Welcome to PyWheat
Python library for simulation of wheat phenological development, crop growth and yield at large scales.
Intro#
The PyWheat simulates the wheat growth and development in a daily time-step at field, local, regional and global scales. Most of the algorithms are based on the original Fortran routines of the CERES-Wheat 2.01.
To accurately simulate wheat growth, development, and yield, the model takes into account the following processes:
- Phenological development, especially as it is affected by genetics and weather.
- Extension growth of leaves, stems, and roots.
- Biomass accumulation and partitioning, especially reproductive organs.
- Soil water balance and water use by the crop.
Features#
- Spatial crop modeling at scale
- GIS and remote sensing supported
- Weather data directly from AgERA5 products
- Wheat Mega-environments
- Yield Forecasting
- Risk management
- Among others
Quick start#
The package for estimating wheat grain yield using pywheat can be installed with pip:
This will add a command-line interface (CLI) that you can then use like so:
This simple command shows the following message:Usage: pywheat [OPTIONS] COMMAND [ARGS]...
Options:
-h, --help Show this message and exit.
Commands:
pheno
phenology
You can see two functions or commands you will be able to run. Use the help option (-h) to see how to proceed.
Usage: pywheat phenology [OPTIONS]
Options:
-lat, --latitude FLOAT Latitude of the site [required]
-lon, --longitude FLOAT Longitude of the site
-sd, --sowing_date TEXT Sowing date of the crop. eg. 1972-03-13
[required]
-tbase, --tbase FLOAT Base temperature for estimate Thermal time.
Default 0.0
-tt_topt, --tt_topt FLOAT Thermal time optimum temperature. Default 26
-tt_tmax, --tt_tmax FLOAT Thermal time maximum temperature. Default 34
-sa, --sunangle FLOAT Sun angle with the horizon. eg. p = 6.0 : civil
twilight. Default 0.0
-sn, --snow FLOAT Snow fall. Default 0.0
-sdepth, --sdepth FLOAT Sowing depth in cm. Default 3.0 cm
-gdde, --gdde FLOAT Growing degree days per cm seed depth required
for emergence, Default 6.2 GDD/cm.
-dsgft, --dsgft FLOAT GDD from End Ear Growth to Start Grain Filling
period. Default 200 degree-days
-vreq, --vreq FLOAT Vernalization required for max.development rate
(VDays). Default 505 degree-days
-phint, --phint FLOAT Phyllochron. A good estimate for PHINT is 95
degree days. This value for PHINT is
appropriate except for spring sown wheat in
latitudes greater than 30 degrees north and 30
degrees south, in which cases a value for PHINT
of 75 degree days is suggested. Default 95.0
degree-days
-p1v, --p1v FLOAT Development genetic coefficients,
vernalization. 1 for spring type, 5 for winter
type. Default 4.85
-p1d, --p1d FLOAT Development genetic coefficients, Photoperiod
(1 - 6, low- high sensitive to day length).
Default 3.675
-p5, --p5 FLOAT Grain filling degree days. Old value was
divided by 10. Default 500 degree-days.
-p6, --p6 FLOAT Approximate the thermal time from physiological
maturity to harvest. Default 250.
-glim, --glim FLOAT Threshold for days to germination. Default 40
-elim, --elim FLOAT Threshold for thermal time to emergence.
Default 300
-tdu, --tdu FLOAT Threshold for thermal development units (TDU).
Default 400
-fmt, --inputformat TEXT File format of the input weather file. Options
CSV, DSSAT .WTH or Parquet
-ofmt, --outputformat TEXT File format of the output phenology file.
Options txt or csv
-best, --bestmodel BOOLEAN Use the calibration parameters to estimate
phenology
-w, --weather FILE Path to input weather file in CSV or Parquet
format [required]
-o, --output FILE Path to output phenology file.
-verbose, --verbose BOOLEAN Display comments
-h, --help Show this message and exit.
Usage in CLI#
pywheat phenology -lat 37.18 -lon -99.75 -sd '1981-10-16' \
-w ./pywheat/data/example/KSAS.WTH -fmt wth -o ./outputs.txt -verbose False
Note
The above instruction use 3 variables (latitude, longitude and sowing date of the site) to run the phenology model. It also requires the path of the weather data file in this case in DSSAT format. This will take a minute or so at the first time to compile the main functions and save them to the cache. Next time will be much faster.
RSTG GROWTH STAGE DAP DOY CROP AGE SUMDTT DATE
7 Sowing 0 289 0 0 1981-10-16
8 Germinate 1 290 1 28 1981-10-17
9 Emergence 5 294 5 66 1981-10-21
1 Term Spklt 36 325 31 1683 1981-11-21
2 End Veg 147 71 111 290 1982-03-12
3 End Ear Gr 169 93 22 202 1982-04-03
4 Beg Gr Fil 184 108 15 158 1982-04-18
5 End Gr Fil 214 138 30 459 1982-05-18
6 Harvest 228 152 14 267 1982-06-01
Usage in a python session#
>>> import pywheat
>>> print(pywheat.__version__)
PyWheat version 0.0.9
>>> from pywheat.data import load_dataset
>>> # Load Kansas data
>>> data = load_dataset()
Loading example weather dataset
from Kansas State University (Wagger,M.G. 1983) stored in DSSAT v4.8.
>>> data['Weather']
DATE SRAD TMAX TMIN RAIN
0 1981-10-01 18.9 23.3 10.0 0.0
1 1981-10-02 18.2 22.2 5.6 0.0
2 1981-10-03 2.4 16.7 11.1 0.3
3 1981-10-04 13.8 26.1 12.8 34.0
4 1981-10-05 12.1 26.7 15.6 0.0
.. ... ... ... ... ...
299 1982-07-27 19.9 31.7 22.2 0.0
300 1982-07-28 24.9 29.4 20.0 0.0
301 1982-07-29 20.9 30.0 16.7 0.0
302 1982-07-30 26.4 30.0 18.9 0.0
303 1982-07-31 26.5 33.3 14.4 0.0
[304 rows x 5 columns]
>>> # Initialization of variables
>>> # Default variables are commented
>>> params = dict(
... sowing_date = "1981-10-16", # Sowing date in YYYY-MM-DD
... latitude = 39.0, # Latitude of the site
... )
>>> from pywheat.pheno import determine_phenology_stage
>>> import matplotlib.pylab as plt
>>> growstages = determine_phenology_stage(initparams=params, weather=data['Weather'],
... dispDates=True, dispFigPhenology=True, verbose=False)
RSTG GROWTH STAGE DAP DOY CROP AGE SUMDTT DATE
7 Sowing 0 289 0 0 1981-10-16
8 Germinate 1 290 1 28 1981-10-17
9 Emergence 5 294 5 66 1981-10-21
1 Term Spklt 23 312 18 503 1981-11-08
2 End Veg 122 46 99 286 1982-02-15
3 End Ear Gr 153 77 31 192 1982-03-18
4 Beg Gr Fil 173 97 20 156 1982-04-07
5 End Gr Fil 207 131 34 468 1982-05-11
6 Harvest 221 145 14 264 1982-05-25
# Display a figure with the phenological stages
plt.show()
For detailed installation instructions visit installation
For detailed instructions of how-to get started, configuration options, and a demo, visit Getting Started
Upgrade pywheat#
If you have installed pywheat before and want to upgrade to the latest version, you can run the following command in your terminal:
Feedback#
If you have any feedback, please reach out to us at Feedback
FAQ#
Please read out frequently asked questions before you send an email.
Authors#
License#
MIT License
Copyright © 2023
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
Additional License please check out License
Sponsors
-
CERES-Wheat version 2.0 by Dr. Joe T. Ritchie and Dr. Doug Godwin. https://nowlin.css.msu.edu/wheat_book/ ↩
-
Ritchie, J.T.1991. Wheat phasic development. p. 31-54. In Hanks and Ritchie (ed.) Modeling plant and soil systems. Agron. Monogr. 31, ASA, CSSSA, SSSA, Madison, WI. ↩
-
Ritchie, J.T. and D.S. NeSmith. 1991. Temperature and Crop Development. p. 5-29. In Hanks and Ritchie (ed.) Modeling plant and soil systems. Agron. Monogr. 31, ASA, CSSSA, SSSA, Madison, WI. ↩