Testing different EDA findPeaks parameters.
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c851ab0763
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@ -118,3 +118,6 @@ site/
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# Docker container and other files
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# Docker container and other files
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.devcontainer
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.devcontainer
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# Calculating features module
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calculatingfeatures/
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@ -3,7 +3,7 @@
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########################################################################################################################
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########################################################################################################################
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# See https://www.rapids.science/latest/setup/configuration/#participant-files
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# See https://www.rapids.science/latest/setup/configuration/#participant-files
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PIDS: [p01] #p01, p02, p03]
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PIDS: [p02] #p01, p02, p03]
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# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
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# See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
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CREATE_PARTICIPANT_FILES:
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CREATE_PARTICIPANT_FILES:
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@ -536,7 +536,7 @@ EMPATICA_ELECTRODERMAL_ACTIVITY:
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'sigTonicDifference', 'freqFeats','maxPeakAmplitudeChangeBefore', 'maxPeakAmplitudeChangeAfter', 'avgPeakAmplitudeChangeBefore',
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'sigTonicDifference', 'freqFeats','maxPeakAmplitudeChangeBefore', 'maxPeakAmplitudeChangeAfter', 'avgPeakAmplitudeChangeBefore',
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'avgPeakAmplitudeChangeAfter', 'avgPeakChangeRatio', 'maxPeakIncreaseTime', 'maxPeakDecreaseTime', 'maxPeakDuration', 'maxPeakChangeRatio',
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'avgPeakAmplitudeChangeAfter', 'avgPeakChangeRatio', 'maxPeakIncreaseTime', 'maxPeakDecreaseTime', 'maxPeakDuration', 'maxPeakChangeRatio',
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'avgPeakIncreaseTime', 'avgPeakDecreaseTime', 'avgPeakDuration', 'signalOverallChange', 'changeDuration', 'changeRate', 'significantIncrease',
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'avgPeakIncreaseTime', 'avgPeakDecreaseTime', 'avgPeakDuration', 'signalOverallChange', 'changeDuration', 'changeRate', 'significantIncrease',
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'significantDecrease', maxPeakResponseSlopeBefore, maxPeakResponseSlopeAfter]
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'significantDecrease']
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WINDOWS:
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WINDOWS:
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COMPUTE: True
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COMPUTE: True
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WINDOW_LENGTH: 60 # specify window length in seconds
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WINDOW_LENGTH: 60 # specify window length in seconds
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@ -30,11 +30,13 @@ def extract_eda_features_from_intraday_data(eda_intraday_data, features, window_
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if window_length is None:
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if window_length is None:
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eda_intraday_features = \
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eda_intraday_features = \
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eda_intraday_data.groupby('local_segment').apply(\
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eda_intraday_data.groupby('local_segment').apply(\
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lambda x: extractGsrFeatures2D(convert_to2d(x['electrodermal_activity'], x.shape[0]), sampleRate=sample_rate, featureNames=features))
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lambda x: extractGsrFeatures2D(convert_to2d(x['electrodermal_activity'], x.shape[0]), sampleRate=sample_rate, featureNames=features,
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threshold=.01, offset=1, riseTime=5, decayTime=15))
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else:
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else:
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eda_intraday_features = \
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eda_intraday_features = \
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eda_intraday_data.groupby('local_segment').apply(\
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eda_intraday_data.groupby('local_segment').apply(\
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lambda x: extractGsrFeatures2D(convert_to2d(x['electrodermal_activity'], window_length*sample_rate), sampleRate=sample_rate, featureNames=features))
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lambda x: extractGsrFeatures2D(convert_to2d(x['electrodermal_activity'], window_length*sample_rate), sampleRate=sample_rate, featureNames=features,
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threshold=.01, offset=1, riseTime=5, decayTime=15))
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eda_intraday_features.reset_index(inplace=True)
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eda_intraday_features.reset_index(inplace=True)
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@ -2,10 +2,11 @@ import pandas as pd
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import seaborn as sns
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import seaborn as sns
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import matplotlib.pyplot as plt
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import matplotlib.pyplot as plt
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participant = "p02"
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# path = "/rapids/data/processed/features/all_participants/all_sensor_features.csv" # all features all participants
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# path = "/rapids/data/processed/features/all_participants/all_sensor_features.csv" # all features all participants
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# path = "/rapids/data/interim/p03/empatica_accelerometer_features/empatica_accelerometer_python_cr_windows.csv"
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# path = "/rapids/data/interim/p03/empatica_accelerometer_features/empatica_accelerometer_python_cr_windows.csv"
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path = "/rapids/data/interim/p01/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_cr_windows.csv"
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path = f"/rapids/data/interim/{participant}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_temperature_features/empatica_temperature_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_temperature_features/empatica_temperature_python_cr_windows.csv"
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@ -15,9 +16,13 @@ print(df)
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is_NaN = df.isnull()
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is_NaN = df.isnull()
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row_has_NaN = is_NaN.any(axis=1)
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row_has_NaN = is_NaN.any(axis=1)
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rows_with_NaN = df[row_has_NaN]
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rows_with_NaN = df[row_has_NaN]
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print(rows_with_NaN.size)
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print("All rows:", len(df.index))
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print("\nCount NaN vals:", rows_with_NaN.size)
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print("\nDf mean:")
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print(df.mean())
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sns.heatmap(df.isna(), cbar=False)
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sns.heatmap(df.isna(), cbar=False)
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plt.savefig('eda_windows_p02_window_60_thresh_default.png', bbox_inches='tight')
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plt.savefig(f'eda_{participant}_windows_NaN.png', bbox_inches='tight')
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@ -3,9 +3,11 @@ import seaborn as sns
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import matplotlib.pyplot as plt
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import matplotlib.pyplot as plt
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from itertools import compress
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from itertools import compress
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participant = "p02"
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# path = "/rapids/data/processed/features/all_participants/all_sensor_features.csv" # all features all participants
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# path = "/rapids/data/processed/features/all_participants/all_sensor_features.csv" # all features all participants
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# path = "/rapids/data/interim/p03/empatica_accelerometer_features/empatica_accelerometer_python_cr_windows.csv"
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# path = "/rapids/data/interim/p03/empatica_accelerometer_features/empatica_accelerometer_python_cr_windows.csv"
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path = "/rapids/data/interim/p01/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_cr_windows.csv"
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path = f"/rapids/data/interim/{participant}/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_temperature_features/empatica_temperature_python_cr_windows.csv"
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# path = "/rapids/data/interim/p02/empatica_temperature_features/empatica_temperature_python_cr_windows.csv"
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@ -17,9 +19,6 @@ columns_num_peaks_zero = df_num_peaks_zero.columns[df_num_peaks_zero.isna().any(
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df_num_peaks_non_zero = df[df["empatica_electrodermal_activity_cr_numPeaks"] != 0]
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df_num_peaks_non_zero = df[df["empatica_electrodermal_activity_cr_numPeaks"] != 0]
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df_num_peaks_non_zero = df_num_peaks_non_zero[columns_num_peaks_zero]
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df_num_peaks_non_zero = df_num_peaks_non_zero[columns_num_peaks_zero]
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print(df_num_peaks_non_zero[df_num_peaks_non_zero["empatica_electrodermal_activity_cr_maxPeakAmplitudeChangeBefore"] != 0])
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pd.set_option('display.max_columns', None)
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pd.set_option('display.max_columns', None)
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df_q = pd.DataFrame()
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df_q = pd.DataFrame()
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@ -27,7 +26,7 @@ for col in df_num_peaks_non_zero:
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df_q[col] = pd.to_numeric(pd.cut(df_num_peaks_non_zero[col], bins=[-1,0,0.000000000001,1000], labels=[-1,0,1], right=False))
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df_q[col] = pd.to_numeric(pd.cut(df_num_peaks_non_zero[col], bins=[-1,0,0.000000000001,1000], labels=[-1,0,1], right=False))
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sns.heatmap(df_q)
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sns.heatmap(df_q)
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plt.savefig('eda_windows_p01_window_values_non_zero_peak_distribution_0thresh.png', bbox_inches='tight')
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plt.savefig(f'eda_{participant}_window_non_zero_peak_other_vals.png', bbox_inches='tight')
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plt.close()
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plt.close()
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# Filter columns that do not contain 0
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# Filter columns that do not contain 0
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