Days: wps_climdex_days

WPS wrapper for climdex.pcic days functions

• climdex.su Computes the SU (summer days) climdexindex: the annual count of days where daily maximum temperature exceeds 25 degreesCelsius.
• climdex.id Computes the ID (icing days) climdexindex: the annual count of days where daily maximum temperature was below 0 degrees Celsius.
• climdex.fd Computes the FD frost days) climdexindex: the annual count of days where daily minimum temperature was below 0 degrees Celsius.
• climdex.tr Computees the TR (tropical nights) climdexindex: the annual count of days where daily minimum temperature stays above 20 degrees Celsius.

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.output_handling import auto_construct_outputs
from wps_tools.R import get_robjects, construct_r_out, rda_to_vector, test_rda_output
from wps_tools.testing import get_target_url

# Ensure we are in the working directory with access to the data
while os.path.basename(os.getcwd()) != "quail":
    os.chdir('../')

# 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

quail = WPSClient(url)

Help for individual processes can be diplayed using the ? command (ex/ bird.process?)

# NBVAL_IGNORE_OUTPUT
quail.climdex_days?

Signature:
quail.climdex_days(
    climdex_input,
    days_type=None,
    loglevel='INFO',
    output_file='output.rda',
    output_formats=None,
)
Docstring:
Takes a climdexInput object as input and computes the annual count of days where daily temperature satisfies some condition.
                "summer": the annual count of days where daily maximum temperature
                exceeds 25 degreesCelsius
                "icing": the annual count of days where daily maximum temperature
                was below 0 degrees Celsius
                "frost": the annual count of days where daily minimum temperature
                was below 0 degrees Celsius
                "tropical nights": the annual count of days where daily minimum
                temperature stays above 20 degrees Celsius

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)
days_type : {'su', 'id', 'fd', 'tr'}string
    Day type condition to compute
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-0>
Type:      method

Run wps_climdex_days process for climdex.su (summer days) with rda input

with NamedTemporaryFile(suffix=".rda", prefix="summer_days_", dir="/tmp", delete=True) as output_file:
    output = quail.climdex_days(
            climdex_input=(files("tests") / "data/climdexInput.rda").resolve(),
            days_type="su",
            output_file=output_file.name,
        )
su_url = output.get()[0]

Run wps_climdex_days process for climdex.id (icing days) with rda input

with NamedTemporaryFile(suffix=".rda", prefix="icing_days_", dir="/tmp", delete=True) as output_file:
    output = quail.climdex_days(
            climdex_input=(files("tests") / "data/climdexInput.rda").resolve(),      
            days_type="id",
            output_file=output_file.name,
        )
id_url = output.get()[0]

Run wps_climdex_days process for climdex.fd (frost days) with rds input

with NamedTemporaryFile(suffix=".rda", prefix="frost_days_", dir="/tmp", delete=True) as output_file:
    output = quail.climdex_days(
            climdex_input=(files("tests") / "data/climdexInput.rda").resolve(),        
            days_type="fd",
            output_file=output_file.name,
        )
fd_url = output.get()[0]

Run wps_climdex_days process for climdex.tr (tropical nights) with rds input

with NamedTemporaryFile(suffix=".rda", prefix="frost_days_", dir="/tmp", delete=True) as output_file:
    output = quail.climdex_days(
            climdex_input=(files("tests") / "data/climdexInput.rds").resolve(),        
            days_type="tr",
            output_file=output_file.name,
        )
tr_url = output.get()[0]

Run with multiple inputs

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="frost_days_", dir="/tmp", delete=True) as output_file:
    output = quail.climdex_days(
            climdex_input=climdex_inputs,        
            days_type="su",
            output_file=output_file.name,
        )

# NBVAL_IGNORE_OUTPUT
construct_r_out(output.get())

[[R object with classes: ('numeric',) mapped to:
  [     nan, 11.000000,      nan,      nan, ..., 4.000000,      nan, 13.000000,      nan],
  R object with classes: ('numeric',) mapped to:
  [     nan, 11.000000,      nan,      nan, ..., 4.000000,      nan, 13.000000,      nan],
  R object with classes: ('numeric',) mapped to:
  [     nan, 11.000000,      nan,      nan, ..., 4.000000,      nan, 13.000000,      nan],
  R object with classes: ('numeric',) mapped to:
  [     nan, 11.000000,      nan,      nan, ..., 4.000000,      nan, 13.000000,      nan]]]

Access the output with rda_to_vector or construct_r_out from wps_tools.R

# use print() to see whole vector
su = rda_to_vector(su_url, "su1_ci")
print(f"SUMMER DAYS\n{su}")
id_ = rda_to_vector(id_url, "id1_ci")
fd = rda_to_vector(fd_url, "fd1_ci")
tr = rda_to_vector(tr_url, "tr1_ci")

SUMMER DAYS
1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 
  NA   11   NA   NA    2   NA    3    4    6   11    6    4   10    5    6    4 
1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 
   1   NA   NA    5    3    2    5    3    4   NA   NA    6   NA    4    2    8 
1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 
  NA   10   NA   NA    7   12    8   15    2    8    4   NA   13   NA 

construct_r_out([su_url, id_url, fd_url, tr_url])

[[R object with classes: ('numeric',) mapped to:
  [     nan, 11.000000,      nan,      nan, ..., 4.000000,      nan, 13.000000,      nan]],
 [R object with classes: ('numeric',) mapped to:
  [     nan, 0.000000,      nan,      nan, ..., 0.000000,      nan, 0.000000,      nan]],
 [R object with classes: ('numeric',) mapped to:
  [     nan, 10.000000,      nan,      nan, ..., 1.000000,      nan, 0.000000,      nan]],
 [R object with classes: ('numeric',) mapped to:
  [     nan, 0.000000,      nan,      nan, ..., 0.000000,      nan, 0.000000,      nan]]]

Test output against expected output

test_rda_output(
        su_url, "su1_ci", "expected_days_data.rda", "expected_summer_days"
    )
test_rda_output(
        id_url, "id1_ci", "expected_days_data.rda", "expected_icing_days"
    )
test_rda_output(
        fd_url, "fd1_ci", "expected_days_data.rda", "expected_frost_days"
    )
test_rda_output(
        tr_url, "tr1_ci", "expected_days_data.rda", "expected_tropical_nights"
    )