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

Example 61 with ImageReader

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

the class TestTools method getFiles.

/**
 * Recursively generate a list of files to test.
 */
public static void getFiles(String root, List files, final ConfigurationTree config, String toplevelConfig, String[] subdirs, String configFileSuffix) {
    Location f = new Location(root);
    String[] subs = f.list();
    if (subs == null)
        subs = new String[0];
    if (subdirs != null) {
        subs = subdirs;
    }
    boolean isToplevel = toplevelConfig != null && new File(toplevelConfig).exists();
    Arrays.sort(subs);
    List<String> subsList = new ArrayList<String>();
    if (config.getConfigDirectory() != null) {
        // Look for a configuration file under the configuration directory
        String configRoot = config.relocateToConfig(root);
        Location configFile = new Location(configRoot, baseConfigName);
        if (configFile.exists()) {
            LOGGER.debug("found config file: {}", configFile.getAbsolutePath());
            subsList.add(configFile.getAbsolutePath());
        }
    }
    // make sure that if a config file exists, it is first on the list
    for (int i = 0; i < subs.length; i++) {
        Location file = new Location(root, subs[i]);
        if ((!isToplevel && isConfigFile(file, configFileSuffix)) || (isToplevel && subs[i].equals(toplevelConfig))) {
            if (config.getConfigDirectory() != null) {
                LOGGER.debug("adding config file: {}", file.getAbsolutePath());
                subsList.add(0, file.getAbsolutePath());
            }
        } else {
            subsList.add(file.getAbsolutePath());
        }
    }
    // special config file for the test suite
    LOGGER.debug("\tconfig file");
    try {
        LOGGER.debug("Parsing {}:", subsList.get(0));
        config.parseConfigFile(subsList.get(0));
    } catch (IOException exc) {
        LOGGER.debug("", exc);
    } catch (Throwable e) {
    }
    Arrays.sort(subs, new Comparator() {

        @Override
        public int compare(Object o1, Object o2) {
            String s1 = o1.toString();
            String s2 = o2.toString();
            Configuration c1 = null;
            Configuration c2 = null;
            try {
                c1 = config.get(s1);
            } catch (IOException e) {
            }
            try {
                c2 = config.get(s2);
            } catch (IOException e) {
            }
            if (c1 == null && c2 != null) {
                return 1;
            } else if (c1 != null && c2 == null) {
                return -1;
            }
            return s1.compareTo(s2);
        }
    });
    ImageReader typeTester = new ImageReader();
    for (int i = 0; i < subsList.size(); i++) {
        Location file = new Location(subsList.get(i));
        LOGGER.debug("Checking {}:", subsList.get(i));
        if (isConfigFile(file, configFileSuffix)) {
            continue;
        } else if (isIgnoredFile(subsList.get(i), config)) {
            LOGGER.debug("\tignored");
            continue;
        } else if (file.isDirectory()) {
            LOGGER.debug("\tdirectory");
            getFiles(subsList.get(i), files, config, null, null, configFileSuffix);
        } else if (!subsList.get(i).endsWith("readme.txt") && !subsList.get(i).endsWith("test_setup.ini")) {
            if (typeTester.isThisType(subsList.get(i))) {
                LOGGER.debug("\tOK");
                files.add(file.getAbsolutePath());
            } else
                LOGGER.debug("\tunknown type");
        }
        file = null;
    }
}

Example 62 with ImageReader

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

the class SingularityTest method main.

public static void main(String[] args) throws FormatException, IOException {
    if (args.length < 1) {
        LOGGER.info("Usage: java.loci.tests.SingularityTest /path/to/input-file");
        System.exit(1);
    }
    LOGGER.info("Testing {}", args[0]);
    ImageReader reader = new ImageReader();
    boolean isSingleFile = reader.isSingleFile(args[0]);
    reader.setId(args[0]);
    String[] usedFiles = reader.getUsedFiles();
    if (isSingleFile && usedFiles.length > 1) {
        LOGGER.info("  Used files list contains more than one file, " + "but isSingleFile(String) returned true.");
        LOGGER.info("FAILURE");
    } else if (!isSingleFile && usedFiles.length == 1) {
        LOGGER.info("  Used files list only contains one file, " + "but isSingleFile(String) returned false.");
        LOGGER.info("FAILURE");
    } else
        LOGGER.info("SUCCESS");
}

Example 63 with ImageReader

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

the class Configuration method populateINI.

// -- Helper methods --
private void populateINI(IFormatReader reader) {
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    ini = new IniList();
    IniTable globalTable = new IniTable();
    putTableName(globalTable, reader, " global");
    int seriesCount = reader.getSeriesCount();
    globalTable.put(SERIES_COUNT, String.valueOf(seriesCount));
    IFormatReader r = reader;
    if (r instanceof ImageReader) {
        r = ((ImageReader) r).getReader();
    } else if (r instanceof ReaderWrapper) {
        try {
            r = ((ReaderWrapper) r).unwrap();
        } catch (FormatException e) {
        } catch (IOException e) {
        }
    }
    globalTable.put(READER, TestTools.shortClassName(r));
    globalTable.put(TEST, "true");
    globalTable.put(MEMORY, String.valueOf(TestTools.getUsedMemory()));
    long planeSize = (long) FormatTools.getPlaneSize(reader) * 3;
    boolean canOpenImages = planeSize > 0 && TestTools.canFitInMemory(planeSize);
    long t0 = System.currentTimeMillis();
    if (canOpenImages) {
        try {
            reader.openBytes(0);
        } catch (FormatException e) {
        } catch (IOException e) {
        }
    }
    long t1 = System.currentTimeMillis();
    globalTable.put(ACCESS_TIME, String.valueOf(t1 - t0));
    ini.add(globalTable);
    for (int series = 0; series < seriesCount; series++) {
        reader.setSeries(series);
        IniTable seriesTable = new IniTable();
        putTableName(seriesTable, reader, SERIES + series);
        seriesTable.put(SIZE_X, String.valueOf(reader.getSizeX()));
        seriesTable.put(SIZE_Y, String.valueOf(reader.getSizeY()));
        seriesTable.put(SIZE_Z, String.valueOf(reader.getSizeZ()));
        seriesTable.put(SIZE_C, String.valueOf(reader.getSizeC()));
        seriesTable.put(SIZE_T, String.valueOf(reader.getSizeT()));
        seriesTable.put(DIMENSION_ORDER, reader.getDimensionOrder());
        seriesTable.put(IS_INTERLEAVED, String.valueOf(reader.isInterleaved()));
        seriesTable.put(IS_INDEXED, String.valueOf(reader.isIndexed()));
        seriesTable.put(IS_FALSE_COLOR, String.valueOf(reader.isFalseColor()));
        seriesTable.put(IS_RGB, String.valueOf(reader.isRGB()));
        seriesTable.put(THUMB_SIZE_X, String.valueOf(reader.getThumbSizeX()));
        seriesTable.put(THUMB_SIZE_Y, String.valueOf(reader.getThumbSizeY()));
        seriesTable.put(PIXEL_TYPE, FormatTools.getPixelTypeString(reader.getPixelType()));
        seriesTable.put(IS_LITTLE_ENDIAN, String.valueOf(reader.isLittleEndian()));
        seriesTable.put(CHANNEL_COUNT, String.valueOf(retrieve.getChannelCount(series)));
        try {
            planeSize = DataTools.safeMultiply32(reader.getSizeX(), reader.getSizeY(), reader.getEffectiveSizeC(), FormatTools.getBytesPerPixel(reader.getPixelType()));
            canOpenImages = planeSize > 0 && TestTools.canFitInMemory(planeSize);
        } catch (IllegalArgumentException e) {
            canOpenImages = false;
        }
        if (canOpenImages) {
            try {
                byte[] plane = reader.openBytes(0);
                seriesTable.put(MD5, TestTools.md5(plane));
            } catch (FormatException e) {
            // TODO
            } catch (IOException e) {
            // TODO
            }
        }
        try {
            int w = (int) Math.min(TILE_SIZE, reader.getSizeX());
            int h = (int) Math.min(TILE_SIZE, reader.getSizeY());
            byte[] tile = reader.openBytes(0, 0, 0, w, h);
            seriesTable.put(TILE_MD5, TestTools.md5(tile));
        } catch (FormatException e) {
        // TODO
        } catch (IOException e) {
        // TODO
        }
        seriesTable.put(NAME, retrieve.getImageName(series));
        seriesTable.put(DESCRIPTION, retrieve.getImageDescription(series));
        Length physicalX = retrieve.getPixelsPhysicalSizeX(series);
        if (physicalX != null) {
            seriesTable.put(PHYSICAL_SIZE_X, physicalX.value().toString());
            seriesTable.put(PHYSICAL_SIZE_X_UNIT, physicalX.unit().getSymbol());
        }
        Length physicalY = retrieve.getPixelsPhysicalSizeY(series);
        if (physicalY != null) {
            seriesTable.put(PHYSICAL_SIZE_Y, physicalY.value().toString());
            seriesTable.put(PHYSICAL_SIZE_Y_UNIT, physicalY.unit().getSymbol());
        }
        Length physicalZ = retrieve.getPixelsPhysicalSizeZ(series);
        if (physicalZ != null) {
            seriesTable.put(PHYSICAL_SIZE_Z, physicalZ.value().toString());
            seriesTable.put(PHYSICAL_SIZE_Z_UNIT, physicalZ.unit().getSymbol());
        }
        Time timeIncrement = retrieve.getPixelsTimeIncrement(series);
        if (timeIncrement != null) {
            seriesTable.put(TIME_INCREMENT, timeIncrement.value().toString());
            seriesTable.put(TIME_INCREMENT_UNIT, timeIncrement.unit().getSymbol());
        }
        Timestamp acquisition = retrieve.getImageAcquisitionDate(series);
        if (acquisition != null) {
            String date = acquisition.getValue();
            if (date != null) {
                seriesTable.put(DATE, date);
            }
        }
        for (int c = 0; c < retrieve.getChannelCount(series); c++) {
            seriesTable.put(CHANNEL_NAME + c, retrieve.getChannelName(series, c));
            try {
                seriesTable.put(LIGHT_SOURCE + c, retrieve.getChannelLightSourceSettingsID(series, c));
            } catch (NullPointerException e) {
            }
            try {
                int plane = reader.getIndex(0, c, 0);
                if (plane < retrieve.getPlaneCount(series)) {
                    seriesTable.put(EXPOSURE_TIME + c, retrieve.getPlaneExposureTime(series, plane).value().toString());
                    seriesTable.put(EXPOSURE_TIME_UNIT + c, retrieve.getPlaneExposureTime(series, plane).unit().getSymbol());
                }
            } catch (NullPointerException e) {
            }
            Length emWavelength = retrieve.getChannelEmissionWavelength(series, c);
            if (emWavelength != null) {
                seriesTable.put(EMISSION_WAVELENGTH + c, emWavelength.value().toString());
                seriesTable.put(EMISSION_WAVELENGTH_UNIT + c, emWavelength.unit().getSymbol());
            }
            Length exWavelength = retrieve.getChannelExcitationWavelength(series, c);
            if (exWavelength != null) {
                seriesTable.put(EXCITATION_WAVELENGTH + c, exWavelength.value().toString());
                seriesTable.put(EXCITATION_WAVELENGTH_UNIT + c, exWavelength.unit().getSymbol());
            }
            try {
                seriesTable.put(DETECTOR + c, retrieve.getDetectorSettingsID(series, c));
            } catch (NullPointerException e) {
            }
        }
        for (int p = 0; p < reader.getImageCount(); p++) {
            try {
                Time deltaT = retrieve.getPlaneDeltaT(series, p);
                if (deltaT != null) {
                    seriesTable.put(DELTA_T + p, deltaT.value(UNITS.SECOND).toString());
                }
                Length xPos = retrieve.getPlanePositionX(series, p);
                if (xPos != null) {
                    seriesTable.put(X_POSITION + p, String.valueOf(xPos.value().doubleValue()));
                    seriesTable.put(X_POSITION_UNIT + p, xPos.unit().getSymbol());
                }
                Length yPos = retrieve.getPlanePositionY(series, p);
                if (yPos != null) {
                    seriesTable.put(Y_POSITION + p, String.valueOf(yPos.value().doubleValue()));
                    seriesTable.put(Y_POSITION_UNIT + p, yPos.unit().getSymbol());
                }
                Length zPos = retrieve.getPlanePositionZ(series, p);
                if (zPos != null) {
                    seriesTable.put(Z_POSITION + p, String.valueOf(zPos.value().doubleValue()));
                    seriesTable.put(Z_POSITION_UNIT + p, zPos.unit().getSymbol());
                }
            } catch (IndexOutOfBoundsException e) {
            // only happens if no Plane elements were populated
            }
        }
        ini.add(seriesTable);
    }
}

Example 64 with ImageReader

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

the class TiffWriterTest method parse.

@Parameters({ "id" })
@BeforeClass
public void parse(String id) throws Exception {
    ServiceFactory factory = new ServiceFactory();
    service = factory.getInstance(OMEXMLService.class);
    metadata = service.createOMEXMLMetadata();
    reader = new ImageReader();
    reader.setMetadataStore(metadata);
    reader.setId(id);
}

Example 65 with ImageReader

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

the class TiledReaderWriter method initialize.

/**
 * Set up the file reader and writer, ensuring that the input file is
 * associated with the reader and the output file is associated with the
 * writer.
 *
 * @return true if the reader and writer were successfully set up, or false
 *   if an error occurred
 * @throws DependencyException thrown if failed to create an OMEXMLService
 * @throws IOException thrown if unable to setup input or output stream for reader or writer
 * @throws FormatException thrown if invalid ID set for reader or writer or invalid tile size set
 * @throws ServiceException thrown if unable to create OME-XML meta data
 */
private void initialize() throws DependencyException, FormatException, IOException, ServiceException {
    // construct the object that stores OME-XML metadata
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    IMetadata omexml = service.createOMEXMLMetadata();
    // set up the reader and associate it with the input file
    reader = new ImageReader();
    reader.setMetadataStore(omexml);
    reader.setId(inputFile);
    // set up the writer and associate it with the output file
    writer = new OMETiffWriter();
    writer.setMetadataRetrieve(omexml);
    writer.setInterleaved(reader.isInterleaved());
    // set the tile size height and width for writing
    this.tileSizeX = writer.setTileSizeX(tileSizeX);
    this.tileSizeY = writer.setTileSizeY(tileSizeY);
    writer.setId(outputFile);
}