/*
* #%L
* BSD implementations of Bio-Formats readers and writers
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions are met:
*
* 1. Redistributions of source code must retain the above copyright notice,
* this list of conditions and the following disclaimer.
* 2. Redistributions in binary form must reproduce the above copyright notice,
* this list of conditions and the following disclaimer in the documentation
* and/or other materials provided with the distribution.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
* AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
* ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
* LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
* CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
* SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
* INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
* CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
* ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
* POSSIBILITY OF SUCH DAMAGE.
* #L%
*/
package loci.formats.in;
import java.io.IOException;
import loci.common.RandomAccessInputStream;
import loci.formats.CoreMetadata;
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.
*
* @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;
private int[] map;
// -- 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() */
@Override
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() */
@Override
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)
*/
@Override
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]);
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++) {
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) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
start = 0;
binary = isTiff = false;
ifds = null;
map = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
CoreMetadata m = core.get(0);
LOGGER.info("Verifying EPS format");
String line = 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);
map = tp.getColorMap(firstIFD);
m.sizeX = (int) firstIFD.getImageWidth();
m.sizeY = (int) firstIFD.getImageLength();
m.sizeZ = 1;
m.sizeT = 1;
m.sizeC = firstIFD.getSamplesPerPixel();
if (getSizeC() == 2) m.sizeC = 4;
m.littleEndian = firstIFD.isLittleEndian();
m.interleaved = true;
m.rgb = getSizeC() > 1;
m.pixelType = firstIFD.getPixelType();
m.imageCount = 1;
m.dimensionOrder = "XYCZT";
m.metadataComplete = true;
m.indexed = false;
m.falseColor = false;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
return;
}
LOGGER.info("Finding image data");
binary = false;
String image = "image";
int lineNum = 1;
line = readLine().trim();
while (line != null && !line.equals("%%EOF")) {
if (line.endsWith(image)) {
if (!line.startsWith(image)) {
if (line.indexOf("colorimage") != -1) m.sizeC = 3;
String[] t = line.split(" ");
try {
int newX = Integer.parseInt(t[0]);
int newY = Integer.parseInt(t[1]);
if (t.length > 2 && Integer.parseInt(t[2]) >= 8) {
m.sizeX = newX;
m.sizeY = newY;
start = lineNum;
}
}
catch (NumberFormatException exc) {
LOGGER.debug("Could not parse image dimensions", exc);
if (t.length > 3) {
m.sizeC = Integer.parseInt(t[3]);
}
}
}
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());
m.sizeX = Integer.parseInt(t[2].trim()) - originX;
m.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(" ");
m.sizeX = Integer.parseInt(t[0]);
m.sizeY = Integer.parseInt(t[1]);
m.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 = readLine().trim();
}
LOGGER.info("Populating metadata");
if (getSizeC() == 0) m.sizeC = 1;
m.sizeZ = 1;
m.sizeT = 1;
m.dimensionOrder = "XYCZT";
m.pixelType = FormatTools.UINT8;
m.rgb = getSizeC() == 3;
m.interleaved = true;
m.littleEndian = true;
m.imageCount = 1;
// Populate metadata store
// The metadata store we're working with.
MetadataStore store = getMetadataStore();
MetadataTools.populatePixels(store, this);
}
private String readLine() throws IOException {
String s = in.findString("\r", "\n");
return s.length() == 0 ? null : s;
}
}