/*
* #%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.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;
/**
* MolecularImagingReader is the file format reader for Molecular Imaging files.
*/
public class MolecularImagingReader extends FormatReader {
// -- Constants --
private static final String MAGIC_STRING = "UK SOFT";
private static final String DATE_FORMAT = "dd.MM.yyyy HH:mm:ss";
// -- Fields --
private long pixelOffset = 0;
// -- Constructor --
/** Constructs a new Molecular Imaging reader. */
public MolecularImagingReader() {
super("Molecular Imaging", "stp");
domains = new String[] {FormatTools.SEM_DOMAIN};
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 16;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readString(blockLen).indexOf(MAGIC_STRING) > 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(pixelOffset + no * FormatTools.getPlaneSize(this));
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) {
pixelOffset = 0;
}
}
// -- 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);
m.sizeZ = 0;
String date = null;
double pixelSizeX = 0d, pixelSizeY = 0d;
String data = in.findString("Data_section \r\n");
String[] lines = data.split("\n");
for (String line : lines) {
line = line.trim();
int space = line.indexOf(" ");
if (space != -1) {
String key = line.substring(0, space).trim();
String value = line.substring(space + 1).trim();
addGlobalMeta(key, value);
if (key.equals("samples_x")) {
m.sizeX = Integer.parseInt(value);
}
else if (key.equals("samples_y")) {
m.sizeY = Integer.parseInt(value);
}
else if (key.equals("buffer_id")) {
m.sizeZ++;
}
else if (key.equals("Date")) {
date = value;
}
else if (key.equals("time")) {
date += " " + value;
}
else if (key.equals("length_x")) {
pixelSizeX = Double.parseDouble(value) / getSizeX();
}
else if (key.equals("length_y")) {
pixelSizeY = Double.parseDouble(value) / getSizeY();
}
}
}
pixelOffset = in.getFilePointer();
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = getSizeZ();
m.rgb = false;
m.pixelType = FormatTools.UINT16;
m.littleEndian = true;
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 sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
}
}