/*
* #%L
* OME Bio-Formats package for reading and converting biological file formats.
* %%
* Copyright (C) 2005 - 2015 Open Microscopy Environment:
* - Board of Regents of the University of Wisconsin-Madison
* - Glencoe Software, Inc.
* - University of Dundee
* %%
* 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, see
* <http://www.gnu.org/licenses/gpl-2.0.html>.
* #L%
*/
package loci.formats.in;
import java.io.IOException;
import loci.common.DataTools;
import loci.common.DateTools;
import loci.common.Location;
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 ome.xml.model.primitives.PositiveFloat;
import ome.xml.model.primitives.Timestamp;
import ome.units.UNITS;
import ome.units.quantity.Length;
/**
* PDSReader is the file format reader for Perkin Elmer densitometer files.
*/
public class PDSReader extends FormatReader {
// -- Constants --
private static final String PDS_MAGIC_STRING = " IDENTIFICATION";
private static final String DATE_FORMAT = "HH:mm:ss d-MMM-** yyyy";
// -- Fields --
private String pixelsFile;
private int recordWidth;
private int lutIndex = -1;
private boolean reverseX = false, reverseY = false;
// -- Constructor --
/** Constructs a new PDS reader. */
public PDSReader() {
super("Perkin Elmer Densitometer", new String[] {"hdr", "img"});
domains = new String[] {FormatTools.EM_DOMAIN};
suffixSufficient = false;
hasCompanionFiles = true;
datasetDescription = "One .hdr file and a similarly-named .img file";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
if (!open) return false;
if (checkSuffix(name, "hdr")) return super.isThisType(name, open);
else if (checkSuffix(name, "img")) {
String headerFile = name.substring(0, name.lastIndexOf(".")) + ".hdr";
return new Location(headerFile).exists() && isThisType(headerFile, open);
}
return false;
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 15;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(blockLen).equals(PDS_MAGIC_STRING);
}
/* @see loci.formats.IFormatReader#get16BitLookupTable() */
@Override
public short[][] get16BitLookupTable() throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
if (lutIndex < 0 || lutIndex >= 3) return null;
short[][] lut = new short[3][65536];
for (int i=0; i<lut[lutIndex].length; i++) {
lut[lutIndex][i] = (short) i;
}
return lut;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
@Override
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (noPixels) {
return new String[] {currentId};
}
return new String[] {currentId, pixelsFile};
}
/**
* @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);
int pad = recordWidth - (getSizeX() % recordWidth);
RandomAccessInputStream pixels = new RandomAccessInputStream(pixelsFile);
int realX = reverseX ? getSizeX() - w - x : x;
int realY = reverseY ? getSizeY() - h - y : y;
readPlane(pixels, realX, realY, w, h, pad, buf);
pixels.close();
if (reverseX) {
for (int row=0; row<h; row++) {
for (int col=0; col<w/2; col++) {
int begin = 2 * (row * w + col);
int end = 2 * (row * w + (w - col - 1));
byte b0 = buf[begin];
byte b1 = buf[begin + 1];
buf[begin] = buf[end];
buf[begin + 1] = buf[end + 1];
buf[end] = b0;
buf[end + 1] = b1;
}
}
}
if (reverseY) {
for (int row=0; row<h/2; row++) {
byte[] b = new byte[w * 2];
int start = row * w * 2;
int end = (h - row - 1) * w * 2;
System.arraycopy(buf, start, b, 0, b.length);
System.arraycopy(buf, end, buf, start, b.length);
System.arraycopy(b, 0, buf, end, b.length);
}
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
recordWidth = 0;
pixelsFile = null;
lutIndex = -1;
reverseX = reverseY = false;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
if (!checkSuffix(id, "hdr")) {
String headerFile = id.substring(0, id.lastIndexOf(".")) + ".hdr";
if (!new Location(headerFile).exists()) {
headerFile = id.substring(0, id.lastIndexOf(".")) + ".HDR";
if (!new Location(headerFile).exists()) {
throw new FormatException("Could not find matching .hdr file.");
}
}
initFile(headerFile);
return;
}
super.initFile(id);
String[] headerData = DataTools.readFile(id).split("\r\n");
if (headerData.length == 1) {
headerData = headerData[0].split("\r");
}
Length xPos = null, yPos = null;
Double deltaX = null, deltaY = null;
String date = null;
CoreMetadata m = core.get(0);
for (String line : headerData) {
int eq = line.indexOf("=");
if (eq < 0) continue;
int end = line.indexOf("/");
if (end < 0) end = line.length();
String key = line.substring(0, eq).trim();
String value = line.substring(eq + 1, end).trim();
if (key.equals("NXP")) {
m.sizeX = Integer.parseInt(value);
}
else if (key.equals("NYP")) {
m.sizeY = Integer.parseInt(value);
}
else if (key.equals("XPOS")) {
final Double number = Double.valueOf(value);
xPos = new Length(number, UNITS.REFERENCEFRAME);
addGlobalMeta("X position for position #1", xPos);
}
else if (key.equals("YPOS")) {
final Double number = Double.valueOf(value);
yPos = new Length(number, UNITS.REFERENCEFRAME);
addGlobalMeta("Y position for position #1", yPos);
}
else if (key.equals("SIGNX")) {
reverseX = value.replaceAll("'", "").trim().equals("-");
}
else if (key.equals("SIGNY")) {
reverseY = value.replaceAll("'", "").trim().equals("-");
}
else if (key.equals("DELTAX")) {
deltaX = new Double(value);
}
else if (key.equals("DELTAY")) {
deltaY = new Double(value);
}
else if (key.equals("COLOR")) {
int color = Integer.parseInt(value);
if (color == 4) {
m.sizeC = 3;
m.rgb = true;
}
else {
m.sizeC = 1;
m.rgb = false;
lutIndex = color - 1;
m.indexed = lutIndex >= 0;
}
}
else if (key.equals("SCAN TIME")) {
long modTime = new Location(currentId).getAbsoluteFile().lastModified();
String year = DateTools.convertDate(modTime, DateTools.UNIX, "yyyy");
date = value.replaceAll("'", "") + " " + year;
date = DateTools.formatDate(date, DATE_FORMAT);
}
else if (key.equals("FILE REC LEN")) {
recordWidth = Integer.parseInt(value) / 2;
}
addGlobalMeta(key, value);
}
m.sizeZ = 1;
m.sizeT = 1;
m.imageCount = 1;
m.dimensionOrder = "XYCZT";
m.pixelType = FormatTools.UINT16;
m.littleEndian = true;
String base = currentId.substring(0, currentId.lastIndexOf("."));
pixelsFile = base + ".IMG";
if (!new Location(pixelsFile).exists()) {
pixelsFile = base + ".img";
}
boolean minimumMetadata =
getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, !minimumMetadata);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
if (!minimumMetadata) {
store.setPlanePositionX(xPos, 0, 0);
store.setPlanePositionY(yPos, 0, 0);
Length sizeX = FormatTools.getPhysicalSizeX(deltaX);
Length sizeY = FormatTools.getPhysicalSizeY(deltaY);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
}
}