Flight phase separation

.github/workflows/pythonpackage.yml

@@ -30,7 +30,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
           conda-channels: anaconda, conda-forge
     - name: Install dependencies (conda)
-      run: conda install -y cartopy"<=0.17"
+      run: conda install -y cartopy
     - name: Install dependencies (pip)
       run: |
         python -m pip install --upgrade pip

.gitignore

@@ -2,7 +2,8 @@
 .ipynb_checkpoints/
 .idea/
 docs/build
-tests/testdata/
+tests/testdata/goes/
+tests/testdata/obs/
 
 *.nc
 *.png

README.md

@@ -31,14 +31,14 @@ You can:
 
 install cartopy first via conda
 
-    $> conda install -c conda-forge cartopy"<=0.17"
+    $> conda install -c conda-forge cartopy
 
 or manually install the cartopy dependencies (Following [this stack overflow answer](https://stackoverflow.com/a/56956172))
 
     $> apt-get install libproj-dev proj-data proj-bin
     $> apt-get install libgeos-dev
     $> pip install cython
-    $> pip install cartopy"<=0.17"
+    $> pip install cartopy
 
 
 

setup.py

@@ -11,13 +11,14 @@
     "matplotlib",
     "pandas",
     "metpy>=1.0",
-    "cartopy<=0.17",
+    "cartopy",
     "parse",
     "tqdm",
     "cftime",
     "worldview_dl",
     "docopt",
     "netcdf4",
+    "pyyaml",
 ]
 
 setup_requirements = []
@@ -58,5 +59,5 @@
     test_suite="tests",
     tests_require=test_requirements,
     url="",
-    version="0.2.2",
+    version="0.3.0",
 )

tests/conftest.py

@@ -19,6 +19,7 @@
 
 # A testdata folder in this directory
 testdata_dir = Path(__file__).parent / "testdata"
+testdata_twinotter_dir = testdata_dir / "obs"
 testdata_goes_dir = testdata_dir / "goes"
 
 
@@ -43,8 +44,8 @@ def download_goes_testdata():
 @pytest.fixture
 def testdata(scope="session"):
     # Download testdata if it is not there yet
-    if not testdata_dir.exists():
-        testdata_dir.mkdir()
+    if not testdata_twinotter_dir.exists():
+        testdata_twinotter_dir.mkdir()
         download_testdata()
 
     if not testdata_goes_dir.exists():
@@ -72,9 +73,17 @@ def testdata(scope="session"):
         flight_data_file=str(
             flight_data_path / "MASIN" / "core_masin_20200124_r004_flight330_1hz.nc"
         ),
-        flight_legs_data_path=str(flight_data_path / "flight330-legs.csv"),
+        flight_segments_file=str(
+            testdata_dir / "EUREC4A_TO_Flight-Segments_20200124a_0.1.yaml"
+        ),
         goes_path=str(p_root / "goes"),
-        goes_time=datetime.datetime(year=2020, month=1, day=24, hour=14, minute=0,),
+        goes_time=datetime.datetime(
+            year=2020,
+            month=1,
+            day=24,
+            hour=14,
+            minute=0,
+        ),
     )
 
 

tests/test_eurec4a.py

@@ -0,0 +1,18 @@
+import pytest
+
+import twinotter.external.eurec4a
+
+
+@pytest.mark.parametrize(
+    "platform,flight_number,flight_id",
+    [
+        ("TO", 330, "TO-0330"),
+        ("HALO", 119, "HALO-0119"),
+        ("P3", 117, "P3-0117"),
+    ],
+)
+def test_load_segments(platform, flight_number, flight_id):
+    flight_segments = twinotter.external.eurec4a.load_segments(
+        flight_number, platform=platform
+    )
+    assert flight_segments["flight_id"] == flight_id

tests/test_goes.py

@@ -11,7 +11,8 @@
 
 def test_load_nc(testdata):
     ds = twinotter.external.goes.load_nc(
-        path=testdata["goes_path"], time=testdata["goes_time"],
+        path=testdata["goes_path"],
+        time=testdata["goes_time"],
     )
 
     assert len(ds) == 93

tests/test_plots.py

@@ -23,7 +23,8 @@ def test_basic_flight_path(mock_savefig, testdata):
 
 def test_flight_track_frame(testdata):
     ds = twinotter.external.goes.load_nc(
-        path=testdata["goes_path"], time=testdata["goes_time"],
+        path=testdata["goes_path"],
+        time=testdata["goes_time"],
     )
     fig, ax = twinotter.plots.flight_track_frames.make_frame(ds)
 
@@ -50,7 +51,7 @@ def test_vertical_profile_plot(mock_showfig, testdata):
 def test_heights_and_legs_plot(mock_savefig, testdata):
     twinotter.plots.heights_and_legs.generate(
         flight_data_path=testdata["flight_data_path"],
-        legs_file=testdata["flight_legs_data_path"],
+        flight_segments_file=testdata["flight_segments_file"],
     )
     mock_savefig.assert_called_once()
 
@@ -59,23 +60,23 @@ def test_heights_and_legs_plot(mock_savefig, testdata):
 def test_quicklook_plot(mock_savefig, testdata):
     twinotter.quicklook.generate(
         flight_data_path=testdata["flight_data_path"],
-        legs_file=testdata["flight_legs_data_path"],
+        flight_segments_file=testdata["flight_segments_file"],
     )
 
-    with open(testdata["flight_legs_data_path"]) as fh:
+    with open(testdata["flight_segments_file"]) as fh:
         file_content = fh.read()
-        n_legs = len(file_content.split("Leg")) - 1
-        n_profiles = len(file_content.split("Profile")) - 1
+        n_levels = len(file_content.split("level")) - 1
+        n_profiles = len(file_content.split("profile")) - 1
 
-    for n in range(n_legs):
-        fn_fig = "flight330_Leg{}_quicklook.png".format(n)
+    for n in range(n_levels):
+        fn_fig = "flight330_level{}_quicklook.png".format(n)
         mock_savefig.assert_any_call(fn_fig)
 
-        fn_fig = "flight330_Leg{}_paluch.png".format(n)
+        fn_fig = "flight330_level{}_paluch.png".format(n)
         mock_savefig.assert_any_call(fn_fig)
 
     for n in range(n_profiles):
-        fn_fig = "flight330_Profile{}_skewt.png".format(n)
+        fn_fig = "flight330_profile{}_skewt.png".format(n)
         mock_savefig.assert_any_call(fn_fig)
 
 

tests/test_twinotter.py

@@ -33,3 +33,21 @@ def test_load_flight_empty_fails(testdata_empty):
     with pytest.raises(FileNotFoundError):
         twinotter.load_flight(flight_data_path=testdata_empty["flight_data_path"])
     return
+
+
+def test_load_segments(testdata):
+    flight_segments = twinotter.load_segments(testdata["flight_segments_file"])
+
+
+def test_count_segments(testdata):
+    flight_segments = twinotter.load_segments(testdata["flight_segments_file"])
+    assert twinotter.count_segments(flight_segments, "level") == 10
+    assert twinotter.count_segments(flight_segments, "profile") == 7
+
+
+def test_extract_segments(testdata):
+    ds = twinotter.load_flight(flight_data_path=testdata["flight_data_path"])
+    flight_segments = twinotter.load_segments(testdata["flight_segments_file"])
+
+    ds_segs = twinotter.extract_segments(ds, flight_segments, "level")
+    assert len(ds_segs.Time) == 5684

tests/testdata/EUREC4A_TO_Flight-Segments_20200124a_0.1.yaml

@@ -0,0 +1,134 @@
+name: RF01
+mission: EUREC4A
+platform: TO
+flight_id: TO-0330
+contacts: []
+date: 2020-01-24
+flight_report: ''
+takeoff: 2020-01-24 11:06:37
+landing: 2020-01-24 14:02:53
+events: []
+remarks:
+- HUM_ROSE is not well calibrated to absolute values - reference against TDEW_BUCK
+  or H2O_LICOR.
+segments:
+- kinds:
+  - profile
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 11:25:13
+  end: 2020-01-24 11:34:58
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 11:34:58
+  end: 2020-01-24 11:45:28
+- kinds:
+  - profile
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 11:45:28
+  end: 2020-01-24 11:50:21
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 11:50:21
+  end: 2020-01-24 12:01:37
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 12:02:44
+  end: 2020-01-24 12:18:52
+- kinds:
+  - calibration
+  - profile
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 12:17:45
+  end: 2020-01-24 12:27:53
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 12:28:15
+  end: 2020-01-24 12:42:53
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 12:47:24
+  end: 2020-01-24 12:54:09
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 12:56:46
+  end: 2020-01-24 13:06:09
+- kinds:
+  - profile
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 13:06:09
+  end: 2020-01-24 13:08:24
+- kinds:
+  - profile
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 13:08:47
+  end: 2020-01-24 13:12:32
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 13:17:47
+  end: 2020-01-24 13:29:03
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 13:32:03
+  end: 2020-01-24 13:36:11
+- kinds:
+  - profile
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 13:36:33
+  end: 2020-01-24 13:43:41
+- kinds:
+  - profile
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 13:44:03
+  end: 2020-01-24 13:47:26
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 13:47:49
+  end: 2020-01-24 13:56:04
+- kinds:
+  - level
+  name: ''
+  irregularities: []
+  segment_id: TO-0330_
+  start: 2020-01-24 13:59:27
+  end: 2020-01-24 14:01:42