Examples with Location loci.common.Location used on opensource projects

Example 11 with Location

use of loci.common.Location 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 12 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class FlexReader method findFiles.

private String[] findFiles(Location baseFile, String[] suffixes) throws IOException {
    // we're assuming that the directory structure looks something like this:
    // 
    // top level directory
    // /              \
    // top level flex dir       top level measurement dir
    // /     |    \                 /       |     \
    // plate #0   ...   plate #n     plate #0    ...    plate #n
    // /   |  \                        /   \
    // .flex ... .flex                 .mea   .res
    // 
    // or like this:
    // 
    // top level directory
    // /  |  \      /  |  \
    // Flex plate #0  ... #n    #0 ... Measurement plate #n
    // 
    // or that the .mea and .res are in the same directory as the .flex files
    LOGGER.debug("findFiles({})", baseFile.getAbsolutePath());
    LOGGER.info("Looking for files that are in the same dataset as " + baseFile.getAbsolutePath());
    final List<String> fileList = new ArrayList<String>();
    Location plateDir = baseFile.getParentFile();
    String[] files = plateDir.list(true);
    // check if the measurement files are in the same directory
    LOGGER.debug("Looking for files in {}", plateDir.getAbsolutePath());
    for (String file : files) {
        String lfile = file.toLowerCase();
        String path = new Location(plateDir, file).getAbsolutePath();
        if (checkSuffix(file, suffixes)) {
            fileList.add(path);
            LOGGER.debug("Found file {}", path);
        }
    }
    // file list is valid (i.e. can be returned) if there is at least
    // one file with each of the desired suffixes
    LOGGER.debug("Checking to see if at least one file with each suffix was found...");
    boolean validList = true;
    for (String suffix : suffixes) {
        boolean foundSuffix = false;
        for (String file : fileList) {
            if (checkSuffix(file, suffix)) {
                foundSuffix = true;
                break;
            }
        }
        if (!foundSuffix) {
            validList = false;
            break;
        }
    }
    LOGGER.debug("{} required files.", validList ? "Found" : "Did not find");
    if (validList) {
        LOGGER.debug("Returning file list:");
        for (String file : fileList) {
            LOGGER.debug("  {}", file);
            if (checkSuffix(file, MEASUREMENT_SUFFIXES) && !measurementFiles.contains(file)) {
                measurementFiles.add(file);
            }
        }
        return fileList.toArray(new String[fileList.size()]);
    }
    Location flexDir = null;
    try {
        flexDir = plateDir.getParentFile();
    } catch (NullPointerException e) {
    }
    LOGGER.debug("Looking for files in {}", flexDir);
    if (flexDir == null)
        return null;
    // check if the measurement directory and the Flex directory
    // have the same parent
    Location measurementDir = null;
    String[] flexDirList = flexDir.list(true);
    if (flexDirList.length > 1) {
        String plateName = plateDir.getName();
        for (String file : flexDirList) {
            if (!file.equals(plateName) && (plateName.startsWith(file) || file.startsWith(plateName))) {
                measurementDir = new Location(flexDir, file);
                LOGGER.debug("Expect measurement files to be in {}", measurementDir.getAbsolutePath());
                break;
            }
        }
    }
    if (measurementDir == null) {
        Location topDir = flexDir.getParentFile();
        LOGGER.debug("First attempt at finding measurement file directory " + "failed.  Looking for an appropriate measurement directory in {}.", topDir.getAbsolutePath());
        String[] topDirList = topDir.list(true);
        for (String file : topDirList) {
            if (!flexDir.getAbsolutePath().endsWith(file)) {
                measurementDir = new Location(topDir, file);
                LOGGER.debug("Expect measurement files to be in {}", measurementDir.getAbsolutePath());
                break;
            }
        }
        if (measurementDir == null) {
            LOGGER.debug("Failed to find measurement file directory.");
            return null;
        }
    } else
        plateDir = measurementDir;
    if (!plateDir.getAbsolutePath().equals(measurementDir.getAbsolutePath())) {
        LOGGER.debug("Measurement files are in a subdirectory of {}", measurementDir.getAbsolutePath());
        String[] measurementPlates = measurementDir.list(true);
        String plate = plateDir.getName();
        LOGGER.debug("Determining which subdirectory contains the measurements " + "for plate {}", plate);
        plateDir = null;
        if (measurementPlates != null) {
            for (String file : measurementPlates) {
                LOGGER.debug("Checking {}", file);
                if (file.indexOf(plate) != -1 || plate.indexOf(file) != -1) {
                    plateDir = new Location(measurementDir, file);
                    LOGGER.debug("Measurement files are in {}", plateDir.getAbsolutePath());
                    break;
                }
            }
        }
    }
    if (plateDir == null) {
        LOGGER.debug("Could not find appropriate subdirectory.");
        return null;
    }
    files = plateDir.list(true);
    for (String file : files) {
        fileList.add(new Location(plateDir, file).getAbsolutePath());
    }
    LOGGER.debug("Returning file list:");
    for (String file : fileList) {
        LOGGER.debug("  {}", file);
        if (checkSuffix(file, MEASUREMENT_SUFFIXES) && !measurementFiles.contains(file)) {
            measurementFiles.add(file);
        }
    }
    return fileList.toArray(new String[fileList.size()]);
}

Example 13 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class FlexReader method initFlexFile.

private void initFlexFile(String id) throws FormatException, IOException {
    LOGGER.debug("initFlexFile({})", id);
    boolean doGrouping = true;
    Location currentFile = new Location(id).getAbsoluteFile();
    LOGGER.info("Storing well indices");
    try {
        String name = currentFile.getName();
        int[] well = getWell(name);
        if (well[0] > nRows)
            nRows = well[0];
        if (well[1] > nCols)
            nCols = well[1];
    } catch (NumberFormatException e) {
        LOGGER.debug("Could not parse well indices", e);
        doGrouping = false;
    }
    LOGGER.info("Looking for other .flex files");
    if (!isGroupFiles())
        doGrouping = false;
    if (isGroupFiles()) {
        LOGGER.debug("Attempting to find files in the same dataset.");
        try {
            findFiles(currentFile);
        } catch (NullPointerException e) {
            LOGGER.debug("", e);
        } catch (IOException e) {
            LOGGER.debug("", e);
        }
        if (measurementFiles.isEmpty()) {
            LOGGER.warn("Measurement files not found.");
        } else {
            for (String f : measurementFiles) {
                if (checkSuffix(f, RES_SUFFIX)) {
                    parseResFile(f);
                }
            }
        }
    }
    MetadataStore store = makeFilterMetadata();
    LOGGER.info("Making sure that all .flex files are valid");
    final List<String> flex = new ArrayList<String>();
    if (doGrouping) {
        // group together .flex files that are in the same directory
        Location dir = currentFile.getParentFile();
        String[] files = dir.list(true);
        for (String file : files) {
            // file names should be nnnnnnnnn.flex, where 'n' is 0-9
            LOGGER.debug("Checking if {} belongs in the same dataset.", file);
            if (file.endsWith(".flex") && file.length() == 14) {
                flex.add(new Location(dir, file).getAbsolutePath());
                LOGGER.debug("Added {} to dataset.", flex.get(flex.size() - 1));
            }
        }
    }
    String[] files = doGrouping ? flex.toArray(new String[flex.size()]) : new String[] { currentFile.getAbsolutePath() };
    if (files.length == 0) {
        if (Location.getMappedFile(currentFile.getName()) != null) {
            files = new String[] { currentFile.getName() };
        } else {
            files = new String[] { currentFile.getAbsolutePath() };
        }
    }
    LOGGER.debug("Determined that {} .flex files belong together.", files.length);
    groupFiles(files, store);
    populateMetadataStore(store);
}

Example 14 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class FlexReader method populateMetadataStore.

private void populateMetadataStore(MetadataStore store) throws FormatException {
    LOGGER.info("Populating MetadataStore");
    MetadataTools.populatePixels(store, this, true);
    Location currentFile = new Location(getCurrentFile()).getAbsoluteFile();
    int[] lengths = new int[] { fieldCount, wellCount, plateCount };
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    PositiveInteger maxFieldCount = FormatTools.getMaxFieldCount(fieldCount);
    if (maxFieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(maxFieldCount, 0, 0);
    }
    plateAcqStartTime = DateTools.formatDate(plateAcqStartTime, "dd.MM.yyyy  HH:mm:ss");
    if (plateAcqStartTime != null) {
        store.setPlateAcquisitionStartTime(new Timestamp(plateAcqStartTime), 0, 0);
    }
    for (int row = 0; row < wellRows; row++) {
        for (int col = 0; col < wellColumns; col++) {
            int well = row * wellColumns + col;
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellRow(new NonNegativeInteger(row), 0, well);
            store.setWellColumn(new NonNegativeInteger(col), 0, well);
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        int[] pos = FormatTools.rasterToPosition(lengths, i);
        String imageID = MetadataTools.createLSID("Image", i);
        store.setImageID(imageID, i);
        int well = wellNumber[pos[1]][0] * wellColumns + wellNumber[pos[1]][1];
        char wellRow = (char) ('A' + wellNumber[pos[1]][0]);
        store.setImageName("Well " + wellRow + "-" + (wellNumber[pos[1]][1] + 1) + "; Field #" + (pos[0] + 1), i);
        if (acquisitionDates.get(i) != null) {
            store.setImageAcquisitionDate(acquisitionDates.get(i), i);
        }
        if (wellRows == 0 && wellColumns == 0) {
            well = pos[1];
            NonNegativeInteger row = new NonNegativeInteger(wellNumber[pos[1]][0]);
            NonNegativeInteger col = new NonNegativeInteger(wellNumber[pos[1]][1]);
            String wellID = MetadataTools.createLSID("Well", pos[2], well);
            store.setWellID(wellID, pos[2], well);
            store.setWellRow(row, pos[2], pos[1]);
            store.setWellColumn(col, pos[2], pos[1]);
        }
        String wellSample = MetadataTools.createLSID("WellSample", pos[2], well, pos[0]);
        store.setWellSampleID(wellSample, pos[2], well, pos[0]);
        store.setWellSampleIndex(new NonNegativeInteger(i), pos[2], well, pos[0]);
        store.setWellSampleImageRef(imageID, pos[2], well, pos[0]);
        store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        if (plateName == null)
            plateName = currentFile.getParentFile().getName();
        if (plateBarcode != null)
            plateName = plateBarcode + " " + plateName;
        store.setPlateName(plateName, 0);
        store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
        store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
        for (int i = 0; i < getSeriesCount(); i++) {
            int[] pos = FormatTools.rasterToPosition(lengths, i);
            store.setImageInstrumentRef(instrumentID, i);
            int seriesIndex = i * getImageCount();
            if (seriesIndex < objectiveRefs.size()) {
                store.setObjectiveSettingsID(objectiveRefs.get(seriesIndex), i);
            }
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                int channelIndex = seriesIndex + c;
                if (seriesIndex > 0 && channelNames.length == getEffectiveSizeC() * getSeriesCount()) {
                    channelIndex = i * getEffectiveSizeC() + c;
                }
                if (channelNames != null && channelIndex >= channelNames.length) {
                    channelIndex = c;
                }
                if (channelNames != null && channelIndex < channelNames.length) {
                    store.setChannelName(channelNames[channelIndex], i, c);
                }
            }
            if (seriesIndex < lightSourceCombinationRefs.size()) {
                String lightSourceCombo = lightSourceCombinationRefs.get(seriesIndex);
                List<String> lightSources = lightSourceCombinationIDs.get(lightSourceCombo);
                for (int c = 0; c < getEffectiveSizeC(); c++) {
                    int index = seriesIndex + c;
                    if (index < cameraRefs.size()) {
                        store.setDetectorSettingsID(cameraRefs.get(index), i, c);
                        if (index < binnings.size()) {
                            store.setDetectorSettingsBinning(getBinning(binnings.get(index)), i, c);
                        }
                    }
                    if (lightSources != null && c < lightSources.size()) {
                        store.setChannelLightSourceSettingsID(lightSources.get(c), i, c);
                    } else if (c > 0 && lightSources != null && lightSources.size() == 1) {
                        lightSourceCombo = lightSourceCombinationRefs.get(seriesIndex + c);
                        lightSources = lightSourceCombinationIDs.get(lightSourceCombo);
                        store.setChannelLightSourceSettingsID(lightSources.get(0), i, c);
                    }
                    if (index < filterSets.size()) {
                        FilterGroup group = filterSetMap.get(filterSets.get(index));
                        if (group != null) {
                            if (group.emission != null) {
                                store.setLightPathEmissionFilterRef(group.emission, i, c, 0);
                            }
                            if (group.excitation != null) {
                                store.setLightPathExcitationFilterRef(group.excitation, i, c, 0);
                            }
                            if (group.dichroic != null) {
                                store.setLightPathDichroicRef(group.dichroic, i, c);
                            }
                        }
                    }
                }
            }
            if (seriesIndex < xSizes.size()) {
                Length size = FormatTools.getPhysicalSizeX(xSizes.get(seriesIndex));
                if (size != null) {
                    store.setPixelsPhysicalSizeX(size, i);
                }
            }
            if (seriesIndex < ySizes.size()) {
                Length size = FormatTools.getPhysicalSizeY(ySizes.get(seriesIndex));
                if (size != null) {
                    store.setPixelsPhysicalSizeY(size, i);
                }
            }
            int well = wellNumber[pos[1]][0] * wellColumns + wellNumber[pos[1]][1];
            if (wellRows == 0 && wellColumns == 0) {
                well = pos[1];
            }
            if (pos[0] < xPositions.size()) {
                Length l = new Length(xPositions.get(pos[0]), UNITS.REFERENCEFRAME);
                store.setWellSamplePositionX(l, pos[2], well, pos[0]);
            }
            if (pos[0] < yPositions.size()) {
                Length l = new Length(yPositions.get(pos[0]), UNITS.REFERENCEFRAME);
                store.setWellSamplePositionY(l, pos[2], well, pos[0]);
            }
            for (int image = 0; image < getImageCount(); image++) {
                int plane = i * getImageCount() + image;
                int c = getZCTCoords(image)[1];
                if (plane < planePositionX.size()) {
                    store.setPlanePositionX(planePositionX.get(plane), i, image);
                }
                if (plane < planePositionY.size()) {
                    store.setPlanePositionY(planePositionY.get(plane), i, image);
                }
                if (plane < planePositionZ.size()) {
                    store.setPlanePositionZ(planePositionZ.get(plane), i, image);
                }
                if (plane - image + c < planeExposureTime.size()) {
                    if (planeExposureTime.get(plane - image + c) != null) {
                        store.setPlaneExposureTime(new Time(planeExposureTime.get(plane - image + c), UNITS.SECOND), i, image);
                    }
                }
                if (plane < planeDeltaT.size() && planeDeltaT.get(plane) != null) {
                    store.setPlaneDeltaT(new Time(planeDeltaT.get(plane), UNITS.SECOND), i, image);
                }
            }
        }
    }
}

Example 15 with Location

use of loci.common.Location in project bioformats by openmicroscopy.

the class FlexReader method initResFile.

// -- Helper methods --
/**
 * Initialize the dataset from a .res file.
 */
private void initResFile(String id) throws FormatException, IOException {
    LOGGER.debug("initResFile({})", id);
    parseResFile(id);
    Location thisFile = new Location(id).getAbsoluteFile();
    Location parent = thisFile.getParentFile();
    LOGGER.debug("  Looking for an .mea file in {}", parent.getAbsolutePath());
    String[] list = parent.list();
    for (String file : list) {
        if (checkSuffix(file, MEA_SUFFIX)) {
            String mea = new Location(parent, file).getAbsolutePath();
            LOGGER.debug("  Found .mea file {}", mea);
            initMeaFile(mea);
            if (!measurementFiles.contains(thisFile.getAbsolutePath())) {
                measurementFiles.add(thisFile.getAbsolutePath());
            }
            return;
        }
    }
    throw new FormatException("Could not find an .mea file.");
}