@DataProvider(name = "wrappers")
public Object[][] createWrappers() {
Location.mapId(TEST_FILE, TEST_FILE);
Object[][] wrappers =
new Object[][] {
{new ChannelFiller()},
{new ChannelMerger()},
{new ChannelSeparator()},
{new DimensionSwapper()},
{new FileStitcher()},
{new ImageReader()},
{new MinMaxCalculator()}
};
for (int i = 0; i < wrappers.length; i++) {
IFormatReader reader = (IFormatReader) wrappers[i][0];
try {
reader.setId(TEST_FILE);
} catch (FormatException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
}
return wrappers;
}
/**
* Tests whether Bio-Formats is potentially capable of importing the given file IDs. Outputs the
* IDs it can potentially import, one group per line, with elements of the each group separated by
* spaces.
*/
public void testIds(int[] fileIds) throws OmeisException, FormatException, IOException {
Arrays.sort(fileIds);
// set up file path mappings
String[] ids = new String[fileIds.length];
for (int i = 0; i < fileIds.length; i++) {
Hashtable fileInfo = getFileInfo(fileIds[i]);
ids[i] = (String) fileInfo.get("Name");
String path = getLocalFilePath(fileIds[i]);
Location.mapId(ids[i], path);
}
// check types and groups
if (http) printHttpResponseHeader();
boolean[] done = new boolean[fileIds.length];
StringBuffer sb = new StringBuffer();
for (int i = 0; i < fileIds.length; i++) {
if (done[i]) continue; // already part of another group
if (ids[i] == null) continue; // invalid id
if (!reader.isThisType(ids[i])) continue; // unknown format
reader.setId(ids[i]);
String[] files = reader.getUsedFiles();
if (files == null) continue; // invalid files list
sb.setLength(0);
for (int j = files.length - 1; j >= 0; j--) {
for (int ii = i; ii < fileIds.length; ii++) {
if (files[j] == null) {
log("Warning: FileID " + fileIds[ii] + " ('" + ids[ii] + "') has null used file #" + j);
} else if (files[j].equals(ids[ii])) {
if (done[ii]) {
log(
"Warning: FileID "
+ fileIds[ii]
+ " ('"
+ ids[ii]
+ "') already belongs to a group");
}
done[ii] = true;
if (j < files.length - 1) sb.append(" ");
sb.append(fileIds[ii]);
break;
}
}
}
System.out.println(sb.toString());
}
}
/** Constructs and initializes a Bio-Formats reader for the given file. */
private IFormatReader initializeReader(String id) throws FormatException, IOException {
notifyListeners(new StatusEvent("Initializing " + id));
IFormatReader r = null;
r = new ImageReader();
r = new ChannelFiller(r);
r = new ChannelSeparator(r);
try {
r.setMetadataStore(new OMEXMLServiceImpl().createOMEXMLMetadata());
} catch (ServiceException e) {
}
r.setId(id);
return r;
}
private byte[] decodeTile(int no, int row, int col) throws FormatException, IOException {
if (tileMap[getCoreIndex()] == null) {
return new byte[getTileSize()];
}
int[] zct = getZCTCoords(no);
TileCoordinate t = new TileCoordinate(nDimensions[getCoreIndex()]);
t.coordinate[0] = col;
t.coordinate[1] = row;
for (String dim : dimensionOrdering.keySet()) {
int index = dimensionOrdering.get(dim) + 2;
if (dim.equals("Z")) {
t.coordinate[index] = zct[0];
} else if (dim.equals("C")) {
t.coordinate[index] = zct[1];
} else if (dim.equals("T")) {
t.coordinate[index] = zct[2];
}
}
Integer index = (Integer) tileMap[getCoreIndex()].get(t);
if (index == null) {
return new byte[getTileSize()];
}
Long offset = tileOffsets[getCoreIndex()][index];
RandomAccessInputStream ets = new RandomAccessInputStream(usedFiles[getCoreIndex()]);
ets.seek(offset);
CodecOptions options = new CodecOptions();
options.interleaved = isInterleaved();
options.littleEndian = isLittleEndian();
int tileSize = getTileSize();
if (tileSize == 0) {
tileSize = tileX[getCoreIndex()] * tileY[getCoreIndex()] * 10;
}
options.maxBytes = (int) (offset + tileSize);
byte[] buf = null;
long end =
index < tileOffsets[getCoreIndex()].length - 1
? tileOffsets[getCoreIndex()][index + 1]
: ets.length();
IFormatReader reader = null;
String file = null;
switch (compressionType[getCoreIndex()]) {
case RAW:
buf = new byte[tileSize];
ets.read(buf);
break;
case JPEG:
Codec codec = new JPEGCodec();
buf = codec.decompress(ets, options);
break;
case JPEG_2000:
codec = new JPEG2000Codec();
buf = codec.decompress(ets, options);
break;
case PNG:
file = "tile.png";
reader = new APNGReader();
case BMP:
if (reader == null) {
file = "tile.bmp";
reader = new BMPReader();
}
byte[] b = new byte[(int) (end - offset)];
ets.read(b);
Location.mapFile(file, new ByteArrayHandle(b));
reader.setId(file);
buf = reader.openBytes(0);
Location.mapFile(file, null);
break;
}
if (reader != null) {
reader.close();
}
ets.close();
return buf;
}
/**
* Attempts to import the given file IDs using Bio-Formats, as a single group. Pixels are saved to
* the pixels file designated by OMEIS, and an OME-XML metadata block describing the successfully
* imported data is dumped to standard output.
*/
public void importIds(int[] fileIds) throws OmeisException, FormatException, IOException {
boolean doLittle = isLittleEndian();
Arrays.sort(fileIds);
// set up file path mappings
String[] ids = new String[fileIds.length];
for (int i = 0; i < fileIds.length; i++) {
Hashtable fileInfo = getFileInfo(fileIds[i]);
ids[i] = (String) fileInfo.get("Name");
String path = getLocalFilePath(fileIds[i]);
Location.mapId(ids[i], path);
}
// read file group
String id = ids[0];
String path = Location.getMappedId(id);
if (DEBUG) log("Reading file '" + id + "' --> " + path);
// verify that all given file IDs were grouped by the reader
reader.setId(id);
String[] used = reader.getUsedFiles();
if (used == null) {
throw new FormatException("Invalid file list for " + path);
}
if (used.length != ids.length) {
throw new FormatException(
"File list length mismatch for " + path + ": used=" + a2s(used) + "; ids=" + a2s(ids));
}
boolean[] done = new boolean[ids.length];
int numLeft = ids.length;
for (int i = 0; i < used.length; i++) {
for (int j = 0; j < ids.length; j++) {
if (done[j]) continue;
if (used[i].equals(ids[j])) {
done[j] = true;
numLeft--;
break;
}
}
}
if (numLeft > 0) {
throw new FormatException("File list does not correspond to ID list for " + path);
}
int seriesCount = reader.getSeriesCount();
// get DOM and Pixels elements for the file's OME-XML metadata
OMENode ome = (OMENode) omexmlMeta.getRoot();
Document omeDoc = ome.getDOMElement().getOwnerDocument();
Vector pix = DOMUtil.findElementList("Pixels", omeDoc);
if (pix.size() != seriesCount) {
throw new FormatException(
"Pixels element count ("
+ pix.size()
+ ") does not match series count ("
+ seriesCount
+ ") for '"
+ id
+ "'");
}
if (DEBUG) log(seriesCount + " series detected.");
for (int s = 0; s < seriesCount; s++) {
reader.setSeries(s);
// gather pixels information for this series
int sizeX = reader.getSizeX();
int sizeY = reader.getSizeY();
int sizeZ = reader.getSizeZ();
int sizeC = reader.getSizeC();
int sizeT = reader.getSizeT();
int pixelType = reader.getPixelType();
int bytesPerPixel;
boolean isSigned, isFloat;
switch (pixelType) {
case FormatTools.INT8:
bytesPerPixel = 1;
isSigned = true;
isFloat = false;
break;
case FormatTools.UINT8:
bytesPerPixel = 1;
isSigned = false;
isFloat = false;
break;
case FormatTools.INT16:
bytesPerPixel = 2;
isSigned = true;
isFloat = false;
break;
case FormatTools.UINT16:
bytesPerPixel = 2;
isSigned = false;
isFloat = false;
break;
case FormatTools.INT32:
bytesPerPixel = 4;
isSigned = true;
isFloat = false;
break;
case FormatTools.UINT32:
bytesPerPixel = 4;
isSigned = false;
isFloat = false;
break;
case FormatTools.FLOAT:
bytesPerPixel = 4;
isSigned = true;
isFloat = true;
break;
case FormatTools.DOUBLE:
bytesPerPixel = 8;
isSigned = true;
isFloat = true;
break;
default:
throw new FormatException(
"Unknown pixel type for '" + id + "' series #" + s + ": " + pixelType);
}
boolean little = reader.isLittleEndian();
boolean swap = doLittle != little && bytesPerPixel > 1 && !isFloat;
// ask OMEIS to allocate new pixels file
int pixelsId = newPixels(sizeX, sizeY, sizeZ, sizeC, sizeT, bytesPerPixel, isSigned, isFloat);
String pixelsPath = getLocalPixelsPath(pixelsId);
if (DEBUG) {
log("Series #" + s + ": id=" + pixelsId + ", path=" + pixelsPath);
}
// write pixels to file
FileOutputStream out = new FileOutputStream(pixelsPath);
int imageCount = reader.getImageCount();
if (DEBUG) {
log(
"Processing "
+ imageCount
+ " planes (sizeZ="
+ sizeZ
+ ", sizeC="
+ sizeC
+ ", sizeT="
+ sizeT
+ "): ");
}
// OMEIS expects XYZCT order --
// interleaved RGB files will be handled a bit more slowly due to this
// ordering (ChannelSeparator must read each plane three times), but
// caching performed by the OS helps some
for (int t = 0; t < sizeT; t++) {
for (int c = 0; c < sizeC; c++) {
for (int z = 0; z < sizeZ; z++) {
int ndx = reader.getIndex(z, c, t);
if (DEBUG) {
log("Reading plane #" + ndx + ": z=" + z + ", c=" + c + ", t=" + t);
}
byte[] plane = reader.openBytes(ndx);
if (swap) { // swap endianness
for (int b = 0; b < plane.length; b += bytesPerPixel) {
for (int k = 0; k < bytesPerPixel / 2; k++) {
int i1 = b + k;
int i2 = b + bytesPerPixel - k - 1;
byte b1 = plane[i1];
byte b2 = plane[i2];
plane[i1] = b2;
plane[i2] = b1;
}
}
}
out.write(plane);
}
}
}
out.close();
if (DEBUG) log("[done]");
// tell OMEIS we're done
pixelsId = finishPixels(pixelsId);
if (DEBUG) log("finishPixels called (new id=" + pixelsId + ")");
// get SHA1 hash for finished pixels
String sha1 = getPixelsSHA1(pixelsId);
if (DEBUG) log("SHA1=" + sha1);
// inject important extra attributes into proper Pixels element
Element pixels = (Element) pix.elementAt(s);
pixels.setAttribute("FileSHA1", sha1);
pixels.setAttribute("ImageServerID", "" + pixelsId);
pixels.setAttribute("DimensionOrder", "XYZCT"); // ignored anyway
String pType = pixels.getAttribute("PixelType");
if (pType.startsWith("u")) {
pixels.setAttribute("PixelType", pType.replace('u', 'U'));
}
if (DEBUG) log("Pixel attributes injected.");
}
reader.close();
// accumulate XML into buffer
ByteArrayOutputStream xml = new ByteArrayOutputStream();
try {
DOMUtil.writeXML(xml, omeDoc);
} catch (javax.xml.transform.TransformerException exc) {
throw new FormatException(exc);
}
// output OME-XML to standard output
xml.close();
String xmlString = new String(xml.toByteArray());
if (DEBUG) log(xmlString);
if (http) printHttpResponseHeader();
System.out.println(xmlString);
}