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Commit a84b8a1c authored by Vojtech Moravec's avatar Vojtech Moravec
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Use abstract PlaneLoader. 

Use ConcretePlaneLoader instead of RawDataIO.
This allows the use of SCIFIO readers.
parent 4496519f
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src/main/java/azgracompress/benchmark/BenchmarkBase.java
+ 29
− 45
View file @ a84b8a1c
......@@ -33,27 +33,11 @@ abstract class BenchmarkBase {
protected final int workerCount;
protected BenchmarkBase(final String inputFile,
final String outputDirectory,
final int[] planes,
final V3i rawImageDims) {
this.inputFile = inputFile;
this.outputDirectory = outputDirectory;
this.planes = planes;
this.rawImageDims = rawImageDims;
hasReferencePlane = false;
referencePlaneIndex = -1;
codebookSize = 256;
hasCacheFolder = false;
cacheFolder = null;
hasGeneralQuantizer = false;
workerCount = 1;
}
protected final ParsedCliOptions options;
protected BenchmarkBase(final ParsedCliOptions options) {
this.options = options;
final InputFileInfo ifi = options.getInputFileInfo();
this.inputFile = ifi.getFilePath();
this.outputDirectory = options.getOutputFile();
......@@ -98,32 +82,32 @@ abstract class BenchmarkBase {
return file.getAbsolutePath();
}
/**
* Load u16 plane from RAW file.
*
* @param planeIndex Zero based plane index.
* @return u16 plane.
*/
protected ImageU16 loadPlane(final int planeIndex) {
try {
return RawDataIO.loadImageU16(inputFile, rawImageDims, planeIndex);
} catch (Exception ex) {
ex.printStackTrace();
}
return null;
}
/**
* Load U16 plane data from RAW file.
*
* @param planeIndex Zero based plane index.
* @return U16 array of image plane data.
*/
protected int[] loadPlaneData(final int planeIndex) {
ImageU16 plane = loadPlane(planeIndex);
return (plane != null) ? plane.getData() : new int[0];
}
// /**
// * Load u16 plane from RAW file.
// *
// * @param planeIndex Zero based plane index.
// * @return u16 plane.
// */
// protected ImageU16 loadPlane(final int planeIndex) {
// try {
// return RawDataIO.loadImageU16(inputFile, rawImageDims, planeIndex);
// } catch (Exception ex) {
// ex.printStackTrace();
// }
// return null;
// }
// /**
// * Load U16 plane data from RAW file.
// *
// * @param planeIndex Zero based plane index.
// * @return U16 array of image plane data.
// */
// protected int[] loadPlaneData(final int planeIndex) {
// ImageU16 plane = loadPlane(planeIndex);
//
// return (plane != null) ? plane.getData() : new int[0];
// }
/**
......
src/main/java/azgracompress/benchmark/ScalarQuantizationBenchmark.java
+ 26
− 11
View file @ a84b8a1c
......@@ -2,9 +2,9 @@ package azgracompress.benchmark;
import azgracompress.U16;
import azgracompress.cli.ParsedCliOptions;
import azgracompress.data.V3i;
import azgracompress.de.DeException;
import azgracompress.de.shade.ILShadeSolver;
import azgracompress.io.ConcretePlaneLoader;
import azgracompress.quantization.QTrainIteration;
import azgracompress.quantization.QuantizationValueCache;
import azgracompress.quantization.scalar.LloydMaxU16ScalarQuantization;
......@@ -18,13 +18,6 @@ import java.io.OutputStreamWriter;
public class ScalarQuantizationBenchmark extends BenchmarkBase {
private boolean useDiffEvolution = false;
public ScalarQuantizationBenchmark(final String inputFile,
final String outputDirectory,
final int[] planes,
final V3i rawImageDims) {
super(inputFile, outputDirectory, planes, rawImageDims);
}
public ScalarQuantizationBenchmark(final ParsedCliOptions options) {
super(options);
}
......@@ -32,12 +25,22 @@ public class ScalarQuantizationBenchmark extends BenchmarkBase {
@Override
public void startBenchmark() {
ConcretePlaneLoader planeLoader = null;
try {
planeLoader = new ConcretePlaneLoader(options.getInputFileInfo());
} catch (Exception e) {
e.printStackTrace();
System.err.println("Unable to create SCIFIO reader.");
return;
}
if (planes.length < 1) {
return;
}
boolean dirCreated = new File(this.outputDirectory).mkdirs();
System.out.println(String.format("|CODEBOOK| = %d", codebookSize));
ScalarQuantizer quantizer = null;
if (hasCacheFolder) {
System.out.println("Loading codebook from cache");
QuantizationValueCache cache = new QuantizationValueCache(cacheFolder);
......@@ -51,11 +54,16 @@ public class ScalarQuantizationBenchmark extends BenchmarkBase {
}
System.out.println("Created quantizer from cache");
} else if (hasReferencePlane) {
final int[] refPlaneData = loadPlaneData(referencePlaneIndex);
if (refPlaneData.length == 0) {
final int[] refPlaneData;
try {
refPlaneData = planeLoader.loadPlaneU16(referencePlaneIndex).getData();
} catch (IOException e) {
e.printStackTrace();
System.err.println("Failed to load reference plane data.");
return;
}
if (useDiffEvolution) {
quantizer = trainDifferentialEvolution(refPlaneData, codebookSize);
} else {
......@@ -67,7 +75,14 @@ public class ScalarQuantizationBenchmark extends BenchmarkBase {
for (final int planeIndex : planes) {
System.out.println(String.format("Loading plane %d ...", planeIndex));
// NOTE(Moravec): Actual planeIndex is zero based.
final int[] planeData = loadPlaneData(planeIndex);
final int[] planeData;
try {
planeData = planeLoader.loadPlaneU16(planeIndex).getData();
} catch (IOException e) {
e.printStackTrace();
System.err.println("Failed to load plane data.");
return;
}
if (planeData.length == 0) {
System.err.println(String.format("Failed to load plane %d data. Skipping plane.", planeIndex));
return;
......
src/main/java/azgracompress/benchmark/VectorQuantizationBenchmark.java
+ 19
− 11
View file @ a84b8a1c
......@@ -2,6 +2,7 @@ package azgracompress.benchmark;
import azgracompress.cli.ParsedCliOptions;
import azgracompress.data.*;
import azgracompress.io.ConcretePlaneLoader;
import azgracompress.quantization.QuantizationValueCache;
import azgracompress.quantization.vector.CodebookEntry;
import azgracompress.quantization.vector.LBGResult;
......@@ -17,10 +18,6 @@ public class VectorQuantizationBenchmark extends BenchmarkBase {
final static V2i DEFAULT_QVECTOR = new V2i(3, 3);
public VectorQuantizationBenchmark(String inputFile, String outputDirectory, int[] planes, V3i rawImageDims) {
super(inputFile, outputDirectory, planes, rawImageDims);
}
public VectorQuantizationBenchmark(final ParsedCliOptions options) {
super(options);
}
......@@ -51,6 +48,14 @@ public class VectorQuantizationBenchmark extends BenchmarkBase {
if (planes.length < 1) {
return;
}
ConcretePlaneLoader planeLoader = null;
try {
planeLoader = new ConcretePlaneLoader(options.getInputFileInfo());
} catch (Exception e) {
e.printStackTrace();
System.err.println("Unable to create SCIFIO reader.");
return;
}
if (qVector.getY() > 1) {
System.out.println("2D qVector");
} else {
......@@ -77,9 +82,11 @@ public class VectorQuantizationBenchmark extends BenchmarkBase {
}
System.out.println("Created quantizer from cache");
} else if (hasReferencePlane) {
final ImageU16 plane = loadPlane(referencePlaneIndex);
if (plane == null) {
final ImageU16 plane;
try {
plane = planeLoader.loadPlaneU16(referencePlaneIndex);
} catch (IOException e) {
e.printStackTrace();
System.err.println("Failed to load reference plane data.");
return;
}
......@@ -93,11 +100,12 @@ public class VectorQuantizationBenchmark extends BenchmarkBase {
for (final int planeIndex : planes) {
System.out.println(String.format("Loading plane %d ...", planeIndex));
// NOTE(Moravec): Actual planeIndex is zero based.
final ImageU16 plane = loadPlane(planeIndex - 1);
if (plane == null) {
final ImageU16 plane;
try {
plane = planeLoader.loadPlaneU16(planeIndex);
} catch (IOException e) {
e.printStackTrace();
System.err.println(String.format("Failed to load plane %d data. Skipping plane.", planeIndex));
return;
}
......
src/main/java/azgracompress/cli/InputFileInfo.java
+ 10
− 0
View file @ a84b8a1c
......@@ -12,6 +12,8 @@ public class InputFileInfo {
*/
private final String filePath;
private boolean isRAW = true;
private V3i dimension;
private boolean planeIndexSet = false;
......@@ -76,4 +78,12 @@ public class InputFileInfo {
public V2i getPlaneRange() {
return planeRange;
}
public boolean isRAW() {
return isRAW;
}
public void setIsRaw(boolean RAW) {
isRAW = RAW;
}
}
src/main/java/azgracompress/cli/ParsedCliOptions.java
+ 3
− 2
View file @ a84b8a1c
......@@ -130,7 +130,6 @@ public class ParsedCliOptions {
return;
}
inputFileInfo = new InputFileInfo(inputFileArguments[0]);
// Decompress and Inspect methods doesn't require additional file information.
......@@ -159,7 +158,8 @@ public class ParsedCliOptions {
// inputFileInfo is already created with TIFF type.
// assert (inputFileInfo.getFileType() == FileType.TIFF) : "Not TIFF type in parse Tiff arguments.";
Reader reader = null;
inputFileInfo.setIsRaw(false);
Reader reader;
try {
reader = ScifioWrapper.getReader(inputFileInfo.getFilePath());
} catch (IOException | FormatException e) {
......@@ -223,6 +223,7 @@ public class ParsedCliOptions {
return;
}
inputFileInfo.setIsRaw(true);
parseImageDims(inputFileArguments[1], errorBuilder);
// User specified plane index or plane range.
......
src/main/java/azgracompress/cli/functions/MeasurePlaneErrorFunction.java
+ 47
− 56
View file @ a84b8a1c
......@@ -2,15 +2,6 @@ package azgracompress.cli.functions;
import azgracompress.cli.CustomFunctionBase;
import azgracompress.cli.ParsedCliOptions;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i;
import azgracompress.io.RawDataIO;
import azgracompress.utilities.Utils;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStreamWriter;
import java.util.Arrays;
public class MeasurePlaneErrorFunction extends CustomFunctionBase {
public MeasurePlaneErrorFunction(ParsedCliOptions options) {
......@@ -66,53 +57,53 @@ public class MeasurePlaneErrorFunction extends CustomFunctionBase {
}
private boolean reportPlaneDifference(final String compressedFile, final String reportFile) {
final String referenceFile = "D:\\biology\\tiff_data\\benchmark\\fused_tp_10_ch_1_16bit.raw";
final V3i dims = new V3i(1041, 996, 946);
final int planePixelCount = dims.getX() * dims.getY();
System.out.println(options.report());
System.out.println("Run custom function.");
ImageU16 compressedPlane = null;
ImageU16 originalPlane = null;
ImageU16 differencePlane = null;
PlaneError[] planeErrors = new PlaneError[dims.getZ()];
for (int planeIndex = 0; planeIndex < dims.getZ(); planeIndex++) {
try {
originalPlane = RawDataIO.loadImageU16(referenceFile, dims, planeIndex);
compressedPlane = RawDataIO.loadImageU16(compressedFile, dims, planeIndex);
} catch (IOException e) {
e.printStackTrace();
return true;
}
final int[] diffData = Utils.getDifference(originalPlane.getData(), compressedPlane.getData());
Utils.applyAbsFunction(diffData);
final double absDiffSum = Arrays.stream(diffData).mapToDouble(v -> v).sum();
final double meanPixelError = absDiffSum / (double) planePixelCount;
planeErrors[planeIndex] = new PlaneError(planeIndex, absDiffSum, meanPixelError);
// System.out.println("Finished plane: " + planeIndex);
}
try (FileOutputStream fos = new FileOutputStream(reportFile, false);
OutputStreamWriter writer = new OutputStreamWriter(fos)) {
writer.write("PlaneIndex\tErrorSum\tMeanError\n");
for (final PlaneError planeError : planeErrors) {
writer.write(String.format("%d\t%.4f\t%.4f\n",
planeError.getPlaneIndex(),
planeError.getAbsoluteError(),
planeError.getMeanAbsoluteError()));
}
} catch (IOException e) {
e.printStackTrace();
}
System.out.println("Finished reportPlaneDifference");
// final String referenceFile = "D:\\biology\\tiff_data\\benchmark\\fused_tp_10_ch_1_16bit.raw";
//
// final V3i dims = new V3i(1041, 996, 946);
// final int planePixelCount = dims.getX() * dims.getY();
// System.out.println(options.report());
// System.out.println("Run custom function.");
// ImageU16 compressedPlane = null;
// ImageU16 originalPlane = null;
// ImageU16 differencePlane = null;
//
// PlaneError[] planeErrors = new PlaneError[dims.getZ()];
//
// for (int planeIndex = 0; planeIndex < dims.getZ(); planeIndex++) {
// try {
// originalPlane = RawDataIO.loadImageU16(referenceFile, dims, planeIndex);
// compressedPlane = RawDataIO.loadImageU16(compressedFile, dims, planeIndex);
// } catch (IOException e) {
// e.printStackTrace();
// return true;
// }
// final int[] diffData = Utils.getDifference(originalPlane.getData(), compressedPlane.getData());
// Utils.applyAbsFunction(diffData);
//
//
// final double absDiffSum = Arrays.stream(diffData).mapToDouble(v -> v).sum();
// final double meanPixelError = absDiffSum / (double) planePixelCount;
//
// planeErrors[planeIndex] = new PlaneError(planeIndex, absDiffSum, meanPixelError);
// // System.out.println("Finished plane: " + planeIndex);
// }
//
// try (FileOutputStream fos = new FileOutputStream(reportFile, false);
// OutputStreamWriter writer = new OutputStreamWriter(fos)) {
//
// writer.write("PlaneIndex\tErrorSum\tMeanError\n");
//
// for (final PlaneError planeError : planeErrors) {
// writer.write(String.format("%d\t%.4f\t%.4f\n",
// planeError.getPlaneIndex(),
// planeError.getAbsoluteError(),
// planeError.getMeanAbsoluteError()));
// }
//
// } catch (IOException e) {
// e.printStackTrace();
// }
// System.out.println("Finished reportPlaneDifference");
return false;
}
}
src/main/java/azgracompress/compression/SQImageCompressor.java
+ 21
− 15
View file @ a84b8a1c
......@@ -5,8 +5,8 @@ import azgracompress.cli.InputFileInfo;
import azgracompress.cli.ParsedCliOptions;
import azgracompress.compression.exception.ImageCompressionException;
import azgracompress.data.ImageU16;
import azgracompress.io.ConcretePlaneLoader;
import azgracompress.io.OutBitStream;
import azgracompress.io.RawDataIO;
import azgracompress.quantization.QuantizationValueCache;
import azgracompress.quantization.scalar.LloydMaxU16ScalarQuantization;
import azgracompress.quantization.scalar.ScalarQuantizer;
......@@ -85,6 +85,13 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
Stopwatch stopwatch = new Stopwatch();
final boolean hasGeneralQuantizer = options.hasCodebookCacheFolder() || options.hasReferencePlaneIndex();
final ConcretePlaneLoader planeLoader;
try {
planeLoader = new ConcretePlaneLoader(inputFileInfo);
} catch (Exception e) {
throw new ImageCompressionException("Unable to create SCIFIO reader. " + e.getMessage());
}
ScalarQuantizer quantizer = null;
if (options.hasCodebookCacheFolder()) {
Log("Loading codebook from cache file.");
......@@ -96,10 +103,8 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
stopwatch.restart();
ImageU16 referencePlane = null;
try {
referencePlane = RawDataIO.loadImageU16(inputFileInfo.getFilePath(),
inputFileInfo.getDimensions(),
options.getReferencePlaneIndex());
} catch (Exception ex) {
referencePlane = planeLoader.loadPlaneU16(options.getReferencePlaneIndex());
} catch (IOException ex) {
throw new ImageCompressionException("Unable to load reference plane data.", ex);
}
......@@ -121,10 +126,8 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
ImageU16 plane = null;
try {
plane = RawDataIO.loadImageU16(inputFileInfo.getFilePath(),
inputFileInfo.getDimensions(),
planeIndex);
} catch (Exception ex) {
plane = planeLoader.loadPlaneU16(planeIndex);
} catch (IOException ex) {
throw new ImageCompressionException("Unable to load plane data.", ex);
}
......@@ -152,13 +155,17 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
private int[] loadConfiguredPlanesData() throws ImageCompressionException {
final InputFileInfo inputFileInfo = options.getInputFileInfo();
final ConcretePlaneLoader planeLoader;
try {
planeLoader = new ConcretePlaneLoader(inputFileInfo);
} catch (Exception e) {
throw new ImageCompressionException("Unable to create SCIFIO reader. " + e.getMessage());
}
int[] trainData = null;
if (inputFileInfo.isPlaneIndexSet()) {
try {
Log("Loading single plane data.");
trainData = RawDataIO.loadImageU16(inputFileInfo.getFilePath(),
inputFileInfo.getDimensions(),
inputFileInfo.getPlaneIndex()).getData();
trainData = planeLoader.loadPlaneU16(inputFileInfo.getPlaneIndex()).getData();
} catch (IOException e) {
throw new ImageCompressionException("Failed to load reference image data.", e);
}
......@@ -166,7 +173,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
Log("Loading plane range data.");
final int[] planes = getPlaneIndicesForCompression();
try {
trainData = RawDataIO.loadPlanesData(inputFileInfo.getFilePath(), inputFileInfo.getDimensions(), planes);
trainData = planeLoader.loadPlanesU16Data(planes);
} catch (IOException e) {
e.printStackTrace();
throw new ImageCompressionException("Failed to load plane range data.", e);
......@@ -174,7 +181,7 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
} else {
Log("Loading all planes data.");
try {
trainData = RawDataIO.loadAllPlanesData(inputFileInfo.getFilePath(), inputFileInfo.getDimensions());
trainData = planeLoader.loadAllPlanesU16Data();
} catch (IOException e) {
throw new ImageCompressionException("Failed to load all planes data.", e);
}
......@@ -185,7 +192,6 @@ public class SQImageCompressor extends CompressorDecompressorBase implements IIm
@Override
public void trainAndSaveCodebook() throws ImageCompressionException {
int[] trainData = loadConfiguredPlanesData();
LloydMaxU16ScalarQuantization lloydMax = new LloydMaxU16ScalarQuantization(trainData,
......
src/main/java/azgracompress/compression/VQImageCompressor.java
+ 28
− 20
View file @ a84b8a1c
......@@ -5,8 +5,9 @@ import azgracompress.cli.ParsedCliOptions;
import azgracompress.compression.exception.ImageCompressionException;
import azgracompress.data.Chunk2D;
import azgracompress.data.ImageU16;
import azgracompress.io.ConcretePlaneLoader;
import azgracompress.io.IPlaneLoader;
import azgracompress.io.OutBitStream;
import azgracompress.io.RawDataIO;
import azgracompress.quantization.QuantizationValueCache;
import azgracompress.quantization.vector.CodebookEntry;
import azgracompress.quantization.vector.LBGResult;
......@@ -90,6 +91,12 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
final InputFileInfo inputFileInfo = options.getInputFileInfo();
Stopwatch stopwatch = new Stopwatch();
final boolean hasGeneralQuantizer = options.hasCodebookCacheFolder() || options.hasReferencePlaneIndex();
final ConcretePlaneLoader planeLoader;
try {
planeLoader = new ConcretePlaneLoader(inputFileInfo);
} catch (Exception e) {
throw new ImageCompressionException("Unable to create SCIFIO reader. " + e.getMessage());
}
VectorQuantizer quantizer = null;
if (options.hasCodebookCacheFolder()) {
......@@ -102,10 +109,8 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
ImageU16 referencePlane = null;
try {
referencePlane = RawDataIO.loadImageU16(inputFileInfo.getFilePath(),
inputFileInfo.getDimensions(),
options.getReferencePlaneIndex());
} catch (Exception ex) {
referencePlane = planeLoader.loadPlaneU16(options.getReferencePlaneIndex());
} catch (IOException ex) {
throw new ImageCompressionException("Unable to load reference plane data.", ex);
}
......@@ -125,10 +130,8 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
ImageU16 plane = null;
try {
plane = RawDataIO.loadImageU16(inputFileInfo.getFilePath(),
inputFileInfo.getDimensions(),
planeIndex);
} catch (Exception ex) {
plane = planeLoader.loadPlaneU16(planeIndex);
} catch (IOException ex) {
throw new ImageCompressionException("Unable to load plane data.", ex);
}
......@@ -165,33 +168,38 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
* @return Quantization vectors of configured quantization.
* @throws IOException When reading fails.
*/
private int[][] loadPlaneQuantizationVectors(final int planeIndex) throws IOException {
ImageU16 refPlane = RawDataIO.loadImageU16(options.getInputFileInfo().getFilePath(),
options.getInputFileInfo().getDimensions(),
planeIndex);
private int[][] loadPlaneQuantizationVectors(final IPlaneLoader planeLoader,
final int planeIndex) throws IOException {
ImageU16 refPlane = planeLoader.loadPlaneU16(planeIndex);
return refPlane.toQuantizationVectors(options.getVectorDimension());
}
private int[][] loadConfiguredPlanesData() throws ImageCompressionException {
final int vectorSize = options.getVectorDimension().getX() * options.getVectorDimension().getY();
final InputFileInfo ifi = options.getInputFileInfo();
final InputFileInfo inputFileInfo = options.getInputFileInfo();
final ConcretePlaneLoader planeLoader;
try {
planeLoader = new ConcretePlaneLoader(inputFileInfo);
} catch (Exception e) {
throw new ImageCompressionException("Unable to create SCIFIO reader. " + e.getMessage());
}
int[][] trainData = null;
Stopwatch s = new Stopwatch();
s.start();
if (ifi.isPlaneIndexSet()) {
if (inputFileInfo.isPlaneIndexSet()) {
Log("VQ: Loading single plane data.");
try {
trainData = loadPlaneQuantizationVectors(ifi.getPlaneIndex());
trainData = loadPlaneQuantizationVectors(planeLoader, inputFileInfo.getPlaneIndex());
} catch (IOException e) {
throw new ImageCompressionException("Failed to load reference image data.", e);
}
} else {
Log(ifi.isPlaneRangeSet() ? "VQ: Loading plane range data." : "VQ: Loading all planes data.");
Log(inputFileInfo.isPlaneRangeSet() ? "VQ: Loading plane range data." : "VQ: Loading all planes data.");
final int[] planeIndices = getPlaneIndicesForCompression();
final int chunkCountPerPlane = Chunk2D.calculateRequiredChunkCountPerPlane(
ifi.getDimensions().toV2i(),
inputFileInfo.getDimensions().toV2i(),
options.getVectorDimension());
final int totalChunkCount = chunkCountPerPlane * planeIndices.length;
......@@ -201,7 +209,7 @@ public class VQImageCompressor extends CompressorDecompressorBase implements IIm
int planeCounter = 0;
for (final int planeIndex : planeIndices) {
try {
planeVectors = loadPlaneQuantizationVectors(planeIndex);
planeVectors = loadPlaneQuantizationVectors(planeLoader, planeIndex);
assert (planeVectors.length == chunkCountPerPlane) : "Wrong chunk count per plane";
} catch (IOException e) {
throw new ImageCompressionException(String.format("Failed to load plane %d image data.",
......
src/main/java/azgracompress/data/ImageU16.java
+ 5
− 1
View file @ a84b8a1c
......@@ -8,13 +8,17 @@ public class ImageU16 {
private final int height;
private int[] data;
public ImageU16(int width, int height, int[] data) {
public ImageU16(final int width, final int height, final int[] data) {
assert ((width * height) == data.length) : "Wrong data size in ImageU16 constructor.";
this.width = width;
this.height = height;
this.data = data;
}
public ImageU16(final V2i dims, final int[] data) {
this(dims.getX(), dims.getY(), data);
}
private int index(final int x, final int y) {
assert ((x >= 0 && x < height) && (y >= 0 && y < width)) : "Index out of bounds";
return (x * width) + y;
......
src/main/java/azgracompress/io/ConcretePlaneLoader.java 0 → 100644
+ 45
− 0
View file @ a84b8a1c
package azgracompress.io;
import azgracompress.cli.InputFileInfo;
import azgracompress.data.ImageU16;
import java.io.IOException;
public class ConcretePlaneLoader implements IPlaneLoader {
private final IPlaneLoader loader;
private final InputFileInfo inputFileInfo;
/**
* Create plane loader.
*
* @param inputFileInfo Information about input file.
* @throws Exception When fails to create SCIFIO reader.
*/
public ConcretePlaneLoader(final InputFileInfo inputFileInfo) throws Exception {
this.inputFileInfo = inputFileInfo;
if (inputFileInfo.isRAW()) {
loader = new RawDataLoader(inputFileInfo);
} else {
loader = new SCIFIOLoader(inputFileInfo);
}
}
@Override
public ImageU16 loadPlaneU16(int plane) throws IOException {
return loader.loadPlaneU16(plane);
}
@Override
public int[] loadPlanesU16Data(int[] planes) throws IOException {
return loader.loadPlanesU16Data(planes);
}
@Override
public int[] loadAllPlanesU16Data() throws IOException {
return loader.loadAllPlanesU16Data();
}
}
src/main/java/azgracompress/io/IPlaneLoader.java 0 → 100644
+ 14
− 0
View file @ a84b8a1c
package azgracompress.io;
import azgracompress.cli.InputFileInfo;
import azgracompress.data.ImageU16;
import java.io.IOException;
public interface IPlaneLoader {
ImageU16 loadPlaneU16(final int plane) throws IOException;
int[] loadPlanesU16Data(int[] planes) throws IOException;
int[] loadAllPlanesU16Data() throws IOException;
}
src/main/java/azgracompress/io/ImagePlaneIO.java deleted 100644 → 0
+ 0
− 46
View file @ 4496519f
package azgracompress.io;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i;
import io.scif.jj2000.j2k.NotImplementedError;
import java.io.IOException;
/**
* Class handling loading and writing of plane data.
* Multiple data types should be supported.
* For start: RAW, TIFF
*/
public class ImagePlaneIO {
public static ImageU16 loadImageU16(final String rawFile,
final V3i rawDataDimension,
final int plane) throws IOException {
// TODO(Moravec): Handle loading of different types.
// TODO(Moravec): If the loaded image is not U16 convert it to U16 image.
throw new NotImplementedError();
}
public static int[] loadPlanesData(final String rawFile,
final V3i rawDataDims,
int[] planes) throws IOException {
// TODO(Moravec): Handle loading of different types.
// TODO(Moravec): If the loaded image is not U16 convert it to U16 image.
throw new NotImplementedError();
}
public static int[] loadAllPlanesData(final String rawFile, final V3i imageDims) throws IOException {
// TODO(Moravec): Handle loading of different types.
// TODO(Moravec): If the loaded image is not U16 convert it to U16 image.
throw new NotImplementedError();
}
public static void writeImageU16(final String rawFile,
final ImageU16 image,
final boolean littleEndian) throws IOException {
// TODO(Moravec): Handle writing of U16 image to multiple types.
throw new NotImplementedError();
}
}
src/main/java/azgracompress/io/RawDataIO.java
+ 2
− 109
View file @ a84b8a1c
package azgracompress.io;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i;
import azgracompress.utilities.TypeConverter;
import java.io.*;
import java.util.Arrays;
import java.io.FileOutputStream;
import java.io.IOException;
public class RawDataIO {
/**
* Load single U16 image from RAW data file.
*
* @param rawFile Path to the raw file.
* @param rawDataDimension X (Width), Y (Height) of plane and Z(Number of planes)
* @param plane Plane index.
* @return U16 image specified by the plane
*/
public static ImageU16 loadImageU16(final String rawFile,
final V3i rawDataDimension,
final int plane) throws IOException {
byte[] buffer;
try (FileInputStream fileStream = new FileInputStream(rawFile)) {
final long planeSize = (long) rawDataDimension.getX() * (long) rawDataDimension.getY() * 2;
final long expectedFileSize = planeSize * rawDataDimension.getZ();
final long fileSize = fileStream.getChannel().size();
if (expectedFileSize != fileSize) {
throw new IOException(
"File specified by `rawFile` doesn't contains raw data for image of dimensions " +
"`rawDataDimension`");
}
final long planeOffset = plane * planeSize;
buffer = new byte[(int) planeSize];
if (fileStream.skip(planeOffset) != planeOffset) {
throw new IOException("Failed to skip.");
}
if (fileStream.read(buffer, 0, (int) planeSize) != planeSize) {
throw new IOException("Read wrong number of bytes.");
}
}
return new ImageU16(rawDataDimension.getX(),
rawDataDimension.getY(),
TypeConverter.unsignedShortBytesToIntArray(buffer));
}
public static int[] loadPlanesData(final String rawFile,
final V3i rawDataDims,
int[] planes) throws IOException {
if (planes.length < 1)
return new int[0];
final int planeValueCount = rawDataDims.getX() * rawDataDims.getY();
final long planeDataSize = 2 * (long) planeValueCount;
final long totalValueCount = (long) planeValueCount * planes.length;
int[] values = new int[(int) totalValueCount];
if (totalValueCount > (long) Integer.MAX_VALUE) {
throw new IOException("Integer count is too big.");
}
Arrays.sort(planes);
try (FileInputStream fileStream = new FileInputStream(rawFile);
DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {
int lastIndex = 0;
int valIndex = 0;
for (final int planeIndex : planes) {
// Skip specific number of bytes to get to the next plane.
final int requestedSkip = (planeIndex == 0) ? 0 : ((planeIndex - lastIndex) - 1) * (int) planeDataSize;
lastIndex = planeIndex;
final int actualSkip = dis.skipBytes(requestedSkip);
if (requestedSkip != actualSkip) {
throw new IOException("Skip operation failed.");
}
for (int i = 0; i < planeValueCount; i++) {
values[valIndex++] = dis.readUnsignedShort();
}
}
}
return values;
}
public static int[] loadAllPlanesData(final String rawFile, final V3i imageDims) throws IOException {
final long dataSize = (long) imageDims.getX() * (long) imageDims.getY() * (long) imageDims.getZ();
int[] values = new int[(int) dataSize];
if (dataSize > (long) Integer.MAX_VALUE) {
throw new IOException("RawFile size is too big.");
}
try (FileInputStream fileStream = new FileInputStream(rawFile);
DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {
for (int i = 0; i < (int) dataSize; i++) {
values[i] = dis.readUnsignedShort();
}
}
return values;
}
public static void writeImageU16(final String rawFile,
final ImageU16 image,
......
src/main/java/azgracompress/io/RawDataLoader.java 0 → 100644
+ 115
− 0
View file @ a84b8a1c
package azgracompress.io;
import azgracompress.cli.InputFileInfo;
import azgracompress.data.ImageU16;
import azgracompress.data.V3i;
import azgracompress.utilities.TypeConverter;
import java.io.*;
import java.util.Arrays;
public class RawDataLoader implements IPlaneLoader {
private final InputFileInfo inputFileInfo;
public RawDataLoader(final InputFileInfo inputFileInfo) {
this.inputFileInfo = inputFileInfo;
}
@Override
public ImageU16 loadPlaneU16(int plane) throws IOException {
byte[] buffer;
final V3i rawDataDimension = inputFileInfo.getDimensions();
try (FileInputStream fileStream = new FileInputStream(inputFileInfo.getFilePath())) {
final long planeSize = (long) rawDataDimension.getX() * (long) rawDataDimension.getY() * 2;
final long expectedFileSize = planeSize * rawDataDimension.getZ();
final long fileSize = fileStream.getChannel().size();
if (expectedFileSize != fileSize) {
throw new IOException(
"File specified by `rawFile` doesn't contains raw data for image of dimensions " +
"`rawDataDimension`");
}
final long planeOffset = plane * planeSize;
buffer = new byte[(int) planeSize];
if (fileStream.skip(planeOffset) != planeOffset) {
throw new IOException("Failed to skip.");
}
if (fileStream.read(buffer, 0, (int) planeSize) != planeSize) {
throw new IOException("Read wrong number of bytes.");
}
}
return new ImageU16(rawDataDimension.getX(),
rawDataDimension.getY(),
TypeConverter.unsignedShortBytesToIntArray(buffer));
}
@Override
public int[] loadPlanesU16Data(int[] planes) throws IOException {
if (planes.length < 1)
return new int[0];
final int planeValueCount = inputFileInfo.getDimensions().getX() * inputFileInfo.getDimensions().getY();
final long planeDataSize = 2 * (long) planeValueCount;
final long totalValueCount = (long) planeValueCount * planes.length;
int[] values = new int[(int) totalValueCount];
if (totalValueCount > (long) Integer.MAX_VALUE) {
throw new IOException("Integer count is too big.");
}
Arrays.sort(planes);
try (FileInputStream fileStream = new FileInputStream(inputFileInfo.getFilePath());
DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {
int lastIndex = 0;
int valIndex = 0;
for (final int planeIndex : planes) {
// Skip specific number of bytes to get to the next plane.
final int requestedSkip = (planeIndex == 0) ? 0 : ((planeIndex - lastIndex) - 1) * (int) planeDataSize;
lastIndex = planeIndex;
final int actualSkip = dis.skipBytes(requestedSkip);
if (requestedSkip != actualSkip) {
throw new IOException("Skip operation failed.");
}
for (int i = 0; i < planeValueCount; i++) {
values[valIndex++] = dis.readUnsignedShort();
}
}
}
return values;
}
@Override
public int[] loadAllPlanesU16Data() throws IOException {
final V3i imageDims = inputFileInfo.getDimensions();
final long dataSize = (long) imageDims.getX() * (long) imageDims.getY() * (long) imageDims.getZ();
int[] values = new int[(int) dataSize];
if (dataSize > (long) Integer.MAX_VALUE) {
throw new IOException("RawFile size is too big.");
}
try (FileInputStream fileStream = new FileInputStream(inputFileInfo.getFilePath());
DataInputStream dis = new DataInputStream(new BufferedInputStream(fileStream, 8192))) {
for (int i = 0; i < (int) dataSize; i++) {
values[i] = dis.readUnsignedShort();
}
}
return values;
}
}
src/main/java/azgracompress/io/SCIFIOLoader.java 0 → 100644
+ 51
− 0
View file @ a84b8a1c
package azgracompress.io;
import azgracompress.ScifioWrapper;
import azgracompress.cli.InputFileInfo;
import azgracompress.data.ImageU16;
import azgracompress.utilities.TypeConverter;
import io.scif.FormatException;
import io.scif.Reader;
import io.scif.jj2000.j2k.NotImplementedError;
import java.io.IOException;
public class SCIFIOLoader implements IPlaneLoader {
private final InputFileInfo inputFileInfo;
private final Reader reader;
/**
* Create SCIFIO reader from input file.
*
* @param inputFileInfo Input file info.
* @throws IOException When fails to create SCIFIO reader.
* @throws FormatException When fails to create SCIFIO reader.
*/
public SCIFIOLoader(final InputFileInfo inputFileInfo) throws IOException, FormatException {
this.inputFileInfo = inputFileInfo;
this.reader = ScifioWrapper.getReader(this.inputFileInfo.getFilePath());
}
@Override
public ImageU16 loadPlaneU16(int plane) throws IOException {
byte[] planeBytes;
try {
planeBytes = reader.openPlane(0, plane).getBytes();
} catch (FormatException e) {
throw new IOException("Unable to open plane with the reader. " + e.getMessage());
}
final int[] data = TypeConverter.unsignedShortBytesToIntArray(planeBytes);
return new ImageU16(inputFileInfo.getDimensions().toV2i(), data);
}
@Override
public int[] loadPlanesU16Data(int[] planes) throws IOException {
throw new NotImplementedError("NOT IMPLEMENTED");
}
@Override
public int[] loadAllPlanesU16Data() throws IOException {
throw new NotImplementedError("NOT IMPLEMENTED");
}
}
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