/*
* #%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.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.quantity.Length;
/**
* SBIGReader is the file format reader for SBIG files.
* See the specification at http://www.sbig.com/pdffiles/file.format.pdf.
*/
public class SBIGReader extends FormatReader {
// -- Constants --
private static final long HEADER_SIZE = 2048;
private static final String DATE_FORMAT = "MM/dd/yy HH:mm:ss";
// -- Fields --
private boolean compressed;
// -- Constructor --
/** Constructs a new SBIG reader. */
public SBIGReader() {
super("SBIG", "");
domains = new String[] {FormatTools.ASTRONOMY_DOMAIN};
suffixSufficient = false;
suffixNecessary = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = (int) HEADER_SIZE;
final int checkLen = 32;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(checkLen).indexOf("ST-7 Compressed Image") >= 0;
}
/**
* @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);
in.seek(HEADER_SIZE);
int width = getSizeX() * 2;
if (compressed) {
byte[] b = new byte[FormatTools.getPlaneSize(this)];
for (int row=0; row<getSizeY(); row++) {
int rowLen = in.readShort();
if (rowLen == width) {
in.read(b, row * width, rowLen);
}
else {
int bufferPointer = row * width;
in.read(b, bufferPointer, 2);
while (bufferPointer - row * width < width - 2) {
short prevPixel =
DataTools.bytesToShort(b, bufferPointer, isLittleEndian());
bufferPointer += 2;
byte check = in.readByte();
if (check == -128) {
in.read(b, bufferPointer, 2);
}
else {
prevPixel += check;
DataTools.unpackBytes(prevPixel, b, bufferPointer, 2,
isLittleEndian());
}
}
}
}
RandomAccessInputStream stream = new RandomAccessInputStream(b);
readPlane(stream, x, y, w, h, buf);
stream.close();
}
else readPlane(in, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
compressed = false;
}
}
// -- 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);
Double temperature = null;
Double sizeX = null, sizeY = null;
String date = null, description = null;
String[] lines = DataTools.readFile(currentId).split("\n");
for (String line : lines) {
line = line.trim();
int eq = line.indexOf("=");
if (eq != -1) {
String key = line.substring(0, eq).trim();
String value = line.substring(eq + 1).trim();
addGlobalMeta(key, value);
if (key.equals("Width")) {
m.sizeX = Integer.parseInt(value);
}
else if (key.equals("Height")) {
m.sizeY = Integer.parseInt(value);
}
else if (key.equals("Note")) {
description = value;
}
else if (key.equals("X_pixel_size")) {
sizeX = new Double(value) * 1000;
}
else if (key.equals("Y_pixel_size")) {
sizeY = new Double(value) * 1000;
}
else if (key.equals("Date")) {
date = value;
}
else if (key.equals("Time")) {
date += " " + value;
}
}
else if (line.indexOf("Compressed") != -1) {
compressed = true;
}
else if (line.equals("End")) break;
}
m.pixelType = FormatTools.UINT16;
m.littleEndian = true;
m.rgb = false;
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.dimensionOrder = "XYZCT";
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (date != null) {
date = DateTools.formatDate(date, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Length x = FormatTools.getPhysicalSizeX(sizeX);
Length y = FormatTools.getPhysicalSizeY(sizeY);
if (x != null) {
store.setPixelsPhysicalSizeX(x, 0);
}
if (y != null) {
store.setPixelsPhysicalSizeY(y, 0);
}
store.setImageDescription(description, 0);
}
}
}