Examples with SpotList gdsc.smlm.tsf.TaggedSpotFile.SpotList used on opensource projects

Example 1 with SpotList

use of gdsc.smlm.tsf.TaggedSpotFile.SpotList in project GDSC-SMLM by aherbert.

the class ResultsManagerTest method writeTSFMatchesRead.

private void writeTSFMatchesRead(int channels, int slices, int positions, int types) {
    String filename = createFile();
    FileOutputStream out = null;
    try {
        out = new FileOutputStream(filename);
    } catch (Exception e) {
        closeOutput(out);
        e.printStackTrace();
        Assert.fail(e.getMessage());
    }
    // Write the offsets used in the TSF format
    try {
        DataOutputStream dos = new DataOutputStream(out);
        dos.writeInt(0);
        dos.writeLong(0);
    } catch (IOException e) {
        closeOutput(out);
        e.printStackTrace();
        Assert.fail(e.getMessage());
    }
    // Generate random spots
    int size = 1000;
    Spot[] spots = new Spot[size];
    for (int i = 1; i <= size; i++) {
        Spot.Builder builder = Spot.newBuilder();
        builder.setChannel(1 + rand.nextInt(channels));
        builder.setSlice(1 + rand.nextInt(slices));
        builder.setPos(1 + rand.nextInt(positions));
        builder.setFluorophoreType(rand.nextInt(1, types));
        // This is a required field but is ignored when reading
        builder.setMolecule(i);
        builder.setCluster(rand.nextInt(10));
        builder.setFrame(rand.nextInt(1, 100));
        builder.setXPosition(rand.nextInt(50));
        builder.setYPosition(rand.nextInt(50));
        builder.setBackground(rand.next());
        builder.setIntensity(rand.next());
        builder.setX(rand.next());
        builder.setY(rand.next());
        builder.setWidth(TSFPeakResultsWriter.SD_TO_FWHM_FACTOR * rand.next());
        Spot spot = builder.build();
        spots[i - 1] = spot;
        try {
            spot.writeDelimitedTo(out);
        } catch (IOException e) {
            closeOutput(out);
            e.printStackTrace();
            Assert.fail(e.getMessage());
        }
    }
    // Write the header
    // Get the offset to the SpotList message
    long offset = 0;
    try {
        // The offset is the amount to skip forward after reading the int 
        // magic number (4 bytes) and long offset (8 bytes)
        //out.flush();
        offset = out.getChannel().position() - 12;
    } catch (IOException e) {
        closeOutput(out);
        e.printStackTrace();
        Assert.fail(e.getMessage());
    }
    // Record the SpotList message
    SpotList.Builder builder = SpotList.newBuilder();
    builder.setApplicationId(1);
    builder.setNrSpots(size);
    builder.setLocationUnits(LocationUnits.PIXELS);
    builder.setIntensityUnits(IntensityUnits.COUNTS);
    builder.setFitMode(FitMode.ONEAXIS);
    builder.setNrChannels(channels);
    builder.setNrSlices(slices);
    builder.setNrPos(positions);
    for (int type = 1; type <= types; type++) {
        FluorophoreType.Builder typeBuilder = FluorophoreType.newBuilder();
        typeBuilder.setId(type);
        typeBuilder.setDescription("Type " + type);
        typeBuilder.setIsFiducial(rand.next() < 0.5f);
        builder.addFluorophoreTypes(typeBuilder.build());
    }
    SpotList spotList = builder.build();
    try {
        spotList.writeDelimitedTo(out);
    } catch (IOException e) {
        e.printStackTrace();
        Assert.fail(e.getMessage());
    } finally {
        closeOutput(out);
    }
    // Write the offset to the SpotList message into the offset position
    RandomAccessFile f = null;
    try {
        f = new RandomAccessFile(new File(filename), "rw");
        f.seek(4);
        f.writeLong(offset);
    } catch (Exception e) {
        e.printStackTrace();
        Assert.fail(e.getMessage());
    } finally {
        if (f != null) {
            try {
                f.close();
            } catch (IOException e) {
            }
        }
    }
    // Read each combination 
    for (int channel = 1; channel <= channels; channel++) for (int slice = 1; slice <= slices; slice++) for (int position = 1; position <= positions; position++) for (int type = 1; type <= types; type++) {
        StringBuilder sb = new StringBuilder();
        sb.append(" channel=").append(channel);
        sb.append(" slice=").append(slice);
        sb.append(" position=").append(position);
        sb.append(" fluorophore_type=[").append(type).append(":Type ").append(type).append(":fiducial=").append(builder.getFluorophoreTypes(type - 1).getIsFiducial()).append(']');
        // This is needed to trick the Macro class into returning the options 
        // for the thread to the GenericDialog used in the ResultsManager
        Thread.currentThread().setName("Run$_");
        Macro.setOptions(sb.toString());
        ResultsManager.setInputFilename(filename);
        MemoryPeakResults in = ResultsManager.loadInputResults(ResultsManager.INPUT_FILE, false);
        checkEqual(spots, channel, slice, position, type, in);
    }
}

Example 2 with SpotList

use of gdsc.smlm.tsf.TaggedSpotFile.SpotList in project GDSC-SMLM by aherbert.

the class TSFPeakResultsReader method isTSF.

/**
	 * Checks if is a binary TSF file by attempting to read the SpotList header.
	 *
	 * @param filename
	 *            the filename
	 * @return true, if is a TSF file
	 */
public static boolean isTSF(String filename) {
    FileInputStream fi = null;
    try {
        fi = new FileInputStream(filename);
        DataInputStream di = new DataInputStream(fi);
        // the file has an initial 0, then the offset (as long)
        // to the position of spotList
        int magic = di.readInt();
        if (magic != 0) {
            // Magic number should be zero
            return false;
        }
        if (fi.available() == 0) {
            // No more contents
            return false;
        }
        long offset = di.readLong();
        if (offset == 0) {
            // No offset record
            return false;
        }
        fi.skip(offset);
        SpotList spotList = SpotList.parseDelimitedFrom(fi);
        if (spotList != null)
            return true;
    } catch (Exception e) {
    // Fail
    } finally {
        if (fi != null) {
            try {
                fi.close();
            } catch (IOException e) {
            }
        }
    }
    return false;
}

Example 3 with SpotList

use of gdsc.smlm.tsf.TaggedSpotFile.SpotList in project GDSC-SMLM by aherbert.

the class TSFPeakResultsWriter method end.

/*
	 * (non-Javadoc)
	 * 
	 * @see gdsc.utils.fitting.PeakResults#end()
	 */
public void end() {
    // Get the offset to the SpotList message
    long offset = 0;
    try {
        // The offset is the amount to skip forward after reading the int 
        // magic number (4 bytes) and long offset (8 bytes)
        //out.flush();
        offset = out.getChannel().position() - 12;
    } catch (IOException e) {
        // This is bad.
        System.err.println("Failed to determine offset for SpotList message");
        e.printStackTrace();
        closeOutput();
        return;
    }
    // Record the SpotList message
    SpotList.Builder builder = SpotList.newBuilder();
    builder.setApplicationId(APPLICATION_ID);
    builder.setNrSpots(size);
    // Add the standard details the TSF supports. We use extensions to add GDSC SMLM data.
    if (name != null) {
        builder.setName(name);
    }
    if (source != null) {
        builder.setNrPixelsX(source.width);
        builder.setNrPixelsY(source.height);
        builder.setNrFrames(source.frames);
        builder.setSource(singleLine(source.toXML()));
    }
    if (bounds != null) {
        ROI.Builder roiBuilder = builder.getRoiBuilder();
        roiBuilder.setX(bounds.x);
        roiBuilder.setY(bounds.y);
        roiBuilder.setXWidth(bounds.width);
        roiBuilder.setYWidth(bounds.height);
        builder.setRoi(roiBuilder.build());
    }
    if (calibration != null) {
        if (calibration.hasNmPerPixel())
            builder.setPixelSize((float) calibration.getNmPerPixel());
        if (calibration.hasExposureTime())
            builder.setExposureTime(calibration.getExposureTime());
        if (calibration.hasReadNoise())
            builder.setReadNoise(calibration.getReadNoise());
        if (calibration.hasBias())
            builder.setBias(calibration.getBias());
        if (calibration.hasEMCCD())
            builder.setEmCCD(calibration.isEmCCD());
        if (calibration.hasAmplification())
            builder.setAmplification(calibration.getAmplification());
        if (calibration.hasGain()) {
            builder.setGain(calibration.getGain());
            // Use amplification if present (as this is the correct electrons/count value), otherwise use gain
            if (calibration.hasAmplification()) {
                double ecf = calibration.getAmplification();
                double qe = calibration.getGain() / ecf;
                builder.addEcf(ecf);
                builder.addQe(qe);
            } else {
                builder.addEcf(calibration.getGain());
                builder.addQe(1);
            }
        }
    }
    if (configuration != null && configuration.length() > 0) {
        builder.setConfiguration(singleLine(configuration));
    }
    // Have a property so the boxSize can be set
    if (boxSize > 0)
        builder.setBoxSize(boxSize);
    builder.setLocationUnits(LocationUnits.PIXELS);
    builder.setIntensityUnits(IntensityUnits.COUNTS);
    builder.setThetaUnits(ThetaUnits.DEGREES);
    builder.setFitMode(fitMode);
    FluorophoreType.Builder typeBuilder = FluorophoreType.newBuilder();
    typeBuilder.setId(1);
    typeBuilder.setDescription("Default fluorophore");
    typeBuilder.setIsFiducial(false);
    builder.addFluorophoreTypes(typeBuilder.build());
    SpotList spotList = builder.build();
    try {
        spotList.writeDelimitedTo(out);
    } catch (IOException e) {
        System.err.println("Failed to write SpotList message");
        e.printStackTrace();
        return;
    } finally {
        closeOutput();
    }
    // Note: it would be good to be able to use the ability to write to any output stream. However
    // the TSF format requires a seek at the end of writing to record the offset. seek() is not
    // supported by OutputStream. It is supported by: RandomAccessFile, RandomAccessStream (for input). 
    // Write the offset to the SpotList message into the offset position
    RandomAccessFile f = null;
    try {
        f = new RandomAccessFile(new File(filename), "rw");
        f.seek(4);
        f.writeLong(offset);
    } catch (Exception e) {
        System.err.println("Failed to record offset for SpotList message");
        e.printStackTrace();
    } finally {
        if (f != null) {
            try {
                f.close();
            } catch (IOException e) {
            }
        }
    }
}