Examples with PSFType uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFType used on opensource projects

Example 1 with PSFType

use of uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFType in project GDSC-SMLM by aherbert.

the class PeakResultsReader method simplifyTwoAxis.

/**
 * Simplify two axis Gaussian 2D data.
 *
 * @param results the results
 * @param removeTheta the remove theta flag
 */
private void simplifyTwoAxis(MemoryPeakResults results, boolean removeTheta) {
    final int[] indices = PsfHelper.getGaussian2DWxWyIndices(psf);
    final int isx = indices[0];
    final int isy = indices[1];
    // Columns to remove
    int remove = (removeTheta) ? 1 : 0;
    // New PSF type
    PSFType psfType;
    // Determine if sy is redundant
    if (results.forEach((PeakResultProcedureX) peakResult -> peakResult.getParameter(isx) != peakResult.getParameter(isy))) {
        if (!removeTheta) {
            // Already a TwoAxis Gaussian
            return;
        }
        // Otherwise this was a TwoAxisAndTheta with 1 column to remove
        // so it should be simplified
        psfType = PSFType.TWO_AXIS_GAUSSIAN_2D;
    } else {
        // sy is redundant so remove another column
        psfType = PSFType.ONE_AXIS_GAUSSIAN_2D;
        remove++;
    }
    // Update the PSF
    final PSF.Builder builder = psf.toBuilder();
    builder.setPsfType(psfType);
    psf = builder.build();
    results.setPsf(psf);
    // Update the results.
    // We can directly manipulate the params array
    final int newLength = results.getf(0).getNumberOfParameters() - remove;
    if (deviations) {
        results.forEach((PeakResultProcedure) peakResult -> {
            peakResult.resizeParameters(newLength);
            peakResult.resizeParameterDeviations(newLength);
        });
    } else {
        results.forEach((PeakResultProcedure) peakResult -> peakResult.resizeParameters(newLength));
    }
}

Example 2 with PSFType

use of uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFType in project GDSC-SMLM by aherbert.

the class PeakFit method addPsfOptions.

/**
 * Adds the PSF options.
 *
 * <p>Note that if an astigmatic PSF is selected then the model must be created with
 * {@link #configurePsfModel(FitEngineConfiguration, int)}.
 *
 * @param gd the dialog
 * @param fitConfigurationProvider the fit configuration provider
 */
public static void addPsfOptions(final ExtendedGenericDialog gd, final FitConfigurationProvider fitConfigurationProvider) {
    final FitConfiguration fitConfig = fitConfigurationProvider.getFitConfiguration();
    gd.addChoice("PSF", getPsfTypeNames(), PsfProtosHelper.getName(fitConfig.getPsfType()), new OptionListener<Integer>() {

        @Override
        public boolean collectOptions(Integer field) {
            final FitConfiguration fitConfig = fitConfigurationProvider.getFitConfiguration();
            fitConfig.setPsfType(PeakFit.getPsfTypeValues()[field]);
            return collectOptions(false);
        }

        @Override
        public boolean collectOptions() {
            return collectOptions(true);
        }

        private boolean collectOptions(boolean silent) {
            final FitConfiguration localFitConfig = fitConfigurationProvider.getFitConfiguration();
            final PSFType psfType = localFitConfig.getPsfType();
            final ExtendedGenericDialog egd = new ExtendedGenericDialog("PSF Options", null);
            PSF oldPsf = null;
            if (psfType == PSFType.ASTIGMATIC_GAUSSIAN_2D) {
                // The PSF is entirely defined in the model
                String[] list = AstigmatismModelManager.listAstigmatismModels(false, localFitConfig.getCalibrationReader().getNmPerPixel(), 0.1);
                // In case the calibration has not been updated
                if (list.length == 0) {
                    list = AstigmatismModelManager.listAstigmatismModels(false, true);
                }
                egd.addChoice("Z-model", list, localFitConfig.getPsfModelName());
            } else {
                // Collect the PSF parameters
                oldPsf = localFitConfig.getPsf();
                for (int i = 0; i < oldPsf.getParametersCount(); i++) {
                    final PSFParameter p = oldPsf.getParameters(i);
                    egd.addNumericField(String.format("PSF_parameter_%d (%s)", i + 1, p.getName()), p.getValue(), 3);
                }
                if (psfType == PSFType.ONE_AXIS_GAUSSIAN_2D) {
                    egd.addCheckbox("Fixed", localFitConfig.isFixedPsf());
                }
            }
            egd.setSilent(silent);
            egd.showDialog(true, gd);
            if (egd.wasCanceled()) {
                return false;
            }
            if (psfType == PSFType.ASTIGMATIC_GAUSSIAN_2D) {
                // The PSF is entirely defined in the model
                localFitConfig.setPsfModelName(egd.getNextChoice());
                return true;
            }
            @SuppressWarnings("null") final PSF.Builder b = oldPsf.toBuilder();
            final int n = b.getParametersCount();
            for (int i = 0; i < n; i++) {
                b.getParametersBuilder(i).setValue(egd.getNextNumber());
            }
            final PSF newPsf = b.build();
            localFitConfig.setPsf(newPsf);
            boolean changed = !oldPsf.equals(newPsf);
            if (psfType == PSFType.ONE_AXIS_GAUSSIAN_2D) {
                final boolean newFixed = egd.getNextBoolean();
                changed = changed || (newFixed != localFitConfig.isFixedPsf());
                localFitConfig.setFixedPsf(newFixed);
            }
            return changed;
        }
    });
}

Example 3 with PSFType

use of uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFType in project GDSC-SMLM by aherbert.

the class FitConfiguration method updatePsf.

private void updatePsf(boolean resetAstigmatismModel) {
    invalidateGaussianFunction();
    // Reset the astigmatism model. It will be dynamically created from the PSF settings.
    if (resetAstigmatismModel) {
        astigmatismZModel = null;
    }
    int paramCount;
    final PSFType psfType = psf.getPsfType();
    switch(psfType) {
        case ASTIGMATIC_GAUSSIAN_2D:
            flags = GaussianFunctionFactory.FIT_ERF_ASTIGMATISM;
            // nParams = 2; // Store Sx and Sy
            // The PSF stores the full astigmatism model
            paramCount = 8;
            break;
        case ONE_AXIS_GAUSSIAN_2D:
            if (isFixedPsf()) {
                flags = GaussianFunctionFactory.FIT_ERF_FIXED;
            } else {
                flags = GaussianFunctionFactory.FIT_ERF_CIRCLE;
            }
            paramCount = 1;
            break;
        case TWO_AXIS_AND_THETA_GAUSSIAN_2D:
            flags = GaussianFunctionFactory.FIT_ELLIPTICAL;
            paramCount = 3;
            break;
        case TWO_AXIS_GAUSSIAN_2D:
            flags = GaussianFunctionFactory.FIT_ERF_FREE_CIRCLE;
            paramCount = 2;
            break;
        default:
            throw new IllegalStateException("FitSettings must be a Gaussian 2D PSF");
    }
    isTwoAxisGaussian2D = PsfHelper.isTwoAxisGaussian2D(psfType);
    final boolean changed = psf.getParametersCount() > paramCount;
    if (changed) {
        while (psf.getParametersCount() > paramCount) {
            psf.removeParameters(psf.getParametersCount() - 1);
        }
        // Updated names when changing from two-axis to one axis
        if (psf.getParametersCount() == 1) {
            psf.getParametersBuilder(PsfHelper.INDEX_SX).setName(PsfProtosHelper.defaultOneAxisGaussian2DPSF.getParameters(PsfHelper.INDEX_SX).getName());
        }
    }
    // Ensure we have enough parameters
    if (psf.getParametersCount() == 0 && paramCount > 0) {
        // Create a dummy Sx
        final PSFParameter.Builder p = psf.addParametersBuilder();
        p.setName(PsfProtosHelper.defaultOneAxisGaussian2DPSF.getParameters(PsfHelper.INDEX_SX).getName());
        p.setValue(1);
        p.setUnit(PSFParameterUnit.DISTANCE);
    }
    if (psf.getParametersCount() == 1 && paramCount > 1) {
        // Rename S to Sx
        psf.getParametersBuilder(PsfHelper.INDEX_SX).setName(PsfProtosHelper.defaultTwoAxisGaussian2DPSF.getParameters(PsfHelper.INDEX_SX).getName());
        // Duplicate the Sx to Sy
        final PSFParameter.Builder p = psf.addParametersBuilder();
        p.setName(PsfProtosHelper.defaultTwoAxisGaussian2DPSF.getParameters(PsfHelper.INDEX_SY).getName());
        p.setValue(psf.getParameters(PsfHelper.INDEX_SX).getValue());
        p.setUnit(PSFParameterUnit.DISTANCE);
    }
    if (psf.getParametersCount() == 2 && paramCount > 2) {
        // Create a dummy angle
        final PSFParameter.Builder p = psf.addParametersBuilder();
        p.setName(PsfProtosHelper.defaultTwoAxisAndThetaGaussian2DPSF.getParameters(PsfHelper.INDEX_THETA).getName());
        p.setUnit(PSFParameterUnit.ANGLE);
    }
    // These depend on the 2-axis Gaussian flag
    updateWidthThreshold();
    updateMinWidthThreshold();
    // This depends on the width.
    updateCoordinateShift();
}