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

Example 31 with IFormatReader

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

the class FormatReaderTest method testSaneUsedFiles.

@Test(groups = { "all", "type", "automated" })
public void testSaneUsedFiles() {
    if (!initFile())
        return;
    String file = reader.getCurrentFile();
    String testName = "testSaneUsedFiles";
    boolean success = true;
    String msg = null;
    try {
        String[] base = reader.getUsedFiles();
        if (base.length == 1) {
            if (!base[0].equals(file))
                success = false;
        } else {
            Arrays.sort(base);
            IFormatReader r = /*config.noStitching() ? new ImageReader() :*/
            new FileStitcher();
            int maxFiles = (int) Math.min(base.length, 100);
            if (DataTools.indexOf(reader.getDomains(), FormatTools.HCS_DOMAIN) >= 0 || file.toLowerCase().endsWith(".czi")) {
                maxFiles = (int) Math.min(maxFiles, 10);
            }
            for (int i = 0; i < maxFiles && success; i++) {
                // than one dataset
                if (reader.getFormat().equals("InCell 1000/2000")) {
                    if (!base[i].toLowerCase().endsWith(".xdce") && !base[i].toLowerCase().endsWith(".xml")) {
                        continue;
                    }
                }
                // Volocity datasets can only be detected with the .mvd2 file
                if (file.toLowerCase().endsWith(".mvd2") && !base[i].toLowerCase().endsWith(".mvd2")) {
                    continue;
                }
                // 'fid' and 'acqp' files
                if ((file.toLowerCase().endsWith("fid") || file.toLowerCase().endsWith("acqp")) && !base[i].toLowerCase().endsWith("fid") && !base[i].toLowerCase().endsWith("acqp") && reader.getFormat().equals("Bruker")) {
                    continue;
                }
                // CellR datasets cannot be detected with a TIFF file
                if (reader.getFormat().equals("Olympus APL") && base[i].toLowerCase().endsWith("tif")) {
                    continue;
                }
                // Micromanager datasets cannot be detected with an OME-TIFF file
                if (reader.getFormat().equals("Micro-Manager") && (base[i].toLowerCase().endsWith(".ome.tiff") || base[i].toLowerCase().endsWith(".ome.tif"))) {
                    continue;
                }
                // DICOM companion files may not be detected
                if (reader.getFormat().equals("DICOM") && !base[i].equals(file)) {
                    continue;
                }
                // QuickTime resource forks are not detected
                if (reader.getFormat().equals("QuickTime") && !base[i].equals(file)) {
                    continue;
                }
                // SVS files in AFI datasets are detected as SVS
                if (reader.getFormat().equals("Aperio AFI") && base[i].toLowerCase().endsWith(".svs")) {
                    continue;
                }
                if (reader.getFormat().equals("BD Pathway") && (base[i].endsWith(".adf") || base[i].endsWith(".txt")) || base[i].endsWith(".roi")) {
                    continue;
                }
                // Hamamatsu VMS datasets cannot be detected with non-.vms files
                if (reader.getFormat().equals("Hamamatsu VMS") && !base[i].toLowerCase().endsWith(".vms")) {
                    continue;
                }
                if (reader.getFormat().equals("CellVoyager")) {
                    continue;
                }
                if (reader.getFormat().equals("Leica Image File Format")) {
                    continue;
                }
                // pattern datasets can only be detected with the pattern file
                if (reader.getFormat().equals("File pattern")) {
                    continue;
                }
                r.setId(base[i]);
                String[] comp = r.getUsedFiles();
                // are not grouped.  This is expected behavior; see ticket #3701.
                if (base[i].toLowerCase().endsWith(".lsm") && comp.length == 1) {
                    r.close();
                    continue;
                }
                // will give different results.
                if (file.toLowerCase().endsWith(".dv") && base[i].toLowerCase().endsWith(".log")) {
                    r.close();
                    continue;
                }
                // used file count from the text file.
                if (reader.getFormat().equals("Hitachi")) {
                    r.close();
                    continue;
                }
                // separately
                if (reader.getFormat().equals("Trestle")) {
                    r.close();
                    continue;
                }
                // TIFF files in CellR datasets are detected separately
                if (reader.getFormat().equals("Olympus APL") && base[i].toLowerCase().endsWith(".tif")) {
                    r.close();
                    continue;
                }
                // TIFF files in Li-Cor datasets are detected separately
                if (reader.getFormat().equals("Li-Cor L2D") && !base[i].toLowerCase().endsWith("l2d")) {
                    r.close();
                    continue;
                }
                // TIFF files in Prairie datasets may be detected as OME-TIFF
                if (reader.getFormat().equals("Prairie TIFF") && base[i].toLowerCase().endsWith(".tif") && r.getFormat().equals("OME-TIFF")) {
                    r.close();
                    continue;
                }
                if (reader.getFormat().equals("Hamamatsu NDPIS") && r.getFormat().equals("Hamamatsu NDPI")) {
                    r.close();
                    continue;
                }
                if (base[i].endsWith(".bmp") && reader.getFormat().equals("BD Pathway")) {
                    r.close();
                    continue;
                }
                if (comp.length != base.length) {
                    success = false;
                    msg = base[i] + " (file list length was " + comp.length + "; expected " + base.length + ")";
                }
                if (success)
                    Arrays.sort(comp);
                // a test failure (which we can do nothing about).
                if (file.toLowerCase().endsWith(".nhdr") || base[i].toLowerCase().endsWith(".nhdr")) {
                    r.close();
                    continue;
                }
                for (int j = 0; j < comp.length && success; j++) {
                    if (!comp[j].equals(base[j])) {
                        if (base[j].equals(new Location(comp[j]).getCanonicalPath())) {
                            continue;
                        }
                        success = false;
                        msg = base[i] + "(file @ " + j + " was '" + comp[j] + "', expected '" + base[j] + "')";
                    }
                }
                r.close();
            }
        }
    } catch (Throwable t) {
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}

Example 32 with IFormatReader

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

the class FormatReaderTest method testUnflattenedSubimagePixelsHashes.

/*
  @Test(groups = {"all", "pixels"})
  public void testReorderedPixelsHashes() {
    if (config == null) throw new SkipException("No config tree");
    String testName = "testReorderedPixelsHashes";
    if (!initFile()) result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
      for (int i=0; i<reader.getSeriesCount() && success; i++) {
        reader.setSeries(i);
        config.setSeries(i);

        for (int j=0; j<3; j++) {
          int index = (int) (Math.random() * reader.getImageCount());
          reader.openBytes(index);
        }

        String md5 = TestTools.md5(reader.openBytes(0));
        String expected1 = config.getMD5();
        String expected2 = config.getAlternateMD5();

        if (!md5.equals(expected1) && !md5.equals(expected2)) {
          success = false;
          msg = expected1 == null && expected2 == null ? "no configuration" :
            "series " + i;
        }
      }
    }
    catch (Throwable t) {
      LOGGER.info("", t);
      success = false;
    }
    result(testName, success, msg);
  }
  */
@Test(groups = { "all", "pixels", "automated" })
public void testUnflattenedSubimagePixelsHashes() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "testUnflattenedSubimagePixelsHashes";
    if (!initFile())
        result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
        IFormatReader resolutionReader = new BufferedImageReader(new FileStitcher());
        resolutionReader.setFlattenedResolutions(false);
        resolutionReader.setNormalized(true);
        resolutionReader.setOriginalMetadataPopulated(false);
        resolutionReader.setMetadataFiltered(true);
        resolutionReader.setId(id);
        // check the MD5 of the first plane in each resolution
        for (int i = 0; i < resolutionReader.getSeriesCount() && success; i++) {
            resolutionReader.setSeries(i);
            for (int r = 0; r < resolutionReader.getResolutionCount() && success; r++) {
                resolutionReader.setResolution(r);
                config.setSeries(resolutionReader.getCoreIndex());
                int w = (int) Math.min(Configuration.TILE_SIZE, resolutionReader.getSizeX());
                int h = (int) Math.min(Configuration.TILE_SIZE, resolutionReader.getSizeY());
                String expected1 = config.getTileMD5();
                String expected2 = config.getTileAlternateMD5();
                String md5 = null;
                try {
                    md5 = TestTools.md5(resolutionReader.openBytes(0, 0, 0, w, h));
                } catch (Throwable e) {
                    if (TestTools.isOutOfMemory(e)) {
                        result(testName, true, "Image too large");
                        return;
                    }
                    LOGGER.warn("", e);
                }
                if (md5 == null && expected1 == null && expected2 == null) {
                    success = true;
                } else if (!md5.equals(expected1) && !md5.equals(expected2) && (expected1 != null || expected2 != null)) {
                    success = false;
                    msg = "series " + i + ", resolution " + r;
                }
            }
        }
        resolutionReader.close();
    } catch (Throwable t) {
        LOGGER.info("", t);
        success = false;
    }
    result(testName, success, msg);
}

Example 33 with IFormatReader

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

the class FormatReaderTest method testOMEXML.

@Test(groups = { "all", "xml", "fast", "automated" })
public void testOMEXML() {
    String testName = "testOMEXML";
    if (!initFile())
        result(testName, false, "initFile");
    String msg = null;
    try {
        MetadataRetrieve retrieve = (MetadataRetrieve) reader.getMetadataStore();
        boolean success = omexmlService.isOMEXMLMetadata(retrieve);
        if (!success)
            msg = TestTools.shortClassName(retrieve);
        for (int i = 0; i < reader.getSeriesCount() && msg == null; i++) {
            reader.setSeries(i);
            String type = FormatTools.getPixelTypeString(reader.getPixelType());
            if (reader.getSizeX() != retrieve.getPixelsSizeX(i).getValue().intValue()) {
                msg = "SizeX";
            }
            if (reader.getSizeY() != retrieve.getPixelsSizeY(i).getValue().intValue()) {
                msg = "SizeY";
            }
            if (reader.getSizeZ() != retrieve.getPixelsSizeZ(i).getValue().intValue()) {
                msg = "SizeZ";
            }
            if (reader.getSizeC() != retrieve.getPixelsSizeC(i).getValue().intValue()) {
                msg = "SizeC";
            }
            if (reader.getSizeT() != retrieve.getPixelsSizeT(i).getValue().intValue()) {
                msg = "SizeT";
            }
            // NB: OME-TIFF files do not have a BinData element under Pixels
            IFormatReader r = reader.unwrap();
            if (r instanceof FileStitcher)
                r = ((FileStitcher) r).getReader();
            if (r instanceof ReaderWrapper)
                r = ((ReaderWrapper) r).unwrap();
            if (!(r instanceof OMETiffReader)) {
                boolean littleEndian = false;
                if (retrieve.getPixelsBigEndian(i) != null) {
                    littleEndian = !retrieve.getPixelsBigEndian(i).booleanValue();
                } else if (retrieve.getPixelsBinDataCount(i) == 0) {
                    littleEndian = !retrieve.getPixelsBinDataBigEndian(i, 0).booleanValue();
                }
                if (reader.isLittleEndian() != littleEndian) {
                    msg = "BigEndian";
                }
            }
            if (!reader.getDimensionOrder().equals(retrieve.getPixelsDimensionOrder(i).toString())) {
                msg = "DimensionOrder";
            }
            if (!type.equalsIgnoreCase(retrieve.getPixelsType(i).toString())) {
                msg = "PixelType";
            }
        }
    } catch (Throwable t) {
        LOGGER.info("", t);
        msg = t.getMessage();
    }
    result(testName, msg == null, msg);
}

Example 34 with IFormatReader

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

the class FormatReaderTest method testRequiredDirectories.

@Test(groups = { "all", "type", "automated" })
public void testRequiredDirectories() {
    if (!initFile())
        return;
    if (reader.getFormat().equals("Woolz") || reader.getFormat().startsWith("CellH5")) {
        throw new SkipException(SKIP_MESSAGE);
    }
    String testName = "testRequiredDirectories";
    String file = reader.getCurrentFile();
    LOGGER.debug("testRequiredDirectories({})", file);
    int directories = -1;
    try {
        directories = reader.getRequiredDirectories(reader.getUsedFiles());
    } catch (Exception e) {
        LOGGER.warn("Could not retrieve directory count", e);
    }
    LOGGER.debug("directories = {}", directories);
    if (directories < 0) {
        result(testName, false, "Invalid directory count (" + directories + ")");
    } else {
        // make sure the directory count is not too small
        // we can't reliably test for the directory count being too large,
        // since a different fileset in the same format may need more directories
        String[] usedFiles = reader.getUsedFiles();
        String[] newFiles = new String[usedFiles.length];
        // find the common parent
        String commonParent = new Location(usedFiles[0]).getAbsoluteFile().getParent();
        for (int i = 1; i < usedFiles.length; i++) {
            while (!usedFiles[i].startsWith(commonParent)) {
                commonParent = commonParent.substring(0, commonParent.lastIndexOf(File.separator));
            }
        }
        LOGGER.debug("commonParent = {}", commonParent);
        // remove extra directories
        String split = File.separatorChar == '\\' ? "\\\\" : File.separator;
        LOGGER.debug("split = {}", split);
        String[] f = commonParent.split(split);
        StringBuilder toRemove = new StringBuilder();
        for (int i = 0; i < f.length - directories - 1; i++) {
            toRemove.append(f[i]);
            if (i < f.length - directories - 2) {
                toRemove.append(split);
            }
        }
        // map new file names and verify that setId still works
        String newFile = null;
        for (int i = 0; i < usedFiles.length; i++) {
            newFiles[i] = usedFiles[i].replaceAll(toRemove.toString(), "");
            LOGGER.debug("mapping {} to {}", newFiles[i], usedFiles[i]);
            Location.mapId(newFiles[i], usedFiles[i]);
            if (usedFiles[i].equals(file)) {
                newFile = newFiles[i];
            }
        }
        if (newFile == null) {
            newFile = newFiles[0];
        }
        LOGGER.debug("newFile = {}", newFile);
        IFormatReader check = new FileStitcher();
        try {
            check.setId(newFile);
            int nFiles = check.getUsedFiles().length;
            result(testName, nFiles == usedFiles.length, "Found " + nFiles + "; expected " + usedFiles.length);
        } catch (Exception e) {
            LOGGER.info("Initialization failed", e);
            result(testName, false, e.getMessage());
        } finally {
            try {
                check.close();
            } catch (IOException e) {
                LOGGER.warn("Could not close reader", e);
            }
            for (int i = 0; i < newFiles.length; i++) {
                Location.mapId(newFiles[i], null);
            }
        }
    }
}

Example 35 with IFormatReader

use of loci.formats.IFormatReader 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);
    }
}