Start with mhealth geolocation reader

niimpy/config/config.ini

@@ -15,8 +15,9 @@ studentlife_activity = %(sample_data)s/sl_activity.csv
 sqlite_singleuser= %(sample_data)s/singleuser.sqlite3
 sqlite_multiuser= %(sample_data)s/multiuser.sqlite3
 
-mhealth_total_sleep_time= %(sample_data)s/mhealth_total_sleep_time.json
-mhealth_heart_rate= %(sample_data)s/mhealth_heart_rate.json
+mhealth_total_sleep_time = %(sample_data)s/mhealth_total_sleep_time.json
+mhealth_heart_rate = %(sample_data)s/mhealth_heart_rate.json
+mhealth_geolocation = %(sample_data)s/mhealth_geolocation.json
 
 [plotly_settings]
 

niimpy/config/config.py

@@ -23,3 +23,4 @@
 SQLITE_MULTIUSER_PATH =os.path.join(ROOT, config['sample_paths']['sqlite_multiuser']) 
 MHEALTH_TOTAL_SLEEP_TIME_PATH = os.path.join(ROOT, config['sample_paths']['mhealth_total_sleep_time'])
 MHEALTH_HEART_RATE_PATH = os.path.join(ROOT, config['sample_paths']['mhealth_heart_rate'])
+MHEALTH_GEOLOCATION_PATH = os.path.join(ROOT, config['sample_paths']['mhealth_geolocation'])

niimpy/reading/mhealth.py

@@ -258,6 +258,7 @@ def heart_rate(data_list):
     Returns
     -------
 
+    data: A pandas.DataFrame containing geolocation data
     '''
     df = pd.json_normalize(data_list)
 
@@ -325,3 +326,56 @@ def heart_rate_from_file(filename):
     df = heart_rate(data)
 
     return df
+
+
+
+def geolocation(data_list):
+    ''' Format the geolocation json data into a niimpy dataframe.
+
+    Parameters
+    ----------
+
+    data_list: list of dictionaries
+        MHealth formatted geolocation data loaded using json.load().
+
+    Returns
+    -------
+
+    data: A pandas.DataFrame containing geolocation data
+    '''
+    df = pd.json_normalize(data_list)
+
+    # Keep rows where latitude and longitude are given correctly
+    df = df[df["latitude.unit"] == "deg"]
+    df = df[df["longitude.unit"] == "deg"]
+    df.rename(columns={
+        "latitude.value": "latitude",
+        "longitude.value": "longitude",
+    }, inplace=True)
+
+    return df
+
+
+def geolocation_from_file(filename):
+    '''Read mHealth formatted geolocation data from a file and convert it to
+    a Niimpy compatible dataframe.  
+
+    Parameters
+    ----------
+
+    filename: string
+        Path to the file containing mhealth formatted geolocation data.
+    
+    Returns
+    -------
+
+    data: A pandas.DataFrame containing geolocation data
+    '''
+
+    with open(filename) as f:
+        data = json.load(f)
+
+    df = geolocation(data)
+
+    return df
+

niimpy/sampledata/mhealth_geolocation.json

@@ -0,0 +1,40 @@
+[
+    {
+        "latitude": {
+            "value": 60.1867,
+            "unit": "deg"
+        },
+        "longitude": {
+            "value": 24.8283,
+            "unit": "deg"
+        },
+        "effective_time_frame": {
+            "time_interval": {
+                "start_date_time": "2016-02-05T20:35:00-08:00",
+                "end_date_time": "2016-02-06T06:35:00-08:00"
+            }
+        },
+        "positioning_system": "GPS"
+    },
+    {
+        "latitude": {
+            "value": 60.1867,
+            "unit": "deg"
+        },
+        "longitude": {
+            "value": 24.8283,
+            "unit": "deg"
+        },
+        "elevation": {
+            "value": 20.4,
+            "unit": "m"
+        },
+        "effective_time_frame": {
+            "time_interval": {
+                "start_date_time": "2016-02-05T20:35:00-08:00",
+                "end_date_time": "2016-02-06T06:35:00-08:00"
+            }
+        },
+        "positioning_system": "GPS"
+    }
+]

tests/reading/test_read_mhealth.py

@@ -67,7 +67,6 @@ def test_format_time_interval():
 
 
 def test_read_mhealth_total_sleep_time():
-    """test reading mixed mhealth data from the example file."""
     data = niimpy.reading.mhealth.total_sleep_time_from_file(config.MHEALTH_TOTAL_SLEEP_TIME_PATH)
     assert data['total_sleep_time'][0] == pd.Timedelta(465, unit="minutes")
     assert data['descriptive_statistic'][1] == "average"
@@ -81,7 +80,6 @@ def test_read_mhealth_total_sleep_time():
 
 
 def test_read_mhealth_heart_rate():
-    """test reading mixed mhealth data from the example file."""
     data = niimpy.reading.mhealth.heart_rate_from_file(config.MHEALTH_HEART_RATE_PATH)
     assert data['heart_rate'][0] == 70
     assert data['heart_rate'][1] == 65
@@ -91,3 +89,11 @@ def test_read_mhealth_heart_rate():
     assert data['start'][2] == pd.to_datetime("2023-12-20T01:50:00-02:00")
 
 
+def test_read_mhealth_geolocation():
+    data = niimpy.reading.mhealth.geolocation_from_file(config.MHEALTH_GEOLOCATION_PATH)
+
+    assert data['latitude'][0] == 60.1867
+    assert data['longitude'][0] == 24.8283
+    assert data['latitude'][1] == 60.1867
+    assert data['longitude'][1] == 24.8283
+