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Commit 536e90ff authored by payno's avatar payno
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Merge branch 'esrftaskgraph_prototype' into 'master' 

Move Process to Ewoks `Task` and update setup

See merge request workflow/est!40
parents 7dc04564 8a512d0f
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.gitlab-ci.yml
View file @ 536e90ff
......@@ -34,8 +34,6 @@ doc:
- python --version
- python -m pip install pip --upgrade
- python -m pip install setuptools --upgrade
- python -m pip install -r requirements.txt
- python -m pip install -r requirements-doc.txt
- python -m pip install jupyterlab
- python -m pip install pymca --upgrade --pre
- python -m pip install xraylarch
......@@ -43,7 +41,7 @@ doc:
- mkdir artifacts
script:
- python setup.py build
- python -m pip install .
- python -m pip install .[doc]
- python setup.py build_sphinx
- mv build/sphinx/html artifacts/doc
artifacts:
......@@ -75,10 +73,7 @@ doc:
- install_anyqt 'master'
- python -m pip install fabio --upgrade --pre
- python -m pip install silx --upgrade --pre
- python -m pip install -r requirements.txt
- python -m pip install pymca --upgrade --pre
- python -m pip install orange3==3.21
- python -m pip install -r requirements.txt
- python -m pip install .
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python -m pytest est
......@@ -102,13 +97,9 @@ doc:
- source ./ci/install_scripts.sh
- install_anyqt 'master'
- python -m pip install fabio --upgrade --pre
# - python -m pip install -r requirements.txt
- python -m pip install silx --upgrade --pre
- python -m pip install -r requirements.txt
- python -m pip install packaging
- python -m pip install xraylarch
- python -m pip install orange3==3.21
- python -m pip install -r requirements.txt
- python -m pip install .
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python -m pytest est
......@@ -132,14 +123,10 @@ doc:
- source ./ci/install_scripts.sh
- install_anyqt 'master'
- python -m pip install fabio --upgrade --pre
# - python -m pip install -r requirements.txt
- python -m pip install silx --upgrade --pre
- python -m pip install pymca --upgrade --pre
- python -m pip install -r requirements.txt
- python -m pip install packaging
- python -m pip install xraylarch
- python -m pip install orange3==3.21
- python -m pip install -r requirements.txt
- python -m pip install .
- /usr/bin/xvfb-run --server-args="-screen 0 1024x768x24" -a python -m pytest --cov=est est
......@@ -177,7 +164,6 @@ test:test-est-tutorials_pymca:
- python -m pip install ipykernel
- python -m pip install pymca --upgrade --pre
- python -m pip install silx --upgrade --pre
- python -m pip install -r requirements.txt
- python -m pip install .
- ls doc/tutorials/
script:
......
est/__init__.py
View file @ 536e90ff
......@@ -39,11 +39,8 @@ _logging.getLogger(__name__).addHandler(_logging.NullHandler())
project = _os.path.basename(_os.path.dirname(_os.path.abspath(__file__)))
try:
from ._version import __date__ as date # noqa
from ._version import version, version_info, hexversion, strictversion # noqa
except ImportError:
pass
# not raised for now because fail with pip install -e option. Something to
# look at.
# raise RuntimeError("Do NOT use %s from its sources: build it and use the built version" % project)
from .version import __date__ as date # noqa
from .version import version, version_info, hexversion, strictversion # noqa
__version__ = version
est/app/canvas_launcher/__init__.py
View file @ 536e90ff
from .launcher import Launcher
from .launcher import Launcher # noqa
est/app/ows_to_script.py deleted 100644 → 0
View file @ 7dc04564
#!/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.
est/app/process.py
View file @ 536e90ff
import argparse
import sys
from pypushflow.Workflow import ProcessableWorkflow
from pypushflow.representation.scheme.ows_parser import OwsParser
import logging
import signal
from pypushflow.representation.scheme.scheme import Scheme
from silx.io.url import DataUrl
from est.units import ur
from est.io.utils.information import InputInformation
from est.io.utils.information import SpecInputInformation
from ewoksorange.owsconvert import ows_to_ewoks
from .utils import get_unit
from .utils import get_url
from .utils import convert_spectra_dims
from .utils import get_xas_obj
try:
import h5py
has_h5py = True
except:
import h5py # noqa
except ImportError:
has_h5py = False
from typing import Union
else:
has_h5py = True
logging.basicConfig(level=logging.DEBUG)
_logger = logging.getLogger(__name__)
def _insert_input_in_scheme(scheme, input_information):
"""update 'starting' node properties to include the provided input"""
# monkey patch the input file for start nodes if an input is given
for node in scheme.nodes:
if node.properties and "_spec_file_setting" in node.properties:
if input_information.is_spec_input():
node.properties["_spec_file_setting"] = input_information.spec_info
if input_information.spectra_url is not None:
node.properties[
"_spectra_url_setting"
] = input_information.spectra_url.path()
if input_information.dimensions is not None:
node.properties["_dimensions_setting"] = input_information.dimensions
if input_information.channel_url is not None:
node.properties[
"_energy_url_setting"
] = input_information.channel_url.path()
if input_information.configuration_url is not None:
node.properties[
"_configuration_url_setting"
] = input_information.configuration_url.path()
def _insert_output_in_scheme(scheme, output_):
"""update 'starting' node properties to include the provided input"""
found_output = False
# monkey patch the input file for start nodes if an input is given
for node in scheme.nodes:
if node.properties and "_output_file_setting" in node.properties:
node.properties["_output_file_setting"] = output_
found_output = True
if not found_output:
_logger.warning(
"No node for processing output found. output "
"information provided will be ignored"
)
def exec_(
scheme: Scheme,
input_information: InputInformation,
output_: Union[str, None, dict] = None,
timeout: Union[int, None] = None,
):
if not input_information.is_valid():
raise ValueError("You cannot provide an input file and input urls")
_insert_input_in_scheme(input_information=input_information, scheme=scheme)
if output_ is not None:
_insert_output_in_scheme(scheme=scheme, output_=output_)
workflow = ProcessableWorkflow(scheme=scheme)
# add SIGINT capture
def signal_handler(sig, frame):
_logger.warning("stop workflow execution on user request")
workflow._end_actor.join(0)
sys.exit(0)
signal.signal(signal.SIGINT, signal_handler)
xas_obj = get_xas_obj(input_information=input_information)
workflow._start_actor.trigger(("data", xas_obj.to_dict()))
workflow._end_actor.join(timeout)
res = workflow._end_actor.out_data
title = scheme.title or "unknow"
_logger.info(
"workflow '{}' completed with {}".format(title, str(input_information))
)
return res
def main(argv):
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
......@@ -157,7 +76,7 @@ def main(argv):
"--input-dimensions",
"--dimensions",
dest="input_dimensions",
default="None",
default=None,
help="dimension of the input as (Z,Y,X) for example."
"If None will take default unit according to the input type",
)
......@@ -166,28 +85,28 @@ def main(argv):
"--input-I0",
"--I0",
dest="input_I0",
default="None",
default=None,
help="url to I0",
)
parser.add_argument(
"--input-I1",
"--I1",
dest="input_I1",
default="None",
default=None,
help="url to I1",
)
parser.add_argument(
"--input-I2",
"--I2",
dest="input_I2",
default="None",
default=None,
help="url to I2",
)
parser.add_argument(
"--input-mu-ref",
"--mu-ref",
dest="input_mu_ref",
default="None",
default=None,
help="url to mu_ref",
)
# spec file specific inputs
......@@ -201,6 +120,8 @@ def main(argv):
parser.add_argument(
"--input-abs-col-name",
"--abs-col-name",
"--input-mu-col-name",
"--mu-col-name",
dest="input_abs_col_name",
default=None,
help="Provide name of the absorption column for spec file",
......@@ -223,14 +144,13 @@ def main(argv):
parser.add_argument(
"-o",
"--output",
dest="output_",
dest="output_file",
default=None,
help="Output file of the workflow. Require at most one "
"instance of XASOutputOW",
)
options = parser.parse_args(argv[1:])
scheme = OwsParser.scheme_load(options.workflow_file, load_handlers=True)
options = parser.parse_args(argv[1:])
input_information = InputInformation(
spectra_url=get_url(options.input_spectra),
channel_url=get_url(options.input_channel),
......@@ -249,7 +169,15 @@ def main(argv):
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)
exec_(scheme=scheme, input_information=input_information)
graph = ows_to_ewoks(filename=options.workflow_file)
varinfo = {
"input_information": input_information.to_dict(),
}
if options.output_file:
varinfo["output_file"] = options.output_file
graph.execute(varinfo=varinfo)
if __name__ == "__main__":
......
est/app/reprocessing.py deleted 100644 → 0
View file @ 7dc04564
import argparse
import sys
import logging
from est.core.types import XASObject
from est.core.reprocessing import get_process_instance_frm_h5_desc
from typing import Union
try:
import h5py
has_h5py = True
except:
has_h5py = False
logging.basicConfig(level=logging.DEBUG)
_logger = logging.getLogger(__name__)
def exec_(
h5_file: str,
entry: str = "scan1",
spectra_path: Union[None, str] = None,
energy_path: Union[None, str] = None,
configuration_path: Union[None, str] = None,
):