/*
* #%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;
/**
* TopometrixReader is the file format reader for TopoMetrix .tfr, .ffr,
* .zfr, .zfp, and .2fl files.
*/
public class TopometrixReader extends FormatReader {
// -- Fields --
private long pixelOffset;
// -- Constructor --
/** Constructs a new TopoMetrix reader. */
public TopometrixReader() {
super("TopoMetrix", new String[] {"tfr", "ffr", "zfr", "zfp", "2fl"});
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 = 6;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
String check = stream.readString(blockLen);
if (!check.startsWith("#R")) return false;
try {
Double.parseDouble(check.substring(2, 5));
}
catch (NumberFormatException e) { }
return false;
}
/**
* @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);
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.littleEndian = true;
in.order(isLittleEndian());
in.skipBytes(2);
int version = (int) Double.parseDouble(in.readString(4));
in.skipBytes(2);
pixelOffset = Long.parseLong(in.readString(4));
in.skipBytes(2);
long fp = in.getFilePointer();
String date = in.readLine().trim();
int commentLength = (int) (240 - in.getFilePointer() + fp);
String comment = in.readString(commentLength).trim();
if (version == 5) {
in.seek(452);
}
in.skipBytes(152);
m.sizeX = in.readShort();
in.skipBytes(2);
m.sizeY = in.readShort();
double xSize = 0d, ySize = 0d;
double adc = 0d, dacToWorldZero = 0d;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
in.skipBytes(10);
if (version == 5) {
in.skipBytes(4);
xSize = in.readDouble();
in.skipBytes(8);
ySize = in.readDouble();
adc = in.readDouble();
dacToWorldZero = in.readDouble();
in.skipBytes(1176);
double sampleVolts = in.readDouble();
double tunnelCurrent = in.readDouble();
in.skipBytes(16);
double timePerPixel = in.readDouble();
in.skipBytes(40);
double scanAngle = in.readDouble();
addGlobalMeta("Sample volts", sampleVolts);
addGlobalMeta("Tunnel current", tunnelCurrent);
addGlobalMeta("Scan rate", timePerPixel);
addGlobalMeta("Scan angle", scanAngle);
}
else {
xSize = in.readFloat();
in.skipBytes(4);
ySize = in.readFloat();
adc = in.readFloat();
in.skipBytes(764);
dacToWorldZero = in.readFloat();
}
addGlobalMeta("Version", version);
addGlobalMeta("X size (in um)", xSize);
addGlobalMeta("Y size (in um)", ySize);
addGlobalMeta("ADC", adc);
addGlobalMeta("DAC to world zero", dacToWorldZero);
addGlobalMeta("Comment", comment);
addGlobalMeta("Acquisition date", date);
}
m.pixelType = FormatTools.UINT16;
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.dimensionOrder = "XYZCT";
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
date = DateTools.formatDate(date,
new String[] {"MM/dd/yy HH:mm:ss", "MM/dd/yyyy HH:mm:ss"});
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Length sizeX =
FormatTools.getPhysicalSizeX((double) xSize / getSizeX());
Length sizeY =
FormatTools.getPhysicalSizeY((double) ySize / getSizeY());
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
store.setImageDescription(comment, 0);
}
}
}