/** Compiles an N-dimensional list of axis lengths from the given reader. */
private int[] getDimLengths(IFormatReader r) {
final int sizeX = r.getSizeX();
final int sizeY = r.getSizeY();
final int sizeZ = r.getSizeZ();
final int sizeT = r.getSizeT();
// final String[] cDimTypes = r.getChannelDimTypes();
final int[] cDimLengths = r.getChannelDimLengths();
final String dimOrder = r.getDimensionOrder();
final List<Integer> dimLengthsList = new ArrayList<Integer>();
// add core dimensions
for (int i = 0; i < dimOrder.length(); i++) {
final char dim = dimOrder.charAt(i);
switch (dim) {
case 'X':
if (sizeX > 1) dimLengthsList.add(sizeX);
break;
case 'Y':
if (sizeY > 1) dimLengthsList.add(sizeY);
break;
case 'Z':
if (sizeZ > 1) dimLengthsList.add(sizeZ);
break;
case 'T':
if (sizeT > 1) dimLengthsList.add(sizeT);
break;
case 'C':
for (int c = 0; c < cDimLengths.length; c++) {
int len = cDimLengths[c];
if (len > 1) dimLengthsList.add(len);
}
break;
}
}
// convert result to primitive array
final int[] dimLengths = new int[dimLengthsList.size()];
for (int i = 0; i < dimLengths.length; i++) {
dimLengths[i] = dimLengthsList.get(i);
}
return dimLengths;
}
@Test(dataProvider = "wrappers")
public void testCoreMetadata(IFormatReader reader) {
assertNotNull(reader.getCurrentFile());
CoreMetadata[] core = reader.getCoreMetadata();
assertEquals(core.length, reader.getSeriesCount());
for (int i = 0; i < reader.getSeriesCount(); i++) {
reader.setSeries(i);
assertEquals(core[i].sizeX, reader.getSizeX());
assertEquals(core[i].sizeY, reader.getSizeY());
assertEquals(core[i].sizeZ, reader.getSizeZ());
assertEquals(core[i].sizeC, reader.getSizeC());
assertEquals(core[i].sizeT, reader.getSizeT());
assertEquals(core[i].pixelType, reader.getPixelType());
assertEquals(core[i].imageCount, reader.getImageCount());
assertEquals(core[i].dimensionOrder, reader.getDimensionOrder());
assertEquals(core[i].littleEndian, reader.isLittleEndian());
assertEquals(core[i].rgb, reader.isRGB());
assertEquals(core[i].interleaved, reader.isInterleaved());
assertEquals(core[i].indexed, reader.isIndexed());
}
}
private <T extends RealType<T>> void populatePlane(
IFormatReader r, int no, byte[] plane, LocalizablePlaneCursor<T> cursor) {
final int sizeX = r.getSizeX();
final int pixelType = r.getPixelType();
final boolean little = r.isLittleEndian();
final int[] dimLengths = getDimLengths(r);
final int[] pos = new int[dimLengths.length];
final int planeX = 0;
final int planeY = 1;
getPosition(r, no, pos);
cursor.reset(planeX, planeY, pos);
while (cursor.hasNext()) {
cursor.fwd();
final int index = cursor.getPosition(planeX) + cursor.getPosition(planeY) * sizeX;
final double value = decodeWord(plane, index, pixelType, little);
cursor.getType().setReal(value);
}
}
/** Copies the current dimensional position into the given array. */
private void getPosition(IFormatReader r, int no, int[] pos) {
final int sizeX = r.getSizeX();
final int sizeY = r.getSizeY();
final int sizeZ = r.getSizeZ();
final int sizeT = r.getSizeT();
// final String[] cDimTypes = r.getChannelDimTypes();
final int[] cDimLengths = r.getChannelDimLengths();
final String dimOrder = r.getDimensionOrder();
final int[] zct = r.getZCTCoords(no);
int index = 0;
for (int i = 0; i < dimOrder.length(); i++) {
final char dim = dimOrder.charAt(i);
switch (dim) {
case 'X':
if (sizeX > 1) index++; // NB: Leave X axis position alone.
break;
case 'Y':
if (sizeY > 1) index++; // NB: Leave Y axis position alone.
break;
case 'Z':
if (sizeZ > 1) pos[index++] = zct[0];
break;
case 'T':
if (sizeT > 1) pos[index++] = zct[2];
break;
case 'C':
final int[] cPos = FormatTools.rasterToPosition(cDimLengths, zct[1]);
for (int c = 0; c < cDimLengths.length; c++) {
if (cDimLengths[c] > 1) pos[index++] = cPos[c];
}
break;
}
}
}
/** Compiles an N-dimensional list of axis types from the given reader. */
private String[] getDimTypes(IFormatReader r) {
final int sizeX = r.getSizeX();
final int sizeY = r.getSizeY();
final int sizeZ = r.getSizeZ();
final int sizeT = r.getSizeT();
final String[] cDimTypes = r.getChannelDimTypes();
final int[] cDimLengths = r.getChannelDimLengths();
final String dimOrder = r.getDimensionOrder();
final List<String> dimTypes = new ArrayList<String>();
// add core dimensions
for (char dim : dimOrder.toCharArray()) {
switch (dim) {
case 'X':
if (sizeX > 1) dimTypes.add(X);
break;
case 'Y':
if (sizeY > 1) dimTypes.add(Y);
break;
case 'Z':
if (sizeZ > 1) dimTypes.add(Z);
break;
case 'T':
if (sizeT > 1) dimTypes.add(TIME);
break;
case 'C':
for (int c = 0; c < cDimTypes.length; c++) {
int len = cDimLengths[c];
if (len > 1) dimTypes.add(cDimTypes[c]);
}
break;
}
}
return dimTypes.toArray(new String[0]);
}
/**
* 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);
}