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

Example 1 with FilePattern

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

the class ImagePlusReader method constructImageTitle.

private String constructImageTitle(IFormatReader r, String file, String seriesName, boolean groupFiles) {
    String[] used = r.getUsedFiles();
    String title = file.substring(file.lastIndexOf(File.separator) + 1);
    if (used.length > 1 && groupFiles) {
        FilePattern fp = new FilePattern(new Location(file));
        title = fp.getPattern();
        if (title == null) {
            title = file;
            if (title.indexOf('.') != -1) {
                title = title.substring(0, title.lastIndexOf("."));
            }
        }
        title = title.substring(title.lastIndexOf(File.separator) + 1);
    }
    if (seriesName != null && !file.endsWith(seriesName) && r.getSeriesCount() > 1) {
        title += " - " + seriesName;
    }
    if (title.length() > 128) {
        String a = title.substring(0, 62);
        String b = title.substring(title.length() - 62);
        title = a + "..." + b;
    }
    return title;
}

Example 2 with FilePattern

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

the class LeicaReader method parseFilenames.

private void parseFilenames(int seriesIndex) throws IOException {
    int maxPlanes = 0;
    final List<String> f = new ArrayList<String>();
    int tempImages = in.readInt();
    if (((long) tempImages * nameLength) > in.length()) {
        in.order(!isLittleEndian());
        tempImages = in.readInt();
        in.order(isLittleEndian());
    }
    CoreMetadata ms = core.get(seriesIndex);
    ms.sizeX = in.readInt();
    ms.sizeY = in.readInt();
    in.skipBytes(4);
    int samplesPerPixel = in.readInt();
    ms.rgb = samplesPerPixel > 1;
    ms.sizeC = samplesPerPixel;
    boolean tiffsExist = false;
    String dirPrefix = new Location(currentId).getAbsoluteFile().getParent();
    if (!dirPrefix.endsWith(File.separator))
        dirPrefix += File.separator;
    String prefix = "";
    for (int j = 0; j < tempImages; j++) {
        // read in each filename
        prefix = getString(nameLength);
        f.add(dirPrefix + prefix);
        // test to make sure the path is valid
        Location test = new Location(f.get(f.size() - 1)).getAbsoluteFile();
        LOGGER.debug("Expected to find TIFF file {}", test.getAbsolutePath());
        if (!test.exists()) {
            LOGGER.debug("  file does not exist");
        }
        if (!tiffsExist)
            tiffsExist = test.exists();
    }
    if (!tiffsExist) {
        // Strategy for handling renamed files:
        // 1) Assume that files for each series follow a pattern.
        // 2) Assign each file group to the first series with the correct count.
        LOGGER.info("Handling renamed TIFF files");
        String[] listing = getTIFFList();
        // grab the file patterns
        final List<String> filePatterns = new ArrayList<String>();
        for (String q : listing) {
            Location l = new Location(q).getAbsoluteFile();
            if (!l.exists()) {
                l = new Location(dirPrefix, q).getAbsoluteFile();
            }
            FilePattern pattern = new FilePattern(l);
            if (!pattern.isValid())
                continue;
            AxisGuesser guess = new AxisGuesser(pattern, "XYZCT", 1, 1, 1, false);
            String fp = pattern.getPattern();
            if (guess.getAxisCountS() >= 1) {
                String pre = pattern.getPrefix(guess.getAxisCountS());
                final List<String> fileList = new ArrayList<String>();
                for (int n = 0; n < listing.length; n++) {
                    Location p = new Location(dirPrefix, listing[n]);
                    if (p.getAbsolutePath().startsWith(pre)) {
                        fileList.add(listing[n]);
                    }
                }
                fp = FilePattern.findPattern(l.getAbsolutePath(), dirPrefix, fileList.toArray(new String[fileList.size()]));
            }
            if (fp != null && !filePatterns.contains(fp)) {
                filePatterns.add(fp);
            }
        }
        for (String q : filePatterns) {
            String[] pattern = new FilePattern(q).getFiles();
            if (pattern.length == tempImages) {
                // make sure that this pattern hasn't already been used
                boolean validPattern = true;
                for (int n = 0; n < seriesIndex; n++) {
                    if (files[n] == null)
                        continue;
                    if (files[n].contains(pattern[0])) {
                        validPattern = false;
                        break;
                    }
                }
                if (validPattern) {
                    files[seriesIndex] = new ArrayList<String>();
                    files[seriesIndex].addAll(Arrays.asList(pattern));
                }
            }
        }
    } else {
        files[seriesIndex] = f;
        for (int s = 0; s < seriesIndex; s++) {
            if (files[s] != null) {
                if (files[s].get(0).equals(f.get(0))) {
                    valid[s] = false;
                    files[s] = null;
                }
            }
        }
    }
    if (files[seriesIndex] == null)
        valid[seriesIndex] = false;
    else {
        ms.imageCount = files[seriesIndex].size();
        maxPlanes = (int) Math.max(maxPlanes, ms.imageCount);
    }
}

Example 3 with FilePattern

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

the class MIASReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    if (checkSuffix(id, "txt")) {
        // first need to find a relevant TIFF file
        Location base = new Location(id).getAbsoluteFile();
        Location plate = null;
        if (base.getParentFile().getName().equals("Batchresults")) {
            Location experiment = base.getParentFile().getParentFile();
            String[] plates = experiment.list(true);
            Arrays.sort(plates);
            plate = new Location(experiment, plates[0]);
        } else {
            plate = base.getParentFile();
            if (plate.getName().equals("results"))
                plate = plate.getParentFile();
        }
        String[] list = plate.list(true);
        for (String f : list) {
            if (f.startsWith("Well")) {
                Location well = new Location(plate, f);
                String[] wellList = well.list(true);
                for (String file : wellList) {
                    String path = new Location(well, file).getAbsolutePath();
                    if (isThisType(path) && checkSuffix(path, new String[] { "tif", "tiff" })) {
                        initFile(path);
                        return;
                    }
                }
            }
        }
        throw new FormatException("Could not locate an appropriate TIFF file.");
    }
    if (!isGroupFiles()) {
        tiffs = new String[][] { { id } };
        readers = new MinimalTiffReader[1][1];
        readers[0][0] = new MinimalTiffReader();
        TiffReader r = new TiffReader();
        r.setMetadataStore(getMetadataStore());
        r.setId(tiffs[0][0]);
        core = new ArrayList<CoreMetadata>(r.getCoreMetadataList());
        metadataStore = r.getMetadataStore();
        final Map<String, Object> globalMetadata = r.getGlobalMetadata();
        for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
            addGlobalMeta(entry.getKey(), entry.getValue());
        }
        r.close();
        tileRows = 1;
        tileCols = 1;
        return;
    }
    analysisFiles = new ArrayList<AnalysisFile>();
    // MIAS is a high content screening format which supports multiple plates,
    // wells and fields.
    // Most of the metadata comes from the directory hierarchy, as very little
    // metadata is present in the actual files.
    // 
    // The directory hierarchy is either:
    // 
    // <experiment name>                        top level experiment directory
    // Batchresults                           analysis results for experiment
    // <plate number>_<plate barcode>         one directory for each plate
    // results                              analysis results for plate
    // Well<xxxx>                           one directory for each well
    // mode<x>_z<xxx>_t<xxx>_im<x>_<x>.tif
    // 
    // or:
    // 
    // <experiment name>                        top level experiment directory
    // <plate number>                         plate directory (3 digits)
    // <well number>                        well directory (4 digits)
    // <channel number>                   channel directory (1 digit)
    // <tile row>_<tile col>_<Z>_<T>.tif
    // 
    // Each TIFF file contains a single grayscale plane.  The "mode" block
    // refers to the channel number; the "z" and "t" blocks refer to the
    // Z section and timepoint, respectively.  The "im<x>_<x>" block gives
    // the row and column coordinates of the image within a mosaic.
    // 
    // We are initially given one of these TIFF files; from there, we need
    // to find the top level experiment directory and work our way down to
    // determine how many plates and wells are present.
    LOGGER.info("Building list of TIFF files");
    Location baseFile = new Location(id).getAbsoluteFile();
    Location plate = baseFile.getParentFile().getParentFile();
    String plateName = plate.getName();
    if (!(plateName.length() == 3 || (plateName.length() > 3 && plateName.replaceAll("\\d", "").startsWith("-")))) {
        plate = plate.getParentFile();
        plateName = plate.getName();
    }
    int plateNumber = Integer.parseInt(plateName.substring(0, 3));
    Location experiment = plate.getParentFile();
    String[] directories = experiment.list(true);
    Arrays.sort(directories);
    for (String dir : directories) {
        Location f = new Location(experiment, dir);
        if (dir.equals("Batchresults")) {
            String[] results = f.list(true);
            for (String result : results) {
                Location file = new Location(f, result);
                if (result.startsWith("NEO_Results")) {
                    resultFile = file.getAbsolutePath();
                    AnalysisFile af = new AnalysisFile();
                    af.filename = resultFile;
                    analysisFiles.add(af);
                } else if (result.startsWith("NEO_PlateOutput_")) {
                    int plateIndex = Integer.parseInt(result.substring(16, 19));
                    if (plateIndex == plateNumber) {
                        AnalysisFile af = new AnalysisFile();
                        af.filename = file.getAbsolutePath();
                        af.plate = 0;
                        analysisFiles.add(af);
                    }
                }
            }
        }
    }
    String[] list = plate.list(true);
    Arrays.sort(list);
    final List<String> wellDirectories = new ArrayList<String>();
    for (String dir : list) {
        Location f = new Location(plate, dir);
        if (f.getName().startsWith("Well") || f.getName().length() == 4) {
            // directory name is valid, but we need to make sure that the
            // directory contains a TIFF or a subdirectory
            String[] wellList = f.list(true);
            if (wellList != null) {
                boolean validWell = false;
                for (String potentialTIFF : wellList) {
                    if (potentialTIFF.toLowerCase().endsWith(".tif") || new Location(f, potentialTIFF).isDirectory()) {
                        validWell = true;
                        break;
                    }
                }
                if (validWell)
                    wellDirectories.add(f.getAbsolutePath());
            }
        } else if (f.getName().equals("results")) {
            String[] resultsList = f.list(true);
            for (String result : resultsList) {
                // exclude proprietary program state files
                if (!result.endsWith(".sav") && !result.endsWith(".dsv") && !result.endsWith(".dat")) {
                    Location r = new Location(f, result);
                    AnalysisFile af = new AnalysisFile();
                    af.filename = r.getAbsolutePath();
                    af.plate = 0;
                    if (result.toLowerCase().startsWith("well")) {
                        af.well = Integer.parseInt(result.substring(4, 8)) - 1;
                    }
                    analysisFiles.add(af);
                }
            }
        } else if (f.getName().equals("Nugenesistemplate.txt")) {
            templateFile = f.getAbsolutePath();
        }
    }
    int nWells = wellDirectories.size();
    LOGGER.debug("Found {} wells.", nWells);
    readers = new MinimalTiffReader[nWells][];
    tiffs = new String[nWells][];
    int[] zCount = new int[nWells];
    int[] cCount = new int[nWells];
    int[] tCount = new int[nWells];
    String[] order = new String[nWells];
    wellNumber = new int[nWells];
    String[] wells = wellDirectories.toArray(new String[nWells]);
    Arrays.sort(wells);
    for (int j = 0; j < nWells; j++) {
        Location well = new Location(wells[j]);
        String wellName = well.getName().replaceAll("Well", "");
        wellNumber[j] = Integer.parseInt(wellName) - 1;
        String[] tiffFiles = well.list(true);
        final List<String> tmpFiles = new ArrayList<String>();
        for (String tiff : tiffFiles) {
            String name = tiff.toLowerCase();
            if (name.endsWith(".tif") || name.endsWith(".tiff")) {
                tmpFiles.add(new Location(well, tiff).getAbsolutePath());
            }
        }
        if (tmpFiles.size() == 0) {
            LOGGER.debug("No TIFFs in well directory {}", wells[j]);
            // directories which contain the TIFFs
            for (String dir : tiffFiles) {
                Location file = new Location(well, dir);
                if (dir.length() == 1 && file.isDirectory()) {
                    cCount[j]++;
                    String[] tiffs = file.list(true);
                    for (String tiff : tiffs) {
                        String name = tiff.toLowerCase();
                        if (name.endsWith(".tif") || name.endsWith(".tiff")) {
                            tmpFiles.add(new Location(file, tiff).getAbsolutePath());
                        }
                    }
                }
            }
        }
        tiffFiles = tmpFiles.toArray(new String[0]);
        if (ArrayUtils.isEmpty(tiffFiles)) {
            throw new FormatException("Empty dataset - No tiff files were found.");
        }
        Location firstTiff = new Location(tiffFiles[0]);
        List<String> names = new ArrayList<String>();
        for (Location f : firstTiff.getParentFile().listFiles()) {
            names.add(f.getName());
        }
        FilePattern fp = new FilePattern(FilePattern.findPattern(firstTiff.getName(), null, names.toArray(new String[names.size()])));
        String[] blocks = fp.getPrefixes();
        order[j] = "XY";
        int[] count = fp.getCount();
        for (int block = blocks.length - 1; block >= 0; block--) {
            blocks[block] = blocks[block].toLowerCase();
            blocks[block] = blocks[block].substring(blocks[block].lastIndexOf("_") + 1);
            if (blocks[block].equals("z")) {
                zCount[j] = count[block];
                order[j] += 'Z';
            } else if (blocks[block].equals("t")) {
                tCount[j] = count[block];
                order[j] += 'T';
            } else if (blocks[block].equals("mode")) {
                cCount[j] = count[block];
                order[j] += 'C';
            } else if (blocks[block].equals("im"))
                tileRows = count[block];
            else if (blocks[block].equals(""))
                tileCols = count[block];
            else if (blocks[block].replaceAll("\\d", "").length() == 0) {
                if (block == 3)
                    tileRows = count[block];
                else if (block == 2)
                    tileCols = count[block];
                else if (block == 0) {
                    zCount[j] = count[block];
                    order[j] += 'Z';
                } else if (block == 1) {
                    tCount[j] = count[block];
                    order[j] += 'T';
                }
            } else {
                throw new FormatException("Unsupported block '" + blocks[block]);
            }
        }
        Arrays.sort(tiffFiles);
        tiffs[j] = tiffFiles;
        LOGGER.debug("Well {} has {} files.", j, tiffFiles.length);
        readers[j] = new MinimalTiffReader[tiffFiles.length];
        for (int k = 0; k < tiffFiles.length; k++) {
            readers[j][k] = new MinimalTiffReader();
        }
    }
    // Populate core metadata
    LOGGER.info("Populating core metadata");
    int nSeries = tiffs.length;
    bpp = new int[nSeries];
    if (readers.length == 0) {
        throw new FormatException("No wells were found.");
    }
    // assume that all wells have the same width, height, and pixel type
    readers[0][0].setId(tiffs[0][0]);
    tileWidth = readers[0][0].getSizeX();
    tileHeight = readers[0][0].getSizeY();
    if (tileCols == 0)
        tileCols = 1;
    if (tileRows == 0)
        tileRows = 1;
    core.clear();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        ms.sizeZ = zCount[i];
        ms.sizeC = cCount[i];
        ms.sizeT = tCount[i];
        if (ms.sizeZ == 0)
            ms.sizeZ = 1;
        if (ms.sizeC == 0)
            ms.sizeC = 1;
        if (ms.sizeT == 0)
            ms.sizeT = 1;
        ms.sizeX = tileWidth * tileCols;
        ms.sizeY = tileHeight * tileRows;
        ms.pixelType = readers[0][0].getPixelType();
        ms.sizeC *= readers[0][0].getSizeC();
        ms.rgb = readers[0][0].isRGB();
        ms.littleEndian = readers[0][0].isLittleEndian();
        ms.interleaved = readers[0][0].isInterleaved();
        ms.indexed = readers[0][0].isIndexed();
        ms.falseColor = readers[0][0].isFalseColor();
        ms.dimensionOrder = order[i];
        if (ms.dimensionOrder.indexOf('Z') == -1) {
            ms.dimensionOrder += 'Z';
        }
        if (ms.dimensionOrder.indexOf('C') == -1) {
            ms.dimensionOrder += 'C';
        }
        if (ms.dimensionOrder.indexOf('T') == -1) {
            ms.dimensionOrder += 'T';
        }
        ms.imageCount = ms.sizeZ * ms.sizeT * cCount[i];
        if (ms.imageCount == 0) {
            ms.imageCount = 1;
        }
        bpp[i] = FormatTools.getBytesPerPixel(ms.pixelType);
    }
    // Populate metadata hashtable
    LOGGER.info("Populating metadata hashtable");
    if (resultFile != null && getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String[] cols = null;
        final List<String> rows = new ArrayList<String>();
        boolean doKeyValue = true;
        int nStarLines = 0;
        String analysisResults = DataTools.readFile(resultFile);
        String[] lines = analysisResults.split("\n");
        for (String line : lines) {
            line = line.trim();
            if (line.length() == 0)
                continue;
            if (line.startsWith("******") && line.endsWith("******"))
                nStarLines++;
            if (doKeyValue) {
                String[] n = line.split("\t");
                if (n[0].endsWith(":"))
                    n[0] = n[0].substring(0, n[0].length() - 1);
                if (n.length >= 2)
                    addGlobalMeta(n[0], n[1]);
            } else {
                if (cols == null)
                    cols = line.split("\t");
                else
                    rows.add(line);
            }
            if (nStarLines == 2)
                doKeyValue = false;
        }
        for (String row : rows) {
            String[] d = row.split("\t");
            for (int col = 3; col < cols.length; col++) {
                addGlobalMeta("Plate " + d[0] + ", Well " + d[2] + " " + cols[col], d[col]);
                if (cols[col].equals("AreaCode")) {
                    String wellID = d[col].replaceAll("\\D", "");
                    wellColumns = Integer.parseInt(wellID);
                }
            }
        }
    }
    // Populate MetadataStore
    LOGGER.info("Populating MetadataStore");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    // assume that a 96 well plate is 8x12, and a 384 well plate is 16x24
    if (wellColumns == 0) {
        if (nWells == 96) {
            wellColumns = 12;
        } else if (nWells == 384) {
            wellColumns = 24;
        } else {
            LOGGER.warn("Could not determine the plate dimensions.");
            wellColumns = 24;
        }
    }
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    String plateAcqId = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqId, 0, 0);
    store.setPlateAcquisitionMaximumFieldCount(new PositiveInteger(1), 0, 0);
    for (int well = 0; well < nWells; well++) {
        int wellIndex = wellNumber[well];
        int row = wellIndex / wellColumns;
        int wellCol = (wellIndex % wellColumns) + 1;
        char wellRow = (char) ('A' + row);
        store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
        store.setWellRow(new NonNegativeInteger(row), 0, well);
        store.setWellColumn(new NonNegativeInteger(wellCol - 1), 0, well);
        String imageID = MetadataTools.createLSID("Image", well);
        String wellSampleID = MetadataTools.createLSID("WellSample", 0, well, 0);
        store.setWellSampleID(wellSampleID, 0, well, 0);
        store.setWellSampleIndex(new NonNegativeInteger(well), 0, well, 0);
        store.setImageID(imageID, well);
        store.setImageName("Well " + wellRow + wellCol, well);
        store.setWellSampleImageRef(imageID, 0, well, 0);
        store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, well);
    }
    MetadataLevel level = getMetadataOptions().getMetadataLevel();
    if (level != MetadataLevel.MINIMUM) {
        String experimentID = MetadataTools.createLSID("Experiment", 0);
        store.setExperimentID(experimentID, 0);
        store.setExperimentType(getExperimentType("Other"), 0);
        store.setExperimentDescription(experiment.getName(), 0);
        // populate SPW metadata
        store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
        store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
        parseTemplateFile(store);
        plateName = plateName.substring(plateName.indexOf('-') + 1);
        store.setPlateName(plateName, 0);
        store.setPlateExternalIdentifier(plateName, 0);
        for (int well = 0; well < nWells; well++) {
            // populate Image/Pixels metadata
            store.setImageExperimentRef(experimentID, well);
            String instrumentID = MetadataTools.createLSID("Instrument", 0);
            store.setInstrumentID(instrumentID, 0);
            store.setImageInstrumentRef(instrumentID, well);
        }
        roiFiles = new ArrayList<AnalysisFile>();
        for (AnalysisFile af : analysisFiles) {
            String file = af.filename;
            String name = new Location(file).getName();
            if (!name.startsWith("Well"))
                continue;
            if (name.endsWith("AllModesOverlay.tif")) {
                roiFiles.add(af);
            } else if (name.endsWith("overlay.tif")) {
                roiFiles.add(af);
            }
        }
        if (level != MetadataLevel.NO_OVERLAYS) {
            // populate image-level ROIs
            Color[] colors = new Color[getSizeC()];
            int nextROI = 0;
            for (AnalysisFile af : analysisFiles) {
                String file = af.filename;
                String name = new Location(file).getName();
                if (!name.startsWith("Well"))
                    continue;
                int[] position = getPositionFromFile(file);
                int well = position[0];
                if (name.endsWith("detail.txt")) {
                    String data = DataTools.readFile(file);
                    String[] lines = data.split("\n");
                    int start = 0;
                    while (start < lines.length && !lines[start].startsWith("Label")) {
                        start++;
                    }
                    if (start >= lines.length)
                        continue;
                    String[] columns = lines[start].split("\t");
                    List<String> columnNames = Arrays.asList(columns);
                    for (int j = start + 1; j < lines.length; j++) {
                        populateROI(columnNames, lines[j].split("\t"), well, nextROI++, position[1], position[2], store);
                    }
                } else if (name.endsWith("AllModesOverlay.tif")) {
                    // results/Well<nnnn>_mode<n>_z<nnn>_t<nnn>_AllModesOverlay.tif
                    if (colors[position[3]] != null)
                        continue;
                    try {
                        colors[position[3]] = getChannelColorFromFile(file);
                    } catch (IOException e) {
                    }
                    if (colors[position[3]] == null)
                        continue;
                    for (int s = 0; s < getSeriesCount(); s++) {
                        store.setChannelColor(colors[position[3]], s, position[3]);
                    }
                    if (position[3] == 0) {
                        nextROI += parseMasks(store, well, nextROI, file);
                    }
                } else if (name.endsWith("overlay.tif")) {
                    nextROI += parseMasks(store, well, nextROI, file);
                }
            }
        }
    }
}

Example 4 with FilePattern

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

the class FilePatternTest method testVarDir.

@Test
public void testVarDir() {
    String[] prefixes = { "z" };
    String[] blocks = { "<0-1>" };
    String suffix = SEPARATOR + "foo.tif";
    String pattern = mkPattern(prefixes, blocks, suffix);
    FilePattern fp = new FilePattern(pattern);
    assertTrue(fp.isValid());
    assertFalse(fp.isRegex());
    assertEquals(fp.getPattern(), pattern);
    assertEquals(fp.getPrefixes(), prefixes);
    for (int i = 0; i < prefixes.length; i++) {
        assertEquals(fp.getPrefix(i), prefixes[i]);
    }
    assertEquals(fp.getPrefix(), prefixes[0]);
    assertEquals(fp.getBlocks(), blocks);
    for (int i = 0; i < blocks.length; i++) {
        assertEquals(fp.getBlock(i), blocks[i]);
    }
    assertEquals(fp.getSuffix(), suffix);
    assertEquals(fp.getCount(), new int[] { 2 });
    assertEquals(fp.getElements(), new String[][] { { "0", "1" } });
    assertEqualsNoOrder(fp.getFiles(), new String[] { "z0" + suffix, "z1" + suffix });
    assertEquals(fp.getFirst(), new BigInteger[] { BigInteger.ZERO });
    assertEquals(fp.getLast(), new BigInteger[] { BigInteger.ONE });
    assertEquals(fp.getStep(), new BigInteger[] { BigInteger.ONE });
}

Example 5 with FilePattern

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

the class FilePatternTest method testNonRegex.

@Test
public void testNonRegex() {
    String[] prefixes = { "z", "c", "t" };
    String[] blocks = { "<0-1>", "<R,G,B>", "<10-30:10>" };
    String suffix = ".tif";
    String pattern = mkPattern(prefixes, blocks, suffix);
    FilePattern fp = new FilePattern(pattern);
    assertTrue(fp.isValid());
    assertFalse(fp.isRegex());
    assertEquals(fp.getPattern(), pattern);
    assertEquals(fp.getPrefixes(), prefixes);
    for (int i = 0; i < prefixes.length; i++) {
        assertEquals(fp.getPrefix(i), prefixes[i]);
    }
    assertEquals(fp.getPrefix(), prefixes[0]);
    assertEquals(fp.getBlocks(), blocks);
    for (int i = 0; i < blocks.length; i++) {
        assertEquals(fp.getBlock(i), blocks[i]);
    }
    assertEquals(fp.getSuffix(), suffix);
    assertEquals(fp.getCount(), new int[] { 2, 3, 3 });
    assertEquals(fp.getElements(), new String[][] { { "0", "1" }, { "R", "G", "B" }, { "10", "20", "30" } });
    assertEqualsNoOrder(fp.getFiles(), new String[] { "z0cRt10.tif", "z0cRt20.tif", "z0cRt30.tif", "z0cGt10.tif", "z0cGt20.tif", "z0cGt30.tif", "z0cBt10.tif", "z0cBt20.tif", "z0cBt30.tif", "z1cRt10.tif", "z1cRt20.tif", "z1cRt30.tif", "z1cGt10.tif", "z1cGt20.tif", "z1cGt30.tif", "z1cBt10.tif", "z1cBt20.tif", "z1cBt30.tif" });
    assertEquals(fp.getFirst(), new BigInteger[] { new BigInteger("0"), null, new BigInteger("10") });
    assertEquals(fp.getLast(), new BigInteger[] { new BigInteger("1"), null, new BigInteger("30") });
    assertEquals(fp.getStep(), new BigInteger[] { new BigInteger("1"), null, new BigInteger("10") });
}