enhance location plot robustness, load .nc location

handle NAV2 with intermittent missing values

data move test

pep8

vers

MANIFEST.in

@@ -1,2 +1,3 @@
 include LICENSE
 recursive-include tests *.py
+recursive-include tests/data *

georinex/nav2.py

@@ -108,7 +108,12 @@ def rinexnav2(fn: Path,
 
         for i in svi:
             it = np.nonzero(timesu == times[i])[0][0]  # int by defn
-            data[:, it, j] = [float(raws[i][k*Lf:(k+1)*Lf]) for k in range(len(fields))]
+            """
+            some files sometimes drop the last measurement, this fixes that.
+            It assumes the blank is always in the last measurement for now.
+            """
+            dvec = [float(raws[i][k*Lf:(k+1)*Lf]) for k in range(min(len(fields), len(raws[i])//Lf))]
+            data[:len(dvec), it, j] = dvec
 
 # %% assemble output
     # NOTE: time must be datetime64[ns] or .to_netcdf will fail

georinex/plots.py

@@ -1,6 +1,7 @@
 import xarray
 import pandas
 import logging
+import numpy as np
 from matplotlib.pyplot import figure
 
 try:
@@ -55,7 +56,10 @@ def receiver_locations(locs: pandas.DataFrame):
         else:  # large or undefined interval
             c = 'b'
 
-        ax.scatter(loc.lon, loc.lat, s=1000*1/loc.interval, c=c, label=name)
+        if np.isfinite(loc.interval):
+            ax.scatter(loc.lon, loc.lat, s=1000*1/loc.interval, c=c, label=name)
+        else:
+            ax.scatter(loc.lon, loc.lat, c=c, label=name)
 
 
 def navtimeseries(nav: xarray.Dataset):

georinex/utils.py

@@ -13,6 +13,10 @@
 
 def globber(path: Path, glob: Sequence[str]) -> List[Path]:
 
+    path = Path(path).expanduser()
+    if path.is_file():
+        return [path]
+
     if isinstance(glob, str):
         glob = [glob]
 
@@ -69,10 +73,14 @@ def getlocations(flist: Sequence[Path]) -> pandas.DataFrame:
                             columns=['lat', 'lon', 'interval'])
 
     for f in flist:
-        try:
-            hdr = rinexheader(f)
-        except ValueError:
-            continue
+        if f.suffix == '.nc':
+            dat = xarray.open_dataset(f, group='OBS')
+            hdr = dat.attrs
+        else:
+            try:
+                hdr = rinexheader(f)
+            except ValueError:
+                continue
 
         if 'position_geodetic' not in hdr:
             continue

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = georinex
-version = 1.6.7
+version = 1.6.7.1
 author = Michael Hirsch, Ph.D.
 author_email = [email protected]
 description = Python RINEX 2/3 NAV/OBS reader with speed and simplicity.

tests/test_batch_convert.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 import georinex as gr
 
-R = Path(__file__).parent
+R = Path(__file__).parent / 'data'
 
 
 def test_obs():

tests/test_conv.py

@@ -12,7 +12,7 @@
 import os
 WIN32 = os.name == 'nt'
 #
-R = Path(__file__).parent
+R = Path(__file__).parent / 'data'
 
 
 @pytest.mark.xfail(WIN32, reason='Windows PermissionError for missing files')

tests/test_hatanaka.py

@@ -6,7 +6,7 @@
 from datetime import datetime
 import os
 
-R = Path(__file__).parent
+R = Path(__file__).parent / 'data'
 Rexe = Path(__file__).resolve().parents[1] / 'rnxcmp'
 exe = './crx2rnx'
 shell = False

tests/test_nav2.py

@@ -5,9 +5,10 @@
 from pathlib import Path
 from datetime import datetime
 import georinex as gr
+import numpy as np
 import tempfile
 #
-R = Path(__file__).parent
+R = Path(__file__).parent / 'data'
 
 
 def test_blank():
@@ -74,6 +75,24 @@ def test_mangled():
     assert times == datetime(2018, 6, 22, 8)
 
 
+def test_mangled2():
+    fn = R/'brdc2420.18n.gz'
+
+    nav = gr.load(fn)
+
+    G10 = nav.sel(sv='G10').dropna(dim='time', how='all')
+    assert G10['Crc'].values == approx([221.59375, 225.7421875])
+    assert np.isnan(G10['FitIntvl'][0])
+    assert G10['FitIntvl'][1] == approx(4)
+
+    times = nav.time.values.astype('datetime64[us]').astype(datetime)
+    assert (times == [datetime(2018, 8, 29, 22, 0),
+                      datetime(2018, 8, 29, 23, 0),
+                      datetime(2018, 8, 29, 23, 30),
+                      datetime(2018, 8, 29, 23, 59, 12),
+                      datetime(2018, 8, 29, 23, 59, 44)]).all()
+
+
 def test_tlim():
     pytest.importorskip('unlzw')
 

tests/test_nav3.py

@@ -6,7 +6,7 @@
 import tempfile
 from datetime import datetime
 #
-R = Path(__file__).parent
+R = Path(__file__).parent / 'data'
 
 
 def test_blank():

tests/test_obs2.py

@@ -8,7 +8,7 @@
 import numpy as np
 from datetime import datetime
 #
-R = Path(__file__).parent
+R = Path(__file__).parent / 'data'
 
 
 def test_blank():

tests/test_obs3.py

@@ -8,7 +8,7 @@
 import georinex as gr
 import tempfile
 #
-R = Path(__file__).parent
+R = Path(__file__).parent / 'data'
 
 
 def test_blank():

tests/test_scripts.py

@@ -7,7 +7,7 @@
 from pathlib import Path
 import tempfile
 
-R = Path(__file__).parent
+R = Path(__file__).parent / 'data'
 
 
 def test_convenience():