Merge pull request #19 from wpreimes/master

Fix for SMOS L2 NRT

CHANGELOG.rst

@@ -2,6 +2,10 @@
 Changelog
 =========
 
+v0.3.1
+======
+- Changed the default variables reshuffled for SMOS L2 and added option to select variables
+
 v0.3.0
 ======
 - Add support for SMOS L4 RZSM product (`PR #11 <https://github.com/TUW-GEO/smos/pull/11>`_)

README.rst

@@ -96,7 +96,7 @@ Build Docker image
 ==================
 - Check out the repo at the branch/tag/commit you want bake into the image
 - Make sure you have docker installed and run the command (replace the tag `latest`
-with something more meaningful, e.g. a version number)
+  with something more meaningful, e.g. a version number)
 
 .. code::
 

environment.yml

@@ -17,9 +17,9 @@ dependencies:
     - pygeogrids
     - pynetcf
     - pyproj
-    - git+https://github.com/TUW-GEO/repurpose@master
+    - repurpose>=0.13.1
     - trollsift
     - ease_grid
     - more_itertools
     - cf-xarray==0.8.4
-    - git+https://github.com/awst-austria/qa4sm-preprocessing@master
+    - qa4sm_preprocessing==0.3

setup.cfg

@@ -37,7 +37,7 @@ install_requires =
     dask[distributed]
     xarray
     netCDF4
-    repurpose
+    repurpose>=0.13.1
     pyresample
     pygeogrids>=0.3.2
     pynetcf>=0.5.1
@@ -47,7 +47,7 @@ install_requires =
     h5py
     more_itertools
     cf-xarray==0.8.4
-    qa4sm_preprocessing>=0.2
+    qa4sm_preprocessing>=0.3
 # The usage of test_requires is discouraged, see `Dependency Management` docs
 #tests_require = pytest; pytest-cov; coverage
 # Require a specific Python version, e.g. Python 2.7 or >= 3.4

src/smos/smos_l2/cli.py

@@ -3,7 +3,7 @@
 import pandas as pd
 
 from smos.smos_l2.download import SmosDissEoFtp, L2_START_DATE
-from smos.smos_l2.reshuffle import swath2ts, extend_ts
+from smos.smos_l2.reshuffle import swath2ts, extend_ts, _default_variables
 from smos.misc import get_first_last_day_images
 
 @click.command(
@@ -138,14 +138,22 @@ def cli_update_img(path,
     default=None,
     help="Format YYYY-MM-DD | Last day to include in the"
     "time series. [default: Date of the last available image]")
+@click.option(
+    '--variables',
+    '-v',
+    type=click.STRING,
+    default=','.join(_default_variables),
+    help="List of variables in the swath files to reshuffle. Multiple variables"
+         " must be comma-separated.")
 @click.option(
     '--memory',
     '-m',
     type=click.INT,
     default=4,
     help="NUMBER | Available memory (in GB) to use to load image data. "
     "A larger buffer means faster processing.")
-def cli_reshuffle(img_path, ts_path, startdate, enddate, memory):
+def cli_reshuffle(img_path, ts_path, startdate, enddate, variables,
+                  memory):
     """
     Convert SMOS L2 image data into a (5x5 degrees chunked) time series format
     following CF conventions (Indexed Ragged format).
@@ -158,18 +166,21 @@ def cli_reshuffle(img_path, ts_path, startdate, enddate, memory):
     Required Parameters
     -------------------
     IMG_PATH: string
-        Path where previously downloaded C3S SM images are stored. Use the
-        `c3s_sm download` command to retrieve image data.
+        Path where previously downloaded SMOS images are stored. Use the
+        `smos_l2 download` command to retrieve image data.
     TS_PATH: string
         Path where the newly created time series files should be stored.
     """
     # The docstring above is slightly different to the normal python one to
     # display it properly on the command line.
     print(f"Convert image data in {img_path} to time series in {ts_path}")
 
+    variables = [str(v.strip()) for v in variables.split(',')]
+
     swath2ts(
         img_path,
         ts_path,
+        variables=variables,
         startdate=startdate,
         enddate=enddate,
         memory=int(memory))
@@ -193,7 +204,7 @@ def cli_update_ts(img_path, ts_path):
     Required Parameters
     -------------------
     IMG_PATH: string
-        Path where previously downloaded C3S SM images are stored.
+        Path where previously downloaded SMOS files are stored.
     TS_PATH: string
         Path where the time series to update are stored
     """

src/smos/smos_l2/reshuffle.py

@@ -1,12 +1,24 @@
+import numpy as np
 import pandas as pd
 import os
 import yaml
 from qa4sm_preprocessing.level2.smos import SMOSL2Reader
 from smos.misc import read_summary_yml, get_first_last_day_images
 from datetime import datetime
 
-
-def swath2ts(img_path, ts_path, startdate=None, enddate=None, memory=4):
+_default_variables = (
+    "Soil_Moisture",
+    "Science_Flags",
+    "Confidence_Flags",
+    "Chi_2_P",
+    "RFI_Prob",
+    "N_RFI_X",
+    "N_RFI_Y",
+    "M_AVA0",
+)
+
+def swath2ts(img_path, ts_path, variables=_default_variables,
+             startdate=None, enddate=None, memory=4):
     """
     Convert SMOS L2 swath data to time series in IndexedRaggedTs format.
 
@@ -17,6 +29,19 @@ def swath2ts(img_path, ts_path, startdate=None, enddate=None, memory=4):
         swath data are found.
     ts_path: str
         Local directory where the converted time series data will be stored.
+    variables: tuple or str, optional (default: None)
+        List of variables to include, None will use the default variables
+        "Soil_Moisture",
+        "Soil_Moisture_DQX",
+        "Science_Flags",
+        "Confidence_Flags",
+        "Processing_Flags",
+        "Chi_2_P",
+        "RFI_Prob",
+        "N_RFI_X",
+        "N_RFI_Y",
+        "M_AVA0",
+        "acquisition_time"
     startdate: str or datetime, optional (default: None)
         First day of the available swath data that should be included in the
         time series. If None is passed, then the first available day is used.
@@ -27,7 +52,13 @@ def swath2ts(img_path, ts_path, startdate=None, enddate=None, memory=4):
         Size of available memory in GB. More memory will lead to a faster
         conversion.
     """
-    reader = SMOSL2Reader(img_path)
+    variables = [v for v in np.atleast_1d(variables)]
+
+    if "acquisition_time" not in variables:
+        variables.append("acquisition_time")
+
+    reader = SMOSL2Reader(img_path, varnames=variables,
+                          add_overpass_flag=True)
 
     first_day, last_day = get_first_last_day_images(img_path)
 
@@ -122,4 +153,3 @@ def extend_ts(img_path, ts_path, memory=4):
 
     else:
         print(f"No extension required From: {startdate} To: {last_day}")
-

tests/smos_l2/test_l2_reshuffle.py

@@ -1,7 +1,7 @@
 import os
 import pandas as pd
 from tempfile import TemporaryDirectory
-from smos.smos_l2.reshuffle import swath2ts, extend_ts
+from smos.smos_l2.reshuffle import swath2ts, extend_ts, _default_variables
 from smos.misc import read_summary_yml
 from pynetcf.time_series import GriddedNcIndexedRaggedTs
 from pygeogrids.netcdf import load_grid
@@ -42,6 +42,11 @@ def test_reshuffle_and_update():
             ts.loc['2022-01-02', 'Soil_Moisture'].values[0],
             0.52442, 5
         )
+        for var in _default_variables:
+            assert var in ts.columns
+
+        assert 'Overpass' in ts.columns
+
         assert 1 in ts.index.day
         assert 2 in ts.index.day
         assert 3 not in ts.index.day  # this must be excluded