Merge pull request #185 from c-proof/fix-mission-number

Fix mission number

pyglider/ncprocess.py

@@ -312,7 +312,7 @@ def make_gridfiles(inname, outdir, deploymentyaml, *, fnamesuffix='', dz=1, star
     # https://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/build/aphs06.html
     dsout.attrs['featureType'] = 'trajectoryProfile'
     dsout['profile'].attrs['cf_role'] = 'profile_id'
-    dsout['mission_number'] = int(1)
+    dsout['mission_number'] = np.int32(1)
     dsout['mission_number'].attrs['cf_role'] = 'trajectory_id'
     dsout = dsout.set_coords(['latitude', 'longitude', 'time'])
     for k in dsout:

pyglider/slocum.py

@@ -789,7 +789,8 @@ def raw_to_timeseries(indir, outdir, deploymentyaml, *,
 def binary_to_timeseries(indir, cachedir, outdir, deploymentyaml, *,
                          search='*.[D|E]BD', fnamesuffix='',
                          time_base='sci_water_temp', profile_filt_time=100,
-                         profile_min_time=300, maxgap=300):
+                         profile_min_time=300, maxgap=300,
+                         replace_attrs=None):
     """
     Convert directly from binary files to netcdf timeseries file.  Requires
     dbdreader to be installed.
@@ -821,6 +822,11 @@ def binary_to_timeseries(indir, cachedir, outdir, deploymentyaml, *,
     profile_min_time : float
         minimum time to consider a profile an actual profile (seconds)
 
+    replace_attrs : dict or None
+        replace global attributes in the metadata after reading the metadata
+        file in.  Helpful when processing runs with only a couple things that
+        change.
+
     Returns
     -------
     outname : string
@@ -831,6 +837,9 @@ def binary_to_timeseries(indir, cachedir, outdir, deploymentyaml, *,
         raise ImportError('Cannot import dbdreader')
 
     deployment = utils._get_deployment(deploymentyaml)
+    if replace_attrs:
+        for att in replace_attrs:
+            deployment['metadata'][att] = replace_attrs[att]
 
     ncvar = deployment['netcdf_variables']
     device_data = deployment['glider_devices']

pyglider/utils.py

@@ -7,6 +7,7 @@
 from scipy.signal import argrelextrema
 import gsw
 import logging
+from pathlib import Path
 import yaml
 
 
@@ -28,11 +29,15 @@ def get_distance_over_ground(ds):
     ds : `.xarray.Dataset`
         With ``distance_over_ground`` key.
     """
+
     good = ~np.isnan(ds.latitude + ds.longitude)
-    dist = gsw.distance(ds.longitude[good].values, ds.latitude[good].values)/1000
-    dist = np.roll(np.append(dist, 0), 1)
-    dist = np.cumsum(dist)
-    dist = np.interp(ds.time, ds.time[good], dist)
+    if np.any(good):
+        dist = gsw.distance(ds.longitude[good].values, ds.latitude[good].values)/1000
+        dist = np.roll(np.append(dist, 0), 1)
+        dist = np.cumsum(dist)
+        dist = np.interp(ds.time, ds.time[good], dist)
+    else:
+        dist = 0 * ds.latitude.values
     attr = {'long_name': 'distance over ground flown since mission start',
             'method': 'get_distance_over_ground',
             'units': 'km',
@@ -464,10 +469,17 @@ def fill_metadata(ds, metadata, sensor_data):
 
     """
     good = ~np.isnan(ds.latitude.values + ds.longitude.values)
-    ds.attrs['geospatial_lat_max'] = np.max(ds.latitude.values[good])
-    ds.attrs['geospatial_lat_min'] = np.min(ds.latitude.values[good])
-    ds.attrs['geospatial_lon_max'] = np.max(ds.longitude.values[good])
-    ds.attrs['geospatial_lon_min'] = np.min(ds.longitude.values[good])
+    if np.any(good):
+        ds.attrs['geospatial_lat_max'] = np.max(ds.latitude.values[good])
+        ds.attrs['geospatial_lat_min'] = np.min(ds.latitude.values[good])
+        ds.attrs['geospatial_lon_max'] = np.max(ds.longitude.values[good])
+        ds.attrs['geospatial_lon_min'] = np.min(ds.longitude.values[good])
+    else:
+        ds.attrs['geospatial_lat_max'] = np.nan
+        ds.attrs['geospatial_lat_min'] = np.nan
+        ds.attrs['geospatial_lon_max'] = np.nan
+        ds.attrs['geospatial_lon_min'] = np.nan
+
     ds.attrs['geospatial_lat_units'] = 'degrees_north'
     ds.attrs['geospatial_lon_units'] = 'degrees_east'
     ds.attrs['netcdf_version'] = '4.0'  # TODO get this somehow...
@@ -711,6 +723,40 @@ def _get_deployment(deploymentyaml):
     return deployment
 
 
+def _any_newer(dirname, filename):
+    """
+    Check if any files in dirname are newer than filename
+    """
+    filename = Path(filename)
+    dirname = Path(dirname)
+    print(filename, filename.exists())
+    if not filename.exists():
+        return True
+
+    mod_time = filename.stat().st_mtime
+    is_newer = False
+    for file_path in dirname.iterdir():
+        if file_path.is_file():
+            if file_path.stat().st_mtime > mod_time:
+                is_newer = True
+                break
+
+    return is_newer
+
+
+def _get_glider_name_slocum(current_directory):
+    glider = current_directory.parts[-2]
+    mission = current_directory.parts[-1]
+    print(f'Glider {glider} and mission: {mission}')
+    slocum_glider = glider[4:]
+    if slocum_glider[-4:-3].isnumeric():
+        slocum_glider = slocum_glider[:-4] + '_' + slocum_glider[-4:]
+    else:
+        slocum_glider = slocum_glider[:-3] + '_' + slocum_glider[-3:]
+
+    return glider, mission, slocum_glider
+
+
 __all__ = ['get_distance_over_ground', 'get_glider_depth', 'get_profiles_new',
            'get_derived_eos_raw', "fill_metadata", "nmea2deg",
            "gappy_fill_vertical", "oxygen_concentration_correction"]