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legacy BDV server transforms on-the-fly the data to gray16 for BDV #26

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legacy BDV server transforms on-the-fly the data to gray16 for BDV #26

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60 changes: 57 additions & 3 deletions src/main/java/cz/it4i/fiji/datastore/bdv_server/CellHandlerTS.java
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,14 @@
import net.imglib2.img.cell.Cell;
import net.imglib2.realtransform.AffineTransform3D;

import org.janelia.saalfeldlab.n5.DataBlock;
import org.janelia.saalfeldlab.n5.DataType;
import org.janelia.saalfeldlab.n5.DataBlock;
import org.janelia.saalfeldlab.n5.ByteArrayDataBlock;
import org.janelia.saalfeldlab.n5.IntArrayDataBlock;
import org.janelia.saalfeldlab.n5.LongArrayDataBlock;
import org.janelia.saalfeldlab.n5.ShortArrayDataBlock;
import org.janelia.saalfeldlab.n5.FloatArrayDataBlock;
import org.janelia.saalfeldlab.n5.DoubleArrayDataBlock;
import org.janelia.saalfeldlab.n5.DatasetAttributes;
import org.janelia.saalfeldlab.n5.N5Writer;
import org.jdom2.Document;
Expand Down Expand Up @@ -205,12 +211,60 @@ private DataBlock<?> readBlock(
}*/
gridPosition[i] = cellMin[i] / blockSizes[key.level][i];
}
DataBlock<?> result = writer.readBlock(path, datasetAttributes,
gridPosition);

DataBlock<?> result = writer.readBlock(path, datasetAttributes, gridPosition);
//if the data is not native to BDV (i.e., data type != gray16), we convert on the fly for BDV (to gray16)
//because that's what BDV expects and that's how it interprets the incoming buffers (e.g., if gray8 would
//be sent instead, expect black rectangles be displayed on the BDV screen)
if (! (result instanceof ShortArrayDataBlock) )
return convertBlock(result);

return result;
}

private ShortArrayDataBlock convertBlock(DataBlock<?> nonGray16Block) {
short[] shortArray;

if (nonGray16Block instanceof ByteArrayDataBlock) {
byte[] byteArray = ((ByteArrayDataBlock)nonGray16Block).getData();
shortArray = new short[ byteArray.length ];
for (int i=0; i < shortArray.length; ++i) {
//double aux = byteArray[i];
//aux += aux < 0 ? 256 : 0; //signed byte -> unsigned short
//shortArray[i] = (short)aux;
shortArray[i] = byteArray[i];
shortArray[i] += shortArray[i] < 0 ? 256 : 0; //signed byte -> unsigned short
}
//
} else if (nonGray16Block instanceof IntArrayDataBlock) {
int[] data = ((IntArrayDataBlock)nonGray16Block).getData();
shortArray = new short[ data.length ];
for (int i=0; i < shortArray.length; ++i) shortArray[i] = (short)data[i];
//
} else if (nonGray16Block instanceof LongArrayDataBlock) {
long[] data = ((LongArrayDataBlock)nonGray16Block).getData();
shortArray = new short[ data.length ];
for (int i=0; i < shortArray.length; ++i) shortArray[i] = (short)data[i];
//
} else if (nonGray16Block instanceof FloatArrayDataBlock) {
float[] data = ((FloatArrayDataBlock)nonGray16Block).getData();
shortArray = new short[ data.length ];
for (int i=0; i < shortArray.length; ++i) shortArray[i] = (short)data[i];
//
} else if (nonGray16Block instanceof DoubleArrayDataBlock) {
double[] data = ((DoubleArrayDataBlock)nonGray16Block).getData();
shortArray = new short[ data.length ];
for (int i=0; i < shortArray.length; ++i) shortArray[i] = (short)data[i];
//
} else {
throw new IllegalArgumentException("Don't know how to convert "+nonGray16Block.getClass().getName()
+" to ShortArrayDataBlock during the legacy BDV on-the-fly data transform");
}

return new ShortArrayDataBlock(nonGray16Block.getSize(),
nonGray16Block.getGridPosition(), shortArray);
}

public DatasetAttributes getDatasetAttributes(
Map<String, DatasetAttributes> perPathDatasetAttribute, N5Writer writer,
String path)
Expand Down