/*
* #%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;
/**
* AIMReader is the file format reader for .aim files.
*/
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)
*/
@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);
int planeSize = FormatTools.getPlaneSize(this);
long offset = pixelOffset + planeSize * (long) no;
if (offset < in.length()) {
in.seek(offset);
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());
// check for newer version of AIM format with wider offsets
String version = in.readString(16);
boolean widerOffsets = version.startsWith("AIMDATA_V030");
if (widerOffsets) {
in.seek(96);
m.sizeX = (int) in.readLong();
m.sizeY = (int) in.readLong();
m.sizeZ = (int) in.readLong();
in.seek(280);
}
else {
in.seek(56);
m.sizeX = in.readInt();
m.sizeY = in.readInt();
m.sizeZ = in.readInt();
in.seek(160);
}
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = getSizeZ();
m.pixelType = FormatTools.INT16;
m.dimensionOrder = "XYZCT";
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", ".");
}
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.setImageAcquisitionDate(new Timestamp(date), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (xSize != null && xLength != null) {
Double size = xLength / xSize;
Length physicalSize = FormatTools.getPhysicalSizeX(size);
if (physicalSize != null) {
store.setPixelsPhysicalSizeX(physicalSize, 0);
}
}
if (ySize != null && yLength != null) {
Double size = yLength / ySize;
Length physicalSize = FormatTools.getPhysicalSizeY(size);
if (physicalSize != null) {
store.setPixelsPhysicalSizeY(physicalSize, 0);
}
}
if (zSize != null && zLength != null) {
Double size = zLength / zSize;
Length physicalSize = FormatTools.getPhysicalSizeZ(size);
if (physicalSize != null) {
store.setPixelsPhysicalSizeZ(physicalSize, 0);
}
}
}
}
}