/**
* Returns list of mapped files, that should be transformed. Files can by specified via attributes
* (srcFile, srcDir) or resources (FileSet, FileList, DirSet, etc). Mapped file represents input
* and output file for transformation.
*
* @return list of mapped files
*/
public List<MappedFile> getMappedFiles() {
mappedFiles.clear();
// one src file
if (getSrcFile() != null) {
addMappedFile(getSrcFile());
}
if (getSrcDir() != null) {
addMappedFile(getSrcDir());
}
Iterator element = resources.iterator();
while (element.hasNext()) {
ResourceCollection rc = (ResourceCollection) element.next();
if (rc instanceof FileSet && rc.isFilesystemOnly()) {
FileSet fs = (FileSet) rc;
File fromDir = fs.getDir(getProject());
DirectoryScanner ds;
try {
ds = fs.getDirectoryScanner(getProject());
} catch (BuildException ex) {
log("Could not scan directory " + fromDir, ex, Project.MSG_ERR);
continue;
}
for (String f : ds.getIncludedFiles()) {
addMappedFile(new File(fromDir + System.getProperty("file.separator") + f), fromDir);
}
} else {
if (!rc.isFilesystemOnly()) {
log("Only filesystem resources are supported", Project.MSG_WARN);
continue;
}
Iterator rcIt = rc.iterator();
while (rcIt.hasNext()) {
Resource r = (Resource) rcIt.next();
if (!r.isExists()) {
log("Could not find resource " + r.toLongString(), Project.MSG_VERBOSE);
continue;
}
if (r instanceof FileResource) {
FileResource fr = (FileResource) r;
addMappedFile(fr.getFile(), fr.getBaseDir());
} else {
log(
"Only file resources are supported (" + r.getClass().getSimpleName() + " found)",
Project.MSG_WARN);
continue;
}
}
}
}
return mappedFiles;
}
@Override
public void putImage(TaggedImage taggedImage) throws MMException {
if (!newDataSet_) {
throw new MMException("This ImageFileManager is read-only.");
}
int fileSetIndex = 0;
if (splitByXYPosition_) {
try {
fileSetIndex = MDUtils.getPositionIndex(taggedImage.tags);
} catch (JSONException ex) {
ReportingUtils.logError(ex);
}
}
String label = MDUtils.getLabel(taggedImage.tags);
if (fileSets_ == null) {
try {
fileSets_ = new HashMap<Integer, FileSet>();
createDirectory(directory_);
} catch (Exception ex) {
ReportingUtils.logError(ex);
}
}
if (omeTiff_) {
if (omeMetadata_ == null) {
omeMetadata_ = new OMEMetadata(this);
}
}
if (fileSets_.get(fileSetIndex) == null) {
fileSets_.put(fileSetIndex, new FileSet(taggedImage.tags, this));
}
FileSet set = fileSets_.get(fileSetIndex);
try {
set.writeImage(taggedImage);
} catch (IOException ex) {
ReportingUtils.showError("problem writing image to file");
}
tiffReadersByLabel_.put(label, set.getCurrentReader());
int frame;
try {
frame = MDUtils.getFrameIndex(taggedImage.tags);
} catch (JSONException ex) {
frame = 0;
}
lastFrameOpenedDataSet_ = Math.max(frame, lastFrameOpenedDataSet_);
cached_.add(taggedImage, label);
}
/**
* Call this function when no more images are expected Finishes writing the metadata file and
* closes it. After calling this function, the imagestorage is read-only
*/
@Override
public synchronized void finished() {
if (finished_) {
return;
}
newDataSet_ = false;
try {
if (fileSets_ != null) {
for (FileSet p : fileSets_.values()) {
p.finishAbortedAcqIfNeeded();
}
for (FileSet p : fileSets_.values()) {
p.finished();
}
}
} catch (IOException ex) {
ReportingUtils.logError(ex);
}
finished_ = true;
}