wps_climdex_dtr¶
WPS wrapper for climdex.pcic's climdex.dtr function
climdex.dtr computes the mean daily diurnal temperature range. The frequency of observationcan be either monthly or annual.
In [1]:
import os
import requests
from birdy import WPSClient
from rpy2 import robjects
from urllib.request import urlretrieve
from importlib.resources import files
from tempfile import NamedTemporaryFile
from wps_tools.R import rda_to_vector, construct_r_out, test_rda_output
from wps_tools.testing import get_target_url
In [2]:
# Ensure we are in the working directory with access to the data
while os.path.basename(os.getcwd()) != "quail":
os.chdir('../')
In [3]:
# NBVAL_IGNORE_OUTPUT
url = get_target_url("quail")
print(f"Using quail on {url}")
Using quail on https://marble-dev01.pcic.uvic.ca/twitcher/ows/proxy/quail/wps
In [4]:
quail = WPSClient(url)
Help for individual processes can be diplayed using the ? command (ex/ bird.process?)¶
In [5]:
# NBVAL_IGNORE_OUTPUT
quail.climdex_dtr?
Signature: quail.climdex_dtr( climdex_input=None, loglevel='INFO', output_file='output.rda', freq='monthly', output_formats=None, ) Docstring: Computes the mean daily diurnal temperature range. Parameters ---------- climdex_input : ComplexData:mimetype:`application/x-gzip` RDS or Rdata (.rds, .rda, .rdata) file containing R Object of type climdexInput output_file : string Filename to store the output Rdata (extension .rda) freq : {'monthly', 'annual'}string Time frequency to aggregate to loglevel : {'CRITICAL', 'ERROR', 'WARNING', 'INFO', 'DEBUG', 'NOTSET'}string Logging level Returns ------- rda_output : ComplexData:mimetype:`application/x-gzip` Rda file containing R output data File: ~/github/quail/</tmp/quail-venv/lib/python3.8/site-packages/birdy/client/base.py-9> Type: method
Run wps_climdex_dtr Process with rda input¶
In [6]:
with NamedTemporaryFile(suffix=".rda", prefix="dtr_", dir="/tmp", delete=True) as output_file:
output = quail.climdex_dtr(
climdex_input=(files("tests") / "data/climdexInput.rda").resolve(),
freq="annual",
output_file=output_file.name,
)
dtr_url = output.get()[0]
You can also pass rds input
In [7]:
with NamedTemporaryFile(suffix=".rda", prefix="dtr_", dir="/tmp", delete=True) as output_file:
output = quail.climdex_dtr(
climdex_input=(files("tests") / "data/climdexInput.rds").resolve(),
output_file=output_file.name,
)
dtr_url_rds = output.get()[0]
Run with multiple inputs
In [8]:
climdex_inputs = [
(files("tests") / "data/climdexInput.rds").resolve(),
(files("tests") / "data/climdexInput.rda").resolve(),
(files("tests") / "data/climdex_input_multiple.rda").resolve(),
]
with NamedTemporaryFile(suffix=".rda", prefix="dtr_", dir="/tmp", delete=True) as output_file:
output = quail.climdex_dtr(
climdex_input=climdex_inputs,
output_file=output_file.name,
)
In [9]:
# NBVAL_IGNORE_OUTPUT
construct_r_out(output.get())
Out[9]:
[[R object with classes: ('numeric',) mapped to:
[ nan, nan, nan, nan, ..., 7.883333, 7.048387, nan, nan],
R object with classes: ('numeric',) mapped to:
[ nan, nan, nan, nan, ..., 7.883333, 7.048387, nan, nan],
R object with classes: ('numeric',) mapped to:
[ nan, nan, nan, nan, ..., 7.883333, 7.048387, nan, nan],
R object with classes: ('numeric',) mapped to:
[ nan, nan, nan, nan, ..., 7.883333, 7.048387, nan, nan]]]
Access the output with rda_to_vector or construct_r_out from wps_tools.R
In [10]:
dtr = rda_to_vector(dtr_url, "dtr1_ci")
# use print() to see whole vector
print(dtr)
1959 1960 1961 1962 1963 1964 1965 1966
NA 6.870492 NA NA 7.286575 NA 6.472603 6.230137
1967 1968 1969 1970 1971 1972 1973 1974
6.578082 7.060109 6.800549 6.810989 7.092329 7.986612 7.094795 6.835890
1975 1976 1977 1978 1979 1980 1981 1982
7.049589 NA NA 6.324658 7.215068 7.183060 7.382192 8.236915
1983 1984 1985 1986 1987 1988 1989 1990
8.259615 NA NA 6.004110 NA 5.945355 6.176712 6.322802
1991 1992 1993 1994 1995 1996 1997 1998
NA 6.551913 NA NA 6.978022 6.223140 6.282192 6.527473
1999 2000 2001 2002 2003 2004
6.589286 6.407104 6.331956 NA 7.064560 NA
In [11]:
# NBVAL_IGNORE_OUTPUT
construct_r_out(output.get())
Out[11]:
[[R object with classes: ('numeric',) mapped to:
[ nan, nan, nan, nan, ..., 7.883333, 7.048387, nan, nan],
R object with classes: ('numeric',) mapped to:
[ nan, nan, nan, nan, ..., 7.883333, 7.048387, nan, nan],
R object with classes: ('numeric',) mapped to:
[ nan, nan, nan, nan, ..., 7.883333, 7.048387, nan, nan],
R object with classes: ('numeric',) mapped to:
[ nan, nan, nan, nan, ..., 7.883333, 7.048387, nan, nan]]]
Testing output against expected output¶
In [12]:
test_rda_output(
dtr_url, "dtr1_ci", "expected_dtr.rda", "expected_dtr_annual"
)