def test_csv_modelisotherm(self, basic_modelisotherm, tmpdir_factory):
"""Test creation of the ModelIsotherm CSV."""
path = tmpdir_factory.mktemp('csv').join('isotherm.csv').strpath
pygaps.isotherm_to_csv(basic_modelisotherm, path)
isotherm = pygaps.isotherm_from_csv(path)
assert isotherm.to_dict() == basic_modelisotherm.to_dict()
def test_csv_pointisotherm(self, basic_pointisotherm, tmpdir_factory):
"""Tests creation of the regular csv file"""
path = tmpdir_factory.mktemp('csv').join('isotherm.csv').strpath
pygaps.isotherm_to_csv(basic_pointisotherm, path)
isotherm = pygaps.isotherm_from_csv(path)
assert isotherm == basic_pointisotherm
def load(self, path, name, ext):
"""Load isotherm from disk."""
isotherm = None
if ext == '.csv':
isotherm = pygaps.isotherm_from_csv(path)
elif ext == '.json':
isotherm = pygaps.isotherm_from_json(path)
elif ext == '.xls' or ext == '.xlsx':
isotherm = pygaps.isotherm_from_xl(path)
elif ext == '.aif':
isotherm = pygaps.isotherm_from_aif(path)
else:
raise Exception(f"Unknown isotherm type '{ext}'.")
if not isotherm:
return
self.add_isotherm(name, isotherm)
def test_csv_isotherm_checks(self):
"""Sanity checks for the CSV parser."""
# basic from string
text = "material,test\nadsorbate,test\ntemperature,303\n"
assert pygaps.isotherm_from_csv(text)
# empty value
text = "material,test\nadsorbate,test\ntemperature,303\nnew,"
assert pygaps.isotherm_from_csv(text).new is None
# multiple value errors
text = "material,test\nadsorbate,test\ntemperature,303\nnew,1,2"
with pytest.raises(ParsingError):
pygaps.isotherm_from_csv(text)
# bool in csv
text = "material,test\nadsorbate,test\ntemperature,303\nnew,True"
assert pygaps.isotherm_from_csv(text).new is True
# list in csv
text = "material,test\nadsorbate,test\ntemperature,303\nnew,[1 2 3]"
assert pygaps.isotherm_from_csv(text).new == [1, 2, 3]
def main():
"""
The main entrypoint for the cli.
Currently the CLI can read any pyGAPS format (JSON, CSV, Excel) and then:
* print isotherm to output (default if no argument is passed)
* plot the isotherm using a Matplotlib window (``-p/--plot``)
* run basic automated characterization tests (``-ch/--characterize a_bet``
for the BET area for example)
* attempt to model the isotherm using a requested model or guess the best
fitting model (``-md/--model guess``) and save the resulting isotherm model
using the ``-o/--outfile`` path.
* convert the isotherm to any unit/basis
(``-cv/--convert pressure_mode=absolute,pressure_unit=bar``) and save the
resulting isotherm model using the ``-o/--outfile`` path.
"""
# Create the parser
prs = argparse.ArgumentParser(
description='Command-line interface to pyGAPS')
# Add the arguments
prs.add_argument(
'iso',
metavar='isotherm',
type=pathlib.Path,
help='isotherm to display or process',
)
prs.add_argument(
'-p',
'--plot',
action='store_true',
help='plot the isotherm',
)
prs.add_argument(
'-ch',
'--characterize',
help='run characterization methods (BET area, PSD, etc).',
choices=['a_bet', 'a_lang', 'kh'],
)
prs.add_argument(
'-md',
'--model',
choices=['guess', 'henry', 'langmuir', 'dslangmuir', 'bet'],
help='model an isotherm, saved as the file specified at \'-o\'',
)
prs.add_argument(
'-cv',
'--convert',
help='convert to another unit/basis, savepath using \'-o\'',
)
prs.add_argument(
'-o',
'--outfile',
type=pathlib.Path,
help='output path for a resulting isotherm',
)
prs.add_argument(
'-v',
'--verbose',
action='store_true',
help='increase verbosity',
)
# Execute the parse_args() method
args = prs.parse_args()
import pygaps as pg
# Read the isotherm
if not args.iso.exists():
raise FileNotFoundError("Path does not exist.")
ext = args.iso.suffix
if ext == '.json':
iso = pg.isotherm_from_json(args.iso)
elif ext == '.csv':
iso = pg.isotherm_from_csv(args.iso)
elif ext == '.xls':
iso = pg.isotherm_from_xl(args.iso)
else:
from pygaps.utilities.exceptions import ParsingError
raise ParsingError(f"Cannot read '{ext}' files")
plot = False
out_iso = None
# pass to various characterization functions
if args.characterize:
plot = args.verbose
if args.characterize == 'a_bet':
res = pg.area_BET(iso, verbose=args.verbose)
print(res)
elif args.characterize == 'a_lang':
res = pg.area_langmuir(iso, verbose=args.verbose)
elif args.characterize == 'kh':
res = pg.initial_henry_slope(iso, verbose=args.verbose)
# model isotherm using `model_iso`
elif args.model:
plot = args.verbose
out_iso = pg.model_iso(iso, model=args.model, verbose=args.verbose)
# convert an isotherm to a different basis/unit
elif args.convert:
convert_args = {
keyval.split('=')[0]: keyval.split('=')[1]
for keyval in map(str.strip, args.convert.split(','))
}
convert_args['verbose'] = args.verbose
iso.convert(**convert_args)
out_iso = iso
# simply plot the isotherm
elif args.plot:
iso.plot()
plot = True
# default to printing isotherm to stdout
else:
print(iso)
if out_iso:
if args.outfile:
ext = args.outfile.suffix
if ext == '.json':
out_iso.to_json(args.outfile)
elif ext == '.csv':
out_iso.to_csv(args.outfile)
elif ext == '.xls':
out_iso.to_xl(args.outfile)
else:
from pygaps.utilities.exceptions import ParsingError
raise ParsingError(f"Cannot export as '{ext}' files")
if args.verbose:
print(out_iso)
if plot:
import matplotlib.pyplot as plt
plt.show()
