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Commit 15f05e23 authored by Raphael GIRARDOT's avatar Raphael GIRARDOT
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Added the possibility, for block data reading, to get extracted block as FlatData array or FlatData

parent aceb571d
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src/main/java/fr/soleil/cdma/box/data/ImageStack.java
+ 41
− 41
View file @ 15f05e23
......@@ -67,32 +67,32 @@ public class ImageStack extends StackedData {
}
return image;
}
//
// /**
// * Returns a block of image ROIs, starting at given position.
// *
// * @param x The ROI x coordinate in the image.
// * @param y The ROI y coordinate in the image.
// * @param width The ROI width.
// * @param height The ROI height.
// * @param nbOfImages The number of images in the block.
// * @param position The image position in the stack.
// * @return A {@link FlatData}.
// */
// public FlatData getROIBlockAt(int x, int y, int width, int height, int nbOfImages, int... position) {
// FlatData block = null;
// if ((stackFullShape != null) && (position != null) && (dataShape != null) && (dataShape.length == 2) && (x > -1)
// && (y > -1) && (height > 0) && (width > 0) && (x + width <= dataShape[1])
// && (y + height <= dataShape[0]) && (nbOfImages > 0)) {
// if (position.length != stackFullShape.length) {
// position = Arrays.copyOf(position, stackFullShape.length);
// }
// position[position.length - 1] = x;
// position[position.length - 2] = y;
// block = getData(position, new int[] { nbOfImages, height, width });
// }
// return block;
// }
/**
* Returns a block of image ROIs, starting at given position.
*
* @param x The ROI x coordinate in the image.
* @param y The ROI y coordinate in the image.
* @param width The ROI width.
* @param height The ROI height.
* @param nbOfImages The number of images in the block.
* @param position The image position in the stack.
* @return A {@link FlatData}.
*/
public FlatData getROIFlatBlockAt(int x, int y, int width, int height, int nbOfImages, int... position) {
FlatData block = null;
if ((stackFullShape != null) && (position != null) && (dataShape != null) && (dataShape.length == 2) && (x > -1)
&& (y > -1) && (height > 0) && (width > 0) && (x + width <= dataShape[1])
&& (y + height <= dataShape[0]) && (nbOfImages > 0)) {
if (position.length != stackFullShape.length) {
position = Arrays.copyOf(position, stackFullShape.length);
}
position[position.length - 1] = x;
position[position.length - 2] = y;
block = getData(position, new int[] { nbOfImages, height, width });
}
return block;
}
/**
* Returns a block of image ROIs, starting at given position.
......@@ -125,21 +125,21 @@ public class ImageStack extends StackedData {
return getDataAt(position);
}
// /**
// * Returns a block of images, starting at given position.
// *
// * @param nbOfImages The number of images in the block.
// * @param position The image position in the stack.
// * @return A {@link FlatData}.
// */
// public FlatData getImageBlockAt(int nbOfImages, int... position) {
// FlatData block = null;
// if ((stackFullShape != null) && (position != null) && (dataShape != null) && (dataShape.length == 2)
// && (nbOfImages > 0)) {
// block = getData(position, new int[] { nbOfImages, dataShape[0], dataShape[1] });
// }
// return block;
// }
/**
* Returns a block of images, starting at given position.
*
* @param nbOfImages The number of images in the block.
* @param position The image position in the stack.
* @return A {@link FlatData}.
*/
public FlatData getImageFlatBlockAt(int nbOfImages, int... position) {
FlatData block = null;
if ((stackFullShape != null) && (position != null) && (dataShape != null) && (dataShape.length == 2)
&& (nbOfImages > 0)) {
block = getData(position, new int[] { nbOfImages, dataShape[0], dataShape[1] });
}
return block;
}
/**
* Returns a block of images, starting at given position.
......
src/main/java/fr/soleil/cdma/box/data/SpectrumStack.java
+ 38
− 37
View file @ 15f05e23
......@@ -12,6 +12,7 @@ import fr.soleil.cdma.box.reader.ICDMAReader;
import fr.soleil.cdma.box.util.PositionKey;
import fr.soleil.lib.project.data.FlatData;
import fr.soleil.lib.project.math.ArrayUtils;
import fr.soleil.lib.project.math.MathConst;
import fr.soleil.lib.project.math.NumberArrayUtils;
/**
......@@ -159,43 +160,43 @@ public class SpectrumStack extends StackedData {
return result;
}
// @Override
// public FlatData getBlockAt(int nbOfData, int... position) {
// FlatData result;
// if (useMap) {
// if ((nbOfData > 0) && (spectrumLength > 0) && (position != null) && (stackShape != null)
// && (position.length == stackShape.length)) {
// int count = Math.min(nbOfData, stackShape[stackShape.length - 1] - position[position.length - 1]);
// if (count > 0) {
// double[] array = new double[count * spectrumLength];
// Arrays.fill(array, MathConst.NAN_FOR_NULL);
// int[] index = position.clone();
// int i = 0;
// while (ArrayUtils.isPosition(stackShape, index)) {
// SoftIndexedData<double[]> data = spectra.get(new PositionKey(index));
// if (data != null) {
// double[] spectrum = data.getData();
// if (spectrum != null) {
// System.arraycopy(spectrum, 0, array, i * spectrumLength, spectrumLength);
// }
// }
// ArrayUtils.incrementPosition(stackShape, index);
// if (++i >= count) {
// break;
// }
// }
// result = new FlatData(new int[] { count, spectrumLength }, array);
// } else {
// result = null;
// }
// } else {
// result = null;
// }
// } else {
// result = super.getBlockAt(nbOfData, position);
// }
// return result;
// }
@Override
public FlatData getFlatBlockAt(int nbOfData, int... position) {
FlatData result;
if (useMap) {
if ((nbOfData > 0) && (spectrumLength > 0) && (position != null) && (stackShape != null)
&& (position.length == stackShape.length)) {
int count = Math.min(nbOfData, stackShape[stackShape.length - 1] - position[position.length - 1]);
if (count > 0) {
double[] array = new double[count * spectrumLength];
Arrays.fill(array, MathConst.NAN_FOR_NULL);
int[] index = position.clone();
int i = 0;
while (ArrayUtils.isPosition(stackShape, index)) {
SoftIndexedData<double[]> data = spectra.get(new PositionKey(index));
if (data != null) {
double[] spectrum = data.getData();
if (spectrum != null) {
System.arraycopy(spectrum, 0, array, i * spectrumLength, spectrumLength);
}
}
ArrayUtils.incrementPosition(stackShape, index);
if (++i >= count) {
break;
}
}
result = new FlatData(new int[] { count, spectrumLength }, array);
} else {
result = null;
}
} else {
result = null;
}
} else {
result = super.getFlatBlockAt(nbOfData, position);
}
return result;
}
@Override
public FlatData[] getBlockAt(int nbOfData, int... position) {
......
src/main/java/fr/soleil/cdma/box/data/StackedData.java
+ 21
− 21
View file @ 15f05e23
......@@ -103,27 +103,27 @@ public abstract class StackedData extends ReferencedData {
return getData(position, dataShape);
}
// /**
// * Returns a block of data, starting at given position.
// *
// * @param nbOfData The number of data in a block
// * @param position The data position in the stack.
// * @return A {@link FlatData}.
// */
// public FlatData getBlockAt(int nbOfData, int... position) {
// FlatData block = null;
// int rank = getDataRank();
// if ((stackFullShape != null) && (stackFullShape.length > rank) && (rank > -1) && (position != null)
// && (dataShape != null) && (dataShape.length == rank) && (nbOfData > 0)) {
// int[] shape = new int[rank + 1];
// shape[0] = nbOfData;
// if (rank > 0) {
// System.arraycopy(dataShape, 0, shape, 1, rank);
// }
// block = getData(position, shape);
// }
// return block;
// }
/**
* Returns a block of data, starting at given position.
*
* @param nbOfData The number of data in a block
* @param position The data position in the stack.
* @return A {@link FlatData}.
*/
public FlatData getFlatBlockAt(int nbOfData, int... position) {
FlatData block = null;
int rank = getDataRank();
if ((stackFullShape != null) && (stackFullShape.length > rank) && (rank > -1) && (position != null)
&& (dataShape != null) && (dataShape.length == rank) && (nbOfData > 0)) {
int[] shape = new int[rank + 1];
shape[0] = nbOfData;
if (rank > 0) {
System.arraycopy(dataShape, 0, shape, 1, rank);
}
block = getData(position, shape);
}
return block;
}
/**
* Returns a block of data, starting at given position.
......
src/main/java/fr/soleil/cdma/box/data/scan/ScanData.java
+ 49
− 0
View file @ 15f05e23
......@@ -399,6 +399,36 @@ public class ScanData {
return result;
}
/**
* Returns the image block at a particular coordinate
*
* @param index The coordinate
* @param nbOfImages The number of images inside the block.
* @return A {@link FlatData}. <code>null</code> if no such image.
*/
public FlatData[] getImageBlockAt(int nbOfImages, int... index) {
FlatData[] result = null;
if (images != null) {
result = images.getImageBlockAt(nbOfImages, index);
}
return result;
}
/**
* Returns the image block at a particular coordinate
*
* @param index The coordinate
* @param nbOfImages The number of images inside the block.
* @return A {@link FlatData}. <code>null</code> if no such image.
*/
public FlatData getImageFlatBlockAt(int nbOfImages, int... index) {
FlatData result = null;
if (images != null) {
result = images.getImageFlatBlockAt(nbOfImages, index);
}
return result;
}
// public FlatData getSpectraAt(int... index) {
// FlatData result = null;
//
......@@ -466,6 +496,25 @@ public class ScanData {
return result;
}
/**
* Returns a block of image ROI at a particular coordinate
*
* @param x the desired ROI x
* @param y the desired ROI y
* @param width the desired ROI width
* @param height the desired ROI height
* @param nbOfImages The number of images in the block
* @param index The coordinate
* @return A {@link FlatData} array. <code>null</code> if no such image block.
*/
public FlatData getImageROIFlatBlockAt(int x, int y, int width, int height, int nbOfImages, int... index) {
FlatData result = null;
if (images != null) {
result = images.getROIFlatBlockAt(x, y, width, height, nbOfImages, index);
}
return result;
}
public Object getSpectrumAt(int... position) {
Object spectrum = null;
if (spectrumStack != null) {
......
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