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

Example 6 with ReaderWrapper

use of loci.formats.ReaderWrapper 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);
    }
}