Examples with Region org.apache.sis.internal.storage.io.Region used on opensource projects

Example 1 with Region

use of org.apache.sis.internal.storage.io.Region in project sis by apache.

the class VariableInfo method readArray.

/**
 * Reads the data from this variable and returns them as an array of a Java primitive type.
 * Multi-dimensional variables are flattened as a one-dimensional array (wrapped in a vector).
 * Fill values/missing values are replaced by NaN if {@link #hasRealValues()} is {@code true}.
 * Array elements are in "natural" order (inverse of netCDF order).
 *
 * @param  area         indices (in "natural" order) of cell values to read, or {@code null} for whole variable.
 * @param  subsampling  subsampling along each dimension, or {@code null} if none. Ignored if {@code area} is null.
 * @return the data as an array of a Java primitive type.
 * @throws ArithmeticException if the size of the variable exceeds {@link Integer#MAX_VALUE}, or other overflow occurs.
 *
 * @see #read()
 * @see #read(GridExtent, int[])
 */
private Object readArray(final GridExtent area, int[] subsampling) throws IOException, DataStoreException {
    if (reader == null) {
        throw new DataStoreContentException(unknownType());
    }
    final int dimension = dimensions.length;
    final long[] lower = new long[dimension];
    final long[] upper = new long[dimension];
    final long[] size = (area != null) ? new long[dimension] : upper;
    /*
         * NetCDF sorts datas in reverse dimension order. Example:
         *
         * DIMENSIONS:
         *   time: 3
         *   lat : 2
         *   lon : 4
         *
         * VARIABLES:
         *   temperature (time,lat,lon)
         *
         * DATA INDICES:
         *   (0,0,0) (0,0,1) (0,0,2) (0,0,3)
         *   (0,1,0) (0,1,1) (0,1,2) (0,1,3)
         *   (1,0,0) (1,0,1) (1,0,2) (1,0,3)
         *   (1,1,0) (1,1,1) (1,1,2) (1,1,3)
         *   (2,0,0) (2,0,1) (2,0,2) (2,0,3)
         *   (2,1,0) (2,1,1) (2,1,2) (2,1,3)
         */
    for (int i = 0; i < dimension; i++) {
        size[i] = dimensions[(dimension - 1) - i].length();
        if (area != null) {
            lower[i] = area.getLow(i);
            upper[i] = Math.incrementExact(area.getHigh(i));
        }
    }
    if (subsampling == null) {
        subsampling = new int[dimension];
        Arrays.fill(subsampling, 1);
    }
    final Region region = new Region(size, lower, upper, subsampling);
    /*
         * If this variable uses the unlimited dimension, we have to skip the records of all other unlimited variables
         * before to reach the next record of this variable.  Current implementation can do that only if the number of
         * bytes to skip is a multiple of the data type size. It should be the case most of the time because variables
         * in netCDF files have a 4 bytes padding. It may not work however if the variable uses {@code long} or
         * {@code double} type.
         */
    if (isUnlimited()) {
        if (offsetToNextRecord < 0) {
            throw canNotComputePosition(null);
        }
        region.setAdditionalByteOffset(dimensions.length - 1, offsetToNextRecord);
    }
    Object array = reader.read(region);
    replaceNaN(array);
    if (area == null && array instanceof double[]) {
        /*
             * If we can convert a double[] array to a float[] array, we should do that before
             * to invoke `setValues(array)` - we can not rely on data.compress(tolerance). The
             * reason is because we assume that float[] arrays are accurate in base 10 even if
             * the data were originally stored as doubles. The Vector class does not make such
             * assumption since it is specific to what we observe with netCDF files. To enable
             * this assumption, we need to convert to float[] before createDecimalVector(…).
             */
        final float[] copy = ArraysExt.copyAsFloatsIfLossless((double[]) array);
        if (copy != null)
            array = copy;
    }
    return array;
}

Example 2 with Region

use of org.apache.sis.internal.storage.io.Region in project sis by apache.

the class DataSubset method readSlice.

/**
 * Reads a two-dimensional slice of the data cube from the given input channel. This method is usually
 * invoked for reading the tile in full, in which case the {@code lower} argument is (0,0) and the
 * {@code upper} argument is the tile size. But those arguments may identify a smaller region if the
 * {@link DataSubset} contains only one (potentially large) tile.
 *
 * <p>The length of {@code lower}, {@code upper} and {@code subsampling} arrays shall be 2.</p>
 *
 * <h4>Default implementation</h4>
 * The default implementation in this base class assumes uncompressed data without band subset.
 * Subsampling on the <var>X</var> axis is not supported if the image has interleaved pixels.
 * Packed pixels (é.g. bilevel images with 8 pixels per byte) are not supported.
 * Those restrictions are verified by {@link DataCube#canReadDirect(TiledGridResource.Subset)}.
 * Subclasses must override for handling decompression or for resolving above-cited limitations.
 *
 * @todo It is possible to relax a little bit some restrictions. If the tile width is a divisor
 *       of the sample size, we could round {@code lower[0]} and {@code upper[0]} to a multiple
 *       of {@code sampleSize}. We would need to adjust the coordinates of returned image accordingly.
 *       This adjustment need to be done by the caller.
 *
 * @param  offsets      position in the channel where tile data begins, one value per bank.
 * @param  byteCounts   number of bytes for the compressed tile data, one value per bank.
 * @param  lower        (<var>x</var>, <var>y</var>) coordinates of the first pixel to read relative to the tile.
 * @param  upper        (<var>x</var>, <var>y</var>) coordinates after the last pixel to read relative to the tile.
 * @param  subsampling  (<var>sx</var>, <var>sy</var>) subsampling factors.
 * @param  location     pixel coordinates in the upper-left corner of the tile to return.
 * @return a single tile decoded from the GeoTIFF file.
 * @throws IOException if an I/O error occurred.
 * @throws DataStoreException if a logical error occurred.
 * @throws RuntimeException if the Java2D image can not be created for another reason
 *         (too many exception types to list them all).
 *
 * @see DataCube#canReadDirect(TiledGridResource.Subset)
 */
Raster readSlice(final long[] offsets, final long[] byteCounts, final long[] lower, final long[] upper, final int[] subsampling, final Point location) throws IOException, DataStoreException {
    final DataType type = getDataType();
    // Assumed same as `SampleModel.getSampleSize(…)` by pre-conditions.
    final int sampleSize = type.size();
    final long width = subtractExact(upper[X_DIMENSION], lower[X_DIMENSION]);
    final long height = subtractExact(upper[Y_DIMENSION], lower[Y_DIMENSION]);
    /*
         * The number of bytes to read should not be greater than `byteCount`. It may be smaller however if only
         * a subregion is read. Note that the `length` value may be different than `capacity` if the tile to read
         * is smaller than the "standard" tile size of the image. It happens often when reading the last strip.
         * This length is used only for verification purpose so it does not need to be exact.
         */
    final long length = ceilDiv(width * height * sourcePixelStride * sampleSize, Byte.SIZE);
    final long[] size = new long[] { multiplyFull(sourcePixelStride, getTileSize(X_DIMENSION)), getTileSize(Y_DIMENSION) };
    /*
         * If we use an interleaved sample model, each "element" from `HyperRectangleReader` perspective is actually a
         * group of `sourcePixelStride` values. Note that in such case, we can not handle subsampling on the first axis.
         * Such case should be handled by the `CompressedSubset` subclass instead, even if there is no compression.
         */
    assert sourcePixelStride == 1 || subsampling[X_DIMENSION] == 1;
    lower[X_DIMENSION] *= sourcePixelStride;
    upper[X_DIMENSION] *= sourcePixelStride;
    /*
         * Read each plane ("banks" in Java2D terminology). Note that a single bank contains all bands
         * in the interleaved sample model case. This block assumes that each bank element contains
         * exactly one sample value (verified by assertion), as documented in the Javadoc of this method.
         * If that assumption was not true, we would have to adjust `capacity`, `lower[0]` and `upper[0]`
         * (we may do that as an optimization in a future version).
         */
    final HyperRectangleReader hr = new HyperRectangleReader(ImageUtilities.toNumberEnum(type.toDataBufferType()), input());
    final Region region = new Region(size, lower, upper, subsampling);
    final Buffer[] banks = new Buffer[numBanks];
    for (int b = 0; b < numBanks; b++) {
        if (b < byteCounts.length && length > byteCounts[b]) {
            throw new DataStoreContentException(source.reader.resources().getString(Resources.Keys.UnexpectedTileLength_2, length, byteCounts[b]));
        }
        hr.setOrigin(offsets[b]);
        // See above comment.
        assert model.getSampleSize(b) == sampleSize;
        final Buffer bank = hr.readAsBuffer(region, getBankCapacity(1));
        fillRemainingRows(bank);
        banks[b] = bank;
    }
    final DataBuffer buffer = RasterFactory.wrap(type, banks);
    return Raster.createWritableRaster(model, buffer, location);
}