10 Commits

Author SHA1 Message Date
d1e035e01e Update repo with template version v1.2.8
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2026-02-27 15:49:26 +01:00
d49d9cef33 Update repo with template version v1.2.7
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2026-02-27 12:11:40 +01:00
a62fe77b56 fix: ipython startup
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2026-01-17 18:24:39 +01:00
e642cbaae8 refactor: upgrade copier to v1-2-2
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2025-09-11 18:24:35 +02:00
37bfc1c2a2 Merge branch 'update_copier_template' into 'main'
feat: update repository with copier changes for gitea migration

See merge request bec/addams_bec!4
2025-09-11 15:16:27 +02:00
63ded2bf7d feat: update repository with copier changes for gitea migration 2025-09-11 15:10:02 +02:00
0c3e7acea6 Merge branch 'chore/migrate_to_copier' into 'main'
chore: migrate to new plugin template

See merge request bec/addams_bec!2
2025-06-02 14:03:54 +02:00
e724ff4869 chore: migrate to new plugin template 2025-06-02 13:16:20 +02:00
2e52f6b274 Merge branch 'feature/energy_optimizer' into 'main'
Feature/energy optimizer

See merge request bec/addams_bec!1
2025-05-24 11:26:12 +02:00
dbda93ee12 feat: add EnergyOptimizer class with transition step calculation and tests 2025-05-24 11:24:05 +02:00
25 changed files with 597 additions and 216 deletions

9
.copier-answers.yml Normal file
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@@ -0,0 +1,9 @@
# Do not edit this file!
# It is needed to track the repo template version, and editing may break things.
# This file will be overwritten by copier on template updates.
_commit: v1.2.8
_src_path: https://github.com/bec-project/plugin_copier_template.git
make_commit: false
project_name: addams_bec
widget_plugins_input: []

102
.gitea/workflows/ci.yml Normal file
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@@ -0,0 +1,102 @@
name: CI for addams_bec
on:
push:
pull_request:
workflow_dispatch:
inputs:
BEC_WIDGETS_BRANCH:
description: "Branch of BEC Widgets to install"
required: false
type: string
default: "main"
BEC_CORE_BRANCH:
description: "Branch of BEC Core to install"
required: false
type: string
default: "main"
OPHYD_DEVICES_BRANCH:
description: "Branch of Ophyd Devices to install"
required: false
type: string
default: "main"
BEC_PLUGIN_REPO_BRANCH:
description: "Branch of the BEC Plugin Repository to install"
required: false
type: string
default: "main"
PYTHON_VERSION:
description: "Python version to use"
required: false
type: string
default: "3.12"
permissions:
pull-requests: write
jobs:
test:
runs-on: ubuntu-latest
env:
QTWEBENGINE_DISABLE_SANDBOX: 1
QT_QPA_PLATFORM: "offscreen"
steps:
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: "${{ inputs.PYTHON_VERSION || '3.12' }}"
- name: Checkout BEC Plugin Repository
uses: actions/checkout@v4
with:
repository: bec/addams_bec
ref: "${{ inputs.BEC_PLUGIN_REPO_BRANCH || github.head_ref || github.sha }}"
path: ./addams_bec
- name: Lint for merge conflicts from template updates
shell: bash
# Find all Copier conflicts except this line
run: '! grep -r "<<<<<<< before updating" | grep -v "grep -r \"<<<<<<< before updating"'
- name: Checkout BEC Core
uses: actions/checkout@v4
with:
repository: bec/bec
ref: "${{ inputs.BEC_CORE_BRANCH || 'main' }}"
path: ./bec
- name: Checkout Ophyd Devices
uses: actions/checkout@v4
with:
repository: bec/ophyd_devices
ref: "${{ inputs.OPHYD_DEVICES_BRANCH || 'main' }}"
path: ./ophyd_devices
- name: Checkout BEC Widgets
uses: actions/checkout@v4
with:
repository: bec/bec_widgets
ref: "${{ inputs.BEC_WIDGETS_BRANCH || 'main' }}"
path: ./bec_widgets
- name: Install dependencies
shell: bash
run: |
sudo apt-get update
sudo apt-get install -y libgl1 libegl1 x11-utils libxkbcommon-x11-0 libdbus-1-3 xvfb
sudo apt-get -y install libnss3 libxdamage1 libasound2t64 libatomic1 libxcursor1
- name: Install Python dependencies
shell: bash
run: |
pip install uv
uv pip install --system -e ./ophyd_devices
uv pip install --system -e ./bec/bec_lib[dev]
uv pip install --system -e ./bec/bec_ipython_client
uv pip install --system -e ./bec/bec_server[dev]
uv pip install --system -e ./bec_widgets[dev,pyside6]
uv pip install --system -e ./addams_bec
- name: Run Pytest with Coverage
id: coverage
run: pytest --random-order --cov=./addams_bec --cov-config=./addams_bec/pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./addams_bec/tests/ || test $? -eq 5

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@@ -0,0 +1,62 @@
name: Create template upgrade PR for addams_bec
on:
workflow_dispatch:
permissions:
pull-requests: write
jobs:
create_update_branch_and_pr:
runs-on: ubuntu-latest
permissions:
contents: write
pull-requests: write
steps:
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Install tools
run: |
pip install copier PySide6
- name: Checkout
uses: actions/checkout@v4
- name: Perform update
run: |
git config --global user.email "bec_ci_staging@psi.ch"
git config --global user.name "BEC automated CI"
branch="chore/update-template-$(python -m uuid)"
echo "switching to branch $branch"
git checkout -b $branch
echo "Running copier update..."
output="$(copier update --trust --defaults --conflict inline 2>&1)"
echo "$output"
msg="$(printf '%s\n' "$output" | head -n 1)"
if ! grep -q "make_commit: true" .copier-answers.yml ; then
echo "Autocommit not made, committing..."
git add -A
git commit -a -m "$msg"
fi
if diff-index --quiet HEAD ; then
echo "No changes detected"
exit 0
fi
git push -u origin $branch
curl -X POST "https://gitea.psi.ch/api/v1/repos/${{ gitea.repository }}/pulls" \
-H "Authorization: token ${{ secrets.CI_REPO_WRITE }}" \
-H "Content-Type: application/json" \
-d "{
\"title\": \"Template: $(echo $msg)\",
\"body\": \"This PR was created by Gitea Actions\",
\"head\": \"$(echo $branch)\",
\"base\": \"main\"
}"

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@@ -1,4 +0,0 @@
include:
- file: /templates/plugin-repo-template.yml
inputs: {name: addams_bec, target: addams_bec}
project: bec/awi_utils

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@@ -1,6 +1,7 @@
BSD 3-Clause License
Copyright (c) 2024, Paul Scherrer Institute
Copyright (c) 2025, Paul Scherrer Institute
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:
@@ -25,4 +26,4 @@ DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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@@ -1,75 +1,57 @@
import builtins
import collections
import functools
import json
import math
import pathlib
import numpy
from bec_ipython_client.main import BECClientPrompt
from bec_ipython_client.prettytable import PrettyTable
__all__ = [
'setlat',
'setlambda',
'setmode',
'freeze',
'unfreeze',
'br',
'ubr',
'mvhkl',
'umvhkl',
'ca',
'wh',
'pa',
'orientAdd',
'orientRemove',
'orientShow',
'orientFit',
'ct'
"setlat",
"setlambda",
"setmode",
"freeze",
"unfreeze",
"br",
"ubr",
"mvhkl",
"umvhkl",
"ca",
"wh",
"pa",
"orientAdd",
"orientRemove",
"orientShow",
"orientFit",
"ct",
]
bec = builtins.__dict__.get("bec")
dev = builtins.__dict__.get("dev")
scans = builtins.__dict__.get("scans")
class BECClientPromptDiffractometer(BECClientPrompt):
@property
def username(self):
"""current username"""
if "x04v" in dev:
return "x04v"
if "x04h" in dev:
return "x04h"
return "demo"
bec._ip.prompts = BECClientPromptDiffractometer(ip=bec._ip, username="demo", client=bec._client, status=1)
# check for diffractometer device
diffract = None
if dev is not None:
if 'x04h' in dev:
if "x04h" in dev:
diffract = dev.x04h
elif 'x04v' in dev:
elif "x04v" in dev:
diffract = dev.x04v
if diffract is not None:
RealPosition = collections.namedtuple('RealPosition', ' '.join(diffract.get_real_positioners()))
RealPosition = collections.namedtuple("RealPosition", " ".join(diffract.get_real_positioners()))
def freeze(
angle: float | None
):
def freeze(angle: float | None):
"""
Freeze the value of the mode dependent angle, so when calculating motor positions
corresponding to an arbitrary (H, K, L ), the angle will be reset to the frozen value
Freeze the value of the mode dependent angle, so when calculating motor positions
corresponding to an arbitrary (H, K, L ), the angle will be reset to the frozen value
before the calculation no matter what the current position of the diffractometer.
"""
diffract.freeze(angle)
def unfreeze():
"""
Subsequent angle calculations will use whatever the current value of the associated
@@ -77,74 +59,69 @@ def unfreeze():
"""
diffract.unfreeze()
def setlat(
a: float, b: float, c: float, alpha: float, beta: float, gamma: float
):
def setlat(a: float, b: float, c: float, alpha: float, beta: float, gamma: float):
"""
Set sample lattice parameters
"""
diffract.set_lattice((a, b, c, alpha, beta, gamma))
def setlambda(
wavelength: float
):
def setlambda(wavelength: float):
"""
Set the x-ray wavelength (in Angstroms)
"""
if wavelength <= 0:
print('Invalid input: wavelength <=0!')
print("Invalid input: wavelength <=0!")
return
current_wavelength = diffract.get_wavelength()
if math.isclose(wavelength, current_wavelength):
print(f'Still using {current_wavelength} A')
print(f"Still using {current_wavelength} A")
else:
diffract.set_wavelength(wavelength)
print(f'Lambda reset from {current_wavelength} to {wavelength} A')
print(f"Lambda reset from {current_wavelength} to {wavelength} A")
def setmode(
mode: int
):
def setmode(mode: int):
"""
Set the geometry mode
"""
if mode < 0 or mode > 2:
print('Valid mode is from 0 to 2')
print("Valid mode is from 0 to 2")
return
current_mode = diffract.get_mode()
if mode == current_mode:
print(f'Still using mode {current_mode}')
print(f"Still using mode {current_mode}")
else:
diffract.set_mode(mode)
print(f'Mode reset from {current_mode} to {mode}')
print(f"Mode reset from {current_mode} to {mode}")
def mvhkl(
h: float, k: float, l: float, auto=False
):
def mvhkl(h: float, k: float, l: float, auto=False):
"""
Move to the reciprocol space coordinates
"""
try:
angles = diffract.forward(h, k, l)[:-2]
except Exception as exc:
print(f'{h} {k} {l} is not obtainable: {exc}')
print(f"{h} {k} {l} is not obtainable: {exc}")
return
if not auto:
for axis, current, target in zip(RealPosition._fields, _currentPosition(), angles):
print('%7s = %9.4f --> %9.4f' % (axis, current, target))
print("%7s = %9.4f --> %9.4f" % (axis, current, target))
answer = input('Move to these values? [Y/n]: ')
if answer.startswith(('N', 'n')):
print('Move abandoned.')
answer = input("Move to these values? [Y/n]: ")
if answer.startswith(("N", "n")):
print("Move abandoned.")
return
br(h, k, l)
def br(
h: float, k: float, l: float
):
def br(h: float, k: float, l: float):
"""
Move to the reciprocol space coordinates
"""
@@ -156,9 +133,8 @@ def br(
scans.mv(*args, relative=False)
def ubr(
h: float, k: float, l: float
):
def ubr(h: float, k: float, l: float):
"""
Move to the reciprocol space coordinates with updates
"""
@@ -170,44 +146,43 @@ def ubr(
scans.umv(*args, relative=False)
def umvhkl(
h: float, k: float, l: float, auto=False
):
def umvhkl(h: float, k: float, l: float, auto=False):
"""
Move to the reciprocol space coordinates with updates
"""
try:
angles = diffract.forward(h, k, l)[:-2]
except Exception as exc:
print(f'{h} {k} {l} is not obtainable: {exc}')
print(f"{h} {k} {l} is not obtainable: {exc}")
return
if not auto:
for axis, current, target in zip(RealPosition._fields, _currentPosition(), angles):
print('%7s = %9.4f --> %9.4f' % (axis, current, target))
print("%7s = %9.4f --> %9.4f" % (axis, current, target))
answer = input('Move to these values? [Y/n]: ')
if answer.startswith(('N', 'n')):
print('Move abandoned.')
answer = input("Move to these values? [Y/n]: ")
if answer.startswith(("N", "n")):
print("Move abandoned.")
return
ubr(h, k, l)
def ca(
h: float, k: float, l: float
):
def ca(h: float, k: float, l: float):
"""
Calculate angle positions for a given point in reciprocol space
"""
angles = diffract.forward(h, k, l)
print("\nCalculated positions:\n")
print(f'H K L = {h} {k} {l}')
print('BetaIn = %.5f BetaOut = %.5f' %(angles[-2], angles[-1]))
print('Lambda = %.3f' % diffract.get_wavelength())
print(f"H K L = {h} {k} {l}")
print("BetaIn = %.5f BetaOut = %.5f" % (angles[-2], angles[-1]))
print("Lambda = %.3f" % diffract.get_wavelength())
print()
_showAngles(angles[:-2])
def wh():
"""
Show where principal axes and reciprocal space
@@ -218,41 +193,45 @@ def wh():
betaIn = diffract.betaIn.position
betaOut = diffract.betaOut.position
print(f'H K L = {h:.4f} {k:.4f} {l:.4f}')
print('BetaIn = %.5f BetaOut = %.5f' %(betaIn, betaOut))
print('Lambda = %.3f' % diffract.get_wavelength())
print(f"H K L = {h:.4f} {k:.4f} {l:.4f}")
print("BetaIn = %.5f BetaOut = %.5f" % (betaIn, betaOut))
print("Lambda = %.3f" % diffract.get_wavelength())
print()
_showAngles()
def pa():
"""
Show geometry parameters
"""
if diffract.name == 'x04v':
print('x04v (Newport Microcontrols 2+3 at SLS) vertical geometry')
elif diffract.name == 'x04h':
print('x04h (Newport Microcontrols 2+3 at SLS) horizontal geometry')
if diffract.name == "x04v":
print("x04v (Newport Microcontrols 2+3 at SLS) vertical geometry")
elif diffract.name == "x04h":
print("x04h (Newport Microcontrols 2+3 at SLS) horizontal geometry")
match mode := diffract.get_mode():
case 0:
print(f' BetaIn Fixed (mode {mode})')
print(f" BetaIn Fixed (mode {mode})")
case 1:
print(f' BetaOut Fixed (mode {mode})')
print(f" BetaOut Fixed (mode {mode})")
case 2:
print(f' BetaIn equals BetaOut (mode {mode})')
print(f" BetaIn equals BetaOut (mode {mode})")
if beta_frozen := diffract.get_frozen():
print(f' Frozen coordinate: {beta_frozen}')
print(f" Frozen coordinate: {beta_frozen}")
def orientShow():
"""
Display list of measured reflections
"""
print('\n(Using lattice constants:)')
print("\n(Using lattice constants:)")
lattice = diffract.get_lattice()
print('a = %.4g, b = %.4g, b = %.4g, alpha = %.6g, beta = %.6g, gamma = %.6g' %
(lattice[0], lattice[1], lattice[2], lattice[3], lattice[4], lattice[5]))
print(
"a = %.4g, b = %.4g, b = %.4g, alpha = %.6g, beta = %.6g, gamma = %.6g"
% (lattice[0], lattice[1], lattice[2], lattice[3], lattice[4], lattice[5])
)
print("\n------------------------------------------------\n")
@@ -263,17 +242,15 @@ def orientShow():
_showUB()
def orientRemove(
h: float, k: float, l: float
):
def orientRemove(h: float, k: float, l: float):
"""
Remove a measured reflection from the list
"""
diffract.remove_reflection(h, k, l)
def orientAdd(
h: float, k: float, l: float, *args
):
def orientAdd(h: float, k: float, l: float, *args):
"""
Add a reflection to the list of measured reflections
"""
@@ -282,63 +259,67 @@ def orientAdd(
response = diffract.real_position
# The original return value is of namedtuple type,
# which gets serialized to a dictionary by the device server.
angles = tuple(response['values'][axis] for axis in response['fields'] if axis != 'nu')
angles = tuple(response["values"][axis] for axis in response["fields"] if axis != "nu")
if len(angles) < 4:
print('Please specify all angles')
print("Please specify all angles")
return
diffract.add_reflection(h, k, l, angles)
def orientSave(
filename: str
):
def orientSave(filename: str):
"""
Save the current reflections
"""
configuration = {}
configuration['geometry'] = diffract.name
configuration['wavelength'] = diffract.get_wavelength()
configuration['lattice'] = diffract.get_lattice()
configuration['reflections'] = diffract.get_reflections()
configuration["geometry"] = diffract.name
configuration["wavelength"] = diffract.get_wavelength()
configuration["lattice"] = diffract.get_lattice()
configuration["reflections"] = diffract.get_reflections()
filepath = pathlib.Path(filename)
if filepath.exists():
answer = input('File "%s" already exists. Do you want to overwrite it? [y/N]: ' %(filepath.absolute()))
if not answer.startswith(('Y', 'y')):
answer = input(
'File "%s" already exists. Do you want to overwrite it? [y/N]: ' % (filepath.absolute())
)
if not answer.startswith(("Y", "y")):
return
with open(filepath, 'w') as f:
with open(filepath, "w") as f:
json.dump(configuration, f)
def orientLoad(
filename: str
):
def orientLoad(filename: str):
"""
Load relfections from file
"""
with open(filename, 'r') as f:
with open(filename, "r") as f:
configuration = json.load(f)
if configuration['geometry'] != diffract.name:
print('Saved orientation is for a different geometry "%s", current is "%s".' % configuration['geometry'], diffract.name)
if configuration["geometry"] != diffract.name:
print(
'Saved orientation is for a different geometry "%s", current is "%s".'
% configuration["geometry"],
diffract.name,
)
return
# save current wavelength, lattice and reflections
saved_wavelength = diffract.get_wavelength()
saved_lattice = diffract.get_lattice()
saved_reflections = diffract.get_reflections()
try:
diffract.set_lattice(configuration['lattice'])
diffract.set_lattice(configuration["lattice"])
diffract.clear_reflections()
for reflection in configuration['reflections']:
for reflection in configuration["reflections"]:
diffract.add_reflection(*reflection)
_showReflections(configuration['reflections'])
_showReflections(configuration["reflections"])
print("\n------------------------------------------------\n")
# set wavelength temporarily for orientFit and restore later
diffract.set_wavelength(configuration['wavelength'])
diffract.set_wavelength(configuration["wavelength"])
orientFit()
except Exception as exc:
# restore saved lattice and reflections
@@ -352,6 +333,7 @@ def orientLoad(
# restore wavelength
diffract.set_wavelength(saved_wavelength)
def orientFit():
"""
Fit UB matrix from given reflections
@@ -364,19 +346,22 @@ def orientFit():
diffract.compute_UB()
_showUB()
def ct(exp_time: float):
"""
Acquire all detectors
"""
scans.acquire(exp_time=exp_time)
def _showUB():
UB = diffract.get_UB()
print('Orientation matrix by row:')
print(' Row 1: %8.5f %8.5f %8.5f' % (UB[0,0], UB[0,1], UB[0,2]))
print(' Row 2: %8.5f %8.5f %8.5f' % (UB[1,0], UB[1,1], UB[1,2]))
print(' Row 3: %8.5f %8.5f %8.5f' % (UB[2,0], UB[2,1], UB[2,2]))
print("Orientation matrix by row:")
print(" Row 1: %8.5f %8.5f %8.5f" % (UB[0, 0], UB[0, 1], UB[0, 2]))
print(" Row 2: %8.5f %8.5f %8.5f" % (UB[1, 0], UB[1, 1], UB[1, 2]))
print(" Row 3: %8.5f %8.5f %8.5f" % (UB[2, 0], UB[2, 1], UB[2, 2]))
def _showAngles(angles=None):
if angles is None:
@@ -384,23 +369,25 @@ def _showAngles(angles=None):
table = PrettyTable(RealPosition._fields, padding=12)
print(table.get_header())
text = tuple(f'{x:9.4f}' for x in angles)
text = tuple(f"{x:9.4f}" for x in angles)
print(table.get_row(*text))
def _currentPosition():
response = diffract.real_position
# The original return value is of namedtuple type,
# which gets serialized to a dictionary by the device server.
angles = RealPosition(*(response['values'][axis] for axis in response['fields']))
angles = RealPosition(*(response["values"][axis] for axis in response["fields"]))
return angles
def _showReflections(reflections):
print('The defined reflections are:')
header = ['h', 'k', 'l'] + diffract.real_position['fields'][:-1]
print("The defined reflections are:")
header = ["h", "k", "l"] + diffract.real_position["fields"][:-1]
table = PrettyTable(header, padding=12)
print(' ', table.get_header())
print(" ", table.get_header())
for reflection in reflections:
h, k, l, angles = reflection
text = [f'{h:9.4f}', f'{k:9.4f}', f'{l:9.4f}'] + [f'{x:9.4f}' for x in angles]
print(' ', table.get_row(*text))
text = [f"{h:9.4f}", f"{k:9.4f}", f"{l:9.4f}"] + [f"{x:9.4f}" for x in angles]
print(" ", table.get_row(*text))

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@@ -0,0 +1,83 @@
from __future__ import annotations
from typing import TYPE_CHECKING, List, Tuple
if TYPE_CHECKING: # pragma: no cover
from bec_lib.devicemanager import DeviceManagerBase as DeviceManager
class EnergyOptimizer:
def __init__(self, device_manager: DeviceManager):
self.device_manager = device_manager
self.strips = {
"Si": {"energy_range": [5, 10]},
"Rh": {"energy_range": [8, 23]},
"Pt": {"energy_range": [20, 40]},
}
self.overlap_energyies = {"Si": {"Rh": 9}, "Rh": {"Si": 9, "Pt": 22}, "Pt": {"Rh": 22}}
@staticmethod
def get_transition_steps(start_energy: float, target_energy: float) -> List[Tuple[float, str]]:
"""
Get the required steps to transition from one energy to another.
Args:
start_energy: The starting energy in keV.
target_energy: The target energy in keV.
Returns:
A list of tuples containing the energy and the strip name for each step.
"""
strips = {"Si": (5, 10), "Rh": (8, 23), "Pt": (20, 40)}
overlap_energyies = {"Si": {"Rh": 9}, "Rh": {"Si": 9, "Pt": 22}, "Pt": {"Rh": 22}}
def get_strip(energy: float) -> str:
for strip, (low, high) in strips.items():
if low <= energy <= high:
return strip
return ""
def find_overlap(from_strip: str, to_strip: str) -> float:
return overlap_energyies[from_strip][to_strip]
path = []
if get_strip(start_energy) == "":
raise ValueError("Start energy is out of range for available strips")
if not any(low <= target_energy <= high for low, high in strips.values()):
raise ValueError("End energy is out of range for available strips")
current_energy = start_energy
# TODO: this should be replaced with a readout from the PV
current_strip = get_strip(current_energy)
# if the target energy is covered by the current strip, return the path
if strips[current_strip][0] <= target_energy <= strips[current_strip][1]:
return [(target_energy, current_strip)]
target_strip = get_strip(target_energy)
available_strips = list(strips.keys())
current_index = available_strips.index(current_strip)
target_index = available_strips.index(target_strip)
step = 1 if target_index > current_index else -1
for i in range(current_index, target_index, step):
next_strip = available_strips[i + step]
overlap_energy = find_overlap(available_strips[i], next_strip)
path.append((overlap_energy, next_strip))
current_strip = next_strip
path.append((target_energy, target_strip))
return path
if __name__ == "__main__": # pragma: no cover
from unittest.mock import MagicMock
device_manager = MagicMock()
optimizer = EnergyOptimizer(device_manager)
steps = optimizer.get_transition_steps(30, 20)
print(steps)

View File

@@ -34,7 +34,27 @@ to setup the prompts.
"""
# pylint: disable=invalid-name, unused-import, import-error, undefined-variable, unused-variable, unused-argument, no-name-in-module
import builtins
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from bec_ipython_client.main import BECIPythonClient
bec: BECIPythonClient = BECIPythonClient()
dev = bec.device_manager.devices
scans = bec.scans
else:
bec = builtins.__dict__.get("bec")
dev = builtins.__dict__.get("dev")
scans = builtins.__dict__.get("scans")
bec.load_high_level_interface("bec_hli")
bec.load_high_level_interface("spec_hli")
bec.load_high_level_interface("hkl_hli")
if "x04v" in dev:
bec._ip.prompts.session_name = "x04v"
elif "x04h" in dev:
bec._ip.prompts.session_name = "x04h"

View File

@@ -1,10 +1,14 @@
"""
Pre-startup script for BEC client. This script is executed before the BEC client
is started. It can be used to add additional command line arguments.
is started. It can be used to add additional command line arguments.
"""
import os
from bec_lib.service_config import ServiceConfig
import addams_bec
def extend_command_line_args(parser):
"""
@@ -15,9 +19,13 @@ def extend_command_line_args(parser):
return parser
# def get_config() -> ServiceConfig:
# """
# Create and return the service configuration.
# """
# return ServiceConfig(redis={"host": "localhost", "port": 6379})
def get_config() -> ServiceConfig:
"""
Create and return the ServiceConfig for the plugin repository
"""
deployment_path = os.path.dirname(os.path.dirname(os.path.dirname(addams_bec.__file__)))
files = os.listdir(deployment_path)
if "bec_config.yaml" in files:
return ServiceConfig(config_path=os.path.join(deployment_path, "bec_config.yaml"))
else:
return ServiceConfig(redis={"host": "localhost", "port": 6379})

View File

@@ -0,0 +1,6 @@
# Macros
This directory is intended to store macros which will be loaded automatically when starting BEC.
Macros are small functions to make repetitive tasks easier. Functions defined in python files in this directory will be accessible from the BEC console.
Please do not put any code outside of function definitions here. If you wish for code to be automatically run when starting BEC, see the startup script at addams_bec/bec_ipython_client/startup/post_startup.py
For a guide on writing macros, please see: https://bec.readthedocs.io/en/latest/user/command_line_interface.html#how-to-write-a-macro

View File

View File

@@ -1,2 +1,2 @@
from .fly_scan import HklFlyScan
from .hkl_scan import HklScan
from .fly_scan import HklFlyScan

View File

@@ -0,0 +1,12 @@
# from .metadata_schema_template import ExampleSchema
METADATA_SCHEMA_REGISTRY = {
# Add models which should be used to validate scan metadata here.
# Make a model according to the template, and import it as above
# Then associate it with a scan like so:
# "example_scan": ExampleSchema
}
# Define a default schema type which should be used as the fallback for everything:
DEFAULT_SCHEMA = None

View File

@@ -0,0 +1,34 @@
# # By inheriting from BasicScanMetadata you can define a schema by which metadata
# # supplied to a scan must be validated.
# # This schema is a Pydantic model: https://docs.pydantic.dev/latest/concepts/models/
# # but by default it will still allow you to add any arbitrary information to it.
# # That is to say, when you run a scan with which such a model has been associated in the
# # metadata_schema_registry, you can supply any python dictionary with strings as keys
# # and built-in python types (strings, integers, floats) as values, and these will be
# # added to the experiment metadata, but it *must* contain the keys and values of the
# # types defined in the schema class.
# #
# #
# # For example, say that you would like to enforce recording information about sample
# # pretreatment, you could define the following:
# #
#
# from bec_lib.metadata_schema import BasicScanMetadata
#
#
# class ExampleSchema(BasicScanMetadata):
# treatment_description: str
# treatment_temperature_k: int
#
#
# # If this was used according to the example in metadata_schema_registry.py,
# # then when calling the scan, the user would need to write something like:
# >>> scans.example_scan(
# >>> motor,
# >>> 1,
# >>> 2,
# >>> 3,
# >>> metadata={"treatment_description": "oven overnight", "treatment_temperature_k": 575},
# >>> )
#
# # And the additional metadata would be saved in the HDF5 file created for the scan.

1
bin/.gitignore vendored Normal file
View File

@@ -0,0 +1 @@
# Add anything you don't want to check in to git, e.g. very large files

View File

@@ -5,8 +5,8 @@ build-backend = "hatchling.build"
[project]
name = "addams_bec"
version = "0.0.0"
description = "Custom device implementations based on the ophyd hardware abstraction layer"
requires-python = ">=3.10"
description = "A plugin repository for BEC"
requires-python = ">=3.11"
classifiers = [
"Development Status :: 3 - Alpha",
"Programming Language :: Python :: 3",
@@ -17,6 +17,7 @@ dependencies = []
[project.optional-dependencies]
dev = [
"black",
"copier",
"isort",
"coverage",
"pylint",
@@ -38,12 +39,15 @@ plugin_file_writer = "addams_bec.file_writer"
[project.entry-points."bec.scans"]
plugin_scans = "addams_bec.scans"
[project.entry-points."bec.scans.metadata_schema"]
plugin_metadata_schema = "addams_bec.scans.metadata_schema"
[project.entry-points."bec.ipython_client_startup"]
plugin_ipython_client_pre = "addams_bec.bec_ipython_client.startup.pre_startup"
plugin_ipython_client_post = "addams_bec.bec_ipython_client.startup"
[project.entry-points."bec.widgets.auto_updates"]
plugin_widgets_update = "addams_bec.bec_widgets.auto_updates:PlotUpdate"
plugin_widgets_update = "addams_bec.bec_widgets.auto_updates"
[project.entry-points."bec.widgets.user_widgets"]
plugin_widgets = "addams_bec.bec_widgets.widgets"

View File

@@ -1,31 +1,34 @@
# Getting Started with Testing using pytest
BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework.
It can be install via
``` bash
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```bash
pip install pytest
```
in your *python environment*.
in your _python environment_.
We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
## Introduction
Tests in this package should be stored in the `tests` directory.
We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
It is mandatory for test files to begin with `test_` for pytest to discover them.
To run all tests, navigate to the directory of the plugin from the command line, and run the command
To run all tests, navigate to the directory of the plugin from the command line, and run the command
``` bash
```bash
pytest -v --random-order ./tests
```
Note, the python environment needs to be active.
The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
## Test examples
Writing tests can be quite specific for the given function.
Writing tests can be quite specific for the given function.
We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).

View File

@@ -0,0 +1,38 @@
from unittest import mock
import pytest
from addams_bec.bec_ipython_client.plugins.energy_optimizer.addams_energy_optimizer import (
EnergyOptimizer,
)
@pytest.fixture
def optimizer():
dm = mock.MagicMock()
yield EnergyOptimizer(dm)
@pytest.mark.parametrize(
"start_energy, target_energy, expected",
[
(5, 10, [(10, "Si")]),
(5, 20, [(9, "Rh"), (20, "Rh")]),
(5, 40, [(9, "Rh"), (22, "Pt"), (40, "Pt")]),
(5, 5, [(5, "Si")]),
(5, 4, ValueError),
(5, 41, ValueError),
(2, 8, ValueError),
(18, 40, [(22, "Pt"), (40, "Pt")]),
(18, 5, [(9, "Si"), (5, "Si")]),
(18, 10, [(10, "Rh")]),
(18, 20, [(20, "Rh")]),
(25, 7, [(22, "Rh"), (9, "Si"), (7, "Si")]),
],
)
def test_get_transition_steps(optimizer, start_energy, target_energy, expected):
if expected == ValueError:
with pytest.raises(ValueError):
optimizer.get_transition_steps(start_energy, target_energy)
else:
assert optimizer.get_transition_steps(start_energy, target_energy) == expected

View File

@@ -1,31 +1,34 @@
# Getting Started with Testing using pytest
BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework.
It can be install via
``` bash
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```bash
pip install pytest
```
in your *python environment*.
in your _python environment_.
We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
## Introduction
Tests in this package should be stored in the `tests` directory.
We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
It is mandatory for test files to begin with `test_` for pytest to discover them.
To run all tests, navigate to the directory of the plugin from the command line, and run the command
To run all tests, navigate to the directory of the plugin from the command line, and run the command
``` bash
```bash
pytest -v --random-order ./tests
```
Note, the python environment needs to be active.
The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
## Test examples
Writing tests can be quite specific for the given function.
Writing tests can be quite specific for the given function.
We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).

View File

@@ -1,31 +1,34 @@
# Getting Started with Testing using pytest
BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework.
It can be install via
``` bash
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```bash
pip install pytest
```
in your *python environment*.
in your _python environment_.
We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
## Introduction
Tests in this package should be stored in the `tests` directory.
We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
It is mandatory for test files to begin with `test_` for pytest to discover them.
To run all tests, navigate to the directory of the plugin from the command line, and run the command
To run all tests, navigate to the directory of the plugin from the command line, and run the command
``` bash
```bash
pytest -v --random-order ./tests
```
Note, the python environment needs to be active.
The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
## Test examples
Writing tests can be quite specific for the given function.
Writing tests can be quite specific for the given function.
We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).

View File

@@ -1,31 +1,34 @@
# Getting Started with Testing using pytest
BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework.
It can be install via
``` bash
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```bash
pip install pytest
```
in your *python environment*.
in your _python environment_.
We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
## Introduction
Tests in this package should be stored in the `tests` directory.
We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
It is mandatory for test files to begin with `test_` for pytest to discover them.
To run all tests, navigate to the directory of the plugin from the command line, and run the command
To run all tests, navigate to the directory of the plugin from the command line, and run the command
``` bash
```bash
pytest -v --random-order ./tests
```
Note, the python environment needs to be active.
The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
## Test examples
Writing tests can be quite specific for the given function.
Writing tests can be quite specific for the given function.
We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).

View File

@@ -1,31 +1,34 @@
# Getting Started with Testing using pytest
BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework.
It can be install via
``` bash
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```bash
pip install pytest
```
in your *python environment*.
in your _python environment_.
We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
## Introduction
Tests in this package should be stored in the `tests` directory.
We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
It is mandatory for test files to begin with `test_` for pytest to discover them.
To run all tests, navigate to the directory of the plugin from the command line, and run the command
To run all tests, navigate to the directory of the plugin from the command line, and run the command
``` bash
```bash
pytest -v --random-order ./tests
```
Note, the python environment needs to be active.
The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
## Test examples
Writing tests can be quite specific for the given function.
Writing tests can be quite specific for the given function.
We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).

View File

@@ -1,31 +1,34 @@
# Getting Started with Testing using pytest
BEC is using the [pytest](https://docs.pytest.org/en/8.0.x/) framework.
It can be install via
``` bash
BEC is using the [pytest](https://docs.pytest.org/en/latest/) framework.
It can be installed via
```bash
pip install pytest
```
in your *python environment*.
in your _python environment_.
We note that pytest is part of the optional-dependencies `[dev]` of the plugin package.
## Introduction
Tests in this package should be stored in the `tests` directory.
We suggest to sort tests of different submodules, i.e. `scans` or `devices` in the respective folder structure, and to folow a naming convention of `<test_module_name.py>`.
It is mandatory for test files to begin with `test_` for pytest to discover them.
To run all tests, navigate to the directory of the plugin from the command line, and run the command
To run all tests, navigate to the directory of the plugin from the command line, and run the command
``` bash
```bash
pytest -v --random-order ./tests
```
Note, the python environment needs to be active.
The additional arg `-v` allows pytest to run in verbose mode which provides more detailed information about the tests being run.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
The argument `--random-order` instructs pytest to run the tests in random order, which is the default in the CI pipelines.
## Test examples
Writing tests can be quite specific for the given function.
Writing tests can be quite specific for the given function.
We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes.
A very useful class to enable isolated testing is [MagicMock](https://docs.python.org/3/library/unittest.mock.html).
In addition, we also recommend to take a look at the [How-to guides from pytest](https://docs.pytest.org/en/8.0.x/how-to/index.html).