/*
* #%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 ome.xml.model.primitives.Timestamp;
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.units.quantity.Length;
import ome.units.UNITS;
/**
* GatanDM2Reader is the file format reader for Gatan .dm2 files.
*/
public class GatanDM2Reader extends FormatReader {
// -- Constants --
private static final int HEADER_SIZE = 24;
private static final int DM2_MAGIC_BYTES = 0x3d0000;
// -- Fields --
private Double pixelSizeX;
private Double pixelSizeY;
private String pixelSizeUnits;
// -- Constructor --
/** Constructs a new Gatan .dm2 reader. */
public GatanDM2Reader() {
super("Gatan DM2", "dm2");
domains = new String[] {FormatTools.SPM_DOMAIN};
suffixNecessary = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 4;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return stream.readInt() == DM2_MAGIC_BYTES;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
pixelSizeX = null;
pixelSizeY = null;
pixelSizeUnits = null;
}
}
/**
* @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(HEADER_SIZE);
readPlane(in, x, y, w, h, buf);
return buf;
}
// -- 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);
in.setEncoding("ISO-8859-1");
int magicBytes = in.readInt();
if (magicBytes != DM2_MAGIC_BYTES) {
throw new FormatException("Invalid DM2 file");
}
in.skipBytes(8);
long footerOffset = in.readInt() + 16;
CoreMetadata m = core.get(0);
m.sizeX = in.readShort();
m.sizeY = in.readShort();
int bpp = in.readShort();
boolean signed = in.readShort() == 1;
m.pixelType = FormatTools.pixelTypeFromBytes(bpp, signed, true);
m.sizeC = 1;
m.sizeT = 1;
m.sizeZ = 1;
m.imageCount = 1;
m.dimensionOrder = "XYZCT";
m.littleEndian = false;
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
store.setImageInstrumentRef(instrumentID, 0);
String date = null, time = null, name = null;
in.skipBytes(FormatTools.getPlaneSize(this) + 35);
MetadataLevel level = getMetadataOptions().getMetadataLevel();
while (in.getFilePointer() < in.length()) {
if (level == MetadataLevel.MINIMUM && date != null &&
time != null && name != null)
{
break;
}
int strlen = in.readShort();
if (strlen == 0 || strlen > 255) {
in.skipBytes(35);
strlen = in.readShort();
if (strlen < 0 || strlen + in.getFilePointer() >= in.length()) {
in.seek(in.getFilePointer() - 10);
strlen = in.readShort();
}
}
if (strlen < 0 || strlen + in.getFilePointer() >= in.length()) break;
String label = in.readString(strlen);
StringBuffer value = new StringBuffer();
int block = in.readInt();
if (block == 5) {
in.skipBytes(33);
if (in.readShort() == 0) {
if (in.readShort() == 39) {
in.skipBytes(1);
}
else {
in.skipBytes(2);
}
}
else {
in.seek(in.getFilePointer() - 2);
continue;
}
}
else if (block == 0 || (block > 0xffff && block < 0x01000000)) {
if (block != 0 && strlen > 0) {
in.seek(in.getFilePointer() - 4);
value.append(label);
label = "Description";
addGlobalMeta(label, value.toString());
}
else if (block != 0) {
in.skipBytes(15);
}
parseExtraTags();
continue;
}
else if (block >= 0x01000000) {
in.skipBytes(34);
strlen = in.readShort();
if (strlen + in.getFilePointer() >= in.length()) {
break;
}
label = in.readString(strlen);
block = in.readInt();
if (block == 5) {
in.skipBytes(33);
continue;
}
}
int len = in.readInt();
if (len + in.getFilePointer() >= in.length() || len < 0) break;
String type = in.readString(len);
int extra = in.readInt() - 2;
int count = in.readInt();
if (type.equals("TEXT")) {
value.append(in.readString(count));
if (block == 5) {
in.skipBytes(22);
if (in.readInt() == 4) {
if (in.readString(4).equals("TEXT")) {
in.skipBytes(4);
count = in.readInt();
value.append(", " + in.readString(count));
in.skipBytes(37);
}
else {
in.skipBytes(7);
}
}
else {
in.skipBytes(11);
}
}
}
else if (type.equals("long")) {
count /= 8;
for (int i=0; i<count; i++) {
value.append(in.readLong());
if (i < count - 1) value.append(", ");
}
in.skipBytes(4);
}
else if (type.equals("bool")) {
for (int i=0; i<count; i++) {
value.append(in.read() == 1);
if (i < count - 1) value.append(", ");
}
}
else if (type.equals("shor")) {
count /= 2;
for (int i=0; i<count; i++) {
value.append(in.readShort());
if (i < count - 1) value.append(", ");
}
}
else if (type.equals("sing")) {
count /= 4;
for (int i=0; i<count; i++) {
value.append(in.readFloat());
if (i < count - 1) value.append(", ");
}
}
else {
if (count < 0 || count + in.getFilePointer() > in.length()) {
break;
}
in.skipBytes(count);
}
in.skipBytes(16);
addGlobalMeta(label, value.toString());
if (label.equals("Acquisition Date")) {
date = value.toString();
if (date != null && date.indexOf("/") != -1) {
// if the year is stored as a single digit, then it will be parsed
// literally, e.g. '7' -> '0007', when we want '7' -> '2007'
String year = date.substring(date.lastIndexOf("/") + 1);
if (year.length() < 2) {
year = "0" + year;
}
date = date.substring(0, date.lastIndexOf("/") + 1) + year;
}
}
else if (label.equals("Acquisition Time")) {
time = value.toString();
}
else if (label.equals("Binning")) {
int bin = (int) Double.parseDouble(value.toString());
store.setDetectorSettingsBinning(getBinning(bin + "x" + bin), 0, 0);
String detectorID = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detectorID, 0, 0);
store.setDetectorSettingsID(detectorID, 0, 0);
}
else if (label.equals("Name")) {
name = value.toString();
}
else if (label.equals("Operator")) {
String[] experimenterName = value.toString().split(" ");
store.setExperimenterFirstName(experimenterName[0], 0);
if (experimenterName.length > 1) {
store.setExperimenterLastName(experimenterName[1], 0);
}
String expID = MetadataTools.createLSID("Experimenter", 0);
store.setExperimenterID(expID, 0);
store.setImageExperimenterRef(expID, 0);
}
}
if (date != null && time != null) {
String[] format = new String[] {
"M/d/yy h:mm:ss a", "d/M/yy h:mm:ss a",
"M/d/yy H:mm:ss", "d/M/yy H:mm:ss"};
date += " " + time;
date = DateTools.formatDate(date, format);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
if (name != null) {
store.setImageName(name, 0);
}
if (pixelSizeX != null) {
store.setPixelsPhysicalSizeX(FormatTools.createLength(pixelSizeX, UNITS.MICROM), 0);
}
if (pixelSizeY != null) {
store.setPixelsPhysicalSizeY(FormatTools.createLength(pixelSizeY, UNITS.MICROM), 0);
}
}
// -- Helper methods --
private void parseExtraTags() throws IOException {
while (in.getFilePointer() < in.length()) {
int tag = in.readShort();
int length = in.readInt();
String value = "foo";
if (length == 4) {
value = String.valueOf(in.readFloat());
}
else if (length == 2) {
value = String.valueOf(in.readShort());
}
else if (length == 1) {
value = String.valueOf(in.read());
}
else {
value = in.readString(length);
int nullIndex = value.indexOf("\0");
if (nullIndex >= 0) {
value = value.substring(0, nullIndex);
}
}
value = value.trim();
String label = "Tag " + Integer.toHexString(tag);
switch (tag) {
case 17:
label = "BlackContrastLimit";
break;
case 18:
label = "WhiteContrastLimit";
break;
case 22:
label = "Scale";
break;
case 27:
label = "MaxPixelValue";
break;
case 28:
label = "MinPixelValue";
break;
case 31:
label = "Physical width";
pixelSizeX = new Double(value);
break;
case 32:
label = "Physical height";
pixelSizeY = new Double(value);
break;
case 37:
label = "Image label";
break;
case 38:
label = "MinimumContrast";
break;
case 53:
label = "Physical size units";
pixelSizeUnits = value;
break;
case 62:
label = "Origin";
break;
}
addGlobalMeta(label, value);
}
if (pixelSizeUnits != null && !pixelSizeUnits.equals("µm")) {
LOGGER.warn("Unsupported units: " + pixelSizeUnits);
}
}
}