Fix a few anatomical orientation issues after further testing

Author: melissalinkert

components/formats-bsd/src/loci/formats/in/FakeReader.java

@@ -328,6 +328,9 @@ public FakeReader() {
   @Override
   public Orientation[] getAxisOrientations() {
     FormatTools.assertId(currentId, true, 1);
+    if (orientations.size() == 0) {
+      return new Orientation[5];
+    }
     return orientations.toArray(new Orientation[orientations.size()]);
   }
 

components/formats-gpl/src/loci/formats/in/AnalyzeReader.java

@@ -287,39 +287,40 @@ protected void initFile(String id) throws FormatException, IOException {
       // further reference:
       // http://www.grahamwideman.com/gw/brain/analyze/formatdoc.htm
       // https://eeg.sourceforge.net/mri_orientation_notes.html
+      String orientationDescription = String.valueOf(orient);
       switch (orient) {
-        case '0':
-          // transverse unflipped
+        case 0:
+          orientationDescription = "transverse unflipped";
           xAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.RIGHT_TO_LEFT);
           yAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.POSTERIOR_TO_ANTERIOR);
           zAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.INFERIOR_TO_SUPERIOR);
           break;
-        case '1':
-          // coronal unflipped
+        case 1:
+          orientationDescription = "coronal unflipped";
           xAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.RIGHT_TO_LEFT);
           yAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.INFERIOR_TO_SUPERIOR);
           zAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.POSTERIOR_TO_ANTERIOR);
           break;
-        case '2':
-          // sagittal unflipped
+        case 2:
+          orientationDescription = "sagittal unflipped";
           xAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.POSTERIOR_TO_ANTERIOR);
           yAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.INFERIOR_TO_SUPERIOR);
           zAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.RIGHT_TO_LEFT);
           break;
-        case '3':
-          // transverse flipped
+        case 3:
+          orientationDescription = "transverse flipped";
           xAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.RIGHT_TO_LEFT);
           yAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.ANTERIOR_TO_POSTERIOR);
           zAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.INFERIOR_TO_SUPERIOR);
           break;
-        case '4':
-          // coronal flipped
+        case 4:
+          orientationDescription = "coronal flipped";
           xAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.RIGHT_TO_LEFT);
           yAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.SUPERIOR_TO_INFERIOR);
           zAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.POSTERIOR_TO_ANTERIOR);
           break;
-        case '5':
-          // sagittal flipped
+        case 5:
+          orientationDescription = "sagittal flipped";
           xAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.POSTERIOR_TO_ANTERIOR);
           yAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.SUPERIOR_TO_INFERIOR);
           zAxis = new Orientation(OrientationType.ANATOMICAL, AnatomicalOrientation.RIGHT_TO_LEFT);
@@ -345,7 +346,7 @@ protected void initFile(String id) throws FormatException, IOException {
       addGlobalMeta("Pixel minimum", pixelMin);
       addGlobalMeta("Description", description);
       addGlobalMeta("Auxiliary file", auxFile);
-      addGlobalMeta("Orientation", orient);
+      addGlobalMeta("Orientation", orientationDescription);
       addGlobalMeta("Originator", originator);
       addGlobalMeta("Generated", generated);
       addGlobalMeta("Scan Number", scannum);

components/formats-gpl/src/loci/formats/in/BrukerReader.java

@@ -497,10 +497,10 @@ else if (key.equals("##$SUBJECT_type")) {
           subjectType = value;
         }
         else if (key.equals("##$SUBJECT_entry")) {
-          subjectEntry = value.substring(value.indexOf("_") + 1);
+          subjectEntry = value.substring(value.lastIndexOf("_") + 1);
         }
-        else if (key.equals("##$SUBJECT_pose")) {
-          subjectPose = value.substring(value.indexOf("_") + 1);
+        else if (key.equals("##$SUBJECT_position")) {
+          subjectPose = value.substring(value.lastIndexOf("_") + 1);
         }
 
         if (ms != null) {