/*
* #%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.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import loci.common.Constants;
import loci.common.DataTools;
import loci.common.DateTools;
import loci.common.Location;
import loci.common.RandomAccessInputStream;
import loci.common.services.DependencyException;
import loci.common.services.ServiceFactory;
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.services.POIService;
import loci.formats.tiff.IFD;
import loci.formats.tiff.TiffParser;
import ome.xml.model.enums.Binning;
import ome.xml.model.primitives.PositiveFloat;
import ome.xml.model.primitives.Timestamp;
import ome.units.quantity.Length;
import ome.units.quantity.Time;
import ome.units.UNITS;
/**
* PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
*
* @author Melissa Linkert melissa at glencoesoftware.com
*/
public class PCIReader extends FormatReader {
// -- Constants --
public static final int PCI_MAGIC_BYTES = 0xd0cf11e0;
// -- Fields --
private HashMap<Integer, String> imageFiles;
private transient POIService poi;
private HashMap<Integer, Double> timestamps;
private String creationDate;
private int binning;
private List<Double> uniqueZ;
// -- Constructor --
/** Constructs a new SimplePCI reader. */
public PCIReader() {
super("Compix Simple-PCI", "cxd");
domains = new String[] {FormatTools.LM_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, false)) return false;
return stream.readInt() == PCI_MAGIC_BYTES;
}
/* @see loci.formats.IFormatReader#getOptimalTileWidth() */
@Override
public int getOptimalTileWidth() {
FormatTools.assertId(currentId, true, 1);
String file = imageFiles.get(0);
try {
if (poi == null) {
initPOIService();
}
RandomAccessInputStream s = poi.getDocumentStream(file);
TiffParser tp = new TiffParser(s);
if (tp.isValidHeader()) {
IFD ifd = tp.getFirstIFD();
s.close();
return (int) ifd.getTileWidth();
}
s.close();
}
catch (FormatException e) {
LOGGER.debug("Could not retrieve tile width", e);
}
catch (IOException e) {
LOGGER.debug("Could not retrieve tile width", e);
}
return super.getOptimalTileWidth();
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
@Override
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
String file = imageFiles.get(0);
try {
if (poi == null) {
initPOIService();
}
RandomAccessInputStream s = poi.getDocumentStream(file);
TiffParser tp = new TiffParser(s);
if (tp.isValidHeader()) {
IFD ifd = tp.getFirstIFD();
s.close();
return (int) ifd.getTileLength();
}
s.close();
}
catch (FormatException e) {
LOGGER.debug("Could not retrieve tile height", e);
}
catch (IOException e) {
LOGGER.debug("Could not retrieve tile height", e);
}
return super.getOptimalTileHeight();
}
/**
* @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);
if (poi == null) {
initPOIService();
}
String file = imageFiles.get(no);
RandomAccessInputStream s = poi.getDocumentStream(file);
TiffParser tp = new TiffParser(s);
// can be raw pixel data or an embedded TIFF file
if (tp.isValidHeader()) {
IFD ifd = tp.getFirstIFD();
tp.getSamples(ifd, buf, x, y, w, h);
}
else {
s.seek(0);
readPlane(s, x, y, w, h, buf);
}
s.close();
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
imageFiles = null;
timestamps = null;
if (poi != null) poi.close();
poi = null;
binning = 0;
creationDate = null;
uniqueZ = null;
}
}
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
imageFiles = new HashMap<Integer, String>();
timestamps = new HashMap<Integer, Double>();
uniqueZ = new ArrayList<Double>();
CoreMetadata m = core.get(0);
initPOIService();
double scaleFactor = 1;
final List<String> allFiles = poi.getDocumentList();
if (allFiles.isEmpty()) {
throw new FormatException(
"No files were found - the .cxd may be corrupt.");
}
double firstZ = 0d, secondZ = 0d;
int mode = 0;
for (String name : allFiles) {
int separator = name.lastIndexOf(File.separator);
String parent = name.substring(0, separator);
String relativePath = name.substring(separator + 1);
RandomAccessInputStream stream = null;
if (!(relativePath.startsWith("Bitmap") ||
(relativePath.equals("Data") && parent.indexOf("Image") != -1)))
{
stream = poi.getDocumentStream(name);
stream.order(true);
}
if (stream != null && stream.length() == 8) {
double value = stream.readDouble();
stream.seek(0);
String key = name.replace(File.separatorChar, ' ');
key = key.replaceAll("Root Entry ", "");
key = key.replaceAll("Field Data ", "");
key = key.replaceAll("Details ", "");
addGlobalMeta(key, value);
}
if (relativePath.equals("Field Count")) {
m.imageCount = stream.readInt();
}
else if (relativePath.equals("File Has Image")) {
if (stream.readShort() == 0) {
throw new FormatException("This file does not contain image data.");
}
}
else if (relativePath.startsWith("Bitmap") ||
(relativePath.equals("Data") && parent.indexOf("Image") != -1))
{
imageFiles.put(imageFiles.size(), name);
if (getSizeX() != 0 && getSizeY() != 0) {
int bpp = FormatTools.getBytesPerPixel(getPixelType());
int plane = getSizeX() * getSizeY() * bpp;
if (getSizeC() == 0 || getSizeC() * plane > poi.getFileSize(name)) {
m.sizeC = poi.getFileSize(name) / plane;
}
}
}
else if (relativePath.indexOf("Image_Depth") != -1) {
boolean firstBits = m.bitsPerPixel == 0;
int bits = (int) stream.readDouble();
m.bitsPerPixel = bits;
while (bits % 8 != 0 || bits == 0) bits++;
if (bits % 3 == 0) {
m.sizeC = 3;
bits /= 3;
m.bitsPerPixel /= 3;
}
bits /= 8;
m.pixelType = FormatTools.pixelTypeFromBytes(bits, false, false);
if (getSizeC() > 1 && firstBits) {
m.sizeC /= bits;
}
}
else if (relativePath.indexOf("Image_Height") != -1 && getSizeY() == 0) {
m.sizeY = (int) stream.readDouble();
}
else if (relativePath.indexOf("Image_Width") != -1 && getSizeX() == 0) {
m.sizeX = (int) stream.readDouble();
}
else if (relativePath.indexOf("Time_From_Start") != -1) {
timestamps.put(getTimestampIndex(parent), stream.readDouble());
}
else if (relativePath.indexOf("Position_Z") != -1) {
double zPos = stream.readDouble();
if (!uniqueZ.contains(zPos) && getSizeZ() <= 1)
{
uniqueZ.add(zPos);
}
if (name.indexOf("Field 1" + File.separator) != -1) firstZ = zPos;
else if (name.indexOf("Field 2" + File.separator) != -1) secondZ = zPos;
}
else if (relativePath.equals("First Field Date & Time")) {
long date = (long) stream.readDouble() * 1000;
creationDate = DateTools.convertDate(date, DateTools.COBOL);
}
else if (relativePath.equals("GroupMode")) {
mode = stream.readInt();
}
else if (relativePath.equals("GroupSelectedFields")) {
m.sizeZ = (int) (stream.length() / 8);
}
else if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM)
{
if (relativePath.equals("Binning")) {
binning = (int) stream.readDouble();
}
else if (relativePath.equals("Comments")) {
String comments = stream.readString((int) stream.length());
String[] lines = comments.split("\n");
for (String line : lines) {
int eq = line.indexOf("=");
if (eq != -1) {
String key = line.substring(0, eq).trim();
String value = line.substring(eq + 1).trim();
addGlobalMeta(key, value);
if (key.equals("factor")) {
if (value.indexOf(";") != -1) {
value = value.substring(0, value.indexOf(";"));
}
scaleFactor = Double.parseDouble(value.trim());
}
}
}
}
}
if (stream != null) {
stream.close();
}
}
boolean zFirst = Math.abs(firstZ - secondZ) > Constants.EPSILON;
if (getSizeC() == 0) m.sizeC = 1;
if (mode == 0) {
m.sizeZ = 0;
}
if (getSizeZ() <= 1 || (getImageCount() % getSizeZ()) != 0) {
m.sizeZ = uniqueZ.isEmpty() ? 1 : uniqueZ.size();
}
m.sizeT = getImageCount() / getSizeZ();
while (getSizeZ() * getSizeT() < getImageCount()) {
m.sizeZ++;
m.sizeT = getImageCount() / getSizeZ();
}
m.rgb = getSizeC() > 1;
if (imageFiles.size() > getImageCount() && getSizeC() == 1) {
m.sizeC = imageFiles.size() / getImageCount();
m.imageCount *= getSizeC();
}
else {
m.imageCount = getSizeZ() * getSizeT();
}
m.interleaved = false;
m.dimensionOrder = zFirst ? "XYCZT" : "XYCTZ";
m.littleEndian = true;
m.indexed = false;
m.falseColor = false;
m.metadataComplete = true;
// re-index image files
String[] files = imageFiles.values().toArray(new String[imageFiles.size()]);
for (String file : files) {
int separator = file.lastIndexOf(File.separator);
String parent = file.substring(0, separator);
imageFiles.put(getImageIndex(parent), file);
}
int bpp = FormatTools.getBytesPerPixel(m.pixelType);
int expectedPlaneSize = m.sizeX * m.sizeY * bpp * m.sizeC;
String file = imageFiles.get(0);
RandomAccessInputStream s = poi.getDocumentStream(file);
TiffParser tp = new TiffParser(s);
// don't correct the image width if it's stored as a TIFF
if (!tp.isValidHeader() && s.length() > expectedPlaneSize) {
m.sizeX += (s.length() - expectedPlaneSize) / (m.sizeY * bpp * m.sizeC);
}
s.close();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
if (creationDate != null) {
store.setImageAcquisitionDate(new Timestamp(creationDate), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Length sizeX = FormatTools.getPhysicalSizeX(scaleFactor);
Length sizeY = FormatTools.getPhysicalSizeY(scaleFactor);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
for (int i=0; i<timestamps.size(); i++) {
if (i >= getImageCount()) {
break;
}
Double timestamp = timestamps.get(i);
if (timestamp != null) {
store.setPlaneDeltaT(new Time(timestamp, UNITS.S), 0, i);
}
if (i == 2) {
Double first = timestamps.get(1);
Double increment = timestamp - first;
if (increment != null) {
store.setPixelsTimeIncrement(new Time(increment, UNITS.S), 0);
}
}
}
if (binning > 0) {
String instrumentID = MetadataTools.createLSID("Instrument", 0);
String detectorID = MetadataTools.createLSID("Detector", 0);
store.setInstrumentID(instrumentID, 0);
store.setDetectorID(detectorID, 0, 0);
store.setDetectorType(getDetectorType("Other"), 0, 0);
store.setImageInstrumentRef(instrumentID, 0);
Binning binningEnum = getBinning(binning + "x" + binning);
for (int c=0; c<getEffectiveSizeC(); c++) {
store.setDetectorSettingsID(detectorID, 0, c);
store.setDetectorSettingsBinning(binningEnum, 0, c);
}
}
}
}
// -- Helper methods --
private void initPOIService() throws FormatException, IOException {
try {
ServiceFactory factory = new ServiceFactory();
poi = factory.getInstance(POIService.class);
}
catch (DependencyException de) {
throw new FormatException("POI library not found", de);
}
poi.initialize(Location.getMappedId(getCurrentFile()));
}
/** Get the image index from the image file name. */
private Integer getImageIndex(String path) {
int space = path.lastIndexOf(" ") + 1;
if (space >= path.length()) return null;
int end = path.indexOf(File.separator, space);
String field = path.substring(space, end);
String image = "1";
int imageIndex = path.indexOf("Image") + 5;
if (imageIndex >= 0) {
end = path.indexOf(File.separator, imageIndex);
if (end < 0) end = path.length();
image = path.substring(imageIndex, end);
}
try {
int channel = Integer.parseInt(image) - 1;
return getEffectiveSizeC() * (Integer.parseInt(field) - 1) + channel;
}
catch (NumberFormatException e) { }
return null;
}
private Integer getTimestampIndex(String path) {
int space = path.lastIndexOf(" ") + 1;
if (space >= path.length()) return null;
int end = path.indexOf(File.separator, space);
return Integer.parseInt(path.substring(space , end)) - 1;
}
}