Merge pull request #806 from INM-6/fix/nix_empty_arrayannotations

Support Empty Array Annotations in NixIO

Author: JuliaSprenger

neo/io/nixio.py

@@ -1008,7 +1008,7 @@ def _write_analogsignal(self, anasig, nixblock, nixgroup):
         if anasig.array_annotations:
             for k, v in anasig.array_annotations.items():
                 p = self._write_property(metadata, k, v)
-                p.definition = ARRAYANNOTATION
+                p.type = ARRAYANNOTATION
 
         self._signal_map[nix_name] = nixdas
 
@@ -1141,7 +1141,7 @@ def _write_irregularlysampledsignal(self, irsig, nixblock, nixgroup):
         if irsig.array_annotations:
             for k, v in irsig.array_annotations.items():
                 p = self._write_property(metadata, k, v)
-                p.definition = ARRAYANNOTATION
+                p.type = ARRAYANNOTATION
 
         self._signal_map[nix_name] = nixdas
 
@@ -1191,7 +1191,7 @@ def _write_event(self, event, nixblock, nixgroup):
         if event.array_annotations:
             for k, v in event.array_annotations.items():
                 p = self._write_property(metadata, k, v)
-                p.definition = ARRAYANNOTATION
+                p.type = ARRAYANNOTATION
 
         nixgroup.multi_tags.append(nixmt)
 
@@ -1252,7 +1252,7 @@ def _write_epoch(self, epoch, nixblock, nixgroup):
         if epoch.array_annotations:
             for k, v in epoch.array_annotations.items():
                 p = self._write_property(metadata, k, v)
-                p.definition = ARRAYANNOTATION
+                p.type = ARRAYANNOTATION
 
         nixgroup.multi_tags.append(nixmt)
 
@@ -1311,7 +1311,7 @@ def _write_spiketrain(self, spiketrain, nixblock, nixgroup):
         if spiketrain.array_annotations:
             for k, v in spiketrain.array_annotations.items():
                 p = self._write_property(metadata, k, v)
-                p.definition = ARRAYANNOTATION
+                p.type = ARRAYANNOTATION
 
         if nixgroup:
             nixgroup.multi_tags.append(nixmt)
@@ -1513,7 +1513,7 @@ def _nix_attr_to_neo(nix_obj):
                     values = values[0]
                 if prop.definition in (DATEANNOTATION, TIMEANNOTATION, DATETIMEANNOTATION):
                     values = dt_from_nix(values, prop.definition)
-                if prop.definition == ARRAYANNOTATION:
+                if prop.type == ARRAYANNOTATION:
                     if 'array_annotations' in neo_attrs:
                         neo_attrs['array_annotations'][prop.name] = values
                     else:

neo/test/iotest/test_nixio.py

@@ -420,7 +420,7 @@ def create_full_nix_file(cls, filename):
             asig_md.create_property(arr_ann_name,
                                     arr_ann_val.magnitude.flatten())
             asig_md.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
-            asig_md.props[arr_ann_name].definition = 'ARRAYANNOTATION'
+            asig_md.props[arr_ann_name].type = 'ARRAYANNOTATION'
 
             for idx in range(10):
                 da_asig = blk.create_data_array(
@@ -454,7 +454,7 @@ def create_full_nix_file(cls, filename):
             imgseq_md.create_property(arr_ann_name,
                                       arr_ann_val.magnitude.flatten())
             imgseq_md.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
-            imgseq_md.props[arr_ann_name].definition = 'ARRAYANNOTATION'
+            imgseq_md.props[arr_ann_name].type = 'ARRAYANNOTATION'
 
             for idx in range(10):
                 da_imgseq = blk.create_data_array(
@@ -487,7 +487,7 @@ def create_full_nix_file(cls, filename):
             isig_md.create_property(arr_ann_name,
                                     arr_ann_val.magnitude.flatten())
             isig_md.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
-            isig_md.props[arr_ann_name].definition = 'ARRAYANNOTATION'
+            isig_md.props[arr_ann_name].type = 'ARRAYANNOTATION'
             for idx in range(7):
                 da_isig = blk.create_data_array(
                     "{}.{}".format(isig_name, idx),
@@ -529,7 +529,7 @@ def create_full_nix_file(cls, filename):
             mtag_st_md.create_property(arr_ann_name,
                                        arr_ann_val.magnitude.flatten())
             mtag_st_md.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
-            mtag_st_md.props[arr_ann_name].definition = 'ARRAYANNOTATION'
+            mtag_st_md.props[arr_ann_name].type = 'ARRAYANNOTATION'
 
             waveforms = cls.rquant((10, 8, 5), 1)
             wfname = "{}.waveforms".format(mtag_st.name)
@@ -581,7 +581,7 @@ def create_full_nix_file(cls, filename):
             mtag_ep.metadata.create_property(arr_ann_name,
                                              arr_ann_val.magnitude.flatten())
             mtag_ep.metadata.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
-            mtag_ep.metadata.props[arr_ann_name].definition = 'ARRAYANNOTATION'
+            mtag_ep.metadata.props[arr_ann_name].type = 'ARRAYANNOTATION'
 
             label_dim = mtag_ep.positions.append_set_dimension()
             label_dim.labels = cls.rsentence(5).split(" ")
@@ -614,7 +614,7 @@ def create_full_nix_file(cls, filename):
             mtag_ev.metadata.create_property(arr_ann_name,
                                              arr_ann_val.magnitude.flatten())
             mtag_ev.metadata.props[arr_ann_name].unit = str(arr_ann_val.dimensionality)
-            mtag_ev.metadata.props[arr_ann_name].definition = 'ARRAYANNOTATION'
+            mtag_ev.metadata.props[arr_ann_name].type = 'ARRAYANNOTATION'
 
             label_dim = mtag_ev.positions.append_set_dimension()
             label_dim.labels = cls.rsentence(5).split(" ")
@@ -1570,6 +1570,24 @@ def test_annotations_special_cases(self):
 
         # TODO: multi dimensional value (GH Issue #501)
 
+    def test_empty_array_annotations(self):
+        wblock = Block("block with spiketrain")
+        wseg = Segment()
+        wseg.spiketrains = [SpikeTrain(times=[] * pq.s, t_stop=1 * pq.s,
+                                       array_annotations={'empty': []})]
+        wblock.segments = [wseg]
+        self.writer.write_block(wblock)
+        try:
+            rblock = self.writer.read_block(neoname="block with spiketrain")
+        except Exception as exc:
+            self.fail('The following exception was raised when'
+                      + ' reading the block with an empty array annotation:\n'
+                      + str(exc))
+        rst = rblock.segments[0].spiketrains[0]
+        self.assertEqual(len(rst.array_annotations), 1)
+        self.assertIn('empty', rst.array_annotations.keys())
+        self.assertEqual(len(rst.array_annotations['empty']), 0)
+
     def test_write_proxyobjects(self):
 
         def generate_complete_block():