//
// AIMReader.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
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, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.in;
import java.io.IOException;
import loci.common.DateTools;
import loci.common.RandomAccessInputStream;
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;
/**
* AIMReader is the file format reader for .aim files.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/AIMReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/AIMReader.java;hb=HEAD">Gitweb</a></dd></dl>
*/
public class AIMReader extends FormatReader {
// -- Fields --
private long pixelOffset;
// -- Constructor --
/** Constructs a new AIM reader. */
public AIMReader() {
super("AIM", "aim");
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
}
// -- IFormatReader API methods --
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
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 + FormatTools.getPlaneSize(this) * no);
readPlane(in, x, y, w, h, buf);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
pixelOffset = 0;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
core[0].littleEndian = true;
in.order(isLittleEndian());
in.seek(56);
core[0].sizeX = in.readInt();
core[0].sizeY = in.readInt();
core[0].sizeZ = in.readInt();
core[0].sizeC = 1;
core[0].sizeT = 1;
core[0].imageCount = getSizeZ();
core[0].pixelType = FormatTools.INT16;
core[0].dimensionOrder = "XYZCT";
in.seek(160);
String processingLog = in.readCString();
pixelOffset = in.getFilePointer();
String date = null;
Double xSize = null, xLength = null;
Double ySize = null, yLength = null;
Double zSize = null, zLength = null;
String[] lines = processingLog.split("\n");
for (String line : lines) {
line = line.trim();
int split = line.indexOf(" ");
if (split > 0) {
String key = line.substring(0, split).trim();
String value = line.substring(split).trim();
addGlobalMeta(key, value);
if (key.equals("Original Creation-Date")) {
date = DateTools.formatDate(value, "dd-MMM-yyyy HH:mm:ss.SS");
}
else if (key.equals("Orig-ISQ-Dim-p")) {
String[] tokens = value.split(" ");
for (String token : tokens) {
token = token.trim();
if (token.length() > 0) {
if (xSize == null) {
xSize = new Double(token);
}
else if (ySize == null) {
ySize = new Double(token);
}
else if (zSize == null) {
zSize = new Double(token);
}
}
}
}
else if (key.equals("Orig-ISQ-Dim-um")) {
String[] tokens = value.split(" ");
for (String token : tokens) {
token = token.trim();
if (token.length() > 0) {
if (xLength == null) {
xLength = new Double(token);
}
else if (yLength == null) {
yLength = new Double(token);
}
else if (zLength == null) {
zLength = new Double(token);
}
}
}
}
}
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (date != null) {
store.setImageAcquiredDate(date, 0);
}
else MetadataTools.setDefaultCreationDate(store, id, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (xSize != null && xLength != null) {
store.setPixelsPhysicalSizeX(new PositiveFloat(xLength / xSize), 0);
}
if (ySize != null && yLength != null) {
store.setPixelsPhysicalSizeY(new PositiveFloat(yLength / ySize), 0);
}
if (zSize != null && zLength != null) {
store.setPixelsPhysicalSizeZ(new PositiveFloat(zLength / zSize), 0);
}
}
}
}