Merge pull request #116 from zmoon/fix/openaq

Fix OpenAQ reader

monetio/obs/openaq.py

@@ -93,16 +93,20 @@ def add_data(self, dates, num_workers=1):
         dfs = [dask.delayed(self.read_json)(f) for f in urls]
         dff = dd.from_delayed(dfs)
         z = dff.compute(num_workers=num_workers)
-        z.coordinates.replace(to_replace=[None], value=pd.np.nan, inplace=True)
+        z.coordinates.replace(to_replace=[None], value=NaN, inplace=True)
         z = z.dropna().reset_index(drop=True)
         js = json.loads(z[["coordinates", "date"]].to_json(orient="records"))
         dff = pd.io.json.json_normalize(js)
         dff.columns = dff.columns.str.split(".").str[1]
         dff.rename({"local": "time_local", "utc": "time"}, axis=1, inplace=True)
 
         dff["time"] = pd.to_datetime(dff.time)
-        dff["time_local"] = pd.to_datetime(dff.time_local)
+        dff["utcoffset"] = pd.to_datetime(dff.time_local).apply(lambda x: x.utcoffset())
         zzz = z.join(dff).drop(columns=["coordinates", "date", "attribution", "averagingPeriod"])
+        zzz = self._fix_units(zzz)
+        assert (
+            zzz[~zzz.parameter.isin(["pm25", "pm4", "pm10", "bc"])].unit.dropna() == "ppm"
+        ).all()
         zp = self._pivot_table(zzz)
         zp["siteid"] = (
             zp.country
@@ -114,8 +118,8 @@ def add_data(self, dates, num_workers=1):
         )
 
         zp["time"] = zp.time.dt.tz_localize(None)
-        tzinfo = zp.time_local.apply(lambda x: x.tzinfo.utcoffset(x))
-        zp["time_local"] = zp["time"] + tzinfo
+        zp["time_local"] = zp["time"] + zp["utcoffset"]
+
         return zp.loc[zp.time >= dates.min()]
 
     def read_json(self, url):
@@ -161,10 +165,17 @@ def local(x):
 
     def _fix_units(self, df):
         df.loc[df.value <= 0] = NaN
-        df.loc[(df.parameter == "co") & (df.unit != "ppm"), "value"] /= 1145
-        df.loc[(df.parameter == "o3") & (df.unit != "ppm"), "value"] /= 2000
-        df.loc[(df.parameter == "so2") & (df.unit != "ppm"), "value"] /= 2620
-        df.loc[(df.parameter == "no2") & (df.unit != "ppm"), "value"] /= 1880
+        # For a certain parameter, different site-times may have different units.
+        # https://docs.openaq.org/docs/parameters
+        # These conversion factors are based on
+        # - air average molecular weight: 29 g/mol
+        # - air density: 1.2 kg m -3
+        # rounded to 3 significant figures.
+        fs = {"co": 1160, "o3": 1990, "so2": 2650, "no2": 1900, "ch4": 664, "no": 1240}
+        for vn, f in fs.items():
+            is_ug = (df.parameter == vn) & (df.unit == "µg/m³")
+            df.loc[is_ug, "value"] /= f
+            df.loc[is_ug, "unit"] = "ppm"
         return df
 
     def _pivot_table(self, df):
@@ -178,7 +189,7 @@ def _pivot_table(self, df):
                 "sourceType",
                 "city",
                 "country",
-                "time_local",
+                "utcoffset",
             ],
             columns="parameter",
         ).reset_index()
@@ -188,10 +199,13 @@ def _pivot_table(self, df):
                 o3="o3_ppm",
                 no2="no2_ppm",
                 so2="so2_ppm",
+                ch4="ch4_ppm",
+                no="no_ppm",
                 bc="bc_umg3",
                 pm25="pm25_ugm3",
                 pm10="pm10_ugm3",
             ),
             axis=1,
+            errors="ignore",
         )
         return w

tests/test_openaq.py

@@ -0,0 +1,17 @@
+import sys
+
+import pandas as pd
+import pytest
+
+from monetio import openaq
+
+
+@pytest.mark.skipif(sys.version_info < (3, 7), reason="requires Python 3.7+")
+def test_openaq():
+    # First date in the archive, just one file
+    # Browse the archive at https://openaq-fetches.s3.amazonaws.com/index.html
+    dates = pd.date_range(start="2013-11-26", end="2013-11-27", freq="H")[:-1]
+    df = openaq.add_data(dates)
+    assert not df.empty
+    assert df.siteid.nunique() == 1
+    assert (df.country == "CN").all() and ((df.time_local - df.time) == pd.Timedelta(hours=8)).all()