Merge pull request #584 from LinkedEarth/depth_nans

Depth nans

pyleoclim/core/geoseries.py

@@ -167,7 +167,17 @@ def __init__(self, time, value, lat, lon, elevation = None, time_unit=None, time
                 time_name='Time'
         else:
             pass
-
+
+        if dropna:
+            if depth is not None:
+                matrix = np.array([time,value,depth])
+                matrix = tsbase.dropna_matrix(matrix)
+                time = matrix[0,:]
+                value = matrix[1,:]
+                depth = matrix[2,:]
+            else:
+                pass
+
         # assign latitude
         if lat is not None:
             lat = float(lat) 

pyleoclim/tests/test_core_GeoSeries.py

@@ -45,6 +45,47 @@ def multiple_pinkgeoseries(nrecs = 20, seed = 108, geobox=[-85.0,85.0,-180,180])
 
     return pyleo.MultipleGeoSeries(ts_list, label='Multiple Pink GeoSeries')
 
+class TestUIGeoSeriesInit:
+    ''' Test for GeoSeries instantiation '''
+
+    def test_init_no_dropna_depth(self, evenly_spaced_series):
+            ts = evenly_spaced_series
+            t = ts.time
+            v = ts.value
+            d = np.arange(len(t))
+            v[0] = np.nan
+            ts2 = pyleo.GeoSeries(time=t,value=v,depth=d,dropna=False, verbose=False,lat=0,lon=0)
+            assert np.isnan(ts2.value[0])
+            assert ts2.depth[0] == d[0]
+
+    def test_init_dropna_depth(self, evenly_spaced_series):
+            ts = evenly_spaced_series
+            t = ts.time
+            v = ts.value
+            d = np.arange(len(t))
+            v[0] = np.nan
+            ts2 = pyleo.GeoSeries(time=t,value=v,depth=d,dropna=True, verbose=False,lat=0,lon=0)
+            print(ts2.value)
+            assert ~np.isnan(ts2.value[0])
+            assert ts2.depth[0] == d[1]
+
+    def test_init_no_dropna(self, evenly_spaced_series):
+            ts = evenly_spaced_series
+            t = ts.time
+            v = ts.value
+            v[0] = np.nan
+            ts2 = pyleo.GeoSeries(time=t,value=v,dropna=False, verbose=False,lat=0,lon=0)
+            assert np.isnan(ts2.value[0])
+
+    def test_init_dropna(self, evenly_spaced_series):
+            ts = evenly_spaced_series
+            t = ts.time
+            v = ts.value
+            v[0] = np.nan
+            ts2 = pyleo.GeoSeries(time=t,value=v,dropna=True, verbose=False,lat=0,lon=0)
+            print(ts2.value)
+            assert ~np.isnan(ts2.value[0])
+
 @pytest.mark.xfail   # will fail until pandas is fixed
 class TestUIGeoSeriesResample():
     ''' test GeoSeries.Resample()

pyleoclim/utils/tsbase.py

@@ -384,6 +384,36 @@ def dropna(ys, ts, verbose=False):
 
     return ys, ts
 
+def dropna_matrix(matrix, verbose=False):
+    '''Drop NaN values from matrix
+
+    Remove columns from matrix that contain nans
+
+    Parameters
+    ----------
+    matrix : array
+        A matrix, NaNs allowed
+    verbose : bool
+        If True, will print a warning message
+
+    Returns
+    -------
+    matrix : array
+        The matrix without nans
+
+    See Also
+    --------
+
+    https://pandas.pydata.org/docs/reference/api/pandas.Series.dropna.html
+
+    '''
+    matrix = matrix[:, ~np.isnan(matrix).any(axis=0)]
+
+    if verbose and any(np.isnan(matrix)):
+        print('NaNs have been detected and dropped.')
+
+    return matrix
+
 def sort_ts(ys, ts, ascending = True, verbose=False):
     ''' Sort timeseries