Examples with FilePattern loci.formats.FilePattern used on opensource projects

Example 16 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class FilePatternDialog method constructDialog.

@Override
protected GenericDialog constructDialog() {
    // CTR - CHECK
    Location idLoc = new Location(options.getId());
    String id = FilePattern.findPattern(idLoc);
    if (id == null) {
        if (!options.isQuiet()) {
            IJ.showMessage("Bio-Formats", "Warning: Bio-Formats was unable to determine a grouping that\n" + "includes the file you chose. The most common reason for this\n" + "situation is that the folder contains extraneous files with\n" + "similar names and numbers that confuse the detection algorithm.\n" + " \n" + "For example, if you have multiple datasets in the same folder\n" + "named series1_z*_c*.tif, series2_z*_c*.tif, etc., Bio-Formats\n" + "may try to group all such files into a single series.\n" + " \n" + "For best results, put each image series's files in their own\n" + "folder, or type in a file pattern manually.\n");
        }
        id = idLoc.getAbsolutePath();
    }
    // construct dialog
    GenericDialog gd = new GenericDialog("Bio-Formats File Stitching") {

        @Override
        public void itemStateChanged(ItemEvent e) {
            super.itemStateChanged(e);
            Object source = e.getSource();
            if (!(source instanceof Checkbox)) {
                return;
            }
            boolean selected = e.getStateChange() == ItemEvent.SELECTED;
            Vector checkboxes = getCheckboxes();
            for (Object checkbox : checkboxes) {
                if (!checkbox.equals(source)) {
                    if (selected) {
                        ((Checkbox) checkbox).setState(false);
                    }
                } else if (!selected && checkbox.equals(source)) {
                    ((Checkbox) checkbox).setState(true);
                }
            }
        }
    };
    gd.addMessage("The list of files to be grouped can be specified in one of the following ways:");
    // option one
    int len = id.length() + 1;
    if (len > 80)
        len = 80;
    originalID = id;
    fp = new FilePattern(id);
    String[] prefixes = fp.getPrefixes();
    if (prefixes.length > 0) {
        gd.addCheckbox("Dimensions", true);
        int[] counts = fp.getCount();
        paddingZeros = new int[counts.length];
        String[][] elements = fp.getElements();
        BigInteger[] first = fp.getFirst();
        BigInteger[] step = fp.getStep();
        for (int i = 0; i < prefixes.length; i++) {
            String prefix = "Axis_" + (i + 1);
            gd.addStringField(prefix + "_number_of_images", "" + counts[i]);
            gd.addStringField(prefix + "_axis_first_image", first[i].toString());
            gd.addStringField(prefix + "_axis_increment", step[i].toString());
            try {
                paddingZeros[i] = elements[i][0].length() - String.valueOf(Integer.parseInt(elements[i][0])).length();
            } catch (NumberFormatException e) {
            }
        }
    }
    // option two
    gd.addCheckbox("File_name", false);
    gd.addStringField("contains", "");
    // option three
    gd.addCheckbox("Pattern", false);
    gd.addStringField("name", id, len);
    rebuild(gd);
    return gd;
}

Example 17 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class ImportProcess method createBaseReader.

/**
 * Initializes an {@link loci.formats.IFormatReader}
 * according to the current configuration.
 */
private void createBaseReader() throws FormatException, IOException {
    if (options.isLocal() || options.isHTTP()) {
        BF.status(options.isQuiet(), "Identifying " + idName);
        imageReader = LociPrefs.makeImageReader();
        baseReader = imageReader.getReader(options.isUsingPatternIds() ? new FilePattern(options.getId()).getFiles()[0] : options.getId());
    } else if (options.isOMERO()) {
        BF.status(options.isQuiet(), "Establishing server connection");
        try {
            ReflectedUniverse r = new ReflectedUniverse();
            r.exec("import loci.ome.io.OmeroReader");
            r.exec("baseReader = new OmeroReader()");
            ClassList<IFormatReader> classes = new ClassList<IFormatReader>(IFormatReader.class);
            r.setVar("classes", classes);
            r.exec("class = baseReader.getClass()");
            r.exec("classes.addClass(class)");
            imageReader = new ImageReader(classes);
            baseReader = imageReader.getReader(options.getId());
        } catch (Exception exc) {
            WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem communicating with the server.");
            cancel();
            return;
        }
    } else {
        WindowTools.reportException(null, options.isQuiet(), "Sorry, there has been an internal error: unknown data source");
        cancel();
        return;
    }
    // attach OME-XML metadata store
    Exception exc = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.createOMEXMLMetadata();
        omeXML = null;
    } catch (DependencyException de) {
        exc = de;
    } catch (ServiceException se) {
        exc = se;
    }
    if (exc != null) {
        WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem constructing the OME-XML metadata store");
        throw new FormatException(exc);
    }
    baseReader.setMetadataStore(meta);
    BF.status(options.isQuiet(), "");
    DebugTools.enableIJLogging(IJ.debugMode);
}

Example 18 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class MetamorphTiffReader method findTIFFs.

private void findTIFFs() throws IOException {
    Location baseFile = new Location(currentId).getAbsoluteFile();
    Location parent = baseFile.getParentFile();
    FilePattern pattern = new FilePattern(baseFile);
    String[] tiffs = pattern.getFiles();
    NumericComparator comparator = new NumericComparator();
    Arrays.sort(tiffs, comparator);
    final List<String> validTIFFs = new ArrayList<String>();
    for (String tiff : tiffs) {
        if (!new Location(tiff).exists()) {
            String base = tiff.substring(tiff.lastIndexOf(File.separator) + 1);
            base = base.substring(0, base.indexOf('.'));
            String suffix = tiff.substring(tiff.lastIndexOf("."));
            while (base.length() < 3) {
                base = "0" + base;
            }
            Location test = new Location(parent, base + suffix);
            if (test.exists()) {
                tiff = test.getAbsolutePath();
            } else
                continue;
        }
        if (File.separator.equals("\\")) {
            tiff = tiff.replaceAll("\\\\\\\\", "\\\\");
        }
        validTIFFs.add(tiff);
    }
    files = validTIFFs.toArray(new String[validTIFFs.size()]);
}

Example 19 with FilePattern

use of loci.formats.FilePattern in project bioformats by openmicroscopy.

the class SewTiffs method main.

public static void main(String[] args) throws Exception {
    if (args.length < 2) {
        System.out.println("Usage: java SewTiffs base_name channel_num [time_count]");
        System.exit(1);
    }
    String base = args[0];
    int c = Integer.parseInt(args[1]);
    int num;
    if (args.length < 3) {
        FilePattern fp = new FilePattern(new Location(base + "_C" + c + "_TP1.tiff"));
        int[] count = fp.getCount();
        num = count[count.length - 1];
    } else
        num = Integer.parseInt(args[2]);
    System.out.println("Fixing " + base + "_C" + c + "_TP<1-" + num + ">.tiff");
    TiffReader in = new TiffReader();
    TiffWriter out = new TiffWriter();
    String outId = base + "_C" + c + ".tiff";
    System.out.println("Writing " + outId);
    out.setId(outId);
    System.out.print("   ");
    boolean comment = false;
    for (int t = 0; t < num; t++) {
        String inId = base + "_C" + c + "_TP" + (t + 1) + ".tiff";
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata meta = service.createOMEXMLMetadata();
        in.setMetadataStore(meta);
        in.setId(inId);
        out.setMetadataRetrieve(meta);
        // read first image plane
        byte[] image = in.openBytes(0);
        in.close();
        if (t == 0) {
            // read first IFD
            RandomAccessInputStream ras = new RandomAccessInputStream(inId);
            TiffParser parser = new TiffParser(ras);
            IFD ifd = parser.getFirstIFD();
            ras.close();
            // preserve TIFF comment
            String desc = ifd.getComment();
            if (desc != null) {
                ifd = new IFD();
                ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, desc);
                comment = true;
                out.saveBytes(t, image, ifd);
                System.out.print(".");
                continue;
            }
        }
        // write image plane
        out.saveBytes(t, image);
        // update status
        System.out.print(".");
        if (t % DOTS == DOTS - 1) {
            System.out.println(" " + (t + 1));
            System.out.print("   ");
        }
    }
    System.out.println();
    if (comment)
        System.out.println("OME-TIFF comment saved.");
    else
        System.out.println("No OME-TIFF comment found.");
}