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Commit 91e4ce03 authored by Vojtech Moravec's avatar Vojtech Moravec
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Clean and improve loader code. 

Remove loadPlaneU16 from IPlaneLoader interface. At the same time add loadPlaneData method, which is more general.

Also we have implemented general loadVoxels in `BasicLoader` which uses the abstract loadPlaneData method.
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src/main/java/azgracompress/io/loader/BasicLoader.java
+ 50
− 0
View file @ 91e4ce03
...@@ -2,6 +2,8 @@ package azgracompress.io.loader; ...@@ -2,6 +2,8 @@ package azgracompress.io.loader;
import azgracompress.data.V3i; import azgracompress.data.V3i;
import java.io.IOException;
public abstract class BasicLoader { public abstract class BasicLoader {
protected final V3i dims; protected final V3i dims;
...@@ -9,6 +11,15 @@ public abstract class BasicLoader { ...@@ -9,6 +11,15 @@ public abstract class BasicLoader {
this.dims = datasetDims; this.dims = datasetDims;
} }
/**
* Abstract method to load specified plane data.
*
* @param plane Zero based plane index.
* @return Plane data.
* @throws IOException when fails to load plane data for some reason.
*/
public abstract int[] loadPlaneData(final int plane) throws IOException;
/** /**
* Check whether the coordinates are inside voxel of dimension `dims`. * Check whether the coordinates are inside voxel of dimension `dims`.
* *
...@@ -63,4 +74,43 @@ public abstract class BasicLoader { ...@@ -63,4 +74,43 @@ public abstract class BasicLoader {
final int zChunkCount = (int) Math.ceil((double) datasetDims.getZ() / (double) voxelDims.getZ()); final int zChunkCount = (int) Math.ceil((double) datasetDims.getZ() / (double) voxelDims.getZ());
return (xChunkCount * yChunkCount * zChunkCount); return (xChunkCount * yChunkCount * zChunkCount);
} }
/**
* Load dataset into voxel data.
*
* @param voxelDim Single voxel dimensions.
* @return Voxel data arranged in arrays.
* @throws IOException When fails to load plane data.
*/
protected int[][] loadVoxelsImplGray16(final V3i voxelDim) throws IOException {
final int xVoxelCount = (int) Math.ceil((double) dims.getX() / (double) voxelDim.getX());
final int yVoxelCount = (int) Math.ceil((double) dims.getY() / (double) voxelDim.getY());
int[][] voxels = new int[calculateRequiredVoxelCount(dims, voxelDim)][(int) voxelDim.multiplyTogether()];
int dstZ, dstY, dstX, voxelX, voxelY, voxelZ, voxelIndex;
for (int srcZ = 0; srcZ < dims.getZ(); srcZ++) {
final int[] srcPlaneBuffer = loadPlaneData(srcZ);
dstZ = srcZ / voxelDim.getZ();
voxelZ = srcZ - (dstZ * voxelDim.getZ());
for (int srcY = 0; srcY < dims.getY(); srcY++) {
dstY = srcY / voxelDim.getY();
voxelY = srcY - (dstY * voxelDim.getY());
for (int srcX = 0; srcX < dims.getX(); srcX++) {
dstX = srcX / voxelDim.getX();
voxelX = srcX - (dstX * voxelDim.getX());
voxelIndex = (dstZ * (xVoxelCount * yVoxelCount)) + (dstY * xVoxelCount) + dstX;
voxels[voxelIndex][voxelDataIndex(voxelX, voxelY, voxelZ, voxelDim)] = srcPlaneBuffer[(srcY * dims.getX()) + srcX];
}
}
}
return voxels;
}
} }
src/main/java/azgracompress/io/loader/IPlaneLoader.java
+ 2
− 5
View file @ 91e4ce03
package azgracompress.io.loader; package azgracompress.io.loader;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i; import azgracompress.data.V3i;
import java.io.IOException; import java.io.IOException;
public interface IPlaneLoader { public interface IPlaneLoader {
ImageU16 loadPlaneU16(final int plane) throws IOException; int[] loadPlaneData(final int plane) throws IOException;
int[] loadPlanesU16Data(int[] planes) throws IOException; int[] loadPlanesU16Data(int[] planes) throws IOException;
int[] loadAllPlanesU16Data() throws IOException; int[] loadAllPlanesU16Data() throws IOException;
default int[][] loadVoxels(final V3i voxelDim) throws IOException { int[][] loadVoxels(final V3i voxelDim) throws IOException;
throw new IOException("NOT IMPLEMENTED");
}
} }
src/main/java/azgracompress/io/loader/ImageJBufferLoader.java
+ 35
− 196
View file @ 91e4ce03
package azgracompress.io.loader; package azgracompress.io.loader;
import azgracompress.data.Chunk3D;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i; import azgracompress.data.V3i;
import azgracompress.io.BufferInputData; import azgracompress.io.BufferInputData;
import azgracompress.io.InputData; import azgracompress.io.InputData;
import azgracompress.utilities.TypeConverter; import azgracompress.utilities.TypeConverter;
import java.io.IOException; import java.io.IOException;
import java.io.PrintStream;
import java.util.Arrays; import java.util.Arrays;
public class ImageJBufferLoader implements IPlaneLoader { public final class ImageJBufferLoader extends BasicLoader implements IPlaneLoader {
private final BufferInputData bufferInputData; private final BufferInputData bufferInputData;
public ImageJBufferLoader(BufferInputData bufferDataInfo) { public ImageJBufferLoader(BufferInputData bufferDataInfo) {
super(bufferDataInfo.getDimensions());
this.bufferInputData = bufferDataInfo; this.bufferInputData = bufferDataInfo;
// FIXME: Support more pixel types.
assert (this.bufferInputData.getPixelType() == InputData.PixelType.Gray16); assert (this.bufferInputData.getPixelType() == InputData.PixelType.Gray16);
} }
private int[] copyShortArray(short[] srcArray, int copyLen) {
int[] destArray = new int[copyLen];
for (int i = 0; i < copyLen; i++) {
destArray[i] = TypeConverter.shortToInt(srcArray[i]);
}
return destArray;
}
private void copyShortArrayIntoBuffer(short[] srcArray, int[] destBuffer, int destOffset, int copyLen) { private void copyShortArrayIntoBuffer(short[] srcArray, int[] destBuffer, int destOffset, int copyLen) {
for (int i = 0; i < copyLen; i++) { for (int i = 0; i < copyLen; i++) {
destBuffer[destOffset + i] = TypeConverter.shortToInt(srcArray[i]); destBuffer[destOffset + i] = TypeConverter.shortToInt(srcArray[i]);
...@@ -34,19 +25,9 @@ public class ImageJBufferLoader implements IPlaneLoader { ...@@ -34,19 +25,9 @@ public class ImageJBufferLoader implements IPlaneLoader {
} }
@Override @Override
public ImageU16 loadPlaneU16(int plane) throws IOException { public int[] loadPlaneData(final int plane) {
assert (plane >= 0);
switch (bufferInputData.getPixelType()) {
case Gray16: {
final int planePixelCount = bufferInputData.getDimensions().getX() * bufferInputData.getDimensions().getY();
final short[] srcBuffer = (short[]) bufferInputData.getPixelBuffer(plane); final short[] srcBuffer = (short[]) bufferInputData.getPixelBuffer(plane);
return new ImageU16(bufferInputData.getDimensions().getX(), return TypeConverter.shortArrayToIntArray(srcBuffer);
bufferInputData.getDimensions().getY(),
copyShortArray(srcBuffer, planePixelCount));
}
default:
throw new IOException("Unable to load unsupported pixel type.");
}
} }
@Override @Override
...@@ -54,13 +35,12 @@ public class ImageJBufferLoader implements IPlaneLoader { ...@@ -54,13 +35,12 @@ public class ImageJBufferLoader implements IPlaneLoader {
if (planes.length < 1) { if (planes.length < 1) {
return new int[0]; return new int[0];
} else if (planes.length == 1) { } else if (planes.length == 1) {
return loadPlaneU16(planes[0]).getData(); return loadPlaneData(planes[0]);
} else if (planes.length == bufferInputData.getDimensions().getZ()) { // Maybe? } else if (planes.length == bufferInputData.getDimensions().getZ()) { // Maybe?
return loadAllPlanesU16Data(); return loadAllPlanesU16Data();
} }
switch (bufferInputData.getPixelType()) { final int planePixelCount =
case Gray16: { bufferInputData.getDimensions().getX() * bufferInputData.getDimensions().getY();
final int planePixelCount = bufferInputData.getDimensions().getX() * bufferInputData.getDimensions().getY();
final long totalValueCount = (long) planePixelCount * (long) planes.length; final long totalValueCount = (long) planePixelCount * (long) planes.length;
if (totalValueCount > (long) Integer.MAX_VALUE) { if (totalValueCount > (long) Integer.MAX_VALUE) {
...@@ -78,15 +58,9 @@ public class ImageJBufferLoader implements IPlaneLoader { ...@@ -78,15 +58,9 @@ public class ImageJBufferLoader implements IPlaneLoader {
} }
return destBuffer; return destBuffer;
} }
default:
throw new IOException("Unable to load unsupported pixel type.");
}
}
@Override @Override
public int[] loadAllPlanesU16Data() throws IOException { public int[] loadAllPlanesU16Data() throws IOException {
switch (bufferInputData.getPixelType()) {
case Gray16: {
final V3i imageDims = bufferInputData.getDimensions(); final V3i imageDims = bufferInputData.getDimensions();
final long totalValueCount = imageDims.multiplyTogether(); final long totalValueCount = imageDims.multiplyTogether();
final int planePixelCount = imageDims.getX() * imageDims.getY(); final int planePixelCount = imageDims.getX() * imageDims.getY();
...@@ -104,145 +78,10 @@ public class ImageJBufferLoader implements IPlaneLoader { ...@@ -104,145 +78,10 @@ public class ImageJBufferLoader implements IPlaneLoader {
} }
return destBuffer; return destBuffer;
} }
default:
throw new IOException("Unable to load unsupported pixel type.");
}
}
@Override @Override
public int[][] loadVoxels(final V3i voxelDim) throws IOException { public int[][] loadVoxels(final V3i voxelDim) throws IOException {
assert (bufferInputData.getPixelType() == InputData.PixelType.Gray16); return loadVoxelsImplGray16(voxelDim);
final V3i dims = bufferInputData.getDimensions();
final int xVoxelCount = (int) Math.ceil((double) dims.getX() / (double) voxelDim.getX());
final int yVoxelCount = (int) Math.ceil((double) dims.getY() / (double) voxelDim.getY());
final int voxelSize = (int) voxelDim.multiplyTogether();
final int voxelCount = Chunk3D.calculateRequiredChunkCount(bufferInputData.getDimensions(), voxelDim);
int[][] voxels = new int[voxelCount][voxelSize];
int dstZ, dstY, dstX;
// THIS IS WRONG
// FIXME
for (int srcZ = 0; srcZ < dims.getZ(); srcZ++) {
final short[] srcBuffer = (short[]) bufferInputData.getPixelBuffer(srcZ);
dstZ = srcZ / voxelDim.getZ();
for (int srcY = 0; srcY < dims.getY(); srcY++) {
dstY = srcY / voxelDim.getY();
for (int srcX = 0; srcX < dims.getX(); srcX++) {
dstX = srcX / voxelDim.getX();
final int voxelIndex = (dstZ * (xVoxelCount * yVoxelCount)) + (dstY * xVoxelCount) + dstX;
final int indexInsideVoxel = ((srcZ % voxelDim.getZ()) * (voxelDim.getX() * voxelDim.getY())) +
((srcY % voxelDim.getY()) * voxelDim.getX()) +
(srcX % voxelDim.getX());
voxels[voxelIndex][indexInsideVoxel] = srcBuffer[(srcY * bufferInputData.getDimensions().getX()) + srcX];
// System.out.printf("SRC: [%d;%d;%d] -> %d_[%d]\n", srcX, srcY, srcZ, voxelIndex, indexInsideVoxel);
}
}
}8
return voxels;
}
/**
* Copy this chunk data to chunk vector.
*
* @param vector Chunk vector.
* @param qVectorDims Dimensions of the vector.
* @param chunkXOffset Chunk X offset
* @param chunkYOffset Chunk Y offset.
* @param chunkZOffset Chunk Z offset.
*/
private void copyDataToVector(int[] vector,
final V3i qVectorDims,
final int chunkXOffset,
final int chunkYOffset,
final int chunkZOffset) {
int srcZ;
for (int z = 0; z < qVectorDims.getZ(); z++) {
srcZ = chunkZOffset + z;
fillVoxelFromPlane(vector, qVectorDims, srcZ, z, chunkXOffset, chunkYOffset);
}
}
private void fillVoxelFromPlane(int[] vector,
final V3i qVectorDims,
final int srcZ,
final int z,
final int chunkXOffset,
final int chunkYOffset) {
if (srcZ >= bufferInputData.getDimensions().getZ())
return;
final short[] srcBuffer = (short[]) bufferInputData.getPixelBuffer(srcZ);
final int width = bufferInputData.getDimensions().getX();
int srcX, srcY;
for (int y = 0; y < qVectorDims.getY(); y++) {
srcY = chunkYOffset + y;
for (int x = 0; x < qVectorDims.getX(); x++) {
srcX = chunkXOffset + x;
final int dstIndex = index(x, y, z, qVectorDims);
vector[dstIndex] = isInside(srcX, srcY, srcZ) ? srcBuffer[(srcY * width) + srcX] : 0;
}
}
}
private boolean isInside(final int x, final int y, final int z) {
return (((x >= 0) && (x < bufferInputData.getDimensions().getX())) && (y >= 0) &&
(y < bufferInputData.getDimensions().getY()) && (z >= 0) &&
(z < bufferInputData.getDimensions().getZ()));
}
/**
* Calculate the index inside data array.
*
* @param x Zero based x coordinate.
* @param y Zero based y coordinate.
* @param z Zero based z coordinate.
* @return Index inside data array.
*/
private int index(final int x, final int y, final int z) {
return index(x, y, z, bufferInputData.getDimensions());
}
/**
* Calculate the index inside array of dimensions specified by chunkDims.
*
* @param x Zero based x coordinate.
* @param y Zero based y coordinate.
* @param z Zero based z coordinate.
* @param chunkDims Chunk dimensions.
* @return Index inside chunk dimension data array.
*/
private int index(final int x, final int y, final int z, final V3i chunkDims) {
assert (x >= 0 && x < chunkDims.getX()) : "Index X out of bounds.";
assert (y >= 0 && y < chunkDims.getY()) : "Index Y out of bounds.";
assert (z >= 0 && z < chunkDims.getZ()) : "Index Z out of bounds.";
// NOTE(Moravec): Description of the following calculation
// plane index * plane pixel count
// | |
// V V
// planeOffset = chunkDims.getZ() * (chunkDims.getX() * chunkDims.getY())
// row * pixels in row
// | |
// V V
// rowOffset = y * chunkDims.getX();
// column
// |
// V
// colOffset = x;
return (z * (chunkDims.getX() * chunkDims.getY())) + (y * chunkDims.getX()) + x;
} }
} }
src/main/java/azgracompress/io/loader/RawDataLoader.java
+ 12
− 12
View file @ 91e4ce03
package azgracompress.io.loader; package azgracompress.io.loader;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i; import azgracompress.data.V3i;
import azgracompress.io.FileInputData; import azgracompress.io.FileInputData;
import azgracompress.utilities.TypeConverter; import azgracompress.utilities.TypeConverter;
...@@ -11,24 +10,23 @@ import java.io.FileInputStream; ...@@ -11,24 +10,23 @@ import java.io.FileInputStream;
import java.io.IOException; import java.io.IOException;
import java.util.Arrays; import java.util.Arrays;
public class RawDataLoader implements IPlaneLoader { public final class RawDataLoader extends BasicLoader implements IPlaneLoader {
private final FileInputData inputDataInfo; private final FileInputData inputDataInfo;
public RawDataLoader(final FileInputData inputDataInfo) { public RawDataLoader(final FileInputData inputDataInfo) {
super(inputDataInfo.getDimensions());
this.inputDataInfo = inputDataInfo; this.inputDataInfo = inputDataInfo;
} }
@Override @Override
public ImageU16 loadPlaneU16(int plane) throws IOException { public int[] loadPlaneData(final int plane) throws IOException {
byte[] buffer; byte[] buffer;
final V3i rawDataDimension = inputDataInfo.getDimensions();
try (FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath())) { try (FileInputStream fileStream = new FileInputStream(inputDataInfo.getFilePath())) {
final long planeSize = (long) rawDataDimension.getX() * (long) rawDataDimension.getY() * 2; final long planeSize = (long) dims.getX() * (long) dims.getY() * 2;
final long expectedFileSize = planeSize * rawDataDimension.getZ(); final long expectedFileSize = planeSize * dims.getZ();
final long fileSize = fileStream.getChannel().size(); final long fileSize = fileStream.getChannel().size();
if (expectedFileSize != fileSize) { if (expectedFileSize != fileSize) {
throw new IOException( throw new IOException(
"File specified by `rawFile` doesn't contains raw data for image of dimensions " + "File specified by `rawFile` doesn't contains raw data for image of dimensions " +
...@@ -45,10 +43,7 @@ public class RawDataLoader implements IPlaneLoader { ...@@ -45,10 +43,7 @@ public class RawDataLoader implements IPlaneLoader {
throw new IOException("Read wrong number of bytes."); throw new IOException("Read wrong number of bytes.");
} }
} }
return TypeConverter.unsignedShortBytesToIntArray(buffer);
return new ImageU16(rawDataDimension.getX(),
rawDataDimension.getY(),
TypeConverter.unsignedShortBytesToIntArray(buffer));
} }
@Override @Override
...@@ -56,7 +51,7 @@ public class RawDataLoader implements IPlaneLoader { ...@@ -56,7 +51,7 @@ public class RawDataLoader implements IPlaneLoader {
if (planes.length < 1) { if (planes.length < 1) {
return new int[0]; return new int[0];
} else if (planes.length == 1) { } else if (planes.length == 1) {
return loadPlaneU16(planes[0]).getData(); return loadPlaneData(planes[0]);
} }
final int planeValueCount = inputDataInfo.getDimensions().getX() * inputDataInfo.getDimensions().getY(); final int planeValueCount = inputDataInfo.getDimensions().getX() * inputDataInfo.getDimensions().getY();
...@@ -119,4 +114,9 @@ public class RawDataLoader implements IPlaneLoader { ...@@ -119,4 +114,9 @@ public class RawDataLoader implements IPlaneLoader {
return values; return values;
} }
@Override
public int[][] loadVoxels(V3i voxelDim) throws IOException {
return loadVoxelsImplGray16(voxelDim);
}
} }
src/main/java/azgracompress/io/loader/SCIFIOLoader.java
+ 12
− 7
View file @ 91e4ce03
package azgracompress.io.loader; package azgracompress.io.loader;
import azgracompress.ScifioWrapper; import azgracompress.ScifioWrapper;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i; import azgracompress.data.V3i;
import azgracompress.io.FileInputData; import azgracompress.io.FileInputData;
import azgracompress.utilities.TypeConverter; import azgracompress.utilities.TypeConverter;
...@@ -11,7 +10,7 @@ import io.scif.Reader; ...@@ -11,7 +10,7 @@ import io.scif.Reader;
import java.io.IOException; import java.io.IOException;
import java.util.Arrays; import java.util.Arrays;
public class SCIFIOLoader implements IPlaneLoader { public final class SCIFIOLoader extends BasicLoader implements IPlaneLoader {
private final FileInputData inputDataInfo; private final FileInputData inputDataInfo;
private final Reader reader; private final Reader reader;
...@@ -24,29 +23,28 @@ public class SCIFIOLoader implements IPlaneLoader { ...@@ -24,29 +23,28 @@ public class SCIFIOLoader implements IPlaneLoader {
* @throws FormatException When fails to create SCIFIO reader. * @throws FormatException When fails to create SCIFIO reader.
*/ */
public SCIFIOLoader(final FileInputData inputDataInfo) throws IOException, FormatException { public SCIFIOLoader(final FileInputData inputDataInfo) throws IOException, FormatException {
super(inputDataInfo.getDimensions());
this.inputDataInfo = inputDataInfo; this.inputDataInfo = inputDataInfo;
this.reader = ScifioWrapper.getReader(this.inputDataInfo.getFilePath()); this.reader = ScifioWrapper.getReader(this.inputDataInfo.getFilePath());
} }
@Override @Override
public ImageU16 loadPlaneU16(int plane) throws IOException { public int[] loadPlaneData(final int plane) throws IOException {
byte[] planeBytes; byte[] planeBytes;
try { try {
planeBytes = reader.openPlane(0, plane).getBytes(); planeBytes = reader.openPlane(0, plane).getBytes();
} catch (FormatException e) { } catch (FormatException e) {
throw new IOException("Unable to open plane with the reader. " + e.getMessage()); throw new IOException("Unable to open plane with the reader. " + e.getMessage());
} }
final int[] data = TypeConverter.unsignedShortBytesToIntArray(planeBytes); return TypeConverter.unsignedShortBytesToIntArray(planeBytes);
return new ImageU16(inputDataInfo.getDimensions().toV2i(), data);
} }
@SuppressWarnings("DuplicatedCode")
@Override @Override
public int[] loadPlanesU16Data(int[] planes) throws IOException { public int[] loadPlanesU16Data(int[] planes) throws IOException {
if (planes.length < 1) { if (planes.length < 1) {
return new int[0]; return new int[0];
} else if (planes.length == 1) { } else if (planes.length == 1) {
return loadPlaneU16(planes[0]).getData(); return loadPlaneData(planes[0]);
} }
final int planeValueCount = inputDataInfo.getDimensions().getX() * inputDataInfo.getDimensions().getY(); final int planeValueCount = inputDataInfo.getDimensions().getX() * inputDataInfo.getDimensions().getY();
...@@ -105,4 +103,11 @@ public class SCIFIOLoader implements IPlaneLoader { ...@@ -105,4 +103,11 @@ public class SCIFIOLoader implements IPlaneLoader {
return values; return values;
} }
@Override
public int[][] loadVoxels(final V3i voxelDim) throws IOException {
return loadVoxelsImplGray16(voxelDim);
}
} }
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