diff --git a/.gitignore b/.gitignore index 6cf83e29..e783159f 100644 --- a/.gitignore +++ b/.gitignore @@ -114,7 +114,7 @@ sn_profile_*/ settings.dcf tests/fakedata_generation/ site/ -credentials.yaml +!credentials.yaml # Docker container and other files .devcontainer diff --git a/config.yaml b/config.yaml index 5aba8dde..248342e1 100644 --- a/config.yaml +++ b/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: diff --git a/credentials.yaml b/credentials.yaml new file mode 100644 index 00000000..7b20cd95 --- /dev/null +++ b/credentials.yaml @@ -0,0 +1,7 @@ +PSQL_STRAW: + database: staw + user: staw_db + password: kizi-x2yf-mate + host: 212.235.208.113 + port: 5432 + \ No newline at end of file diff --git a/environment.yml b/environment.yml index 19e4a252..b0faa871 100644 --- a/environment.yml +++ b/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 diff --git a/src/data/streams/empatica_zip/container.py b/src/data/streams/empatica_zip/container.py index 80224893..f1fe9bcd 100644 --- a/src/data/streams/empatica_zip/container.py +++ b/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) - ibi_data, ibi_start_timestamp = empatica2d_to_array(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'])