Small misc changes

2022-06-02 06:41:53 +00:00 · 2022-06-02 06:41:53 +00:00 · fbf6a77dfc
parent 5532043b1f
commit fbf6a77dfc
4 changed files with 229 additions and 224 deletions
--- a/config.yaml
+++ b/config.yaml
@ -3,7 +3,7 @@
 ########################################################################################################################

 # See https://www.rapids.science/latest/setup/configuration/#participant-files
-PIDS: [p01] #p01, p02, p03]
+PIDS: [p02, p03] #p01, p02, p03]

 # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files
 CREATE_PARTICIPANT_FILES:
@ -484,18 +484,11 @@ EMPATICA_ACCELEROMETER:
      FEATURES: ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
      SRC_SCRIPT: src/features/empatica_accelerometer/dbdp/main.py
    CR:
-      COMPUTE: False
-      FEATURES: ["fqHighestPeakFreqs", "fqHighestPeaks", "fqEnergyFeat", "fqEntropyFeat", "fqHistogramBins","fqAbsMean", "fqSkewness", "fqKurtosis", "fqInterquart", # Freq features
-                  "meanLow", "areaLow", "totalAbsoluteAreaBand", "totalMagnitudeBand", "entropyBand", "skewnessBand", "kurtosisBand", 
-                  "postureDistanceLow", "absoluteMeanBand", "absoluteAreaBand", "quartilesBand", "interQuartileRangeBand", "varianceBand", 
-                  "coefficientOfVariationBand", "amplitudeBand", "totalEnergyBand", "dominantFrequencyEnergyBand", "meanCrossingRateBand", 
-                  "correlationBand", "quartilesMagnitudesBand", "interQuartileRangeMagnitudesBand", "areaUnderAccelerationMagnitude", 
-                  "peaksDataLow", "sumPerComponentBand", "velocityBand", "meanKineticEnergyBand", "totalKineticEnergyBand", "squareSumOfComponent", 
-                  "sumOfSquareComponents", "averageVectorLength", "averageVectorLengthPower", "rollAvgLow", "pitchAvgLow", "rollStdDevLow", 
-                  "pitchStdDevLow", "rollMotionAmountLow", "rollMotionRegularityLow", "manipulationLow", "rollPeaks", "pitchPeaks", "rollPitchCorrelation"] # Acc features
+      COMPUTE: True
+      FEATURES: ["totalMagnitudeBand", "absoluteMeanBand", "varianceBand"] # Acc features
      WINDOWS:
        COMPUTE: True
-        WINDOW_LENGTH: 10 # specify window length in seconds
+        WINDOW_LENGTH: 15 # specify window length in seconds
        SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'max', 'min']
      SRC_SCRIPT: src/features/empatica_accelerometer/cr/main.py

@ -518,15 +511,12 @@ EMPATICA_TEMPERATURE:
      FEATURES: ["maxtemp", "mintemp", "avgtemp", "mediantemp", "modetemp", "stdtemp", "diffmaxmodetemp", "diffminmodetemp", "entropytemp"]
      SRC_SCRIPT: src/features/empatica_temperature/dbdp/main.py
    CR:
-      COMPUTE: False
-      FEATURES: ["autocorrelations", "countAboveMean", "countBelowMean", "maximum", "minimum", "meanAbsChange", "longestStrikeAboveMean", 
-                  "longestStrikeBelowMean", "stdDev", "median", "meanChange", "numberOfZeroCrossings", "absEnergy", "linearTrendSlope", 
-                  "ratioBeyondRSigma", "binnedEntropy", "numOfPeaksAutocorr", "numberOfZeroCrossingsAutocorr", "areaAutocorr",
-                  "calcMeanCrossingRateAutocorr", "countAboveMeanAutocorr", "sumPer", "sumSquared", "squareSumOfComponent", 
-                  "sumOfSquareComponents"]
+      COMPUTE: True
+      FEATURES: ["countAboveMean", "countBelowMean", "maximum", "minimum", "meanAbsChange", "longestStrikeAboveMean", "longestStrikeBelowMean", 
+                  "stdDev", "median", "meanChange", "sumSquared", "squareSumOfComponent", "sumOfSquareComponents"]
      WINDOWS:
        COMPUTE: True
-        WINDOW_LENGTH: 600 # specify window length in seconds
+        WINDOW_LENGTH: 300 # specify window length in seconds
        SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'max', 'min']
      SRC_SCRIPT: src/features/empatica_temperature/cr/main.py

@ -539,15 +529,15 @@ EMPATICA_ELECTRODERMAL_ACTIVITY:
      FEATURES: ["maxeda", "mineda", "avgeda", "medianeda", "modeeda", "stdeda", "diffmaxmodeeda", "diffminmodeeda", "entropyeda"]
      SRC_SCRIPT: src/features/empatica_electrodermal_activity/dbdp/main.py
    CR:
-      COMPUTE: False
+      COMPUTE: True
      FEATURES: ['mean', 'std', 'q25', 'q75', 'qd', 'deriv', 'power', 'numPeaks', 'ratePeaks', 'powerPeaks', 'sumPosDeriv', 'propPosDeriv', 'derivTonic', 
                  'sigTonicDifference', 'freqFeats','maxPeakAmplitudeChangeBefore', 'maxPeakAmplitudeChangeAfter', 'avgPeakAmplitudeChangeBefore', 
                  'avgPeakAmplitudeChangeAfter', 'avgPeakChangeRatio', 'maxPeakIncreaseTime', 'maxPeakDecreaseTime', 'maxPeakDuration', 'maxPeakChangeRatio',
-                  'avgPeakIncreaseTime', 'avgPeakDecreaseTime', 'avgPeakDuration', 'maxPeakResponseSlopeBefore', 'maxPeakResponseSlopeAfter', 
-                  'signalOverallChange', 'changeDuration', 'changeRate', 'significantIncrease', 'significantDecrease']
+                  'avgPeakIncreaseTime', 'avgPeakDecreaseTime', 'avgPeakDuration', 'signalOverallChange', 'changeDuration', 'changeRate', 'significantIncrease', 
+                  'significantDecrease']
      WINDOWS:
        COMPUTE: True
-        WINDOW_LENGTH: 300 # specify window length in seconds
+        WINDOW_LENGTH: 60 # specify window length in seconds
        SECOND_ORDER_FEATURES: ['mean', 'median', 'sd', 'max', 'min']
      SRC_SCRIPT: src/features/empatica_electrodermal_activity/cr/main.py

@ -560,7 +550,7 @@ EMPATICA_BLOOD_VOLUME_PULSE:
      FEATURES: ["maxbvp", "minbvp", "avgbvp", "medianbvp", "modebvp", "stdbvp", "diffmaxmodebvp", "diffminmodebvp", "entropybvp"]
      SRC_SCRIPT: src/features/empatica_blood_volume_pulse/dbdp/main.py
    CR:
-      COMPUTE: False
+      COMPUTE: True
      FEATURES: ['meanHr', 'ibi', 'sdnn', 'sdsd', 'rmssd', 'pnn20', 'pnn50', 'sd', 'sd2', 'sd1/sd2', 'numRR', # Time features
                  'VLF', 'LF', 'LFnorm', 'HF', 'HFnorm', 'LF/HF', 'fullIntegral'] # Freq features
      WINDOWS:
--- a/renv.lock
+++ b/renv.lock
--- a/renv/activate.R
+++ b/renv/activate.R
@ -15,9 +15,6 @@ local({
  Sys.setenv("RENV_R_INITIALIZING" = "true")
  on.exit(Sys.unsetenv("RENV_R_INITIALIZING"), add = TRUE)

-  if(grepl("Darwin", Sys.info()["sysname"], fixed = TRUE) & grepl("ARM64", Sys.info()["version"], fixed = TRUE)) # M1 Macs
-    Sys.setenv("TZDIR" = file.path(R.home(), "share", "zoneinfo"))
-
  # signal that we've consented to use renv
  options(renv.consent = TRUE)

--- a/tests/scripts/missing_values_heatmap.py
+++ b/tests/scripts/missing_values_heatmap.py
@ -0,0 +1,18 @@
+import pandas as pd
+import seaborn as sns
+import matplotlib.pyplot as plt
+
+
+# path = "/rapids/data/processed/features/all_participants/all_sensor_features.csv" # all features all participants
+# path = "/rapids/data/interim/p03/empatica_accelerometer_features/empatica_accelerometer_python_cr_windows.csv" 
+path = "/rapids/data/interim/p02/empatica_electrodermal_activity_features/empatica_electrodermal_activity_python_cr_windows.csv" 
+# path = "/rapids/data/interim/p02/empatica_inter_beat_interval_features/empatica_inter_beat_interval_python_cr_windows.csv" 
+# path = "/rapids/data/interim/p02/empatica_blood_volume_pulse_features/empatica_blood_volume_pulse_python_cr_windows.csv" 
+# path = "/rapids/data/interim/p02/empatica_temperature_features/empatica_temperature_python_cr_windows.csv" 
+
+df = pd.read_csv(path)
+print(df)
+sns.heatmap(df.isna(), cbar=False)
+plt.savefig('eda_windows_p02_window_60_more_peaks.png', bbox_inches='tight')
+
+