use of loci.formats.services.POIService in project bioformats by openmicroscopy.
the class TillVisionReader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
if (!checkSuffix(id, "vws")) {
Location pst = new Location(id).getAbsoluteFile();
String name = pst.getParentFile().getName();
Location parent = pst.getParentFile().getParentFile();
Location vwsFile = new Location(parent, name.replaceAll(".pst", ".vws"));
if (vwsFile.exists() && !vwsFile.isDirectory()) {
id = vwsFile.getAbsolutePath();
} else if (vwsFile.isDirectory()) {
parent = pst.getParentFile();
String[] list = parent.list(true);
boolean foundVWS = false;
for (String f : list) {
if (checkSuffix(f, "vws")) {
id = new Location(parent, f).getAbsolutePath();
foundVWS = true;
break;
}
}
if (!foundVWS) {
throw new FormatException("Could not find .vws file.");
}
} else
throw new FormatException("Could not find .vws file.");
}
super.initFile(id);
exposureTimes = new HashMap<Integer, Double>();
POIService poi = null;
try {
ServiceFactory factory = new ServiceFactory();
poi = factory.getInstance(POIService.class);
} catch (DependencyException de) {
throw new FormatException("POI library not found", de);
}
poi.initialize(id);
Vector<String> documents = poi.getDocumentList();
int nImages = 0;
final Hashtable<String, Object> tmpSeriesMetadata = new Hashtable<String, Object>();
for (String name : documents) {
LOGGER.debug("Reading {}", name);
if (name.equals("Root Entry" + File.separator + "Contents")) {
RandomAccessInputStream s = poi.getDocumentStream(name);
s.order(true);
boolean specialCImage = false;
int nFound = 0;
Long[] cimages = null;
Location dir = new Location(id).getAbsoluteFile().getParentFile();
String[] list = dir.list(true);
boolean hasPST = false;
for (String f : list) {
if (checkSuffix(f, "pst")) {
hasPST = true;
break;
}
}
if (!hasPST) {
cimages = findImages(s);
nFound = cimages.length;
if (nFound == 0) {
s.seek(13);
int len = s.readShort();
String type = s.readString(len);
if (type.equals("CImage")) {
nFound = 1;
cimages = new Long[] { s.getFilePointer() + 6 };
specialCImage = true;
}
}
embeddedImages = nFound > 0;
}
LOGGER.debug("Images are {}embedded", embeddedImages ? "" : "not ");
if (embeddedImages) {
core.clear();
embeddedOffset = new long[nFound];
for (int i = 0; i < nFound; i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);
s.seek(cimages[i]);
int len = s.read();
String imageName = s.readString(len);
imageNames.add(imageName);
if (specialCImage) {
s.seek(1280);
} else {
while (true) {
if (s.readString(2).equals("sB")) {
break;
} else
s.seek(s.getFilePointer() - 1);
}
}
s.skipBytes(20);
ms.sizeX = s.readInt();
ms.sizeY = s.readInt();
ms.sizeZ = s.readInt();
ms.sizeC = s.readInt();
ms.sizeT = s.readInt();
ms.pixelType = convertPixelType(s.readInt());
if (specialCImage) {
embeddedOffset[i] = s.getFilePointer() + 27;
} else {
embeddedOffset[i] = s.getFilePointer() + 31;
}
}
if (in != null)
in.close();
in = poi.getDocumentStream(name);
s.close();
break;
}
s.seek(0);
int lowerBound = 0;
int upperBound = 0x1000;
while (s.getFilePointer() < s.length() - 2) {
LOGGER.debug(" Looking for image at {}", s.getFilePointer());
s.order(false);
int nextOffset = findNextOffset(s);
if (nextOffset < 0 || nextOffset >= s.length())
break;
s.seek(nextOffset);
s.skipBytes(3);
int len = s.readShort();
if (len <= 0)
continue;
imageNames.add(s.readString(len));
if (s.getFilePointer() + 8 >= s.length())
break;
s.skipBytes(6);
s.order(true);
len = s.readShort();
if (nImages == 0 && len > upperBound * 2 && len < upperBound * 4) {
lowerBound = 512;
upperBound = 0x4000;
}
if (len < lowerBound || len > upperBound)
continue;
String description = s.readString(len);
LOGGER.debug("Description: {}", description);
// parse key/value pairs from description
String dateTime = "";
String[] lines = description.split("[\r\n]");
for (String line : lines) {
line = line.trim();
int colon = line.indexOf(':');
if (colon != -1 && !line.startsWith(";")) {
String key = line.substring(0, colon).trim();
String value = line.substring(colon + 1).trim();
String metaKey = "Series " + nImages + " " + key;
addMeta(metaKey, value, tmpSeriesMetadata);
if (key.equals("Start time of experiment")) {
// HH:mm:ss aa OR HH:mm:ss.sss aa
dateTime += " " + value;
} else if (key.equals("Date")) {
// mm/dd/yy ?
dateTime = value + " " + dateTime;
} else if (key.equals("Exposure time [ms]")) {
double exp = Double.parseDouble(value) / 1000;
exposureTimes.put(nImages, exp);
} else if (key.equals("Image type")) {
types.add(value);
}
}
}
dateTime = dateTime.trim();
if (!dateTime.equals("")) {
boolean success = false;
for (String format : DATE_FORMATS) {
try {
dateTime = DateTools.formatDate(dateTime, format, ".");
success = true;
} catch (NullPointerException e) {
}
}
dates.add(success ? dateTime : "");
}
nImages++;
}
s.close();
}
}
Location directory = new Location(currentId).getAbsoluteFile().getParentFile();
String[] pixelsFile = new String[nImages];
if (!embeddedImages) {
if (nImages == 0) {
throw new FormatException("No images found.");
}
// look for appropriate pixels files
String[] files = directory.list(true);
String name = currentId.substring(currentId.lastIndexOf(File.separator) + 1, currentId.lastIndexOf("."));
int nextFile = 0;
for (String f : files) {
if (checkSuffix(f, "pst")) {
Location pst = new Location(directory, f);
if (pst.isDirectory() && f.startsWith(name)) {
String[] subfiles = pst.list(true);
Arrays.sort(subfiles);
for (String q : subfiles) {
if (checkSuffix(q, "pst") && nextFile < nImages) {
pixelsFile[nextFile++] = f + File.separator + q;
}
}
}
}
}
if (nextFile == 0) {
for (String f : files) {
if (checkSuffix(f, "pst")) {
pixelsFile[nextFile++] = new Location(directory, f).getAbsolutePath();
}
}
if (nextFile == 0)
throw new FormatException("No image files found.");
}
}
Arrays.sort(pixelsFile);
int nSeries = core.size();
if (!embeddedImages) {
core.clear();
nSeries = nImages;
}
pixelsFiles = new String[nSeries];
infFiles = new String[nSeries];
Object[] metadataKeys = tmpSeriesMetadata.keySet().toArray();
IniParser parser = new IniParser();
for (int i = 0; i < nSeries; i++) {
CoreMetadata ms;
if (!embeddedImages) {
ms = new CoreMetadata();
core.add(ms);
setSeries(i);
// make sure that pixels file exists
String file = pixelsFile[i];
file = file.replace('/', File.separatorChar);
file = file.replace('\\', File.separatorChar);
String oldFile = file;
Location f = new Location(directory, oldFile);
if (!f.exists()) {
oldFile = oldFile.substring(oldFile.lastIndexOf(File.separator) + 1);
f = new Location(directory, oldFile);
if (!f.exists()) {
throw new FormatException("Could not find pixels file '" + file);
}
}
file = f.getAbsolutePath();
pixelsFiles[i] = file;
// read key/value pairs from .inf files
int dot = file.lastIndexOf(".");
String inf = file.substring(0, dot) + ".inf";
infFiles[i] = inf;
BufferedReader reader = new BufferedReader(new InputStreamReader(new FileInputStream(inf), Constants.ENCODING));
IniList data = parser.parseINI(reader);
reader.close();
IniTable infoTable = data.getTable("Info");
ms.sizeX = Integer.parseInt(infoTable.get("Width"));
ms.sizeY = Integer.parseInt(infoTable.get("Height"));
ms.sizeC = Integer.parseInt(infoTable.get("Bands"));
ms.sizeZ = Integer.parseInt(infoTable.get("Slices"));
ms.sizeT = Integer.parseInt(infoTable.get("Frames"));
int dataType = Integer.parseInt(infoTable.get("Datatype"));
ms.pixelType = convertPixelType(dataType);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
HashMap<String, String> iniMap = data.flattenIntoHashMap();
ms.seriesMetadata.putAll(iniMap);
}
} else {
ms = core.get(i);
setSeries(i);
}
ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
ms.rgb = false;
ms.littleEndian = true;
ms.dimensionOrder = "XYCZT";
ms.seriesMetadata = new Hashtable<String, Object>();
for (Object key : metadataKeys) {
String keyName = key.toString();
if (keyName.startsWith("Series " + i + " ")) {
keyName = keyName.replaceAll("Series " + i + " ", "");
ms.seriesMetadata.put(keyName, tmpSeriesMetadata.get(key));
}
}
}
setSeries(0);
populateMetadataStore();
poi.close();
poi = null;
}
use of loci.formats.services.POIService in project bioformats by openmicroscopy.
the class MissingPOIServiceTest method testInstantiate.
@Test(expectedExceptions = { DependencyException.class })
public void testInstantiate() throws DependencyException {
POIService service = sf.getInstance(POIService.class);
assertNotNull(service);
}
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