Examples with TemplateSettings uk.ac.sussex.gdsc.smlm.data.config.TemplateProtos.TemplateSettings used on opensource projects

Example 1 with TemplateSettings

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

the class DoubletAnalysis method itemStateChanged.

@Override
public void itemStateChanged(ItemEvent event) {
    if (event.getSource() instanceof Choice) {
        // Update the settings from the template
        final Choice choice = (Choice) event.getSource();
        final String templateName = choice.getSelectedItem();
        // Get the configuration template
        final TemplateSettings template = ConfigurationTemplate.getTemplate(templateName);
        if (textCoordinateShiftFactor != null) {
            // Start with a default. This will cause a reset.
            final FitConfiguration fitConfig = new FitConfiguration();
            if (template != null) {
                fitConfig.setFitSettings(template.getFitEngineSettings().getFitSettings());
            }
            cbSmartFilter.setState(fitConfig.isSmartFilter());
            textCoordinateShiftFactor.setText("" + fitConfig.getCoordinateShiftFactor());
            textSignalStrength.setText("" + fitConfig.getSignalStrength());
            textMinPhotons.setText("" + fitConfig.getMinPhotons());
            textMinWidthFactor.setText("" + fitConfig.getMinWidthFactor());
            textWidthFactor.setText("" + fitConfig.getMaxWidthFactor());
            textPrecisionThreshold.setText("" + fitConfig.getPrecisionThreshold());
            textPrecisionMethod.select(fitConfig.getPrecisionMethod().ordinal());
        } else if (template != null) {
            if (template.hasFitEngineSettings()) {
                final boolean custom = ConfigurationTemplate.isCustomTemplate(templateName);
                final FitEngineConfiguration config2 = new FitEngineConfiguration(template.getFitEngineSettings(), template.getCalibration(), template.getPsf());
                final FitConfiguration fitConfig2 = config2.getFitConfiguration();
                if (custom && template.hasPsf()) {
                    textPsf.select(PeakFit.getPsfTypeNames()[fitConfig2.getPsfType().ordinal()]);
                }
                textDataFilterType.select(config2.getDataFilterType().ordinal());
                textDataFilter.select(config2.getDataFilterMethod(0).ordinal());
                textSmooth.setText("" + config2.getDataFilterParameterValue(0));
                textSearch.setText("" + config2.getSearch());
                textBorder.setText("" + config2.getBorder());
                textFitting.setText("" + config2.getFitting());
                textFitSolver.select(FitProtosHelper.getName(fitConfig2.getFitSolver()));
                // Copy settings not in the dialog for the fit solver
                final FitConfiguration fitConfig = config.getFitConfiguration();
                if (custom) {
                    fitConfig.setPsf(fitConfig2.getPsf());
                }
                fitConfig.setFitSolverSettings(fitConfig2.getFitSolverSettings());
            }
        } else {
        // Ignore
        }
    } else if (event.getSource() instanceof Checkbox) {
        final Checkbox checkbox = (Checkbox) event.getSource();
        if (!checkbox.getState()) {
            return;
        }
        if (textCoordinateShiftFactor != null) {
            if (!updateFilterConfiguration(filterFitConfig)) {
                return;
            }
            cbSmartFilter.setState(filterFitConfig.isSmartFilter());
            textCoordinateShiftFactor.setText("" + filterFitConfig.getCoordinateShiftFactor());
            textSignalStrength.setText("" + filterFitConfig.getSignalStrength());
            textMinPhotons.setText("" + filterFitConfig.getMinPhotons());
            textMinWidthFactor.setText("" + filterFitConfig.getMinWidthFactor());
            textWidthFactor.setText("" + filterFitConfig.getMaxWidthFactor());
            textPrecisionThreshold.setText("" + filterFitConfig.getPrecisionThreshold());
            textPrecisionMethod.select(filterFitConfig.getPrecisionMethod().ordinal());
        } else {
            if (!updateFitConfiguration(config)) {
                return;
            }
            final FitConfiguration fitConfig = config.getFitConfiguration();
            textPsf.select(PeakFit.getPsfTypeNames()[fitConfig.getPsfType().ordinal()]);
            textDataFilterType.select(config.getDataFilterType().ordinal());
            textDataFilter.select(config.getDataFilterMethod(0).ordinal());
            textSmooth.setText("" + config.getDataFilterParameterValue(0));
            textSearch.setText("" + config.getSearch());
            textBorder.setText("" + config.getBorder());
            textFitting.setText("" + config.getFitting());
            textFitSolver.select(FitProtosHelper.getName(fitConfig.getFitSolver()));
            textMatchDistance.setText("" + settings.matchDistance);
            textLowerDistance.setText("" + settings.lowerDistance);
            textSignalFactor.setText("" + settings.signalFactor);
            textLowerFactor.setText("" + settings.lowerSignalFactor);
        }
    }
}

Example 2 with TemplateSettings

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

the class SpotFinderPreview method itemStateChanged.

private void itemStateChanged(ItemEvent event) {
    if (event.getSource() instanceof Choice) {
        // Update the settings from the template
        final Choice choice = (Choice) event.getSource();
        final String templateName = choice.getSelectedItem();
        // Get the configuration template
        final TemplateSettings template = ConfigurationTemplate.getTemplate(templateName);
        if (template != null) {
            refreshing = true;
            IJ.log("Applying template: " + templateName);
            for (final String note : template.getNotesList()) {
                IJ.log(note);
            }
            final boolean custom = ConfigurationTemplate.isCustomTemplate(templateName);
            if (template.hasPsf()) {
                refreshSettings(template.getPsf(), custom);
            }
            if (template.hasFitEngineSettings()) {
                refreshSettings(template.getFitEngineSettings(), custom);
            }
            refreshing = false;
        }
    }
}

Example 3 with TemplateSettings

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

the class Configuration method itemStateChanged.

private void itemStateChanged(ItemEvent event) {
    if (event.getSource() instanceof Choice) {
        // Update the settings from the template
        final Choice choice = (Choice) event.getSource();
        final String templateName = choice.getSelectedItem();
        // Get the configuration template
        final TemplateSettings template = ConfigurationTemplate.getTemplate(templateName);
        if (template != null) {
            IJ.log("Applying template: " + templateName);
            final File file = ConfigurationTemplate.getTemplateFile(templateName);
            if (file != null) {
                pluginSettings.templateFilename = file.getPath();
            }
            final StringBuilder sb = new StringBuilder();
            for (final String note : template.getNotesList()) {
                sb.append(note);
                if (!note.endsWith("\n")) {
                    sb.append("\n");
                }
                IJ.log(note);
            }
            pluginSettings.notes = sb.toString();
            final boolean custom = ConfigurationTemplate.isCustomTemplate(templateName);
            if (template.hasCalibration()) {
                refreshSettings(template.getCalibration());
            }
            if (template.hasPsf()) {
                refreshSettings(template.getPsf(), custom);
            }
            if (template.hasFitEngineSettings()) {
                refreshSettings(template.getFitEngineSettings());
            }
        }
    } else if (event.getSource() instanceof Checkbox) {
        if (event.getSource() == textSmartFilter) {
            textDisableSimpleFilter.setState(textSmartFilter.getState());
        }
        updateFilterInput();
    }
}

Example 4 with TemplateSettings

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

the class ConfigurationTemplate method showTemplateInfo.

/**
 * Show the info from the template.
 *
 * @param name the name
 */
private void showTemplateInfo(String name) {
    final TemplateSettings settings = getTemplate(name);
    if (settings == null || settings.getNotesCount() == 0) {
        return;
    }
    if (infoWindow == null || !infoWindow.isVisible()) {
        infoWindow = new TextWindow(title + " Info", "", "", 450, 250);
        // Put underneath the results window
        if (resultsWindow != null) {
            final Point p = resultsWindow.getLocation();
            p.y += resultsWindow.getHeight();
            infoWindow.setLocation(p);
        }
    }
    infoWindow.getTextPanel().clear();
    for (final String note : settings.getNotesList()) {
        // Text window cannot show tabs
        infoWindow.append(note.replace('\t', ','));
    }
}

Example 5 with TemplateSettings

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

the class BenchmarkFilterAnalysis method saveTemplate.

/**
 * Save PeakFit configuration template using the current benchmark settings.
 *
 * @param topFilterSummary the top filter summary
 */
private void saveTemplate(String topFilterSummary) {
    final FitEngineConfiguration config = new FitEngineConfiguration();
    if (!updateAllConfiguration(config, true)) {
        IJ.log("Unable to create the template configuration");
        return;
    }
    // Remove the PSF width to make the template generic
    config.getFitConfiguration().setInitialPeakStdDev(0);
    // Only get this once when doing iterative analysis
    String filename;
    final boolean localSaveTemplateIsSet = saveTemplateIsSet;
    if (localSaveTemplateIsSet) {
        filename = settings.templateFilename;
    } else {
        filename = getFilename("Template_File", settings.templateFilename);
        saveTemplateIsSet = true;
    }
    if (filename != null) {
        settings.templateFilename = filename;
        Prefs.set(Settings.KEY_TEMPLATE_FILENAME, filename);
        final TemplateSettings.Builder templateSettings = TemplateSettings.newBuilder();
        getNotes(templateSettings, topFilterSummary);
        templateSettings.setFitEngineSettings(config.getFitEngineSettings());
        if (!SettingsManager.toJson(templateSettings.build(), filename, SettingsManager.FLAG_SILENT | SettingsManager.FLAG_JSON_WHITESPACE)) {
            IJ.log("Unable to save the template configuration");
            return;
        }
        // This need only be performed once as the sample image is the same for all iterations.
        if (localSaveTemplateIsSet) {
            return;
        }
        // Save some random frames from the test image data
        final ImagePlus imp = CreateData.getImage();
        if (imp == null) {
            return;
        }
        // Get the number of frames
        final ResultsImageSampler sampler = getSampler(results, imp);
        if (!sampler.isValid()) {
            return;
        }
        // Iteratively show the example until the user is happy.
        // Yes = OK, No = Repeat, Cancel = Do not save
        final String keyNo = "nNo";
        final String keyLow = "nLower";
        final String keyHigh = "nHigher";
        if (ImageJUtils.isMacro()) {
            // Collect the options if running in a macro
            final String options = Macro.getOptions();
            settings.countNo = Integer.parseInt(Macro.getValue(options, keyNo, Integer.toString(settings.countNo)));
            settings.countLow = Integer.parseInt(Macro.getValue(options, keyLow, Integer.toString(settings.countLow)));
            settings.countHigh = Integer.parseInt(Macro.getValue(options, keyHigh, Integer.toString(settings.countHigh)));
        } else if (settings.countLow + settings.countHigh == 0) {
            settings.countLow = settings.countHigh = 1;
        }
        final ImagePlus[] out = new ImagePlus[1];
        out[0] = sampler.getSample(settings.countNo, settings.countLow, settings.countHigh);
        if (!ImageJUtils.isMacro()) {
            // Show the template results
            final ConfigurationTemplate configTemplate = new ConfigurationTemplate();
            // Interactively show the sample image data
            final boolean[] close = new boolean[1];
            final ImagePlus[] outImp = new ImagePlus[1];
            if (out[0] != null) {
                final WindowOrganiser windowOrganiser = new WindowOrganiser();
                outImp[0] = display(out[0], windowOrganiser);
                if (windowOrganiser.isNotEmpty()) {
                    close[0] = true;
                    // Zoom a bit
                    final ImageWindow iw = outImp[0].getWindow();
                    for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                        iw.getCanvas().zoomIn(0, 0);
                    }
                }
                configTemplate.createResults(outImp[0]);
            }
            // TODO - fix this when a second sample is made as the results are not updated.
            final ImageListener listener = new ImageListener() {

                @Override
                public void imageOpened(ImagePlus imp) {
                // Do nothing
                }

                @Override
                public void imageClosed(ImagePlus imp) {
                // Do nothing
                }

                @Override
                public void imageUpdated(ImagePlus imp) {
                    if (imp != null && imp == outImp[0]) {
                        configTemplate.updateResults(imp.getCurrentSlice());
                    }
                }
            };
            ImagePlus.addImageListener(listener);
            // Turn off the recorder when the dialog is showing
            final boolean record = Recorder.record;
            Recorder.record = false;
            final NonBlockingGenericDialog gd = new NonBlockingGenericDialog(TITLE);
            ImageJUtils.addMessage(gd, "Showing image data for the template example.\n \nSample Frames:\nEmpty = %d\n" + "Lower density = %d\nHigher density = %d\n", sampler.getNumberOfEmptySamples(), sampler.getNumberOfLowDensitySamples(), sampler.getNumberOfHighDensitySamples());
            gd.addSlider(keyNo, 0, 10, settings.countNo);
            gd.addSlider(keyLow, 0, 10, settings.countLow);
            gd.addSlider(keyHigh, 0, 10, settings.countHigh);
            gd.addDialogListener((genDialog, event) -> {
                // image the user has not seen.
                if (event == null) {
                    return true;
                }
                settings.countNo = (int) genDialog.getNextNumber();
                settings.countLow = (int) genDialog.getNextNumber();
                settings.countHigh = (int) genDialog.getNextNumber();
                out[0] = sampler.getSample(settings.countNo, settings.countLow, settings.countHigh);
                if (out[0] != null) {
                    final WindowOrganiser windowOrganiser = new WindowOrganiser();
                    outImp[0] = display(out[0], windowOrganiser);
                    if (windowOrganiser.isNotEmpty()) {
                        close[0] = true;
                        // Zoom a bit
                        final ImageWindow iw = outImp[0].getWindow();
                        for (int i = 7; i-- > 0 && Math.max(iw.getWidth(), iw.getHeight()) < 512; ) {
                            iw.getCanvas().zoomIn(0, 0);
                        }
                    }
                    configTemplate.createResults(outImp[0]);
                }
                return true;
            });
            gd.showDialog();
            if (gd.wasCanceled()) {
                out[0] = null;
                // For the recorder
                settings.countNo = settings.countLow = settings.countHigh = 0;
            }
            if (close[0]) {
                // Because closing the image sets the stack pixels array to null
                if (out[0] != null) {
                    out[0] = out[0].duplicate();
                }
                outImp[0].close();
            }
            configTemplate.closeResults();
            ImagePlus.removeImageListener(listener);
            if (record) {
                Recorder.record = true;
                Recorder.recordOption(keyNo, Integer.toString(settings.countNo));
                Recorder.recordOption(keyLow, Integer.toString(settings.countLow));
                Recorder.recordOption(keyHigh, Integer.toString(settings.countHigh));
            }
        }
        if (out[0] == null) {
            return;
        }
        final ImagePlus example = out[0];
        filename = FileUtils.replaceExtension(filename, ".tif");
        IJ.save(example, filename);
    }
}