added spectrum block reading

src/main/java/fr/soleil/cdma/box/data/SpectrumStack.java

@@ -125,6 +125,31 @@ public class SpectrumStack extends StackedData {
         return spectrum;
     }
 
+    public FlatData[] getSpectrumBlockAt(int sizeBlock, int... position) {
+        FlatData[] spectrum = null;
+        if (useMap) {
+            SoftIndexedData<double[]> data = spectra.get(new PositionKey(position));
+            if (data != null) {
+                spectrum = new FlatData[1];
+                spectrum[0] = new FlatData(data.getShape(), data.getData());
+            }
+        } else {
+            ICDMAReader cdmaReader = getReader();
+            if ((cdmaReader != null) && (stackFullShape != null) && (position != null)) {
+                if (position.length != stackFullShape.length) {
+                    position = Arrays.copyOf(position, stackFullShape.length);
+                }
+                // For spectra, we don't need FlatData, as resulting data is already a single dimension array
+                spectrum = cdmaReader.readCDMFlatComplexArrayBlockWithCtx(contextDataItem, position, dataFullShape,
+                        sizeBlock);
+                // spectrum = cdmaReader.readCDMSimpleArrayWithCtx(contextDataItem, position, dataFullShape);
+            }
+
+        }
+        return spectrum;
+
+    }
+
     @Override
     public Object getCompleteStack() {
         Object result;

src/main/java/fr/soleil/cdma/box/data/scan/ScanData.java

@@ -53,6 +53,7 @@ public class ScanData {
     private final String scanOrigin;
     private String comments;
     private IAcquisitionDataManager acquisitionDataManager;
+//    private long durationRead = 0;
 
     /**
      * Constructs this {@link ScanData}
@@ -334,6 +335,7 @@ public class ScanData {
         int[] reducedShape = Arrays.copyOf(stack, stack.length - 1);
         int[] position = new int[stackShape.length];
 
+        // TODO CREATE TASK FOR READING SPECTRUM BY BLOCK
         while (ArrayUtils.isPosition(reducedShape, position)) {
             Object spectrum = spectrumStack.getSpectrumAt(position);
 
@@ -522,6 +524,28 @@ public class ScanData {
             spectrum = spectrumStack.getSpectrumAt(position);
         }
 
+//      if ((index != null) && (spectra != null)) {
+//      if ((stackShape != null) && (index.length != stackShape.length)) {
+//          index = Arrays.copyOf(index, stackShape.length);
+//      }
+//      result = spectra.get(new PositionKey(index));
+//  }
+//  return result;
+        return spectrum;
+    }
+
+    public FlatData[] getSpectrumBlockAt(int sizeBlock, int... position) {
+        FlatData[] spectrum = null;
+        // TODO clean code!
+//        long startReadingBlock = System.nanoTime();
+        if (spectrumStack != null) {
+            spectrum = spectrumStack.getSpectrumBlockAt(sizeBlock, position);
+        }
+
+//        long duration = System.nanoTime() - startReadingBlock;
+//        durationRead += duration;
+        // System.out.println("current total duration read is " + durationRead);
+
 //      if ((index != null) && (spectra != null)) {
 //      if ((stackShape != null) && (index.length != stackShape.length)) {
 //          index = Arrays.copyOf(index, stackShape.length);