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Commit ae3c1b65 authored by Vojtech Moravec's avatar Vojtech Moravec
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Choose endianess when writing binary data.

parent 205248a6
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src/main/java/DataCompressor.java
+ 18
− 7
View file @ ae3c1b65
......@@ -38,16 +38,27 @@ public class DataCompressor {
// VectorQuantizer vq = new VectorQuantizer(codebook.getCodebook());
ScalarQuantizationBenchmark sqBenchmark = new ScalarQuantizationBenchmark(
"D:\\biology\\tiff_data\\benchmark\\fused_tp_10_ch_1_16bit.raw",
"D:\\biology\\benchmark\\test",
new int[]{358},
// new int[]{234, 294, 365, 463, 593, 682, 696},
ScalarQuantizationBenchmark[] benchmarks = new ScalarQuantizationBenchmark[3];
benchmarks[0] = new ScalarQuantizationBenchmark("D:\\biology\\tiff_data\\benchmark\\fused_tp_10_ch_0_16bit.raw",
"D:\\biology\\benchmark\\fused_tp_10_ch_0_16bit",
new int[]{198, 240, 280, 351, 573, 663, 695},
new V3i(1041, 996, 946));
benchmarks[1] = new ScalarQuantizationBenchmark(
"D:\\biology\\tiff_data\\benchmark\\fused_tp_10_ch_0_16bit_edited.raw",
"D:\\biology\\benchmark\\fused_tp_10_ch_0_16bit_edited",
new int[]{198, 240, 280, 351, 573, 663, 695},
new V3i(1041, 996, 946));
sqBenchmark.startBenchmark();
benchmarks[2] = new ScalarQuantizationBenchmark("D:\\biology\\tiff_data\\benchmark\\fused_tp_10_ch_1_16bit.raw",
"D:\\biology\\benchmark\\fused_tp_10_ch_1_16bit",
new int[]{235, 295, 366, 464, 594, 683, 697},
new V3i(1041, 996, 946));
for (ScalarQuantizationBenchmark benchmark : benchmarks)
{
benchmark.startBenchmark();
}
// ScalarQuantizationBenchmark sqBenchmark = new ScalarQuantizationBenchmark(
// "D:\\biology\\tiff_data\\fused_tp_10_ch_1_16bit_edited.raw",
// "D:\\biology\\benchmark\\scalar_edited",
......
src/main/java/compression/benchmark/ScalarQuantizationBenchmark.java
+ 10
− 6
View file @ ae3c1b65
......@@ -47,7 +47,8 @@ public class ScalarQuantizationBenchmark {
private boolean saveQuantizedPlaneData(final short[] data, final String filename) {
ImageU16 img = new ImageU16(rawImageDims.getX(), rawImageDims.getY(), data);
try {
RawDataIO.writeImageU16(getFileNamePath(filename), img);
// NOTE(Moravec): Use big endian so that FIJI can read the image.
RawDataIO.writeImageU16(getFileNamePath(filename), img, false);
System.out.println(String.format("Saved %s", filename));
} catch (Exception e) {
e.printStackTrace();
......@@ -63,7 +64,8 @@ public class ScalarQuantizationBenchmark {
rawImageDims.getY(),
TypeConverter.intArrayToShortArray(differenceData));
try {
RawDataIO.writeImageU16(path, img);
// NOTE(Moravec): Use little endian so that gnuplot can read the array.
RawDataIO.writeImageU16(path, img, true);
System.out.println("Saved difference to: " + path);
} catch (Exception e) {
e.printStackTrace();
......@@ -77,7 +79,8 @@ public class ScalarQuantizationBenchmark {
for (final int planeIndex : planes) {
System.out.println(String.format("Loading plane %d ...", planeIndex));
final short[] planeData = loadPlaneData(planeIndex);
// NOTE(Moravec): Actual planeIndex is zero based.
final short[] planeData = loadPlaneData(planeIndex-1);
if (planeData.length == 0) {
System.err.println(String.format("Failed to load plane %d data. Skipping plane.", planeIndex));
return;
......@@ -106,16 +109,17 @@ public class ScalarQuantizationBenchmark {
codebookSize,
method));
if (!RawDataIO.writeDataI32(centroidsFile, quantizer.getCentroids())) {
// NOTE(Moravec): Centroids are saved in little endian order.
if (!RawDataIO.writeDataI32(centroidsFile, quantizer.getCentroids(), true)) {
System.err.println("Failed to save quantizer centroids.");
return;
}
final String quantizedFile = String.format("p%d_cb%d%s.raw", (planeIndex + 1), codebookSize, method);
final String quantizedFile = String.format("p%d_cb%d%s.raw", planeIndex, codebookSize, method);
final String absoluteDiffFile = String.format("p%d_cb%d%s_diff.raw",
(planeIndex + 1),
planeIndex,
codebookSize,
method);
......
src/main/java/compression/io/RawDataIO.java
+ 6
− 4
View file @ ae3c1b65
......@@ -50,14 +50,16 @@ public class RawDataIO {
return image;
}
public static void writeImageU16(final String rawFile, final ImageU16 image) throws IOException {
byte[] buffer = TypeConverter.shortArrayToByteArray(image.getData());
public static void writeImageU16(final String rawFile,
final ImageU16 image,
final boolean littleEndian) throws IOException {
byte[] buffer = TypeConverter.shortArrayToByteArray(image.getData(), littleEndian);
writeBytesToFile(rawFile, buffer);
}
public static boolean writeDataI32(String rawFile, int[] differenceData) {
public static boolean writeDataI32(String rawFile, int[] differenceData, final boolean littleEndian) {
byte[] buffer = TypeConverter.intArrayToByteArray(differenceData);
byte[] buffer = TypeConverter.intArrayToByteArray(differenceData, littleEndian);
try {
writeBytesToFile(rawFile, buffer);
} catch (IOException e) {
......
src/main/java/compression/utilities/TypeConverter.java
+ 21
− 11
View file @ ae3c1b65
......@@ -53,7 +53,6 @@ public class TypeConverter {
public static short[] intArrayToShortArray(final int[] src) {
short[] result = new short[src.length];
short shortValue;
for (int i = 0; i < src.length; i++) {
if (src[i] < 0 || src[i] > U16.Max) {
throw new RuntimeException("Source value is outside of bounds for 16-bit unsigned integer.");
......@@ -63,27 +62,38 @@ public class TypeConverter {
return result;
}
public static byte[] shortArrayToByteArray(final short[] data) {
public static byte[] shortArrayToByteArray(final short[] data, final boolean littleEndian) {
byte[] buffer = new byte[data.length * 2];
int j = 0;
for (final short s : data) {
// NOTE(Moravec): Use little endian.
buffer[j++] = (byte) (s & 0xff);
buffer[j++] = (byte) ((s >> 8) & 0xff);
if (littleEndian) {
buffer[j++] = (byte) (s & 0xff);
buffer[j++] = (byte) ((s >> 8) & 0xff);
} else {
buffer[j++] = (byte) ((s >> 8) & 0xff);
buffer[j++] = (byte) (s & 0xff);
}
}
return buffer;
}
public static byte[] intArrayToByteArray(final int[] data) {
public static byte[] intArrayToByteArray(final int[] data, final boolean littleEndian) {
byte[] buffer = new byte[data.length * 4];
int j = 0;
for (final int v : data) {
// NOTE(Moravec): Use little endian.
buffer[j++] = (byte) (v & 0xFF);
buffer[j++] = (byte) ((v >>> 8) & 0xFF);
buffer[j++] = (byte) ((v >>> 16) & 0xFF);
buffer[j++] = (byte) ((v >>> 24) & 0xFF);
if (littleEndian) {
buffer[j++] = (byte) (v & 0xFF);
buffer[j++] = (byte) ((v >>> 8) & 0xFF);
buffer[j++] = (byte) ((v >>> 16) & 0xFF);
buffer[j++] = (byte) ((v >>> 24) & 0xFF);
} else {
buffer[j++] = (byte) ((v >>> 24) & 0xFF);
buffer[j++] = (byte) ((v >>> 16) & 0xFF);
buffer[j++] = (byte) ((v >>> 8) & 0xFF);
buffer[j++] = (byte) (v & 0xFF);
}
}
return buffer;
}
......
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