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Commit de635f03 authored by payno's avatar payno
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remove ows_to_script

parent c3a99a5c
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est/app/ows_to_script.py deleted 100644 → 0
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
import sys
import argparse
from pypushflow.representation.scheme.ows_parser import OwsParser
from pypushflow import Workflow
import est.version
import pypushflow.version
import subprocess
import os
logging.basicConfig(level=logging.DEBUG)
_logger = logging.getLogger(__name__)
def _convert(scheme, output_file, overwrite):
"""
:param scheme:
:param scan:
:param timeout:
:return:
"""
_logger.warning("translate {} to {}".format(scheme, output_file))
if os.path.exists(output_file):
if overwrite is True:
os.remove(output_file)
else:
raise ValueError("{} already exists.".format(output_file))
with open(output_file, "w+") as file_:
file_.write(_dump_info_generation())
workflow = Workflow.ProcessableWorkflow(scheme)
converter = Workflow.Converter(
workflow=workflow, output_file=output_file, with_opts=True
)
converter.process()
# set up workflow
with open(output_file, mode="a") as file_:
file_.write(_dump_executable_script_section())
# call `black` on it if available
try:
# use help because there is no information regarding version
subprocess.call(["python", "-m", "black", output_file], stdout=subprocess.PIPE)
except Exception as e:
_logger.error(
"Fail to apply black on {}. Error is " "{}".format(output_file, e)
)
_logger.info(
"translation finished. You can execute python {} [[--input --input-spectra --input-spectra-dims --input-channel --input-energy-unit --input-dimensions]]".format(
output_file
)
)
def _dump_info_generation():
return (
"# This file has been generated automatically using \n"
"# pypushflow {} and est {}\n".format(
pypushflow.version.version, est.version.version
)
)
def _dump_executable_script_section():
return """
from pypushflow.utils import IgnoreProcess
if __name__ == '__main__':
import sys
import argparse
from est.app.utils import get_xas_obj
from est.app.utils import get_url
from est.app.utils import get_unit
from est.app.utils import convert_spectra_dims
from silx.io.url import DataUrl
from est.core.types import Dim
from est.io.utils.information import InputInformation
from est.io.utils.information import SpecInputInformation
parser = argparse.ArgumentParser(description=__doc__)
# single file input option
parser.add_argument(
"-i",
"--input",
dest="input_",
default=None,
help="Input of the workflow. Should be a path to a file",
)
# input url option
parser.add_argument(
"--input-spectra",
"--spectra",
dest="input_spectra",
default=None,
help="Input spectra url",
)
parser.add_argument(
"--input-spectra-dims",
"--spectra-dims",
dest="input_spectra_dims",
default=None,
help="Input spectra dimension. Should be a tuple of three values: "
"(X,Y,channel). If None will take the default dimension "
"according to the input type.",
)
parser.add_argument(
"--input-energy",
"--input-channel",
"--channel",
dest="input_channel",
default=None,
help="Input channel url (usually energy)",
)
parser.add_argument(
"--input-configuration",
"--configuration",
dest="input_configuration",
default=None,
help="Input configuration url",
)
parser.add_argument(
"--input-energy-unit",
"--energy-unit",
dest="input_energy_unit",
default="eV",
help="energy unit",
)
parser.add_argument(
"--input-dimensions",
"--dimensions",
dest="input_dimensions",
default="None",
help="dimension of the input as (Z,Y,X) for example."
"If None will take default unit according to the input type",
)
# I0, I1, I2 & mu_ref
parser.add_argument(
"--input-I0",
"--I0",
dest="input_I0",
default="None",
help="url to I0",
)
parser.add_argument(
"--input-I1",
"--I1",
dest="input_I1",
default="None",
help="url to I1",
)
parser.add_argument(
"--input-I2",
"--I2",
dest="input_I2",
default="None",
help="url to I2",
)
parser.add_argument(
"--input-mu-ref",
"--mu-ref",
dest="input_mu_ref",
default="None",
help="url to mu_ref",
)
# spec file specific inputs
parser.add_argument(
"--input-energy-col-name",
"--energy-col-name",
dest="input_energy_col_name",
default=None,
help="Provide name of the energy column for spec file",
)
parser.add_argument(
"--input-abs-col-name",
"--abs-col-name",
dest="input_abs_col_name",
default=None,
help="Provide name of the absorption column for spec file",
)
parser.add_argument(
"--input-monitor-col-name",
"--monitor-col-name",
dest="input_monitor_col_name",
default=None,
help="Provide name of the monitor column for spec file",
)
parser.add_argument(
"--input-scan-title",
"--scan-title",
dest="input_scan_title_name",
default=None,
help="Provide scan title name to consider",
)
# handle larch settings
parser.add_argument(
"--set-autobk-params",
dest="set_autobk_params",
default=None,
help="set autobk settings",
)
parser.add_argument(
"--set-mback-params",
dest="set_mback_params",
default=None,
help="set mback settings",
)
parser.add_argument(
"--set-mback-norm-params",
dest="set_mback_norm_params",
default=None,
help="set mback norm settings",
)
parser.add_argument(
"--set-pre-edge-params",
dest="set_pre_edge_params",
default=None,
help="set pre-edge settings",
)
parser.add_argument(
"--set-xftf-params",
dest="set_xftf_params",
default=None,
help="set xftf settings",
)
# handle noise settings
parser.add_argument(
"--set-noise-params",
dest="set_noise_params",
default=None,
help="set noise settings",
)
# handle output settings
parser.add_argument(
"--set-output-params",
dest="set_output_params",
default=None,
help="set output settings",
)
# handle energy roi settings
parser.add_argument(
"--set-energyroi-params",
dest="set_energyroi_params",
default=None,
help="set energy roi settings",
)
options = parser.parse_args(sys.argv[1:])
input_information = InputInformation(
spectra_url=get_url(options.input_spectra),
channel_url=get_url(options.input_channel),
dimensions=convert_spectra_dims(options.input_spectra_dims),
config_url=get_url(options.input_configuration),
energy_unit=get_unit(options.input_energy_unit),
spec_input=SpecInputInformation(
options.input_,
options.input_energy_col_name,
options.input_abs_col_name,
options.input_monitor_col_name,
options.input_scan_title_name,
),
)
input_information.I0 = get_url(options.input_I0)
input_information.I1 = get_url(options.input_I1)
input_information.I2 = get_url(options.input_I2)
input_information.mu_ref = get_url(options.input_mu_ref)
xas_obj = get_xas_obj(input_information)
main(input_data=xas_obj, channel="xas_obj", options=options)
"""
def main(argv):
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
"workflow_file",
help="Path to the .ows file defining the workflow to process with the"
"provided scan",
)
parser.add_argument("output_file", help="Output python file")
parser.add_argument(
"--overwrite",
help="Overwrite output file if exists",
default=False,
action="store_true",
)
parser.add_argument(
"--debug",
dest="debug",
action="store_true",
default=False,
help="Set logging system in debug mode",
)
options = parser.parse_args(argv[1:])
if not options.output_file.lower().endswith(".py"):
options.output_file = options.output_file + ".py"
# tune the log level
log_level = logging.INFO
if options.debug is True:
log_level = logging.DEBUG
for log_ in ("est", "pypushflow"):
logging.getLogger(log_).setLevel(log_level)
scheme = OwsParser.scheme_load(options.workflow_file, load_handlers=True)
_convert(
scheme=scheme, output_file=options.output_file, overwrite=options.overwrite
)
if __name__ == "__main__":
main(sys.argv)
# convert an ows file to a script calling est low level processes.
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