- No more use of region: a detector region is a detector

- Simplified external tools : HarvestSignalAttributes is useless and removed. Use HarvestEquipmentAttributes instead.

src/main/java/fr/soleil/cdma/box/data/acquisition/Acquisition.java

@@ -18,7 +18,6 @@ import org.apache.commons.lang.ArrayUtils;
 import fr.soleil.cdma.box.data.SoftData;
 import fr.soleil.cdma.box.data.scan.ScanData;
 import fr.soleil.cdma.box.data.scan.ScanData.Dimension;
-import fr.soleil.cdma.box.data.sensor.PhotoElectronAnalyzerConfig;
 import fr.soleil.cdma.box.data.sensor.SensorConfig;
 import fr.soleil.lib.project.math.MathConst;
 
@@ -31,26 +30,24 @@ public class Acquisition {
 
     private final String sourceURI;
     private final String uriSimpleName;
-    private final SensorConfig sensorConfig;
+    private final String detector;
     private final List<ScanData> scanList;
     private double[] spectrumX;
     private boolean energyAcquisition;
 
     /**
-     * Constructs this {@link Acquisition} and associates a source URI and a {@link SensorConfig} to
-     * it
+     * Constructs this {@link Acquisition} and associates a source URI and a detector to it.
      * 
      * @param sourceURI The path of the URI
      * @param uriSimpleName The path of the URI, or a simple name for the URI, that can be understood by human beings.
-     * @param sensorConfig The {@link SensorConfig}
+     * @param detector The detector
      */
-    public Acquisition(String sourceURI, String uriSimpleName, SensorConfig sensorConfig) {
+    public Acquisition(String sourceURI, String uriSimpleName, String detector) {
         scanList = new ArrayList<ScanData>();
         this.sourceURI = sourceURI;
         this.uriSimpleName = uriSimpleName;
-        this.sensorConfig = sensorConfig;
-        spectrumX = (sensorConfig instanceof PhotoElectronAnalyzerConfig
-                ? ((PhotoElectronAnalyzerConfig) sensorConfig).getPixelToEnergy() : null);
+        this.detector = detector;
+        spectrumX = null;
 
         energyAcquisition = false;
     }
@@ -64,12 +61,12 @@ public class Acquisition {
     }
 
     /**
-     * Returns the {@link SensorConfig} of this {@link Acquisition}
+     * Returns this {@link Acquisition}'s detector.
      * 
-     * @return A {@link SensorConfig}
+     * @return A {@link String}.
      */
-    public SensorConfig getSensorConfig() {
-        return sensorConfig;
+    public String getDetector() {
+        return detector;
     }
 
     /**

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

@@ -309,8 +309,10 @@ public class ScanData {
      */
     public double[] getMeanSpectrum() {
         double[] result = getSumSpectrum();
-        int[] stack = spectrumStack.getStackFullShape();
-        int[] reducedShape = Arrays.copyOf(stack, stack.length - 1);
+        if (spectrumStack != null) {
+            int[] stackFullShape = spectrumStack.getStackFullShape();
+            if (stackFullShape != null) {
+                int[] reducedShape = Arrays.copyOf(stackFullShape, stackFullShape.length - 1);
                 int size = 1;
 
                 for (int i = 0; i < reducedShape.length; i++) {
@@ -320,6 +322,8 @@ public class ScanData {
                 for (int i = 0; i < result.length; i++) {
                     result[i] /= size;
                 }
+            } // end if (stackFullShape != null)
+        } // end if (spectrumStack != null)
         return result;
     }
 
@@ -330,9 +334,11 @@ public class ScanData {
      */
     public double[] getSumSpectrum() {
         double[] sumSpectrum = new double[0];
-        int[] stack = spectrumStack.getStackFullShape();
+        if (spectrumStack != null) {
+            int[] stackFullShape = spectrumStack.getStackFullShape();
+            if (stackFullShape != null) {
                 int index = 0;
-        int[] reducedShape = Arrays.copyOf(stack, stack.length - 1);
+                int[] reducedShape = Arrays.copyOf(stackFullShape, stackFullShape.length - 1);
                 int[] position = new int[stackShape.length];
 
                 // TODO CREATE TASK FOR READING SPECTRUM BY BLOCK
@@ -354,6 +360,8 @@ public class ScanData {
                         index++;
                     }
                 }
+            } // end if (stackFullShape != null)
+        } // end if (spectrumStack != null)
         return sumSpectrum;
     }
 

src/main/java/fr/soleil/cdma/box/data/sensor/ExperimentConfig.java

@@ -7,13 +7,9 @@
  ******************************************************************************/
 package fr.soleil.cdma.box.data.sensor;
 
-import java.text.Collator;
 import java.util.Collection;
-import java.util.Comparator;
-import java.util.LinkedHashMap;
-import java.util.Map;
-import java.util.Set;
-import java.util.TreeSet;
+import java.util.Collections;
+import java.util.LinkedHashSet;
 
 /**
  * 
@@ -21,46 +17,24 @@ import java.util.TreeSet;
  */
 public class ExperimentConfig {
 
-    private final Map<String, SensorConfig> acquisitionConfigCache;
-    private final Map<Sensor, Set<SensorConfig>> detectorMap;
+    private Collection<String> detectors;
 
     public ExperimentConfig() {
-        detectorMap = new LinkedHashMap<Sensor, Set<SensorConfig>>();
-        acquisitionConfigCache = new LinkedHashMap<String, SensorConfig>();
+        detectors = new LinkedHashSet<>();
     }
 
-    public void addConfig(Sensor detector, SensorConfig acquisitionConfig) {
-        if (detector != null && acquisitionConfig != null) {
-            // Test if config already exists in cache
-            String configName = detector + acquisitionConfig.getName();
-            SensorConfig cachedAcquisitionConfig = acquisitionConfigCache.get(configName);
-            if (cachedAcquisitionConfig == null) {
-                acquisitionConfigCache.put(configName, acquisitionConfig);
-                cachedAcquisitionConfig = acquisitionConfig;
-            }
-            Set<SensorConfig> regions = detectorMap.get(detector);
-            if (regions == null) {
-                regions = new TreeSet<SensorConfig>(new Comparator<SensorConfig>() {
-                    Collator collator = Collator.getInstance();
-
-                    @Override
-                    public int compare(SensorConfig o1, SensorConfig o2) {
-                        return collator.compare(o1.getName(), o2.getName());
-                    }
-                });
-            }
-            if (acquisitionConfig != null) {
-                regions.add(cachedAcquisitionConfig);
-            }
-            detectorMap.put(detector, regions);
+    public void addDetector(String detector) {
+        if (detector != null) {
+            detectors.add(detector);
         }
     }
 
-    public Collection<Sensor> getDetectorList() {
-        return detectorMap.keySet();
+    public boolean hasDetector(String detector) {
+        return ((detector != null) && detectors.contains(detector));
     }
 
-    public Collection<SensorConfig> getAcquisitionConfigListForDetector(Sensor detector) {
-        return detectorMap.get(detector);
+    public Collection<String> getDetectorList() {
+        return Collections.unmodifiableCollection(detectors);
     }
+
 }

src/main/java/fr/soleil/cdma/box/manager/AcquisitionManager.java

@@ -11,7 +11,6 @@ import java.util.HashSet;
 import java.util.Set;
 
 import fr.soleil.cdma.box.data.LoadableData;
-import fr.soleil.cdma.box.data.sensor.SensorConfig;
 import fr.soleil.cdma.box.exception.CDMAAccessException;
 import fr.soleil.cdma.box.reader.ICDMAReader;
 
@@ -23,7 +22,7 @@ import fr.soleil.cdma.box.reader.ICDMAReader;
 public class AcquisitionManager {
 
     protected final ICDMAReader cdmaReader;
-    private SensorConfig sensorConfig;
+    private String detector;
     private final Set<LoadableData> dataToLoad;
 
     /**
@@ -33,7 +32,7 @@ public class AcquisitionManager {
      */
     public AcquisitionManager(ICDMAReader cdmaReader) {
         this.cdmaReader = cdmaReader;
-        sensorConfig = null;
+        detector = null;
         dataToLoad = new HashSet<LoadableData>();
     }
 
@@ -48,26 +47,26 @@ public class AcquisitionManager {
             synchronized (dataToLoad) {
                 toLoad = dataToLoad.toArray(new LoadableData[dataToLoad.size()]);
             }
-            cdmaReader.loadAcquisition(sensorConfig, toLoad);
+            cdmaReader.loadAcquisition(detector, toLoad);
         }
     }
 
     /**
-     * Returns the previously set {@link SensorConfig}
+     * Returns the previously set detector.
      * 
-     * @return A {@link SensorConfig}
+     * @return A {@link String}.
      */
-    public SensorConfig getSensorConfig() {
-        return sensorConfig;
+    public String getDetector() {
+        return detector;
     }
 
     /**
-     * Sets the {@link SensorConfig} to use for acquisition loading
+     * Sets the detector to use for acquisition loading.
      * 
-     * @param sensorConfig The {@link SensorConfig} to use
+     * @param detector The detector to use.
      */
-    public void setSensorConfig(SensorConfig sensorConfig) {
-        this.sensorConfig = sensorConfig;
+    public void setDetector(String detector) {
+        this.detector = detector;
     }
 
     /**

src/main/java/fr/soleil/cdma/box/reader/ICDMAReader.java

@@ -16,7 +16,6 @@ import fr.soleil.cdma.box.data.ContextDataItem;
 import fr.soleil.cdma.box.data.LoadableData;
 import fr.soleil.cdma.box.data.acquisition.Acquisition;
 import fr.soleil.cdma.box.data.sensor.ExperimentConfig;
-import fr.soleil.cdma.box.data.sensor.SensorConfig;
 import fr.soleil.cdma.box.exception.CDMAAccessException;
 import fr.soleil.data.source.AbstractDataSource;
 import fr.soleil.lib.project.ICancelable;
@@ -42,7 +41,6 @@ public interface ICDMAReader extends ICancelable {
     public static final String STACK_NAME_KEY = "stack_name";
 
     public static final String ATTR_EQUIPMENT_NAME = "equipment";
-    public static final String ATTR_EQUIPMENT_REGION = "region";
     public static final String ATTR_LONG_NAME = "long_name";
     public static final String ATTR_UNIT = "unit";
     public static final String ATTR_FORMAT = "format";
@@ -59,7 +57,7 @@ public interface ICDMAReader extends ICancelable {
     public static final String SCIENTA_DETECTOR = "Scienta";
     public static final String KEITHLEY_DETECTOR = "Keithley";
     public static final String XIA_DETECTOR = "Xia";
-//    public static final String MBS_DETECTOR_PATTERN = "MBSAcquisition[_]*\\d*";
+    public static final String XIA_DETECTOR_PATTERN = "Xia.*";
     public static final String MBS_DETECTOR_PATTERN = "MBS.*";
     public static final String LIVE_TIME_KEY = "liveTime";
     public static final String CHANNEL_SCALE_KEY = "channelScale";
@@ -80,6 +78,7 @@ public interface ICDMAReader extends ICancelable {
     public static final String SLICES_KEY = "slices";
 
     public static final String IMAGES_KEY = "images";
+    public static final String SPECTRA_KEY = "spectra";
     public static final String SPECTRA_XIA_KEY = "spectra_xia";
     public static final String SPECTRA_SCIENTA_KEY = "spectra_scienta";
     public static final String SPECTRA_MBS_KEY = "spectra_mbs";
@@ -91,6 +90,15 @@ public interface ICDMAReader extends ICancelable {
     public static final String SAMPLE_THETA_KEY = "sampleTheta";
     public static final String APERTURE_ANGLE_KEY = "apertureAngle";
 
+    public static final String SCALARS_DISPLAY_NAME = SCALARS_KEY;
+    public static final String SPECTRA_DISPLAY_NAME = SPECTRA_KEY;
+    public static final String IMAGES_DISPLAY_NAME = IMAGES_KEY;
+    public static final String TOTAL_SPECTRUM_DISPLAY_NAME = "total spectrum";
+    public static final String BEAM_ENERGY_DISPLAY_NAME = "beam energy";
+    public static final String SAMPLE_PHI_DISPLAY_NAME = "sample phi";
+    public static final String SAMPLE_THETA_DISPLAY_NAME = "theta";
+    public static final String APERTURE_ANGLE_DISPLAY_NAME = "aperture angle";
+
     public static final String MOTORS_GROUP = "motors";
     public static final String MOTOR_PARAMETER = "motor";
     public static final String MOTOR_POSITION_KEY = "motor_position";
@@ -419,13 +427,13 @@ public interface ICDMAReader extends ICancelable {
     public double getBias(String im, LogicalGroup monitorGroup);
 
     /**
-     * Recovers an {@link Acquisition} from a {@link SensorConfig}
+     * Recovers an {@link Acquisition} from a detector
      * 
-     * @param sensorConfig The concerned {@link SensorConfig}
+     * @param detector The concerned detector
      * @param dataToLoad The optional data to load
      * @throws CDMAAccessException If a problem occurred during acquisition loading
      */
-    public void loadAcquisition(SensorConfig sensorConfig, LoadableData... dataToLoad) throws CDMAAccessException;
+    public void loadAcquisition(String detector, LoadableData... dataToLoad) throws CDMAAccessException;
 
     /**
      * Returns the {@link AbstractDataSource} that contains the loaded {@link ExperimentConfig}