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zorbage-scifio: code for using the SCIFIO data file loading library to populate data into zorbage structures for further processing
/*
* zorbage-scifio: code for using the SCIFIO data file library to open files into zorbage data structures for further processing
*
* Copyright (C) 2020-2022 Barry DeZonia
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in all
* copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
* SOFTWARE.
*/
package nom.bdezonia.zorbage.scifio;
import java.math.BigDecimal;
import java.util.List;
import io.scif.img.ImgOpener;
import io.scif.img.SCIFIOImgPlus;
import net.imglib2.RandomAccess;
import net.imglib2.type.numeric.ARGBType;
import net.imglib2.type.numeric.complex.ComplexDoubleType;
import net.imglib2.type.numeric.complex.ComplexFloatType;
import net.imglib2.type.numeric.integer.ByteType;
import net.imglib2.type.numeric.integer.IntType;
import net.imglib2.type.numeric.integer.LongType;
import net.imglib2.type.numeric.integer.ShortType;
import net.imglib2.type.numeric.integer.Unsigned128BitType;
import net.imglib2.type.numeric.integer.Unsigned12BitType;
import net.imglib2.type.numeric.integer.Unsigned2BitType;
import net.imglib2.type.numeric.integer.Unsigned4BitType;
import net.imglib2.type.numeric.integer.UnsignedByteType;
import net.imglib2.type.numeric.integer.UnsignedIntType;
import net.imglib2.type.numeric.integer.UnsignedLongType;
import net.imglib2.type.numeric.integer.UnsignedShortType;
import net.imglib2.type.numeric.integer.UnsignedVariableBitLengthType;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.type.numeric.real.FloatType;
import nom.bdezonia.zorbage.algebra.Allocatable;
import nom.bdezonia.zorbage.algorithm.GridIterator;
import nom.bdezonia.zorbage.coordinates.LinearNdCoordinateSpace;
import nom.bdezonia.zorbage.data.DimensionedDataSource;
import nom.bdezonia.zorbage.data.DimensionedStorage;
import nom.bdezonia.zorbage.dataview.PlaneView;
import nom.bdezonia.zorbage.misc.DataBundle;
import nom.bdezonia.zorbage.procedure.Procedure2;
import nom.bdezonia.zorbage.sampling.IntegerIndex;
import nom.bdezonia.zorbage.sampling.SamplingIterator;
import nom.bdezonia.zorbage.type.color.ArgbMember;
import nom.bdezonia.zorbage.type.complex.float32.ComplexFloat32Member;
import nom.bdezonia.zorbage.type.complex.float64.ComplexFloat64Member;
import nom.bdezonia.zorbage.type.integer.int1.UnsignedInt1Member;
import nom.bdezonia.zorbage.type.integer.int10.UnsignedInt10Member;
import nom.bdezonia.zorbage.type.integer.int11.UnsignedInt11Member;
import nom.bdezonia.zorbage.type.integer.int12.UnsignedInt12Member;
import nom.bdezonia.zorbage.type.integer.int128.UnsignedInt128Member;
import nom.bdezonia.zorbage.type.integer.int13.UnsignedInt13Member;
import nom.bdezonia.zorbage.type.integer.int14.UnsignedInt14Member;
import nom.bdezonia.zorbage.type.integer.int15.UnsignedInt15Member;
import nom.bdezonia.zorbage.type.integer.int16.SignedInt16Member;
import nom.bdezonia.zorbage.type.integer.int16.UnsignedInt16Member;
import nom.bdezonia.zorbage.type.integer.int2.UnsignedInt2Member;
import nom.bdezonia.zorbage.type.integer.int3.UnsignedInt3Member;
import nom.bdezonia.zorbage.type.integer.int32.SignedInt32Member;
import nom.bdezonia.zorbage.type.integer.int32.UnsignedInt32Member;
import nom.bdezonia.zorbage.type.integer.int4.UnsignedInt4Member;
import nom.bdezonia.zorbage.type.integer.int5.UnsignedInt5Member;
import nom.bdezonia.zorbage.type.integer.int6.UnsignedInt6Member;
import nom.bdezonia.zorbage.type.integer.int64.SignedInt64Member;
import nom.bdezonia.zorbage.type.integer.int64.UnsignedInt64Member;
import nom.bdezonia.zorbage.type.integer.int7.UnsignedInt7Member;
import nom.bdezonia.zorbage.type.integer.int8.SignedInt8Member;
import nom.bdezonia.zorbage.type.integer.int8.UnsignedInt8Member;
import nom.bdezonia.zorbage.type.integer.int9.UnsignedInt9Member;
import nom.bdezonia.zorbage.type.integer.unbounded.UnboundedIntMember;
import nom.bdezonia.zorbage.type.real.float32.Float32Member;
import nom.bdezonia.zorbage.type.real.float64.Float64Member;
/**
*
* @author Barry DeZonia
*
*/
public class Scifio {
/**
*
* @param filename
* @return
*/
@SuppressWarnings("unchecked")
public static DataBundle loadAllDatasets(String filename) {
DataBundle bundle = new DataBundle();
ImgOpener opener = new ImgOpener();
List> results = opener.openImgs(filename);
for (SCIFIOImgPlus scifImgPlus : results) {
Object elem = scifImgPlus.firstElement();
if (elem instanceof UnsignedByteType)
bundle.mergeUInt8( loadUnsignedByteImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof ByteType)
bundle.mergeInt8( loadByteImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof UnsignedShortType)
bundle.mergeUInt16( loadUnsignedShortImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof ShortType)
bundle.mergeInt16( loadShortImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof UnsignedIntType)
bundle.mergeUInt32( loadUnsignedIntImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof IntType)
bundle.mergeInt32( loadIntImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof UnsignedLongType)
bundle.mergeUInt64( loadUnsignedLongImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof LongType)
bundle.mergeInt64( loadLongImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof FloatType)
bundle.mergeFlt32( loadFloatImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof DoubleType)
bundle.mergeFlt64( loadDoubleImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof Unsigned2BitType)
bundle.mergeUInt2( loadUnsigned2BitImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof Unsigned4BitType)
bundle.mergeUInt4( loadUnsigned4BitImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof Unsigned12BitType)
bundle.mergeUInt12( loadUnsigned12BitImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof Unsigned128BitType)
bundle.mergeUInt128( loadUnsigned128BitImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof ComplexFloatType)
bundle.mergeComplexFlt32( loadComplexFloatImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof ComplexDoubleType)
bundle.mergeComplexFlt64( loadComplexDoubleImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof ARGBType)
bundle.mergeArgb( loadARGBTypeImage( (SCIFIOImgPlus) scifImgPlus) );
else if (elem instanceof UnsignedVariableBitLengthType) {
UnsignedVariableBitLengthType type = (UnsignedVariableBitLengthType) elem;
int bpp = type.getBitsPerPixel();
if (bpp < 1)
throw new IllegalArgumentException("bit per pix must be > 0");
switch (bpp) {
case 1:
bundle.mergeUInt1( loadUnsignedV1BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 2:
bundle.mergeUInt2( loadUnsignedV2BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 3:
bundle.mergeUInt3( loadUnsignedV3BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 4:
bundle.mergeUInt4( loadUnsignedV4BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 5:
bundle.mergeUInt5( loadUnsignedV5BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 6:
bundle.mergeUInt6( loadUnsignedV6BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 7:
bundle.mergeUInt7( loadUnsignedV7BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 8:
bundle.mergeUInt8( loadUnsignedV8BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 9:
bundle.mergeUInt9( loadUnsignedV9BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 10:
bundle.mergeUInt10( loadUnsignedV10BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 11:
bundle.mergeUInt11( loadUnsignedV11BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 12:
bundle.mergeUInt12( loadUnsignedV12BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 13:
bundle.mergeUInt13( loadUnsignedV13BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 14:
bundle.mergeUInt14( loadUnsignedV14BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 15:
bundle.mergeUInt15( loadUnsignedV15BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
case 16:
bundle.mergeUInt16( loadUnsignedV16BitImage( (SCIFIOImgPlus) scifImgPlus) );
break;
default:
if (bpp <= 32)
bundle.mergeUInt32( loadUnsignedV32BitImage( (SCIFIOImgPlus) scifImgPlus) );
else if (bpp <= 64)
bundle.mergeUInt64( loadUnsignedV64BitImage( (SCIFIOImgPlus) scifImgPlus) );
else if (bpp <= 128)
bundle.mergeUInt128( loadUnsignedV128BitImage( (SCIFIOImgPlus) scifImgPlus) );
else // bpp > 128
bundle.mergeBigInt( loadUnsignedBigIntImage( (SCIFIOImgPlus) scifImgPlus) );
break;
}
}
else
System.out.println("scifio image is of unknown type: " + elem);
}
return bundle;
}
private static DimensionedDataSource
loadUnsignedByteImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedByteType in, UnsignedInt8Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt8Member());
fillDataset(input, proc, new UnsignedInt8Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadByteImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(ByteType in, SignedInt8Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new SignedInt8Member());
fillDataset(input, proc, new SignedInt8Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedShortImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedShortType in, UnsignedInt16Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt16Member());
fillDataset(input, proc, new UnsignedInt16Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadShortImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(ShortType in, SignedInt16Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new SignedInt16Member());
fillDataset(input, proc, new SignedInt16Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedIntImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedIntType in, UnsignedInt32Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt32Member());
fillDataset(input, proc, new UnsignedInt32Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadIntImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(IntType in, SignedInt32Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new SignedInt32Member());
fillDataset(input, proc, new SignedInt32Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedLongImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedLongType in, UnsignedInt64Member out) {
out.setV(in.getBigInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt64Member());
fillDataset(input, proc, new UnsignedInt64Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadLongImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(LongType in, SignedInt64Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new SignedInt64Member());
fillDataset(input, proc, new SignedInt64Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadFloatImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(FloatType in, Float32Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new Float32Member());
fillDataset(input, proc, new Float32Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadDoubleImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(DoubleType in, Float64Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new Float64Member());
fillDataset(input, proc, new Float64Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadComplexFloatImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(ComplexFloatType in, ComplexFloat32Member out) {
out.setR(in.getRealFloat());
out.setI(in.getImaginaryFloat());
}
};
DimensionedDataSource output =
makeDataset(input, new ComplexFloat32Member());
fillDataset(input, proc, new ComplexFloat32Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadComplexDoubleImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(ComplexDoubleType in, ComplexFloat64Member out) {
out.setR(in.getRealDouble());
out.setI(in.getImaginaryDouble());
}
};
DimensionedDataSource output =
makeDataset(input, new ComplexFloat64Member());
fillDataset(input, proc, new ComplexFloat64Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsigned2BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(Unsigned2BitType in, UnsignedInt2Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt2Member());
fillDataset(input, proc, new UnsignedInt2Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsigned4BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(Unsigned4BitType in, UnsignedInt4Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt4Member());
fillDataset(input, proc, new UnsignedInt4Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsigned12BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(Unsigned12BitType in, UnsignedInt12Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt12Member());
fillDataset(input, proc, new UnsignedInt12Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsigned128BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(Unsigned128BitType in, UnsignedInt128Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt128Member());
fillDataset(input, proc, new UnsignedInt128Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV1BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt1Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt1Member());
fillDataset(input, proc, new UnsignedInt1Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV2BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt2Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt2Member());
fillDataset(input, proc, new UnsignedInt2Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV3BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt3Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt3Member());
fillDataset(input, proc, new UnsignedInt3Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV4BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt4Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt4Member());
fillDataset(input, proc, new UnsignedInt4Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV5BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt5Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt5Member());
fillDataset(input, proc, new UnsignedInt5Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV6BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt6Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt6Member());
fillDataset(input, proc, new UnsignedInt6Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV7BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt7Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt7Member());
fillDataset(input, proc, new UnsignedInt7Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV8BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt8Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt8Member());
fillDataset(input, proc, new UnsignedInt8Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV9BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt9Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt9Member());
fillDataset(input, proc, new UnsignedInt9Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV10BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt10Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt10Member());
fillDataset(input, proc, new UnsignedInt10Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV11BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt11Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt11Member());
fillDataset(input, proc, new UnsignedInt11Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV12BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt12Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt12Member());
fillDataset(input, proc, new UnsignedInt12Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV13BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt13Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt13Member());
fillDataset(input, proc, new UnsignedInt13Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV14BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt14Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt14Member());
fillDataset(input, proc, new UnsignedInt14Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV15BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt15Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt15Member());
fillDataset(input, proc, new UnsignedInt15Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV16BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt16Member out) {
out.setV(in.getInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt16Member());
fillDataset(input, proc, new UnsignedInt16Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV32BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt32Member out) {
out.setV(in.get());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt32Member());
fillDataset(input, proc, new UnsignedInt32Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV64BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt64Member out) {
out.setV(in.getBigInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt64Member());
fillDataset(input, proc, new UnsignedInt64Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedV128BitImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnsignedInt128Member out) {
out.setV(in.getBigInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnsignedInt128Member());
fillDataset(input, proc, new UnsignedInt128Member(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadUnsignedBigIntImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(UnsignedVariableBitLengthType in, UnboundedIntMember out) {
out.setV(in.getBigInteger());
}
};
DimensionedDataSource output =
makeDataset(input, new UnboundedIntMember());
fillDataset(input, proc, new UnboundedIntMember(), output);
updateMetadata(input, output);
return output;
}
private static DimensionedDataSource
loadARGBTypeImage(SCIFIOImgPlus input)
{
Procedure2 proc =
new Procedure2()
{
@Override
public void call(ARGBType in, ArgbMember out) {
int value = in.get();
out.setA(ARGBType.alpha(value));
out.setR(ARGBType.red(value));
out.setG(ARGBType.green(value));
out.setB(ARGBType.blue(value));
}
};
DimensionedDataSource output =
makeDataset(input, new ArgbMember());
fillDataset(input, proc, new ArgbMember(), output);
updateMetadata(input, output);
return output;
}
private static > DimensionedDataSource
makeDataset(SCIFIOImgPlus sciImgPlus, U type)
{
long[] dims = new long[sciImgPlus.numDimensions()];
for (int i = 0; i < dims.length; i++) {
dims[i] = sciImgPlus.dimension(i);
}
return DimensionedStorage.allocate(type, dims);
}
private static
void fillDataset(SCIFIOImgPlus input, Procedure2 converter, W outValue, DimensionedDataSource output)
{
PlaneView planes = new PlaneView<>(output, 0, 1);
int numPlaneDims = output.numDimensions() - 2;
long[] planeDims = new long[numPlaneDims];
for (int i = 0; i < numPlaneDims; i++) {
planeDims[i] = output.dimension(i+2);
}
RandomAccess r = input.randomAccess();
IntegerIndex planeIndex = new IntegerIndex(numPlaneDims);
if (numPlaneDims == 0) {
// iterate within the plane and copy values
for (long y = 0; y < planes.d1(); y++) {
r.setPosition(y, 1);
for (long x = 0; x < planes.d0(); x++) {
r.setPosition(x, 0);
U inValue = r.get();
converter.call(inValue, outValue);
planes.set(x, y, outValue);
}
}
}
else {
SamplingIterator planeIter = GridIterator.compute(planeDims);
// iterate through planes
while (planeIter.hasNext()) {
// find next plane
planeIter.next(planeIndex);
// move the imglib index and our planes index to match this plane
for (int i = 0; i < numPlaneDims; i++) {
r.setPosition(planeIndex.get(i), i+2);
planes.setPositionValue(i, planeIndex.get(i));
}
// iterate within the plane and copy values
for (long y = 0; y < planes.d1(); y++) {
r.setPosition(y, 1);
for (long x = 0; x < planes.d0(); x++) {
r.setPosition(x, 0);
U inValue = r.get();
converter.call(inValue, outValue);
planes.set(x, y, outValue);
}
}
}
}
}
private static void updateMetadata(SCIFIOImgPlus input, DimensionedDataSource output)
{
BigDecimal[] scales = new BigDecimal[input.numDimensions()];
BigDecimal[] offsets = new BigDecimal[input.numDimensions()];
output.setName(input.getName());
output.setSource(input.getSource());
for (int i = 0; i < input.numDimensions(); i++) {
output.setAxisType(i, input.axis(i).type().toString());
output.setAxisUnit(i, input.axis(i).unit());
if (input.dimension(i) < 2)
scales[i] = BigDecimal.ONE;
else
scales[i] = BigDecimal.valueOf(input.axis(i).averageScale(0, input.dimension(i)-1));
offsets[i] = BigDecimal.valueOf(input.axis(i).calibratedValue(0));
}
output.setCoordinateSpace(new LinearNdCoordinateSpace(scales, offsets));
output.metadata().putString("input-dataset-name", input.getMetadata().getDatasetName());
output.metadata().putLong("input-dataset-size", input.getMetadata().getDatasetSize());
// surprisingly this one might hang or just takes a long time with ImageJ's lena-std
// image. maybe a scifio bug? I reported it as one.
//output.metadata().put("input-destination-location", input.getMetadata().getDestinationLocation().toString());
output.metadata().putString("input-format-name", input.getMetadata().getFormatName());
output.metadata().putString("input-identifier", input.getMetadata().getIdentifier());
output.metadata().putString("input-location", input.getMetadata().getLocation());
output.metadata().putString("input-source-location", input.getMetadata().getSourceLocation().toString());
output.metadata().putString("input-version", input.getMetadata().getVersion());
}
}
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