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

sociality-task
primoz 2022-06-02 11:43:49 +00:00
parent fbf6a77dfc
commit d300f0f8f0
5 changed files with 29 additions and 7 deletions

2
.gitignore vendored
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@ -114,7 +114,7 @@ sn_profile_*/
settings.dcf settings.dcf
tests/fakedata_generation/ tests/fakedata_generation/
site/ site/
credentials.yaml !credentials.yaml
# Docker container and other files # Docker container and other files
.devcontainer .devcontainer

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

7
credentials.yaml 100644
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@ -0,0 +1,7 @@
PSQL_STRAW:
database: staw
user: staw_db
password: kizi-x2yf-mate
host: 212.235.208.113
port: 5432

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

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@ -68,8 +68,11 @@ def extract_empatica_data(data, sensor):
elif sensor == 'EMPATICA_INTER_BEAT_INTERVAL': elif sensor == 'EMPATICA_INTER_BEAT_INTERVAL':
df = pd.read_csv(sensor_data_file, names=['timestamp', column], header=None) df = pd.read_csv(sensor_data_file, names=['timings', column], header=None)
df['timings'] = df['timestamp'] df['timestamp'] = df['timings']
if df.empty:
df = df.set_index('timestamp')
return df
timestampstart = float(df['timestamp'][0]) timestampstart = float(df['timestamp'][0])
df['timestamp'] = (df['timestamp'][1:len(df)]).astype(float) + timestampstart df['timestamp'] = (df['timestamp'][1:len(df)]).astype(float) + timestampstart
df = df.drop([0]) 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 = BytesIO(ibi_data).getvalue().decode('utf-8')
ibi_data_file = StringIO(ibi_data_file) 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) 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 = BytesIO(bvp_data).getvalue().decode('utf-8')
bvp_data_file = StringIO(bvp_data_file) 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, winsorize_value=25, hampel_fiter=False, median_filter=False,
mod_z_score_filter=True, sampling=64, feature_names=['meanHr']) 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 = \ df = \
pd.DataFrame(np.array([ibi_timings, ibi_rr]).transpose(), columns=['timestamp', 'inter_beat_interval']) pd.DataFrame(np.array([ibi_timings, ibi_rr]).transpose(), columns=['timestamp', 'inter_beat_interval'])