/*
* #%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;
/**
* QuesantReader is the file format reader for Quesant .afm files.
*/
public class QuesantReader extends FormatReader {
// -- Constants --
public static final int MAX_HEADER_SIZE = 1024;
// -- Fields --
private int pixelsOffset;
private double xSize = 0d;
private String date = null, comment = null;
// -- Constructor --
/** Constructs a new Quesant reader. */
public QuesantReader() {
super("Quesant AFM", "afm");
domains = new String[] {FormatTools.SEM_DOMAIN};
}
// -- IFormatReader API methods --
/**
* @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(pixelsOffset);
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) {
pixelsOffset = 0;
xSize = 0d;
date = comment = null;
}
}
// -- 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());
while (in.getFilePointer() < MAX_HEADER_SIZE) {
readVariable();
}
in.seek(pixelsOffset);
m.sizeX = in.readShort();
pixelsOffset += 2;
m.sizeY = getSizeX();
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);
if (date != null) {
// Insert fake separator between seconds and milliseconds to use
// DateTools.formatDate()
int separator = date.lastIndexOf(":");
if (separator > 0 && date.length() > (separator + 5)) {
date = date.substring(0, separator + 3) + "." +
date.substring(separator + 3);
}
date = DateTools.formatDate(date, "MMM dd yyyy HH:mm:ss", ".");
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(comment, 0);
Length sizeX =
FormatTools.getPhysicalSizeX((double) xSize / getSizeX());
Length sizeY =
FormatTools.getPhysicalSizeY((double) xSize / getSizeY());
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
}
// -- Helper methods --
private void readVariable() throws IOException {
String code = in.readString(4);
if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM &&
!code.equals("IMAG"))
{
in.skipBytes(4);
return;
}
int offset = in.readInt();
long fp = in.getFilePointer();
if (offset <= 0 || offset > in.length()) return;
in.seek(offset);
if (code.equals("SDES")) {
String sdes = in.readCString().trim();
if (comment == null) comment = sdes;
else comment += " " + sdes;
}
else if (code.equals("DESC")) {
int length = in.readShort();
String desc = in.readString(length);
if (comment == null) comment = desc;
else comment += " " + desc;
}
else if (code.equals("DATE")) {
date = in.readCString();
}
else if (code.equals("IMAG")) {
pixelsOffset = offset;
}
else if (code.equals("HARD")) {
xSize = in.readFloat();
float scanRate = in.readFloat();
float tunnelCurrent = (in.readFloat() * 10) / 32768;
in.skipBytes(12);
float integralGain = in.readFloat();
float proportGain = in.readFloat();
boolean isSTM = in.readShort() == 10;
float dynamicRange = in.readFloat();
addGlobalMeta("Scan rate (Hz)", scanRate);
addGlobalMeta("Tunnel current", tunnelCurrent);
addGlobalMeta("Is STM image", isSTM);
addGlobalMeta("Integral gain", integralGain);
addGlobalMeta("Proportional gain", proportGain);
addGlobalMeta("Z dynamic range", dynamicRange);
}
in.seek(fp);
}
}