** Flag indicating binary data. */
private boolean binary;
private boolean isTiff;
private IFDList ifds;
// -- Constructor --
/** Constructs a new EPS reader. */
public EPSReader() {
super("Encapsulated PostScript", new String[] {"eps", "epsi", "ps"});
domains = new String[] {FormatTools.GRAPHICS_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
public int getOptimalTileWidth() {
FormatTools.assertId(currentId, true, 1);
try {
if (isTiff) {
return (int) ifds.get(0).getTileWidth();
}
}
catch (FormatException e) {
LOGGER.debug("Could not retrieve tile width", e);
}
return super.getOptimalTileWidth();
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
try {
if (isTiff) {
return (int) ifds.get(0).getTileLength();
}
}
catch (FormatException e) {
LOGGER.debug("Could not retrieve tile height", e);
}
return super.getOptimalTileHeight();
}
/**
* @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);
if (isTiff) {
long[] offsets = ifds.get(0).getStripOffsets();
in.seek(offsets[0]);
int[] map = ifds.get(0).getIFDIntArray(IFD.COLOR_MAP);
if (map == null) {
readPlane(in, x, y, w, h, buf);
return buf;
}
byte[] b = new byte[w * h];
in.skipBytes(2 * y * getSizeX());
for (int row=0; row<h; row++) {
in.skipBytes(x * 2);
for (int col=0; col<w; col++) {
b[row * w + col] = (byte) (in.readShort() & 0xff);
}
in.skipBytes(2 * (getSizeX() - w - x));
}
for (int i=0; i<b.length; i++) {
int ndx = b[i] & 0xff;
for (int j=0; j<getSizeC(); j++) {
if (j < 3) {
buf[i*getSizeC() + j] = (byte) map[ndx + j*256];
}
else {
boolean zero =
map[ndx] == 0 && map[ndx + 256] == 0 && map[ndx + 512] == 0;
buf[i * getSizeC() + j] = zero ? (byte) 0 : (byte) 255;
}
}
}
return buf;
}
if (start == 0) {
throw new FormatException("Vector data not supported.");
}
in.seek(0);
for (int line=0; line<=start; line++) {
in.readLine();
}
int bytes = FormatTools.getBytesPerPixel(getPixelType());
if (binary) {
// pixels are stored as raw bytes
readPlane(in, x, y, w, h, buf);
}
else {
// pixels are stored as a 2 character hexadecimal value
String pix = in.readString((int) (in.length() - in.getFilePointer()));
pix = pix.replaceAll("\n", "");
pix = pix.replaceAll("\r", "");
int ndx = getSizeC() * y * bytes * getSizeX();
int destNdx = 0;
for (int row=0; row<h; row++) {
ndx += x * getSizeC() * bytes;
for (int col=0; col<w*getSizeC()*bytes; col++) {
buf[destNdx++] =
(byte) Integer.parseInt(pix.substring(2*ndx, 2*(ndx+1)), 16);
ndx++;
}
ndx += getSizeC() * bytes * (getSizeX() - w - x);
}
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
start = 0;
binary = isTiff = false;
ifds = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
LOGGER.info("Verifying EPS format");
String line = in.readLine();
if (!line.trim().startsWith("%!PS")) {
// read the TIFF preview
isTiff = true;
in.order(true);
in.seek(20);
int offset = in.readInt();
int len = in.readInt();
byte[] b = new byte[len];
in.seek(offset);
in.read(b);
in = new RandomAccessInputStream(b);
TiffParser tp = new TiffParser(in);
ifds = tp.getIFDs();
IFD firstIFD = ifds.get(0);
core[0].sizeX = (int) firstIFD.getImageWidth();
core[0].sizeY = (int) firstIFD.getImageLength();
core[0].sizeZ = 1;
core[0].sizeT = 1;
core[0].sizeC = firstIFD.getSamplesPerPixel();
if (getSizeC() == 2) core[0].sizeC = 4;
core[0].littleEndian = firstIFD.isLittleEndian();
core[0].interleaved = true;
core[0].rgb = getSizeC() > 1;
core[0].pixelType = firstIFD.getPixelType();
core[0].imageCount = 1;
core[0].dimensionOrder = "XYCZT";
core[0].metadataComplete = true;
core[0].indexed = false;
core[0].falseColor = false;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, id, 0);
return;
}
LOGGER.info("Finding image data");
binary = false;
String image = "image";
int lineNum = 1;
line = in.readLine().trim();
while (line != null && !line.equals("%%EOF")) {
if (line.endsWith(image)) {
if (!line.startsWith(image)) {
if (line.indexOf("colorimage") != -1) core[0].sizeC = 3;
String[] t = line.split(" ");
try {
core[0].sizeX = Integer.parseInt(t[0]);
core[0].sizeY = Integer.parseInt(t[1]);
}
catch (NumberFormatException exc) {
LOGGER.debug("Could not parse image dimensions", exc);
core[0].sizeC = Integer.parseInt(t[3]);
}
}
start = lineNum;
break;
}
else if (line.startsWith("%%")) {
if (line.startsWith("%%BoundingBox:")) {
line = line.substring(14).trim();
String[] t = line.split(" ");
try {
int originX = Integer.parseInt(t[0].trim());
int originY = Integer.parseInt(t[1].trim());
core[0].sizeX = Integer.parseInt(t[2].trim()) - originX;
core[0].sizeY = Integer.parseInt(t[3].trim()) - originY;
addGlobalMeta("X-coordinate of origin", originX);
addGlobalMeta("Y-coordinate of origin", originY);
}
catch (NumberFormatException e) {
throw new FormatException(
"Files without image data are not supported.");
}
}
else if (line.startsWith("%%BeginBinary")) {
binary = true;
}
else {
// parse key/value pairs
int ndx = line.indexOf(":");
if (ndx != -1) {
String key = line.substring(0, ndx);
String value = line.substring(ndx + 1);
addGlobalMeta(key, value);
}
}
}
else if (line.startsWith("%ImageData:")) {
line = line.substring(11);
String[] t = line.split(" ");
core[0].sizeX = Integer.parseInt(t[0]);
core[0].sizeY = Integer.parseInt(t[1]);
core[0].sizeC = Integer.parseInt(t[3]);
for (int i=4; i<t.length; i++) {
image = t[i].trim();
if (image.length() > 1) {
image = image.substring(1, image.length() - 1);
}
}
}
lineNum++;
line = in.readLine().trim();
}
LOGGER.info("Populating metadata");
if (getSizeC() == 0) core[0].sizeC = 1;
core[0].sizeZ = 1;
core[0].sizeT = 1;
core[0].dimensionOrder = "XYCZT";
core[0].pixelType = FormatTools.UINT8;
core[0].rgb = getSizeC() == 3;
core[0].interleaved = true;
core[0].littleEndian = true;
core[0].imageCount = 1;
// Populate metadata store
// The metadata store we're working with.
MetadataStore store = getMetadataStore();
MetadataTools.populatePixels(store, this);
MetadataTools.setDefaultCreationDate(store, currentId, 0);
}
}