User/wbodo/add row names to analog (#498)

NovelaNeuro · Jul 22, 2020 · 9401bf1 · 9401bf1
1 parent 255964a
commit 9401bf1
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Showing 6 changed files with 24 additions and 11 deletions.
diff --git a/rec_to_nwb/processing/nwb/components/analog/analog_creator.py b/rec_to_nwb/processing/nwb/components/analog/analog_creator.py
@@ -14,6 +14,7 @@ def create(cls, fl_analog, unit):
         behavioral_events.add_timeseries(
             AnalogCreator.__build_timeseries(
                 name='analog',
+                description=fl_analog.description,
                 data=fl_analog.data,
                 timestamps=fl_analog.timestamps,
                 unit=unit
@@ -27,9 +28,9 @@ def __create_behavioral_events():
         return BehavioralEvents(name="analog")
 
     @staticmethod
-    def __build_timeseries(name, data, timestamps, unit):
+    def __build_timeseries(name, description, data, timestamps, unit):
         return TimeSeries(name=name,
-                          description='-',
+                          description=description,
                           data=data,
                           timestamps=timestamps,
                           unit=unit

diff --git a/rec_to_nwb/processing/nwb/components/analog/fl_analog.py b/rec_to_nwb/processing/nwb/components/analog/fl_analog.py
@@ -1,5 +1,6 @@
 class FlAnalog:
 
-    def __init__(self, data, timestamps):
+    def __init__(self, data, timestamps, description):
         self.data = data
-        self.timestamps = timestamps
+        self.timestamps = timestamps
+        self.description = description
diff --git a/rec_to_nwb/processing/nwb/components/analog/fl_analog_builder.py b/rec_to_nwb/processing/nwb/components/analog/fl_analog_builder.py
@@ -4,5 +4,5 @@
 class FlAnalogBuilder:
 
     @staticmethod
-    def build(data, timestamps):
-        return FlAnalog(data, timestamps)
+    def build(data, timestamps, description):
+        return FlAnalog(data, timestamps, description)
diff --git a/rec_to_nwb/processing/nwb/components/analog/fl_analog_extractor.py b/rec_to_nwb/processing/nwb/components/analog/fl_analog_extractor.py
@@ -20,7 +20,7 @@ def extract_analog_for_single_dataset(analog_files, continuous_time_file):
             if not 'timestamps' in analog_file:
                 analog_data = readTrodesExtractedDataFile(analog_files[analog_file])
                 values = analog_data['data']
-                single_dataset_data[analog_file] = values
+                single_dataset_data[analog_data['id']] = values
             else:
                 continuous_time_dict = ContinuousTimeExtractor.get_continuous_time_dict_file(continuous_time_file)
                 timestamp = readTrodesExtractedDataFile(analog_files[analog_file])
@@ -29,3 +29,5 @@ def extract_analog_for_single_dataset(analog_files, continuous_time_file):
         return single_dataset_data
 
 
+
+
diff --git a/rec_to_nwb/processing/nwb/components/analog/fl_analog_manager.py b/rec_to_nwb/processing/nwb/components/analog/fl_analog_manager.py
@@ -30,17 +30,26 @@ def get_analog(self) -> FlAnalog:
                 )
             )
         merged_epochs = self.__merge_epochs(all_analog_data)
+        description = self.__merge_row_description(all_analog_data)
         analog_data = self.__merge_analog_sensors(merged_epochs)
-        return FlAnalogBuilder.build(analog_data, self.__get_timestamps(merged_epochs))
+        return FlAnalogBuilder.build(analog_data, self.__get_timestamps(merged_epochs), description)
 
     @staticmethod
     def __merge_epochs(data_from_multiple_datasets):
         merged_epochs = data_from_multiple_datasets[0]
         for single_dataset_data in data_from_multiple_datasets[1:]:
-            for analog_file in single_dataset_data.keys():
-                merged_epochs[analog_file] = np.hstack((merged_epochs[analog_file], single_dataset_data[analog_file]))
+            for row in single_dataset_data.keys():
+                merged_epochs[row] = np.hstack((merged_epochs[row], single_dataset_data[row]))
         return merged_epochs
 
+    @staticmethod
+    def __merge_row_description(data_from_multiple_datasets):
+        row_ids = data_from_multiple_datasets[0].keys()
+        description = ''
+        for id in row_ids:
+            description += id + '   '
+        return description
+
     @classmethod
     def __merge_analog_sensors(cls, merged_epochs):
         analog_sensors = [merged_epochs[analog_sensor] for analog_sensor in merged_epochs.keys() if 'timestamp' not in analog_sensor]

diff --git a/rec_to_nwb/test/processing/analog/test_analogCreator.py b/rec_to_nwb/test/processing/analog/test_analogCreator.py
@@ -24,7 +24,7 @@ def setUp(self):
         )
 
         self.timestamp = numpy.array([1, 2, 3, 4])
-        self.fl_analog = FlAnalog(self.data, self.timestamp)
+        self.fl_analog = FlAnalog(self.data, self.timestamp, 'description')
 
     def test_creator_create_analog_successfully(self):
         analog = AnalogCreator.create(self.fl_analog, 'um')