use of loci.common.services.ServiceException in project bioformats by openmicroscopy.
the class ImportProcess method getOMEXML.
/**
* Valid only after {@link ImportStep#READER}.
*/
public String getOMEXML() {
if (omeXML == null) {
// NB: Extract the OME-XML once, then keep it cached.
try {
ServiceFactory factory = new ServiceFactory();
OMEXMLService service = factory.getInstance(OMEXMLService.class);
omeXML = service.getOMEXML(getOMEMetadata());
} catch (DependencyException de) {
} catch (ServiceException se) {
}
}
return omeXML;
}
use of loci.common.services.ServiceException in project bioformats by openmicroscopy.
the class MINCReader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
try {
ServiceFactory factory = new ServiceFactory();
netcdf = factory.getInstance(NetCDFService.class);
netcdf.setFile(id);
} catch (DependencyException e) {
throw new MissingLibraryException(e);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Vector<String> variableList = netcdf.getVariableList();
for (String variable : variableList) {
Hashtable<String, Object> attributes = netcdf.getVariableAttributes(variable);
String[] keys = attributes.keySet().toArray(new String[0]);
Arrays.sort(keys);
for (String key : keys) {
if (attributes.get(key) instanceof Object[]) {
final StringBuilder sb = new StringBuilder();
Object[] o = (Object[]) attributes.get(key);
for (Object q : o) {
sb.append(q.toString());
}
addGlobalMeta(variable + " " + key, sb.toString());
} else {
addGlobalMeta(variable + " " + key, attributes.get(key));
}
}
}
}
CoreMetadata m = core.get(0);
try {
Object pixels = netcdf.getVariableValue("/image");
if (pixels == null) {
pixels = netcdf.getVariableValue("/minc-2.0/image/0/image");
isMINC2 = true;
}
m.littleEndian = isMINC2;
boolean signed = false;
if (isMINC2) {
Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/minc-2.0/image/0/image");
String unsigned = attrs.get("_Unsigned").toString();
if (!unsigned.startsWith("true")) {
signed = true;
}
} else {
Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/image");
String signtype = attrs.get("signtype").toString();
if (signtype.startsWith("signed")) {
signed = true;
}
}
if (pixels instanceof byte[][][]) {
m.pixelType = signed ? FormatTools.INT8 : FormatTools.UINT8;
pixelData = (byte[][][]) pixels;
} else if (pixels instanceof byte[][][][]) {
byte[][][][] actualPixels = (byte[][][][]) pixels;
m.pixelType = signed ? FormatTools.INT8 : FormatTools.UINT8;
pixelData = new byte[actualPixels.length * actualPixels[0].length][][];
int nextPlane = 0;
for (int t = 0; t < actualPixels.length; t++) {
for (int z = 0; z < actualPixels[t].length; z++) {
pixelData[nextPlane++] = actualPixels[t][z];
}
}
} else if (pixels instanceof short[][][]) {
m.pixelType = signed ? FormatTools.INT16 : FormatTools.UINT16;
short[][][] s = (short[][][]) pixels;
pixelData = new byte[s.length][][];
for (int i = 0; i < s.length; i++) {
pixelData[i] = new byte[s[i].length][];
for (int j = 0; j < s[i].length; j++) {
pixelData[i][j] = DataTools.shortsToBytes(s[i][j], isLittleEndian());
}
}
} else if (pixels instanceof int[][][]) {
m.pixelType = signed ? FormatTools.INT32 : FormatTools.UINT32;
int[][][] s = (int[][][]) pixels;
pixelData = new byte[s.length][][];
for (int i = 0; i < s.length; i++) {
pixelData[i] = new byte[s[i].length][];
for (int j = 0; j < s[i].length; j++) {
pixelData[i][j] = DataTools.intsToBytes(s[i][j], isLittleEndian());
}
}
} else if (pixels instanceof float[][][]) {
m.pixelType = FormatTools.FLOAT;
float[][][] s = (float[][][]) pixels;
pixelData = new byte[s.length][][];
for (int i = 0; i < s.length; i++) {
pixelData[i] = new byte[s[i].length][];
for (int j = 0; j < s[i].length; j++) {
pixelData[i][j] = DataTools.floatsToBytes(s[i][j], isLittleEndian());
}
}
} else if (pixels instanceof double[][][]) {
m.pixelType = FormatTools.DOUBLE;
double[][][] s = (double[][][]) pixels;
pixelData = new byte[s.length][][];
for (int i = 0; i < s.length; i++) {
pixelData[i] = new byte[s[i].length][];
for (int j = 0; j < s[i].length; j++) {
pixelData[i][j] = DataTools.doublesToBytes(s[i][j], isLittleEndian());
}
}
}
} catch (ServiceException e) {
throw new FormatException(e);
}
Length physicalX = null;
Length physicalY = null;
Length physicalZ = null;
Length xPosition = null;
Length yPosition = null;
Length zPosition = null;
if (isMINC2) {
Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/xspace");
m.sizeX = Integer.parseInt(attrs.get("length").toString());
physicalX = getStepSize(attrs);
xPosition = getStart(attrs);
attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/yspace");
m.sizeY = Integer.parseInt(attrs.get("length").toString());
physicalY = getStepSize(attrs);
yPosition = getStart(attrs);
attrs = netcdf.getVariableAttributes("/minc-2.0/dimensions/zspace");
m.sizeZ = Integer.parseInt(attrs.get("length").toString());
physicalZ = getStepSize(attrs);
zPosition = getStart(attrs);
} else {
m.sizeX = netcdf.getDimension("/xspace");
m.sizeY = netcdf.getDimension("/yspace");
m.sizeZ = netcdf.getDimension("/zspace");
Hashtable<String, Object> attrs = netcdf.getVariableAttributes("/xspace");
physicalX = getStepSize(attrs);
xPosition = getStart(attrs);
attrs = netcdf.getVariableAttributes("/yspace");
physicalY = getStepSize(attrs);
yPosition = getStart(attrs);
attrs = netcdf.getVariableAttributes("/zspace");
physicalZ = getStepSize(attrs);
zPosition = getStart(attrs);
}
try {
m.sizeT = netcdf.getDimension("/time");
} catch (NullPointerException e) {
m.sizeT = 1;
}
m.sizeC = 1;
m.imageCount = getSizeZ() * getSizeT() * getSizeC();
m.rgb = false;
m.indexed = false;
m.dimensionOrder = "XYZCT";
String history = null;
if (isMINC2) {
history = netcdf.getAttributeValue("/minc-2.0/ident");
} else {
history = netcdf.getAttributeValue("/history");
}
addGlobalMeta("Comment", history);
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, xPosition != null || yPosition != null || zPosition != null);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(history, 0);
if (physicalX != null) {
store.setPixelsPhysicalSizeX(physicalX, 0);
}
if (physicalY != null) {
store.setPixelsPhysicalSizeY(physicalY, 0);
}
if (physicalZ != null) {
store.setPixelsPhysicalSizeZ(physicalZ, 0);
}
for (int i = 0; i < getImageCount(); i++) {
if (xPosition != null) {
store.setPlanePositionX(xPosition, 0, i);
}
if (yPosition != null) {
store.setPlanePositionY(yPosition, 0, i);
}
if (zPosition != null) {
int z = getZCTCoords(i)[0];
Double pos = zPosition.value().doubleValue();
if (physicalZ != null && z > 0) {
pos += z * physicalZ.value().doubleValue();
}
store.setPlanePositionZ(FormatTools.createLength(pos, zPosition.unit()), 0, i);
}
}
}
}
use of loci.common.services.ServiceException in project bioformats by openmicroscopy.
the class NDPIReader method openBytes.
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
if (x == 0 && y == 0 && w == 1 && h == 1) {
return buf;
} else if (getSizeX() <= MAX_SIZE || getSizeY() <= MAX_SIZE) {
int ifdIndex = getIFDIndex(getCoreIndex(), no);
in = new RandomAccessInputStream(currentId);
tiffParser = new TiffParser(in);
tiffParser.setUse64BitOffsets(true);
tiffParser.setYCbCrCorrection(false);
byte[] b = tiffParser.getSamples(ifds.get(ifdIndex), buf, x, y, w, h);
in.close();
tiffParser.getStream().close();
return b;
}
if (initializedSeries != getCoreIndex() || initializedPlane != no) {
IFD ifd = ifds.get(getIFDIndex(getCoreIndex(), no));
long offset = ifd.getStripOffsets()[0];
long byteCount = ifd.getStripByteCounts()[0];
if (in != null) {
in.close();
}
in = new RandomAccessInputStream(currentId);
in.seek(offset);
in.setLength(offset + byteCount);
try {
service.close();
long[] markers = ifd.getIFDLongArray(MARKER_TAG);
if (!use64Bit) {
for (int i = 0; i < markers.length; i++) {
markers[i] = markers[i] & 0xffffffffL;
}
}
if (markers != null) {
service.setRestartMarkers(markers);
}
service.initialize(in, getSizeX(), getSizeY());
} catch (ServiceException e) {
throw new FormatException(e);
}
initializedSeries = getCoreIndex();
initializedPlane = no;
}
service.getTile(buf, x, y, w, h);
return buf;
}
use of loci.common.services.ServiceException in project bioformats by openmicroscopy.
the class HamamatsuVMSReader method openBytes.
/**
* @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
*/
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
int startCol = x / MAX_JPEG_SIZE;
int startRow = y / MAX_JPEG_SIZE;
String file = null;
switch(getCoreIndex()) {
case 0:
file = tileFiles[no][startRow][startCol];
break;
case 1:
file = macroFile;
break;
case 2:
file = mapFile;
break;
}
if (getSizeX() <= MAX_SIZE || getSizeY() <= MAX_SIZE) {
JPEGReader reader = new JPEGReader();
reader.setId(file);
reader.openBytes(0, buf, x, y, w, h);
reader.close();
return buf;
}
if (service == null) {
service = new JPEGTurboServiceImpl();
}
try {
Region image = new Region(x, y, w, h);
for (int row = startRow; row < nRows; row++) {
for (int col = startCol; col < nCols; col++) {
Region tile = new Region(col * MAX_JPEG_SIZE, row * MAX_JPEG_SIZE, col == nCols - 1 ? getSizeX() % MAX_JPEG_SIZE : MAX_JPEG_SIZE, row == nRows - 1 ? getSizeY() % MAX_JPEG_SIZE : MAX_JPEG_SIZE);
if (!tile.intersects(image)) {
continue;
}
file = tileFiles[no][row][col];
if (initializedSeries != getCoreIndex() || initializedPlane != no || !file.equals(initializedFile)) {
service.close();
if (restartMarkers.containsKey(file)) {
service.setRestartMarkers(restartMarkers.get(file));
} else {
service.setRestartMarkers(null);
}
// closing the service will close this file
RandomAccessInputStream s = new RandomAccessInputStream(file);
service.initialize(s, tile.width, tile.height);
restartMarkers.put(file, service.getRestartMarkers());
initializedSeries = getCoreIndex();
initializedPlane = no;
initializedFile = file;
}
Region intersection = tile.intersection(image);
int tileX = intersection.x % MAX_JPEG_SIZE;
int tileY = intersection.y % MAX_JPEG_SIZE;
int rowLen = intersection.width * getRGBChannelCount();
byte[] b = new byte[rowLen * intersection.height];
service.getTile(b, tileX, tileY, intersection.width, intersection.height);
for (int tileRow = 0; tileRow < intersection.height; tileRow++) {
int src = tileRow * rowLen;
int dest = (((intersection.y + tileRow - y) * w) + (intersection.x - x)) * getRGBChannelCount();
System.arraycopy(b, src, buf, dest, rowLen);
}
}
}
} catch (ServiceException e) {
throw new FormatException(e);
}
return buf;
}
use of loci.common.services.ServiceException in project bioformats by openmicroscopy.
the class OMEXMLServiceImpl method validateOMEXML.
/**
* @see OMEXMLService#validateOMEXML(java.lang.String, boolean)
*/
@Override
public boolean validateOMEXML(String xml, boolean pixelsHack) {
// HACK: Inject a TiffData element beneath any childless Pixels elements.
if (pixelsHack) {
// convert XML string to DOM
Document doc = null;
Exception exception = null;
try {
doc = XMLTools.parseDOM(xml);
} catch (ParserConfigurationException exc) {
exception = exc;
} catch (SAXException exc) {
exception = exc;
} catch (IOException exc) {
exception = exc;
}
if (exception != null) {
LOGGER.info("Malformed OME-XML", exception);
return false;
}
// inject TiffData elements as needed
NodeList list = doc.getElementsByTagName("Pixels");
for (int i = 0; i < list.getLength(); i++) {
Node node = list.item(i);
NodeList children = node.getChildNodes();
boolean needsTiffData = true;
for (int j = 0; j < children.getLength(); j++) {
Node child = children.item(j);
String name = child.getLocalName();
if ("TiffData".equals(name) || "BinData".equals(name)) {
needsTiffData = false;
break;
}
}
if (needsTiffData) {
// inject TiffData element
Node tiffData = doc.createElement("TiffData");
node.insertBefore(tiffData, node.getFirstChild());
}
}
// convert tweaked DOM back to XML string
try {
xml = XMLTools.getXML(doc);
} catch (TransformerConfigurationException exc) {
exception = exc;
} catch (TransformerException exc) {
exception = exc;
}
if (exception != null) {
LOGGER.info("Internal XML conversion error", exception);
return false;
}
}
try {
OMEXMLMetadata omexml = createOMEXMLMetadata(xml);
OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) omexml.getRoot();
for (int image = 0; image < root.sizeOfImageList(); image++) {
Image img = root.getImage(image);
for (int i = 0; i < img.sizeOfLinkedAnnotationList(); i++) {
Annotation annotation = img.getLinkedAnnotation(i);
if (!(annotation instanceof XMLAnnotation)) {
continue;
}
String annotationXML = ((XMLAnnotation) annotation).getValue();
Document annotationRoot = XMLTools.parseDOM(annotationXML);
NodeList nodes = annotationRoot.getElementsByTagName("ModuloAlongZ");
if (nodes.getLength() > 0) {
((XMLAnnotation) annotation).setValue("");
}
nodes = annotationRoot.getElementsByTagName("ModuloAlongC");
if (nodes.getLength() > 0) {
((XMLAnnotation) annotation).setValue("");
}
nodes = annotationRoot.getElementsByTagName("ModuloAlongT");
if (nodes.getLength() > 0) {
((XMLAnnotation) annotation).setValue("");
}
}
}
omexml.setRoot(root);
xml = getOMEXML(omexml);
} catch (ServiceException | ParserConfigurationException | SAXException | IOException e) {
LOGGER.warn("Could not remove Modulo annotations", e);
}
return XMLTools.validateXML(xml, "OME-XML", SCHEMA_CLASSPATH_READER);
}
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