Examples with TrackProgressAdaptor uk.ac.sussex.gdsc.core.logging.TrackProgressAdaptor used on opensource projects

Example 1 with TrackProgressAdaptor

use of uk.ac.sussex.gdsc.core.logging.TrackProgressAdaptor in project GDSC-SMLM by aherbert.

the class PeakFit method setup.

@Override
public int setup(String arg, ImagePlus imp) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    pluginFlags = FLAGS;
    extraOptions = ImageJUtils.isExtraOptions();
    maximaIdentification = StringUtils.contains(arg, "spot");
    fitMaxima = StringUtils.contains(arg, "maxima");
    simpleFit = StringUtils.contains(arg, "simple");
    final boolean runSeries = StringUtils.contains(arg, "series");
    ImageSource imageSource = null;
    if (fitMaxima) {
        // The image source will be found from the peak results.
        if (!showMaximaDialog()) {
            return DONE;
        }
        final MemoryPeakResults localResults = ResultsManager.loadInputResults(settings.inputOption, false, DistanceUnit.PIXEL);
        if (localResults == null || localResults.size() == 0) {
            IJ.error(TITLE, "No results could be loaded");
            return DONE;
        }
        if (settings.fitAcrossAllFrames) {
            // Allow the user to select a different image. The source will be set as per the
            // main fit routine from the image (imp).
            singleFrame = 0;
        } else {
            // Check for single frame
            singleFrame = getSingleFrame(localResults);
            // Forces the maxima to be used with their original source.
            imp = null;
            imageSource = localResults.getSource();
            pluginFlags |= NO_IMAGE_REQUIRED;
        }
    } else if (runSeries) {
        imp = null;
        // Select input folder
        final String inputDirectory = IJ.getDirectory("Select image series ...");
        if (inputDirectory == null) {
            return DONE;
        }
        // Load input series ...
        SeriesOpener series;
        if (extraOptions) {
            final String helpKey = maximaIdentification ? "spot-finder-series" : "peak-fit-series";
            series = SeriesOpener.create(inputDirectory, true, HelpUrls.getUrl(helpKey));
        } else {
            series = new SeriesOpener(inputDirectory);
        }
        if (series.getNumberOfImages() == 0) {
            IJ.error(TITLE, "No images in the selected directory:\n" + inputDirectory);
            return DONE;
        }
        final SeriesImageSource seriesImageSource = new SeriesImageSource(getName(series.getImageList()), series);
        // TrackProgress logging is very verbose if the series has many images
        // Status is used only when reading TIFF info.
        // seriesImageSource.setTrackProgress(SimpleImageJTrackProgress.getInstance());
        seriesImageSource.setTrackProgress(new TrackProgressAdaptor() {

            @Override
            public void status(String format, Object... args) {
                ImageJUtils.showStatus(() -> String.format(format, args));
            }
        });
        imageSource = seriesImageSource;
        pluginFlags |= NO_IMAGE_REQUIRED;
    }
    // If the image source has not been set then use the input image
    if (imageSource == null) {
        if (imp == null) {
            IJ.noImage();
            return DONE;
        }
        // Check it is not a previous result
        if (imp.getTitle().endsWith(ImageJImagePeakResults.IMAGE_SUFFIX)) {
            IJImageSource ijImageSource = null;
            // Check the image to see if it has an image source XML structure in the info property
            final Object o = imp.getProperty("Info");
            final Pattern pattern = Pattern.compile("Source: (<.*IJImageSource>.*<.*IJImageSource>)", Pattern.DOTALL);
            final Matcher match = pattern.matcher((o == null) ? "" : o.toString());
            if (match.find()) {
                final ImageSource tmpSource = ImageSource.fromXml(match.group(1));
                if (tmpSource instanceof IJImageSource) {
                    ijImageSource = (IJImageSource) tmpSource;
                    if (!ijImageSource.open()) {
                        ijImageSource = null;
                    } else {
                        imp = WindowManager.getImage(ijImageSource.getName());
                    }
                }
            }
            if (ijImageSource == null) {
                // Look for a parent using the title
                final String parentTitle = imp.getTitle().substring(0, imp.getTitle().length() - ImageJImagePeakResults.IMAGE_SUFFIX.length() - 1);
                final ImagePlus parentImp = WindowManager.getImage(parentTitle);
                if (parentImp != null) {
                    ijImageSource = new IJImageSource(parentImp);
                    imp = parentImp;
                }
            }
            String message = "The selected image may be a previous fit result";
            if (ijImageSource != null) {
                if (!TextUtils.isNullOrEmpty(ijImageSource.getName())) {
                    message += " of: \n \n" + ijImageSource.getName();
                }
                message += " \n \nFit the parent?";
            } else {
                message += " \n \nDo you want to continue?";
            }
            final YesNoCancelDialog d = new YesNoCancelDialog(null, TITLE, message);
            if (ijImageSource == null) {
                if (!d.yesPressed()) {
                    return DONE;
                }
            } else {
                if (d.yesPressed()) {
                    imageSource = ijImageSource;
                }
                if (d.cancelPressed()) {
                    return DONE;
                }
            }
        }
        if (imageSource == null) {
            try {
                imageSource = new IJImageSource(imp);
            } catch (final IllegalArgumentException ex) {
                // This can happen if the image has an origin not in integer pixels
                // e.g. the plugin is run on a plot
                IJ.error(TITLE, "Error using image: " + imp.getTitle() + "\n \n" + ex.getMessage());
                return DONE;
            }
        }
    }
    time = -1;
    if (!initialiseImage(imageSource, getBounds(imp), false)) {
        IJ.error(TITLE, "Failed to initialise the source image: " + imageSource.getName());
        return DONE;
    }
    final int flags = showDialog(imp);
    if ((flags & DONE) == 0) {
        initialiseFitting();
    }
    return flags;
}

Example 2 with TrackProgressAdaptor

use of uk.ac.sussex.gdsc.core.logging.TrackProgressAdaptor in project GDSC-SMLM by aherbert.

the class TiffSeriesViewer method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    settings = Settings.load();
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addChoice("Mode", Settings.MODE, settings.inputMode, new OptionListener<Integer>() {

        @Override
        public boolean collectOptions(Integer value) {
            settings.inputMode = value;
            return collectOptions(false);
        }

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

        private boolean collectOptions(boolean silent) {
            // This has limited silent support to fake running in a macro
            if (settings.inputMode == 0) {
                String dir = null;
                final String title = "Select image series ...";
                if (silent) {
                    final String macroOptions = Macro.getOptions();
                    if (macroOptions != null) {
                        dir = Macro.getValue(macroOptions, title, null);
                    }
                } else {
                    dir = ImageJUtils.getDirectory(title, settings.inputDirectory);
                }
                if (TextUtils.isNullOrEmpty(dir)) {
                    return false;
                }
                settings.inputDirectory = dir;
            } else {
                String file = null;
                final String title = "Select image ...";
                if (silent) {
                    final String macroOptions = Macro.getOptions();
                    if (macroOptions != null) {
                        file = Macro.getValue(macroOptions, title, null);
                    }
                } else {
                    file = ImageJUtils.getFilename(title, settings.inputFile);
                }
                if (TextUtils.isNullOrEmpty(file)) {
                    return false;
                }
                settings.inputFile = file;
            }
            updateLabel();
            return true;
        }
    });
    gd.addMessage("");
    label = gd.getLastLabel();
    if (ImageJUtils.isShowGenericDialog()) {
        final Choice choice = gd.getLastChoice();
        choice.addItemListener(event -> {
            settings.inputMode = choice.getSelectedIndex();
            updateLabel();
        });
        updateLabel();
    }
    gd.addCheckbox("Log_progress", settings.logProgress);
    gd.addChoice("Output_mode", Settings.OUTPUT_MODE, settings.outputMode, new OptionListener<Integer>() {

        @Override
        public boolean collectOptions(Integer value) {
            settings.outputMode = value;
            return collectOptions(false);
        }

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

        private boolean collectOptions(boolean silent) {
            if (settings.outputMode == 0) {
                // Nothing to do
                return false;
            }
            final ExtendedGenericDialog egd = new ExtendedGenericDialog("Output Options");
            egd.addNumericField("Slices_per_image", settings.imageCount, 0);
            egd.addDirectoryField("Output_directory", settings.outputDirectory);
            egd.setSilent(silent);
            egd.showDialog(true, gd);
            if (egd.wasCanceled()) {
                return false;
            }
            settings.imageCount = (int) egd.getNextNumber();
            settings.outputDirectory = egd.getNextString();
            updateLabel2();
            return true;
        }
    });
    gd.addMessage("");
    label2 = gd.getLastLabel();
    if (ImageJUtils.isShowGenericDialog()) {
        final Choice choice = gd.getLastChoice();
        choice.addItemListener(event -> {
            settings.outputMode = choice.getSelectedIndex();
            updateLabel2();
        });
        updateLabel2();
    }
    gd.addHelp(HelpUrls.getUrl("tiff-series-viewer"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    settings.inputMode = gd.getNextChoiceIndex();
    settings.logProgress = gd.getNextBoolean();
    settings.outputMode = gd.getNextChoiceIndex();
    settings.save();
    SeriesImageSource source;
    if (settings.inputMode == 0) {
        final SeriesOpener series = new SeriesOpener(settings.inputDirectory);
        if (series.getNumberOfImages() == 0) {
            IJ.error(TITLE, "No images in the selected directory:\n" + settings.inputDirectory);
            return;
        }
        source = new SeriesImageSource(PeakFit.getName(series.getImageList()), series);
    } else {
        source = new SeriesImageSource(FileUtils.getName(settings.inputFile), new String[] { settings.inputFile });
    }
    // No memory buffer
    source.setBufferLimit(0);
    source.setReadHint(ReadHint.NONSEQUENTIAL);
    if (!source.isTiffSeries) {
        IJ.error(TITLE, "Not a TIFF image");
        return;
    }
    ImageJUtils.showStatus("Opening TIFF ...");
    final TrackProgressAdaptor progress = new TrackProgressAdaptor() {

        @Override
        public void progress(double fraction) {
            IJ.showProgress(fraction);
        }

        @Override
        public void progress(long position, long total) {
            IJ.showProgress((double) position / total);
        }

        @Override
        public void log(String format, Object... args) {
            if (settings.logProgress) {
                ImageJUtils.log(format, args);
            }
        }

        @Override
        public void status(String format, Object... args) {
            ImageJUtils.showStatus(() -> String.format(format, args));
        }

        @Override
        public boolean isLog() {
            return settings.logProgress;
        }
    };
    source.setTrackProgress(progress);
    if (!source.open()) {
        IJ.error(TITLE, "Cannot open the image");
        return;
    }
    ImageJUtils.showStatus("");
    // Create a virtual stack
    final TiffSeriesVirtualStack stack = new TiffSeriesVirtualStack(source);
    if (settings.outputMode == 0) {
        stack.show();
    } else {
        final int nImages = Math.max(1, settings.imageCount);
        final ImagePlus imp = stack.createImp();
        // The calibration only has the offset so ignore for speed.
        // Calibration cal = imp.getCalibration();
        final int size = stack.getSize();
        // Create the format string
        final int digits = String.format("%d", size).length();
        final String format = new File(settings.outputDirectory, imp.getShortTitle() + "%0" + digits + "d.tif").getPath();
        IJ.showStatus("Saving image ...");
        try {
            for (int i = 1; i <= size; i += nImages) {
                if (ImageJUtils.isInterrupted()) {
                    break;
                }
                ImageJUtils.showSlowProgress(i, size);
                final String path = String.format(format, i);
                final ImageStack out = new ImageStack(source.getWidth(), source.getHeight());
                for (int j = 0, k = i; j < nImages && k <= size; j++, k++) {
                    out.addSlice(null, stack.getPixels(k));
                }
                final ImagePlus outImp = new ImagePlus(path, out);
                // outImp.setCalibration(cal);
                saveAsTiff(outImp, path);
            }
            IJ.showStatus("Saved image");
        } catch (final IOException ex) {
            IJ.log(ExceptionUtils.getStackTrace(ex));
            IJ.error(TITLE, "Failed to save image: " + ex.getMessage());
            IJ.showStatus("Failed to save image");
        } finally {
            ImageJUtils.clearSlowProgress();
        }
    }
}