TC wind hazard for tracks from MIT TC downscale model

.github/workflows/tcrm-pylint.yml

@@ -0,0 +1,34 @@
+name: Pylint tests for TCRM 
+
+on: 
+  push:
+    branches:  [ master, develop ]
+
+jobs:
+  build:
+    name: Pylint TCRM
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python env
+      uses: conda-incubator/[email protected]
+      with: 
+        activate-environment: tcrm
+        environment-file: tcrmenv.yml
+        python-version: 3.7
+        auto-activate-base: false
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install pylint
+    - name: Analysing the code with pylint
+      run: |
+        pylint --rcfile pylintrc --fail-under=7 `find -regextype egrep -regex '(.*.py)$'` |
+        tee pylint.txt
+    - name: Upload pylint.txt as artifact
+      uses: actions/upload-artifact@v2
+      with:
+        name: pylint report
+        path: pylint.txt

.github/workflows/tcrm-tests.yml

@@ -0,0 +1,34 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unit tests for TCRM
+
+on:
+  push:
+    branches: [ master, develop ]
+  pull_request:
+    branches: [ master, develop ]
+
+jobs:
+  TCRM:
+    name: Test TCRM
+    runs-on: ubuntu-latest
+    strategy: 
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up environment
+      uses: conda-incubator/[email protected]
+      with:
+        activate-environment: tcrm
+        environment-file: tcrmenv.yml
+        python-version: ${{ matrix.python-version }}
+        auto-activate-base: false
+
+    - name: Test with pytest
+      env: 
+        PYTHONPATH: ~/tcrm;~/tcrm/Utilities
+      shell: bash -l {0}
+      run: |
+        pytest -x --cov=. --cov-report xml

.readthedocs.yaml

@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  builder: html
+   configuration: conf.py
+
+# Optionally build your docs in additional formats such as PDF
+formats:
+   - pdf
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+   version: 3.7
+
+conda:
+   environment: tcrmenv.yml

Evaluate/evaluate.py

@@ -1600,5 +1600,25 @@ def process_args(argv):
 
     log.info("Completed {0}".format(sys.argv[0]))
 
+
+def bom2tcrm(df, trackId):
+    """
+    Transforms a dataframe in BoM format into a tcrm track.
+
+    """
+    df['Datetime'] = pd.to_datetime(df.validtime)
+    df['Speed'] = df.translation_speed
+    df['CentralPressure'] = df.pcentre
+    df['Longitude'] = df.longitude
+    df['Latitude'] = df.latitude
+    df['EnvPressure'] = df.poci
+    df['rMax'] = df.rmax
+    df['trackId'] = df.disturbance.values
+
+    track = Track(df)
+    track.trackId = [trackId]
+    return track
+
+
 if __name__ == '__main__':
     process_args(sys.argv[1:])

Evaluate/interpolateTracks.py

@@ -3,12 +3,15 @@
 import numpy as np
 
 from datetime import datetime, timedelta
-from matplotlib.dates import num2date
+from matplotlib.dates import num2date, date2num
 from scipy.interpolate import interp1d, splev, splrep
 
 from Utilities.maputils import latLon2Azi
 from Utilities.loadData import loadTrackFile, maxWindSpeed
+from Utilities.parallel import disableOnWorkers
 from Utilities.track import Track, ncSaveTracks
+from pycxml.pycxml import loadfile
+import pandas as pd
 
 LOG = logging.getLogger(__name__)
 LOG.addHandler(logging.NullHandler())
@@ -70,7 +73,7 @@ def interpolate(track, delta, interpolation_type=None):
                                           track.Minute)]
     else:
         day_ = track.Datetime
-    
+
     timestep = timedelta(delta/24.)
     try:
         time_ = np.array([d.toordinal() + (d.hour + d.minute/60.)/24.0
@@ -84,24 +87,24 @@ def interpolate(track, delta, interpolation_type=None):
         else:
             raise
     dt_ = 24.0 * np.diff(time_)
-    dt = np.empty(len(track.data), dtype=float)
+    dt = np.zeros(len(track.data), dtype=float)
     dt[1:] = dt_
 
     # Convert all times to a time after initial observation:
     timestep = 24.0*(time_ - time_[0])
 
     newtime = np.arange(timestep[0], timestep[-1] + .01, delta)
     newtime[-1] = timestep[-1]
-    _newtime = (newtime / 24.) + time_[0]
-
+    _newtime = (newtime / 24.) + time_[0] + date2num(np.datetime64('0000-12-31'))     #  Before Matplotlib 3.3, the epoch was 0000-12-31, later it changes to 1970-01-01 UTC 
     newdates = num2date(_newtime)
     newdates = np.array([n.replace(tzinfo=None) for n in newdates])
 
     if not hasattr(track, 'Speed'):
         idx = np.zeros(len(track.data))
         idx[0] = 1
+        # TODO: Possibly could change `np.mean(dt)` to `dt`?
         track.WindSpeed = maxWindSpeed(idx, np.mean(dt), track.Longitude,
-                                       track.Latitude, track.CentralPressure, 
+                                       track.Latitude, track.CentralPressure,
                                        track.EnvPressure)
     # Find the indices of valid pressure observations:
     validIdx = np.where(track.CentralPressure < sys.maxsize)[0]
@@ -140,7 +143,7 @@ def interpolate(track, delta, interpolation_type=None):
             # Use the Akima interpolation method:
             try:
                 import akima
-            except ImportError:
+            except ModuleNotFoundError:
                 LOG.exception(("Akima interpolation module unavailable "
                                " - default to scipy.interpolate"))
                 nLon = splev(newtime, splrep(timestep, track.Longitude, s=0),
@@ -262,6 +265,7 @@ def saveTracks(tracks, outputFile):
         if len(data) > 0:
             np.savetxt(fp, data, fmt=OUTPUT_FMTS)
 
+@disableOnWorkers
 def parseTracks(configFile, trackFile, source, delta, outputFile=None,
                 interpolation_type=None):
     """
@@ -299,6 +303,9 @@ def parseTracks(configFile, trackFile, source, delta, outputFile=None,
     if trackFile.endswith("nc"):
         from Utilities.track import ncReadTrackData
         tracks = ncReadTrackData(trackFile)
+    elif trackFile.endswith("xml"):
+        dfs = loadfile(trackFile)
+        tracks = [bom2tcrm(df, i) for i, df in enumerate(dfs)]
     else:
         tracks = loadTrackFile(configFile, trackFile, source)
 
@@ -317,3 +324,22 @@ def parseTracks(configFile, trackFile, source, delta, outputFile=None,
 
 
     return results
+
+
+def bom2tcrm(df, trackId):
+    """
+    Transforms a dataframe in BoM format into a tcrm track.
+
+    """
+    df['Datetime'] = pd.to_datetime(df.validtime)
+    df['Speed'] = df.translation_speed
+    df['CentralPressure'] = df.pcentre
+    df['Longitude'] = df.longitude
+    df['Latitude'] = df.latitude
+    df['EnvPressure'] = df.poci
+    df['rMax'] = df.rmax
+    df['trackId'] = df.disturbance.values
+
+    track = Track(df)
+    track.trackId = [trackId, trackId]
+    return track