Updates for data conversion (#1052)

Merging this now. As agreed, we will update the name-overwriting strategy after the Hackathon tutorial this afternoon, so that name changes are only applied when duplicate names are found.

Author: legouee

neo/io/nwbio.py

@@ -73,7 +73,8 @@
     "experiment_description", "session_id", "institution", "keywords", "notes",
     "pharmacology", "protocol", "related_publications", "slices", "source_script",
     "source_script_file_name", "data_collection", "surgery", "virus", "stimulus_notes",
-    "lab", "session_description"
+    "lab", "session_description",
+    "rec_datetime",
 )
 
 POSSIBLE_JSON_FIELDS = (
@@ -273,7 +274,7 @@ def read_all_blocks(self, lazy=False, **kwargs):
                 "session_start_time"]
         if "file_create_date" in self.global_block_metadata:
             self.global_block_metadata["file_datetime"] = self.global_block_metadata[
-                "file_create_date"]
+                "rec_datetime"]
 
         self._blocks = {}
         self._read_acquisition_group(lazy=lazy)
@@ -435,11 +436,13 @@ def write_all_blocks(self, blocks, **kwargs):
             annotations["session_description"] = blocks[0].description or self.filename
             # todo: concatenate descriptions of multiple blocks if different
         if "session_start_time" not in annotations:
-            raise Exception("Writing to NWB requires an annotation 'session_start_time'")
+            annotations["session_start_time"] = blocks[0].rec_datetime
+            if annotations["session_start_time"] is None:
+                raise Exception("Writing to NWB requires an annotation 'session_start_time'")
+        self.annotations = {"rec_datetime": "rec_datetime"}
+        self.annotations["rec_datetime"] = blocks[0].rec_datetime
         # todo: handle subject
-        # todo: store additional Neo annotations somewhere in NWB file
         nwbfile = NWBFile(**annotations)
-
         assert self.nwb_file_mode in ('w',)  # possibly expand to 'a'ppend later
         if self.nwb_file_mode == "w" and os.path.exists(self.filename):
             os.remove(self.filename)
@@ -514,8 +517,9 @@ def _write_segment(self, nwbfile, segment, electrodes):
         for i, signal in enumerate(
                 chain(segment.analogsignals, segment.irregularlysampledsignals)):
             assert signal.segment is segment
+            signal.name = "%s %s %i" % (signal.name, segment.name, i)
             if not signal.name:
-                signal.name = "%s : analogsignal%d" % (segment.name, i)
+                signal.name = "%s : analogsignal%d %i" % (segment.name, i, i)
             self._write_signal(nwbfile, signal, electrodes)
 
         for i, train in enumerate(segment.spiketrains):
@@ -526,6 +530,7 @@ def _write_segment(self, nwbfile, segment, electrodes):
 
         for i, event in enumerate(segment.events):
             assert event.segment is segment
+            event.name = "%s  %s %i" % (event.name, segment.name, i)
             if not event.name:
                 event.name = "%s : event%d" % (segment.name, i)
             self._write_event(nwbfile, event)
@@ -626,7 +631,8 @@ class AnalogSignalProxy(BaseAnalogSignalProxy):
     common_metadata_fields = (
         # fields that are the same for all TimeSeries subclasses
         "comments", "description", "unit", "starting_time", "timestamps", "rate",
-        "data", "starting_time_unit", "timestamps_unit", "electrode"
+        "data", "starting_time_unit", "timestamps_unit", "electrode",
+        "stream_id",
     )
 
     def __init__(self, timeseries, nwb_group):

neo/test/iotest/test_nwbio.py

@@ -63,16 +63,18 @@ def test_roundtrip(self):
             for seg in blk.segments:  # AnalogSignal objects
 
                 # 3 Neo AnalogSignals
-                a = AnalogSignal(np.random.randn(44, num_chan) * pq.nA,
+                a = AnalogSignal(name='Signal_a %s' % (seg.name),
+                                 signal=np.random.randn(44, num_chan) * pq.nA,
                                  sampling_rate=10 * pq.kHz,
                                  t_start=50 * pq.ms)
-                b = AnalogSignal(np.random.randn(64, num_chan) * pq.mV,
+                b = AnalogSignal(name='Signal_b %s' % (seg.name),
+                                 signal=np.random.randn(64, num_chan) * pq.mV,
                                  sampling_rate=8 * pq.kHz,
                                  t_start=40 * pq.ms)
-                c = AnalogSignal(np.random.randn(33, num_chan) * pq.uA,
+                c = AnalogSignal(name='Signal_c %s' % (seg.name),
+                                 signal=np.random.randn(33, num_chan) * pq.uA,
                                  sampling_rate=10 * pq.kHz,
                                  t_start=120 * pq.ms)
-
                 # 2 Neo IrregularlySampledSignals
                 d = IrregularlySampledSignal(np.arange(7.0) * pq.ms,
                                              np.random.randn(7, num_chan) * pq.mV)
@@ -83,7 +85,8 @@ def test_roundtrip(self):
                 # todo: add waveforms
 
                 # 1 Neo Event
-                evt = Event(times=np.arange(0, 30, 10) * pq.ms,
+                evt = Event(name='Event',
+                            times=np.arange(0, 30, 10) * pq.ms,
                             labels=np.array(['ev0', 'ev1', 'ev2']))
 
                 # 2 Neo Epochs
@@ -228,17 +231,17 @@ def test_roundtrip_with_annotations(self):
 
         nwbfile = pynwb.NWBHDF5IO(test_file_name, mode="r").read()
 
-        self.assertIsInstance(nwbfile.acquisition["response"], pynwb.icephys.CurrentClampSeries)
-        self.assertIsInstance(nwbfile.stimulus["stimulus"],
+        self.assertIsInstance(nwbfile.acquisition[response.name], pynwb.icephys.CurrentClampSeries)
+        self.assertIsInstance(nwbfile.stimulus[stimulus.name],
                               pynwb.icephys.CurrentClampStimulusSeries)
-        self.assertEqual(nwbfile.acquisition["response"].bridge_balance,
+        self.assertEqual(nwbfile.acquisition[response.name].bridge_balance,
                          response_annotations["nwb:bridge_balance"])
 
         ior = NWBIO(filename=test_file_name, mode='r')
         retrieved_block = ior.read_all_blocks()[0]
 
-        original_response = original_block.segments[0].filter(name="response")[0]
-        retrieved_response = retrieved_block.segments[0].filter(name="response")[0]
+        original_response = original_block.segments[0].filter(name=response.name)[0]
+        retrieved_response = retrieved_block.segments[0].filter(name=response.name)[0]
         for attr_name in ("name", "units", "sampling_rate", "t_start"):
             retrieved_attribute = getattr(retrieved_response, attr_name)
             original_attribute = getattr(original_response, attr_name)