refactor: improve argument parsing of dates inputs: startTime, endTim…

…e and csvStartTime

The changes in this commit allow more flexible date inputs e.g. '2000-12-31T23:59:59', '2000-12-31 23:59:59', '12/31/2000 23:59:59' etc. should all work.

src/accelerometer/accProcess.py

@@ -44,13 +44,13 @@ def main():  # noqa: C901
                             minutes. Not to be confused with timezone offsets.
                             (default : %(default)s""")
     parser.add_argument('--startTime',
-                        metavar='e.g. 1991-01-01T23:59', default=None,
-                        type=str2date, help="""removes data before this
+                        metavar='e.g. 2000-12-31 23:59:59', default=None,
+                        type=str, help="""removes data before this
                             time (local) in the final analysis
                             (default : %(default)s)""")
     parser.add_argument('--endTime',
-                        metavar='e.g 1991-01-01T23:59', default=None,
-                        type=str2date, help="""removes data after this
+                        metavar='e.g 2000-12-31 23:59:59', default=None,
+                        type=str, help="""removes data after this
                             time (local) in the final analysis
                             (default : %(default)s)""")
     parser.add_argument('--processInputFile',
@@ -75,8 +75,8 @@ def main():  # noqa: C901
                         help="""Filter ENMOtrunc values?
                              (default : %(default)s)""")
     parser.add_argument('--csvStartTime',
-                        metavar='e.g. 2020-01-01T00:01', default=None,
-                        type=str2date, help="""start time for csv file
+                        metavar='e.g. 2000-12-31 23:59:59', default=None,
+                        type=str, help="""start time for csv file
                             when time column is not available
                             (default : %(default)s)""")
     parser.add_argument('--csvSampleRate',
@@ -281,10 +281,10 @@ def deleteIntermediateFiles():
 
     # Check user-specified end time is not before start time
     if args.startTime and args.endTime:
-        assert args.startTime <= args.endTime, (
+        assert pd.Timestamp(args.startTime) <= pd.Timestamp(args.endTime), (
             "startTime and endTime arguments are invalid!\n"
-            f"startTime: {args.startTime.strftime('%Y-%m-%dT%H:%M')}\n"
-            f"endTime:, {args.endTime.strftime('%Y-%m-%dT%H:%M')}\n"
+            f"startTime: {args.startTime}\n"
+            f"endTime: {args.endTime}\n"
         )
 
     # Print processing options to screen
@@ -367,32 +367,6 @@ def str2bool(v):
     return v.lower() in ("yes", "true", "t", "1")
 
 
-def str2date(v):
-    """
-    Used to parse date values from the command line. E.g. "1994-11-30T12:00" -> time.datetime
-    """
-
-    eg = "1994-11-30T12:00"  # example date
-    if v.count("-") != eg.count("-"):
-        print("ERROR: Not enough dashes in date")
-    elif v.count("T") != eg.count("T"):
-        print("ERROR: No T seperator in date")
-    elif v.count(":") != eg.count(":"):
-        print("ERROR: No ':' seperator in date")
-    elif len(v.split("-")[0]) != 4:
-        print("ERROR: Year in date must be 4 numbers")
-    elif len(v.split("-")[1]) != 2 and len(v.split("-")[1]) != 1:
-        print("ERROR: Month in date must be 1-2 numbers")
-    elif len(v.split("-")[2].split("T")[0]) != 2 and len(v.split("-")[2].split("T")[0]) != 1:
-        print("ERROR: Day in date must be 1-2 numbers")
-    else:
-        return pd.datetime.strptime(v, "%Y-%m-%dT%H:%M")
-    print("Please change your input date:")
-    print('"' + v + '"')
-    print("to match the example date format:")
-    print('"' + eg + '"')
-    raise ValueError("Date in incorrect format")
-
 
 if __name__ == '__main__':
     main()  # Standard boilerplate to call the main() function to begin the program.

src/accelerometer/device.py

@@ -4,6 +4,7 @@
 import gzip
 import numpy as np
 import os
+import dateutil
 import pandas as pd
 import statsmodels.api as sm
 import struct
@@ -104,7 +105,7 @@ def processInputFileToEpoch(  # noqa: C901
             if javaHeapSpace:
                 commandArgs.insert(1, javaHeapSpace)
             if csvStartTime:
-                commandArgs.append("csvStartTime:" + csvStartTime.strftime("%Y-%m-%dT%H:%M"))
+                commandArgs.append("csvStartTime:" + to_iso_datetime(csvStartTime))
             if csvSampleRate:
                 commandArgs.append("csvSampleRate:" + str(csvSampleRate))
             if csvTimeFormat:
@@ -163,9 +164,9 @@ def processInputFileToEpoch(  # noqa: C901
         if javaHeapSpace:
             commandArgs.insert(1, javaHeapSpace)
         if startTime:
-            commandArgs.append("startTime:" + startTime.strftime("%Y-%m-%dT%H:%M"))
+            commandArgs.append("startTime:" + to_iso_datetime(startTime))
         if endTime:
-            commandArgs.append("endTime:" + endTime.strftime("%Y-%m-%dT%H:%M"))
+            commandArgs.append("endTime:" + to_iso_datetime(endTime))
         if csvStartTime:
             commandArgs.append("csvStartTime:" + csvStartTime.strftime("%Y-%m-%dT%H:%M"))
         if csvSampleRate:
@@ -531,3 +532,9 @@ def getGT3XDeviceId(gt3xFile):
      this usually occurs when the file is not an Actigraph .gt3x accelerometer
      file. Exiting...""")
     sys.exit(-8)
+
+
+def to_iso_datetime(dt):
+    """ Given input string representing a datetime, return its ISO formatted
+    datetime string. """
+    return dateutil.parser.parse(dt).isoformat()

src/accelerometer/summarisation.py

@@ -1,6 +1,5 @@
 """Module to generate overall activity summary from epoch data."""
 import sys
-import pytz
 import numpy as np
 import pandas as pd
 from pandas.tseries.frequencies import to_offset
@@ -73,13 +72,10 @@ def getActivitySummary(  # noqa: C901
 
     # Remove data before/after user specified start/end times
     rows = data.shape[0]
-    tz = pytz.timezone(timeZone)
     if startTime:
-        localStartTime = tz.localize(startTime)
-        data = data[data.index >= localStartTime]
+        data = data.loc[pd.Timestamp(startTime, tz=timeZone):]
     if endTime:
-        localEndTime = tz.localize(endTime)
-        data = data[data.index <= localEndTime]
+        data = data.loc[:pd.Timestamp(endTime, tz=timeZone)]
     # Quit if no data left
     if data.shape[0] == 0:
         print("No rows remaining after start/end time removal")