/** Constructs a new pattern reader. */
public FilePatternReader() {
super("File pattern", new String[] {"pattern"});
ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses();
Class<? extends IFormatReader>[] classArray = classes.getClasses();
ClassList<IFormatReader> newClasses = new ClassList<IFormatReader>(IFormatReader.class);
for (Class<? extends IFormatReader> c : classArray) {
if (!c.equals(FilePatternReader.class)) {
newClasses.addClass(c);
}
}
helper = new FileStitcher(new ImageReader(newClasses));
suffixSufficient = true;
}
/**
* 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);
};