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CellRandomAccess unexpected behavior
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import java.io.IOException; | |
import java.util.Arrays; | |
import org.janelia.saalfeldlab.n5.GzipCompression; | |
import org.janelia.saalfeldlab.n5.N5FSWriter; | |
import org.janelia.saalfeldlab.n5.N5Writer; | |
import org.janelia.saalfeldlab.n5.imglib2.N5Utils; | |
import net.imglib2.Cursor; | |
import net.imglib2.FinalInterval; | |
import net.imglib2.Interval; | |
import net.imglib2.RandomAccessibleInterval; | |
import net.imglib2.img.array.ArrayImg; | |
import net.imglib2.img.array.ArrayImgs; | |
import net.imglib2.img.basictypeaccess.array.ShortArray; | |
import net.imglib2.img.cell.CellGrid; | |
import net.imglib2.type.NativeType; | |
import net.imglib2.type.numeric.IntegerType; | |
import net.imglib2.type.numeric.integer.ShortType; | |
import net.imglib2.util.Intervals; | |
import net.imglib2.view.Views; | |
public class N5CellAccessTest { | |
static private final String testDirPath = System.getProperty("user.home") + "/tmp/n5-imglib2-test"; | |
static private final String dataset = "test-cell-access"; | |
static private final long[] dimensions = {8, 8, 8}; | |
static private final int[] blockSize = {2, 2, 2}; | |
public static <T extends NativeType<T> & IntegerType<T>> void main(final String[] args) throws IOException { | |
// fill image data | |
final short[] data = new short[(int) Intervals.numElements(dimensions)]; | |
for (int i = 0; i < data.length; ++i) | |
data[i] = (short) (i + 1); | |
final ArrayImg<ShortType, ShortArray> arrayImg = ArrayImgs.shorts(data, dimensions); | |
// save the image as n5 | |
final N5Writer n5 = new N5FSWriter(testDirPath); | |
N5Utils.save(arrayImg, n5, dataset, blockSize, new GzipCompression()); | |
// create an interval for cell at grid position [2,2,2] | |
final CellGrid cellGrid = new CellGrid(dimensions, blockSize); | |
final long[] cellMin = new long[3], cellMax = new long[3]; | |
final int[] cellDims = new int[3]; | |
cellGrid.getCellDimensions(new long[] {2, 2, 2}, cellMin, cellDims); | |
Arrays.setAll(cellMax, d -> cellMin[d] + cellDims[d] - 1); | |
final Interval cellInterval = new FinalInterval(cellMin, cellMax); | |
// open the image and iterate inside the cell [2,2,2] | |
final RandomAccessibleInterval<T> img = N5Utils.open(n5, dataset); | |
final RandomAccessibleInterval< T > crop = Views.interval(img, cellInterval); | |
final Cursor<T> cursor = Views.flatIterable(crop).cursor(); | |
while (cursor.hasNext()) | |
System.out.println(cursor.next().getInteger()); | |
// The above loop is expected to only load cell [2,2,2]. | |
// However, if I add code to log accessed cells in N5CellLoader, it shows that these cells have been accessed: | |
// [0,0,0], [2,2,2], [1,2,2], [2,3,2] | |
n5.remove(); | |
} | |
} |
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To see positions of accessed cells you would need to modify
N5CellLoader::load()
and trace the requested grid position there