Examples with IDirectFilter gdsc.smlm.results.filter.IDirectFilter used on opensource projects

Example 1 with IDirectFilter

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

the class BenchmarkFilterAnalysis method readFilterSets.

@SuppressWarnings("unchecked")
private List<FilterSet> readFilterSets() {
    if (extraOptions && BenchmarkSpotFit.multiFilter != null) {
        IDirectFilter f = BenchmarkSpotFit.multiFilter.getFilter();
        if (f instanceof DirectFilter) {
            GenericDialog gd = new GenericDialog(TITLE);
            gd.addMessage("Use an identical filter to " + BenchmarkSpotFit.TITLE);
            gd.enableYesNoCancel();
            gd.hideCancelButton();
            gd.showDialog();
            if (gd.wasOKed()) {
                setLastFile(null);
                List<FilterSet> filterSets = new ArrayList<FilterSet>(1);
                List<Filter> filters = new ArrayList<Filter>(1);
                filters.add((DirectFilter) f);
                FilterSet filterSet = new FilterSet(filters);
                filterSets.add(filterSet);
                resetParametersFromFitting();
                createResultsPrefix2();
                return filterSets;
            }
        }
    }
    GlobalSettings gs = SettingsManager.loadSettings();
    FilterSettings filterSettings = gs.getFilterSettings();
    String filename = Utils.getFilename("Filter_File", filterSettings.filterSetFilename);
    if (filename != null) {
        IJ.showStatus("Reading filters ...");
        filterSettings.filterSetFilename = filename;
        // Allow the filters to be cached
        if (isSameFile(filename)) {
            GenericDialog gd = new GenericDialog(TITLE);
            gd.hideCancelButton();
            gd.addMessage("The same filter file was selected.");
            gd.addCheckbox("Re-use_filters", reUseFilters);
            gd.showDialog();
            if (!gd.wasCanceled()) {
                if ((reUseFilters = gd.getNextBoolean())) {
                    SettingsManager.saveSettings(gs);
                    return filterList;
                }
            }
        }
        BufferedReader input = null;
        setLastFile(null);
        try {
            FileInputStream fis = new FileInputStream(filename);
            input = new BufferedReader(new UnicodeReader(fis, null));
            Object o = XStreamWrapper.getInstance().fromXML(input);
            if (o != null && o instanceof List<?>) {
                SettingsManager.saveSettings(gs);
                List<FilterSet> filterSets = (List<FilterSet>) o;
                if (containsStandardFilters(filterSets)) {
                    IJ.log("Filter sets must contain 'Direct' filters");
                    return null;
                }
                // Check they are not empty lists
                List<FilterSet> filterSets2 = new LinkedList<FilterSet>();
                for (FilterSet filterSet : filterSets) {
                    if (filterSet.size() != 0) {
                        filterSets2.add(filterSet);
                    } else {
                        IJ.log("Filter set empty: " + filterSet.getName());
                    }
                }
                if (filterSets2.isEmpty()) {
                    IJ.log("All Filter sets are empty");
                    return null;
                }
                // Maintain the same list type
                filterSets.clear();
                filterSets.addAll(filterSets2);
                filterList = filterSets;
                // Option to enumerate filters
                expandFilters();
                setLastFile(filename);
                return filterList;
            }
            IJ.log("No filter sets defined in the specified file: " + filename);
        } catch (Exception e) {
            IJ.log("Unable to load the filter sets from file: " + e.getMessage());
        } finally {
            if (input != null) {
                try {
                    input.close();
                } catch (IOException e) {
                // Ignore
                }
            }
            IJ.showStatus("");
        }
    }
    return null;
}