/*
* #%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.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.units.quantity.Length;
import ome.units.quantity.Time;
import ome.units.UNITS;
/**
* ImarisReader is the file format reader for Bitplane Imaris files.
* Specifications available at
* http://flash.bitplane.com/wda/interfaces/public/faqs/faqsview.cfm?inCat=0&inQuestionID=104
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class ImarisReader extends FormatReader {
// -- Constants --
/** Magic number; present in all files. */
private static final int IMARIS_MAGIC_BYTES = 5021964;
/** Specifies endianness. */
private static final boolean IS_LITTLE = false;
// -- Fields --
/** Offsets to each image. */
private int[] offsets;
// -- Constructor --
/** Constructs a new Imaris reader. */
public ImarisReader() {
super("Bitplane Imaris", "ims");
suffixSufficient = false;
domains = new String[] {FormatTools.UNKNOWN_DOMAIN};
}
// -- 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, IS_LITTLE)) {
return false;
}
return stream.readInt() == IMARIS_MAGIC_BYTES;
}
/**
* @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(offsets[no] + getSizeX() * (getSizeY() - y - h));
for (int row=h-1; row>=0; row--) {
in.skipBytes(x);
in.read(buf, row*w, w);
in.skipBytes(getSizeX() - w - x);
}
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) offsets = 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);
LOGGER.info("Verifying Imaris RAW format");
in.order(IS_LITTLE);
long magic = in.readInt();
if (magic != IMARIS_MAGIC_BYTES) {
throw new FormatException("Imaris magic number not found.");
}
LOGGER.info("Reading header");
int version = in.readInt();
in.skipBytes(4);
String imageName = in.readString(128);
CoreMetadata m = core.get(0);
m.sizeX = in.readShort();
m.sizeY = in.readShort();
m.sizeZ = in.readShort();
in.skipBytes(2);
m.sizeC = in.readInt();
in.skipBytes(2);
String date = in.readString(32);
float dx = in.readFloat();
float dy = in.readFloat();
float dz = in.readFloat();
int mag = in.readShort();
String description = in.readString(128);
int isSurvey = in.readInt();
LOGGER.info("Calculating image offsets");
m.imageCount = getSizeZ() * getSizeC();
offsets = new int[getImageCount()];
float[] gains = new float[getSizeC()];
float[] detectorOffsets = new float[getSizeC()];
float[] pinholes = new float[getSizeC()];
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
for (int i=0; i<getSizeC(); i++) {
addGlobalMeta("Channel #" + i + " Comment", in.readString(128));
gains[i] = in.readFloat();
detectorOffsets[i] = in.readFloat();
pinholes[i] = in.readFloat();
in.skipBytes(24);
}
}
int offset = 336 + (164 * getSizeC());
for (int i=0; i<getSizeC(); i++) {
for (int j=0; j<getSizeZ(); j++) {
offsets[i*getSizeZ() + j] = offset + (j * getSizeX() * getSizeY());
}
offset += getSizeX() * getSizeY() * getSizeZ();
}
addGlobalMeta("Version", version);
addGlobalMeta("Image name", imageName);
addGlobalMeta("Image comment", description);
addGlobalMeta("Survey performed", isSurvey == 0);
addGlobalMeta("Original date", date);
LOGGER.info("Populating metadata");
m.sizeT = getImageCount() / (getSizeC() * getSizeZ());
m.dimensionOrder = "XYZCT";
m.rgb = false;
m.interleaved = false;
m.littleEndian = IS_LITTLE;
m.indexed = false;
m.falseColor = false;
m.metadataComplete = true;
m.pixelType = FormatTools.UINT8;
// The metadata store we're working with.
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
// populate Image data
store.setImageName(imageName, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(description, 0);
// link Instrument and Image
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
store.setImageInstrumentRef(instrumentID, 0);
// populate Dimensions data
Length sizeX = FormatTools.getPhysicalSizeX((double) dx);
Length sizeY = FormatTools.getPhysicalSizeY((double) dy);
Length sizeZ = FormatTools.getPhysicalSizeZ((double) dz);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
if (sizeZ != null) {
store.setPixelsPhysicalSizeZ(sizeZ, 0);
}
store.setPixelsTimeIncrement(new Time(1.0, UNITS.S), 0);
// populate LogicalChannel data
for (int i=0; i<getSizeC(); i++) {
if (pinholes[i] > 0) {
store.setChannelPinholeSize(new Length(pinholes[i], UNITS.MICROM), 0, i);
}
}
// populate Detector data
for (int i=0; i<getSizeC(); i++) {
if (gains[i] > 0) {
store.setDetectorSettingsGain((double) gains[i], 0, i);
}
store.setDetectorSettingsOffset((double) offsets[i], i, 0);
// link DetectorSettings to an actual Detector
String detectorID = MetadataTools.createLSID("Detector", 0, i);
store.setDetectorID(detectorID, 0, i);
store.setDetectorType(getDetectorType("Other"), 0, i);
store.setDetectorSettingsID(detectorID, 0, i);
}
}
}
}