/*
* #%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.EOFException;
import java.io.IOException;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.Hashtable;
import java.util.Vector;
import loci.common.Constants;
import loci.common.DataTools;
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 loci.formats.MissingLibraryException;
import ome.xml.model.primitives.PositiveFloat;
import ome.units.quantity.Length;
import ome.units.quantity.Time;
import ome.units.UNITS;
import org.scijava.nativelib.NativeLibraryUtil;
/**
* SlideBook6Reader is a file format reader for 3i SlideBook SLD files that uses
* the SlideBook SBReadFile SDK via the (Windows only) dlls:
* SBReadFile.dll and SlideBook6Reader.dll
*
* @author Richard Myers, richard at intelligent-imaging.com
*
*/
public class SlideBook6Reader extends FormatReader {
// -- Constants --
public static final int SLD_MAGIC_BYTES_1_0 = 0x006c;
public static final int SLD_MAGIC_BYTES_1_1 = 0x0100;
public static final int SLD_MAGIC_BYTES_1_2 = 0x0200;
public static final int SLD_MAGIC_BYTES_2_0 = 0x01f5;
public static final int SLD_MAGIC_BYTES_2_1 = 0x0102;
public static final long SLD_MAGIC_BYTES_3 = 0xf6010101L;
private static final String URL_3I_SLD =
"http://www.openmicroscopy.org/site/support/bio-formats/formats/3i-slidebook6.html";
private static final String NO_3I_MSG = "3i SlideBook SlideBook6Reader library not found. " +
"Please see " + URL_3I_SLD + " for details.";
private static final String GENERAL_3I_MSG = "3i SlideBook SlideBook6Reader library problem. " +
"Please see " + URL_3I_SLD + " for details.";
// -- Static initializers --
private static boolean libraryFound = false;
static {
try {
// load JNI wrapper of SBReadFile.dll
NativeLibraryUtil.Architecture arch = NativeLibraryUtil.getArchitecture();
if (arch != NativeLibraryUtil.Architecture.WINDOWS_64 && arch != NativeLibraryUtil.Architecture.WINDOWS_32) {
// TODO: add compiled linux and OS X architecture libraries to class
throw new UnsatisfiedLinkError();
}
if (!libraryFound) {
libraryFound = NativeLibraryUtil.loadNativeLibrary(SlideBook6Reader.class, "SlideBook6Reader");
}
}
catch (UnsatisfiedLinkError e) {
// log level debug, otherwise a warning will be printed every time a file is initialized without the .dll present
LOGGER.debug(NO_3I_MSG, e);
libraryFound = false;
}
catch (SecurityException e) {
LOGGER.warn("Insufficient permission to load native library", e);
libraryFound = false;
}
}
// -- Constructor --
public SlideBook6Reader() {
super("SlideBook 6 SLD (native)", new String[] {"sld"});
domains = new String[] {FormatTools.LM_DOMAIN};
suffixSufficient = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 8;
stream.seek(4);
boolean littleEndian = stream.readString(2).equals("II");
if (!FormatTools.validStream(stream, blockLen, littleEndian)) return false;
int magicBytes1 = stream.readShort();
int magicBytes2 = stream.readShort();
boolean isMatch = ((magicBytes2 & 0xff00) == SLD_MAGIC_BYTES_1_1 ||
(magicBytes2 & 0xff00) == SLD_MAGIC_BYTES_1_2) &&
(magicBytes1 == SLD_MAGIC_BYTES_1_0 ||
magicBytes1 == SLD_MAGIC_BYTES_2_0);
return isMatch;
}
/* @see loci.formats.IFormatReader#isThisType(String, boolean) */
public boolean isThisType(String file, boolean open) {
// Check the first few bytes to determine if the file can be read by this reader.
return libraryFound && super.isThisType(file, open);
}
/**
* @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);
int[] zct = FormatTools.getZCTCoords(this, no);
int bpc = FormatTools.getBytesPerPixel(getPixelType());
byte[] b = new byte[FormatTools.getPlaneSize(this)];
readImagePlaneBuf(b, getSeries(), 0, zct[2], zct[0], zct[1]);
int pixel = bpc * getRGBChannelCount();
int rowLen = w * pixel;
for (int row=0; row<h; row++) {
System.arraycopy(b, pixel * ((row + y) * getSizeX() + x), buf,
row * rowLen, rowLen);
}
if (isRGB()) {
int bpp = getSizeC() * bpc;
int line = w * bpp;
for (int row=0; row<h; row++) {
for (int col=0; col<w; col++) {
int base = row * line + col * bpp;
for (int bb=0; bb<bpc; bb++) {
byte blue = buf[base + bpc*(getSizeC() - 1) + bb];
buf[base + bpc*(getSizeC() - 1) + bb] = buf[base + bb];
buf[base + bb] = blue;
}
}
}
}
return buf;
}
// -- Internal FormatReader API methods --
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (libraryFound) {
closeFile();
}
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
try {
openFile(id);
// read basic meta data
int numCaptures = getNumCaptures();
int[] numPositions = new int[numCaptures];
int[] numTimepoints = new int[numCaptures];
int[] numZPlanes = new int[numCaptures];
int[] numChannels = new int[numCaptures];
for (int capture=0; capture < numCaptures; capture++) {
numPositions[capture] = getNumPositions(capture);
numTimepoints[capture] = getNumTimepoints(capture) / numPositions[capture];
numZPlanes[capture] = getNumZPlanes(capture);
numChannels[capture] = getNumChannels(capture);
}
core.clear();
// set up basic meta data
for (int capture=0; capture < numCaptures; capture++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);
setSeries(capture);
ms.sizeX = getNumXColumns(capture);
if (ms.sizeX % 2 != 0) ms.sizeX++;
ms.sizeY = getNumYRows(capture);
ms.sizeZ = numZPlanes[capture];
ms.sizeT = numTimepoints[capture] * numPositions[capture];
ms.sizeC = numChannels[capture];
int bytes = getBytesPerPixel(capture);
if (bytes % 3 == 0) {
ms.sizeC *= 3;
bytes /= 3;
ms.rgb = true;
}
else ms.rgb = false;
ms.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, true);
ms.imageCount = ms.sizeZ * ms.sizeT;
if (!ms.rgb)
ms.imageCount *= ms.sizeC;
ms.interleaved = true;
ms.littleEndian = true;
ms.dimensionOrder = "XYCZT";
ms.indexed = false;
ms.falseColor = false;
}
setSeries(0);
// fill in meta data
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
// add extended meta data
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
// set instrument information
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
// set up extended meta data
for (int capture=0; capture < numCaptures; capture++) {
// link Instrument and Image
store.setImageInstrumentRef(instrumentID, capture);
// set image name
String imageName = getImageName(capture);
store.setImageName(imageName, capture);
// store.setImageName("Image " + (capture + 1), capture);
// set description
String imageDescription = getImageComments(capture);
store.setImageDescription(imageDescription, capture);
// set voxel size per image (microns)
double voxelsize = getVoxelSize(capture);
Length physicalSizeX = FormatTools.getPhysicalSizeX(voxelsize);
Length physicalSizeY = FormatTools.getPhysicalSizeY(voxelsize);
if (physicalSizeX != null) {
store.setPixelsPhysicalSizeX(physicalSizeX, capture);
}
if (physicalSizeY != null) {
store.setPixelsPhysicalSizeY(physicalSizeY, capture);
}
double stepSize = 0;
if (numZPlanes[capture] > 1) {
double plane0 = getZPosition(capture, 0, 0);
double plane1 = getZPosition(capture, 0, getNumChannels(capture));
// distance between plane 0 and 1 is step size, assume constant for all planes
stepSize = plane1 - plane0;
}
Length physicalSizeZ = FormatTools.getPhysicalSizeZ(stepSize);
if (physicalSizeZ != null) {
store.setPixelsPhysicalSizeZ(physicalSizeZ, capture);
}
int imageIndex = 0;
// if numPositions[capture] > 1 then we have a montage
for (int timepoint = 0; timepoint < numTimepoints[capture]; timepoint++) {
int deltaT = getElapsedTime(capture, timepoint);
for (int position = 0; position < numPositions[capture]; position++) {
for (int zplane = 0; zplane < numZPlanes[capture]; zplane++) {
for (int channel = 0; channel < numChannels[capture]; channel++, imageIndex++) {
// set elapsed time
store.setPlaneDeltaT(new Time(deltaT, UNITS.MS), capture, imageIndex);
// set exposure time
int expTime = getExposureTime(capture, channel);
store.setPlaneExposureTime(new Time(expTime, UNITS.MS), capture, imageIndex);
// set tile xy position
double numberX = getXPosition(capture, position);
Length positionX = new Length(numberX, UNITS.MICROM);
store.setPlanePositionX(positionX, capture, imageIndex);
double numberY = getYPosition(capture, position);
Length positionY = new Length(numberY, UNITS.MICROM);
store.setPlanePositionY(positionY, capture, imageIndex);
// set tile z position
double positionZ = getZPosition(capture, position, zplane);
Length zPos = new Length(positionZ, UNITS.MICROM);
store.setPlanePositionZ(zPos, capture, imageIndex);
}
}
}
}
// set channel names
for (int channel = 0; channel < numChannels[capture]; channel++) {
String theChannelName = getChannelName(capture, channel);
store.setChannelName(theChannelName.trim(), capture, channel);
}
}
// populate Objective data
int objectiveIndex = 0;
for (int capture = 0; capture < numCaptures; capture++) {
// link Objective to Image
String objectiveID = MetadataTools.createLSID("Objective", 0, objectiveIndex);
store.setObjectiveID(objectiveID, 0, objectiveIndex);
store.setObjectiveSettingsID(objectiveID, capture);
String objective = getLensName(capture);
if (objective != null) {
store.setObjectiveModel(objective, 0, objectiveIndex);
}
store.setObjectiveCorrection(getCorrection("Other"), 0, objectiveIndex);
store.setObjectiveImmersion(getImmersion("Other"), 0, objectiveIndex);
double magnification = getMagnification(capture);
if (magnification > 0) {
store.setObjectiveNominalMagnification(magnification, 0, objectiveIndex);
}
objectiveIndex++;
}
}
}
catch (UnsatisfiedLinkError e) {
throw new MissingLibraryException(GENERAL_3I_MSG, e);
}
catch (Exception e) {
throw new MissingLibraryException(GENERAL_3I_MSG, e);
}
}
// -- Native methods --
public native boolean openFile(String path);
public native void closeFile();
public native int getNumCaptures();
public native int getNumPositions(int inCapture);
public native int getNumTimepoints(int inCapture);
public native int getNumChannels(int inCapture);
public native int getNumXColumns(int inCapture);
public native int getNumYRows(int inCapture);
public native int getNumZPlanes(int inCapture);
public native int getElapsedTime(int inCapture, int inTimepoint);
public native int getExposureTime(int inCapture, int inChannel);
public native float getVoxelSize(int inCapture);
public native double getXPosition(int inCapture, int inPosition);
public native double getYPosition(int inCapture, int inPosition);
public native double getZPosition(int inCapture, int inPosition, int inZPlane);
public native int getMontageRow(int inCapture, int inPosition);
public native int getMontageColumn(int inCapture, int inPosition);
public native String getChannelName(int inCapture, int inChannel);
public native String getLensName(int inCapture);
public native double getMagnification(int inCapture);
public native String getImageName(int inCapture);
public native String getImageComments(int inCapture);
public native int getBytesPerPixel(int inCapture);
public native boolean readImagePlaneBuf( byte outPlaneBuffer[],
int inCapture,
int inPosition,
int inTimepoint,
int inZ,
int inChannel );
}