setting up xtreme plugins

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# X-Treme Bec
# X-Treme BEC
## Getting started
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
## Add your files
- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
```
cd existing_repo
git remote add origin https://gitlab.psi.ch/bec/xtreme-bec.git
git branch -M main
git push -uf origin main
```
## Integrate with your tools
- [ ] [Set up project integrations](https://gitlab.psi.ch/bec/xtreme-bec/-/settings/integrations)
## Collaborate with your team
- [ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
- [ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
- [ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
- [ ] [Enable merge request approvals](https://docs.gitlab.com/ee/user/project/merge_requests/approvals/)
- [ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
## Test and Deploy
Use the built-in continuous integration in GitLab.
- [ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
- [ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
- [ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
- [ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
- [ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
## Name
Choose a self-explaining name for your project.
## Description
Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
## Badges
On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
## Visuals
Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
## Installation
Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.
## Usage
Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
## Support
Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
## Roadmap
If you have ideas for releases in the future, it is a good idea to list them in the README.
## Contributing
State if you are open to contributions and what your requirements are for accepting them.
For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
## Authors and acknowledgment
Show your appreciation to those who have contributed to the project.
## License
For open source projects, say how it is licensed.
## Project status
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
X-Treme specific plugins and configs for BEC

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from .bec_client import *

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from .plugins import *

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from bec_client.scan_manager import ScanReport
from bec_utils.devicemanager import Device
# pylint:disable=undefined-variable
# pylint: disable=too-many-arguments
def dscan(
motor1: Device, m1_from: float, m1_to: float, steps: int, exp_time: float, **kwargs
) -> ScanReport:
"""Relative line scan with one device.
Args:
motor1 (Device): Device that should be scanned.
m1_from (float): Start position relative to the current position.
m1_to (float): End position relative to the current position.
steps (int): Number of steps.
exp_time (float): Exposure time.
Returns:
ScanReport: Status object.
Examples:
>>> dscan(dev.motor1, -5, 5, 10, 0.1)
"""
return scans.line_scan(
motor1, m1_from, m1_to, steps=steps, exp_time=exp_time, relative=True, **kwargs
)
def d2scan(
motor1: Device,
m1_from: float,
m1_to: float,
motor2: Device,
m2_from: float,
m2_to: float,
steps: int,
exp_time: float,
**kwargs
) -> ScanReport:
"""Relative line scan with two devices.
Args:
motor1 (Device): First device that should be scanned.
m1_from (float): Start position of the first device relative to its current position.
m1_to (float): End position of the first device relative to its current position.
motor2 (Device): Second device that should be scanned.
m2_from (float): Start position of the second device relative to its current position.
m2_to (float): End position of the second device relative to its current position.
steps (int): Number of steps.
exp_time (float): Exposure time
Returns:
ScanReport: Status object.
Examples:
>>> d2scan(dev.motor1, -5, 5, dev.motor2, -8, 8, 10, 0.1)
"""
return scans.line_scan(
motor1,
m1_from,
m1_to,
motor2,
m2_from,
m2_to,
steps=steps,
exp_time=exp_time,
relative=True,
**kwargs
)
def ascan(motor1, m1_from, m1_to, steps, exp_time, **kwargs):
"""Absolute line scan with one device.
Args:
motor1 (Device): Device that should be scanned.
m1_from (float): Start position.
m1_to (float): End position.
steps (int): Number of steps.
exp_time (float): Exposure time.
Returns:
ScanReport: Status object.
Examples:
>>> ascan(dev.motor1, -5, 5, 10, 0.1)
"""
return scans.line_scan(
motor1, m1_from, m1_to, steps=steps, exp_time=exp_time, relative=False, **kwargs
)
def a2scan(motor1, m1_from, m1_to, motor2, m2_from, m2_to, steps, exp_time, **kwargs):
"""Absolute line scan with two devices.
Args:
motor1 (Device): First device that should be scanned.
m1_from (float): Start position of the first device.
m1_to (float): End position of the first device.
motor2 (Device): Second device that should be scanned.
m2_from (float): Start position of the second device.
m2_to (float): End position of the second device.
steps (int): Number of steps.
exp_time (float): Exposure time
Returns:
ScanReport: Status object.
Examples:
>>> a2scan(dev.motor1, -5, 5, dev.motor2, -8, 8, 10, 0.1)
"""
return scans.line_scan(
motor1,
m1_from,
m1_to,
motor2,
m2_from,
m2_to,
steps=steps,
exp_time=exp_time,
relative=False,
**kwargs
)
def dmesh(motor1, m1_from, m1_to, m1_steps, motor2, m2_from, m2_to, m2_steps, exp_time, **kwargs):
"""Relative mesh scan (grid scan) with two devices.
Args:
motor1 (Device): First device that should be scanned.
m1_from (float): Start position of the first device relative to its current position.
m1_to (float): End position of the first device relative to its current position.
m1_steps (int): Number of steps for motor1.
motor2 (Device): Second device that should be scanned.
m2_from (float): Start position of the second device relative to its current position.
m2_to (float): End position of the second device relative to its current position.
m2_steps (int): Number of steps for motor2.
exp_time (float): Exposure time
Returns:
ScanReport: Status object.
Examples:
>>> dmesh(dev.motor1, -5, 5, 10, dev.motor2, -8, 8, 10, 0.1)
"""
return scans.grid_scan(
motor1,
m1_from,
m1_to,
m1_steps,
motor2,
m2_from,
m2_to,
m2_steps,
exp_time=exp_time,
relative=True,
)
def amesh(motor1, m1_from, m1_to, m1_steps, motor2, m2_from, m2_to, m2_steps, exp_time, **kwargs):
"""Absolute mesh scan (grid scan) with two devices.
Args:
motor1 (Device): First device that should be scanned.
m1_from (float): Start position of the first device.
m1_to (float): End position of the first device.
m1_steps (int): Number of steps for motor1.
motor2 (Device): Second device that should be scanned.
m2_from (float): Start position of the second device.
m2_to (float): End position of the second device.
m2_steps (int): Number of steps for motor2.
exp_time (float): Exposure time
Returns:
ScanReport: Status object.
Examples:
>>> amesh(dev.motor1, -5, 5, 10, dev.motor2, -8, 8, 10, 0.1)
"""
return scans.grid_scan(
motor1,
m1_from,
m1_to,
m1_steps,
motor2,
m2_from,
m2_to,
m2_steps,
exp_time=exp_time,
relative=False,
)
def umv(*args) -> ScanReport:
"""Updated absolute move (i.e. blocking) for one or more devices.
Returns:
ScanReport: Status object.
Examples:
>>> umv(dev.samx, 1)
>>> umv(dev.samx, 1, dev.samy, 2)
"""
return scans.umv(*args, relative=False)
def umvr(*args) -> ScanReport:
"""Updated relative move (i.e. blocking) for one or more devices.
Returns:
ScanReport: Status object.
Examples:
>>> umvr(dev.samx, 1)
>>> umvr(dev.samx, 1, dev.samy, 2)
"""
return scans.umv(*args, relative=True)
def mv(*args) -> ScanReport:
"""Absolute move for one or more devices.
Returns:
ScanReport: Status object.
Examples:
>>> mv(dev.samx, 1)
>>> mv(dev.samx, 1, dev.samy, 2)
"""
return scans.mv(*args, relative=False)
def mvr(*args) -> ScanReport:
"""Relative move for one or more devices.
Returns:
ScanReport: Status object.
Examples:
>>> mvr(dev.samx, 1)
>>> mvr(dev.samx, 1, dev.samy, 2)
"""
return scans.mv(*args, relative=True)

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"""
Post startup script for the BEC client. This script is executed after the
IPython shell is started. It is used to load the beamline specific
information and to setup the prompts.
The script is executed in the global namespace of the IPython shell. This
means that all variables defined here are available in the shell.
If needed, bec command-line arguments can be parsed here. For example, to
parse the --session argument, add the following lines to the script:
import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--session", help="Session name", type=str, default="my_default_session")
args = parser.parse_args()
if args.session == "my_session":
print("Loading my_session session")
from bec_plugins.bec_client.plugins.my_session import *
else:
print("Loading default session")
from bec_plugins.bec_client.plugins.default_session import *
"""
# pylint: disable=invalid-name, unused-import, import-error, undefined-variable, unused-variable, unused-argument, no-name-in-module
from bec_lib.core import bec_logger
logger = bec_logger.logger
logger.info("Using the XTreme startup script.")
# SETUP BEAMLINE INFO
from bec_client.plugins.SLS.sls_info import OperatorInfo, SLSInfo
bec._beamline_mixin._bl_info_register(SLSInfo)
bec._beamline_mixin._bl_info_register(OperatorInfo)
# SETUP PROMPTS
bec._ip.prompts.username = "XTreme"
bec._ip.prompts.status = 1

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"""
Pre-startup script for BEC client. This script is executed before the BEC client
is started. It can be used to set up the BEC client configuration. The script is
executed in the global namespace of the BEC client. This means that all
variables defined here are available in the BEC client.
To set up the BEC client configuration, use the ServiceConfig class. For example,
to set the configuration file path, add the following lines to the script:
import pathlib
from bec_lib.core import ServiceConfig
current_path = pathlib.Path(__file__).parent.resolve()
CONFIG_PATH = f"{current_path}/<path_to_my_config_file.yaml>"
config = ServiceConfig(CONFIG_PATH)
If this startup script defined a ServiceConfig object, the BEC client will use
it to configure itself. Otherwise, the BEC client will use the default config.
"""
CONFIG_PATH = "/sls/X07MA/data/x07maop/SW/bec/bec/bec_client_config.yaml"
config = ServiceConfig(CONFIG_PATH)

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import os
def setup_epics_ca():
os.environ["EPICS_CA_AUTO_ADDR_LIST"] = "NO"
os.environ["EPICS_CA_ADDR_LIST"] = "129.129.112.255 sls-x07ma-cagw.psi.ch:5836"
os.environ["PYTHONIOENCODING"] = "latin1"
def run():
setup_epics_ca()

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import time
import numpy as np
from bec_lib.core import bec_logger
from scan_server.scans import FlyScanBase, ScanArgType, ScanBase
logger = bec_logger.logger
class OTFScan(FlyScanBase):
scan_name = "otf_scan"
scan_report_hint = "table"
required_kwargs = ["e1", "e2", "time"]
arg_input = []
arg_bundle_size = len(arg_input)
def __init__(self, *args, parameter=None, **kwargs):
"""Scans the energy from e1 to e2 in <time> minutes.
Examples:
>>> scans.otf_scan(e1=700, e2=740, time=4)
"""
super().__init__(parameter=parameter, **kwargs)
self.axis = []
self.scan_motors = []
self.num_pos = 0
self.mono = self.caller_kwargs.get("mono", "mono")
self.otf_device = self.caller_kwargs.get("otf", "otf")
def scan_core(self):
yield from self.stubs.set(
device=self.mono, value=self.caller_kwargs["e1"], wait_group="flyer"
)
yield from self.stubs.wait(device=[self.mono], wait_group="flyer", wait_type="move")
yield from self.stubs.kickoff(
device=self.otf_device,
parameter={
key: val for key, val in self.caller_kwargs.items() if key in ["e1", "e2", "time"]
},
)
yield from self.stubs.wait(device=[self.otf_device], wait_group="kickoff", wait_type="move")
yield from self.stubs.complete(device=self.otf_device)
target_diid = self.DIID - 1
while True:
yield from self.stubs.read_and_wait(group="primary", wait_group="readout_primary")
status = self.stubs.get_req_status(
device=self.otf_device, RID=self.metadata["RID"], DIID=target_diid
)
progress = self.stubs.get_device_progress(
device=self.otf_device, RID=self.metadata["RID"]
)
if progress:
self.num_pos = progress
if status:
break
time.sleep(1)
class HystScan(ScanBase):
scan_name = "hyst_scan"
scan_report_hint = "table"
required_kwargs = []
arg_input = [
ScanArgType.DEVICE,
ScanArgType.FLOAT,
ScanArgType.FLOAT,
ScanArgType.DEVICE,
ScanArgType.FLOAT,
ScanArgType.FLOAT,
]
arg_bundle_size = 3
scan_type = "step"
default_ramp_rate = 2
def __init__(self, *args, parameter=None, **kwargs):
"""
A hysteresis scan.
scans.hyst_scan(field_motor, start_field, end_field, mono, energy1, energy2)
Examples:
>>> scans.hyst_scan(dev.field_x, 0, 0.5, dev.mono, 600, 640, ramp_rate=2)
"""
super().__init__(parameter=parameter, **kwargs)
self.axis = []
self.flyer = list(self.caller_args.keys())[0]
self.energy_motor = list(self.caller_args.keys())[1]
self.scan_motors = [self.energy_motor, self.flyer]
self.flyer_positions = self.caller_args[self.flyer]
self._current_scan_motor_index = 0
self._scan_motor_direction = 1
self.ramp_rate = self.caller_kwargs.get("ramp_rate", self.default_ramp_rate)
def _calculate_positions(self) -> None:
self.positions = [[pos] for pos in self.caller_args[self.energy_motor]]
def prepare_positions(self):
self._calculate_positions()
self.num_pos = 0
yield None
self._check_limits()
def _at_each_point(self):
yield from self.stubs.read(group="primary", wait_group="primary", pointID=self.pointID)
self.pointID += 1
def _get_next_scan_motor_position(self):
while True:
yield self.positions[self._current_scan_motor_index][0]
if len(self.positions) - 1 == self._current_scan_motor_index or (
self._current_scan_motor_index == 0 and self._scan_motor_direction < 0
):
self._scan_motor_direction *= -1
self._current_scan_motor_index += self._scan_motor_direction
def scan_core(self):
# yield from self._move_and_wait(self.positions[0])
status = yield from self.stubs.send_rpc_and_wait(
"field_x", "ramprate.set", self.default_ramp_rate
)
status.wait()
yield from self.stubs.set(
device=self.flyer, value=self.flyer_positions[0], wait_group="flyer"
)
yield from self.stubs.wait(device=[self.flyer], wait_group="flyer", wait_type="move")
status = yield from self.stubs.send_rpc_and_wait("field_x", "ramprate.set", self.ramp_rate)
status.wait()
# send the slow motor on its way
yield from self.stubs.set(
device=self.flyer,
value=self.flyer_positions[1],
wait_group="flyer",
)
flyer_done = False
pos_generator = self._get_next_scan_motor_position()
target_DIID = self.DIID - 1
dev = self.device_manager.devices
while not flyer_done:
flyer_done = bool(
self.stubs.get_req_status(
device=self.flyer, DIID=target_DIID, RID=self.metadata["RID"]
)
)
val = next(pos_generator)
logger.info(f"Moving mono to {val}.")
yield from self.stubs.set(device=self.energy_motor, value=val, wait_group="mono")
yield from self.stubs.wait(
device=[self.energy_motor], wait_group="mono", wait_type="move"
)
monitored_devices = [dev.name for dev in dev.monitored_devices([])]
yield from self.stubs.read_and_wait(
device=[self.flyer, self.scan_motors[0], *monitored_devices],
wait_group="readout_primary",
pointID=self.pointID,
)
# time.sleep(1)
self.pointID += 1
self.scan_motors[0]
self.num_pos += 1
status = yield from self.stubs.send_rpc_and_wait(
"field_x", "ramprate.set", self.default_ramp_rate
)
status.wait()
def return_to_start(self):
yield None

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# This file is used to select the BEC and Ophyd Devices version for the auto deployment process.
# Do not edit this file unless you know what you are doing!
# The version can be a git tag, branch or commit hash.
# BEC version to use
BEC_AUTODEPLOY_VERSION="master"
# ophyd_devices version to use
OPHYD_DEVICES_AUTODEPLOY_VERSION="master"

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redis:
host: localhost
port: 6379
mongodb:
host: localhost
port: 27017
scibec:
host: http://[::1]
port: 3030
beamline: "XTREME"
service_config:
general:
reset_queue_on_cancel: True
enforce_ACLs: False
file_writer:
plugin: default_NeXus_format
base_path: ./

28
deployment/deploy.sh Executable file
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# deployment script to be translated to Ansible
# NOT NEEDED since the beamline repo will be autodeployed
# BEAMLINE_REPO=gitlab.psi.ch:bec/csaxs-bec.git
# git clone git@$BEAMLINE_REPO
module add psi-python38/2020.11
# start redis
docker run --network=host --name redis-bec -d redis
# alternative:
# conda install -y redis; redis-server &
# get the target versions for ophyd_devices and BEC
source ./csaxs-bec/deployment/autodeploy_versions
git clone -b $OPHYD_DEVICES_AUTODEPLOY_VERSION https://gitlab.psi.ch/bec/ophyd_devices.git
git clone -b $BEC_AUTODEPLOY_VERSION https://gitlab.psi.ch/bec/bec.git
# install BEC
cd bec
source ./bin/install_bec_dev.sh
cd ../
# start the BEC server
bec-server start --config ./xtreme-bec/deployment/bec-server-config.yaml

21
setup.cfg Normal file
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[metadata]
name = bec_plugins
description = BEC plugins to modify the behaviour of services within the BEC framework
long_description = file: README.md
long_description_content_type = text/markdown
url = https://gitlab.psi.ch/bec/bec
project_urls =
Bug Tracker = https://gitlab.psi.ch/bec/bec/issues
classifiers =
Programming Language :: Python :: 3
Development Status :: 3 - Alpha
Topic :: Scientific/Engineering
[options]
package_dir =
= .
packages = find:
python_requires = >=3.8
[options.packages.find]
where = .

7
setup.py Normal file
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from setuptools import setup
if __name__ == "__main__":
setup(
install_requires=[],
extras_require={"dev": ["pytest", "pytest-random-order", "coverage"]},
)