/*
* #%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 java.util.ArrayList;
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;
/**
* ImspectorReader is the file format reader for Imspector .msr files.
*/
public class ImspectorReader extends FormatReader {
// -- Constants --
/** The header for each file contains this string. */
private static final String MAGIC_STRING = "CDataStack";
// -- Fields --
/** List of offsets to each block of pixel data. */
private ArrayList<Long> pixelsOffsets = new ArrayList<Long>();
/** List of PMTs active during acquisition. */
private ArrayList<String> uniquePMTs = new ArrayList<String>();
/**
* Number of planes in each block of pixel data. The blocks will
* often (though not always) be of equal size.
*/
private ArrayList<Integer> planesPerBlock = new ArrayList<Integer>();
/** Whether or not this file contains FLIM data. */
private boolean isFLIM = false;
/** The number of mosaic tiles stored in the file. */
private int tileCount = 1;
// -- Constructor --
/** Constructs a new Imspector reader. */
public ImspectorReader() {
super("Lavision Imspector", "msr");
domains = new String[] {FormatTools.FLIM_DOMAIN};
suffixSufficient = false;
}
// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
final int blockLen = 32;
if (!FormatTools.validStream(stream, blockLen, false)) return false;
return (stream.readString(blockLen)).indexOf(MAGIC_STRING) >= 0;
}
/**
* @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);
// calculate the block index from the series and image numbers
int index = 0;
for (int i=0; i<getSeries(); i++) {
index += core.get(i).imageCount;
}
index += no;
int[] zct = getZCTCoords(no);
int block = getSeries() * getSizeC() + zct[1];
int plane = getIndex(zct[0], 0, zct[2]);
if (plane < planesPerBlock.get(block)) {
in.seek(pixelsOffsets.get(block) + FormatTools.getPlaneSize(this) * plane);
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) {
pixelsOffsets.clear();
uniquePMTs.clear();
planesPerBlock.clear();
isFLIM = false;
tileCount = 1;
}
}
// -- 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);
// pixel data is stored uncompressed in blocks of one or more planes
// as far as we know, pixels are always little-endian unsigned 16-bit
m.littleEndian = true;
in.order(isLittleEndian());
in.skipBytes(20);
int length = in.readShort();
String tag = in.readString(length);
int count = in.readInt();
skipTags(count);
if (in.getFilePointer() % 2 == 1) {
in.skipBytes(1);
}
else {
int check = in.read() & 0xff;
if (check != 0xff) {
in.seek(in.getFilePointer() - 1);
}
}
length = in.readShort();
String metadata = in.readString(length);
String[] values = metadata.split("::");
// Correct alignment when length is an even number of bytes
if (length % 2 == 0) {
if (in.read() != 13) {
in.seek(in.getFilePointer() - 1);
}
}
int check = in.readShort();
while (check != 3 && check != 2) {
check = in.readShort();
}
in.skipBytes(26);
int pmtMarkerLength = in.read();
String pmtMarker = in.readString(pmtMarkerLength);
uniquePMTs.add(pmtMarker);
in.skipBytes(6);
m.sizeX = in.readInt();
m.sizeY = in.readInt();
m.sizeZ = in.readInt();
m.sizeT = in.readInt();
planesPerBlock.add(m.sizeT * m.sizeZ);
in.skipBytes(16);
for (int i=0; i<4; i++) {
int len = in.read();
String pmtSetting = in.readString(len);
}
pixelsOffsets.add(in.getFilePointer());
for (int i=0; i<values.length-1; i+=2) {
addGlobalMeta(values[i], values[i + 1]);
if (values[i].equals("Instrument Mode")) {
isFLIM =
values[i + 1].startsWith("TCSPC") || values[i + 1].startsWith("FLIM");
}
}
m.pixelType = FormatTools.UINT16;
int bpp = FormatTools.getBytesPerPixel(m.pixelType);
in.skipBytes(m.sizeX * m.sizeY * planesPerBlock.get(0) * bpp + 2);
int tileX = 1;
int tileY = 1;
double timeBase = 1.0;
// read through the file looking for metadata and pixels offsets
// 0x8003 and 0xffff appear to be special markers for metadata sections
while (in.getFilePointer() < in.length()) {
check = in.readShort() & 0xffff;
if (check != 0x8003) {
in.skipBytes(2);
length = in.readShort();
}
else {
length = in.read() & 0xff;
}
if (length == 0 && check == 65535) {
in.skipBytes(46);
skipTagBlock();
in.skipBytes(50);
findOffset();
continue;
}
else if (length == 3 && check == 65535) {
in.seek(in.getFilePointer() - 2);
findOffset(false);
continue;
}
if (length < 0) {
continue;
}
tag = in.readString(length);
while (in.getFilePointer() < in.length()) {
if (tag.equals("CImageStack")) {
readStackHeader();
in.skipBytes(60);
while ((in.read() & 0xff) != 0xff);
length = in.readShort();
if (length == 0) {
in.skipBytes(1);
if ((in.read() & 0xff) == 0xff) {
length = in.readShort();
}
else {
in.seek(in.getFilePointer() - 1);
length = in.readShort();
in.skipBytes(length - 2);
break;
}
}
in.skipBytes(length + 50);
findOffset();
break;
}
else if (tag.equals("Label")) {
in.skipBytes(4);
}
length = in.read();
if (length < 0) {
break;
}
String key = in.readString(length);
int type = in.readInt();
String value = null;
if (type == 5) {
length = in.read();
if (length == 0) {
in.skipBytes(4);
length = in.read();
}
value = in.readString(length);
}
else if (type > 0xffff && type != 0x80000) {
in.seek(in.getFilePointer() - 2);
value = String.valueOf(in.readDouble());
}
else {
length = in.read();
value = in.readString(length);
}
if (tag.equals("Label")) {
in.skipBytes(350);
findOffset();
break;
}
int valueType = in.readShort();
int valueLen = in.readShort();
int check1 = 0, check2 = 0;
// type codes were determined by trial and error, and may not be correct
switch (valueType) {
case 10:
case 11:
case 12:
key = value;
value = String.valueOf(in.readInt() == 1);
break;
case 2:
case 9:
case 13:
case 14:
key = value;
value = String.valueOf(in.readFloat());
break;
case 0:
case 1:
case 4:
case 5:
case 6:
case 8:
key = value;
value = String.valueOf(in.readInt());
break;
default:
LOGGER.debug("found type {}", valueType);
check1 = valueType;
check2 = valueLen;
}
// parse the tile dimensions, if present
if (key.equals("Stitching X")) {
try {
tileX = Integer.parseInt(value);
}
catch (NumberFormatException e) { }
}
else if (key.equals("Stitching Y")) {
try {
tileY = Integer.parseInt(value);
}
catch (NumberFormatException e) { }
}
check1 = in.readShort();
check2 = in.readShort();
// read the real value
// ends with 0x03, 0x80
if (check1 == 0 && check2 == 8) {
if (in.readShort() != 0x8003) {
in.seek(in.getFilePointer() - 2);
int v = in.readInt();
if (v < 0xffff) {
value = String.valueOf(v);
if (key.equals("StitchingX")) {
tileX = v;
}
else if (key.equals("StitchingY")) {
tileY = v;
}
}
else {
in.seek(in.getFilePointer() - 4);
}
}
else {
in.seek(in.getFilePointer() - 2);
}
}
else {
in.seek(in.getFilePointer() - 4);
}
// find the end of this metadata section
check1 = in.read() & 0xff;
check2 = in.read() & 0xff;
while (!(check1 == 3 && check2 == 128) &&
!(type == 5 && check1 == 255 && check2 == 255) &&
in.getFilePointer() < in.length())
{
check1 = check2;
check2 = in.read() & 0xff;
}
addGlobalMeta(key, value);
if (key.equals("TCSPC Z Length")) {
try {
timeBase = Double.parseDouble(value);
}
catch (NumberFormatException e) { }
}
if (check1 == 255 && check2 == 255) {
in.seek(in.getFilePointer() - 2);
break;
}
}
}
for (Integer blockSize : planesPerBlock) {
m.imageCount += blockSize;
}
if (isFLIM) {
if (getSizeZ() == 1 || getSizeT() == 1) {
m.sizeZ = 1;
m.sizeT = m.imageCount;
}
LOGGER.debug("m.imageCount = {}", m.imageCount);
m.moduloT.parentType = FormatTools.SPECTRA;
m.moduloT.type = FormatTools.LIFETIME;
m.sizeC = m.imageCount / (m.sizeZ * m.sizeT);
if (getSizeZ() > 1 && getSizeT() > 1) {
m.dimensionOrder = "XYTZC";
}
else {
m.dimensionOrder = "XYZTC";
}
// convert time base to picoseconds
if (timeBase > 1) {
timeBase *= 1000;
}
m.moduloT.step = timeBase / m.sizeT;
m.moduloT.end = m.moduloT.step * (m.sizeT - 1);
m.moduloT.unit = "ps";
m.moduloT.typeDescription = "TCSPC";
}
else {
if (uniquePMTs.size() <= pixelsOffsets.size()) {
m.sizeC = uniquePMTs.size();
}
else {
m.sizeC = 1;
}
if (m.imageCount != m.sizeZ * m.sizeC * m.sizeT) {
if (planesPerBlock.size() > 1) {
m.sizeZ = 1;
for (Integer block : planesPerBlock) {
if (block > m.sizeZ) {
m.sizeZ = block;
}
}
m.imageCount = m.sizeZ * m.sizeC * m.sizeT;
}
else {
m.sizeZ = m.imageCount / m.sizeC;
m.sizeT = m.imageCount / (m.sizeZ * m.sizeC);
}
}
if (m.sizeC > 1 && m.sizeT != 1) {
m.dimensionOrder = "XYZTC";
}
else {
m.dimensionOrder = "XYZCT";
}
}
tileCount = tileX * tileY;
// correct the tile count if it doesn't make sense
// the count may have been incorrectly recorded or parsed
if (tileCount == 0 || (m.imageCount % tileCount) != 0) {
tileCount = 1;
}
// recalculate image counts based upon the tile count
// tiles are assumed to have the same dimensions
if (tileCount > 1) {
m.imageCount /= tileCount;
if (m.sizeT >= tileCount) {
m.sizeT /= tileCount;
}
else if (m.sizeC >= tileCount) {
m.sizeC /= tileCount;
}
else {
m.sizeZ /= tileCount;
}
for (int i=1; i<tileCount; i++) {
core.add(m);
}
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
/** Read the header for an image stack. */
private void readStackHeader() throws IOException {
int count = in.readInt();
if (count > 0xffff) {
in.seek(in.getFilePointer() - 2);
int len = in.readShort();
in.skipBytes(len);
count = in.readInt() + 1;
}
skipTags(count);
skipTagBlock();
}
/** Skip a block of unknown string values. */
private void skipTags(int count) throws IOException {
for (int i=0; i<count; i++) {
int length = in.read();
if (length == 0) {
i--;
}
if (length < 0) {
return;
}
String tag = in.readString(length);
}
}
/** Skip an unknown tag. */
private void skipTagBlock() throws IOException {
in.skipBytes(1);
int length = in.readShort();
in.skipBytes(length);
}
/** Find the offset to the next block of pixel data. */
private void findOffset() throws IOException {
findOffset(true);
}
private void findOffset(boolean readStackHeader) throws IOException {
if (readStackHeader) {
readStackHeader();
}
int pmtCheck = in.readShort();
while (pmtCheck != 3 && pmtCheck != 2) {
in.seek(in.getFilePointer() - 1);
pmtCheck = in.readShort();
if (pmtCheck == 2) {
if (in.readShort() == 0) {
in.seek(in.getFilePointer() - 2);
}
else {
pmtCheck = 0;
}
}
}
in.skipBytes(26);
int len = in.read();
if (len < 0) {
return;
}
String pmt = in.readString(len);
// as far as we know, valid PMT names only start with "PMT" or "TCSPC",
// depending upon the acquisition mode
if (!uniquePMTs.contains(pmt) && (pmt.startsWith("PMT") ||
pmt.startsWith("TCSPC")))
{
uniquePMTs.add(pmt);
}
boolean noPMT = len == 0;
CoreMetadata m = core.get(0);
in.skipBytes(14);
int newT = in.readInt();
int newZ = in.readInt();
long planeSize = (long) getSizeX() * getSizeY() * FormatTools.getBytesPerPixel(getPixelType());
long newCount = (long) newZ * newT;
if (newZ > getSizeZ() && newT > getSizeT() &&
newCount * planeSize < in.length() - in.getFilePointer() &&
newCount > 0 && newCount * planeSize > 0)
{
planesPerBlock.remove(planesPerBlock.size() - 1);
pixelsOffsets.remove(pixelsOffsets.size() - 1);
m.sizeZ = newZ;
m.sizeT = newT;
}
planesPerBlock.add(newZ * newT);
in.skipBytes(noPMT ? 12 : 16);
for (int i=0; i<4; i++) {
len = in.read();
if (len < 0) {
noPMT = true;
break;
}
String pmtSetting = in.readString(len);
}
if (noPMT) {
while ((in.readShort() & 0xffff) != 0x8003);
in.seek(in.getFilePointer() - 2);
planesPerBlock.remove(planesPerBlock.size() - 1);
return;
}
planeSize = (long) m.sizeX * m.sizeY *
planesPerBlock.get(planesPerBlock.size() - 1) * 2;
if (planeSize > 0 && in.getFilePointer() + planeSize < in.length()) {
pixelsOffsets.add(in.getFilePointer());
in.skipBytes((int) planeSize + 2);
}
else {
planesPerBlock.remove(planesPerBlock.size() - 1);
}
}
}