Empatica zips must be placed in pid folder and small fixes

Snakefile

@@ -367,18 +367,19 @@ for provider in config["EMPATICA_INTER_BEAT_INTERVAL"]["PROVIDERS"].keys():
         files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
         files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
 
-for provider in config["EMPATICA_TAGS"]["PROVIDERS"].keys():
-    if config["EMPATICA_TAGS"]["PROVIDERS"][provider]["COMPUTE"]:
-        for pid in config["PIDS"]:
-            suffixes = get_zip_suffixes(pid)
-            files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_unzipped_{suffix}.csv", pid=pid, suffix=suffixes))
-            files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_raw_{suffix}.csv", pid=pid, suffix=suffixes))
-        files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_joined.csv", pid=config["PIDS"]))
-        files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_with_datetime.csv", pid=config["PIDS"]))
-        files_to_compute.extend(expand("data/interim/{pid}/empatica_tags_features/empatica_tags_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["EMPATICA_TAGS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
-        files_to_compute.extend(expand("data/processed/features/{pid}/empatica_tags.csv", pid=config["PIDS"]))
-        files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
-        files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
+if isinstance(config["EMPATICA_TAGS"]["PROVIDERS"], dict):
+    for provider in config["EMPATICA_TAGS"]["PROVIDERS"].keys():
+        if config["EMPATICA_TAGS"]["PROVIDERS"][provider]["COMPUTE"]:
+            for pid in config["PIDS"]:
+                suffixes = get_zip_suffixes(pid)
+                files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_unzipped_{suffix}.csv", pid=pid, suffix=suffixes))
+                files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_raw_{suffix}.csv", pid=pid, suffix=suffixes))
+            files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_joined.csv", pid=config["PIDS"]))
+            files_to_compute.extend(expand("data/raw/{pid}/empatica_tags_with_datetime.csv", pid=config["PIDS"]))
+            files_to_compute.extend(expand("data/interim/{pid}/empatica_tags_features/empatica_tags_{language}_{provider_key}.csv", pid=config["PIDS"], language=config["EMPATICA_TAGS"]["PROVIDERS"][provider]["SRC_LANGUAGE"].lower(), provider_key=provider.lower()))
+            files_to_compute.extend(expand("data/processed/features/{pid}/empatica_tags.csv", pid=config["PIDS"]))
+            files_to_compute.extend(expand("data/processed/features/{pid}/all_sensor_features.csv", pid=config["PIDS"]))
+            files_to_compute.append("data/processed/features/all_participants/all_sensor_features.csv")
 
 # Visualization for Data Exploration
 if config["HISTOGRAM_PHONE_DATA_YIELD"]["PLOT"]:

config.yaml

@@ -424,7 +424,7 @@ EMPATICA_DATA_CONFIGURATION:
 
 # See https://www.rapids.science/latest/features/fitbit-heartrate-summary/
 EMPATICA_ACCELEROMETER:
-  TABLE: acc
+  TABLE: ACC
   PROVIDERS:
     DBDP:
       COMPUTE: False
@@ -433,7 +433,7 @@ EMPATICA_ACCELEROMETER:
       SRC_LANGUAGE: "python"
 
 EMPATICA_HEARTRATE:
-  TABLE: hr
+  TABLE: HR
   PROVIDERS:
     DBDP:
       COMPUTE: False
@@ -442,7 +442,7 @@ EMPATICA_HEARTRATE:
       SRC_LANGUAGE: "python"
 
 EMPATICA_TEMPERATURE:
-  TABLE: temp
+  TABLE: TEMP
   PROVIDERS:
     DBDP:
       COMPUTE: False
@@ -451,40 +451,36 @@ EMPATICA_TEMPERATURE:
       SRC_LANGUAGE: "python"
 
 EMPATICA_ELECTRODERMAL_ACTIVITY:
-  TABLE: eda
+  TABLE: EDA
   PROVIDERS:
     DBDP:
       COMPUTE: False
       FEATURES: ["maxeda", "mineda", "avgeda", "medianeda", "modeeda", "stdeda", "diffmaxmodeeda", "diffminmodeeda", "entropyeda"]
-      SRC_FOLDER: "dbdp" # inside src/features/empatica_heartrate
+      SRC_FOLDER: "dbdp" # inside src/features/empatica_electrodermal_activity
       SRC_LANGUAGE: "python"
 
 EMPATICA_BLOOD_VOLUME_PULSE:
-  TABLE: bvp
+  TABLE: BVP
   PROVIDERS:
     DBDP:
       COMPUTE: False
       FEATURES: ["maxbvp", "minbvp", "avgbvp", "medianbvp", "modebvp", "stdbvp", "diffmaxmodebvp", "diffminmodebvp", "entropybvp"]
-      SRC_FOLDER: "dbdp" # inside src/features/empatica_heartrate
+      SRC_FOLDER: "dbdp" # inside src/features/empatica_blood_volume_pulse
       SRC_LANGUAGE: "python"
 
 EMPATICA_INTER_BEAT_INTERVAL:
-  TABLE: ibi
+  TABLE: IBI
   PROVIDERS:
     DBDP:
       COMPUTE: False
       FEATURES: ["maxibi", "minibi", "avgibi", "medianibi", "modeibi", "stdibi", "diffmaxmodeibi", "diffminmodeibi", "entropyibi"]
-      SRC_FOLDER: "dbdp" # inside src/features/empatica_heartrate
+      SRC_FOLDER: "dbdp" # inside src/features/inter_beat_interval
       SRC_LANGUAGE: "python"
 
 EMPATICA_TAGS:
-  TABLE: tags
-  PROVIDERS:
-    DBDP:
-      COMPUTE: False
-      FEATURES: []
-      SRC_FOLDER: "dbdp" # inside src/features/empatica_heartrate
-      SRC_LANGUAGE: "python"
+  TABLE: TAGS
+  PROVIDERS:  # None implemented yet
+
 
 ########################################################################################################################
 #                                                 PLOTS                                                                #

rules/common.smk

@@ -31,16 +31,11 @@ def get_phone_sensor_names():
     return phone_sensor_names
 
 from pathlib import Path
-import re
-
 def get_zip_suffixes(pid):
-    zipfiles = list(Path("data/external/empatica").rglob(pid+"*.zip"))
+    zipfiles = list((Path("data/external/empatica/") / Path(pid)).rglob("*.zip"))
     suffixes = []
-    pattern = re.compile("{}(.*)".format(pid))
     for zipfile in zipfiles:
-        name = zipfile.stem
-        results = pattern.search(name)
-        suffixes.append(results.group(1))
+        suffixes.append(zipfile.stem)
     return suffixes
 
 def get_all_raw_empatica_sensor_files(wildcards):

rules/preprocessing.smk

@@ -246,7 +246,7 @@ rule fitbit_readable_datetime:
 from pathlib import Path
 rule unzip_empatica_data:
     input:
-        input_file = Path(config["EMPATICA_DATA_CONFIGURATION"]["SOURCE"]["FOLDER"]) / Path("{pid}{suffix}.zip"),
+        input_file = Path(config["EMPATICA_DATA_CONFIGURATION"]["SOURCE"]["FOLDER"]) / Path("{pid}") / Path("{suffix}.zip"),
         participant_file = "data/external/participant_files/{pid}.yaml"
     params:
         sensor = "{sensor}"

src/features/empatica_tags/dbdp/main.py

@@ -1,21 +0,0 @@
-import pandas as pd
-import numpy as np
-
-def dbdp_features(sensor_data_files, time_segment, provider, filter_data_by_segment, *args, **kwargs):
-
-    sensor_data = pd.read_csv(sensor_data_files["sensor_data"])
-    requested_features = provider["FEATURES"]
-    # name of the features this function can compute
-    base_features_names = [] # ["maxmagnitude", "minmagnitude", "avgmagnitude", "medianmagnitude", "stdmagnitude"]
-    # the subset of requested features this function can compute
-    features_to_compute = list(set(requested_features) & set(base_features_names))
-
-    features = pd.DataFrame(columns=["local_segment"] + features_to_compute)
-    if not sensor_data.empty:
-        sensor_data = filter_data_by_segment(sensor_data, time_segment)
-        
-        if not sensor_data.empty:
-            features = pd.DataFrame()
-            
-
-    return features