/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
reader = new ImageReader();
reader.setMetadataOptions(getMetadataOptions());
reader.setMetadataFiltered(isMetadataFiltered());
reader.setOriginalMetadataPopulated(isOriginalMetadataPopulated());
reader.setNormalized(isNormalized());
reader.setMetadataStore(getMetadataStore());
// NB: We need a raw handle on the ZIP data itself, not a ZipHandle.
IRandomAccess rawHandle = Location.getHandle(id, false, false);
in = new RandomAccessInputStream(rawHandle, id);
ZipInputStream zip = new ZipInputStream(in);
while (true) {
ZipEntry ze = zip.getNextEntry();
if (ze == null) break;
ZipHandle handle = new ZipHandle(id, ze);
Location.mapFile(ze.getName(), handle);
mappedFiles.add(ze.getName());
}
ZipHandle base = new ZipHandle(id);
reader.setId(base.getEntryName());
metadataStore = reader.getMetadataStore();
core = reader.getCoreMetadata();
metadata = reader.getGlobalMetadata();
base.close();
}
/**
* Wrapper for bio-formats
*
* @param config - ImportConfit
*/
public OMEROWrapper(ImportConfig config) {
if (config == null) {
throw new IllegalArgumentException(
"An ImportConfig must be instantitated \n "
+ "in order to properly configure all readers.");
}
this.config = config;
try {
String readersPath = config.readersPath.get();
// Since we now use all readers apart from the ZipReader, just
// initialize in this manner which helps us by not requiring
// us to keep up with all changes in readers.txt and removes
// the requirement for importer_readers.txt (See #2859).
// Chris Allan <*****@*****.**> -- Fri 10 Sep 2010 17:24:49 BST
ClassList<IFormatReader> readers = ImageReader.getDefaultReaderClasses();
readers.removeClass(ZipReader.class);
if (readersPath != null) {
Class<?> k = getClass();
if (new File(readersPath).exists()) {
k = null;
}
readers = new ClassList<IFormatReader>(readersPath, IFormatReader.class, k);
}
iReader = new ImageReader(readers);
filler = new ChannelFiller(iReader);
} catch (IOException e) {
throw new RuntimeException("Unable to load readers.txt.");
}
reader = separator = new ChannelSeparator(filler);
// Force unreadable characters to be removed from metadata key/value pairs
iReader.setMetadataFiltered(true);
filler.setMetadataFiltered(true);
separator.setMetadataFiltered(true);
};
