Fix of missing SE entry with empty array, minor modifiction of new file type structure

eos/file_reader.py

@@ -33,7 +33,7 @@ NO_DEFAULT_VALUE = object() # just for allowing None default value in AmorHeader
 
 class AmorHeader:
     """
-    Collects header information from Amor NeXus fiel without reading event data.
+    Collects header information from Amor NeXus file without reading event data.
     """
     # mapping of names to (hdf_path, dtype, nicos_key[, suffix])
     hdf_paths = dict(
@@ -44,7 +44,7 @@ class AmorHeader:
             user_affiliation=('entry1/user/affiliation', str),
             sample_name=('entry1/sample/name', str),
             sample_model=('entry1/sample/model', str),
-            sample_geometry=('entry1/sample/geometry', dict),
+            sample_geometry=('entry1/sample/geometry', str),
             source_name=('entry1/Amor/source/name', str),
             start_time=('entry1/start_time', str),
             start_time_fallback=('entry1/Amor/measurement_configuration/start_time', str),
@@ -52,7 +52,7 @@ class AmorHeader:
 
             chopper_separation=('entry1/Amor/chopper/pair_separation', float),
             chopper_distance=('entry1/Amor/chopper/distance', float),
-            detector_distance=('entry1/Amor/detector/transformation/distance', float),
+            detector_distance=('entry1/Amor/detector_stage/transformation/distance', float),
             sample_temperature=('entry1/sample/environment/temperature', float),
             sample_magnetic_field=('entry1/sample/environment/magnetic_field', float),
             sample_current=('entry1/sample/environment/current', float),
@@ -68,7 +68,7 @@ class AmorHeader:
             virtual_source_vertical=('entry1/Amor/virtual_source/vertical', float),
             ch1_trigger_phase=('entry1/Amor/chopper/ch1_trigger_phase', float, 'ch1_trigger_phase'),
             ch2_trigger_phase=('entry1/Amor/chopper/ch2_trigger_phase', float, 'ch2_trigger_phase'),
-            chopper_speed=('entry1/Amor/chopper/rotation_speed', float, 'chopper_phase'),
+            chopper_speed=('entry1/Amor/chopper/rotation_speed', float, 'chopper_speed'),
             chopper_phase=('entry1/Amor/chopper/phase', float, 'chopper_phase'),
 
             polarization_config_label=('entry1/Amor/polarization/configuration', int, 'polarization_config_label', '/*'),
@@ -262,7 +262,8 @@ class AmorHeader:
                 )
         sample_geometry = self.rv('sample_geometry', default=None)
         if sample_geometry:
-            self.sample.geometry = sample_geometry
+            import yaml
+            self.sample.geometry = yaml.safe_load(sample_geometry)
         # while event times are not evaluated, use first value reported in file for SEE
         for param in self.SEE_PARAMS:
             key = f'sample_{param}'
@@ -488,8 +489,11 @@ class AmorEventData(AmorHeader):
         sample_keys = [f'sample_{param}' for param in self.SEE_PARAMS]
         relevant_items += sample_keys
         for key, log in self.data.device_logs.items():
+            # if SE is missing there can be a missing key or empty dataset
             if key not in relevant_items:
                 continue
+            if log.value.size == 0:
+                continue
             if log.value.dtype in [np.int8, np.int16, np.int32, np.int64]:
                 # for integer items (flags) report the most common one
                 value = np.bincount(log.value).argmax()