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

Example 1 with IntensityUnits

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

the class TSFPeakResultsReader method read.

/**
	 * Read the results from the TSF file into memory
	 * 
	 * @return The results set (or null if an error occurred)
	 */
public MemoryPeakResults read() {
    readHeader();
    if (spotList == null)
        return null;
    MemoryPeakResults results = createResults();
    // Read the messages that contain the spot data
    FileInputStream fi = null;
    try {
        fi = new FileInputStream(filename);
        // size of int + size of long
        fi.skip(12);
    } catch (Exception e) {
        System.err.println("Failed to read open TSF file: " + filename);
        e.printStackTrace();
        if (fi != null) {
            try {
                fi.close();
            } catch (IOException ex) {
            }
        }
        return null;
    }
    LocationUnits locationUnits = spotList.getLocationUnits();
    boolean locationUnitsWarning = false;
    float locationConversion = 1;
    switch(locationUnits) {
        case PIXELS:
            break;
        case NM:
            locationConversion = 1 / getNmPerPixel(results.getCalibration());
            break;
        case UM:
            float nmPerPixel = getNmPerPixel(results.getCalibration());
            if (nmPerPixel != 1) {
                float umPerPixel = nmPerPixel / 1000;
                locationConversion = 1 / umPerPixel;
            }
            break;
        default:
            System.err.println("Unsupported location units conversion: " + locationUnits);
    }
    IntensityUnits intensityUnits = spotList.getIntensityUnits();
    boolean intensityUnitsWarning = false;
    float intensityConversion = 1;
    switch(intensityUnits) {
        case COUNTS:
            break;
        case PHOTONS:
            intensityConversion = getGain(results.getCalibration());
            break;
        default:
            System.err.println("Unsupported intensity units conversion: " + intensityUnits);
    }
    final float bias = (results.getCalibration().hasBias()) ? (float) results.getCalibration().getBias() : 0f;
    ThetaUnits thetaUnits = spotList.getThetaUnits();
    float thetaConversion = 1;
    switch(thetaUnits) {
        case DEGREES:
            break;
        case RADIANS:
            thetaConversion = (float) (180.0 / Math.PI);
            break;
        default:
            System.err.println("Unsupported theta units conversion: " + thetaUnits);
    }
    FitMode fitMode = FitMode.ONEAXIS;
    if (spotList.hasFitMode())
        fitMode = spotList.getFitMode();
    final boolean filterPosition = position > 0;
    final boolean filterSlice = slice > 0;
    long expectedSpots = getExpectedSpots();
    try {
        long totalSpots = 0;
        while (fi.available() > 0 && (totalSpots < expectedSpots || expectedSpots == 0)) {
            totalSpots++;
            Spot spot = Spot.parseDelimitedFrom(fi);
            // Only read the specified channel, position, slice and fluorophore type
            if (spot.getChannel() != channel)
                continue;
            if (filterPosition && spot.hasPos() && spot.getPos() != position)
                continue;
            if (filterSlice && spot.hasSlice() && spot.getSlice() != slice)
                continue;
            if (spot.hasFluorophoreType() && spot.getFluorophoreType() != fluorophoreType)
                continue;
            if (spot.hasLocationUnits() && !locationUnitsWarning && spot.getLocationUnits() != locationUnits) {
                System.err.println("Spot message has different location units, the units will be ignored: " + spot.getLocationUnits());
                locationUnitsWarning = true;
            }
            if (spot.hasIntensityUnits() && !intensityUnitsWarning && spot.getIntensityUnits() != intensityUnits) {
                System.err.println("Spot message has different intensity units, the units will be ignored: " + spot.getIntensityUnits());
                intensityUnitsWarning = true;
            }
            // Required fields
            int frame = spot.getFrame();
            float[] params = new float[7];
            params[Gaussian2DFunction.X_POSITION] = spot.getX() * locationConversion;
            params[Gaussian2DFunction.Y_POSITION] = spot.getY() * locationConversion;
            params[Gaussian2DFunction.SIGNAL] = spot.getIntensity() * intensityConversion;
            if (spot.hasBackground()) {
                // The writer of the TSF file should have removed the bias (as documented in the format).
                // We can add it back for GSDC results
                params[Gaussian2DFunction.BACKGROUND] = spot.getBackground() * intensityConversion + bias;
            }
            // Support different Gaussian shapes
            if (fitMode == FitMode.ONEAXIS) {
                params[Gaussian2DFunction.X_SD] = params[Gaussian2DFunction.Y_SD] = spot.getWidth() / TSFPeakResultsWriter.SD_TO_FWHM_FACTOR;
            } else {
                if (!spot.hasA()) {
                    params[Gaussian2DFunction.X_SD] = params[Gaussian2DFunction.Y_SD] = spot.getWidth() / TSFPeakResultsWriter.SD_TO_FWHM_FACTOR;
                } else {
                    double a = Math.sqrt(spot.getA());
                    double sd = spot.getWidth() / TSFPeakResultsWriter.SD_TO_FWHM_FACTOR;
                    params[Gaussian2DFunction.X_SD] = (float) (sd * a);
                    params[Gaussian2DFunction.Y_SD] = (float) (sd / a);
                }
                if (fitMode == FitMode.TWOAXISANDTHETA && spot.hasTheta()) {
                    params[Gaussian2DFunction.SHAPE] = spot.getTheta() * thetaConversion;
                }
            }
            // We can use the original position in pixels used for fitting
            int origX = (spot.hasXPosition()) ? spot.getXPosition() : 0;
            int origY = (spot.hasYPosition()) ? spot.getYPosition() : 0;
            // Q. Should we use the required field 'molecule'?
            float origValue = 0;
            double error = 0;
            float noise = 0;
            float[] paramsStdDev = null;
            int id = 0;
            int endFrame = frame;
            if (isGDSC) {
                error = spot.getError();
                noise = spot.getNoise();
                id = spot.getCluster();
                origValue = spot.getOriginalValue();
                endFrame = spot.getEndFrame();
                if (spot.getParamsStdDevCount() != 0) {
                    paramsStdDev = new float[spot.getParamsStdDevCount()];
                    for (int i = 0; i < paramsStdDev.length; i++) paramsStdDev[i] = spot.getParamsStdDev(i);
                }
            } else // Use the standard cluster field for the ID
            if (spot.hasCluster()) {
                id = spot.getCluster();
            }
            // Allow storing any of the optional attributes
            AttributePeakResult peakResult = new AttributePeakResult(frame, origX, origY, origValue, error, noise, params, paramsStdDev);
            peakResult.setEndFrame(endFrame);
            peakResult.setId(id);
            if (spot.hasXPrecision() || spot.hasYPrecision()) {
                // Use the average. Note this is not the Euclidean distance since we divide by n!
                double p = 0;
                int n = 0;
                if (spot.hasXPrecision()) {
                    p = spot.getXPrecision() * spot.getXPrecision();
                    n++;
                }
                if (spot.hasYPrecision()) {
                    p += spot.getYPrecision() * spot.getYPrecision();
                    n++;
                }
                peakResult.setPrecision(Math.sqrt(p / n));
            }
            results.add(peakResult);
        }
    } catch (IOException e) {
        System.err.println("Failed to read Spot message");
        e.printStackTrace();
        // Only fail if there is a number of expected spots. 
        if (expectedSpots != 0) {
            System.err.println("Unexpected error in reading Spot messages, no results will be returned");
            return null;
        }
    } finally {
        if (fi != null) {
            try {
                fi.close();
            } catch (IOException e) {
            }
        }
    }
    return results;
}