//
// PCIReader.java
//
/*
OME Bio-Formats package for reading and converting biological file formats.
Copyright (C) 2005-@year@ UW-Madison LOCI and Glencoe Software, Inc.
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, write to the Free Software
Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*/
package loci.formats.in;
import java.io.File;
import java.io.IOException;
import java.util.HashMap;
import java.util.Vector;
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.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 loci.formats.services.POIService;
import loci.formats.tiff.IFD;
import loci.formats.tiff.TiffParser;
/**
* PCIReader is the file format reader for SimplePCI (Compix) .cxd files.
*
* <dl><dt><b>Source code:</b></dt>
* <dd><a href="http://trac.openmicroscopy.org.uk/ome/browser/bioformats.git/components/bio-formats/src/loci/formats/in/PCIReader.java">Trac</a>,
* <a href="http://git.openmicroscopy.org/?p=bioformats.git;a=blob;f=components/bio-formats/src/loci/formats/in/PCIReader.java;hb=HEAD">Gitweb</a></dd></dl>
*
* @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 POIService poi;
private HashMap<Integer, Double> timestamps;
private String creationDate;
private int binning;
private Vector<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) */
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() */
public int getOptimalTileWidth() {
FormatTools.assertId(currentId, true, 1);
String file = imageFiles.get(0);
try {
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() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
String file = imageFiles.get(0);
try {
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)
*/
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);
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) */
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) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
imageFiles = new HashMap<Integer, String>();
timestamps = new HashMap<Integer, Double>();
uniqueZ = new Vector<Double>();
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(currentId));
double scaleFactor = 1;
Vector<String> allFiles = poi.getDocumentList();
if (allFiles.size() == 0) {
throw new FormatException(
"No files were found - the .cxd may be corrupt.");
}
double firstZ = 0d, secondZ = 0d;
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")) {
core[0].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) {
core[0].sizeC = poi.getFileSize(name) / plane;
}
}
}
else if (relativePath.indexOf("Image_Depth") != -1) {
boolean firstBits = core[0].bitsPerPixel == 0;
int bits = (int) stream.readDouble();
core[0].bitsPerPixel = bits;
while (bits % 8 != 0 || bits == 0) bits++;
if (bits % 3 == 0) {
core[0].sizeC = 3;
bits /= 3;
core[0].bitsPerPixel /= 3;
}
bits /= 8;
core[0].pixelType = FormatTools.pixelTypeFromBytes(bits, false, false);
if (getSizeC() > 1 && firstBits) {
core[0].sizeC /= bits;
}
}
else if (relativePath.indexOf("Image_Height") != -1 && getSizeY() == 0) {
core[0].sizeY = (int) stream.readDouble();
}
else if (relativePath.indexOf("Image_Width") != -1 && getSizeX() == 0) {
core[0].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)) uniqueZ.add(zPos);
if (name.indexOf("Field 1/") != -1) firstZ = zPos;
else if (name.indexOf("Field 2/") != -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 (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 = !new Double(firstZ).equals(new Double(secondZ));
if (getSizeC() == 0) core[0].sizeC = 1;
core[0].sizeZ = uniqueZ.size() == 0 ? 1 : uniqueZ.size();
core[0].sizeT = getImageCount() / getSizeZ();
core[0].rgb = getSizeC() > 1;
if (imageFiles.size() > getImageCount() && getSizeC() == 1) {
core[0].sizeC = imageFiles.size() / getImageCount();
core[0].imageCount *= getSizeC();
}
else {
core[0].imageCount = getSizeZ() * getSizeT();
}
core[0].interleaved = false;
core[0].dimensionOrder = zFirst ? "XYCZT" : "XYCTZ";
core[0].littleEndian = true;
core[0].indexed = false;
core[0].falseColor = false;
core[0].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);
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
if (creationDate != null) {
store.setImageAcquiredDate(creationDate, 0);
}
else MetadataTools.setDefaultCreationDate(store, id, 0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setPixelsPhysicalSizeX(new PositiveFloat(scaleFactor), 0);
store.setPixelsPhysicalSizeY(new PositiveFloat(scaleFactor), 0);
for (int i=0; i<timestamps.size(); i++) {
Double timestamp = new Double(timestamps.get(i).doubleValue());
store.setPlaneDeltaT(timestamp, 0, i);
if (i == 2) {
double first = timestamps.get(1).doubleValue();
Double increment = new Double(timestamp.doubleValue() - first);
store.setPixelsTimeIncrement(increment, 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);
for (int c=0; c<getEffectiveSizeC(); c++) {
store.setDetectorSettingsID(detectorID, 0, c);
store.setDetectorSettingsBinning(
getBinning(binning + "x" + binning), 0, c);
}
}
}
}
// -- Helper methods --
/** 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;
}
}