Examples with IMetadata loci.formats.meta.IMetadata used on opensource projects

Example 51 with IMetadata

use of loci.formats.meta.IMetadata 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 52 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testPlanePositions.

@Test(groups = { "all", "fast", "automated" })
public void testPlanePositions() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "PlanePositions";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        for (int p = 0; p < reader.getImageCount(); p++) {
            Length posX = null;
            Length posY = null;
            Length posZ = null;
            try {
                posX = retrieve.getPlanePositionX(i, p);
            } catch (IndexOutOfBoundsException e) {
            }
            try {
                posY = retrieve.getPlanePositionY(i, p);
            } catch (IndexOutOfBoundsException e) {
            }
            try {
                posZ = retrieve.getPlanePositionZ(i, p);
            } catch (IndexOutOfBoundsException e) {
            }
            Double expectedX = config.getPositionX(p);
            Double expectedY = config.getPositionY(p);
            Double expectedZ = config.getPositionZ(p);
            String expectedXUnit = config.getPositionXUnit(p);
            String expectedYUnit = config.getPositionYUnit(p);
            String expectedZUnit = config.getPositionZUnit(p);
            if (posX == null && expectedX == null) {
            } else if (posX == null) {
                result(testName, false, "missing X position for series " + i + ", plane " + p);
                return;
            } else if (expectedX != null && expectedXUnit != null) {
                Double x = posX.value().doubleValue();
                if (!expectedXUnit.equals(posX.unit().getSymbol())) {
                    result(testName, false, "X position unit series " + i + ", plane " + p + " (expected " + expectedXUnit + ", actual " + posX.unit().getSymbol() + ")");
                    return;
                }
                if (Math.abs(x - expectedX) > Constants.EPSILON) {
                    result(testName, false, "X position series " + i + ", plane " + p + " (expected " + expectedX + ", actual " + x + ")");
                    return;
                }
            }
            if (posY == null && expectedY == null) {
            } else if (posY == null) {
                result(testName, false, "missing Y position for series " + i + ", plane " + p);
                return;
            } else if (expectedY != null && expectedYUnit != null) {
                Double y = posY.value().doubleValue();
                if (!expectedYUnit.equals(posY.unit().getSymbol())) {
                    result(testName, false, "Y position unit series " + i + ", plane " + p + " (expected " + expectedYUnit + ", actual " + posY.unit().getSymbol() + ")");
                    return;
                }
                if (Math.abs(y - expectedY) > Constants.EPSILON) {
                    result(testName, false, "Y position series " + i + ", plane " + p + " (expected " + expectedY + ", actual " + y + ")");
                    return;
                }
            }
            if (posZ == null && expectedZ == null) {
            } else if (posZ == null) {
                result(testName, false, "missing Z position for series " + i + ", plane " + p);
                return;
            } else if (expectedZ != null && expectedZUnit != null) {
                Double z = posZ.value().doubleValue();
                if (!expectedZUnit.equals(posZ.unit().getSymbol())) {
                    result(testName, false, "Z position unit series " + i + ", plane " + p + " (expected " + expectedZUnit + ", actual " + posZ.unit().getSymbol() + ")");
                    return;
                }
                if (Math.abs(z - expectedZ) > Constants.EPSILON) {
                    result(testName, false, "Z position series " + i + ", plane " + p + " (expected " + expectedZ + ", actual " + z + ")");
                    return;
                }
            }
        }
    }
    result(testName, true);
}

Example 53 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testLightSources.

@Test(groups = { "all", "fast", "automated" })
public void testLightSources() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "LightSources";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        for (int c = 0; c < config.getChannelCount(); c++) {
            String expectedLightSource = config.getLightSource(c);
            String realLightSource = null;
            try {
                realLightSource = retrieve.getChannelLightSourceSettingsID(i, c);
            } catch (NullPointerException e) {
            }
            if (!(expectedLightSource == null && realLightSource == null) && !expectedLightSource.equals(realLightSource)) {
                result(testName, false, "Series " + i + " channel " + c + " (expected " + expectedLightSource + ", actual " + realLightSource + ")");
            }
        }
    }
    result(testName, true);
}

Example 54 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testDeltaT.

@Test(groups = { "all", "fast", "automated" })
public void testDeltaT() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "DeltaT";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        // Test image acquisition date
        String expectedDate = config.getDate();
        String date = null;
        if (retrieve.getImageAcquisitionDate(i) != null) {
            date = retrieve.getImageAcquisitionDate(i).getValue();
        }
        if (expectedDate != null && date != null && !expectedDate.equals(date)) {
            result(testName, false, "series " + i + " (expected " + expectedDate + ", actual " + date + ")");
            return;
        }
        for (int p = 0; p < reader.getImageCount(); p++) {
            Time deltaT = null;
            try {
                deltaT = retrieve.getPlaneDeltaT(i, p);
            } catch (IndexOutOfBoundsException e) {
            }
            Double expectedDeltaT = config.getDeltaT(p);
            if (deltaT == null && expectedDeltaT == null) {
                continue;
            }
            if (deltaT == null) {
                result(testName, false, "missing series " + i + ", plane " + p);
                return;
            }
            if (expectedDeltaT != null) {
                Double seconds = deltaT.value(UNITS.SECOND).doubleValue();
                if (Math.abs(seconds - expectedDeltaT) > Constants.EPSILON) {
                    result(testName, false, "series " + i + ", plane " + p + " (expected " + expectedDeltaT + ", actual " + seconds + ")");
                    return;
                }
            }
        }
    }
    result(testName, true);
}

Example 55 with IMetadata

use of loci.formats.meta.IMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testPhysicalSizeY.

@Test(groups = { "all", "fast", "automated" })
public void testPhysicalSizeY() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "PhysicalSizeY";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        Length expectedSize = config.getPhysicalSizeY();
        Length realSize = retrieve.getPixelsPhysicalSizeY(i);
        if (!isAlmostEqual(realSize, expectedSize)) {
            result(testName, false, "Series " + i + " (expected " + expectedSize + ", actual " + realSize + ")");
        }
    }
    result(testName, true);
}