Examples with ImagePlus ij.ImagePlus used on opensource projects

Example 26 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class FolderOpenerDialog method filterImageList.

private void filterImageList() {
    String[] list = imageList;
    ImagePlus imp = nextImage();
    // Reset image list
    currentImage = 0;
    imageList = new String[0];
    if (imp != null && showDialog(imp, list)) {
        // Filter by name
        if (filter != null && (filter.equals("") || filter.equals("*")))
            filter = null;
        if (filter != null) {
            int filteredImages = 0;
            for (int i = 0; i < list.length; i++) {
                if (isRegex && list[i].matches(filter))
                    filteredImages++;
                else if (list[i].indexOf(filter) >= 0)
                    filteredImages++;
                else
                    list[i] = null;
            }
            if (filteredImages == 0) {
                if (isRegex)
                    IJ.error("Import Sequence", "None of the file names match the regular expression.");
                else
                    IJ.error("Import Sequence", "None of the " + list.length + " files contain\n the string '" + filter + "' in their name.");
                return;
            }
            String[] list2 = new String[filteredImages];
            int j = 0;
            for (int i = 0; i < list.length; i++) {
                if (list[i] != null)
                    list2[j++] = list[i];
            }
            list = list2;
        }
        // Process only the requested number of images
        if (n < 1)
            n = list.length;
        if (start < 1 || start > list.length)
            start = 1;
        imageList = new String[list.length];
        int count = 0;
        for (int i = start - 1; i < list.length && count < n; i += increment, count++) {
            imageList[count] = list[i];
        }
        imageList = Arrays.copyOf(imageList, count);
    }
}

Example 27 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class FIRE method showQEstimationInputDialog.

private boolean showQEstimationInputDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    // Build a list of all images with a region ROI
    List<String> titles = new LinkedList<String>();
    if (WindowManager.getWindowCount() > 0) {
        for (int imageID : WindowManager.getIDList()) {
            ImagePlus imp = WindowManager.getImage(imageID);
            if (imp != null && imp.getRoi() != null && imp.getRoi().isArea())
                titles.add(imp.getTitle());
        }
    }
    gd.addMessage("Estimate the blinking correction parameter Q for Fourier Ring Correlation");
    ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
    if (!titles.isEmpty())
        gd.addCheckbox((titles.size() == 1) ? "Use_ROI" : "Choose_ROI", chooseRoi);
    gd.addMessage("Image construction options:");
    //gd.addCheckbox("Use_signal (if present)", useSignal);
    gd.addChoice("Image_scale", SCALE_ITEMS, SCALE_ITEMS[imageScaleIndex]);
    gd.addChoice("Auto_image_size", IMAGE_SIZE_ITEMS, IMAGE_SIZE_ITEMS[imageSizeIndex]);
    gd.addNumericField("Block_size", blockSize, 0);
    gd.addCheckbox("Random_split", randomSplit);
    gd.addNumericField("Max_per_bin", maxPerBin, 0);
    gd.addMessage("Fourier options:");
    String[] fourierMethodNames = SettingsManager.getNames((Object[]) FRC.FourierMethod.values());
    gd.addChoice("Fourier_method", fourierMethodNames, fourierMethodNames[fourierMethodIndex]);
    String[] samplingMethodNames = SettingsManager.getNames((Object[]) FRC.SamplingMethod.values());
    gd.addChoice("Sampling_method", samplingMethodNames, samplingMethodNames[samplingMethodIndex]);
    gd.addSlider("Sampling_factor", 0.2, 4, perimeterSamplingFactor);
    gd.addMessage("Estimation options:");
    String[] thresholdMethodNames = SettingsManager.getNames((Object[]) FRC.ThresholdMethod.values());
    gd.addChoice("Threshold_method", thresholdMethodNames, thresholdMethodNames[thresholdMethodIndex]);
    String[] precisionMethodNames = SettingsManager.getNames((Object[]) PrecisionMethod.values());
    gd.addChoice("Precision_method", precisionMethodNames, precisionMethodNames[precisionMethodIndex]);
    gd.addNumericField("Precision_Mean", mean, 2, 6, "nm");
    gd.addNumericField("Precision_Sigma", sigma, 2, 6, "nm");
    gd.addCheckbox("Sample_decay", sampleDecay);
    gd.addCheckbox("LOESS_smoothing", loessSmoothing);
    gd.addCheckbox("Fit_precision", fitPrecision);
    gd.addSlider("MinQ", 0, 0.4, minQ);
    gd.addSlider("MaxQ", 0.1, 0.5, maxQ);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    inputOption = ResultsManager.getInputSource(gd);
    if (!titles.isEmpty())
        chooseRoi = gd.getNextBoolean();
    //useSignal = gd.getNextBoolean();
    imageScaleIndex = gd.getNextChoiceIndex();
    imageSizeIndex = gd.getNextChoiceIndex();
    blockSize = Math.max(1, (int) gd.getNextNumber());
    randomSplit = gd.getNextBoolean();
    maxPerBin = Math.abs((int) gd.getNextNumber());
    fourierMethodIndex = gd.getNextChoiceIndex();
    fourierMethod = FourierMethod.values()[fourierMethodIndex];
    samplingMethodIndex = gd.getNextChoiceIndex();
    samplingMethod = SamplingMethod.values()[samplingMethodIndex];
    perimeterSamplingFactor = gd.getNextNumber();
    thresholdMethodIndex = gd.getNextChoiceIndex();
    thresholdMethod = FRC.ThresholdMethod.values()[thresholdMethodIndex];
    precisionMethodIndex = gd.getNextChoiceIndex();
    precisionMethod = PrecisionMethod.values()[precisionMethodIndex];
    mean = Math.abs(gd.getNextNumber());
    sigma = Math.abs(gd.getNextNumber());
    sampleDecay = gd.getNextBoolean();
    loessSmoothing = gd.getNextBoolean();
    fitPrecision = gd.getNextBoolean();
    minQ = Maths.clip(0, 0.5, gd.getNextNumber());
    maxQ = Maths.clip(0, 0.5, gd.getNextNumber());
    // Check arguments
    try {
        Parameters.isAboveZero("Perimeter sampling factor", perimeterSamplingFactor);
        if (precisionMethod == PrecisionMethod.FIXED) {
            Parameters.isAboveZero("Precision Mean", mean);
            Parameters.isAboveZero("Precision Sigma", sigma);
        }
        Parameters.isAbove("MaxQ", maxQ, minQ);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    if (!titles.isEmpty() && chooseRoi) {
        if (titles.size() == 1) {
            roiImage = titles.get(0);
            Recorder.recordOption("Image", roiImage);
        } else {
            String[] items = titles.toArray(new String[titles.size()]);
            gd = new ExtendedGenericDialog(TITLE);
            gd.addMessage("Select the source image for the ROI");
            gd.addChoice("Image", items, roiImage);
            gd.showDialog();
            if (gd.wasCanceled())
                return false;
            roiImage = gd.getNextChoice();
        }
        ImagePlus imp = WindowManager.getImage(roiImage);
        roiBounds = imp.getRoi().getBounds();
        roiImageWidth = imp.getWidth();
        roiImageHeight = imp.getHeight();
    } else {
        roiBounds = null;
    }
    return true;
}

Example 28 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class BenchmarkFilterAnalysis method showOverlay.

/**
	 * Show overlay.
	 *
	 * @param allAssignments
	 *            The assignments generated from running the filter (or null)
	 * @param filter
	 *            the filter
	 * @return The results from running the filter (or null)
	 */
private PreprocessedPeakResult[] showOverlay(ArrayList<FractionalAssignment[]> allAssignments, DirectFilter filter) {
    ImagePlus imp = CreateData.getImage();
    if (imp == null)
        return null;
    // Run the filter manually to get the results that pass.
    if (allAssignments == null)
        allAssignments = getAssignments(filter);
    final Overlay o = new Overlay();
    // Do TP
    final TIntHashSet actual = new TIntHashSet();
    final TIntHashSet predicted = new TIntHashSet();
    //int tp = 0, fp = 0, fn = 0;
    for (FractionalAssignment[] assignments : allAssignments) {
        if (assignments == null || assignments.length == 0)
            continue;
        float[] tx = null, ty = null;
        int t = 0;
        //tp += assignments.length;
        if (showTP) {
            tx = new float[assignments.length];
            ty = new float[assignments.length];
        }
        int frame = 0;
        for (int i = 0; i < assignments.length; i++) {
            CustomFractionalAssignment c = (CustomFractionalAssignment) assignments[i];
            IdPeakResult peak = (IdPeakResult) c.peak;
            BasePreprocessedPeakResult spot = (BasePreprocessedPeakResult) c.peakResult;
            actual.add(peak.uniqueId);
            predicted.add(spot.getUniqueId());
            frame = spot.getFrame();
            if (showTP) {
                tx[t] = spot.getX();
                ty[t++] = spot.getY();
            }
        }
        if (showTP)
            SpotFinderPreview.addRoi(frame, o, tx, ty, t, Color.green);
    }
    float[] x = new float[10];
    float[] y = new float[x.length];
    float[] x2 = new float[10];
    float[] y2 = new float[x2.length];
    // Do FP (all remaining results that are not a TP)
    PreprocessedPeakResult[] filterResults = null;
    if (showFP) {
        final MultiPathFilter multiPathFilter = createMPF(filter, minimalFilter);
        //multiPathFilter.setDebugFile("/tmp/filter.txt");
        filterResults = filterResults(multiPathFilter);
        int frame = 0;
        int c = 0;
        int c2 = 0;
        for (int i = 0; i < filterResults.length; i++) {
            if (frame != filterResults[i].getFrame()) {
                if (c != 0)
                    SpotFinderPreview.addRoi(frame, o, x, y, c, Color.red);
                if (c2 != 0)
                    SpotFinderPreview.addRoi(frame, o, x2, y2, c2, Color.magenta);
                c = c2 = 0;
            }
            frame = filterResults[i].getFrame();
            if (predicted.contains(filterResults[i].getUniqueId()))
                continue;
            if (filterResults[i].ignore()) {
                if (x2.length == c2) {
                    x2 = Arrays.copyOf(x2, c2 * 2);
                    y2 = Arrays.copyOf(y2, c2 * 2);
                }
                x2[c2] = filterResults[i].getX();
                y2[c2++] = filterResults[i].getY();
            } else {
                if (x.length == c) {
                    x = Arrays.copyOf(x, c * 2);
                    y = Arrays.copyOf(y, c * 2);
                }
                x[c] = filterResults[i].getX();
                y[c++] = filterResults[i].getY();
            }
        }
        //fp += c;
        if (c != 0)
            SpotFinderPreview.addRoi(frame, o, x, y, c, Color.red);
        if (c2 != 0)
            SpotFinderPreview.addRoi(frame, o, x2, y2, c2, Color.magenta);
    }
    // Do TN (all remaining peaks that have not been matched)
    if (showFN) {
        final boolean checkBorder = (BenchmarkSpotFilter.lastAnalysisBorder != null && BenchmarkSpotFilter.lastAnalysisBorder.x != 0);
        final float border, xlimit, ylimit;
        if (checkBorder) {
            final Rectangle lastAnalysisBorder = BenchmarkSpotFilter.lastAnalysisBorder;
            border = lastAnalysisBorder.x;
            xlimit = lastAnalysisBorder.x + lastAnalysisBorder.width;
            ylimit = lastAnalysisBorder.y + lastAnalysisBorder.height;
        } else
            border = xlimit = ylimit = 0;
        // Add the results to the lists
        actualCoordinates.forEachEntry(new CustomTIntObjectProcedure(x, y, x2, y2) {

            public boolean execute(int frame, IdPeakResult[] results) {
                int c = 0, c2 = 0;
                if (x.length <= results.length) {
                    x = new float[results.length];
                    y = new float[results.length];
                }
                if (x2.length <= results.length) {
                    x2 = new float[results.length];
                    y2 = new float[results.length];
                }
                for (int i = 0; i < results.length; i++) {
                    // Ignore those that were matched by TP
                    if (actual.contains(results[i].uniqueId))
                        continue;
                    if (checkBorder && outsideBorder(results[i], border, xlimit, ylimit)) {
                        x2[c2] = results[i].getXPosition();
                        y2[c2++] = results[i].getYPosition();
                    } else {
                        x[c] = results[i].getXPosition();
                        y[c++] = results[i].getYPosition();
                    }
                }
                //fn += c;
                if (c != 0)
                    SpotFinderPreview.addRoi(frame, o, x, y, c, Color.yellow);
                if (c2 != 0)
                    SpotFinderPreview.addRoi(frame, o, x2, y2, c2, Color.orange);
                return true;
            }
        });
    }
    //System.out.printf("TP=%d, FP=%d, FN=%d, N=%d (%d)\n", tp, fp, fn, tp + fn, results.size());
    imp.setOverlay(o);
    return filterResults;
}

Example 29 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class BenchmarkFilterAnalysis method saveTemplate.

/**
	 * Save PeakFit configuration template using the current benchmark settings.
	 * 
	 * @param topFilterSummary
	 */
private void saveTemplate(String topFilterSummary) {
    FitEngineConfiguration config = new FitEngineConfiguration(new FitConfiguration());
    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);
    String filename = getFilename("Template_File", templateFilename);
    if (filename != null) {
        templateFilename = filename;
        Prefs.set(KEY_TEMPLATE_FILENAME, filename);
        GlobalSettings settings = new GlobalSettings();
        settings.setNotes(getNotes(topFilterSummary));
        settings.setFitEngineConfiguration(config);
        if (!SettingsManager.saveSettings(settings, filename, true)) {
            IJ.log("Unable to save the template configuration");
            return;
        }
        // Save some random frames from the test image data
        ImagePlus imp = CreateData.getImage();
        if (imp == null)
            return;
        // Get the number of frames
        final ImageStack stack = imp.getImageStack();
        if (sampler == null || sampler.getResults() != results) {
            sampler = new ResultsImageSampler(results, stack, 32);
            sampler.analyse();
        }
        if (!sampler.isValid())
            return;
        // Iteratively show the example until the user is happy.
        // Yes = OK, No = Repeat, Cancel = Do not save
        String keyNo = "nNo";
        String keyLow = "nLower";
        String keyHigh = "nHigher";
        if (Utils.isMacro()) {
            // Collect the options if running in a macro
            String options = Macro.getOptions();
            nNo = Integer.parseInt(Macro.getValue(options, keyNo, Integer.toString(nNo)));
            nLow = Integer.parseInt(Macro.getValue(options, keyLow, Integer.toString(nLow)));
            nHigh = Integer.parseInt(Macro.getValue(options, keyHigh, Integer.toString(nHigh)));
        } else {
            if (nLow + nHigh == 0)
                nLow = nHigh = 1;
        }
        final ImagePlus[] out = new ImagePlus[1];
        out[0] = sampler.getSample(nNo, nLow, nHigh);
        if (!Utils.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) {
                outImp[0] = display(out[0]);
                if (Utils.isNewWindow()) {
                    close[0] = true;
                    // Zoom a bit
                    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.
            ImageListener listener = new ImageListener() {

                public void imageOpened(ImagePlus imp) {
                }

                public void imageClosed(ImagePlus imp) {
                }

                public void imageUpdated(ImagePlus imp) {
                    if (imp != null && imp == outImp[0]) {
                        configTemplate.updateResults(imp.getCurrentSlice());
                    }
                }
            };
            ImagePlus.addImageListener(listener);
            // For the dialog
            String msg = String.format("Showing image data for the template example.\n \nSample Frames:\nEmpty = %d\nLower density = %d\nHigher density = %d\n", sampler.getNumberOfEmptySamples(), sampler.getNumberOfLowDensitySamples(), sampler.getNumberOfHighDensitySamples());
            // Turn off the recorder when the dialog is showing
            boolean record = Recorder.record;
            Recorder.record = false;
            NonBlockingGenericDialog gd = new NonBlockingGenericDialog(TITLE);
            gd.addMessage(msg);
            //gd.enableYesNoCancel(" Save ", " Resample ");
            gd.addSlider(keyNo, 0, 10, nNo);
            gd.addSlider(keyLow, 0, 10, nLow);
            gd.addSlider(keyHigh, 0, 10, nHigh);
            gd.addDialogListener(new DialogListener() {

                public boolean dialogItemChanged(GenericDialog gd, AWTEvent e) {
                    // image the user has not seen.
                    if (e == null)
                        return true;
                    nNo = (int) gd.getNextNumber();
                    nLow = (int) gd.getNextNumber();
                    nHigh = (int) gd.getNextNumber();
                    out[0] = sampler.getSample(nNo, nLow, nHigh);
                    if (out[0] != null) {
                        outImp[0] = display(out[0]);
                        if (Utils.isNewWindow()) {
                            close[0] = true;
                            // Zoom a bit
                            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
                nNo = nLow = nHigh = 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(nNo));
                Recorder.recordOption(keyLow, Integer.toString(nLow));
                Recorder.recordOption(keyHigh, Integer.toString(nHigh));
            }
        }
        if (out[0] == null)
            return;
        ImagePlus example = out[0];
        filename = Utils.replaceExtension(filename, ".tif");
        IJ.save(example, filename);
    }
}

Example 30 with ImagePlus

use of ij.ImagePlus in project GDSC-SMLM by aherbert.

the class PSFCombiner method selectNextImage.

private boolean selectNextImage() {
    // Show a dialog allowing the user to select an input image
    if (titles.isEmpty())
        return false;
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage("Select the next input PSF image.\n(Each PSF must have the nm/pixel scale)");
    int n = (input.size() + 1);
    if (IJ.isMacro())
        gd.addStringField("PSF_" + n, "");
    else
        gd.addChoice("PSF_" + n, titles.toArray(new String[titles.size()]), "");
    gd.addMessage("Cancel to finish");
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    String title;
    if (IJ.isMacro())
        title = gd.getNextString();
    else
        title = gd.getNextChoice();
    // Check the image exists. If not then exit. This is mainly relevant for Macro mode since
    // the
    // loop will continue otherwise since the titles list is not empty.
    ImagePlus imp = WindowManager.getImage(title);
    if (imp == null)
        return false;
    titles.remove(title);
    input.add(new PSF(title));
    return true;
}