/*
* #%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.quantity.Length;
/**
* UnisokuReader is the file format reader for Unisoku STM files.
*/
public class UnisokuReader extends FormatReader {
// -- Constants --
protected static final String UNISOKU_MAGIC_STRING = ":STM data";
// -- Fields --
private String datFile;
// -- Constructor --
/** Constructs a new Unisoku reader. */
public UnisokuReader() {
super("Unisoku STM", new String[] {"hdr", "dat"});
domains = new String[] {FormatTools.SPM_DOMAIN};
suffixSufficient = false;
hasCompanionFiles = true;
datasetDescription = "One .HDR file plus one similarly-named .DAT file";
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
@Override
public boolean isThisType(String name, boolean open) {
if (checkSuffix(name, "hdr")) {
return super.isThisType(name, open);
}
if (name.indexOf(".") < 0) {
return false;
}
String baseName = name.substring(0, name.lastIndexOf("."));
Location file = new Location(baseName + ".HDR");
if (!file.exists()) {
file = new Location(baseName + ".hdr");
}
if (!file.exists()) {
return false;
}
return super.isThisType(file.getAbsolutePath(), open);
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 9;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return (stream.readString(blockLen)).indexOf(UNISOKU_MAGIC_STRING) >= 0;
}
/* @see loci.formats.IFormatReader#getUsedFiles(boolean) */
@Override
public String[] getUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (noPixels) return new String[] {currentId};
return new String[] {currentId, datFile};
}
/**
* @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);
RandomAccessInputStream dat = new RandomAccessInputStream(datFile);
dat.order(isLittleEndian());
readPlane(dat, x, y, w, h, buf);
dat.close();
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
datFile = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
id = new Location(id).getAbsolutePath();
if (checkSuffix(id, "dat")) {
id = id.substring(0, id.lastIndexOf(".")) + ".HDR";
}
super.initFile(id);
CoreMetadata m = core.get(0);
datFile = id.substring(0, id.lastIndexOf(".")) + ".DAT";
String header = DataTools.readFile(id);
String[] lines = header.split("\r");
String imageName = null, remark = null, date = null;
double pixelSizeX = 0d, pixelSizeY = 0d;
for (int i=0; i<lines.length; ) {
lines[i] = lines[i].trim();
if (lines[i].startsWith(":")) {
String key = lines[i++];
StringBuffer data = new StringBuffer();
while (i < lines.length && !lines[i].trim().startsWith(":")) {
data.append(" ");
data.append(lines[i++].trim());
}
String value = data.toString().trim();
addGlobalMeta(key, value);
String[] v = value.split(" ");
if (key.equals(":data volume(x*y)")) {
m.sizeX = Integer.parseInt(v[0]);
m.sizeY = Integer.parseInt(v[1]);
}
else if (key.equals(":date; time")) {
date = DateTools.formatDate(value, "MM/dd/yy HH:mm:ss");
}
else if (key.startsWith(":ascii flag; data type")) {
value = value.substring(value.indexOf(" ") + 1);
int type = Integer.parseInt(value);
boolean signed = type % 2 == 1;
int bytes = type / 2;
m.pixelType =
FormatTools.pixelTypeFromBytes(bytes, signed, bytes == 4);
}
else if (getMetadataOptions().getMetadataLevel() !=
MetadataLevel.MINIMUM)
{
if (key.equals(":sample name")) {
imageName = value;
}
else if (key.equals(":remark")) {
remark = value;
}
else if (key.startsWith(":x_data ->")) {
String unit = v[0];
pixelSizeX = Double.parseDouble(v[2]) - Double.parseDouble(v[1]);
pixelSizeX /= getSizeX();
if (unit.equals("nm")) {
pixelSizeX /= 1000;
}
}
else if (key.startsWith(":y_data ->")) {
String unit = v[0];
pixelSizeY = Double.parseDouble(v[2]) - Double.parseDouble(v[1]);
pixelSizeY /= getSizeY();
if (unit.equals("nm")) {
pixelSizeY /= 1000;
}
}
}
}
}
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.rgb = false;
m.interleaved = false;
m.indexed = false;
m.dimensionOrder = "XYZCT";
m.littleEndian = true;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
store.setImageName(imageName, 0);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(remark, 0);
Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
}
}