Add comments for event_related_script understanding.

src/features/phone_esm/straw/process_user_event_related_segments.py

@@ -10,6 +10,15 @@ from esm import classify_sessions_by_completion_time, preprocess_esm
 input_data_files = dict(snakemake.input)
 
 def format_timestamp(x):
+    """This method formates inputed timestamp into format "HH MM SS". Including spaces. If there is no hours or minutes present
+    that part is ignored, e.g., "MM SS" or just "SS". 
+
+    Args:
+        x (int): unix timestamp in seconds
+
+    Returns:
+        str: formatted timestamp using "HH MM SS" sintax
+    """
     tstring=""
     space = False
     if x//3600 > 0:
@@ -23,8 +32,23 @@ def format_timestamp(x):
     return tstring
 
 
-def extract_ers(esm_df, device_id): 
+def extract_ers(esm_df):
+    """This method has two major functionalities: 
+        (1) It prepares STRAW event-related segments file with the use of esm file. The execution protocol is depended on 
+            the targets method specified in the config.yaml file.
+        (2) It prepares and writes csv with targets and corresponding time segments labels. This is later used 
+            in the overall cleaning script (straw).
     
+    Details about each target method are listed below by each corresponding condition. Refer to the RAPIDS documentation for the 
+    ERS file format: https://www.rapids.science/1.9/setup/configuration/#time-segments -> event segments
+
+    Args:
+        esm_df (DataFrame): read esm file that is dependend on the current participant.
+
+    Returns:
+        extracted_ers (DataFrame): dataframe with all necessary information to write event-related segments file 
+        in the correct format.
+    """
     pd.set_option("display.max_rows", 20)
     pd.set_option("display.max_columns", None)
 
@@ -42,6 +66,10 @@ def extract_ers(esm_df, device_id):
     
     targets_method = config["TIME_SEGMENTS"]["TAILORED_EVENTS"]["TARGETS_METHOD"]
     if targets_method in ["30_before", "90_before"]: # takes 30-minute peroid before the questionnaire + the duration of the questionnaire
+    """ '30-minutes and 90-minutes before' have the same fundamental logic with couple of deviations that will be explained below.
+    Both take x-minute period before the questionnaire that is summed with the questionnaire duration.
+    All questionnaire durations over 15 minutes are excluded from the querying.
+    """
         # Extract time-relevant information
         extracted_ers = esm_df.groupby(["device_id", "esm_session"])['timestamp'].apply(lambda x: math.ceil((x.max() - x.min()) / 1000)).reset_index() # questionnaire length
         extracted_ers["label"] = f"straw_event_{targets_method}_" + snakemake.params["pid"] + "_" + extracted_ers.index.astype(str).str.zfill(3) 
@@ -50,6 +78,9 @@ def extract_ers(esm_df, device_id):
         extracted_ers["shift_direction"] = -1 
 
         if targets_method == "30_before":
+        """The method 30-minutes before simply takes 30 minutes before the questionnaire and sums it with the questionnaire duration.
+        The timestamps are formatted with the help of format_timestamp() method.
+        """
             time_before_questionnaire = 30 * 60 # in seconds (30 minutes)
 
             extracted_ers["length"] = (extracted_ers["timestamp"] + time_before_questionnaire).apply(lambda x: format_timestamp(x))
@@ -57,6 +88,9 @@ def extract_ers(esm_df, device_id):
             extracted_ers["shift"] = extracted_ers["shift"].apply(lambda x: format_timestamp(x))
         
         elif targets_method == "90_before":
+        """The method 90-minutes before has an important condition. If the time between the current and the previous questionnaire is
+        longer then 90 minutes it takes 90 minutes, otherwise it takes the original time difference between the questionnaires.
+        """
             time_before_questionnaire = 90 * 60 # in seconds (90 minutes)
 
             extracted_ers[['end_event_timestamp', 'device_id']] = esm_df.groupby(["device_id", "esm_session"])['timestamp'].max().reset_index()[['timestamp', 'device_id']]
@@ -70,6 +104,17 @@ def extract_ers(esm_df, device_id):
             extracted_ers["shift"] = extracted_ers["diffs"].apply(lambda x: format_timestamp(x))
 
     elif targets_method == "stress_event":
+        """This is a special case of the method as it consists of two important parts:
+            (1) Generating of the ERS file (same as the methods above) and
+            (2) Generating targets file alongside with the correct time segment labels.
+        
+        This extracts event-related segments, depended on the event time and duration specified by the participant in the next
+        questionnaire. Additionally, 5 minutes before the specified start time of this event is taken to take into a account the 
+        possiblity of the participant not remembering the start time percisely => this parameter can be manipulated with the variable
+        "time_before_event" which is defined below. 
+        
+        By default, this method also excludes all events that are longer then 2.5 hours so that the segments are easily comparable. 
+        """
         # Get and join required data
         extracted_ers = esm_df.groupby(["device_id", "esm_session"])['timestamp'].apply(lambda x: math.ceil((x.max() - x.min()) / 1000)).reset_index().rename(columns={'timestamp': 'session_length'}) # questionnaire end timestamp
         extracted_ers = extracted_ers[extracted_ers["session_length"] <= 15 * 60].reset_index(drop=True) # ensure that the longest duration of the questionnaire anwsering is 15 min
@@ -83,7 +128,9 @@ def extract_ers(esm_df, device_id):
                                      .join(se_duration, on=['device_id', 'esm_session'], how='inner') \
                                      .join(se_intensity, on=['device_id', 'esm_session'], how='inner')
                             
-        # Filter sessions that are not useful
+        # Filter sessions that are not useful. Because of the ambiguity this excludes: 
+        # (1) straw event times that are marked as "0 - I don't remember"
+        # (2) straw event durations that are marked as "0 - I don't remember" 
         extracted_ers = extracted_ers[(~extracted_ers.se_time.str.startswith("0 - ")) & (~extracted_ers.se_duration.str.startswith("0 - "))]
 
         # Transform data into its final form, ready for the extraction
@@ -93,6 +140,8 @@ def extract_ers(esm_df, device_id):
         extracted_ers['event_timestamp'] = pd.to_datetime(extracted_ers['se_time']).apply(lambda x: x.timestamp() * 1000).astype('int64')
         extracted_ers['shift_direction'] = -1
 
+        # Checks whether the duration is marked with "1 - It's still ongoing" which means that the end of the current questionnaire
+        # is taken as end time of the segment. Else the user input duration is taken. 
         extracted_ers['se_duration'] = \
             np.where(
                 extracted_ers['se_duration'].str.startswith("1 - "),
@@ -100,15 +149,18 @@ def extract_ers(esm_df, device_id):
                 extracted_ers['se_duration']
             )
 
+        # This converts the rows of timestamps in miliseconds and the row with datetime to timestamp in seconds.
         extracted_ers['se_duration'] = \
             extracted_ers['se_duration'].apply(lambda x: math.ceil(x / 1000) if isinstance(x, int) else (pd.to_datetime(x).hour * 60 + pd.to_datetime(x).minute) * 60) + time_before_event
 
-        extracted_ers = extracted_ers[extracted_ers["se_duration"] <= 2.5 * 60 * 60].reset_index(drop=True) # Exclude events that are longer than 2.5 hours
+        # Exclude events that are longer than 2.5 hours
+        extracted_ers = extracted_ers[extracted_ers["se_duration"] <= 2.5 * 60 * 60].reset_index(drop=True) 
 
         extracted_ers["label"] = f"straw_event_{targets_method}_" + snakemake.params["pid"] + "_" + extracted_ers.index.astype(str).str.zfill(3)
         extracted_ers['shift'] = format_timestamp(time_before_event)
         extracted_ers['length'] = extracted_ers['se_duration'].apply(lambda x: format_timestamp(x))
 
+        # Write the csv of extracted ERS labels with targets (stress event intensity)   
         extracted_ers[["label", "intensity"]].to_csv(snakemake.output[1], index=False)
         
     else:
@@ -118,14 +170,20 @@ def extract_ers(esm_df, device_id):
     return extracted_ers[["label", "event_timestamp", "length", "shift", "shift_direction", "device_id"]]
 
 
-# Actual code execution
+"""
+Here the code is executed - this .py file is used both for extraction of the STRAW time_segments file for the individual
+participant, and also for merging all participant's files into one combined file which is later used for assignments of the
+time segments to all sensors.
+
+There are two files involved (see rules extract_event_information_from_esm and merge_event_related_segments_files in preprocessing.smk)
+(1) ERS file which contains all the information about the time segment timings and
+(2) targets file which has corresponding target value for the segment label which is later used to merge with other features in the cleaning script.
+For more information, see the comment in the method above.
+"""
 if snakemake.params["stage"] == "extract": 
     esm_df = pd.read_csv(input_data_files['esm_raw_input'])
 
-    with open(input_data_files['pid_file'], 'r') as stream:
+    extracted_ers = extract_ers(esm_df)
-        pid_file = yaml.load(stream, Loader=yaml.FullLoader)
-
-    extracted_ers = extract_ers(esm_df, pid_file["PHONE"]["DEVICE_IDS"][0])
 
     extracted_ers.to_csv(snakemake.output[0], index=False)