Example 81 with Length
use of ome.units.quantity.Length in project bioformats by openmicroscopy.
the class DeltavisionReader method initPixels.
protected void initPixels() throws FormatException, IOException {
LOGGER.info("Reading header");
MetadataStore store = makeFilterMetadata();
in.seek(96);
in.order(true);
boolean little = in.readShort() == LITTLE_ENDIAN;
in.order(little);
in.seek(0);
int sizeX = in.readInt();
int sizeY = in.readInt();
int imageCount = in.readInt();
int filePixelType = in.readInt();
in.seek(180);
int rawSizeT = in.readUnsignedShort();
int sizeT = rawSizeT == 0 ? 1 : rawSizeT;
int sequence = in.readShort();
in.seek(92);
extSize = in.readInt();
in.seek(196);
int rawSizeC = in.readShort();
int sizeC = rawSizeC == 0 ? 1 : rawSizeC;
// --- compute some secondary values ---
String imageSequence = getImageSequence(sequence);
int sizeZ = imageCount / (sizeC * sizeT);
// --- populate core metadata ---
LOGGER.info("Populating core metadata");
CoreMetadata m = core.get(0);
m.littleEndian = little;
m.sizeX = sizeX;
m.sizeY = sizeY;
m.imageCount = imageCount;
String pixel = getPixelString(filePixelType);
m.pixelType = getPixelType(filePixelType);
m.dimensionOrder = "XY" + imageSequence.replaceAll("W", "C");
int planeSize = getSizeX() * getSizeY() * FormatTools.getBytesPerPixel(getPixelType());
int realPlaneCount = (int) ((in.length() - HEADER_LENGTH - extSize) / planeSize);
if (realPlaneCount < getImageCount() && !truncatedFileFlag) {
LOGGER.debug("Truncated file");
m.imageCount = realPlaneCount;
if (sizeZ == 1) {
sizeT = realPlaneCount / sizeC;
} else if (sizeT == 1) {
sizeZ = realPlaneCount / sizeC;
if ((realPlaneCount % sizeC) != 0) {
sizeZ++;
m.imageCount = sizeZ * sizeC;
}
} else if (getDimensionOrder().indexOf('Z') < getDimensionOrder().indexOf('T')) {
sizeZ = realPlaneCount / (sizeC * sizeT);
if (sizeZ == 0) {
sizeT = 1;
sizeZ = realPlaneCount / sizeC;
if ((realPlaneCount % sizeC) != 0) {
sizeZ++;
m.imageCount = sizeZ * sizeC;
}
}
if (getImageCount() > (sizeZ * sizeC * sizeT)) {
m.imageCount = imageCount;
sizeC = rawSizeC == 0 ? 1 : rawSizeC;
sizeT = rawSizeT == 0 ? 1 : rawSizeT;
sizeZ = getImageCount() / (sizeC * sizeT);
}
} else {
sizeT = realPlaneCount / (sizeC * sizeZ);
}
}
m.sizeT = sizeT;
m.sizeC = sizeC;
m.sizeZ = sizeZ;
m.rgb = false;
m.interleaved = false;
m.metadataComplete = true;
m.indexed = false;
m.falseColor = false;
// --- parse extended header ---
in.seek(128);
numIntsPerSection = in.readShort();
numFloatsPerSection = in.readShort();
LOGGER.info("Reading extended header");
setOffsetInfo(sequence, getSizeZ(), getSizeC(), getSizeT());
extHdrFields = new DVExtHdrFields[getSizeZ()][getSizeC()][getSizeT()];
ndFilters = new Double[getSizeC()];
final List<Length> uniqueTileX = new ArrayList<Length>();
final List<Length> uniqueTileY = new ArrayList<Length>();
// Run through every image and fill in the
// Extended Header information array for that image
int offset = HEADER_LENGTH + numIntsPerSection * 4;
boolean hasZeroX = false;
boolean hasZeroY = false;
for (int i = 0; i < getImageCount(); i++) {
int[] coords = getZCTCoords(i);
int z = coords[0];
int w = coords[1];
int t = coords[2];
// -- read in the extended header data --
in.seek(offset + getTotalOffset(z, w, t));
DVExtHdrFields hdr = new DVExtHdrFields(in);
extHdrFields[z][w][t] = hdr;
if (!uniqueTileX.contains(hdr.stageXCoord) && hdr.stageXCoord.value().floatValue() != 0) {
uniqueTileX.add(hdr.stageXCoord);
} else if (hdr.stageXCoord.value().floatValue() == 0) {
hasZeroX = true;
}
if (!uniqueTileY.contains(hdr.stageYCoord) && hdr.stageYCoord.value().floatValue() != 0) {
uniqueTileY.add(hdr.stageYCoord);
} else if (hdr.stageYCoord.value().floatValue() == 0) {
hasZeroY = true;
}
}
xTiles = uniqueTileX.size();
yTiles = uniqueTileY.size();
if (xTiles > 1 || yTiles > 1) {
if (hasZeroX) {
xTiles++;
}
if (hasZeroY) {
yTiles++;
}
}
if (yTiles > 1) {
// TODO: use compareTo once Length implements Comparable
final Number y0 = uniqueTileY.get(0).value(UNITS.REFERENCEFRAME);
final Number y1 = uniqueTileY.get(1).value(UNITS.REFERENCEFRAME);
if (y1.floatValue() < y0.floatValue()) {
backwardsStage = true;
}
}
int nStagePositions = xTiles * yTiles;
if (nStagePositions > 0 && nStagePositions <= getSizeT()) {
int t = getSizeT();
m.sizeT /= nStagePositions;
if (getSizeT() * nStagePositions != t) {
m.sizeT = t;
nStagePositions = 1;
} else {
m.imageCount /= nStagePositions;
}
if (nStagePositions > 1) {
CoreMetadata originalCore = core.get(0);
core.clear();
for (int i = 0; i < nStagePositions; i++) {
core.add(originalCore);
}
}
}
lengths = new int[4];
int lengthIndex = 0;
int dimIndex = 0;
while (lengthIndex < lengths.length) {
char dim = imageSequence.charAt(dimIndex++);
switch(dim) {
case 'Z':
lengths[lengthIndex++] = getSizeZ();
break;
case 'W':
lengths[lengthIndex++] = getSizeC();
break;
case 'T':
lengths[lengthIndex++] = getSeriesCount();
lengths[lengthIndex++] = getSizeT();
break;
}
}
// --- populate original metadata ---
LOGGER.info("Populating original metadata");
addGlobalMeta("ImageWidth", sizeX);
addGlobalMeta("ImageHeight", sizeY);
addGlobalMeta("NumberOfImages", imageCount);
addGlobalMeta("PixelType", pixel);
addGlobalMeta("Number of timepoints", rawSizeT);
addGlobalMeta("Image sequence", imageSequence);
addGlobalMeta("Number of wavelengths", rawSizeC);
addGlobalMeta("Number of focal planes", sizeZ);
for (int series = 0; series < getSeriesCount(); series++) {
setSeries(series);
for (int plane = 0; plane < getImageCount(); plane++) {
int[] coords = getZCTCoords(plane);
int tIndex = getSeriesCount() * coords[2] + series;
DVExtHdrFields hdr = extHdrFields[coords[0]][coords[1]][tIndex];
// -- record original metadata --
String prefix = "Extended header Z" + coords[0] + " W" + coords[1] + " T" + coords[2];
for (Map.Entry<String, Object> entry : hdr.asMap().entrySet()) {
addSeriesMeta(prefix + ":" + entry.getKey(), entry.getValue());
}
addGlobalMetaList("X position for position", hdr.stageXCoord);
addGlobalMetaList("Y position for position", hdr.stageYCoord);
addGlobalMetaList("Z position for position", hdr.stageZCoord);
}
}
setSeries(0);
// --- populate OME metadata ---
LOGGER.info("Populating OME metadata");
MetadataTools.populatePixels(store, this, true);
// link Instrument and Image
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
for (int i = 0; i < getSeriesCount(); i++) {
store.setImageInstrumentRef(instrumentID, i);
}
}
Also used :
ArrayList(java.util.ArrayList)
CoreMetadata(loci.formats.CoreMetadata)
MetadataStore(loci.formats.meta.MetadataStore)
Length(ome.units.quantity.Length)
HashMap(java.util.HashMap)
Map(java.util.Map)
Example 82 with Length
use of ome.units.quantity.Length in project bioformats by openmicroscopy.
the class DeltavisionReader method populateObjective.
/**
* Populate an Objective based upon the lens ID.
* This is based upon information received from Applied Precision.
*/
private void populateObjective(MetadataStore store, int lensID) throws FormatException {
Double lensNA = null;
Double workingDistance = null;
Immersion immersion = getImmersion("Other");
Correction correction = getCorrection("Other");
String manufacturer = null;
String model = null;
double magnification = 0;
Double calibratedMagnification = null;
if (lensID >= 10000 && lensID <= 32000) {
if (lensID < 12000) {
manufacturer = "Olympus";
} else if (lensID < 14000) {
manufacturer = "Nikon";
} else if (lensID < 16000) {
manufacturer = "Zeiss";
} else if (lensID < 18000) {
manufacturer = "Leica";
} else if (lensID < 20000) {
manufacturer = "APLLC";
}
magnification = ((lensID % 1000) - (lensID % 100)) / 10.0;
if (magnification == 0) {
magnification = 100;
}
}
switch(lensID) {
case 2001:
lensNA = 1.15;
immersion = getImmersion("Water");
break;
case 10100:
lensNA = 0.30;
immersion = getImmersion("Air");
model = "1-LP134";
correction = getCorrection("Achromat");
break;
case 10101:
lensNA = 0.40;
immersion = getImmersion("Air");
model = "1-LB331";
correction = getCorrection("Apo");
break;
case 10102:
lensNA = 0.30;
immersion = getImmersion("Air");
model = "1-LP134";
break;
case 10103:
lensNA = 0.13;
calibratedMagnification = 4.0;
immersion = getImmersion("Air");
model = "1-LP124";
break;
case 10104:
lensNA = 0.40;
immersion = getImmersion("Air");
model = "1-LB331";
break;
case 10105:
lensNA = 0.40;
workingDistance = 3.10;
immersion = getImmersion("Air");
model = "1-LP331";
break;
case 10106:
lensNA = 0.16;
calibratedMagnification = 4.0;
workingDistance = 13.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "1-UB822";
break;
case 10107:
lensNA = 0.40;
immersion = getImmersion("Air");
workingDistance = 3.10;
model = "1-UB823";
correction = getCorrection("PlanApo");
break;
case 10108:
lensNA = 0.25;
workingDistance = 9.8;
immersion = getImmersion("Air");
model = "1-UC243";
break;
case 10109:
lensNA = 0.30;
immersion = getImmersion("Air");
model = "1-UB532";
correction = getCorrection("PlanFluor");
break;
case 10110:
lensNA = 0.13;
calibratedMagnification = 4.0;
immersion = getImmersion("Air");
break;
case 10111:
lensNA = 0.08;
calibratedMagnification = 2.0;
immersion = getImmersion("Air");
break;
case 10112:
lensNA = 0.13;
calibratedMagnification = 4.0;
immersion = getImmersion("Air");
model = "1-UB522";
break;
case 10113:
lensNA = 0.04;
calibratedMagnification = 1.25;
workingDistance = 5.1;
immersion = getImmersion("Air");
model = "1-UB920";
correction = getCorrection("PlanApo");
break;
case 10114:
lensNA = 0.08;
calibratedMagnification = 2.0;
workingDistance = 6.0;
immersion = getImmersion("Air");
model = "1-UB921";
correction = getCorrection("PlanApo");
break;
case 10200:
lensNA = 0.40;
workingDistance = 3.0;
immersion = getImmersion("Air");
break;
case 10201:
lensNA = 0.65;
workingDistance = 1.03;
immersion = getImmersion("Air");
model = "1-LB343";
correction = getCorrection("Apo");
break;
case 10202:
lensNA = 0.40;
immersion = getImmersion("Air");
model = "1-LP146";
break;
case 10203:
lensNA = 0.80;
immersion = getImmersion("Oil");
model = "1-LB342";
correction = getCorrection("PlanApo");
break;
case 10204:
lensNA = 0.70;
immersion = getImmersion("Air");
model = "1-LB341";
break;
case 10205:
lensNA = 0.75;
workingDistance = 0.55;
immersion = getImmersion("Air");
model = "1-UB765";
correction = getCorrection("Apo");
break;
case 10206:
lensNA = 0.50;
workingDistance = 0.55;
immersion = getImmersion("Air");
model = "1-UC525";
break;
case 10207:
lensNA = 0.40;
workingDistance = 3.0;
immersion = getImmersion("Air");
model = "1-UC145";
correction = getCorrection("Achromat");
break;
case 10208:
lensNA = 0.50;
workingDistance = 0.55;
immersion = getImmersion("Air");
model = "1-UB525";
break;
case 10209:
lensNA = 0.40;
workingDistance = 6.9;
immersion = getImmersion("Air");
model = "1-UC345";
break;
case 10210:
lensNA = 0.40;
workingDistance = 6.9;
immersion = getImmersion("Air");
model = "1-UB345";
break;
case 10400:
lensNA = 0.55;
workingDistance = 2.04;
immersion = getImmersion("Air");
break;
case 10401:
lensNA = 0.85;
workingDistance = 0.25;
immersion = getImmersion("Air");
break;
case 10402:
lensNA = 1.30;
workingDistance = 0.12;
immersion = getImmersion("Oil");
model = "1-LB356";
break;
case 10403:
lensNA = 1.35;
workingDistance = 0.10;
immersion = getImmersion("Oil");
model = "1-UB768";
break;
case 10404:
lensNA = 0.85;
workingDistance = 0.20;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "1-UB827";
break;
case 10405:
lensNA = 0.95;
workingDistance = 0.14;
immersion = getImmersion("Air");
model = "1-UB927";
correction = getCorrection("PlanApo");
break;
case 10406:
lensNA = 1.0;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "1-UB828";
break;
case 10407:
lensNA = 0.75;
correction = getCorrection("PlanFluor");
immersion = getImmersion("Air");
model = "1-UB527";
break;
case 10408:
lensNA = 0.60;
workingDistance = 2.15;
immersion = getImmersion("Air");
model = "1-UB347";
break;
case 10409:
lensNA = 0.60;
workingDistance = 2.15;
immersion = getImmersion("Air");
model = "1-UC347";
break;
case 10410:
lensNA = 1.15;
immersion = getImmersion("Water");
model = "1-UB769";
break;
case 10411:
lensNA = 0.75;
immersion = getImmersion("Air");
model = "1-UC527";
correction = getCorrection("PlanFluor");
break;
case 10412:
lensNA = 1.34;
workingDistance = 0.10;
immersion = getImmersion("Oil");
correction = getCorrection("Apo");
break;
case 10000:
lensNA = 1.30;
correction = getCorrection("Apo");
immersion = getImmersion("Oil");
model = "1-LB393";
break;
case 10001:
lensNA = 1.30;
immersion = getImmersion("Oil");
model = "1-LB392";
break;
case 10002:
lensNA = 1.40;
workingDistance = 0.10;
immersion = getImmersion("Oil");
model = "1-UB935";
correction = getCorrection("PlanApo");
break;
case 10003:
lensNA = 1.35;
workingDistance = 0.10;
immersion = getImmersion("Oil");
model = "1-UB836";
correction = getCorrection("PlanApo");
break;
case 10004:
lensNA = 1.30;
immersion = getImmersion("Oil");
model = "1-UB535";
break;
case 10005:
lensNA = 1.35;
workingDistance = 0.10;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
break;
case 10006:
lensNA = 1.40;
workingDistance = 0.10;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
break;
case 10007:
lensNA = 1.40;
workingDistance = 0.13;
immersion = getImmersion("Oil");
;
model = "1-U2B836";
break;
case 10600:
lensNA = 1.40;
workingDistance = 0.30;
immersion = getImmersion("Oil");
break;
case 10601:
lensNA = 1.40;
immersion = getImmersion("Oil");
model = "1-LB751";
break;
case 10602:
lensNA = 1.40;
workingDistance = 0.1;
immersion = getImmersion("Oil");
model = "1-UB932";
correction = getCorrection("PlanApo");
break;
case 10603:
lensNA = 1.20;
workingDistance = 0.25;
immersion = getImmersion("Water");
model = "1-UB891";
break;
case 10604:
lensNA = 1.20;
workingDistance = 0.25;
immersion = getImmersion("Water");
break;
case 10605:
lensNA = 0.70;
workingDistance = 1.10;
immersion = getImmersion("Air");
model = "1-UB351";
break;
case 10606:
lensNA = 0.70;
workingDistance = 1.10;
immersion = getImmersion("Air");
model = "1-UC351";
break;
case 10607:
lensNA = 1.40;
immersion = getImmersion("Oil");
model = "1-UC932";
correction = getCorrection("PlanApo");
break;
case 10608:
lensNA = 1.25;
immersion = getImmersion("Oil");
model = "1-UB532";
break;
case 10609:
lensNA = 1.40;
workingDistance = 0.15;
immersion = getImmersion("Oil");
model = "1-UB933";
correction = getCorrection("PlanApo");
break;
case 10610:
lensNA = 1.40;
workingDistance = 0.15;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
break;
case 10611:
lensNA = 1.20;
workingDistance = 0.25;
immersion = getImmersion("Water");
correction = getCorrection("PlanApo");
break;
case 10612:
lensNA = 1.42;
workingDistance = 0.15;
immersion = getImmersion("Oil");
model = "1-U2B933";
correction = getCorrection("PlanApo");
break;
case 12201:
lensNA = 0.75;
immersion = getImmersion("Air");
correction = getCorrection("PlanFluor");
model = "93146";
break;
case 12203:
lensNA = 0.45;
workingDistance = 8.1;
immersion = getImmersion("Air");
correction = getCorrection("PlanFluor");
model = "93150";
break;
case 12204:
lensNA = 0.45;
workingDistance = 4.50;
immersion = getImmersion("Air");
model = "MUE01200/92777";
break;
case 12205:
lensNA = 0.50;
workingDistance = 2.10;
immersion = getImmersion("Air");
correction = getCorrection("PlanFluor");
model = "MRH00200/93135";
break;
case 12401:
lensNA = 1.30;
workingDistance = 0.16;
immersion = getImmersion("Oil");
model = "85028";
break;
case 12402:
lensNA = 1.30;
workingDistance = 0.22;
immersion = getImmersion("Oil");
model = "85004";
break;
case 12403:
lensNA = 0.75;
immersion = getImmersion("Air");
model = "140508";
break;
case 12404:
lensNA = 1.30;
workingDistance = 0.22;
immersion = getImmersion("Oil");
break;
case 12405:
lensNA = 0.95;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "93105";
break;
case 12406:
lensNA = 1.00;
workingDistance = 0.16;
immersion = getImmersion("Oil");
model = "93106";
break;
case 12600:
lensNA = 1.40;
workingDistance = 0.17;
immersion = getImmersion("Oil");
model = "85020";
break;
case 12601:
lensNA = 1.40;
workingDistance = 0.21;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "93108";
break;
case 12602:
lensNA = 1.20;
workingDistance = 0.22;
immersion = getImmersion("Water");
correction = getCorrection("PlanApo");
model = "93109";
break;
case 12000:
lensNA = 1.40;
workingDistance = 0.1;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "85025";
break;
case 12001:
lensNA = 1.30;
workingDistance = 0.14;
immersion = getImmersion("Oil");
model = "85005";
break;
case 12002:
lensNA = 1.30;
workingDistance = 0.14;
immersion = getImmersion("Oil");
correction = getCorrection("UV");
model = "85005";
break;
case 12003:
lensNA = 1.40;
workingDistance = 0.13;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "93110";
break;
case 12004:
lensNA = 1.30;
workingDistance = 0.20;
immersion = getImmersion("Oil");
model = "93129";
break;
case 12101:
lensNA = 0.10;
calibratedMagnification = 2.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "202294";
break;
case 12102:
lensNA = 0.20;
calibratedMagnification = 4.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "108388";
break;
case 12103:
lensNA = 0.2;
calibratedMagnification = 4.0;
workingDistance = 15.7;
correction = getCorrection("PlanApo");
immersion = getImmersion("Air");
model = "93102";
break;
case 12104:
lensNA = 0.45;
workingDistance = 4.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "93103";
break;
case 12105:
lensNA = 0.30;
workingDistance = 16.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanFluor");
model = "93134";
break;
case 12106:
lensNA = 0.50;
workingDistance = 1.20;
immersion = getImmersion("Air");
correction = getCorrection("SuperFluor");
model = "93126";
break;
case 12107:
lensNA = 0.25;
workingDistance = 10.5;
immersion = getImmersion("Air");
model = "93183";
break;
case 12108:
lensNA = 0.25;
workingDistance = 6.10;
immersion = getImmersion("Air");
correction = getCorrection("Achromat");
model = "93161";
break;
case 14001:
lensNA = 1.40;
workingDistance = 0.1;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "44 07 08 (02)";
break;
case 14002:
lensNA = 1.30;
workingDistance = 0.1;
immersion = getImmersion("Oil");
model = "44 07 86";
break;
case 14003:
lensNA = 1.40;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "44 07 80 (02)";
break;
case 14004:
lensNA = 1.30;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "46 19 46 - 9903";
break;
case 14005:
lensNA = 1.40;
immersion = getImmersion("Oil");
model = "44 07 86 (02)";
break;
case 14006:
lensNA = 1.30;
immersion = getImmersion("Oil");
break;
case 14601:
lensNA = 1.40;
calibratedMagnification = 63.0;
workingDistance = 0.09;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "44 07 60 (03)";
break;
case 14602:
lensNA = 1.40;
calibratedMagnification = 63.0;
workingDistance = 0.09;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "44 07 62 (02)";
break;
case 14603:
lensNA = 0.90;
calibratedMagnification = 63.0;
immersion = getImmersion("Water");
model = "44 00 69";
break;
case 14604:
lensNA = 1.20;
workingDistance = 0.09;
calibratedMagnification = 63.0;
immersion = getImmersion("Water");
model = "44 06 68";
break;
case 14401:
lensNA = 1.30;
workingDistance = 0.14;
immersion = getImmersion("Oil");
correction = getCorrection("Fluar");
model = "44 02 55 (01)";
break;
case 14402:
lensNA = 1.00;
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
model = "44 07 51";
break;
case 14403:
lensNA = 1.20;
immersion = getImmersion("Water");
correction = getCorrection("Apo");
model = "44 00 52";
break;
case 14404:
lensNA = 0.75;
immersion = getImmersion("Air");
correction = getCorrection("PlanNeofluar");
model = "44 03 51";
break;
case 14405:
lensNA = 1.30;
workingDistance = 0.15;
immersion = getImmersion("Oil");
correction = getCorrection("PlanNeofluar");
model = "44 04 50";
break;
case 14406:
lensNA = 0.60;
immersion = getImmersion("Air");
model = "44 08 65";
break;
case 14407:
lensNA = 1.30;
immersion = getImmersion("Air");
correction = getCorrection("PlanNeofluar");
break;
case 14301:
lensNA = 0.80;
calibratedMagnification = 25.0;
workingDistance = 0.80;
correction = getCorrection("PlanNeofluar");
model = "44 05 44";
break;
case 14302:
lensNA = 0.80;
workingDistance = 0.80;
calibratedMagnification = 25.0;
correction = getCorrection("PlanNeofluar");
model = "44 05 42";
break;
case 14303:
lensNA = 0.80;
calibratedMagnification = 25.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanNeofluar");
model = "44 05 45";
break;
case 14201:
lensNA = 0.50;
immersion = getImmersion("Air");
correction = getCorrection("PlanNeofluar");
model = "44 03 41 (01)";
break;
case 14202:
lensNA = 0.60;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "44 06 40";
break;
case 14203:
lensNA = 0.75;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "44 06 49";
break;
case 14204:
lensNA = 0.75;
immersion = getImmersion("Air");
correction = getCorrection("Fluar");
model = "44 01 45";
break;
case 14101:
lensNA = 0.30;
immersion = getImmersion("Air");
correction = getCorrection("PlanNeofluar");
model = "44 03 30";
break;
case 14102:
lensNA = 0.25;
immersion = getImmersion("Air");
model = "44 01 31";
break;
case 14103:
lensNA = 0.25;
immersion = getImmersion("Air");
model = "44 00 31";
break;
case 14104:
lensNA = 0.45;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "44 06 39";
break;
case 14105:
lensNA = 0.16;
calibratedMagnification = 5.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
model = "44 06 20";
break;
case 18101:
lensNA = 0.20;
workingDistance = 3.33;
calibratedMagnification = 4.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
break;
case 18102:
lensNA = 0.20;
workingDistance = 2.883;
calibratedMagnification = 2.46;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
break;
case 18103:
lensNA = 0.20;
workingDistance = 2.883;
calibratedMagnification = 4.0;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
break;
case 18104:
lensNA = 0.45;
calibratedMagnification = 6.15;
workingDistance = 2.883;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
break;
case 18105:
lensNA = 0.45;
workingDistance = 2.883;
immersion = getImmersion("Air");
correction = getCorrection("PlanApo");
break;
case 18106:
lensNA = 0.1;
workingDistance = 24.00;
calibratedMagnification = 1.0;
immersion = getImmersion("Air");
break;
case 18201:
lensNA = 0.55;
workingDistance = 13.00;
immersion = getImmersion("Air");
break;
case 18202:
lensNA = 0.50;
workingDistance = 13.00;
immersion = getImmersion("Air");
break;
case 18204:
lensNA = 0.45;
workingDistance = 4.50;
immersion = getImmersion("Air");
model = "MUE01200/92777";
break;
case 18205:
lensNA = 0.50;
workingDistance = 2.10;
immersion = getImmersion("Air");
model = "MRH00200/93135";
break;
case 1:
lensNA = 0.25;
manufacturer = "Zeiss";
calibratedMagnification = 10.0;
immersion = getImmersion("Air");
break;
case 2:
lensNA = 0.50;
manufacturer = "Zeiss";
calibratedMagnification = 25.0;
immersion = getImmersion("Air");
break;
case 3:
lensNA = 1.00;
manufacturer = "Zeiss";
calibratedMagnification = 50.0;
immersion = getImmersion("Oil");
break;
case 4:
lensNA = 1.25;
manufacturer = "Zeiss";
calibratedMagnification = 63.0;
immersion = getImmersion("Oil");
break;
case 5:
lensNA = 1.30;
manufacturer = "Zeiss";
calibratedMagnification = 100.0;
immersion = getImmersion("Oil");
break;
case 6:
lensNA = 1.30;
calibratedMagnification = 100.0;
correction = getCorrection("Neofluor");
immersion = getImmersion("Oil");
break;
case 7:
lensNA = 1.40;
calibratedMagnification = 63.0;
manufacturer = "Leitz";
immersion = getImmersion("Oil");
correction = getCorrection("PlanApo");
break;
case 8:
lensNA = 1.20;
calibratedMagnification = 63.0;
immersion = getImmersion("Water");
break;
case 9:
lensNA = 0.40;
workingDistance = 0.30;
calibratedMagnification = 10.0;
manufacturer = "Olympus";
immersion = getImmersion("Air");
break;
case 10:
lensNA = 0.80;
workingDistance = 0.30;
manufacturer = "Olympus";
calibratedMagnification = 20.0;
immersion = getImmersion("Oil");
break;
case 11:
lensNA = 1.30;
calibratedMagnification = 40.0;
manufacturer = "Olympus";
workingDistance = 0.30;
immersion = getImmersion("Oil");
break;
case 12:
lensNA = 1.40;
workingDistance = 0.30;
manufacturer = "Olympus";
calibratedMagnification = 60.0;
immersion = getImmersion("Oil");
break;
case 13:
lensNA = 1.40;
workingDistance = 0.30;
manufacturer = "Nikon";
calibratedMagnification = 100.0;
immersion = getImmersion("Oil");
break;
}
String objectiveID = "Objective:" + lensID;
store.setObjectiveID(objectiveID, 0, 0);
for (int series = 0; series < getSeriesCount(); series++) {
store.setObjectiveSettingsID(objectiveID, series);
}
store.setObjectiveLensNA(lensNA, 0, 0);
store.setObjectiveImmersion(immersion, 0, 0);
store.setObjectiveCorrection(correction, 0, 0);
store.setObjectiveManufacturer(manufacturer, 0, 0);
store.setObjectiveModel(model, 0, 0);
store.setObjectiveNominalMagnification(magnification, 0, 0);
if (calibratedMagnification != null) {
store.setObjectiveCalibratedMagnification(calibratedMagnification, 0, 0);
}
if (workingDistance != null) {
store.setObjectiveWorkingDistance(new Length(workingDistance, UNITS.MILLIMETER), 0, 0);
}
}
Also used :
Length(ome.units.quantity.Length)
Immersion(ome.xml.model.enums.Immersion)
Correction(ome.xml.model.enums.Correction)
Example 83 with Length
use of ome.units.quantity.Length in project bioformats by openmicroscopy.
the class DeltavisionReader method initExtraMetadata.
protected void initExtraMetadata() throws FormatException, IOException {
MetadataStore store = makeFilterMetadata();
// --- read in the image header data ---
LOGGER.info("Reading header");
in.seek(16);
int subImageStartX = in.readInt();
int subImageStartY = in.readInt();
int subImageStartZ = in.readInt();
int pixelSamplingX = in.readInt();
int pixelSamplingY = in.readInt();
int pixelSamplingZ = in.readInt();
float pixX = in.readFloat();
float pixY = in.readFloat();
float pixZ = in.readFloat();
float xAxisAngle = in.readFloat();
float yAxisAngle = in.readFloat();
float zAxisAngle = in.readFloat();
int xAxisSeq = in.readInt();
int yAxisSeq = in.readInt();
int zAxisSeq = in.readInt();
float[] minWave = new float[5];
float[] maxWave = new float[5];
minWave[0] = in.readFloat();
maxWave[0] = in.readFloat();
float meanIntensity = in.readFloat();
int spaceGroupNumber = in.readInt();
in.seek(132);
short numSubResSets = in.readShort();
short zAxisReductionQuotient = in.readShort();
for (int i = 1; i <= 3; i++) {
minWave[i] = in.readFloat();
maxWave[i] = in.readFloat();
}
int type = in.readShort();
int lensID = in.readShort();
in.seek(172);
minWave[4] = in.readFloat();
maxWave[4] = in.readFloat();
in.seek(184);
float xTiltAngle = in.readFloat();
float yTiltAngle = in.readFloat();
float zTiltAngle = in.readFloat();
in.skipBytes(2);
short[] waves = new short[5];
for (int i = 0; i < waves.length; i++) {
waves[i] = in.readShort();
}
float xOrigin = in.readFloat();
float yOrigin = in.readFloat();
float zOrigin = in.readFloat();
in.skipBytes(4);
String[] title = new String[10];
for (int i = 0; i < title.length; i++) {
// Make sure that "null" characters are stripped out
title[i] = in.readByteToString(80).replaceAll("\0", "");
}
// --- compute some secondary values ---
String imageType = type < IMAGE_TYPES.length ? IMAGE_TYPES[type] : "unknown";
String imageDesc = title[0];
if (imageDesc != null && imageDesc.length() == 0)
imageDesc = null;
// --- populate original metadata ---
LOGGER.info("Populating original metadata");
addGlobalMeta("Sub-image starting point (X)", subImageStartX);
addGlobalMeta("Sub-image starting point (Y)", subImageStartY);
addGlobalMeta("Sub-image starting point (Z)", subImageStartZ);
addGlobalMeta("Pixel sampling size (X)", pixelSamplingX);
addGlobalMeta("Pixel sampling size (Y)", pixelSamplingY);
addGlobalMeta("Pixel sampling size (Z)", pixelSamplingZ);
addGlobalMeta("X element length (in um)", pixX);
addGlobalMeta("Y element length (in um)", pixY);
addGlobalMeta("Z element length (in um)", pixZ);
addGlobalMeta("X axis angle", xAxisAngle);
addGlobalMeta("Y axis angle", yAxisAngle);
addGlobalMeta("Z axis angle", zAxisAngle);
addGlobalMeta("Column axis sequence", xAxisSeq);
addGlobalMeta("Row axis sequence", yAxisSeq);
addGlobalMeta("Section axis sequence", zAxisSeq);
addGlobalMeta("Image Type", imageType);
addGlobalMeta("Lens ID Number", lensID);
addGlobalMeta("X axis tilt angle", xTiltAngle);
addGlobalMeta("Y axis tilt angle", yTiltAngle);
addGlobalMeta("Z axis tilt angle", zTiltAngle);
for (int i = 0; i < waves.length; i++) {
addGlobalMeta("Wavelength " + (i + 1) + " (in nm)", waves[i]);
}
addGlobalMeta("X origin (in um)", xOrigin);
addGlobalMeta("Y origin (in um)", yOrigin);
addGlobalMeta("Z origin (in um)", zOrigin);
for (String t : title) {
addGlobalMetaList("Title", t);
}
for (int i = 0; i < minWave.length; i++) {
addGlobalMeta("Wavelength " + (i + 1) + " min. intensity", minWave[i]);
addGlobalMeta("Wavelength " + (i + 1) + " max. intensity", maxWave[i]);
}
addGlobalMeta("Wavelength 1 mean intensity", meanIntensity);
addGlobalMeta("Space group number", spaceGroupNumber);
addGlobalMeta("Number of Sub-resolution sets", numSubResSets);
addGlobalMeta("Z axis reduction quotient", zAxisReductionQuotient);
// --- populate OME metadata ---
LOGGER.info("Populating OME metadata");
for (int series = 0; series < getSeriesCount(); series++) {
if (store instanceof IMinMaxStore) {
IMinMaxStore minMaxStore = (IMinMaxStore) store;
for (int i = 0; i < minWave.length; i++) {
if (i < getEffectiveSizeC()) {
minMaxStore.setChannelGlobalMinMax(i, minWave[i], maxWave[i], series);
}
}
}
Double x = new Double(pixX);
Length sizeX = FormatTools.getPhysicalSizeX(x);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, series);
}
Double y = new Double(pixY);
Length sizeY = FormatTools.getPhysicalSizeY(y);
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, series);
}
Double z = new Double(pixZ);
Length sizeZ = FormatTools.getPhysicalSizeZ(z);
if (sizeZ != null) {
store.setPixelsPhysicalSizeZ(sizeZ, series);
}
store.setImageDescription(imageDesc, series);
}
populateObjective(store, lensID);
// if matching log file exists, extract key/value pairs from it
boolean logFound = isGroupFiles() ? parseLogFile(store) : false;
if (isGroupFiles())
parseDeconvolutionLog(store);
if (getSeriesCount() == 1) {
xTiles = 1;
yTiles = 1;
backwardsStage = false;
}
for (int series = 0; series < getSeriesCount(); series++) {
int seriesIndex = series;
if (backwardsStage) {
int x = series % xTiles;
int y = series / xTiles;
seriesIndex = (yTiles - y - 1) * xTiles + (xTiles - x - 1);
}
for (int i = 0; i < getImageCount(); i++) {
int[] coords = getZCTCoords(i);
int tIndex = getSeriesCount() * coords[2] + seriesIndex;
DVExtHdrFields hdr = extHdrFields[coords[0]][coords[1]][tIndex];
// plane timing
store.setPlaneDeltaT(new Time(new Double(hdr.timeStampSeconds), UNITS.SECOND), series, i);
store.setPlaneExposureTime(new Time(new Double(extHdrFields[0][coords[1]][0].expTime), UNITS.SECOND), series, i);
// stage position
if (!logFound || getSeriesCount() > 1) {
store.setPlanePositionX(hdr.stageXCoord, series, i);
store.setPlanePositionY(hdr.stageYCoord, series, i);
store.setPlanePositionZ(hdr.stageZCoord, series, i);
}
}
for (int w = 0; w < getSizeC(); w++) {
DVExtHdrFields hdrC = extHdrFields[0][w][series];
Length emission = FormatTools.getEmissionWavelength(new Double(waves[w]));
Length excitation = FormatTools.getExcitationWavelength(new Double(hdrC.exWavelen));
if (emission != null) {
store.setChannelEmissionWavelength(emission, series, w);
}
if (excitation != null) {
store.setChannelExcitationWavelength(excitation, series, w);
}
if (ndFilters[w] == null)
ndFilters[w] = new Double(hdrC.ndFilter);
store.setChannelNDFilter(ndFilters[w], series, w);
}
}
}
Also used :
Time(ome.units.quantity.Time)
MetadataStore(loci.formats.meta.MetadataStore)
Length(ome.units.quantity.Length)
IMinMaxStore(loci.formats.meta.IMinMaxStore)
Example 84 with Length
use of ome.units.quantity.Length in project bioformats by openmicroscopy.
the class FV1000Reader method parseROIFile.
private int parseROIFile(String filename, MetadataStore store, int nextROI, int plane) throws FormatException, IOException {
int[] coordinates = getZCTCoords(plane);
IniList roiFile = null;
try {
roiFile = getIniFile(filename);
} catch (FormatException e) {
LOGGER.debug("Could not parse ROI file {}", filename, e);
return nextROI;
} catch (IOException e) {
LOGGER.debug("Could not parse ROI file {}", filename, e);
return nextROI;
}
boolean validROI = false;
int shape = -1;
int shapeType = -1;
String[] xc = null, yc = null;
int divide = 0;
int fontSize = 0, lineWidth = 0, angle = 0;
String fontName = null, name = null;
for (IniTable table : roiFile) {
String tableName = table.get(IniTable.HEADER_KEY);
if (tableName.equals("ROIBase FileInformation")) {
try {
String roiName = table.get("Name").replaceAll("\"", "");
validROI = Integer.parseInt(roiName) > 1;
} catch (NumberFormatException e) {
validROI = false;
}
if (!validROI)
continue;
} else if (tableName.equals("ROIBase Body")) {
shapeType = Integer.parseInt(table.get("SHAPE"));
divide = Integer.parseInt(table.get("DIVIDE"));
String[] fontAttributes = table.get("FONT").split(",");
fontName = fontAttributes[0];
fontSize = Integer.parseInt(fontAttributes[1]);
Length font = FormatTools.getFontSize(fontSize);
lineWidth = Integer.parseInt(table.get("LINEWIDTH"));
name = table.get("NAME");
angle = Integer.parseInt(table.get("ANGLE"));
xc = table.get("X").split(",");
yc = table.get("Y").split(",");
int x = Integer.parseInt(xc[0]);
int width = xc.length > 1 ? Integer.parseInt(xc[1]) - x : 0;
int y = Integer.parseInt(yc[0]);
int height = yc.length > 1 ? Integer.parseInt(yc[1]) - y : 0;
if (width + x <= getSizeX() && height + y <= getSizeY()) {
shape++;
final Integer zIndex = coordinates[0];
final Integer tIndex = coordinates[2];
if (shape == 0) {
nextROI++;
if (shapeType == POINT || shapeType == GRID || shapeType == RECTANGLE || shapeType == LINE || shapeType == CIRCLE || shapeType == ELLIPSE || shapeType == POLYGON || shapeType == FREE_SHAPE || shapeType == POLYLINE || shapeType == FREE_LINE) {
String roiID = MetadataTools.createLSID("ROI", nextROI);
store.setROIID(roiID, nextROI);
store.setImageROIRef(roiID, 0, nextROI);
}
}
String shapeID = MetadataTools.createLSID("Shape", nextROI, shape);
if (shapeType == POINT) {
store.setPointID(shapeID, nextROI, shape);
store.setPointTheZ(new NonNegativeInteger(zIndex), nextROI, shape);
store.setPointTheT(new NonNegativeInteger(tIndex), nextROI, shape);
if (font != null) {
store.setPointFontSize(font, nextROI, shape);
}
Length l = new Length((double) lineWidth, UNITS.PIXEL);
store.setPointStrokeWidth(l, nextROI, shape);
store.setPointX(new Double(xc[0]), nextROI, shape);
store.setPointY(new Double(yc[0]), nextROI, shape);
} else if (shapeType == GRID || shapeType == RECTANGLE) {
if (shapeType == RECTANGLE)
divide = 1;
width /= divide;
height /= divide;
for (int row = 0; row < divide; row++) {
for (int col = 0; col < divide; col++) {
double realX = x + col * width;
double realY = y + row * height;
shapeID = MetadataTools.createLSID("Shape", nextROI, shape);
store.setRectangleID(shapeID, nextROI, shape);
store.setRectangleX(realX, nextROI, shape);
store.setRectangleY(realY, nextROI, shape);
store.setRectangleWidth((double) width, nextROI, shape);
store.setRectangleHeight((double) height, nextROI, shape);
store.setRectangleTheZ(new NonNegativeInteger(zIndex), nextROI, shape);
store.setRectangleTheT(new NonNegativeInteger(tIndex), nextROI, shape);
if (font != null) {
store.setRectangleFontSize(font, nextROI, shape);
}
Length l = new Length((double) lineWidth, UNITS.PIXEL);
store.setRectangleStrokeWidth(l, nextROI, shape);
double centerX = realX + (width / 2);
double centerY = realY + (height / 2);
store.setRectangleTransform(getRotationTransform(angle), nextROI, shape);
if (row < divide - 1 || col < divide - 1)
shape++;
}
}
} else if (shapeType == LINE) {
store.setLineID(shapeID, nextROI, shape);
store.setLineX1((double) x, nextROI, shape);
store.setLineY1((double) y, nextROI, shape);
store.setLineX2((double) (x + width), nextROI, shape);
store.setLineY2((double) (y + height), nextROI, shape);
store.setLineTheZ(new NonNegativeInteger(zIndex), nextROI, shape);
store.setLineTheT(new NonNegativeInteger(tIndex), nextROI, shape);
if (font != null) {
store.setLineFontSize(font, nextROI, shape);
}
Length l = new Length((double) lineWidth, UNITS.PIXEL);
store.setLineStrokeWidth(l, nextROI, shape);
int centerX = x + (width / 2);
int centerY = y + (height / 2);
store.setLineTransform(getRotationTransform(angle), nextROI, shape);
} else if (shapeType == CIRCLE || shapeType == ELLIPSE) {
double rx = width / 2;
double ry = shapeType == CIRCLE ? rx : height / 2;
store.setEllipseID(shapeID, nextROI, shape);
store.setEllipseX(x + rx, nextROI, shape);
store.setEllipseY(y + ry, nextROI, shape);
store.setEllipseRadiusX(rx, nextROI, shape);
store.setEllipseRadiusY(ry, nextROI, shape);
store.setEllipseTheZ(new NonNegativeInteger(zIndex), nextROI, shape);
store.setEllipseTheT(new NonNegativeInteger(tIndex), nextROI, shape);
if (font != null) {
store.setEllipseFontSize(font, nextROI, shape);
}
Length l = new Length((double) lineWidth, UNITS.PIXEL);
store.setEllipseStrokeWidth(l, nextROI, shape);
store.setEllipseTransform(getRotationTransform(angle), nextROI, shape);
} else if (shapeType == POLYGON || shapeType == FREE_SHAPE || shapeType == POLYLINE || shapeType == FREE_LINE) {
final StringBuilder points = new StringBuilder();
for (int point = 0; point < xc.length; point++) {
points.append(xc[point]);
points.append(",");
points.append(yc[point]);
if (point < xc.length - 1)
points.append(" ");
}
if (shapeType == POLYLINE || shapeType == FREE_LINE) {
store.setPolylineID(shapeID, nextROI, shape);
store.setPolylinePoints(points.toString(), nextROI, shape);
store.setPolylineTransform(getRotationTransform(angle), nextROI, shape);
store.setPolylineTheZ(new NonNegativeInteger(zIndex), nextROI, shape);
store.setPolylineTheT(new NonNegativeInteger(tIndex), nextROI, shape);
if (font != null) {
store.setPolylineFontSize(font, nextROI, shape);
}
Length l = new Length((double) lineWidth, UNITS.PIXEL);
store.setPolylineStrokeWidth(l, nextROI, shape);
} else {
store.setPolygonID(shapeID, nextROI, shape);
store.setPolygonPoints(points.toString(), nextROI, shape);
store.setPolygonTransform(getRotationTransform(angle), nextROI, shape);
store.setPolygonTheZ(new NonNegativeInteger(zIndex), nextROI, shape);
store.setPolygonTheT(new NonNegativeInteger(tIndex), nextROI, shape);
if (font != null) {
store.setPolygonFontSize(font, nextROI, shape);
}
Length l = new Length((double) lineWidth, UNITS.PIXEL);
store.setPolygonStrokeWidth(l, nextROI, shape);
}
} else {
if (shape == 0)
nextROI--;
shape--;
}
}
}
}
return nextROI;
}
Also used :
IniList(loci.common.IniList)
NonNegativeInteger(ome.xml.model.primitives.NonNegativeInteger)
IOException(java.io.IOException)
FormatException(loci.formats.FormatException)
NonNegativeInteger(ome.xml.model.primitives.NonNegativeInteger)
Length(ome.units.quantity.Length)
IniTable(loci.common.IniTable)
Example 85 with Length
use of ome.units.quantity.Length in project bioformats by openmicroscopy.
the class Ecat7Reader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
CoreMetadata ms0 = core.get(0);
String check = in.readString(14).trim();
if (!check.matches(ECAT7_MAGIC_REGEX)) {
throw new FormatException("Invalid ECAT 7 file.");
}
String originalPath = in.readString(32);
short version = in.readShort();
short systemType = in.readShort();
short fileType = in.readShort();
String serialNumber = in.readString(10);
int scanStart = in.readInt();
String isotopeName = in.readString(8);
float isotopeHalflife = in.readFloat();
String radioPharmaceutical = in.readString(32);
float gantryTilt = in.readFloat();
float gantryRotation = in.readFloat();
float bedElevation = in.readFloat();
float intrinsicTilt = in.readFloat();
short wobbleSpeed = in.readShort();
short sourceType = in.readShort();
float distanceScanned = in.readFloat();
float transaxialFOV = in.readFloat();
short angularCompression = in.readShort();
short coinSampleMode = in.readShort();
short axialSampleMode = in.readShort();
float calibrationFactor = in.readFloat();
short calibrationUnits = in.readShort();
short calibrationLabel = in.readShort();
short compression = in.readShort();
String studyType = in.readString(12);
String patientID = in.readString(16);
String patientName = in.readString(32);
String patientSex = in.readString(1);
String patientDexterity = in.readString(1);
float patientAge = in.readFloat();
float patientHeight = in.readFloat();
float patientWeight = in.readFloat();
int patientBirthDate = in.readInt();
String physicianName = in.readString(32);
String operatorName = in.readString(32);
String description = in.readString(32);
short acquisitionType = in.readShort();
short patientOrientation = in.readShort();
String facilityName = in.readString(20);
ms0.sizeZ = in.readShort();
ms0.sizeT = in.readShort();
short numGates = in.readShort();
short numBedPositions = in.readShort();
float initBedPosition = in.readFloat();
float[] bedPositions = new float[15];
for (int i = 0; i < bedPositions.length; i++) {
bedPositions[i] = in.readFloat();
}
float planeSeparation = in.readFloat();
short lowerThreshold = in.readShort();
short trueLowerThreshold = in.readShort();
short trueUpperThreshold = in.readShort();
String processCode = in.readString(10);
short acquisitionMode = in.readShort();
float binSize = in.readFloat();
float branchingFraction = in.readFloat();
int doseStartTime = in.readInt();
float dosage = in.readFloat();
float wellCounterCorrectionFactor = in.readFloat();
String dataUnits = in.readString(32);
short septaState = in.readShort();
short[] fillCTI = new short[6];
for (int i = 0; i < fillCTI.length; i++) {
fillCTI[i] = in.readShort();
}
in.skipBytes(512);
short dataType = in.readShort();
short numDimensions = in.readShort();
ms0.sizeX = in.readShort();
ms0.sizeY = in.readShort();
in.skipBytes(2);
float xOffset = in.readFloat();
float yOffset = in.readFloat();
float zOffset = in.readFloat();
float reconZoom = in.readFloat();
float scaleFactor = in.readFloat();
short imageMin = in.readShort();
short imageMax = in.readShort();
float xPixelSize = in.readFloat();
float yPixelSize = in.readFloat();
float zPixelSize = in.readFloat();
int frameDuration = in.readInt();
int frameStartTime = in.readInt();
short filterCode = in.readShort();
float xResolution = in.readFloat();
float yResolution = in.readFloat();
float zResolution = in.readFloat();
float numRElements = in.readFloat();
float numAngles = in.readFloat();
float zRotationAngle = in.readFloat();
float decayCorrectionFactor = in.readFloat();
int processingCode = in.readInt();
int gateDuration = in.readInt();
int rWaveOffset = in.readInt();
int numAcceptedBeats = in.readInt();
float filterCutoffFrequency = in.readFloat();
float filterResolution = in.readFloat();
float filterRampSlope = in.readFloat();
short filterOrder = in.readShort();
float filterScatterFraction = in.readFloat();
float filterScatterSlope = in.readFloat();
String annotation = in.readString(40);
float[][] matrix = new float[3][4];
for (int i = 0; i < matrix.length; i++) {
for (int j = 0; j < matrix[i].length - 1; j++) {
matrix[i][j] = in.readFloat();
}
}
float rFilterCutoff = in.readFloat();
float rFilterResolution = in.readFloat();
short rFilterCode = in.readShort();
short rFilterOrder = in.readShort();
float zFilterCutoff = in.readFloat();
float zFilterResolution = in.readFloat();
short zFilterCode = in.readShort();
short zFilterOrder = in.readShort();
matrix[0][3] = in.readFloat();
matrix[1][3] = in.readFloat();
matrix[2][3] = in.readFloat();
short scatterType = in.readShort();
short reconType = in.readShort();
short reconViews = in.readShort();
short[] ctiFill = new short[87];
for (int i = 0; i < ctiFill.length; i++) {
ctiFill[i] = in.readShort();
}
short[] userFill = new short[48];
for (int i = 0; i < userFill.length; i++) {
userFill[i] = in.readShort();
}
ms0.sizeC = 1;
ms0.imageCount = getSizeZ() * getSizeT() * getSizeC();
ms0.dimensionOrder = "XYZTC";
switch(dataType) {
case 6:
ms0.pixelType = FormatTools.UINT16;
break;
default:
throw new FormatException("Unsupported data type: " + dataType);
}
addGlobalMeta("Original path", originalPath);
addGlobalMeta("Version", version);
addGlobalMeta("System type", systemType);
addGlobalMeta("File type", fileType);
addGlobalMeta("Serial number", serialNumber);
addGlobalMeta("Scan start", scanStart);
addGlobalMeta("Isotope Name", isotopeName);
addGlobalMeta("Isotope half-life", isotopeHalflife);
addGlobalMeta("Radiopharmaceutical", radioPharmaceutical);
addGlobalMeta("Gantry tilt", gantryTilt);
addGlobalMeta("Gantry rotation", gantryRotation);
addGlobalMeta("Bed elevation", bedElevation);
addGlobalMeta("Intrinsic tilt", intrinsicTilt);
addGlobalMeta("Wobble speed", wobbleSpeed);
addGlobalMeta("Source type", sourceType);
addGlobalMeta("Distance scanned", distanceScanned);
addGlobalMeta("Transaxial FOV", transaxialFOV);
addGlobalMeta("Angular compression", angularCompression);
addGlobalMeta("Coin. sample mode", coinSampleMode);
addGlobalMeta("Axial sample mode", axialSampleMode);
addGlobalMeta("Calibration factor", calibrationFactor);
addGlobalMeta("Calibration units", calibrationUnits);
addGlobalMeta("Calibration units label", calibrationLabel);
addGlobalMeta("Compression", compression);
addGlobalMeta("Study type", studyType);
addGlobalMeta("Patient ID", patientID);
addGlobalMeta("Patient name", patientName);
addGlobalMeta("Patient sex", patientSex);
addGlobalMeta("Patient dexterity", patientDexterity);
addGlobalMeta("Patient age", patientAge);
addGlobalMeta("Patient height", patientHeight);
addGlobalMeta("Patient weight", patientWeight);
addGlobalMeta("Patient birth date", patientBirthDate);
addGlobalMeta("Physician name", physicianName);
addGlobalMeta("Operator name", operatorName);
addGlobalMeta("Description", description);
addGlobalMeta("Acquisition type", acquisitionType);
addGlobalMeta("Patient orientation", patientOrientation);
addGlobalMeta("Facility name", facilityName);
addGlobalMeta("Number of gates", numGates);
addGlobalMeta("Number of bed positions", numBedPositions);
for (float bedPos : bedPositions) {
addGlobalMetaList("Bed position", bedPos);
}
addGlobalMeta("Plane separation", planeSeparation);
addGlobalMeta("Lower threshold", lowerThreshold);
addGlobalMeta("True lower threshold", trueLowerThreshold);
addGlobalMeta("True upper threshold", trueUpperThreshold);
addGlobalMeta("Process code", processCode);
addGlobalMeta("Acquistion mode", acquisitionMode);
addGlobalMeta("Bin size", binSize);
addGlobalMeta("Branching fraction", branchingFraction);
addGlobalMeta("Dose start time", doseStartTime);
addGlobalMeta("Dosage", dosage);
addGlobalMeta("Well counter correction factor", wellCounterCorrectionFactor);
addGlobalMeta("Data units", dataUnits);
addGlobalMeta("Septa state", septaState);
for (float fill : fillCTI) {
addGlobalMetaList("Fill CTI", fill);
}
addGlobalMeta("Data type", dataType);
addGlobalMeta("Number of dimensions", numDimensions);
addGlobalMeta("X offset", xOffset);
addGlobalMeta("Y offset", yOffset);
addGlobalMeta("Z offset", zOffset);
addGlobalMeta("Recon. zoom", reconZoom);
addGlobalMeta("Scale factor", scaleFactor);
addGlobalMeta("Image minimum", imageMin);
addGlobalMeta("Image maximum", imageMax);
addGlobalMeta("X pixel size", xPixelSize);
addGlobalMeta("Y pixel size", yPixelSize);
addGlobalMeta("Z pixel size", zPixelSize);
addGlobalMeta("Frame duration", frameDuration);
addGlobalMeta("Frame start time", frameStartTime);
addGlobalMeta("Filter code", filterCode);
addGlobalMeta("X resolution", xResolution);
addGlobalMeta("Y resolution", yResolution);
addGlobalMeta("Z resolution", zResolution);
addGlobalMeta("Number of R elements", numRElements);
addGlobalMeta("Number of angles", numAngles);
addGlobalMeta("Z rotation angle", zRotationAngle);
addGlobalMeta("Decay correction factor", decayCorrectionFactor);
addGlobalMeta("Processing code", processingCode);
addGlobalMeta("Gate duration", gateDuration);
addGlobalMeta("R wave offset", rWaveOffset);
addGlobalMeta("Number of accepted beats", numAcceptedBeats);
addGlobalMeta("Filter cutoff frequency", filterCutoffFrequency);
addGlobalMeta("Filter resolution", filterResolution);
addGlobalMeta("Filter ramp slope", filterRampSlope);
addGlobalMeta("Filter order", filterOrder);
addGlobalMeta("Filter scatter fraction", filterScatterFraction);
addGlobalMeta("Filter scatter slope", filterScatterSlope);
addGlobalMeta("Annotation", annotation);
for (int i = 0; i < matrix.length; i++) {
for (int j = 0; j < matrix[i].length; j++) {
addGlobalMeta("MT (" + (i + 1) + ", " + (j + 1) + ")", matrix[i][j]);
}
}
addGlobalMeta("R filter cutoff", rFilterCutoff);
addGlobalMeta("R filter resolution", rFilterResolution);
addGlobalMeta("R filter code", rFilterCode);
addGlobalMeta("R filter order", rFilterOrder);
addGlobalMeta("Z filter cutoff", zFilterCutoff);
addGlobalMeta("Z filter resolution", zFilterResolution);
addGlobalMeta("Z filter code", zFilterCode);
addGlobalMeta("Z filter order", zFilterOrder);
addGlobalMeta("Scatter type", scatterType);
addGlobalMeta("Recon. type", reconType);
addGlobalMeta("Recon. views", reconViews);
for (float cti : ctiFill) {
addGlobalMeta("CTI fill", cti);
}
for (float user : userFill) {
addGlobalMeta("User fill", user);
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(description, 0);
Length sizeX = FormatTools.getPhysicalSizeX(new Double(xPixelSize));
Length sizeY = FormatTools.getPhysicalSizeY(new Double(yPixelSize));
Length sizeZ = FormatTools.getPhysicalSizeZ(new Double(zPixelSize));
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
if (sizeZ != null) {
store.setPixelsPhysicalSizeZ(sizeZ, 0);
}
}
}
Also used :
CoreMetadata(loci.formats.CoreMetadata)
FormatException(loci.formats.FormatException)
MetadataStore(loci.formats.meta.MetadataStore)
Length(ome.units.quantity.Length)
RandomAccessInputStream(loci.common.RandomAccessInputStream)
Aggregations
Length (ome.units.quantity.Length)154
MetadataStore (loci.formats.meta.MetadataStore)82
CoreMetadata (loci.formats.CoreMetadata)74
Timestamp (ome.xml.model.primitives.Timestamp)52
RandomAccessInputStream (loci.common.RandomAccessInputStream)48
Time (ome.units.quantity.Time)46
FormatException (loci.formats.FormatException)39
Location (loci.common.Location)34
ArrayList (java.util.ArrayList)29
IMetadata (loci.formats.meta.IMetadata)13
NonNegativeInteger (ome.xml.model.primitives.NonNegativeInteger)13
ServiceFactory (loci.common.services.ServiceFactory)12
IOException (java.io.IOException)11
DependencyException (loci.common.services.DependencyException)11
PositiveInteger (ome.xml.model.primitives.PositiveInteger)11
MetadataRetrieve (loci.formats.meta.MetadataRetrieve)10
ElectricPotential (ome.units.quantity.ElectricPotential)9
Test (org.testng.annotations.Test)9
Element (org.w3c.dom.Element)9
NodeList (org.w3c.dom.NodeList)9
