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Merge pull request #47 from djgagne/djgagne
Speedups to segmentation
2 parents 3d24400 + 26d001c commit fb443b7

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‎.readthedocs.yaml

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# Read the Docs configuration file for Sphinx projects
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# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
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# Required
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version: 2
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# Set the OS, Python version and other tools you might need
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build:
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os: ubuntu-22.04
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tools:
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python: "mambaforge-22.9"
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# You can also specify other tool versions:
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# nodejs: "20"
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# rust: "1.70"
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# golang: "1.20"
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conda:
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environment: environment.yml
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# Build documentation in the "docs/" directory with Sphinx
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sphinx:
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configuration: doc/conf.py
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# You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
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# builder: "dirhtml"
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# Fail on all warnings to avoid broken references
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# fail_on_warning: true
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# Optionally build your docs in additional formats such as PDF and ePub
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# formats:
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# - pdf
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# - epub
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# Optional but recommended, declare the Python requirements required
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# to build your documentation
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# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
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# python:
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# install:
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# - requirements: docs/requirements.txt

‎demos/hwt_2021_eval.ipynb

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‎environment.yml

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name: hagelslag
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channels:
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- conda-forge
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- defaults
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dependencies:
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- python>=3.8
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- python<=3.10
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- numpy
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- scipy
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- s3fs
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- cython
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- sphinx
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- mock
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- dask
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- numba
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- jasper
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- flake8
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- zarr

‎hagelslag/VERSION

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0.6

‎hagelslag/data/GribModelGrid.py

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import datetime
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from os.path import exists
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import pygrib
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import numpy as np
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import pandas as pd
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import pygrib
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from netCDF4 import Dataset
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‎hagelslag/data/ZarrModelGrid.py

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self.end_date = pd.to_datetime(end_date)
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self.frequency = frequency
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self.valid_dates = date_range(start=self.start_date, end=self.end_date, freq=self.frequency)
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self.forecast_hours = (self.valid_dates - self.run_date).astype("timedelta64[h]").astype(int)
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self.forecast_hours = (self.valid_dates - self.run_date).values.astype("timedelta64[h]").astype(int)
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def load_data(self):
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‎hagelslag/mapfiles/GRIB2Table_hrrr_2d.csv

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High Resolution Rapid Refresh (HRRR)
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CONUS 2-D Fields
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GRIB2 Table Documentation
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13 March 2013
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RecordNumber,TableNumber,DisciplineNumber,CategoryNumber,ParameterNumber,WGrib2Name,NCLName,FieldType,Description,Units,
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1,0,0,16,196,var,REFC_P0_L200_GLC0,Composite Reflectivity,Maximum reflectivity in model column,dBZ,
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2,0,0,3,193,var,5WAVH_P0_L3_GLC0,Echo Top,Echo top height of 18dBZ surface,m,
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3,0,0,3,194,var,UGWD_P0_L200_GLC0,VIL,Vertically integrated liquid,kg/m^2,
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4,0,0,3,195,var,VGWD_P0_L200_GLC0,Radar VIL,Radar-derived vertically integrated liquid,kg/m^2,
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5,0,0,19,0,VIS,VIS_P0_L1_GLC0,Visibility,Surface visibility,m,
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6,0,0,16,195,var,REFD_P0_L103_GLC0,Reflectivity,Reflectivity at 1 km above ground level,dBZ,
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7,8,0,3,206,var,NLGSP_P8_2L100_GLC0_1h,Maximum Updraft,Maximum updraft velocity in 1000-400 mb layer over previous hour,m/s,
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8,8,2,0,196,var,CNWAT_P8_2L100_GLC0,Maximum Downdraft,Maximum downdraft velocity in 1000-400 mb layer over previous hour,m/s,
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9,8,0,2,9,DZDT,DZDT_P8_2L104_GLC0,Mean Vertical Velocity,Mean vertical velocity in sigma 0.8-0.5 layer,m/s,
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10,0,0,3,1,PRMSL,PRMSL_P0_L101_GLC0,Pressure,Pressure reduced to mean sea level via MAPS method,Pa,
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11,8,0,1,198,var,MINRH_P8_L103_GLC0_1h,Maximum Reflectivity,Maximum reflectivity at 1 km above ground level over previous hour,dBZ,
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12,8,3,192,2,SBT124,SBT124_P8_2L103_GLC0_1h,Maximum Updraft Helicity,Maximum updraft helicity in layer 2-5 km above ground level over previous hour,m^2/s^2,
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13,8,3,192,3,SBT126,SBT125_P8_2L103_GLC0_1h,Maximum Updraft Helicity,Maximum updraft helicity in layer 1-6 km above ground level over previous hour,m^2/s^2,
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14,8,10,3,192,var,SURGE_P8_L200_GLC0_1h,Vertically Integrated Graupel,Maximum vertically integrated graupel in model column over previous hour,kg/m^2,
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15,8,2,0,206,var,RDRIP_P8_L200_GLC0_1h,Lightning Threat 1,Maximum lightning threat 1 based on vertical flux of graupel at -15C over previous hour,flashes/km^2/(5 min),
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16,8,0,1,206,var,TIPD_P8_L200_GLC0_1h,Lightning Threat 2,Maximum lightning threat 2 based on vertically integrated graupel snow and cloud ice over previous hour,flashes/km^2/(5 min),
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17,0,0,17,192,var,LTNG_P8_L200_GLC0_1h,Lightning Threat 3,Maximum lightning threat 3 based on a weighted combination of lightning threat 1 and 2 over previous hour,flashes/km^2/(5 min),
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18,0,0,7,197,var,UPHL_P8_2L103_GLC0,Updraft Helicity,Updraft helicity in layer 2-5 km above ground level,m^2/s^2,
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19,0,3,192,1,SBT123,SBT123_P8_2L103_GLC0,Updraft Helicity,Updraft helicity in layer 1-6 km above ground level,m^2/s^2,
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20,0,0,0,195,var,LRGHR_P0_L200_GLC0,Heating Rate,Large scale condensate heating rate,K/s,
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21,0,0,0,196,var,CNVHR_P0_L200_GLC0,Heating Rate,Deep convective heating rate,K/s,
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22,0,0,1,213,var,CNVMR_P0_L200_GLC0,Moistening Rate,Deep convective moistening rate,kg/kg/s,
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23,0,0,0,201,var,SHAHR_P0_L200_GLC0,Heating Rate,Shallow convective heating rate,K/s,
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24,0,0,1,214,var,SHAMR_P0_L200_GLC0,Moistening Rate,Shallow convective moistening rate,kg/kg/s,
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25,0,0,0,202,var,VDFHR_P0_L200_GLC0,Heating Rate,Vertical diffusion heating rate,K/s,
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26,0,0,2,19,WMIXE,WMIXE_P0_L103_GLC0,Wind Energy,Wind energy generation potential using 0.5*density*speed^3 at 80 m above ground level,W/m^2,
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27,0,10,1,2,UOGRD,UOGRD_P0_L103_GLC0,Wind,U-component of wind at 80 m above ground level,m/s,
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28,0,10,1,3,VOGRD,VOGRD_P0_L103_GLC0,Wind,V-component of wind at 80 m above ground level,m/s,
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29,0,0,3,0,PRES,PRES_P0_L1_GLC0,Pressure,Surface pressure,Pa,
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30,0,0,0,0,TMP,TMP_P0_L1_GLC0,Temperature,Surface (skin) temperature,K,
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31,0,2,0,2,TSOIL,TSOIL_P0_L1_GLC0,Soil Temperature,Surface (skin) soil temperature,K,
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32,0,2,0,192,var,SOILW_P0_L1_GLC0,Soil Moisture,Surface (skin) volumetric soil moisture content (0 to 0.5 cm layer below surface),fraction,
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33,0,2,0,2,TSOIL,TSOIL_P0_L106_GLC0(0),Soil Temperature,Soil temperature 1 cm below surface,K,
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34,0,2,0,192,var,SOILW_P0_L106_GLC0(0),Soil Moisture,Volumetric soil moisture content 1 cm below surface (0.5 to 2.5 cm layer below surface),fraction,
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35,0,2,0,2,TSOIL,TSOIL_P0_L106_GLC0(1),Soil Temperature,Soil temperature 4 cm below surface,K,
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36,0,2,0,192,var,SOILW_P0_L106_GLC0(1),Soil Moisture,Volumetric soil moisture content 4 cm below surface (2.5 to 7 cm layer below surface),fraction,
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37,0,2,0,2,TSOIL,TSOIL_P0_L106_GLC0(2),Soil Temperature,Soil temperature 10 cm below surface,K,
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38,0,2,0,192,var,SOILW_P0_L106_GLC0(2),Soil Moisture,Volumetric soil moisture content 10 cm below surface (7 to 20 cm layer below surface),fraction,
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39,0,2,0,2,TSOIL,TSOIL_P0_L106_GLC0(3),Soil Temperature,Soil temperature 30 cm below surface,K,
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40,0,2,0,192,var,SOILW_P0_L106_GLC0(3),Soil Moisture,Volumetric soil moisture content 30 cm below surface (20 to 45 cm layer below surface),fraction,
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41,0,2,0,2,TSOIL,TSOIL_P0_L106_GLC0(4),Soil Temperature,Soil temperature 60 cm below surface,K,
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42,0,2,0,192,var,SOILW_P0_L106_GLC0(4),Soil Moisture,Volumetric soil moisture content 60 cm below surface (45 to 80 cm layer below surface),fraction,
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43,0,2,0,2,TSOIL,TSOIL_P0_L106_GLC0(5),Soil Temperature,Soil temperature 100 cm below surface,K,
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44,0,2,0,192,var,SOILW_P0_L106_GLC0(5),Soil Moisture,Volumetric soil moisture content 100 cm below surface (80 to 130 cm layer below surface),fraction,
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45,0,2,0,2,TSOIL,TSOIL_P0_L106_GLC0(6),Soil Temperature,Soil temperature 160 cm below surface,K,
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46,0,2,0,192,var,SOILW_P0_L106_GLC0(6),Soil Moisture,Volumetric soil moisture content 160 cm below surface (130 to 230 cm layer below surface),fraction,
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47,0,2,0,2,TSOIL,TSOIL_P0_L106_GLC0(7),Soil Temperature,Soil temperature 300 cm below surface,K,
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48,0,2,0,192,var,SOILW_P0_L106_GLC0(7),Soil Moisture,Volumetric soil moisture content 300 cm below surface (230 to 300 cm layer below surface),fraction,
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49,0,0,1,13,WEASD,WEASD_P0_L1_GLC0,Snow Water,Water equivalent of accumulated snow depth,kg/m^2,
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50,0,0,0,0,TMP,TMP_P0_L103_GLC0,Temperature,Temperature at 2 m above ground level,K,
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51,0,0,0,2,POT,POT_P0_L103_GLC0,Potential Temperature,Potential temperature at 2 m above ground level,K,
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52,0,0,1,0,SPFH,SPFH_P0_L103_GLC0,Specific Humidity,Specific humidity at 2 m above ground level,kg/kg,
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53,0,0,0,6,DPT,DPT_P0_L103_GLC0,Dewpoint,Dewpoint temperature at 2 m above ground level,K,
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54,0,0,1,1,RH,RH_P0_L103_GLC0,Relative Humidity,Relative humidity at 2 m above ground level,%,
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55.1,0,0,2,2,UGRD,UGRD_P0_L103_GLC0,Wind,U-component of wind at 10 m above ground level,m/s,
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55.2,0,0,2,3,VGRD,VGRD_P0_L103_GLC0,Wind,V-component of wind at 10 m above ground level,m/s,
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56,8,0,0,192,var,SNOHF_P8_L103_GLC0_1h,Maximum Wind,Maximum horizontal wind speed at 10 m above ground level over previous hour,m/s,
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57,8,0,1,8,APCP,APCP_P8_L1_GLC0_accHHh,Precipitation,Total precipitation accumulated since initial time,kg/m^2,
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58,8,0,1,10,ACPCP,ACPCP_P8_L1_GLC0_accHHh,Precipitation,Total convective precipitation accumulated since initial time,kg/m^2,
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59,8,0,1,9,NCPCP,NCPCP_P8_L1_GLC0_accHHh,Precipitation,Total large-scale precipitation accumulated since initial time,kg/m^2,
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60,8,0,1,13,WEASD,WEASD_P8_L1_GLC0_accHHh,Precipitation,Water equivalent of accumulated snow depth since initial time,kg/m^2,
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61,8,0,1,8,APCP,APCP_P8_L1_GLC0_acc1h,Precipitation,Total precipitation accumulated over previous hour,kg/m^2,
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62,8,0,1,10,ACPCP,ACPCP_P8_L1_GLC0_acc1h,Precipitation,Total convective precipitation accumulated over previous hour,kg/m^2,
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63,8,0,1,9,NCPCP,NCPCP_P8_L1_GLC0_acc1h,Precipitation,Total large-scale precipitation accumulated over previous hour,kg/m^2,
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64,8,0,1,13,WEASD,WEASD_P8_L1_GLC0_acc1h,Precipitation,Water equivalent of accumulated snow depth over previous hour,kg/m^2,
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65,0,0,1,195,var,CSNOW_P0_L1_GLC0,Precipitation Type,Categorical snow (yes=1 no=0),flag,
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66,0,0,1,194,var,CICEP_P0_L1_GLC0,Precipitation Type,Categorical ice pellets (yes=1 no=0),flag,
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67,0,0,1,193,var,CFRZR_P0_L1_GLC0,Precipitation Type,Categorical freezing rain (yes=1 no=0),flag,
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68,0,0,1,192,var,CRAIN_P0_L1_GLC0,Precipitation Type,Categorical rain (yes=1 no=0),flag,
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69,0,0,2,197,FRICV,FRICV_P0_L1_GLC0,Wind,Frictional velocity,m/s,
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70,0,0,0,11,SHTFL,SHTFL_P0_L1_GLC0,Heat Flux,Sensible heat net flux at surface,W/m^2,
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71,0,0,0,10,LHTFL,LHTFL_P0_L1_GLC0,Heat Flux,Latent heat net flux at surface,W/m^2,
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72,0,2,0,193,var,GFLUX_P0_L1_GLC0,Heat Flux,Ground heat flux at surface,W/m^2,
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73,0,0,7,192,var,LFTX_P0_2L100_GLC0,Lifted Index,Surface lifted index using 500 mb reference level,K,
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74,0,0,7,6,CAPE,CAPE_P0_L1_GLC0,Instability,Surface CAPE using highest theta-e parcel from lowest 10 mb,J/kg,
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75,0,0,7,7,CIN,CIN_P0_L1_GLC0,Instability,Surface CIN using highest theta-e parcel from lowest 10 mb,J/kg,
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76,0,0,1,3,PWAT,PWAT_P0_L200_GLC0,Precipitable Water,Precipitable water in model column,kg/m^2,
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77,0,0,6,3,LCDC,LCDC_P0_L214_GLC0,Cloud Cover,Low cloud cover,%,
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78,0,0,6,4,MCDC,MCDC_P0_L224_GLC0,Cloud Cover,Medium cloud cover,%,
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79,0,0,6,5,HCDC,HCDC_P0_L234_GLC0,Cloud Cover,High cloud cover,%,
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80,0,0,6,1,TCDC,TCDC_P0_L200_GLC0,Cloud Cover,Total cloud cover,%,
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81,0,0,3,5,HGT,HGT_P0_L2_GLC0,Cloud Base,Geopotential height of cloud base,gpm,
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82,0,0,3,5,HGT,HGT_P0_L3_GLC0,Cloud Top,Geopotential height of cloud top,gpm,
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83,0,0,5,193,var,ULWRF_P0_L8_GLC0,Radiation,Outgoing longwave radiation at top of atmosphere,W/m^2,
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84,0,0,4,192,var,DSWRF_P0_L1_GLC0,Radiation,Incoming shortwave radiation at the surface,W/m^2,
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85,0,0,7,8,HLCY,HLCY_P0_2L103_GLC0(0),Helicity,Storm-relative helicity for 0-3 km above ground level using Bunkers et al. 2000 storm-motion,m^2/s^2,
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86,0,0,7,8,HLCY,HLCY_P0_2L103_GLC0(1),Helicity,Storm-relative helicity for 0-1 km above ground level using Bunkers et al. 2000 storm-motion,m^2/s^2,
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87,0,0,2,194,var,USTM_P0_2L103_GLC0,Storm Motion,U-component of convective storm motion for right-moving cells using Bunkers et al. 2000,m/s,
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88,0,0,2,195,var,VSTM_P0_2L103_GLC0,Storm Motion,V-component of convective storm motion for right-moving cells using Bunkers et al. 2000,m/s,
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89,0,0,2,15,VUCSH,VUCSH_P0_2L103_GLC0(0),Wind Shear,U-component of vector wind difference between 10 m and 1 km above ground level,m/s,
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90,0,0,2,16,VVCSH,VVCSH_P0_2L103_GLC0(0),Wind Shear,V-component of vector wind difference between 10 m and 1 km above ground level,m/s,
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91,0,0,2,15,VUCSH,VUCSH_P0_2L103_GLC0(1),Wind Shear,U-component of vector wind difference between wind in surface-500 m and 5.5-6.0 km layers above ground level,m/s,
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92,0,0,2,16,VVCSH,VVCSH_P0_2L103_GLC0(1),Wind Shear,V-component of vector wind difference between wind in surface-500 m and 5.5-6.0 km layers above ground level,m/s,
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93,0,0,0,0,TMP,TMP_P0_2L108_GLC0,Temperature,Mean temperature in lowest 30 mb,K,
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94,0,0,0,2,POT,POT_P0_2L108_GLC0,Temperature,Mean potential temperature in lowest 30 mb,K,
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95,0,0,1,1,RH,RH_P0_2L108_GLC0,Relative Humidity,Mean relative humidity in lowest 30 mb,%,
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96,0,0,0,6,DPT,DPT_P0_2L108_GLC0,Dewpoint,Mean dewpoint temperature in lowest 30 mb,K,
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97,0,0,7,193,var,4LFTX_P0_2L108_GLC0,Lifted Index,Most unstable lifted index in six lowest 30 mb layers using 500 mb reference level,K,
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98,0,0,7,6,CAPE,CAPE_P0_2L108_GLC0(1),Instability,CAPE using highest average theta-e in six lowest 30 mb layers,J/kg,
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99,0,0,7,7,CIN,CIN_P0_2L108_GLC0(1),Instability,CIN using highest average theta-e in six lowest 30 mb layers,J/kg,
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100,0,0,3,196,var,HPBL_P0_L1_GLC0,Height,Planetary boundary layer height,m,
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101,0,0,3,5,HGT,HGT_P0_L5_GLC0,Height,Adiabatic condensation level above ground (LCL),gpm,
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102,0,0,7,6,CAPE,CAPE_P0_2L108_GLC0(0),Instability,Mixed-layer CAPE (MLCAPE) using average theta-e of the three lowest 30 mb layers,J/kg,
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103,0,0,7,7,CIN,CIN_P0_2L108_GLC0(0),Instability,Mixed-layer CIN (MLCIN) using average theta-e of the three lowest 30 mb layers,J/kg,
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104,0,0,7,6,CAPE,CAPE_P0_2L108_GLC0(2),Instability,Most unstable CAPE (MUCAPE) using parcel with highest theta-e in lowest 300 mb,J/kg,
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105,0,0,7,7,CIN,CIN_P0_2L108_GLC0(2),Instability,Most unstable CIN (MUCIN) using parcel with highest theta-e in lowest 300 mb,J/kg,
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106,0,0,3,200,var,PLPL_P0_2L108_GLC0,Pressure,Pressure level of most unstable parcel in lowest 300 mb,Pa,
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107,0,0,2,22,GUST,GUST_P0_L1_GLC0,Wind,Wind gust speed at 10 m above ground level,m/s,
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108,0,255,255,255,var,VAR_255_255_255_P0_L200_GLC0,Relative Humidity,Relative humidity with respect to precipitable water in model column,%,

‎hagelslag/mapfiles/GRIB2Table_hrrr_nat.csv

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High Resolution Rapid Refresh (HRRR)
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CONUS 3-D Native Level Fields (50 levels)
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GRIB2 Table Documentation
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25 Oct 2012
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RecordNumber,TableNumber,DisciplineNumber,CategoryNumber,ParameterNumber,WGrib2Name,NCLName,FieldType,Description,Units,
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1,0,0,3,0,PRES,PRES_P0_L100_GLC0,Pressure,Pressure,Pa,
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2,0,0,1,22,CLWMR,CLWMR_P0_L100_GLC0,Mixing Ratio,Cloud water mixing ratio,kg/kg,
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3,8,0,6,0,CICE,CICE_P0_L100_GLC0,Mixing Ratio,Cloud ice mixing ratio,kg/kg,
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4,8,0,1,24,RWMR,RWMR_P0_L100_GLC0,Mixing Ratio,Rain mixing ratio,kg/kg,
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5,8,0,1,25,SNMR,SNMR_P0_L100_GLC0,Mixing Ratio,Snow mixing ratio,kg/kg,
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6,0,0,1,32,GRLE,GRLE_P0_L100_GLC0,Mixing Ratio,Graupel mixing ratio,kg/kg,
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7,0,0,6,1,TCDC,TCDC_P0_L100_GLC0,Cloud Cover,Total cloud cover,%,
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8,0,0,3,5,HGT,HGT_P0_L100_GLC0,Geopotential Height,Geopotential height,gpm,
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9,0,0,0,0,TMP,TMP_P0_L100_GLC0,Temperature,Temperature,K,
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10,0,0,1,0,SPFH,SPFH_P0_L100_GLC0,Specific Humidity,Specific humidity,kg/kg,
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11.1,0,0,2,2,UGRD,UGRD_P0_L100_GLC0,Wind,U-component of wind,m/s,
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11.2,0,0,2,3,VGRD,VGRD_P0_L100_GLC0,Wind,V-component of wind,m/s,
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12,0,0,2,8,VVEL,VVEL_P0_L100_GLC0,Vertical Velocity,Vertical velocity (pressure),Pa/s,
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13,0,0,19,11,TKE,TKE_P0_L100_GLC0,Turbulent Kinetic Energy,Turbulent kinetic energy,m^2/s^2,

‎hagelslag/mapfiles/README

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To make VSE_mask.nc
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run python ../hagelslag/util/create_model_grid_us_mask.py -m VSE.txt -s states/states.shp -o t.nc
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and python ../hagelslag/util/create_model_grid_us_mask.py -m VSE.txt -s mexstates/mexstates.shp -o u.nc
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and merge them together
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ncea -y max t.nc u.nc VSE_mask.nc
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‎hagelslag/mapfiles/VSE.txt

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proj=lcc
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a=6370000
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b=6370000
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lat_0=30.8
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lon_0=-90.
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lat_1=30.8
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lat_2=30.8
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units=m
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dx=3000
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dy=3000
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sw_lon=258.714
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sw_lat=24.019
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ne_lon=282.843185435306
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ne_lat=36.4670218542745

‎hagelslag/mapfiles/VSE_mask.nc

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