imagej/ch.psi.imagej.hdf5
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explicit names for method parameters on copyPixels* functions

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This commit is contained in:
ebner 2014-09-29 15:14:09 +02:00
parent 74aae47436
commit 87a195dd4d
1 changed files with 95 additions and 91 deletions
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186
src/main/java/ch/psi/imagej/hdf5/HDF5Reader.java
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@ -96,7 +96,7 @@ public class HDF5Reader implements PlugIn {
List<Dataset> datasets = HDF5Utilities.getDatasets(inFile);
List<Dataset> selectedDatasets = selectDatasets(datasets);
for (Dataset var : selectedDatasets) {
// Read dataset attributes and properties
String datasetName = var.getName();
@ -206,7 +206,7 @@ public class HDF5Reader implements PlugIn {
// long numElements = stackSize * 3;
int endIdx = (int) (startIdx + stackSize * 3 - 1);
copyPixels3(datatypeIfUnsupported, extent, stack, wholeDataset, size, startIdx, endIdx);
copyPixels3(datatypeIfUnsupported, (int)extent[2], (int)extent[3], stack, wholeDataset, size, startIdx, endIdx);
}
}
@ -287,7 +287,7 @@ public class HDF5Reader implements PlugIn {
// startIdx, numElements);
int size = (int) (extent[2] * extent[1]);
copyPixels1(extent, stack, wholeDataset, startIdx, endIdx, size);
copyPixels1((int)extent[1], (int)extent[2], stack, wholeDataset, startIdx, endIdx, size);
}
ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
// new for hyperstack
@ -357,7 +357,7 @@ public class HDF5Reader implements PlugIn {
// start[1] = lev;
// Object slice = var.read();
int startIdx = (int) ((volIDX * singleVolumeSize) + (lev * stackSize));
int endIdx = (int) (startIdx + stackSize - 1);
int endIdx = (int) (startIdx + stackSize);
// long numElements = stackSize;
convertDatatypesAndSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx);
@ -421,7 +421,7 @@ public class HDF5Reader implements PlugIn {
int size = (int) (extent[1] * extent[0]);
// ugly but working: copy pixel by pixel
copyPixels2(extent, stack, slice, size);
copyPixels2((int)extent[0], (int)extent[1], stack, slice, size);
IJ.showProgress(1.f);
ImagePlus imp = new ImagePlus(directory + name + " " + datasetName, stack);
@ -482,7 +482,7 @@ public class HDF5Reader implements PlugIn {
// Object slice = var.read();
int startIdx = (int) (lev * stackSize);
int endIdx = (int) (startIdx + stackSize - 1);
int endIdx = (int) (startIdx + stackSize);
// long numElements = stackSize;
convertDatatypesAndSlice(datatypeIfUnsupported, stack, wholeDataset, startIdx, endIdx);
}
@ -740,22 +740,24 @@ public class HDF5Reader implements PlugIn {
/**
* @param datatypeIfUnsupported
* @param extent
* @param nRows (extent[2])
* @param nColumns (extent[3])
* @param stack
* @param wholeDataset
* @param size
* @param startIdx
* @param endIdx
*/
private void copyPixels3(Datatype datatypeIfUnsupported, long[] extent, ImageStack stack, Object wholeDataset, int size, int startIdx, int endIdx) {
private void copyPixels3(Datatype datatypeIfUnsupported, int nRows, int nColumns, ImageStack stack, Object wholeDataset, int size, int startIdx, int endIdx) {
if (wholeDataset instanceof byte[]) {
byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
byte[] rChannel = new byte[size];
byte[] gChannel = new byte[size];
byte[] bChannel = new byte[size];
for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nRows * 3) + (col * 3);
int offset = (row * nRows) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -769,10 +771,10 @@ public class HDF5Reader implements PlugIn {
short[] rChannel = new short[size];
short[] gChannel = new short[size];
short[] bChannel = new short[size];
for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nRows * 3) + (col * 3);
int offset = (row * nRows) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -787,10 +789,10 @@ public class HDF5Reader implements PlugIn {
float[] rChannel = new float[size];
float[] gChannel = new float[size];
float[] bChannel = new float[size];
for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nRows * 3) + (col * 3);
int offset = (row * nRows) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -805,10 +807,10 @@ public class HDF5Reader implements PlugIn {
short[] rChannel = new short[size];
short[] gChannel = new short[size];
short[] bChannel = new short[size];
for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nRows * 3) + (col * 3);
int offset = (row * nRows) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -824,10 +826,10 @@ public class HDF5Reader implements PlugIn {
float[] rChannel = new float[size];
float[] gChannel = new float[size];
float[] bChannel = new float[size];
for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nRows * 3) + (col * 3);
int offset = (row * nRows) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -842,10 +844,10 @@ public class HDF5Reader implements PlugIn {
short[] rChannel = new short[size];
short[] gChannel = new short[size];
short[] bChannel = new short[size];
for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nRows * 3) + (col * 3);
int offset = (row * nRows) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -860,10 +862,10 @@ public class HDF5Reader implements PlugIn {
float[] rChannel = new float[size];
float[] gChannel = new float[size];
float[] bChannel = new float[size];
for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nRows * 3) + (col * 3);
int offset = (row * nRows) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -877,10 +879,10 @@ public class HDF5Reader implements PlugIn {
float[] rChannel = new float[size];
float[] gChannel = new float[size];
float[] bChannel = new float[size];
for (int row = 0; row < extent[2]; ++row) {
for (int col = 0; col < extent[3]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nRows * 3) + (col * 3);
int offset = (row * nRows) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -896,21 +898,22 @@ public class HDF5Reader implements PlugIn {
/**
* @param extent
* @param nRows (extent[0])
* @param nColumns (extent[1])
* @param stack
* @param slice
* @param size
*/
private void copyPixels2(long[] extent, ImageStack stack, Object slice, int size) {
private void copyPixels2(int nRows, int nColumns, ImageStack stack, Object slice, int size) {
if (slice instanceof byte[]) {
byte[] tmp = (byte[]) slice;
byte[] rChannel = new byte[size];
byte[] gChannel = new byte[size];
byte[] bChannel = new byte[size];
for (int row = 0; row < extent[0]; ++row) {
for (int col = 0; col < extent[1]; ++col) {
int offsetRGB = (row * (int) extent[1] * 3) + (col * 3);
int offset = (row * (int) extent[1]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -924,10 +927,10 @@ public class HDF5Reader implements PlugIn {
short[] rChannel = new short[size];
short[] gChannel = new short[size];
short[] bChannel = new short[size];
for (int row = 0; row < extent[0]; ++row) {
for (int col = 0; col < extent[1]; ++col) {
int offsetRGB = (row * (int) extent[1] * 3) + (col * 3);
int offset = (row * (int) extent[1]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -941,10 +944,10 @@ public class HDF5Reader implements PlugIn {
int[] rChannel = new int[size];
int[] gChannel = new int[size];
int[] bChannel = new int[size];
for (int row = 0; row < extent[0]; ++row) {
for (int col = 0; col < extent[1]; ++col) {
int offsetRGB = (row * (int) extent[1] * 3) + (col * 3);
int offset = (row * (int) extent[1]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -958,10 +961,10 @@ public class HDF5Reader implements PlugIn {
long[] rChannel = new long[size];
long[] gChannel = new long[size];
long[] bChannel = new long[size];
for (int row = 0; row < extent[0]; ++row) {
for (int col = 0; col < extent[1]; ++col) {
int offsetRGB = (row * (int) extent[1] * 3) + (col * 3);
int offset = (row * (int) extent[1]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -975,10 +978,10 @@ public class HDF5Reader implements PlugIn {
float[] rChannel = new float[size];
float[] gChannel = new float[size];
float[] bChannel = new float[size];
for (int row = 0; row < extent[0]; ++row) {
for (int col = 0; col < extent[1]; ++col) {
int offsetRGB = (row * (int) extent[1] * 3) + (col * 3);
int offset = (row * (int) extent[1]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -992,10 +995,10 @@ public class HDF5Reader implements PlugIn {
double[] rChannel = new double[size];
double[] gChannel = new double[size];
double[] bChannel = new double[size];
for (int row = 0; row < extent[0]; ++row) {
for (int col = 0; col < extent[1]; ++col) {
int offsetRGB = (row * (int) extent[1] * 3) + (col * 3);
int offset = (row * (int) extent[1]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -1009,23 +1012,24 @@ public class HDF5Reader implements PlugIn {
/**
* @param extent
* @param nRows
* @param nColumns
* @param stack
* @param wholeDataset
* @param startIdx
* @param endIdx
* @param size
*/
private void copyPixels1(long[] extent, ImageStack stack, Object wholeDataset, int startIdx, int endIdx, int size) {
private void copyPixels1(int nRows, int nColumns, ImageStack stack, Object wholeDataset, int startIdx, int endIdx, int size) {
if (wholeDataset instanceof byte[]) {
byte[] tmp = Arrays.copyOfRange((byte[]) wholeDataset, startIdx, endIdx);
byte[] rChannel = new byte[size];
byte[] gChannel = new byte[size];
byte[] bChannel = new byte[size];
for (int row = 0; row < extent[1]; ++row) {
for (int col = 0; col < extent[2]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -1039,10 +1043,10 @@ public class HDF5Reader implements PlugIn {
short[] rChannel = new short[size];
short[] gChannel = new short[size];
short[] bChannel = new short[size];
for (int row = 0; row < extent[1]; ++row) {
for (int col = 0; col < extent[2]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -1056,10 +1060,10 @@ public class HDF5Reader implements PlugIn {
int[] rChannel = new int[size];
int[] gChannel = new int[size];
int[] bChannel = new int[size];
for (int row = 0; row < extent[1]; ++row) {
for (int col = 0; col < extent[2]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -1073,10 +1077,10 @@ public class HDF5Reader implements PlugIn {
long[] rChannel = new long[size];
long[] gChannel = new long[size];
long[] bChannel = new long[size];
for (int row = 0; row < extent[1]; ++row) {
for (int col = 0; col < extent[2]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -1090,10 +1094,10 @@ public class HDF5Reader implements PlugIn {
float[] rChannel = new float[size];
float[] gChannel = new float[size];
float[] bChannel = new float[size];
for (int row = 0; row < extent[1]; ++row) {
for (int col = 0; col < extent[2]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];
@ -1107,10 +1111,10 @@ public class HDF5Reader implements PlugIn {
double[] rChannel = new double[size];
double[] gChannel = new double[size];
double[] bChannel = new double[size];
for (int row = 0; row < extent[1]; ++row) {
for (int col = 0; col < extent[2]; ++col) {
int offsetRGB = (row * (int) extent[2] * 3) + (col * 3);
int offset = (row * (int) extent[2]) + col;
for (int row = 0; row < nRows; ++row) {
for (int col = 0; col < nColumns; ++col) {
int offsetRGB = (row * nColumns * 3) + (col * 3);
int offset = (row * nColumns) + col;
rChannel[offset] = tmp[offsetRGB + 0];
gChannel[offset] = tmp[offsetRGB + 1];
bChannel[offset] = tmp[offsetRGB + 2];