Examples with FilePeakResults gdsc.smlm.results.FilePeakResults used on opensource projects

Example 1 with FilePeakResults

use of gdsc.smlm.results.FilePeakResults in project GDSC-SMLM by aherbert.

the class NeighbourAnalysis method saveTraces.

private void saveTraces(Trace[] traces) {
    String[] path = Utils.decodePath(filename);
    OpenDialog chooser = new OpenDialog("Traces_File", path[0], path[1]);
    if (chooser.getFileName() != null) {
        filename = chooser.getDirectory() + chooser.getFileName();
        // Remove extension and replace with .xls
        int index = filename.lastIndexOf('.');
        if (index > 0) {
            filename = filename.substring(0, index);
        }
        filename += ".xls";
        boolean showDeviations = (!results.getResults().isEmpty() && results.getHead().paramsStdDev != null);
        FilePeakResults traceResults = new FilePeakResults(filename, showDeviations);
        traceResults.copySettings(results);
        traceResults.begin();
        if (!traceResults.isActive()) {
            IJ.error(TITLE, "Failed to write to file: " + filename);
            return;
        }
        traceResults.addComment(createSettingsComment());
        for (Trace trace : traces) // addTrace(...) does a sort on the results
        traceResults.addCluster(trace);
        traceResults.end();
    }
}

Example 2 with FilePeakResults

use of gdsc.smlm.results.FilePeakResults in project GDSC-SMLM by aherbert.

the class PeakFit method addFileResults.

private void addFileResults(PeakResultsList resultsList) {
    String filename = null;
    if (resultsSettings.resultsDirectory != null && new File(resultsSettings.resultsDirectory).exists()) {
        filename = resultsSettings.resultsDirectory + File.separatorChar + source.getName() + ".results." + resultsSettings.getResultsFileFormat().getExtension();
    } else if (resultsSettings.resultsFilename != null && resultsSettings.resultsFilename.length() > 0) {
        filename = resultsSettings.resultsFilename;
    }
    if (filename != null) {
        PeakResults r;
        switch(resultsSettings.getResultsFileFormat()) {
            case GDSC_BINARY:
                r = new BinaryFilePeakResults(filename, resultsSettings.showDeviations);
                break;
            case GDSC_TEXT:
                r = new FilePeakResults(filename, resultsSettings.showDeviations);
                break;
            case MALK:
                r = new MALKFilePeakResults(resultsSettings.resultsFilename);
                break;
            case TSF:
                r = new TSFPeakResultsWriter(resultsSettings.resultsFilename);
                break;
            default:
                throw new RuntimeException("Unsupported file format: " + resultsSettings.getResultsFileFormat());
        }
        if (r instanceof FilePeakResults) {
            FilePeakResults fr = (FilePeakResults) r;
            fr.setSortAfterEnd(Prefs.getThreads() > 1);
            fr.setPeakIdColumnName("Frame");
        }
        resultsList.addOutput(r);
    }
}

Example 3 with FilePeakResults

use of gdsc.smlm.results.FilePeakResults in project GDSC-SMLM by aherbert.

the class ResultsMatchCalculator method createFilePeakResults.

private FilePeakResults createFilePeakResults(MemoryPeakResults results2) {
    if (!saveClassifications)
        return null;
    String[] path = Utils.decodePath(classificationsFile);
    OpenDialog chooser = new OpenDialog("Classifications_File", path[0], path[1]);
    if (chooser.getFileName() != null) {
        classificationsFile = chooser.getDirectory() + chooser.getFileName();
        FilePeakResults r = new FilePeakResults(classificationsFile, false, false);
        r.copySettings(results2);
        r.setPeakIdColumnName("Frame");
        r.begin();
        return r;
    }
    return null;
}

Example 4 with FilePeakResults

use of gdsc.smlm.results.FilePeakResults in project GDSC-SMLM by aherbert.

the class CreateData method saveImageResults.

private void saveImageResults(MemoryPeakResults results) {
    if (!settings.saveImageResults)
        return;
    String[] path = Utils.decodePath(settings.imageResultsFilename);
    OpenDialog chooser = new OpenDialog("Image_Results_File", path[0], path[1]);
    if (chooser.getFileName() != null) {
        settings.imageResultsFilename = chooser.getDirectory() + chooser.getFileName();
        settings.imageResultsFilename = Utils.replaceExtension(settings.imageResultsFilename, "xls");
        FilePeakResults r = new FilePeakResults(settings.imageResultsFilename, false);
        r.copySettings(results);
        r.setPeakIdColumnName("Frame");
        r.begin();
        r.addAll(results.getResults());
        r.end();
    }
}

Example 5 with FilePeakResults

use of gdsc.smlm.results.FilePeakResults in project GDSC-SMLM by aherbert.

the class ResultsManager method addFileResults.

private void addFileResults(PeakResultsList resultsList, boolean showDeviations, boolean showEndFrame, boolean showId) {
    if (resultsSettings.resultsFilename != null && resultsSettings.resultsFilename.length() > 0) {
        // Remove extension
        resultsSettings.resultsFilename = Utils.replaceExtension(resultsSettings.resultsFilename, resultsSettings.getResultsFileFormat().getExtension());
        if (fileInput && inputFilename.equals(resultsSettings.resultsFilename)) {
            IJ.log(TITLE + ": Input and output files are the same, skipping output ...");
            return;
        }
        // Check if file exists
        File file = new File(resultsSettings.resultsFilename);
        if (file.exists()) {
            YesNoCancelDialog d = new YesNoCancelDialog(IJ.getInstance(), TITLE, "Overwrite existing file?\n" + resultsSettings.resultsFilename);
            if (!d.yesPressed())
                return;
        }
        File parent = file.getParentFile();
        if (parent != null && parent.exists()) {
            PeakResults r;
            switch(resultsSettings.getResultsFileFormat()) {
                case GDSC_BINARY:
                    r = new BinaryFilePeakResults(resultsSettings.resultsFilename, showDeviations, showEndFrame, showId);
                    break;
                case GDSC_TEXT:
                    r = new FilePeakResults(resultsSettings.resultsFilename, showDeviations, showEndFrame, showId);
                    break;
                case MALK:
                    r = new MALKFilePeakResults(resultsSettings.resultsFilename);
                    break;
                case TSF:
                    r = new TSFPeakResultsWriter(resultsSettings.resultsFilename);
                    break;
                default:
                    throw new RuntimeException("Unsupported file format: " + resultsSettings.getResultsFileFormat());
            }
            if (r instanceof FilePeakResults) {
                FilePeakResults fr = (FilePeakResults) r;
                fr.setPeakIdColumnName("Frame");
            }
            resultsList.addOutput(r);
        }
    }
}