/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
if (tiffReader.getCurrentFile() == null) {
setupReader();
}
return tiffReader.getOptimalTileHeight();
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
try {
return (int) ifds.get(getSeries()).getTileLength();
} catch (FormatException e) {
LOGGER.debug("", e);
}
return super.getOptimalTileHeight();
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
if (noPixels) {
return files.toArray(new String[files.size()]);
}
String[] allFiles = new String[files.size() + 1];
files.toArray(allFiles);
allFiles[allFiles.length - 1] = currentId;
return allFiles;
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
if (getCoreIndex() < core.length - ifds.size()) {
return tileY[getCoreIndex()];
}
int ifdIndex = getCoreIndex() - (usedFiles.length - 1);
try {
return (int) ifds.get(ifdIndex).getTileLength();
} catch (FormatException e) {
LOGGER.debug("Could not retrieve tile height", e);
}
return super.getOptimalTileHeight();
}
public void populateMetadataStore(String[] jsonData) throws FormatException, IOException {
FormatTools.assertId(currentId, false, 1);
currentId = "in-memory-json";
core = new CoreMetadata[jsonData.length];
positions = new Vector<Position>();
for (int pos = 0; pos < jsonData.length; pos++) {
core[pos] = new CoreMetadata();
Position p = new Position();
p.metadataFile = "Position #" + (pos + 1);
positions.add(p);
setSeries(pos);
parsePosition(jsonData[pos], pos);
}
setSeries(0);
populateMetadata();
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
Vector<String> files = new Vector<String>();
for (String file : metadataFiles) {
if (file != null) files.add(file);
}
if (!noPixels && tiffs != null) {
int well = getSeries() / (fieldRows * fieldCols);
for (int i = 0; i < tiffs[well].length; i++) {
files.add(tiffs[well][i]);
}
}
return files.toArray(new String[files.size()]);
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
Vector<String> files = new Vector<String>();
for (Position pos : positions) {
files.add(pos.metadataFile);
if (pos.xmlFile != null) {
files.add(pos.xmlFile);
}
if (!noPixels) {
for (String tiff : pos.tiffs) {
if (new Location(tiff).exists()) {
files.add(tiff);
}
}
}
}
return files.toArray(new String[files.size()]);
}
/* @see loci.formats.IFormatHandler#openThumbBytes(int) */
public byte[] openThumbBytes(int no) throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
int currentSeries = getSeries();
int thumbSize =
getThumbSizeX()
* getThumbSizeY()
* FormatTools.getBytesPerPixel(getPixelType())
* getRGBChannelCount();
if (getCoreIndex() >= usedFiles.length - 1 || usedFiles.length >= core.length) {
return super.openThumbBytes(no);
}
setSeries(usedFiles.length);
byte[] thumb = FormatTools.openThumbBytes(this, 0);
setSeries(currentSeries);
if (thumb.length == thumbSize) {
return thumb;
}
return super.openThumbBytes(no);
}
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
FormatTools.assertId(currentId, true, 1);
FormatTools.checkPlaneNumber(this, no);
FormatTools.checkBufferSize(this, buf.length, w, h);
final int[] zct = FormatTools.getZCTCoords(this, no);
final byte[] plane;
try {
plane = store.getPlane(zct[0], zct[1], zct[2]);
} catch (ServerError e) {
throw new FormatException(e);
}
RandomAccessInputStream s = new RandomAccessInputStream(plane);
readPlane(s, x, y, w, h, buf);
s.close();
return buf;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getSeriesUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
return usedFiles;
}
/* @see loci.formats.IFormatReader#getDomains() */
public String[] getDomains() {
FormatTools.assertId(currentId, true, 1);
String[] domain = new String[1];
domain[0] = files.length == 1 ? FormatTools.LM_DOMAIN : FormatTools.HCS_DOMAIN;
return domain;
}
/* @see loci.formats.IFormatReader#getSeriesUsedFiles(boolean) */
public String[] getUsedFiles(boolean noPixels) {
FormatTools.assertId(currentId, true, 1);
return noPixels ? new String[0] : files;
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
return reader.getOptimalTileHeight();
}
/* @see loci.formats.IFormatReader#getDomains() */
public String[] getDomains() {
FormatTools.assertId(currentId, true, 1);
return hasSPW ? new String[] {FormatTools.HCS_DOMAIN} : FormatTools.NON_SPECIAL_DOMAINS;
}