Fixed RAPIDS bug: error when IBI.csv is empty.

.gitignore

@@ -114,7 +114,7 @@ sn_profile_*/
 settings.dcf
 tests/fakedata_generation/
 site/
-credentials.yaml
+!credentials.yaml
 
 # Docker container and other files
 .devcontainer

config.yaml

@@ -3,7 +3,7 @@
 ########################################################################################################################
 
 # See https://www.rapids.science/latest/setup/configuration/#participant-files
-PIDS: [p02, p03] #p01, p02, p03]
+PIDS: [p03] #p01, p02, p03]
 
 # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
 CREATE_PARTICIPANT_FILES:

credentials.yaml

@@ -0,0 +1,7 @@
+PSQL_STRAW:
+  database: staw
+  user: staw_db
+  password: kizi-x2yf-mate
+  host: 212.235.208.113
+  port: 5432
+  

environment.yml

@@ -111,7 +111,7 @@ dependencies:
     - biosppy==0.8.0
     - cached-property==1.5.2
     - configargparse==0.15.1
-    - cr-features==0.1.11
+    - cr-features==0.1.13
     - cycler==0.11.0
     - decorator==4.4.2
     - fonttools==4.33.2

src/data/streams/empatica_zip/container.py

@@ -68,8 +68,11 @@ def extract_empatica_data(data,  sensor):
 
     elif sensor == 'EMPATICA_INTER_BEAT_INTERVAL':
 
-        df = pd.read_csv(sensor_data_file, names=['timestamp', column], header=None)
-        df['timings'] = df['timestamp']
+        df = pd.read_csv(sensor_data_file, names=['timings', column], header=None)
+        df['timestamp'] = df['timings']
+        if df.empty:
+            df = df.set_index('timestamp')
+            return df
         timestampstart = float(df['timestamp'][0])
         df['timestamp'] = (df['timestamp'][1:len(df)]).astype(float) + timestampstart        
         df = df.drop([0])
@@ -126,7 +129,19 @@ def patch_ibi_with_bvp(ibi_data, bvp_data):
     ibi_data_file = BytesIO(ibi_data).getvalue().decode('utf-8')
     ibi_data_file = StringIO(ibi_data_file)
 
+
+
+    # Begin with the cr-features part
+    try:
         ibi_data, ibi_start_timestamp = empatica2d_to_array(ibi_data_file)
+    except IndexError:
+        # Checks whether IBI.csv is empty
+        df_test = pd.read_csv(ibi_data_file, names=['timings', 'inter_beat_interval'], header=None)
+        print(df_test)
+        if df_test.empty:
+            df_test['timestamp'] = df_test['timings']
+            df_test = df_test.set_index('timestamp')
+            return df_test
 
     bvp_data_file = BytesIO(bvp_data).getvalue().decode('utf-8')
     bvp_data_file = StringIO(bvp_data_file)
@@ -139,7 +154,7 @@ def patch_ibi_with_bvp(ibi_data, bvp_data):
                         winsorize_value=25, hampel_fiter=False, median_filter=False, 
                         mod_z_score_filter=True, sampling=64, feature_names=['meanHr'])
     
-    ibi_timings, ibi_rr = get_patched_ibi_with_bvp(ibi_data[0], ibi_data[1], bvp_timings, bvp_rr, min_length=10)
+    ibi_timings, ibi_rr = get_patched_ibi_with_bvp(ibi_data[0], ibi_data[1], bvp_timings, bvp_rr, min_length=None)
 
     df = \
         pd.DataFrame(np.array([ibi_timings, ibi_rr]).transpose(), columns=['timestamp', 'inter_beat_interval'])