fix: bugfix of process

.copier-answers.yml

@@ -1,9 +0,0 @@
-# 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: v1.4.0
-_src_path: https://github.com/bec-project/plugin_copier_template.git
-make_commit: false
-project_name: pxiii_bec
-widget_plugins_input: null

.git_hooks/post-commit

@@ -1,3 +0,0 @@
-SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
-semantic-release changelog -D version_variable=$SCRIPT_DIR/../../semantic_release/__init__.py:__version__
-semantic-release version -D version_variable=$SCRIPT_DIR/../../semantic_release/__init__.py:__version__

.git_hooks/pre-commit

@@ -1,3 +0,0 @@
-black --line-length=100 $(git diff --cached --name-only --diff-filter=ACM -- '*.py')
-isort --line-length=100 --profile=black --multi-line=3 --trailing-comma $(git diff --cached --name-only --diff-filter=ACM -- '*.py')
-git add $(git diff --cached --name-only --diff-filter=ACM -- '*.py')

.gitea/workflows/ci.yml

@@ -1,102 +0,0 @@
-name: CI for pxiii_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: "${{ inputs.PYTHON_VERSION || '3.12' }}"
-
-      - name: Checkout BEC Plugin Repository
-        uses: actions/checkout@v4
-        with:
-          repository: bec/pxiii_bec
-          ref: "${{ inputs.BEC_PLUGIN_REPO_BRANCH || github.head_ref || github.sha }}"
-          path: ./pxiii_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 ./pxiii_bec
-
-      - name: Run Pytest with Coverage
-        id: coverage
-        run: pytest --random-order --cov=./pxiii_bec --cov-config=./pxiii_bec/pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./pxiii_bec/tests/ || test $? -eq 5

.gitea/workflows/create_update_pr.yml

@@ -1,70 +0,0 @@
-name: Create template upgrade PR for pxiii_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: Checkout
-        uses: actions/checkout@v4
-
-      - name: Create virtualenv
-	    run: |
-	      python -m virtualenv .venv
-
-      - name: Install tools
-        run: |
-          source .venv/bin/activate
-          pip install copier PySide6 bec_lib
-
-      - name: Perform update
-        run: |
-          source .venv/bin/activate
-          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 $branch
-
-          echo "Running copier update..."
-          copier update --trust --defaults --conflict inline 2>&1 | tee copier.log
-          status=${PIPESTATUS[0]}
-          output="$(cat copier.log)"
-          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\"
-                }"

.gitignore

@@ -8,9 +8,6 @@
 **/.pytest_cache
 **/*.egg*
 
-# recovery_config files
-recovery_config_*
-
 # file writer data
 **.h5
 

LICENSE

@@ -1,29 +0,0 @@
-
-BSD 3-Clause License
-
-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:
-
-1. Redistributions of source code must retain the above copyright notice, this
-   list of conditions and the following disclaimer.
-
-2. Redistributions in binary form must reproduce the above copyright notice,
-   this list of conditions and the following disclaimer in the documentation
-   and/or other materials provided with the distribution.
-
-3. Neither the name of the copyright holder nor the names of its
-   contributors may be used to endorse or promote products derived from
-   this software without specific prior written permission.
-
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
-AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
-IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
-FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
-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.

bec_plugins/__init__.py

@@ -0,0 +1 @@
+from .bec_client import *

bec_plugins/bec_client/__init__.py

@@ -0,0 +1 @@
+from .plugins import *

bec_plugins/bec_client/hli/spec_hli.py

@@ -0,0 +1,245 @@
+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)

bec_plugins/bec_client/startup/post_startup.py

@@ -16,30 +16,31 @@ parse the --session argument, add the following lines to the script:
 
     if args.session == "my_session":
         print("Loading my_session session")
-        from bec_plugins.bec_ipython_client.plugins.my_session import *
+        from bec_plugins.bec_client.plugins.my_session import *
     else:
         print("Loading default session")
-        from bec_plugins.bec_ipython_client.plugins.default_session import *
+        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
+import argparse
 
-from bec_lib import bec_logger
+from bec_lib.core import bec_logger
 
 logger = bec_logger.logger
 
-logger.info("Using the PX-III startup script.")
+logger.info("Using the PXIII startup script.")
 
-# pylint: disable=import-error
+parser = argparse.ArgumentParser()
-_args = _main_dict["args"]
+parser.add_argument("--session", help="Session name", type=str, default="cSAXS")
+args = parser.parse_args()
 
-_session_name = "PX-III"
+# SETUP BEAMLINE INFO
-if _args.session.lower() == "alignment":
+from bec_client.plugins.SLS.sls_info import OperatorInfo, SLSInfo
-    # load the alignment session
-    _session_name = "Alignment"
-    logger.success("Alignment session loaded.")
 
+bec._beamline_mixin._bl_info_register(SLSInfo)
+bec._beamline_mixin._bl_info_register(OperatorInfo)
 
 # SETUP PROMPTS
-bec._ip.prompts.username = _session_name
+bec._ip.prompts.username = "PXIII"
 bec._ip.prompts.status = 1

bec_plugins/bec_client/startup/pre_startup.py

@@ -0,0 +1,25 @@
+"""
+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.
+"""
+
+# example:
+# current_path = pathlib.Path(__file__).parent.resolve()
+# CONFIG_PATH = f"{current_path}/../../../bec_config.yaml"
+# config = ServiceConfig(CONFIG_PATH)

bec_plugins/data_processing/__init__.py

@@ -0,0 +1 @@
+from .saxs_imaging_processor import SaxsImagingProcessor

bec_plugins/data_processing/saxs_imaging_processor.py

@@ -0,0 +1,430 @@
+from __future__ import annotations
+import numpy as np
+import time
+from queue import Queue
+from typing import Optional, Tuple
+
+from data_processing.stream_processor import StreamProcessor
+from bec_lib.core import BECMessage
+from bec_lib.core.redis_connector import MessageObject, RedisConnector
+
+
+class SaxsImagingProcessor(StreamProcessor):
+    def __init__(self, connector: RedisConnector, config: dict) -> None:
+        """"""
+        super().__init__(connector, config)
+        self.metadata_consumer = None
+        self.parameter_consumer = None
+        self.metadata = {}
+        self.num_received_msgs = 0
+        self.queue = Queue()
+        self._init_parameter(endpoint="px_stream/gui_event")
+        self.start_parameter_consumer(endpoint="px_stream/gui_event")
+        self._init_metadata_and_proj_nr(endpoint="px_stream/proj_nr")
+        self.start_metadata_consumer(endpoint="px_stream/projection_*/metadata")
+
+    def _init_parameter(self, endpoint: str) -> None:
+        """Initialize the parameters azi_angle, contrast and horiz_roi.
+
+        Args:
+            endpoint (str): Endpoint for redis topic.
+
+        Returns:
+            None
+
+        """
+        self.azi_angle = None
+        self.horiz_roi = [20, 50]
+        self.contrast = 0
+        msg = self.producer.get(topic=endpoint)
+        if msg is None:
+            return None
+        msg_raw = BECMessage.DeviceMessage.loads(msg)
+        self._parameter_msg_handler(msg_raw)
+
+    def start_parameter_consumer(self, endpoint: str) -> None:
+        """Initialize the consumers for gui_event parameters.
+        Consumer is started with a callback function that updates
+        the parameters: azi_angle, contrast and horiz_roi.
+
+        Args:
+            endpoint (str): Endpoint for redis topic.
+
+        Returns:
+            None
+
+        """
+
+        if self.parameter_consumer and self.parameter_consumer.is_alive():
+            self.parameter_consumer.shutdown()
+        self.parameter_consumer = self._connector.consumer(
+            pattern=endpoint, cb=self._update_parameter_cb, parent=self
+        )
+        self.parameter_consumer.start()
+
+    @staticmethod
+    def _update_parameter_cb(msg: MessageObject, parent: SaxsImagingProcessor) -> None:
+        """Callback function for the parameter consumer.
+
+        Args:
+            msg (MessageObject): Message object.
+            parent (SaxsImagingProcessor): Parent class.
+
+        Returns:
+            None
+
+        """
+
+        msg_raw = BECMessage.DeviceMessage.loads(msg.value)
+        parent._parameter_msg_handler(msg_raw)
+
+    def _parameter_msg_handler(self, msg: BECMessage) -> None:
+        """Handle the parameter message.
+        There can be updates on three different parameters:
+        azi_angle, contrast and horiz_roi.
+
+        Args:
+            msg (BECMessage): Message object.
+
+        Returns:
+            None
+
+        """
+
+        if msg.content["signals"].get("horiz_roi") is not None:
+            self.horiz_roi = msg.content["signals"]["horiz_roi"]
+        if msg.content["signals"].get("azi_angles") is not None:
+            self.azi_angle = msg.content["signals"]["azi_angle"]
+        if msg.content["signals"].get("contrast") is not None:
+            self.contrast = msg.content["signals"]["contrast"]
+        # self._init_parameter_updated = True
+        # if len(self.metadata) > 0:
+        #     self._update_queue(self.metadata[self.proj_nr], self.proj_nr)
+
+    def _init_metadata_and_proj_nr(self, endpoint: str) -> None:
+        """Initialize the metadata and proj_nr.
+
+        Args:
+            endpoint (str): Endpoint for redis topic.
+
+        Returns:
+            None
+
+        """
+
+        msg = self.producer.get(topic=endpoint)
+        if msg is None:
+            self.proj_nr = None
+            return None
+        msg_raw = BECMessage.DeviceMessage.loads(msg)
+        self.proj_nr = msg_raw.content["signals"]["proj_nr"]
+        # TODO hardcoded endpoint, possibe to use more general solution?
+        msg = self.producer.get(topic=f"px_stream/projection_{self.proj_nr}/metadata")
+        msg_raw = BECMessage.DeviceMessage.loads(msg)
+        self._update_queue(msg_raw.content["signals"], self.proj_nr)
+
+    def _update_queue(self, metadata: dict, proj_nr: int) -> None:
+        """Update the process queue.
+
+        Args:
+            metadata (dict): Metadata for the projection.
+            proj_nr (int): Projection number.
+
+        Returns:
+            None
+
+        """
+
+        self.metadata.update({proj_nr: metadata})
+        self.queue.put((proj_nr, metadata))
+
+    def start_metadata_consumer(self, endpoint: str) -> None:
+        """Start the metadata consumer.
+        Consumer is started with a callback function that updates the metadata.
+
+        Args:
+            endpoint (str): Endpoint for redis topic.
+
+        Returns:
+            None
+
+        """
+
+        if self.metadata_consumer and self.metadata_consumer.is_alive():
+            self.metadata_consumer.shutdown()
+        self.metadata_consumer = self._connector.consumer(
+            pattern=endpoint, cb=self._update_metadata_cb, parent=self
+        )
+        self.metadata_consumer.start()
+
+    @staticmethod
+    def _update_metadata_cb(msg: MessageObject, parent: SaxsImagingProcessor) -> None:
+        """Callback function for the metadata consumer.
+
+        Args:
+            msg (MessageObject): Message object.
+            parent (SaxsImagingProcessor): Parent class.
+
+        Returns:
+            None
+
+        """
+
+        msg_raw = BECMessage.DeviceMessage.loads(msg.value)
+        parent._metadata_msg_handler(msg_raw, msg.topic.decode())
+
+    def _metadata_msg_handler(self, msg: BECMessage, topic) -> None:
+        """Handle the metadata message.
+        If self.metadata is larger than 10, the oldest entry is removed.
+
+        Args:
+            msg (BECMessage): Message object.
+            topic (str): Topic for the message.
+
+        Returns:
+            None
+
+        """
+
+        if len(self.metadata) > 10:
+            first_key = next(iter(self.metadata))
+            self.metadata.pop(first_key)
+        self.proj_nr = int(topic.split("px_stream/projection_")[1].split("/")[0])
+        self._update_queue(msg.content["signals"], self.proj_nr)
+
+    def start_data_consumer(self) -> None:
+        """function from the parent class that we don't want to use here"""
+        pass
+
+    def _run_forever(self) -> None:
+        """Loop that runs forever when the processor is started.
+        Upon update of the queue, the data is loaded and processed.
+        This processing continues as long as the queue is empty,
+        and proceeds to the next projection when the queue is updated.
+
+        Returns:
+            None
+
+        """
+
+        proj_nr, metadata = self.queue.get()
+        self.num_received_msgs = 0
+        self.data = None
+        while self.queue.empty():
+            start = time.time()
+            self._get_data(proj_nr, metadata)
+            start = time.time()
+            result = self.process(self.data, metadata)
+            print(f"Processing took {time.time() - start}")
+            if result is None:
+                continue
+            print(f"Length of data is {result[0][0]['z'].shape}")
+            msg = BECMessage.ProcessedDataMessage(data=result[0][0], metadata=result[1]).dumps()
+            print("Publishing result")
+            self._publish_result(msg)
+
+    def _get_data(self, proj_nr: int, metadata: dict) -> None:
+        """Get data for given proj_nr from redis.
+
+        Args:
+            proj_nr (int): Projection number.
+
+        Returns:
+            list: List of azimuthal integrated data.
+
+        """
+        start = time.time()
+        msgs = self.producer.lrange(
+            f"px_stream/projection_{proj_nr}/data", self.num_received_msgs, -1
+        )
+        print(f"Loading of {len(msgs)} took {time.time() - start}")
+        if not msgs:
+            return None
+
+        frame_shape = BECMessage.DeviceMessage.loads(msgs[0]).content["signals"]["data"].shape[-2:]
+
+        if self.data is None:
+            start = time.time()
+            self.data = np.empty(
+                (
+                    metadata["metadata"]["number_of_rows"],
+                    metadata["metadata"]["number_of_columns"],
+                    *frame_shape,
+                )
+            )
+            print(f"Init output took {time.time() - start}")
+        start = time.time()
+        for msg in msgs:
+            self.data[
+                self.num_received_msgs : self.num_received_msgs + 1, ...
+            ] = BECMessage.DeviceMessage.loads(msg).content["signals"]["data"]
+            self.num_received_msgs += 1
+        print(f"Casting data to array took {time.time() - start}")
+
+    def process(self, data: np.ndarray, metadata: dict) -> Optional[Tuple[dict, dict]]:
+        """Process the scanning SAXS data
+
+        Args:
+            data (list): List of azimuthal integrated data.
+            metadata (dict): Metadata for the projection.
+
+        Returns:
+            Optional[Tuple[dict, dict]]: Processed data and metadata.
+
+        """
+
+        if data is None:
+            return None
+        # TODO np.asarray is repsonsible for 95% of the processing time for function.
+        azint_data = data[0 : self.num_received_msgs, ...]
+        norm_sum = metadata["norm_sum"]
+        q = metadata["q"]
+        out = []
+
+        contrast = self.contrast
+        horiz_roi = self.horiz_roi
+        azi_angle = self.azi_angle
+        if azi_angle is None:
+            azi_angle = 0
+
+        f1amp, f2amp, f2phase = self._colorfulplot(
+            horiz_roi=horiz_roi,
+            q=q,
+            norm_sum=norm_sum,
+            data=azint_data,
+            azi_angle=azi_angle,
+        )
+        if contrast == 0:
+            out = f1amp
+        elif contrast == 1:
+            out = f2amp
+        elif contrast == 2:
+            out = f2phase
+
+        stream_output = {
+            # 0: {"x": np.asarray(x), "y": np.asarray(y), "z": np.asarray(out)},
+            0: {"z": np.asarray(out)},
+            # "input": self.config["input_xy"],
+        }
+        metadata["grid_scan"] = out.shape
+
+        return (stream_output, metadata)
+
+    def _colorfulplot(
+        self,
+        horiz_roi: list,
+        q: np.ndarray,
+        norm_sum: np.ndarray,
+        data: np.ndarray,
+        azi_angle: float,
+        percentile_value: int = 96,
+    ) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
+        """Compute data for sSAXS colorful 2D plot.
+        Pending: hsv_to_rgb conversion for colorful output
+
+        Args:
+            horiz_roi (list): List with q edges for binning.
+            q (np.ndarray): q values.
+            norm_sum (np.ndarray): Normalization sum.
+            data (np.ndarray): Data to be binned.
+            azi_angle (float, optional): Azimuthal angle for first segment, shifts f2phase. Defaults to 0.
+            percentile_value (int, optional): Percentile value for removing outliers above threshold. Defaults to 96, range 0...100.
+
+        Returns:
+            Tuple[np.ndarray, np.ndarray, np.ndarray]: f1amp, f2amp, f2phase
+
+        """
+
+        output, output_norm = self._bin_qrange(
+            horiz_roi=horiz_roi, q=q, norm_sum=norm_sum, data=data
+        )
+        output_sym = self._sym_data(data=output, norm_sum=output_norm)
+        output_sym = output_sym
+        shape = output_sym.shape[0:2]
+
+        fft_data = np.fft.rfft(output_sym.reshape((-1, output_sym.shape[-2])), axis=1)
+
+        f1amp = np.abs(fft_data[:, 0]) / output_sym.shape[2]
+        f2amp = 2 * np.abs(fft_data[:, 1]) / output_sym.shape[2]
+        f2angle = np.angle(fft_data[:, 1]) + np.deg2rad(azi_angle)
+
+        f2phase = (f2angle + np.pi) / (2 * np.pi)
+        f2phase[f2phase > 1] = f2phase[f2phase > 1] - 1
+
+        f1amp = f1amp.reshape(shape)
+        f2amp = f2amp.reshape(shape)
+        f2angle = f2angle.reshape(shape)
+        f2phase = f2phase.reshape(shape)
+
+        h = f2phase
+
+        max_scale = np.percentile(f2amp, percentile_value)
+        s = f2amp / max_scale
+        s[s > 1] = 1
+
+        max_scale = np.percentile(f1amp, percentile_value)
+        v = f1amp
+        v = v / max_scale
+        v[v > 1] = 1
+
+        # hsv = np.stack((h, s, v), axis=2)
+        # comb_all = colors.hsv_to_rgb(hsv)
+
+        return f1amp, f2amp, f2phase  # , comb_all
+
+    def _bin_qrange(self, horiz_roi, q, norm_sum, data) -> Tuple[np.ndarray, np.ndarray]:
+        """Reintegrate data for given q range.
+        Weighted sum for data using norm_sum as weights
+
+        Args:
+            horiz_roi (list): List with q edges for binning.
+            q (np.ndarray): q values.
+            norm_sum (np.ndarray): Normalization sum.
+            data (np.ndarray): Data to be binned.
+
+        Returns:
+            np.ndarray: Binned data.
+            np.ndarray: Binned normalization sum.
+        """
+
+        output = np.zeros((*data.shape[:-1], len(horiz_roi) - 1))
+        output_norm = np.zeros((data.shape[-2], len(horiz_roi) - 1))
+
+        with np.errstate(divide="ignore", invalid="ignore"):
+            q_mask = np.logical_and(q >= q[horiz_roi[0]], q <= q[horiz_roi[1]])
+            output_norm[..., 0] = np.nansum(norm_sum[..., q_mask], axis=-1)
+            output[..., 0] = np.nansum(data[..., q_mask] * norm_sum[..., q_mask], axis=-1)
+            output[..., 0] = np.divide(
+                output[..., 0], output_norm[..., 0], out=np.zeros_like(output[..., 0])
+            )
+
+        return output, output_norm
+
+    def _sym_data(self, data, norm_sum) -> np.ndarray:
+        """Symmetrize data by averaging over the two opposing directions.
+        Helpful to remove detector gaps for x-ray detectors
+
+        Args:
+            data (np.ndarray): Data to be symmetrized.
+            norm_sum (np.ndarray): Normalization sum.
+
+        Returns:
+            np.ndarray: Symmetrized data.
+
+        """
+
+        n_directions = norm_sum.shape[0] // 2
+        output = np.divide(
+            data[..., :n_directions, :] * norm_sum[:n_directions, :]
+            + data[..., n_directions:, :] * norm_sum[n_directions:, :],
+            norm_sum[:n_directions, :] + norm_sum[n_directions:, :],
+            out=np.zeros_like(data[..., :n_directions, :]),
+        )
+        return output
+
+
+if __name__ == "__main__":
+    config = {
+        "output": "px_dap_worker",
+    }
+    dap_process = SaxsImagingProcessor.run(config=config, connector_host=["localhost:6379"])

bec_plugins/data_processing/utils/saxs_imaging_streamsimulator.py

@@ -0,0 +1,155 @@
+import os
+import h5py
+import numpy as np
+import time
+import json
+import argparse
+
+from bec_lib.core import RedisConnector, BECMessage
+
+
+def load_data(datadir: str, metadata_path: str) -> tuple:
+    """Load data from disk
+
+    Args:
+        datapath (str): Path to the data directory with data for projection (h5 files)
+        metadata_path (str): Path to the metadata file
+
+    Returns:
+        tuple: data, q, norm_sum, metadata
+
+    """
+
+    with open(metadata_path) as file:
+        metadata = json.load(file)
+
+    filenames = [fname for fname in os.listdir(datadir) if fname.endswith(".h5")]
+    filenames.sort()
+
+    for ii, fname in enumerate(filenames):
+        with h5py.File(os.path.join(datadir, fname), "r") as h5file:
+            if ii == 0:
+                q = h5file["q"][...].T.squeeze()
+                norm_sum = h5file["norm_sum"][...]
+                data = np.zeros((len(filenames), *h5file["I_all"][...].shape))
+            data[ii, ...] = h5file["I_all"][...]
+
+    return data, q, norm_sum, metadata
+
+
+def _get_projection_keys(producer) -> list:
+    """Get all keys for projections with endpoint px_stream/projection_* in redis
+
+    Args:
+        producer (RedisProducer): Redis producer
+
+    Returns:
+        list: List of keys or [] if no keys are found"""
+    keys = producer.keys("px_stream/projection_*")
+    if not keys:
+        return []
+    return keys
+
+
+def send_data(
+    data: np.ndarray,
+    q: np.ndarray,
+    norm_sum: np.ndarray,
+    bec_producer: RedisConnector.producer,
+    metadata: dict,
+    proj_nr: int,
+) -> None:
+    """Send data to redis and delete old data > 5 projections
+
+    Args:
+        data (np.ndarray): Data to send
+        q (np.ndarray): q values
+        norm_sum (np.ndarray): Normalization sum
+        bec_producer (RedisProducer): Redis producer
+        metadata (dict): Metadata
+        proj_nr (int): Projection number
+
+    Returns:
+        None
+
+    """
+    start = time.time()
+
+    keys = _get_projection_keys(bec_producer)
+    pipe = bec_producer.pipeline()
+    proj_numbers = set(key.decode().split("px_stream/projection_")[1].split("/")[0] for key in keys)
+    if len(proj_numbers) > 5:
+        for entry in sorted(proj_numbers)[0:-5]:
+            for key in bec_producer.keys(f"px_stream/projection_{entry}/*"):
+                bec_producer.delete(topic=key, pipe=pipe)
+                print(f"Deleting {key}")
+
+    return_dict = {"metadata": metadata, "q": q, "norm_sum": norm_sum}
+    msg = BECMessage.DeviceMessage(signals=return_dict).dumps()
+    bec_producer.set_and_publish(f"px_stream/projection_{proj_nr}/metadata", msg=msg, pipe=pipe)
+    return_dict = {"proj_nr": proj_nr}
+    msg = BECMessage.DeviceMessage(signals=return_dict).dumps()
+    bec_producer.set_and_publish(f"px_stream/proj_nr", msg=msg, pipe=pipe)
+    pipe.execute()
+
+    for line in range(data.shape[0]):
+        return_dict = {"data": data[line, ...]}
+        msg = BECMessage.DeviceMessage(signals=return_dict).dumps()
+        print(f"Sending line {line}")
+        bec_producer.rpush(topic=f"px_stream/projection_{proj_nr}/data", msgs=msg)
+    print(f"Time to send {time.time()-start} seconds")
+    print(f"Rate {data.shape[0]/(time.time()-start)} Hz")
+    print(f"Data volume {data.nbytes/1e6} MB")
+
+
+if __name__ == "__main__":
+    """Start the stream simulator, defaults to px_stream/projection_* in redis on localhost:6379
+
+    Example usage:
+        >>> python saxs_imaging_streamsimulator.py -d ~/datadir/ -m ~/metadatafile.json -p 180 -d 30 -r localhost:6379
+    """
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "-d",
+        "--datadir",
+        type=str,
+        help="filepath to datadir for projection files (in h5 format)",
+        required=True,
+    )
+    parser.add_argument(
+        "-m",
+        "--metadata",
+        type=str,
+        help="filepath to metadata json file",
+        required=True,
+    )
+    parser.add_argument(
+        "-p",
+        "--proj_nr",
+        type=int,
+        help="Projection number matching the data",
+        required=True,
+    )
+    parser.add_argument(
+        "-w",
+        "--wait_delay",
+        type=int,
+        help="delay between sending data in seconds (int)",
+        default=30,
+    )
+    parser.add_argument(
+        "-r",
+        "--redis",
+        type=str,
+        help="Redis_host:port",
+        default="localhost:6379",
+    )
+    values = parser.parse_args()
+    data, q, norm_sum, metadata = load_data(datadir=values.datadir, metadata_path=values.metadata)
+    bec_producer = RedisConnector([f"{values.redis}"]).producer()
+    proj_nr = values.proj_nr
+    delay = values.wait_delay
+    while True:
+        send_data(data, q, norm_sum, bec_producer, metadata, proj_nr=proj_nr)
+        time.sleep(delay)
+        bec_producer.delete(topic=f"px_stream/projection_{proj_nr}/data:val")

bin/.gitignore

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

deployment/autodeploy_versions

@@ -0,0 +1,11 @@
+# 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"
+

deployment/bec-server-config.yaml

@@ -0,0 +1,18 @@
+redis:
+  host: localhost
+  port: 6379
+mongodb:
+  host: localhost
+  port: 27017
+scibec:
+  host: http://[::1]
+  port: 3030
+  beamline: "PXIII"
+service_config:
+  general:
+    reset_queue_on_cancel: True
+    enforce_ACLs: False
+  file_writer:
+    plugin: default_NeXus_format
+    base_path: ./
+

deployment/deploy.sh

@@ -0,0 +1,30 @@
+# deployment script to be translated to Ansible
+
+# can be removed once we have the autodeployment in place
+BEAMLINE_REPO=gitlab.psi.ch:bec/pxiii-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 ./pxiii-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 ../
+
+pip install -e ./pxiii-bec
+
+# start the BEC server
+bec-server start --config ./pxiii-bec/deployment/bec-server-config.yaml
+

pxiii_bec/bec_ipython_client/startup/pre_startup.py

@@ -1,32 +0,0 @@
-"""
-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.
-"""
-
-import os
-
-from bec_lib.service_config import ServiceConfig
-
-import pxiii_bec
-
-
-def extend_command_line_args(parser):
-    """
-    Extend the command line arguments of the BEC client.
-    """
-
-    parser.add_argument("--session", help="Session name", type=str, default="PX-III")
-
-    return parser
-
-
-def get_config() -> ServiceConfig:
-    """
-    Create and return the ServiceConfig for the plugin repository
-    """
-    deployment_path = os.path.dirname(os.path.dirname(os.path.dirname(pxiii_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})

pxiii_bec/bec_widgets/ComissioningGUIDraft.ui

@@ -1,135 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>Form</class>
- <widget class="QWidget" name="Form">
-  <property name="geometry">
-   <rect>
-    <x>0</x>
-    <y>0</y>
-    <width>1801</width>
-    <height>1459</height>
-   </rect>
-  </property>
-  <property name="minimumSize">
-   <size>
-    <width>1801</width>
-    <height>1459</height>
-   </size>
-  </property>
-  <property name="windowTitle">
-   <string>Form</string>
-  </property>
-  <layout class="QVBoxLayout" name="verticalLayout">
-   <item>
-    <widget class="QTabWidget" name="tabWidget">
-     <property name="currentIndex">
-      <number>0</number>
-     </property>
-     <widget class="QWidget" name="tab">
-      <attribute name="title">
-       <string>Control Panel</string>
-      </attribute>
-      <layout class="QGridLayout" name="gridLayout" rowstretch="3,4" columnstretch="2,5">
-       <item row="0" column="0">
-        <widget class="Waveform" name="waveform"/>
-       </item>
-       <item row="0" column="1">
-        <widget class="ScanControl" name="scan_control"/>
-       </item>
-       <item row="1" column="0">
-        <widget class="ScanHistory" name="scan_history"/>
-       </item>
-       <item row="1" column="1">
-        <widget class="BECQueue" name="bec_queue"/>
-       </item>
-      </layout>
-     </widget>
-     <widget class="QWidget" name="tab_2">
-      <attribute name="title">
-       <string>Logbook</string>
-      </attribute>
-      <layout class="QGridLayout" name="gridLayout_3">
-       <item row="0" column="0">
-        <widget class="QLabel" name="label">
-         <property name="font">
-          <font>
-           <pointsize>24</pointsize>
-          </font>
-         </property>
-         <property name="text">
-          <string>Coming soon...</string>
-         </property>
-        </widget>
-       </item>
-      </layout>
-     </widget>
-     <widget class="QWidget" name="tab_3">
-      <attribute name="title">
-       <string>Take a break</string>
-      </attribute>
-      <layout class="QGridLayout" name="gridLayout_2">
-       <item row="0" column="0">
-        <widget class="Minesweeper" name="minesweeper"/>
-       </item>
-       <item row="0" column="1">
-        <spacer name="horizontalSpacer">
-         <property name="orientation">
-          <enum>Qt::Orientation::Horizontal</enum>
-         </property>
-         <property name="sizeHint" stdset="0">
-          <size>
-           <width>1073</width>
-           <height>20</height>
-          </size>
-         </property>
-        </spacer>
-       </item>
-       <item row="1" column="0">
-        <spacer name="verticalSpacer">
-         <property name="orientation">
-          <enum>Qt::Orientation::Vertical</enum>
-         </property>
-         <property name="sizeHint" stdset="0">
-          <size>
-           <width>20</width>
-           <height>40</height>
-          </size>
-         </property>
-        </spacer>
-       </item>
-      </layout>
-     </widget>
-    </widget>
-   </item>
-  </layout>
- </widget>
- <customwidgets>
-  <customwidget>
-   <class>ScanControl</class>
-   <extends>QWidget</extends>
-   <header>scan_control</header>
-  </customwidget>
-  <customwidget>
-   <class>Waveform</class>
-   <extends>QWidget</extends>
-   <header>waveform</header>
-  </customwidget>
-  <customwidget>
-   <class>BECQueue</class>
-   <extends>QWidget</extends>
-   <header>bec_queue</header>
-  </customwidget>
-  <customwidget>
-   <class>Minesweeper</class>
-   <extends>QWidget</extends>
-   <header>minesweeper</header>
-  </customwidget>
-  <customwidget>
-   <class>ScanHistory</class>
-   <extends>QWidget</extends>
-   <header>scan_history</header>
-  </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
-</ui>

pxiii_bec/bec_widgets/auto_updates/__init__.py

@@ -1 +0,0 @@
-from .auto_updates import AutoUpdates

pxiii_bec/bec_widgets/auto_updates/auto_updates.py

@@ -1,71 +0,0 @@
-from bec_widgets.widgets.containers.auto_update.auto_updates import AutoUpdates
-
-from bec_lib.messages import ScanStatusMessage
-from bec_widgets.cli.rpc.rpc_base import RPCResponseTimeoutError
-
-
-class PlotUpdate(AutoUpdates):
-
-    #######################################################################
-    ################# GUI Callbacks #######################################
-    #######################################################################
-
-    def on_start(self) -> None:
-        """
-        Procedure to run when the auto updates are enabled.
-        """
-        self.start_default_dock()
-
-    def on_stop(self) -> None:
-        """
-        Procedure to run when the auto updates are disabled.
-        """
-
-    def on_scan_open(self, msg: ScanStatusMessage) -> None:
-        """
-        Procedure to run when a scan starts.
-
-        Args:
-            msg (ScanStatusMessage): The scan status message.
-        """
-        if msg.scan_name == "line_scan" and msg.scan_report_devices:
-            return self.simple_line_scan(msg)
-        if msg.scan_name == "grid_scan" and msg.scan_report_devices:
-            return self.simple_grid_scan(msg)
-        
-        dev_x = msg.scan_report_devices[0]
-        if "kwargs" in msg.request_inputs:
-            dev_y = msg.request_inputs["kwargs"].get("plot", None)
-            if dev_y is not None:
-                # Set the dock to the waveform widget
-                wf = self.set_dock_to_widget("Waveform")
-
-                # Clear the waveform widget and plot the data
-                wf.clear_all()
-                wf.plot(
-                    x_name=dev_x,
-                    y_name=dev_y,
-                    label=f"Scan {msg.info.scan_number} - {dev_y}",
-                    title=f"Scan {msg.info.scan_number}",
-                    x_label=dev_x,
-                    y_label=dev_y,
-                )
-        elif msg.scan_report_devices:
-            return self.best_effort(msg)
-        return None
-
-    def on_scan_closed(self, msg: ScanStatusMessage) -> None:
-        """
-        Procedure to run when a scan ends.
-
-        Args:
-            msg (ScanStatusMessage): The scan status message.
-        """
-
-    def on_scan_abort(self, msg: ScanStatusMessage) -> None:
-        """
-        Procedure to run when a scan is aborted.
-
-        Args:
-            msg (ScanStatusMessage): The scan status message.
-        """

pxiii_bec/bec_widgets/widgets/client.py

@@ -1,42 +0,0 @@
-# This file was automatically generated by generate_cli.py
-# type: ignore
-
-from __future__ import annotations
-
-from bec_lib.logger import bec_logger
-
-from bec_widgets.cli.rpc.rpc_base import RPCBase, rpc_call, rpc_timeout
-
-logger = bec_logger.logger
-
-# pylint: skip-file
-
-
-_Widgets = {
-    "ScanHistory": "ScanHistory",
-}
-
-
-class ScanHistory(RPCBase):
-    _IMPORT_MODULE = "pxiii_bec.bec_widgets.widgets.scan_history.scan_history"
-
-    @rpc_call
-    def select_scan_from_history(self, value: "int") -> "None":
-        """
-        Set scan from CLI.
-
-        Args:
-            value (int) : value from history -1 ...-10000
-        """
-
-    @rpc_call
-    def add_scan_from_history(self) -> "None":
-        """
-        Load selected scan from history.
-        """
-
-    @rpc_call
-    def clear_plot(self) -> "None":
-        """
-        Delete all curves on the plot.
-        """

pxiii_bec/bec_widgets/widgets/designer_plugins.py

@@ -1,13 +0,0 @@
-# This file was automatically generated by generate_cli.py
-# type: ignore
-from __future__ import annotations
-
-# pylint: skip-file
-
-designer_plugins = {
-    "ScanHistory": ("pxiii_bec.bec_widgets.widgets.scan_history.scan_history", "ScanHistory"),
-}
-
-widget_icons = {
-    "ScanHistory": "widgets",
-}

pxiii_bec/bec_widgets/widgets/scan_history/register_scan_history.py

@@ -1,15 +0,0 @@
-def main():  # pragma: no cover
-    from qtpy import PYSIDE6
-
-    if not PYSIDE6:
-        print("PYSIDE6 is not available in the environment. Cannot patch designer.")
-        return
-    from PySide6.QtDesigner import QPyDesignerCustomWidgetCollection
-
-    from pxiii_bec.bec_widgets.widgets.scan_history.scan_history_plugin import ScanHistoryPlugin
-
-    QPyDesignerCustomWidgetCollection.addCustomWidget(ScanHistoryPlugin())
-
-
-if __name__ == "__main__":  # pragma: no cover
-    main()

pxiii_bec/bec_widgets/widgets/scan_history/scan_history.py

@@ -1,191 +0,0 @@
-from __future__ import annotations
-
-import os
-from typing import TYPE_CHECKING, TypedDict
-
-from bec_lib.logger import bec_logger
-from bec_qthemes import material_icon
-from bec_widgets.utils.bec_widget import BECWidget
-
-
-from bec_widgets.utils.error_popups import SafeSlot
-from bec_widgets.utils.ui_loader import UILoader
-from qtpy.QtWidgets import QVBoxLayout, QWidget
-
-logger = bec_logger.logger
-
-if TYPE_CHECKING:
-    from qtpy.QtWidgets import QPushButton, QLabel, QSpinBox
-    from bec_widgets.widgets.plots.waveform.waveform import Waveform
-    from bec_widgets.widgets.control.device_input.device_combobox.device_combobox import DeviceComboBox
-    from bec_widgets.widgets.editors.text_box.text_box import TextBox
-
-
-class ScanHistoryUIComponents(TypedDict):
-    waveform: Waveform
-    metadata_text_box: TextBox
-    monitor_label: QLabel
-    monitor_combobox: DeviceComboBox
-    history_label: QLabel
-    history_spin_box: QSpinBox
-    history_add: QPushButton
-    history_clear: QPushButton
-
-
-class ScanHistory(BECWidget, QWidget):
-    USER_ACCESS = ["select_scan_from_history", "add_scan_from_history", "clear_plot"]
-    PLUGIN = True
-    ui_file = "./scan_history.ui"
-    components: ScanHistoryUIComponents
-
-    def __init__(self, parent=None, **kwargs):
-        super().__init__(parent=parent, **kwargs)
-        self._load_ui()
-
-    def _load_ui(self):
-        current_path = os.path.dirname(__file__)
-        self.ui = UILoader(self).loader(os.path.join(current_path, self.ui_file))
-        layout = QVBoxLayout()
-        layout.addWidget(self.ui)
-        self.setLayout(layout)
-
-        self.components: ScanHistoryUIComponents = {
-            "waveform" : self.ui.waveform,
-            "metadata_text_box" : self.ui.metadata_text_box,
-            "monitor_label" : self.ui.monitor_label,
-            "monitor_combobox" : self.ui.monitor_combobox,
-            "history_label" : self.ui.history_label,
-            "history_spin_box" : self.ui.history_spin_box,
-            "history_add" : self.ui.history_add,
-            "history_clear" : self.ui.history_clear,
-        }
-
-        icon_options = {"size": (16, 16), "convert_to_pixmap": False}
-
-        self.components['monitor_combobox'].apply_filter = False
-        self.components['monitor_combobox'].devices = ['dccm_diode_bottom', 'dccm_diode_top', 'dccm_xbpm', 'ssxbpm', 'xbox_diode']
-
-        self.components['history_spin_box'].setMinimum(-10000)
-        self.components['history_spin_box'].setMaximum(-1)
-        self.components['history_spin_box'].valueChanged.connect(self._scan_history_selected)
-        self._scan_history_selected(-1)
-        self.components['history_spin_box'].setValue(-1)
-        self.components['history_add'].setText("Load")
-        self.components['history_add'].setStyleSheet(
-                "background-color:  #129490; color: white; font-weight: bold; font-size: 12px;"
-            )
-        
-        self.components['history_clear'].setText("Clear")
-        self.components['history_clear'].setStyleSheet(
-                "background-color:  #065143; color: white; font-weight: bold; font-size: 12px;"
-            )
-
-        self.components['history_add'].clicked.connect(self._refresh_plot)
-        self.components['history_clear'].clicked.connect(self.clear_plot)
-        self.setWindowTitle("Scan History")
-        self._scan_history_selected(-1)
-
-    @SafeSlot()
-    def add_scan_from_history(self) -> None:
-        """Load selected scan from history."""
-        self.components['history_add'].click()
-
-    @SafeSlot()
-    def clear_plot(self) -> None:
-        """Delete all curves on the plot."""
-        self.components['waveform'].clear_all()
-
-    @SafeSlot()
-    def _refresh_plot(self) -> None:
-        """Refresh plot."""
-        spin_box_value = self.components['history_spin_box'].value()
-        self._check_scan_in_history(spin_box_value)
-
-        # Get the data from the client 
-        data = self.client.history[spin_box_value]
-
-        # Check that the plot does not already have a curve with the same data
-        scan_number = int(data.metadata.bec['scan_number'])
-        monitor_name = self.components['monitor_combobox'].currentText()
-        # Get signal hints
-        signal_name = getattr(self.client.device_manager.devices, monitor_name)._hints
-        signal_name = signal_name[0] if len(signal_name)>0 else signal_name
-
-        curve_label = f"Scan-{scan_number}-{monitor_name}-{signal_name}"
-        if len([curve for curve in self.components['waveform'].curves if curve.config.label == curve_label]):
-            return
-        if not hasattr(data.devices, monitor_name):
-            raise ValueError(f"Device {monitor_name} not found in data.")
-        
-        # Get scan motors and check that the plot x_axis motor is the same as the scan motor, if not, clear the plot
-        scan_motors = [motor.decode() for motor in data.metadata.bec['scan_motors']]
-        x_motor_name = self.components['waveform'].x_mode
-        if x_motor_name not in scan_motors:
-            self.clear_plot()
-            self.components['waveform'].x_mode = x_motor_name = scan_motors[0]
-
-        # fetching the data
-        monitor_data = getattr(data.devices, monitor_name).read()[signal_name]['value']
-        motor_data = getattr(data.devices, x_motor_name).read()[x_motor_name]['value']
-
-        # Plot custom curve, with custom label
-        self.components['waveform'].plot(x=motor_data, y=monitor_data, label=curve_label)
-        x_label = f"{x_motor_name} / [{getattr(self.client.device_manager.devices, x_motor_name).egu()}]"
-        self.components['waveform'].x_label = x_label
-
-    def _check_scan_in_history(self, history_value:int) -> None:
-        """
-        Check if scan is in history.
-        
-        Args:
-            history_value (int): Value from history -1...-10000
-        """
-        if len(self.client.history) < abs(history_value):
-            self.components['metadata_text_box'].set_plain_text(f"Scan history does not have the request scan {history_value} of history with length: {len(self.client.history)}")
-            return
-
-
-    def select_scan_from_history(self, value:int) -> None:
-        """ 
-        Set scan from CLI.
-        
-        Args:
-            value (int) : value from history -1 ...-10000
-        """
-        if value >=0:
-            raise ValueError(f"Value must be smaller or equal -1, provided {value}")
-        self.components['history_spin_box'].setValue(value)
-
-    @SafeSlot(int)
-    def _scan_history_selected(self, spin_box_value:int) -> None:
-        self._check_scan_in_history(spin_box_value)
-        data = self.client.history[spin_box_value]
-        data.metadata.bec['scan_motors'][0].decode()
-
-        text = str(data)
-        scan_motor_text = "\n" + "Scan Motors: "
-        for motor in data.metadata.bec['scan_motors']:
-            scan_motor_text += f" {motor.decode()}"
-        
-        self.components['metadata_text_box'].set_plain_text(text + scan_motor_text)
-
-    @SafeSlot(str)
-    def _set_x_axis(self, device_x:str) -> None:
-        self.components['waveform'].x_mode = device_x
-
-    @SafeSlot(str)
-    def _plot_new_device(self, device:str) -> None:
-        # if len(curve for curve in self.components["waveform"].curves if curve.config.label == f"{device}-{device}":         
-        self.components["waveform"].plot(device)
-
-
-if __name__ == "__main__":  # pragma: no cover
-    import sys
-
-    from qtpy.QtWidgets import QApplication
-
-    app = QApplication(sys.argv)
-    widget = ScanHistory()
-
-    widget.show()
-    sys.exit(app.exec_())

pxiii_bec/bec_widgets/widgets/scan_history/scan_history.pyproject

@@ -1 +0,0 @@
-{'files': ['scan_history.py']}

pxiii_bec/bec_widgets/widgets/scan_history/scan_history.ui

@@ -1,115 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ui version="4.0">
- <class>Form</class>
- <widget class="QWidget" name="Form">
-  <property name="geometry">
-   <rect>
-    <x>0</x>
-    <y>0</y>
-    <width>955</width>
-    <height>796</height>
-   </rect>
-  </property>
-  <property name="windowTitle">
-   <string>Form</string>
-  </property>
-  <layout class="QVBoxLayout" name="verticalLayout_2" stretch="9,3">
-   <item>
-    <widget class="Waveform" name="waveform">
-     <property name="sizePolicy">
-      <sizepolicy hsizetype="Preferred" vsizetype="Preferred">
-       <horstretch>0</horstretch>
-       <verstretch>0</verstretch>
-      </sizepolicy>
-     </property>
-     <property name="minimumSize">
-      <size>
-       <width>0</width>
-       <height>0</height>
-      </size>
-     </property>
-    </widget>
-   </item>
-   <item>
-    <layout class="QHBoxLayout" name="horizontalLayout_2">
-     <item>
-      <layout class="QVBoxLayout" name="verticalLayout">
-       <item>
-        <widget class="QLabel" name="monitor_label">
-         <property name="font">
-          <font/>
-         </property>
-         <property name="text">
-          <string>BPM Monitor</string>
-         </property>
-        </widget>
-       </item>
-       <item>
-        <widget class="DeviceComboBox" name="monitor_combobox"/>
-       </item>
-       <item>
-        <widget class="QLabel" name="history_label">
-         <property name="text">
-          <string>Scan History</string>
-         </property>
-        </widget>
-       </item>
-       <item>
-        <widget class="QSpinBox" name="history_spin_box"/>
-       </item>
-       <item>
-        <widget class="QPushButton" name="history_add">
-         <property name="text">
-          <string>Add scan</string>
-         </property>
-        </widget>
-       </item>
-       <item>
-        <widget class="QPushButton" name="history_clear">
-         <property name="text">
-          <string>clear all</string>
-         </property>
-        </widget>
-       </item>
-      </layout>
-     </item>
-     <item>
-      <widget class="TextBox" name="metadata_text_box">
-       <property name="sizePolicy">
-        <sizepolicy hsizetype="Preferred" vsizetype="MinimumExpanding">
-         <horstretch>0</horstretch>
-         <verstretch>0</verstretch>
-        </sizepolicy>
-       </property>
-       <property name="minimumSize">
-        <size>
-         <width>795</width>
-         <height>191</height>
-        </size>
-       </property>
-      </widget>
-     </item>
-    </layout>
-   </item>
-  </layout>
- </widget>
- <customwidgets>
-  <customwidget>
-   <class>TextBox</class>
-   <extends>QWidget</extends>
-   <header>text_box</header>
-  </customwidget>
-  <customwidget>
-   <class>DeviceComboBox</class>
-   <extends>QComboBox</extends>
-   <header>device_combobox</header>
-  </customwidget>
-  <customwidget>
-   <class>Waveform</class>
-   <extends>QWidget</extends>
-   <header>waveform</header>
-  </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
-</ui>

pxiii_bec/bec_widgets/widgets/scan_history/scan_history_plugin.py

@@ -1,54 +0,0 @@
-# Copyright (C) 2022 The Qt Company Ltd.
-# SPDX-License-Identifier: LicenseRef-Qt-Commercial OR BSD-3-Clause
-
-from qtpy.QtDesigner import QDesignerCustomWidgetInterface
-
-from bec_widgets.utils.bec_designer import designer_material_icon
-from pxiii_bec.bec_widgets.widgets.scan_history.scan_history import ScanHistory
-
-DOM_XML = """
-<ui language='c++'>
-    <widget class='ScanHistory' name='scan_history'>
-    </widget>
-</ui>
-"""
-
-
-class ScanHistoryPlugin(QDesignerCustomWidgetInterface):  # pragma: no cover
-    def __init__(self):
-        super().__init__()
-        self._form_editor = None
-
-    def createWidget(self, parent):
-        t = ScanHistory(parent)
-        return t
-
-    def domXml(self):
-        return DOM_XML
-
-    def group(self):
-        return ""
-
-    def icon(self):
-        return designer_material_icon(ScanHistory.ICON_NAME)
-
-    def includeFile(self):
-        return "scan_history"
-
-    def initialize(self, form_editor):
-        self._form_editor = form_editor
-
-    def isContainer(self):
-        return False
-
-    def isInitialized(self):
-        return self._form_editor is not None
-
-    def name(self):
-        return "ScanHistory"
-
-    def toolTip(self):
-        return "ScanHistory"
-
-    def whatsThis(self):
-        return self.toolTip()

pxiii_bec/deployment/device_server/startup.py

@@ -1,11 +0,0 @@
-import os
-
-
-def setup_epics_ca():
-    os.environ["EPICS_CA_AUTO_ADDR_LIST"] = "NO"
-    os.environ["EPICS_CA_ADDR_LIST"] = "129.129.110.255"
-    os.environ["PYTHONIOENCODING"] = "latin1"
-
-
-def run():
-    setup_epics_ca()

pxiii_bec/deployments/device_server/startup.py

@@ -1,11 +0,0 @@
-import os
-
-
-def setup_epics_ca():
-    # os.environ["EPICS_CA_AUTO_ADDR_LIST"] = "NO"
-    # os.environ["EPICS_CA_ADDR_LIST"] = "129.129.122.255 sls-x12sa-cagw.psi.ch:5836"
-    os.environ["PYTHONIOENCODING"] = "latin1"
-
-
-def run():
-    setup_epics_ca()

pxiii_bec/device_configs/beamline_states.yaml

@@ -1,151 +0,0 @@
-states:
-  robot_sample_exchange:
-    allow_modifiers: true
-    bl_pos: in
-    bl_bright: 'off'
-    bs_pos: in
-    bs_z: safe
-    coll_y: out
-    cryo_pos: in
-    det_cov: 'close'
-    diag_y: out
-    fl_bright: 'off'
-    gon_x: in
-#    smargon: not implemented
-    xrf_pos: out
-
-  sample_alignment:
-    allow_modifiers: true
-    bl_pos: in
-    bl_bright: 'on'
-    bs_pos: in
-    bs_z: safe
-    coll_y: out
-    cryo_pos: in
-    det_cov: 'close'
-    diag_y: out
-    fl_bright: 'on'
-    gon_x: in
-  #    smargon: not implemented
-    xrf_pos: out
-
-  data_collection:
-    allow_modifiers: true
-    bl_pos: out
-    bl_bright: 'off'
-    bs_pos: in
-    bs_z: safe
-    coll_y: in
-    cryo_pos: in
-    det_cov: 'open'
-    diag_y: out
-    fl_bright: 'on'
-    gon_x: in
-  #  smargon: not implemented
-    xrf_pos: out
-
-  DC_XRF:
-    allow_modifiers: true
-#    bl_pos: out
-    bl_bright: 'off'
-    bs_pos: in
-    bs_z: safe
-    coll_y: in
-    cryo_pos: in
-    det_cov: 'close'
-    diag_y: out
-    fl_bright: 'on'
-    gon_x: in
-    #    smargon: not implemented
-    xrf_pos: in
-
-  manual_sample_exchange:
-    allow_modifiers: true
-    bl_pos: out
-    bl_bright: 'off'
-    bs_pos: out
-    bs_z: safe
-    coll_y: park
-    cryo_pos: in
-    det_cov: 'close'
-    diag_y: park
-    fl_bright: 'off'
-    gon_x: in
-    #    smargon: not implemented
-    xrf_pos: out
-
-  beam_visualisation:
-    bl_pos: out
-    bl_bright: 'off'
-    bs_pos: in
-    bs_z: safe
-    coll_y: out
-    cryo_pos: out
-    det_cov: 'close'
-    diag_y: scint
-    fl_bright: 'off'
-    gon_x: out
-  #    smargon: not implemented
-    xrf_pos: out
-
-  flux_measurement:
-    bl_pos: in
-    bl_bright: 'off'
-    bs_pos: in
-    bs_z: safe
-    coll_y: out
-    cryo_pos: out
-    det_cov: 'close'
-    diag_y: i1
-    fl_bright: 'off'
-    gon_x: out
-    #    smargon: not implemented
-    xrf_pos: out
-
-  beamstop_alignment:
-    bl_pos: out
-    bl_bright: 'off'
-    bs_pos: in
-    bs_z: samp
-    coll_y: out
-    cryo_pos: out
-    det_cov: 'close'
-    diag_y: out
-    fl_bright: 'on'
-    gon_x: out
-    #    smargon: not implemented
-    xrf_pos: out
-
-  maintenance:
-    allow_modifiers: true
-    bl_pos: out
-    bl_bright: 'off'
-    bs_pos: out
-    bs_z: safe
-    coll_y: park
-    cryo_pos: in
-    det_cov: 'close'
-    diag_y: park
-    fl_bright: 'off'
-    gon_x: out
-    #    smargon: not implemented
-    xrf_pos: out
-
-  xtal_snapshot:
-    allow_modifiers: true
-    bl_pos: in
-    bl_bright: 'on'
-    bs_pos: in
-    bs_z: safe
-    coll_y: intermediate
-    cryo_pos: in
-    det_cov: 'close'
-    diag_y: out
-    fl_bright: 'on'
-    gon_x: in
-    #    smargon: not implemented
-    xrf_pos: out
-
-
-
-

pxiii_bec/device_configs/create_yaml.py

@@ -1,81 +0,0 @@
-import csv
-import json
-
-
-
-
-def str_to_bool(val):
-    return str(val).strip().lower() in ["yes", "true", "1"]
-
-def create(INPUT_CSV, OUTPUT_YAML):
-    with open(INPUT_CSV, newline="") as csvfile:
-        reader = csv.DictReader(csvfile)
-
-        with open(OUTPUT_YAML, "w") as yamlfile:
-            for row in reader:
-                include = row["include"]
-                name = row["name"]
-                desc = row["description"]
-                device_class = row["deviceClass"]
-                pv = row["PV"]
-                readout_priority = row["readoutPriority"]
-                tag = row["tag"]
-                read_only = str_to_bool(row["readOnly"])
-                user_param = row.get("userParameter", "").strip()
-
-                if str(include).strip().lower() != "yes":
-                    continue
-
-                yamlfile.write(f"{name}:\n")
-                yamlfile.write(f"  description: {desc}\n")
-
-                if device_class == "Motor" or device_class == "MotorEC":
-                    yamlfile.write(f"  deviceClass: ophyd_devices.Epics{device_class}\n")
-                    yamlfile.write(f"  deviceConfig: {{prefix: '{pv}'}}\n")
-                else:
-                    yamlfile.write(f"  deviceClass: ophyd.Epics{device_class}\n")
-                    yamlfile.write(
-                        f"  deviceConfig: {{read_pv: '{pv}', auto_monitor: true}}\n"
-                    )
-
-                yamlfile.write("  onFailure: buffer\n")
-                yamlfile.write("  enabled: True\n")
-                yamlfile.write(f"  readoutPriority: {readout_priority}\n")
-                yamlfile.write("  deviceTags:\n")
-                yamlfile.write(f"    - {tag}\n")
-                yamlfile.write(f"  readOnly: {read_only}\n")
-                yamlfile.write("  softwareTrigger: false\n")
-
-                # Only add userParameter for Motors if present
-                # if device_class == "Motor" and user_param:
-                if user_param:
-                    try:
-                        parsed = json.loads(user_param)
-                        yamlfile.write("  userParameter:\n")
-                        for k, v in parsed.items():
-                            yamlfile.write(f"    {k}: {v}\n")
-                    except json.JSONDecodeError:
-                        yamlfile.write(f"  userParameter: {user_param}\n")
-
-                yamlfile.write("\n")
-
-    print(f"YAML written to {OUTPUT_YAML}")
-
-def main():
-
-    devices = "pxiii-standard-devices"
-    states = "pxiii-state-devices"
-
-    device_files = [
-        f"{devices}.csv",
-        f"{devices}.yaml"
-    ]
-    state_files = [
-        f"{states}.csv",
-        f"{states}.yaml"
-    ]
-
-    create(device_files[0],device_files[1])
-    create(state_files[0],state_files[1])
-
-main()

pxiii_bec/device_configs/pxiii-standard-devices.csv

@@ -1,127 +0,0 @@
-name,description,deviceClass,PV,readoutPriority,tag,readOnly,include,userParameter,
-sls_current,SLS Current,SignalRO,ARS07-DPCT-0100:CURR,monitored,SLS,yes,yes,,
-fe_sl_xr,FE Slit X Ring,MotorEC,X06DA-FE-SLDI:TRXR,baseline,fe,no,yes,,
-fe_sl_yt,FE Slit Y Top,MotorEC,X06DA-FE-SLDI:TRYT,baseline,fe,no,yes,,
-fe_sl_xw,FE Slit X Wall,MotorEC,X06DA-FE-SLDI:TRXW,baseline,fe,no,yes,,
-fe_sl_yb,FE Slit Y Bottom,MotorEC,X06DA-FE-SLDI:TRYB,baseline,fe,no,yes,,
-fe_sl_xcen,FE Slit X Centre,MotorEC,X06DA-FE-SLDI:CENTERX,baseline,fe,no,yes,,
-fe_sl_xsize,FE Slit X Size,MotorEC,X06DA-FE-SLDI:SIZEX,baseline,fe,no,yes,,
-fe_sl_ycen,FE Slit Y Centre,MotorEC,X06DA-FE-SLDI:CENTERY,baseline,fe,no,yes,,
-fe_sl_ysize,FE Slit Y Size,MotorEC,X06DA-FE-SLDI:SIZEY,baseline,fe,no,yes,,
-tm_xu,TorM Upstream X,MotorEC,X06DA-FE-MI1:TRXU,baseline,tm,no,yes,,
-tm_xd,TorM Downstream X,MotorEC,X06DA-FE-MI1:TRXD,baseline,tm,no,yes,,
-tm_yur,TorM Upstream Ring Y,MotorEC,X06DA-FE-MI1:TRYUR,baseline,tm,no,yes,,
-tm_yw,TorM Wall Y,MotorEC,X06DA-FE-MI1:TRYUW,baseline,tm,no,yes,,
-tm_yd,TorM Downstream Y,MotorEC,X06DA-FE-MI1:TRYD,baseline,tm,no,yes,,
-tm_b1,TorM Bender,MotorEC,X06DA-FE-MI1:BEND1,baseline,tm,no,yes,,
-tm_yaw,TorM Virtual Yaw,MotorEC,X06DA-FE-MI1:YAW,baseline,tm,no,yes,,
-tm_roll,TorM Virtual Roll,MotorEC,X06DA-FE-MI1:ROLL,baseline,tm,no,yes,,
-tm_pitch,TorM Virtual Pitch,MotorEC,X06DA-FE-MI1:PITCH,baseline,tm,no,yes,,
-tm_x,TorM Virtual X,MotorEC,X06DA-FE-MI1:TRX,baseline,tm,no,yes,,
-tm_y,TorM Virtual Y ,MotorEC,X06DA-FE-MI1:TRY,baseline,tm,no,yes,,
-bsf_bpm1,BSF BPM Channel 1,SignalRO,X06DA-OP-BSFBPM:SIGNAL1,monitored,bpm,yes,no,,
-bsf_bpm2,BSF BPM Channel 2,SignalRO,X06DA-OP-BSFBPM:SIGNAL2,monitored,bpm,yes,no,,
-bsf_bpm3,BSF BPM Channel 3,SignalRO,X06DA-OP-BSFBPM:SIGNAL3,monitored,bpm,yes,no,,
-bsf_bpm4,BSF BPM Channel 4,SignalRO,X06DA-OP-BSFBPM:SIGNAL4,monitored,bpm,yes,no,,
-bsf_bpmsum,BSF BPM Summed,SignalRO,X06DA-OP-BSFBPM:SUM,monitored,bpm,yes,no,,
-bsf_sl_xw,BSF Slit outboard,MotorEC,X06DA-OP-BSFSLH:TRXW,baseline,bsf,no,yes,,
-bsf_sl_xr,BSF Slit inboard,MotorEC,X06DA-OP-BSFSLH:TRXR,baseline,bsf,no,yes,,
-bsf_sl_xcen,BSF X Centre,MotorEC,X06DA-OP-BSFSLH:CENTER,baseline,bsf,no,yes,,
-bsf_sl_xsize,BSF X Size,MotorEC,X06DA-OP-BSFSLH:SIZE,baseline,bsf,no,yes,,
-bsf_f1_y,BSF Filter 1 Y,MotorEC,X06DA-OP-BSFFI1:TRY,baseline,bsf,no,yes,,
-dccm_theta1,DCCM Theta Xtal1,MotorEC,X06DA-OP-DCCM:ROTX-CR1,baseline,dccm,no,yes,,
-dccm_theta2,DCCM Theta Xtal2,MotorEC,X06DA-OP-DCCM:ROTX-CR2,baseline,dccm,no,yes,,
-dccm_rotz,DCCM RotZ Xtal 2,MotorEC,X06DA-OP-DCCM:ROTZ-CR2,baseline,dccm,no,yes,,
-dccm_xbpm1_y,DCCM BPM1 Y,MotorEC,X06DA-OP-DCCMXBPM1:TRY,baseline,dccm,no,yes,,
-dccm_xbpm2_y,DCCM BPM2 Y,MotorEC,X06DA-OP-DCCMXBPM2:TRY,baseline,dccm,no,yes,,
-dccm_energy,DCCM Energy,Motor,X06DA-OP-DCCM:ENERGY,baseline,dccm,no,yes,,
-dccm_di_top,DCCM Diode Top,SignalRO,X06DA-OP-DCCMXBPM1T:READOUT,monitored,dccm,no,yes,,
-dccm_di_bot,DCCM Diode Bottom,SignalRO,X06DA-OP-DCCMXBPM1B:READOUT,monitored,dccm,no,yes,,
-dccm_bpm1,DCCM BPM Channel 1,SignalRO,X06DA-OP-DCCMXBPM2:Current1:MeanValue_RBV,monitored,dccm,no,yes,,
-dccm_bpm2,DCCM BPM Channel 2,SignalRO,X06DA-OP-DCCMXBPM2:Current2:MeanValue_RBV,monitored,dccm,no,yes,,
-dccm_bpm3,DCCM BPM Channel 3,SignalRO,X06DA-OP-DCCMXBPM2:Current3:MeanValue_RBV,monitored,dccm,no,yes,,
-dccm_bpm4,DCCM BPM Channel 4,SignalRO,X06DA-OP-DCCMXBPM2:Current4:MeanValue_RBV,monitored,dccm,no,yes,,
-dccm_bpmsum,DCCM BPM Summed,SignalRO,X06DA-OP-DCCMXBPM2:SumAll:MeanValue_RBV,monitored,dccm,no,yes,,
-ss_bpm1,SS BPM Channel 1,SignalRO,X06DA-ES-SSBPM:Current1:MeanValue_RBV,monitored,bpm,yes,yes,,
-ss_bpm2,SS BPM Channel 2,SignalRO,X06DA-ES-SSBPM:Current2:MeanValue_RBV,monitored,bpm,yes,yes,,
-ss_bpm3,SS BPM Channel 3,SignalRO,X06DA-ES-SSBPM:Current3:MeanValue_RBV,monitored,bpm,yes,yes,,
-ss_bpm4,SS BPM Channel 4,SignalRO,X06DA-ES-SSBPM:Current4:MeanValue_RBV,monitored,bpm,yes,yes,,
-ss_bpmsum,SS BPM Summed,SignalRO,X06DA-ES-SSBPM:SumAll:MeanValue_RBV,monitored,bpm,yes,yes,,
-ss_bpm_x,SS BPM X,Motor,X06DA-ES-SSBPM:TRX,baseline,ss,no,yes,,
-ss_bpm_y,SS BPM Y,Motor,X06DA-ES-SSBPM:TRY,baseline,ss,no,yes,,
-ss_sl_xw,SS Slit Wall,Motor,X06DA-ES-SSSLH:TRXW,baseline,ss,no,yes,,
-ss_sl_xr,SS Slit Ring,Motor,X06DA-ES-SSSLH:TRXR,baseline,ss,no,yes,,
-ss_sl_xcen,SS Slit X Centre,Motor,X06DA-ES-SSSLH:CENTER,baseline,ss,no,yes,,
-ss_sl_xsize,SS Slit X Size,Motor,X06DA-ES-SSSLH:SIZE,baseline,ss,no,yes,,
-ss_sl_yt,SS Slit Top,Motor,X06DA-ES-SSSLV:TRYT,baseline,ss,no,yes,,
-ss_sl_yb,SS Slit Bottom,Motor,X06DA-ES-SSSLV:TRYB,baseline,ss,no,yes,,
-ss_sl_ycen,SS Slit Y Centre,Motor,X06DA-ES-SSSLV:CENTER,baseline,ss,no,yes,,
-ss_sl_ysize,SS Slit Y Size,Motor,X06DA-ES-SSSLV:SIZE,baseline,ss,no,yes,,
-ss_xi_x,SS X-ray Eye X,Motor,X06DA-ES-SSXI:TRX,baseline,ss,no,yes,"{""type"": multi-position,""in"": 7.5, ""out"": -2.1}",
-ss_xi_y,SS X-ray Eye Y,Motor,X06DA-ES-SSXI:TRY,baseline,ss,no,yes,,
-ss_xicam_x,SS Camera X,SignalRO,X06DA-ES-SSCAM:Stats5:CentroidX_RBV,baseline,ss,yes,yes,,
-ss_xicam_y,SS Camera Y,SignalRO,X06DA-ES-SSCAM:Stats5:CentroidY_RBV,baseline,ss,yes,yes,,
-ss_xicam_max,SS Cam Max,SignalRO,X06DA-ES-SSCAM:Stats5:MaxValue_RBV,monitored,ss,yes,yes,,
-ss_xicam_exp,SS Camera Exposure,Signal,X06DA-ES-SSCAM:cam1:AcquireTime,baseline,ss,no,yes,,
-ss_xicam_gain,SS Camera Gain,Signal,X06DA-ES-SSCAM:cam1:Gain,baseline,ss,no,yes,,
-ss_xicam_xsig,SS Camera  X Sigma,Signal,X06DA-ES-SSCAM:Stats5:SigmaX_RBV,baseline,ss,yes,yes,,
-ss_xicam_ysig,SS Camera Y Sigma,Signal,X06DA-ES-SSCAM:Stats5:SigmaY_RBV,baseline,ss,yes,yes,,
-vfm_xu,VFM Upstream X,MotorEC,X06DA-ES-VFM:TRXU,baseline,vfm,no,yes,,
-vfm_xd,VFM Downstream X,MotorEC,X06DA-ES-VFM:TRXD,baseline,vfm,no,yes,,
-vfm_yur,VFM Upstream Ring Y,MotorEC,X06DA-ES-VFM:TRYUR,baseline,vfm,no,yes,,
-vfm_yw,VFM Wall Y,MotorEC,X06DA-ES-VFM:TRYW,baseline,vfm,no,yes,,
-vfm_ydr,VFM Downstream Ring Y,MotorEC,X06DA-ES-VFM:TRYDR,baseline,vfm,no,yes,,
-vfm_bu,VFM Upstream Bender,MotorEC,X06DA-ES-VFM:BNDU,baseline,vfm,no,yes,,
-vfm_bd,VFM Downstream Bender,MotorEC,X06DA-ES-VFM:BNDD,baseline,vfm,no,yes,,
-vfm_yaw,VFM Virtual Yaw,MotorEC,X06DA-ES-VFM:YAW,baseline,vfm,no,yes,,
-vfm_roll,VFM Virtual Roll,MotorEC,X06DA-ES-VFM:ROLL,baseline,vfm,no,yes,,
-vfm_pitch,VFM Virtual Pitch,MotorEC,X06DA-ES-VFM:PITCH,baseline,vfm,no,yes,,
-vfm_x,VFM Virtual X,MotorEC,X06DA-ES-VFM:TRX,baseline,vfm,no,yes,,
-vfm_y,VFM Virtual Y ,MotorEC,X06DA-ES-VFM:TRY,baseline,vfm,no,yes,,
-hfm_xu,HFM Upstream X,MotorEC,X06DA-ES-HFM:TRXU,baseline,hfm,no,yes,,
-hfm_xd,HFM Downstream X,MotorEC,X06DA-ES-HFM:TRXD,baseline,hfm,no,yes,,
-hfm_yuw,HFM Upstream Wall Y,MotorEC,X06DA-ES-HFM:TRYUW,baseline,hfm,no,yes,,
-hfm_yr,HFM Ring Y,MotorEC,X06DA-ES-HFM:TRYR,baseline,hfm,no,yes,,
-hfm_ydw,HFM Downstream Wall Y,MotorEC,X06DA-ES-HFM:TRYDW,baseline,hfm,no,yes,,
-hfm_bu,HFM Upstream Bender,MotorEC,X06DA-ES-HFM:BNDU,baseline,hfm,no,yes,,
-hfm_bd,HFM Downstream Bender,MotorEC,X06DA-ES-HFM:BNDD,baseline,hfm,no,yes,,
-hfm_yaw,HFM Virtual Yaw,MotorEC,X06DA-ES-HFM:YAW,baseline,hfm,no,yes,,
-hfm_roll,HFM Virtual Roll,MotorEC,X06DA-ES-HFM:ROLL,baseline,hfm,no,yes,,
-hfm_pitch,HFM Virtual Pitch,MotorEC,X06DA-ES-HFM:PITCH,baseline,hfm,no,yes,,
-hfm_x,HFM Virtual X,MotorEC,X06DA-ES-HFM:TRX,baseline,hfm,no,yes,,
-hfm_y,HFM Virtual Y ,MotorEC,X06DA-ES-HFM:TRY,baseline,hfm,no,yes,,
-bcu_bpm1,BCU BPM Channel 1 ,SignalRO,X06DA-ES-BCBPM:Current1:MeanValue_RBV,monitored,bpm,yes,yes,,
-bcu_bpm2,BCU BPM Channel 2,SignalRO,X06DA-ES-BCBPM:Current2:MeanValue_RBV,monitored,bpm,yes,yes,,
-bcu_bpm3,BCU BPM Channel 3,SignalRO,X06DA-ES-BCBPM:Current3:MeanValue_RBV,monitored,bpm,yes,yes,,
-bcu_bpm4,BCU BPM Channel 4,SignalRO,X06DA-ES-BCBPM:Current4:MeanValue_RBV,monitored,bpm,yes,yes,,
-bcu_bpmsum,BCU BPM Summed,SignalRO,X06DA-ES-BCBPM:SumAll:MeanValue_RBV,monitored,bpm,yes,yes,,
-bcu_bpm_x,BCU BPM X,Motor,X06DA-ES-BCBPM:TRX,baseline,bcu,no,yes,,
-bcu_bpm_y,BCU BPM Y ,Motor,X06DA-ES-BCBPM:TRY,baseline,bcu,no,yes,,
-bcu_sl_xw,BCU Slit Wall,Motor,X06DA-ES-BCSLH:TRXW,baseline,bcu,no,yes,,
-bcu_sl_xr,BCU Slit Ring,Motor,X06DA-ES-BCSLH:TRXR,baseline,bcu,no,yes,,
-bcu_sl_xcen,BCU Slit X Centre,Motor,X06DA-ES-BCSLH:CENTER,baseline,bcu,no,yes,,
-bcu_sl_xsize,BCU Slit X Size,Motor,X06DA-ES-BCSLH:SIZE,baseline,bcu,no,yes,,
-bcu_sl_yt,BCU Slit top,Motor,X06DA-ES-BCSLV:TRYT,baseline,bcu,no,yes,,
-bcu_sl_yb,BCU Slit Bottom,Motor,X06DA-ES-BCSLV:TRYB,baseline,bcu,no,yes,,
-bcu_sl_ycen,BCU Slit Y Centre,Motor,X06DA-ES-BCSLV:CENTER,baseline,bcu,no,yes,,
-bcu_sl_ysize,BCU Slit Y Size,Motor,X06DA-ES-BCSLV:SIZE,baseline,bcu,no,yes,,
-samcam_x,Sample Camera X ,SignalRO,X06DA-ES-MS:Stats5:CentroidX_RBV,baseline,scam,yes,no,,
-samcam_xsig,Sample Camera X Sigma,SignalRO,X06DA-ES-MS:Stats5:SigmaX_RBV,monitored,scam,yes,no,,
-samcam_y,Sample Camera Y ,SignalRO,X06DA-ES-MS:Stats5:CentroidY_RBV,baseline,scam,yes,no,,
-samcam_ysig,Sample Camera Y Sigma,SignalRO,X06DA-ES-MS:Stats5:SigmaY_RBV,monitored,scam,yes,no,,
-samcam_max,Sample Camera Max,SignalRO,X06DA-ES-MS:Stats5:MaxValue_RBV,monitored,scam,yes,no,,
-samcam_exp,Sample Camera Exposure,Signal,X06DA-ES-MS:cam1:AcquireTime,baseline,scam,no,no,,
-samcam_gain,Sample Camera Gain,Signal,X06DA-ES-MS:cam1:Gain,baseline,scam,no,no,,
-scam_zoom,Sample Camera Zoom,Motor,X06DA-ES-MS:ZOOM,baseline,scam,no,yes,,
-coll_x,Collimator X,Motor,X06DA-ES-COL:TRX,baseline,se,no,no,, 
-diag_z,Scintillator/diode Z,Motor,X06DA-ES-SCL:TRZ,baseline,se,no,no,,
-i1,I1 diode,SignalRO,X06DA-ES-SCLDI:READOUT,monitored,bpm,yes,no,,
-bs_x,Beamstop X,Motor,X06DA-ES-BS:TRX,baseline,se,no,no,,
-bs_y,Beamstop Y,Motor,X06DA-ES-BS:TRY,baseline,se,no,no,,
-gon_y,Goniometer Y,Motor,X06DA-ES-DF1:TRY1,baseline,det,no,no,,
-gon_z,Goniometer X,Motor,X06DA-ES-DF1:TRZ1,baseline,det,no,no,,
-omega,Omega,Motor,X06DA-ES-DF1:ROTU,baseline,det,no,no,,
-cryo_x,Cryo X ,Motor,X06DA-ES-CS:TRX,baseline,se,no,no,,
-cryo_temp,Cryo Temperature,SignalRO,X06DA-ES-CS:TEMP_RBV,baseline,se,no,no,,
-det_y,Detector Y,MotorEC,X06DA-ES-DET:TRY,baseline,det,no,no,,
-det_z,Detector Z,MotorEC,X06DA-ES-DET:TRZ,baseline,det,no,no,,

pxiii_bec/device_configs/pxiii-state-devices.csv

@@ -1,11 +0,0 @@
-name,description,deviceClass,PV,readoutPriority,tag,readOnly,include,userParameter
-bl_bright,Backlight Brightness,Signal,X06DA-ES-BL:SET,baseline,state,no,yes,
-bl_pos,Backlight Positioner,Signal,X06DA-ES-BL:POS-SET,baseline,state,no,no,"{""type"":positioner}"
-bs_pos,Beamstop Positioner,Signal,X06DA-ES-BS:POS-SET,baseline,state,no,no,"{""type"":positioner}"
-bs_z,Beamstop Z,Motor,X06DA-ES-BS:TRZ,baseline,state,no,yes,"{""type"": guarded, ""min"": 13, ""samp"": 15, ""work_min"": 20, ""safe"": 41, ""max_blin"": 42, ""max_blout"": 70}"
-coll_y,Collimator Y,Motor,X06DA-ES-COL:TRY,baseline,state,no,yes,"{""type"": multi-position, ""in"": 40, ""out"": 20.0, ""park"": 0,""tol"":0.05}"
-cryo_pos,Cryo positioner,Signal,X06DA-ES-CS:POS-SET,baseline,state,no,no,"{""type"":positioner}"
-det_cov,Detector cover,Signal,X06DA-ES-DETCOV:SET,baseline,state,no,no,"{""type"":positioner}"
-diag_y,Scintillator/diode Y,Motor,X06DA-ES-SCL:TRY,baseline,state,no,yes,"{""type"": multi-position, ""scint"": 39, ""i1"": 44.0, ""out"": 20.0,""park"": 0,""tol"":0.3}"
-fl_bright,Frontlight Brightness,Signal,X06DA-ES-FL:SET,baseline,state,no,yes,
-xrf_pos,XRF Positioner,Signal,X06DA-ES-XRF:POS-SET,baseline,state,no,no,"{""type"":positioner}"

pxiii_bec/device_configs/pxiii-state-devices.yaml

@@ -1,63 +0,0 @@
-bl_bright:
-  description: Backlight Brightness
-  deviceClass: ophyd.EpicsSignal
-  deviceConfig: {read_pv: 'X06DA-ES-BL:SET', auto_monitor: true}
-  onFailure: buffer
-  enabled: True
-  readoutPriority: baseline
-  deviceTags:
-    - state
-  readOnly: False
-  softwareTrigger: false
-
-bs_z:
-  description: Beamstop Z
-  deviceClass: ophyd_devices.EpicsMotor
-  deviceConfig: {prefix: 'X06DA-ES-BS:TRZ'}
-  onFailure: buffer
-  enabled: True
-  readoutPriority: baseline
-  deviceTags:
-    - state
-  readOnly: False
-  softwareTrigger: false
-  userParameter: {"type": guarded, "min": 13, "samp": 15, "work_min": 20, "safe": 41, "max_blin": 42, "max_blout": 70}
-
-coll_y:
-  description: Collimator Y
-  deviceClass: ophyd_devices.EpicsMotor
-  deviceConfig: {prefix: 'X06DA-ES-COL:TRY'}
-  onFailure: buffer
-  enabled: True
-  readoutPriority: baseline
-  deviceTags:
-    - state
-  readOnly: False
-  softwareTrigger: false
-  userParameter: {"type": multi-position, "in": 40, "out": 20.0, "park": 0,"tol":0.05}
-
-diag_y:
-  description: Scintillator/diode Y
-  deviceClass: ophyd_devices.EpicsMotor
-  deviceConfig: {prefix: 'X06DA-ES-SCL:TRY'}
-  onFailure: buffer
-  enabled: True
-  readoutPriority: baseline
-  deviceTags:
-    - state
-  readOnly: False
-  softwareTrigger: false
-  userParameter: {"type": multi-position, "scint": 39, "i1": 44.0, "out": 20.0,"park": 0,"tol":0.3}
-
-fl_bright:
-  description: Frontlight Brightness
-  deviceClass: ophyd.EpicsSignal
-  deviceConfig: {read_pv: 'X06DA-ES-FL:SET', auto_monitor: true}
-  onFailure: buffer
-  enabled: True
-  readoutPriority: baseline
-  deviceTags:
-    - state
-  readOnly: False
-  softwareTrigger: false
-

pxiii_bec/device_configs/x06da_device_config.yaml

@@ -1,4 +0,0 @@
-base_config:
-  - !include ./pxiii-standard-devices.yaml
-states_config:
-  - !include ./pxiii-state-devices.yaml

pxiii_bec/devices/A3200.py

@@ -1,426 +0,0 @@
-"""
-``Aerotech`` --- Aerotech control software
-******************************************
-
-This module provides an object to control the Aerotech Abr rotational stage.
-
-Methods in the Abr class
-========================
-
-Standard bluesky interface:
-    AerotechAbrStage.configure(d={...})
-    AerotechAbrStage.kickoff()
-    AerotechAbrStage.stop()
-Additional bluesky functionality:
-
-
-
-
-
-Aerotech.is_homed()
-Aerotech.do_homing(wait=True)
-Aerotech.get_ready(ostart=None, orange=None, etime=None, wait=True)
-Aerotech.is_done()
-Aerotech.is_ready()
-Aerotech.is_busy()
-Aerotech.start_exposure()
-Aerotech.wait_status(status)
-Aerotech.move(angle, wait=False, speed=None)
-Aerotech.set_shutter(state)
-
-
-    Returns the axis mode: ``-ES-DF1:AXES-MODE``
-
-Examples
-========
-
-    abr = AerotechAbrStage(prefix="X06DA-ES-DF1", name="abr")
-
-      # move omega to 270.0 degrees
-      abr.omega = 270.0
-
-      # move omega to 180 degrees and wait for movement to finish
-      abr.move(180, wait=True)
-
-      # move omega to 3000 degrees at 360 degrees/s and wait for movement to finish
-      abr.move(3000, velocity=360, wait=True)
-
-      # stop any movement
-      abr.stop() # this function only returns after the STATUS is back to OK
-
-"""
-
-import time
-from ophyd import Device, Component, EpicsSignal, EpicsSignalRO, Kind
-from ophyd.status import SubscriptionStatus
-from ophyd_devices.interfaces.base_classes.psi_device_base import PSIDeviceBase
-
-try:
-    from .A3200enums import AbrCmd, AbrMode
-except ImportError:
-    from A3200enums import AbrCmd, AbrMode
-
-
-from bec_lib import bec_logger
-
-logger = bec_logger.logger
-
-
-# pylint: disable=logging-fstring-interpolation
-class AerotechAbrStage(PSIDeviceBase, Device):
-    """Standard PX stage on A3200 controller
-
-    This is the wrapper class for the standard rotation stage layout for the PX
-    beamlines at SLS. It wraps the main rotation axis OMEGA (Aerotech ABR)and
-    the associated motion axes GMX, GMY and GMZ. The ophyd class associates to
-    the general PX measurement procedure, which is that the actual scan script
-    is running as an AeroBasic program on the controller and we communicate to
-    it via 10+1 global variables.
-    """
-
-    USER_ACCESS = ["reset", "kickoff", "complete", "set_axis_mode", "arm", "disarm"]
-
-    taskStop = Component(EpicsSignal, "-AERO:TSK-STOP", put_complete=True, kind=Kind.omitted)
-    status = Component(EpicsSignal, "-AERO:STAT", put_complete=True, kind=Kind.omitted)
-    clear = Component(EpicsSignal, "-AERO:CTRL-CLFT", put_complete=True, kind=Kind.omitted)
-
-    # Enable/disable motor movement via the IOC (i.e. make it task-only)
-    axisModeLocked = Component(EpicsSignal, "-DF1:LOCK", put_complete=True, kind=Kind.omitted)
-    axisModeDirect = Component(
-        EpicsSignal, "-DF1:MODE-DIRECT", put_complete=True, kind=Kind.omitted
-    )
-    axisAxesMode = Component(EpicsSignal, "-DF1:AXES-MODE", put_complete=True, kind=Kind.omitted)
-
-    # Shutter box is missing readback so the -GET signal is installed on the VME
-    # _shutter = Component(
-    #     EpicsSignal, "-PH1:GET", write_pv="-PH1:SET", put_complete=True, kind=Kind.config,
-    # )
-
-    # Status flags for all axes
-    omega_done = Component(EpicsSignalRO, "-DF1:OMEGA-DONE", kind=Kind.normal)
-    gmx_done = Component(EpicsSignalRO, "-DF1:GMX-DONE", kind=Kind.normal)
-    gmy_done = Component(EpicsSignalRO, "-DF1:GMY-DONE", kind=Kind.normal)
-    gmz_done = Component(EpicsSignalRO, "-DF1:GMZ-DONE", kind=Kind.normal)
-
-    # For some reason the task interface is called PSO...
-    scan_command = Component(EpicsSignal, "-PSO:CMD", put_complete=True, kind=Kind.omitted)
-    start_command = Component(
-        EpicsSignal, "-PSO:START-TEST.PROC", put_complete=True, kind=Kind.omitted
-    )
-    stop_command = Component(
-        EpicsSignal, "-PSO:STOP-TEST.PROC", put_complete=True, kind=Kind.omitted
-    )
-
-    # Global variables to controll AeroBasic scripts
-    _var_1 = Component(EpicsSignal, "-PSO:VAR-1", put_complete=True, kind=Kind.omitted)
-    _var_2 = Component(EpicsSignal, "-PSO:VAR-2", put_complete=True, kind=Kind.omitted)
-    _var_3 = Component(EpicsSignal, "-PSO:VAR-3", put_complete=True, kind=Kind.omitted)
-    _var_4 = Component(EpicsSignal, "-PSO:VAR-4", put_complete=True, kind=Kind.omitted)
-    _var_5 = Component(EpicsSignal, "-PSO:VAR-5", put_complete=True, kind=Kind.omitted)
-    _var_6 = Component(EpicsSignal, "-PSO:VAR-6", put_complete=True, kind=Kind.omitted)
-    _var_7 = Component(EpicsSignal, "-PSO:VAR-7", put_complete=True, kind=Kind.omitted)
-    _var_8 = Component(EpicsSignal, "-PSO:VAR-8", put_complete=True, kind=Kind.omitted)
-    _var_9 = Component(EpicsSignal, "-PSO:VAR-9", put_complete=True, kind=Kind.omitted)
-    _var_10 = Component(EpicsSignal, "-PSO:VAR-10", put_complete=True, kind=Kind.omitted)
-
-    # Task status PVs (programs always run on task 1)
-    task1 = Component(EpicsSignalRO, "-AERO:TSK1-DONE", auto_monitor=True)
-    task2 = Component(EpicsSignalRO, "-AERO:TSK2-DONE", auto_monitor=True)
-    task3 = Component(EpicsSignalRO, "-AERO:TSK3-DONE", auto_monitor=True)
-    task4 = Component(EpicsSignalRO, "-AERO:TSK4-DONE", auto_monitor=True)
-    scan_done = Component(EpicsSignal, "-GRD:SCAN-DONE", kind=Kind.config)
-
-    def __init__(
-        self,
-        prefix="",
-        *,
-        name,
-        kind=None,
-        read_attrs=None,
-        configuration_attrs=None,
-        parent=None,
-        scan_info=None,
-        **kwargs,
-    ):
-        # super() will call the mixin class
-        super().__init__(
-            prefix=prefix,
-            name=name,
-            kind=kind,
-            read_attrs=read_attrs,
-            configuration_attrs=configuration_attrs,
-            parent=parent,
-            scan_info=scan_info,
-            **kwargs,
-        )
-
-    def set_axis_mode(self, mode: str, settle_time=0.1) -> None:
-        """Set axis mode to direct/measurement mode.
-
-        Measurement ensures that the scrips run undisturbed by blocking axis
-        motion commands from the IOC (i.e. internal only).
-
-        Parameters:
-        -----------
-        mode : str
-            Valid values are 'direct' and 'measuring'.
-        """
-        if mode == "direct":
-            self.axisModeDirect.set(37, settle_time=settle_time).wait()
-        if mode == "measuring":
-            self.axisAxesMode.set(AbrMode.MEASURING, settle_time=settle_time).wait()
-
-    def on_stage(self):
-        """
-
-        NOTE: Zac's request is that stage is essentially ARM, i.e. get ready and don't do anything.
-        """
-        d = {}
-        # FIXME: I don't care about how we fish out config parameters from scan info
-        scan_args = {
-            **self.scan_info.msg.request_inputs["inputs"],
-            **self.scan_info.msg.request_inputs["kwargs"],
-            **self.scan_info.msg.scan_parameters,
-        }
-        scanname = self.scan_info.msg.scan_name
-
-        if scanname in (
-            "standardscan",
-            "helicalscan",
-            "helicalscan1",
-            "helicalscan2",
-            "helicalscan3",
-        ):
-            d["scan_command"] = AbrCmd.MEASURE_STANDARD
-            d["var_1"] = scan_args["start"]
-            d["var_2"] = scan_args["range"]
-            d["var_3"] = scan_args["move_time"]
-            d["var_4"] = scan_args.get("ready_rate", 500)
-            d["var_5"] = 0
-            d["var_6"] = 0
-            d["var_7"] = 0
-            # d["var_8"] = 0
-            # d["var_9"] = 0
-        if scanname in ("verticallinescan", "vlinescan"):
-            d["scan_command"] = AbrCmd.VERTICAL_LINE_SCAN
-            d["var_1"] = scan_args["range"] / scan_args["steps"]
-            d["var_2"] = scan_args["steps"]
-            d["var_3"] = scan_args["exp_time"]
-            d["var_4"] = 0
-            d["var_5"] = 0
-            d["var_6"] = 0
-            d["var_7"] = 0
-            # d["var_8"] = 0
-            # d["var_9"] = 0
-        if scanname in ("screeningscan"):
-            d["scan_command"] = AbrCmd.SCREENING
-            d["var_1"] = scan_args["start"]
-            d["var_2"] = scan_args["oscrange"]
-            d["var_3"] = scan_args["exp_time"]
-            d["var_4"] = scan_args["range"] / scan_args["steps"]
-            d["var_5"] = scan_args["steps"]
-            d["var_6"] = scan_args.get("delta", 0.5)
-            d["var_7"] = 0
-            # d["var_8"] = 0
-            # d["var_9"] = 0
-        if scanname in ("rasterscan", "rastersimplescan"):
-            d["scan_command"] = AbrCmd.RASTER_SCAN_SIMPLE
-            d["var_1"] = scan_args["exp_time"]
-            d["var_2"] = scan_args["range_x"] / scan_args["steps_x"]
-            d["var_3"] = scan_args["range_y"] / scan_args["steps_y"]
-            d["var_4"] = scan_args["steps_x"]
-            d["var_5"] = scan_args["steps_y"]
-            d["var_6"] = 0
-            d["var_7"] = 0
-            # d["var_8"] = 0
-            # d["var_9"] = 0
-
-        # Reconfigure if got a valid scan config
-        if len(d) > 0:
-            self.configure(d)
-
-        # Stage the ABR stage
-        self.arm()
-
-    def on_unstage(self):
-        """Unstage the ABR controller"""
-        self.disarm()
-
-    def configure(self, d: dict) -> tuple:
-        """ " Configure the exposure scripts
-
-        Script execution at the PX beamlines is based on scripts that are always
-        running on the controller that execute commands when commanded by
-        setting a pre-defined set of global variables. This method performs the
-        configuration of the exposure scrips by setting the required global
-        variables.
-
-        Parameters in d: dict
-        ---------------------
-        scan_command: int
-            The index of the desired AeroBasic program to be executed.
-            Usually supported values are taken from an Enum.
-        var_1:
-        var_2:
-        var_3:
-        var_4:
-        var_5:
-        var_6:
-        var_7:
-        var_8:
-        var_9:
-        var_10:
-        """
-        old = self.read_configuration()
-
-        # ToDo: Check if idle before reconfiguring
-        self.scan_command.set(d["scan_command"]).wait()
-        # Set the corresponding global variables
-        if "var_1" in d and d["var_1"] is not None:
-            self._var_1.set(d["var_1"]).wait()
-        if "var_2" in d and d["var_2"] is not None:
-            self._var_2.set(d["var_2"]).wait()
-        if "var_3" in d and d["var_3"] is not None:
-            self._var_3.set(d["var_3"]).wait()
-        if "var_4" in d and d["var_4"] is not None:
-            self._var_4.set(d["var_4"]).wait()
-        if "var_5" in d and d["var_5"] is not None:
-            self._var_5.set(d["var_5"]).wait()
-        if "var_6" in d and d["var_6"] is not None:
-            self._var_6.set(d["var_6"]).wait()
-        if "var_7" in d and d["var_7"] is not None:
-            self._var_7.set(d["var_7"]).wait()
-        if "var_8" in d and d["var_8"] is not None:
-            self._var_8.set(d["var_8"]).wait()
-        if "var_9" in d and d["var_9"] is not None:
-            self._var_9.set(d["var_9"]).wait()
-        if "var_10" in d and d["var_10"] is not None:
-            self._var_10.set(d["var_10"]).wait()
-
-        new = self.read_configuration()
-        return old, new
-
-    def arm(self):
-        """Bluesky-style stage
-
-        Since configuration synchronization is not guaranteed, this does
-        nothing. The script launched by kickoff().
-        """
-
-    def on_kickoff(self, timeout=1) -> SubscriptionStatus:
-        """Kick off the set program"""
-        self.start_command.set(1).wait()
-
-        # Define wait until the busy flag goes high
-        def is_busy(*, value, **_):
-            return bool(value == 0)
-
-        # Subscribe and wait for update
-        status = SubscriptionStatus(self.scan_done, is_busy, timeout=timeout, settle_time=0.1)
-        status.wait()
-        # return status
-
-    def disarm(self, settle_time=0.1):
-        """Stops current script and releases the axes"""
-        # Disarm commands
-        self.scan_command.set(AbrCmd.NONE, settle_time=settle_time).wait()
-        self.stop_command.set(1).wait()
-        # Go to direct mode
-        self.set_axis_mode("direct", settle_time=settle_time)
-
-    def complete(self, timeout=None) -> SubscriptionStatus:
-        """Waits for task execution
-
-        NOTE:  Original complete was raster scanner complete...
-        """
-
-        # Define wait until the busy flag goes down (excluding initial update)
-        def is_idle(*, value, **_):
-            return bool(value == 1)
-
-        # Subscribe and wait for update
-        # status = SubscriptionStatus(self.task1, is_idle, timeout=timeout, settle_time=0.5)
-        status = SubscriptionStatus(self.scan_done, is_idle, timeout=timeout, settle_time=0.5)
-        return status
-
-    def reset(self, settle_time=0.1, wait_after_reload=1) -> None:
-        """Resets the Aerotech controller state
-
-        Attempts to reset the currently running measurement task on the A3200
-        by stopping current motions, reloading aerobasic programs and going
-        to DIRECT mode.
-
-        This will stop movements in both DIRECT and MEASURING modes.  During the
-        stop the `status` temporarely goes to ERROR but reverts to OK after a
-        couple of seconds.
-        """
-        # Disarm commands
-        self.scan_command.set(AbrCmd.NONE, settle_time=settle_time).wait()
-        self.stop_command.set(1, settle_time=settle_time)
-        # Reload tasks
-        self.taskStop.set(1, settle_time=wait_after_reload).wait()
-        # Go to direct mode
-        self.set_axis_mode("direct", settle_time=settle_time)
-
-    # pylint: disable=arguments-differ
-    def stop(self, settle_time=1.0) -> None:
-        """Stops current motions"""
-        # Disarm commands
-        self.scan_command.set(AbrCmd.NONE, settle_time=settle_time).wait()
-        self.stop_command.set(1).wait()
-        # Go to direct mode
-        self.set_axis_mode("direct", settle_time=settle_time)
-
-    def is_ioc_ok(self):
-        """Checks execution status"""
-        return 0 == self.status.get()
-
-    @property
-    def axis_mode(self):
-        """Read axis mode"""
-        return self.axisAxesMode.get()
-
-    # @property
-    # def shutter(self):
-    #     return self._shutter.get()
-
-    # @shutter.setter
-    # def shutter(self, value):
-    #     if self.axisAxesMode.get():
-    #         print("ABR is not in direct mode; cannot manipulate shutter")
-    #         return False
-    #     state = str(state).lower()
-    #     if state not in ["1", "0", "closed", "open"]:
-    #         print("unknown shutter state requested")
-    #         return None
-    #     elif state in ["1", "open"]:
-    #         state = 1
-    #     elif state == ["0", "closed"]:
-    #         state = 0
-    #     self._shutter.set(state).wait()
-    #     return state == self._shutter.get()
-
-    def wait_for_movements(self, timeout=60.0):
-        """Waits for all motor movements"""
-        t_start = time.time()
-        t_elapsed = 0
-
-        while self.is_moving() and t_elapsed < timeout:
-            t_elapsed = time.time() - t_start
-            if timeout is not None and t_elapsed > timeout:
-                raise TimeoutError("Timeout waiting for all axis to stop moving")
-            time.sleep(0.5)
-
-    def is_moving(self):
-        """Chechs if all axes are DONE"""
-        return not (
-            self.omega_done.get()
-            and self.gmx_done.get()
-            and self.gmy_done.get()
-            and self.gmz_done.get()
-        )
-
-
-if __name__ == "__main__":
-    abr = AerotechAbrStage(prefix="X06DA-ES", name="abr")
-    abr.wait_for_connection()

pxiii_bec/devices/A3200enums.py

@@ -1,74 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Enumerations for the MX specific Aerotech A3200 stage.
-
-@author: mohacsi_i
-"""
-# pylint: disable=too-few-public-methods
-
-
-class AbrStatus:
-    """ABR measurement task status"""
-
-    DONE = 0
-    READY = 1
-    BUSY = 2
-
-
-class AbrGridStatus:
-    """ABR grid scan status"""
-
-    BUSY = 0
-    DONE = 1
-
-
-class AbrMode:
-    """ABR mode status"""
-
-    DIRECT = 0
-    MEASURING = 1
-
-
-class AbrShutterStatus:
-    """ABR shutter status"""
-
-    CLOSE = 0
-    OPEN = 1
-
-
-class AbrCmd:
-    """ABR command table"""
-
-    NONE = 0
-    RASTER_SCAN_SIMPLE = 1
-    MEASURE_STANDARD = 2
-    VERTICAL_LINE_SCAN = 3
-    SCREENING = 4
-    SUPER_FAST_OMEGA = 5
-    STILL_WEDGE = 6
-    STILLS = 7
-    REPEAT_SINGLE_OSCILLATION = 8
-    SINGLE_OSCILLATION = 9
-    OLD_FASHIONED = 10
-    RASTER_SCAN = 11
-    JET_ROTATION = 12
-    X_HELICAL = 13
-    X_RUNSEQ = 14
-    JUNGFRAU = 15
-    MSOX = 16
-    SLIT_SCAN = 17
-    RASTER_SCAN_STILL = 18
-    SCAN_SASTT = 19
-    SCAN_SASTT_V2 = 20
-    SCAN_SASTT_V3 = 21
-
-
-class AbrAxis:
-    """ABR axis index"""
-
-    OMEGA = 1
-    GMX = 2
-    GMY = 3
-    GMZ = 4
-    STY = 5
-    STZ = 6

pxiii_bec/devices/A3200utils.py

@@ -1,259 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Tue Jun 11 11:28:38 2024
-
-@author: mohacsi_i
-"""
-import types
-from collections import OrderedDict
-from ophyd import Component, PVPositioner, Signal, EpicsSignal, EpicsSignalRO, Kind, PositionerBase
-from ophyd.status import Status, MoveStatus
-
-from bec_lib import bec_logger
-
-from .A3200enums import AbrMode
-
-logger = bec_logger.logger
-
-
-# ABR_DONE = 0
-# ABR_READY = 1
-# ABR_BUSY = 2
-
-# GRID_SCAN_BUSY = 0
-# GRID_SCAN_DONE = 1
-
-# DIRECT_MODE = 0
-# MEASURING_MODE = 1
-
-
-class A3200Axis(PVPositioner):
-    """Positioner wrapper for A3200 axes
-
-
-    Positioner wrapper for motors on the Aerotech A3200 controller. As the IOC
-    does not provide a motor record, this class simply wraps axes into a
-    standard Ophyd positioner for the BEC. It also has some additional
-    functionality for error checking and diagnostics.
-
-    Examples
-    --------
-    omega = A3200Axis('X06DA-ES-DF1:OMEGA', base_pv='X06DA-ES')
-
-    Parameters
-    ----------
-    prefix : str
-        Axis PV name root.
-    base_pv : str (situational)
-        IOC PV name root, i.e. X06DA-ES if standalone class.
-    """
-
-    USER_ACCESS = ["omove"]
-
-    abr_mode_direct = Component(
-        EpicsSignal, "-DF1:MODE-DIRECT", put_complete=True, kind=Kind.omitted
-    )
-    abr_mode = Component(
-        EpicsSignal, "-DF1:AXES-MODE", auto_monitor=True, put_complete=True, kind=Kind.omitted
-    )
-
-    # Basic PV positioner interface
-    done = Component(EpicsSignalRO, "-DONE", auto_monitor=True, kind=Kind.config)
-    readback = Component(EpicsSignalRO, "-RBV", auto_monitor=True, kind=Kind.hinted)
-    # Setpoint is one of the two...
-    setpoint = Component(EpicsSignal, "-SETP", kind=Kind.config)
-    # setpoint = Component(EpicsSignal, "-VAL", kind=Kind.config)
-
-    velocity = Component(EpicsSignal, "-SETV", kind=Kind.config)
-    status = Component(EpicsSignalRO, "-STAT", auto_monitor=True, kind=Kind.config)
-    # PV to issue native relative movements on the A3200
-    relmove = Component(EpicsSignal, "-INCP", put_complete=True, kind=Kind.config)
-    # PV to home axis
-    home = Component(EpicsSignal, "-HOME", kind=Kind.config)
-    ishomed = Component(EpicsSignal, "-AS00", kind=Kind.config)
-
-    # HW status words
-    dshw = Component(EpicsSignalRO, "-DSHW", auto_monitor=True, kind=Kind.normal)
-    ashw = Component(EpicsSignalRO, "-ASHW", auto_monitor=True, kind=Kind.normal)
-    fslw = Component(EpicsSignalRO, "-FSLW", auto_monitor=True, kind=Kind.normal)
-
-    # Rock movement
-    _rock = Component(EpicsSignal, "-ROCK", put_complete=True, kind=Kind.config)
-    _rock_dist = Component(EpicsSignal, "-RINCP", put_complete=True, kind=Kind.config)
-    _rock_velo = Component(EpicsSignal, "-RSETV", put_complete=True, kind=Kind.config)
-    _rock_count = Component(EpicsSignal, "-COUNT", put_complete=True, kind=Kind.config)
-    # _rock_accel = Component(EpicsSignal, "-RRATE", put_complete=True, kind=Kind.config)
-
-    hlm = Component(Signal, kind=Kind.config)
-    llm = Component(Signal, kind=Kind.config)
-    vmin = Component(Signal, kind=Kind.config)
-    vmax = Component(Signal, kind=Kind.config)
-    offset = Component(EpicsSignal, "-OFF", put_complete=True, kind=Kind.config)
-
-    # pylint: disable=too-many-arguments
-    def __init__(
-        self,
-        prefix="",
-        *,
-        name,
-        base_pv="",
-        kind=None,
-        read_attrs=None,
-        configuration_attrs=None,
-        parent=None,
-        llm=0,
-        hlm=0,
-        vmin=0,
-        vmax=0,
-        **kwargs,
-    ):
-        """__init__ MUST have a full argument list"""
-
-        # Patching the parent's PVs into the axis class to check for direct/locked mode
-        if parent is None:
-
-            def maybe_add_prefix(self, _, kw, suffix):
-                # Patched not to enforce parent prefix when no parent
-                if kw in self.add_prefix:
-                    return suffix
-                return suffix
-
-            self.__class__.__dict__["abr_mode"].maybe_add_prefix = types.MethodType(
-                maybe_add_prefix, self.__class__.__dict__["abr_mode"]
-            )
-            self.__class__.__dict__["abr_mode_direct"].maybe_add_prefix = types.MethodType(
-                maybe_add_prefix, self.__class__.__dict__["abr_mode_direct"]
-            )
-            logger.info(self.__class__.__dict__["abr_mode"].kwargs)
-            self.__class__.__dict__["abr_mode"].suffix = base_pv + "-DF1:AXES-MODE"
-            self.__class__.__dict__["abr_mode_direct"].suffix = base_pv + "-DF1:MODE-DIRECT"
-
-        super().__init__(
-            prefix=prefix,
-            name=name,
-            kind=kind,
-            read_attrs=read_attrs,
-            configuration_attrs=configuration_attrs,
-            parent=parent,
-            **kwargs,
-        )
-        self.llm.set(llm).wait()
-        self.hlm.set(hlm).wait()
-        self.vmin.set(vmin).wait()
-        self.vmax.set(vmax).wait()
-
-    def omove(
-        self,
-        position,
-        wait=True,
-        timeout=None,
-        # moved_cb=None,
-        velocity=None,
-        relative=False,
-        direct=False,
-        **kwargs,
-    ) -> MoveStatus:
-        """Native absolute/relative movement on the A3200"""
-
-        # Check if we're in direct movement mode
-        if self.abr_mode.value not in (AbrMode.DIRECT, "DIRECT"):
-            if direct:
-                self.abr_mode_direct.set(1).wait()
-            else:
-                raise RuntimeError(f"ABR axis not in direct mode: {self.abr_mode.value}")
-
-        # Before moving, ensure we can stop (if a stop_signal is configured).
-        if self.stop_signal is not None:
-            self.stop_signal.wait_for_connection()
-
-        # Set velocity if provided
-        if velocity is not None:
-            self.velocity.set(velocity).wait()
-
-        # This is adapted from pv_positioner.py
-        self.check_value(position)
-
-        # Get MoveStatus from parent of parent
-        status = PositionerBase.move(self, position=position, timeout=timeout, **kwargs)
-
-        has_done = self.done is not None
-        if not has_done:
-            moving_val = 1 - self.done_value
-            self._move_changed(value=self.done_value)
-            self._move_changed(value=moving_val)
-
-        try:
-            if relative:
-                # Relative movement instead of setpoint
-                self.relmove.put(position, wait=True)
-            else:
-                # Standard absolute movement
-                self.setpoint.put(position, wait=True)
-            if wait:
-                status.wait()
-        except KeyboardInterrupt:
-            self.stop()
-            raise
-        return status
-
-    def describe(self):
-        """Workaround to schema expected by the BEC"""
-        d = super().describe()
-        d[str(self.name)] = d[f"{self.name}_readback"]
-        return d
-
-    def read(self) -> OrderedDict[str, dict]:
-        """Workaround to schema expected by the BEC"""
-        d = super().read()
-        d[str(self.name)] = d[f"{self.name}_readback"]
-        return d
-
-    def move(self, position, wait=True, timeout=None, moved_cb=None, **kwargs) -> MoveStatus:
-        """Exposes the ophyd move command through BEC abstraction"""
-        return self.omove(position, wait=wait, timeout=timeout, moved_cb=moved_cb, **kwargs)
-
-    def rock(self, distance, counts: int, velocity=None, wait=True) -> Status:
-        """Repeated single axis zigzag scan I guess PSO should be configured for this"""
-
-        self._rock_dist.put(distance)
-        self._rock_count.put(counts)
-        if velocity is not None:
-            self._rock_velo.put(velocity)
-        # if acceleration is not None:
-        #    self._rock_accel.put(acceleration)
-        self._rock.put(1)
-
-        status = super().move(position=distance)
-        if wait:
-            status.wait()
-        return status
-
-    # def is_omega_ok(self):
-    #     """Checks omega axis status"""
-    #     return 0 == self.self.omega.status.get()
-
-    # def is_homed(self):
-    #     """Checks if omega is homed"""
-    #     return 1 == self.omega.is_homed.get()
-
-    # def do_homing(self, wait=True):
-    #     """Execute the homing procedure.
-
-    #     Executes the homing procedure on omega and waits (default) until it is completed.
-
-    #     TODO: Return a status object to do this wwith futures and monitoring.
-
-    #     PARAMETERS
-    #        `wait` true / false if the routine is to wait for the homing to finish.
-    #     """
-    #     self.omega.home.set(1, settle_time=1).wait()
-    #     if not wait:
-    #         return
-    #     while not self.omega.is_homed():
-    #         time.sleep(0.2)
-
-
-# Automatically start an axis if directly invoked
-if __name__ == "__main__":
-    omega = A3200Axis(prefix="X06DA-ES-DF1:OMEGA", base_pv="X06DA-ES", name="omega")
-    omega.wait_for_connection()

pxiii_bec/devices/NDArrayPreview.py

@@ -1,97 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-``NDArrayPreview`` --- Standalone Preview for ImagePlugin
-*********************************************************
-
-This module provides a standalone object to receive images to ophyd from the
-AreaDetector's ImagePlugin.
-
-Created on Wed Jan 29 2025
-
-@author: mohacsi_i
-"""
-import numpy as np
-from ophyd import Device, Component, EpicsSignal, EpicsSignalWithRBV, Kind, Staged
-from ophyd.areadetector import NDDerivedSignal
-
-
-from bec_lib import bec_logger
-
-logger = bec_logger.logger
-
-
-class SilentNDDerivedSignal(NDDerivedSignal):
-    """Silent version of NDDerivedSignal, it does not spam the terminal on
-    every defective frame (shit happens, ok?)."""
-
-    def _array_shape_callback(self, **kwargs):
-        try:
-            super()._array_shape_callback(**kwargs)
-        except RuntimeError:
-            pass
-
-
-class NDArrayPreview(Device):
-    """Wrapper class around AreaDetector's NDStdArray plugins
-
-    This is a standalone class to display images from AreaDetector's
-    ImagePlugin without using a parent device. It also offers BEC exposed
-    methods to transfer image and change image array Kind-ness.
-
-    NOTE: As an explicit request, it can toggle data recording
-    """
-
-    # Subscriptions for plotting image
-    USER_ACCESS = ["image", "savemode"]
-    SUB_MONITOR = "device_monitor_2d"
-    _default_sub = SUB_MONITOR
-
-    # Status attributes
-    min_callback_time = Component(
-        EpicsSignalWithRBV, "MinCallbackTime", kind=Kind.config, put_complete=True
-    )
-    array_size_x = Component(EpicsSignal, "ArraySize0_RBV", kind=Kind.config)
-    array_size_y = Component(EpicsSignal, "ArraySize1_RBV", kind=Kind.config)
-    array_size_z = Component(EpicsSignal, "ArraySize2_RBV", kind=Kind.config)
-    ndimensions = Component(EpicsSignal, "NDimensions_RBV", kind=Kind.config)
-    array_data = Component(EpicsSignal, "ArrayData", kind=Kind.omitted)
-    shaped_image = Component(
-        SilentNDDerivedSignal,
-        derived_from="array_data",
-        shape=("array_size_z", "array_size_y", "array_size_x"),
-        num_dimensions="ndimensions",
-        kind=Kind.omitted,
-    )
-
-    def read(self):
-        """Stream out data on every read()"""
-        if self._staged == Staged.yes:
-            image = self.shaped_image.get()
-            self._run_subs(sub_type=self.SUB_MONITOR, value=image)
-        return super().read()
-
-    def savemode(self, save=False):
-        """Toggle save mode for the shaped image"""
-        # pylint: disable=protected-access
-        if save:
-            self.shaped_image._kind = Kind.normal
-        else:
-            self.shaped_image._kind = Kind.omitted
-
-    def image(self):
-        """Fallback method in case image streaming fills up the BEC"""
-        array_size = (self.array_size_z.get(), self.array_size_y.get(), self.array_size_x.get())
-        if array_size == (0, 0, 0):
-            raise RuntimeError("Invalid image; ensure array_callbacks are on")
-
-        if array_size[-1] == 0:
-            array_size = array_size[:-1]
-
-        image = self.array_data.get()
-        return np.array(image).reshape(array_size)
-
-
-# Automatically connect to SAMCAM at PXIII if directly invoked
-if __name__ == "__main__":
-    img = NDArrayPreview("X06DA-SAMCAM:image1:", name="samimg")
-    img.wait_for_connection()

pxiii_bec/devices/PneumaticValve.py

@@ -1,47 +0,0 @@
-from ophyd import EpicsSignal
-from ophyd.status import SubscriptionStatus
-
-
-class PneumaticValve(EpicsSignal):
-    """Wrapper around EpicsSignal to wait until reaching target. Use the
-    status returned by set() to wait until movement is finished. Do NOT
-    use put if you want to wait, that's a low-level PV write op.
-
-    NOTE: The SET and GET states do not match exactly
-    """
-
-    def set(self, value, *, timeout=5, settle_time=0.1):
-        """Overloaded setter that waits for target state
-
-        NOTE: The SubscriptionStatus callback does not run in put()
-        """
-        # Lazy hardcoded state lookup
-        target = 1 if value in (1, "Measure") else 2
-
-        # Define wait until an end state is reached
-        def on_target(*, value, **_):
-            return bool(value == target)
-
-        # Subscribe a monitor in advance and wait for update
-        status = SubscriptionStatus(self, on_target, timeout=timeout, settle_time=0.1)
-        # Set value to start movement
-        super().set(value, settle_time=settle_time).wait()
-        # Return the monitor
-        return status
-
-    def check_value(self, value):
-        """Input validation"""
-        if value not in (0, 1, "Measure", "Park"):
-            raise ValueError(f"Unsupported pneumatic valve target {value}")
-        return super().check_value(value)
-
-
-if __name__ == "__main__":
-    pneum = PneumaticValve(
-        read_pv="X06DA-ES-BS:GET-POS",
-        write_pv="X06DA-ES-BS:SET-POS",
-        auto_monitor=True,
-        put_complete=True,
-        name="bspump",
-    )
-    pneum.wait_for_connection()

pxiii_bec/devices/SamCamDetector.py

@@ -1,52 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-``SamCam`` --- Sample Camera control software
-*********************************************
-
-This module provides an object to control the sample camera at the PX III
-beamline. The camera should run continously and stream data via ZMQ for
-the GUI and alignment scripts.
-
-Created on Thu Jan 30 2025
-
-@author: mohacsi_i
-"""
-from ophyd import ADComponent
-from ophyd_devices.devices.areadetector.cam import GenICam
-
-# from ophyd_devices.devices.areadetector.plugins import ImagePlugin_V35
-from ophyd_devices.interfaces.base_classes.psi_detector_base import (
-    PSIDetectorBase,
-    CustomDetectorMixin,
-)
-
-from bec_lib import bec_logger
-
-logger = bec_logger.logger
-
-
-class SamCamSetup(CustomDetectorMixin):
-    """Simple camera mixin class, the SAMCAM is usually streaming"""
-
-    def on_stage(self):
-        """Just make sure it's running continously"""
-        self.parent.cam.acquire.put(1, wait=True)
-
-    def on_unstage(self):
-        """Should run continously"""
-
-    def on_stop(self):
-        """Should run continously"""
-
-
-class SamCamDetector(PSIDetectorBase):
-    """Sample camera device
-
-    The SAMCAM continously streams images to the GUI and sample alignment
-    scripts via ZMQ.
-    """
-
-    custom_prepare_cls = SamCamSetup
-
-    cam = ADComponent(GenICam, "cam1:")
-    # image = ADComponent(ImagePlugin_V35, "image1:")

pxiii_bec/devices/SmarGonA.py

@@ -1,284 +0,0 @@
-"""
-``SmarGon`` --- SmarGon control software
-******************************************
-
-The module provides an object to control the SmarGon goniometer axes at PX III.
-The SmarGon axes are interfaced as positioners.
-"""
-
-import time
-from threading import Thread, Lock
-import requests
-from requests.adapters import HTTPAdapter, Retry
-from collections import OrderedDict
-from ophyd import Component, Kind, Signal, PVPositioner
-from ophyd.status import SubscriptionStatus
-
-try:
-    from bec_lib import bec_logger
-
-    logger = bec_logger.logger
-except ModuleNotFoundError:
-    import logging
-
-    logger = logging.getLogger("SmarGon")
-
-
-# SmarGon contoller can't really handle multiple connections
-# Use this mutex to ensure one access at a time
-mutex = Lock()
-
-
-class SmarGonSignal(Signal):
-    """SmarGonSignal (R/W)
-
-    Small helper class to read/write parameters from SmarGon. As there is no
-    motion status readback from smargopolo, this should be substituted with
-    setting with 'settle_time'.
-    """
-
-    def __init__(self, *args, write_addr="targetSCS", low_limit=None, high_limit=None, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.write_addr = write_addr
-        self.addr = self.parent.name
-        self._limits = (low_limit, high_limit)
-        # self.get()
-
-    def put(self, value, *, timestamp=None, **kwargs):
-        """Overriden put to add communication with smargopolo"""
-        # Validate new value and get timestamp
-        self.check_value(value)
-        if timestamp is None:
-            timestamp = time.time()
-
-        # Perform the actual write to SmargoPolo
-        # pylint: disable=protected-access
-        r = self.parent._go_n_put(f"{self.write_addr}?{self.addr.upper()}={value}")
-
-        # pylint: disable=attribute-defined-outside-init
-        old_value = self._readback
-        self._timestamp = timestamp
-        self._readback = r[self.addr.upper()]
-        self._value = r[self.addr.upper()]
-
-        # Notify subscribers
-        self._run_subs(
-            sub_type=self.SUB_VALUE, old_value=old_value, value=value, timestamp=self._timestamp
-        )
-
-    @property
-    def limits(self):
-        return self._limits
-
-    def check_value(self, value, **kwargs):
-        """Check if value falls within limits"""
-        lol = self.limits[0]
-        if lol is not None:
-            if value < lol:
-                raise ValueError(f"Target {value} outside of limits {self.limits}")
-        hil = self.limits[1]
-        if hil is not None:
-            if value > hil:
-                raise ValueError(f"Target {value} outside of limits {self.limits}")
-
-    def get(self, **kwargs):
-        # pylint: disable=protected-access
-        r = self.parent._go_n_get(self.write_addr)
-
-        # pylint: disable=attribute-defined-outside-init
-        self._value = r[self.addr.upper()] if isinstance(r, dict) else r
-        return super().get(**kwargs)
-
-
-class SmarGonSignalRO(Signal):
-    """Small helper class for read-only parameters PVs from SmarGon.
-
-    Reads and optionally monitors a variable on the SmarGon.
-
-    """
-
-    def __init__(self, *args, read_addr="readbackSCS", auto_monitor=False, **kwargs):
-        super().__init__(*args, **kwargs)
-        self._metadata["write_access"] = False
-        self.read_addr = read_addr
-        self.addr = self.parent.name
-
-        if auto_monitor:
-            self._mon = Thread(target=self.poll, daemon=True)
-            self._mon.start()
-
-    def get(self, **kwargs):
-        # pylint: disable=protected-access
-        r = self.parent._go_n_get(self.read_addr)
-
-        if isinstance(r, dict):
-            self.put(r[self.addr.upper()], force=True)
-        else:
-            self.put(r, force=True)
-        return self._readback
-
-    def poll(self):
-        """Fooo"""
-        time.sleep(2)
-        while True:
-            time.sleep(0.25)
-            try:
-                self.get()
-            except requests.ConnectTimeout as ex:
-                logger.error(f"[{self.name}] {ex}")
-
-
-class SmarGonAxis(PVPositioner):
-    """SmarGon client deice
-
-    This class controls the SmarGon goniometer via the REST interface. All
-    SmarGon axes share a common mutex to manage actual HW access.
-    """
-
-    USER_ACCESS = ["omove"]
-
-    # Status attributes
-    sg_url = Component(Signal, kind=Kind.config, metadata={"write_access": False})
-    corr = Component(SmarGonSignalRO, read_addr="corr_type", kind=Kind.config)
-    mode = Component(SmarGonSignalRO, read_addr="mode", kind=Kind.config)
-
-    # Axis parameters
-    readback = Component(SmarGonSignalRO, kind=Kind.hinted, auto_monitor=True)
-    setpoint = Component(SmarGonSignal, kind=Kind.normal)
-    done = Component(Signal, value=1, kind=Kind.normal)
-    # moving = Component(SmarGonMovingSignalRO, kind=Kind.config)
-    _tol = 0.001
-
-    # pylint: disable=too-many-arguments
-    def __init__(
-        self,
-        prefix="SCS",
-        *,
-        name,
-        kind=None,
-        read_attrs=None,
-        configuration_attrs=None,
-        parent=None,
-        sg_url: str = "http://x06da-smargopolo.psi.ch:3000",
-        low_limit=None,
-        high_limit=None,
-        **kwargs,
-    ) -> None:
-        self.__class__.__dict__["readback"].kwargs["read_addr"] = f"readback{prefix}"
-        self.__class__.__dict__["setpoint"].kwargs["write_addr"] = f"target{prefix}"
-        self.__class__.__dict__["setpoint"].kwargs["low_limit"] = low_limit
-        self.__class__.__dict__["setpoint"].kwargs["high_limit"] = high_limit
-        self.__class__.__dict__["sg_url"].kwargs["value"] = sg_url
-        # Fine-tune HTTP connection behavior
-        # NOTE: SmarGon has a few failed requests every one in a while
-        self._s = requests.Session()
-        retries = Retry(total=5, backoff_factor=0.05, status_forcelist=[500, 502, 503, 504])
-        self._s.mount("http://", HTTPAdapter(max_retries=retries))
-
-        super().__init__(
-            prefix=prefix,
-            name=name,
-            kind=kind,
-            read_attrs=read_attrs,
-            configuration_attrs=configuration_attrs,
-            parent=parent,
-            **kwargs,
-        )
-
-    def initialize(self):
-        """Helper function for initial readings"""
-        # self.corr.get()
-        # self.mode.get()
-        r = self._go_n_get("corr_type")
-        print(r)
-
-    def move(self, position, wait=True, timeout=None, moved_cb=None):
-        """Move command that's masked by BEC"""
-        return self.omove(position, wait, timeout, moved_cb)
-
-    def omove(self, position, wait=True, timeout=2.0, moved_cb=None):
-        """Original move command without the BEC wrappers"""
-        status = self.setpoint.set(position, settle_time=0.1)
-        status.wait()
-        if not wait:
-            return status
-
-        def on_target(*, value, **_):
-            distance = abs(value - self.setpoint._value)
-            print(f"[self.name] Distance: {distance}")
-            return bool(distance < self._tol)
-
-        status = SubscriptionStatus(self.readback, on_target, timeout=timeout, settle_time=0.1)
-        return status
-
-    def describe(self):
-        """Workaround to schema expected by the BEC"""
-        d = super().describe()
-        d[str(self.name)] = d[f"{self.name}_readback"]
-        return d
-
-    def read(self) -> OrderedDict[str, dict]:
-        """Workaround to schema expected by the BEC"""
-        d = super().read()
-        d[str(self.name)] = d[f"{self.name}_readback"]
-        return d
-
-    def _pos_changed(self, timestamp=None, value=None, **kwargs):
-        pass
-
-    def _go_n_get(self, address, **kwargs):
-        """Helper function to connect to smargopolo"""
-        cmd = f"{self.sg_url.get()}/{address}"
-        try:
-            with mutex:
-                r = self._s.get(cmd, timeout=1, **kwargs)
-        except TimeoutError:
-            try:
-                time.sleep(0.05)
-                with mutex:
-                    r = self._s.get(cmd, timeout=0.5, **kwargs)
-            except TimeoutError:
-                time.sleep(0.05)
-                with mutex:
-                    r = self._s.get(cmd, timeout=0.5, **kwargs)
-        if not r.ok:
-            raise RuntimeError(
-                f"[{self.name}] Error getting {address}; reply was {r.status_code} => {r.reason}"
-            )
-        return r.json()
-
-    def _go_n_put(self, address, **kwargs):
-        """Helper function to connect to smargopolo"""
-        cmd = f"{self.sg_url.get()}/{address}"
-        try:
-            with mutex:
-                r = self._s.put(cmd, timeout=1, **kwargs)
-        except TimeoutError:
-            try:
-                time.sleep(0.05)
-                with mutex:
-                    r = self._s.put(cmd, timeout=0.5, **kwargs)
-            except TimeoutError:
-                time.sleep(0.05)
-                with mutex:
-                    r = self._s.put(cmd, timeout=0.5, **kwargs)
-        if not r.ok:
-            raise RuntimeError(
-                f"[{self.name}] Error putting {address}; reply was {r.status_code} => {r.reason}"
-            )
-        return r.json()
-
-
-if __name__ == "__main__":
-    shx = SmarGonAxis(prefix="SCS", name="shx", sg_url="http://x06da-smargopolo.psi.ch:3000")
-    shy = SmarGonAxis(prefix="SCS", name="shy", sg_url="http://x06da-smargopolo.psi.ch:3000")
-    shz = SmarGonAxis(
-        prefix="SCS",
-        name="shz",
-        low_limit=10,
-        high_limit=22,
-        sg_url="http://x06da-smargopolo.psi.ch:3000",
-    )
-    shx.wait_for_connection()
-    shy.wait_for_connection()
-    shz.wait_for_connection()

pxiii_bec/devices/SmarGonB.py

@@ -1,249 +0,0 @@
-"""
-``SmarGon`` --- SmarGon control software
-******************************************
-
-The module provides an object to control the SmarGon goniometer axes at PX III.
-The SmarGon axes are interfaced as positioners.
-"""
-
-import time
-import threading
-from collections import OrderedDict
-import requests
-from requests.adapters import HTTPAdapter, Retry
-from ophyd import Component, Kind, Signal, PVPositioner
-from ophyd.status import SubscriptionStatus
-
-try:
-    from bec_lib import bec_logger
-
-    logger = bec_logger.logger
-except ModuleNotFoundError:
-    import logging
-
-    logger = logging.getLogger("SmarGon")
-
-
-# SmarGon contoller can't really handle multiple connections
-# Use this mutex to ensure one access at a time
-mutex = threading.Lock()
-
-
-class LimitedSmarGonSignal(Signal):
-    """SmarGonSignal (R/W)
-
-    Small helper class to read/write parameters from SmarGon. As there is no
-    motion status readback from smargopolo, this should be substituted with
-    setting with 'settle_time'.
-    """
-
-    def __init__(self, *args, write_addr="targetSCS", low_limit=None, high_limit=None, **kwargs):
-        self._limits = (low_limit, high_limit)
-        super().__init__(*args, **kwargs)
-        self.write_addr = write_addr
-
-    @property
-    def limits(self):
-        return self._limits
-
-    def check_value(self, value, **kwargs):
-        """Check if value falls within limits"""
-        lol = self.limits[0]
-        if lol is not None:
-            if value < lol:
-                raise ValueError(f"Target {value} outside of limits {self.limits}")
-        hil = self.limits[1]
-        if hil is not None:
-            if value > hil:
-                raise ValueError(f"Target {value} outside of limits {self.limits}")
-
-    def put(self, value, *, timestamp=None, force=False, metadata=None, **kwargs):
-        """Overriden put to add communication with smargopolo"""
-        # Validate new value and get timestamp
-        if not force:
-            self.check_value(value)
-        if timestamp is None:
-            timestamp = time.time()
-
-        # Perform the actual write to SmargoPolo
-        # pylint: disable=protected-access
-        r = self.parent._go_n_put(f"{self.write_addr}?{self.parent.name.upper()}={value}")
-
-        # pylint: disable=attribute-defined-outside-init
-        old_value = self._readback
-        self._timestamp = timestamp
-        self._readback = r[self.parent.name.upper()]
-        self._value = r[self.parent.name.upper()]
-
-        # Notify subscribers
-        self._run_subs(
-            sub_type=self.SUB_VALUE, old_value=old_value, value=value, timestamp=self._timestamp
-        )
-
-
-class SmarGonAxis(PVPositioner):
-    """SmarGon client deice
-
-    This class controls the SmarGon goniometer via the REST interface. All
-    SmarGon axes share a common mutex to manage actual HW access.
-    """
-
-    USER_ACCESS = ["omove", "oldmove"]
-
-    # Status attributes
-    sg_url = Component(Signal, kind=Kind.config, metadata={"write_access": False})
-
-    # Axis parameters
-    readback = Component(Signal, kind=Kind.hinted, metadata={"write_access": False})
-    setpoint = Component(LimitedSmarGonSignal, kind=Kind.normal)
-    done = Component(Signal, value=1, kind=Kind.normal, metadata={"write_access": False})
-    _tol = 0.001
-
-    # pylint: disable=too-many-arguments
-    def __init__(
-        self,
-        prefix="SCS",
-        *,
-        name,
-        kind=None,
-        read_attrs=None,
-        configuration_attrs=None,
-        parent=None,
-        sg_url: str = "http://x06da-smargopolo.psi.ch:3000",
-        low_limit=None,
-        high_limit=None,
-        **kwargs,
-    ) -> None:
-        # self.__class__.__dict__["setpoint"].kwargs["write_addr"] = f"target{prefix}"
-        self.__class__.__dict__["setpoint"].kwargs["low_limit"] = low_limit
-        self.__class__.__dict__["setpoint"].kwargs["high_limit"] = high_limit
-        self.__class__.__dict__["sg_url"].kwargs["value"] = sg_url
-        # Fine-tune HTTP connection behavior
-        # NOTE: SmarGon has a few failed requests every one in a while
-        self._s = requests.Session()
-        retries = Retry(total=5, backoff_factor=0.05, status_forcelist=[500, 502, 503, 504])
-        self._s.mount("http://", HTTPAdapter(max_retries=retries))
-
-        super().__init__(
-            prefix=prefix,
-            name=name,
-            kind=kind,
-            read_attrs=read_attrs,
-            configuration_attrs=configuration_attrs,
-            parent=parent,
-            **kwargs,
-        )
-
-        def on_target():
-            """Monitors the setpoint and readback and calculates the on_target flag"""
-            time.sleep(2)
-            while True:
-                # Read back target and setpoint values
-                # pylint: disable=protected-access
-                r = self._go_n_get("readbackSCS")
-                rb = r[self.name.upper()]
-                self.readback.set(rb, force=True).wait()
-                r = self._go_n_get("targetSCS")
-                sp = r[self.name.upper()]
-                self.setpoint._value = sp
-                # print(f"Readback: {rb}\tSetpoint: {sp}")
-                # Check if they're within tolerance
-                distance = abs(rb - sp)
-                done = 1 if distance < self._tol else 0
-                self.done.put(done, force=True)
-                time.sleep(0.2)
-
-        self._mon = threading.Thread(target=on_target, daemon=True)
-        self._mon.start()
-
-    def omove(self, position, wait=True, timeout=None, moved_cb=None):
-        """Move command that's masked by BEC"""
-        self.done.put(0, force=True)
-        return self.move(position, wait, timeout, moved_cb)
-
-    def oldmove(self, position, wait=True, timeout=2.0, moved_cb=None):
-        """Original move command without the BEC wrappers"""
-        status = self.setpoint.set(position, settle_time=0.1).wait()
-        if not wait:
-            return status
-
-        def on_target(*, value, **_):
-            distance = abs(value - self.setpoint._value)
-            print(f"[self.name] Distance: {distance}")
-            return bool(distance < self._tol)
-
-        status = SubscriptionStatus(self.readback, on_target, timeout=timeout, settle_time=0.1)
-        return status
-
-    def describe(self):
-        """Workaround to schema expected by the BEC"""
-        d = super().describe()
-        d[str(self.name)] = d[f"{self.name}_readback"]
-        return d
-
-    def read(self) -> OrderedDict[str, dict]:
-        """Workaround to schema expected by the BEC"""
-        d = super().read()
-        d[str(self.name)] = d[f"{self.name}_readback"]
-        return d
-
-    def _pos_changed(self, timestamp=None, value=None, **kwargs):
-        """Remove EPICS dependency"""
-        pass
-
-    def _go_n_get(self, address, **kwargs):
-        """Helper function to connect to smargopolo"""
-        cmd = f"{self.sg_url.get()}/{address}"
-        try:
-            with mutex:
-                r = self._s.get(cmd, timeout=1, **kwargs)
-        except TimeoutError:
-            try:
-                time.sleep(0.05)
-                with mutex:
-                    r = self._s.get(cmd, timeout=0.5, **kwargs)
-            except TimeoutError:
-                time.sleep(0.05)
-                with mutex:
-                    r = self._s.get(cmd, timeout=0.5, **kwargs)
-        if not r.ok:
-            raise RuntimeError(
-                f"[{self.name}] Error getting {address}; reply was {r.status_code} => {r.reason}"
-            )
-        return r.json()
-
-    def _go_n_put(self, address, **kwargs):
-        """Helper function to connect to smargopolo"""
-        cmd = f"{self.sg_url.get()}/{address}"
-        try:
-            with mutex:
-                r = self._s.put(cmd, timeout=1, **kwargs)
-        except TimeoutError:
-            try:
-                time.sleep(0.05)
-                with mutex:
-                    r = self._s.put(cmd, timeout=0.5, **kwargs)
-            except TimeoutError:
-                time.sleep(0.05)
-                with mutex:
-                    r = self._s.put(cmd, timeout=0.5, **kwargs)
-        if not r.ok:
-            raise RuntimeError(
-                f"[{self.name}] Error putting {address}; reply was {r.status_code} => {r.reason}"
-            )
-        return r.json()
-
-
-if __name__ == "__main__":
-    shx = SmarGonAxis(prefix="SCS", name="shx", sg_url="http://x06da-smargopolo.psi.ch:3000")
-    shy = SmarGonAxis(prefix="SCS", name="shy", sg_url="http://x06da-smargopolo.psi.ch:3000")
-    shz = SmarGonAxis(
-        prefix="SCS",
-        name="shz",
-        low_limit=10,
-        high_limit=22,
-        sg_url="http://x06da-smargopolo.psi.ch:3000",
-    )
-    shx.wait_for_connection()
-    shy.wait_for_connection()
-    shz.wait_for_connection()

pxiii_bec/devices/SmarGon_orig.py

@@ -1,393 +0,0 @@
-# #!/usr/bin/env python3
-
-# from time import sleep, time
-# from typing import Tuple
-
-# from requests import get, put
-
-# from beamline import beamline
-# from mx_redis import SMARGON
-
-# try:
-#     from mx_preferences import get_config
-
-#     host = get_config(beamline)["smargon"]["host"]
-#     port = get_config(beamline)["smargon"]["port"]
-# except Exception:
-#     host = "x06da-smargopolo.psi.ch"
-#     port = 3000
-# base = f"http://{host}:{port}"
-
-
-# def gonget(thing: str, **kwargs) -> dict:
-#     """issue a GET for some API component on the smargopolo server"""
-#     cmd = f"{base}/{thing}"
-#     if kwargs.get("verbose", False):
-#         print(cmd)
-#     r = get(cmd)
-#     if not r.ok:
-#         raise Exception(f"error getting {thing}; server returned {r.status_code} => {r.reason}")
-#     return r.json()
-
-
-# def gonput(thing: str, **kwargs):
-#     """issue a PUT for some API component on the smargopolo server"""
-#     cmd = f"{base}/{thing}"
-#     if kwargs.get("verbose", False):
-#         print(cmd)
-#     put(cmd)
-
-
-# def scsput(**kwargs):
-#     """
-#     Issue a new absolute target in the SH coordinate system.
-
-#     The key "verbose" may be passed in kwargs with any true
-#     value for verbose behaviour.
-
-
-#     :param kwargs: a dict containing keys ("shx", "shy", "shz", "chi", "phi")
-#     :type kwargs: dict
-#     :return:
-#     :rtype:
-#     """
-#     xyz = {
-#         k.upper(): v for k, v in kwargs.items() if k.lower() in ("shx", "shy", "shz", "chi", "phi")
-#     }
-#     thing = "&".join([f"{k.upper()}={float(v):.5f}" for k, v in xyz.items()])
-#     cmd = f"{base}/targetSCS?{thing}"
-#     if kwargs.get("verbose", False):
-#         print(cmd)
-#     put(cmd)
-
-
-# def bcsput(**kwargs):
-#     """
-#     Issue a new absolute target in the beamline coordinate system.
-
-#     The key "verbose" may be passed in kwargs with any true
-#     value for verbose behaviour.
-
-
-#     :param kwargs: a dict containing keys ("bx", "by", "bz", "chi", "phi")
-#     :return:
-#     :rtype:
-#     """
-#     xyz = {k.upper(): v for k, v in kwargs.items() if k.lower() in ("bx", "by", "bz", "chi", "phi")}
-#     thing = "&".join([f"{k.upper()}={float(v):.5f}" for k, v in xyz.items()])
-#     cmd = f"{base}/targetBCS?{thing}"
-#     if kwargs.get("verbose", False):
-#         print(cmd)
-#     put(cmd)
-
-
-# def scsrelput(**kwargs) -> None:
-#     """
-#     Issue relative increments to current SH coordinate system.
-
-#     The key "verbose" may be passed in kwargs with any true
-#     value for verbose behaviour.
-
-
-#     :param kwargs: a dict containing keys ("shx", "shy", "shz", "chi", "phi")
-#     :type kwargs: dict
-#     :return:
-#     :rtype:
-#     """
-#     xyz = {
-#         k.upper(): v for k, v in kwargs.items() if k.lower() in ("shx", "shy", "shz", "chi", "phi")
-#     }
-#     thing = "&".join([f"{k.upper()}={float(v):.5f}" for k, v in xyz.items()])
-#     cmd = f"{base}/targetSCS_rel?{thing}"
-#     if kwargs.get("verbose", False):
-#         print(cmd)
-#     put(cmd)
-
-
-# def bcsrelput(**kwargs):
-#     """
-#     Issue relative increments to current beamline coordinate system.
-
-#     The key "verbose" may be passed in kwargs with any true
-#     value for verbose behaviour.
-
-#     :param kwargs: a dict containing keys ("bx", "by", "bz")
-#     :type kwargs: dict
-#     :return:
-#     :rtype:
-#     """
-#     xyz = {k.upper(): v for k, v in kwargs.items() if k.lower() in ("bx", "by", "bz")}
-#     thing = "&".join([f"{k.upper()}={float(v):.5f}" for k, v in xyz.items()])
-#     cmd = f"{base}/targetBCS_rel?{thing}"
-#     if kwargs.get("verbose", False):
-#         print(cmd)
-#     put(cmd)
-
-
-# # url_redis = f"{beamline}-cons-705.psi.ch"
-# # print(f"connecting to redis DB #3 on host: {url_redis}")
-# # redis_handle = redis.StrictRedis(host=url_redis, db=3)
-# # pubsub = redis_handle.pubsub()
-
-# MODE_UNINITIALIZED = 0
-# MODE_INITIALIZING = 1
-# MODE_READY = 2
-# MODE_ERROR = 99
-
-
-# class SmarGon(object):
-#     def __init__(self):
-#         super(SmarGon, self).__init__()
-#         self.__dict__.update(target=None)
-#         self.__dict__.update(bookmarks={})
-#         self.__dict__.update(_latest_message={})
-#         # pubsub.psubscribe(**{f"__keyspace@{SMARGON.value}__:*": self._cb_readbackSCS})
-#         # pubsub.run_in_thread(sleep_time=0.5, daemon=True)
-
-#     def __repr__(self):
-#         BX, BY, BZ, OMEGA, CHI, PHI, a, b, c = self.readback_bcs().values()
-#         return f"<{self.__class__.__name__}  X={BX:.3f}, Y={BY:.3f}, Z={BZ:.3f}, CHI={CHI:.3f}, PHI={PHI:.3f}, OMEGA={OMEGA:.3f}>"
-
-#     def _cb_readbackSCS(self, msg):
-#         if msg["data"] in ["hset"]:
-#             self._latest_message = msg
-
-#     def move_home(self, wait=False) -> None:
-#         """move to beamline coordinate system X, Y, Z, Chi, Phi = 0 0 0 0 0"""
-#         self.apply_bookmark_sh({"shx": 0.0, "shy": 0.0, "shz": 18.0, "chi": 0.0, "phi": 0.0})
-#         if wait:
-#             self.wait_home()
-
-#     def xyz(self, coords: Tuple[float, float, float], wait: bool = True) -> None:
-#         """
-#         Move smargon in absolute beamline coordinates
-
-#         :param coords: a tuple of floats representing X, Y, Z coordinates
-#         :type coords:
-#         :param wait:
-#         :type wait:
-#         :return:
-#         :rtype:
-#         """
-#         x, y, z = coords
-#         # the two steps below are necessary otherwise the control system
-#         # remembers *a* previous CHI
-#         bcs = self.bcs
-#         bcs.update({"BX": x, "BY": y, "BZ": z})
-#         self.bcs = bcs
-#         if wait:
-#             self.wait()
-
-#     def wait_home(self, timeout: float = 20.0) -> None:
-#         """
-#         wait for the smargon to reach its home position:
-#             SHX = 0.0
-#             SHY = 0.0
-#             SHZ = 18.0
-#             CHI = 0.0
-#             PHI = 0.0
-
-#         :param timeout: time to wait for positions to be reached raises TimeoutError if timeout reached
-#         :type timeout: float
-#         :return:
-#         :rtype:
-#         """
-#         tout = timeout + time()
-#         in_place = [False, False]
-#         rbv = -999.0
-#         while not all(in_place) and time() < tout:
-#             rbv = self.readback_scs()
-#             in_place = []
-#             for k, v in {"SHX": 0.0, "SHY": 0.0, "SHZ": 18.0, "CHI": 0.0, "PHI": 0.0}.items():
-#                 in_place.append(abs(rbv[k] - v) < 0.01)
-#         if time() > tout:
-#             raise TimeoutError(f"timeout waiting for smargon to reach home position: {rbv}")
-
-#     def push_bookmark(self):
-#         """
-#         save current absolute coordinates in FIFO stack
-#         :return:
-#         :rtype:
-#         """
-#         t = round(time())
-#         self.bookmarks[t] = self.readback_scs()
-
-#     def pop_bookmark(self):
-#         return self.bookmarks.popitem()[1]
-
-#     def apply_bookmark_sh(self, scs):
-#         scsput(**scs)
-
-#     def apply_last_bookmark_sh(self):
-#         scs = self.pop_bookmark()
-#         scsput(**scs)
-
-#     def readback_mcs(self):
-#         """current motor positions of the smargon sliders"""
-#         return gonget("readbackMCS")
-
-#     def readback_scs(self):
-#         """current SH coordinates of the smargon model"""
-#         return gonget("readbackSCS")
-
-#     def readback_bcs(self):
-#         """current beamline coordinates of the smargon"""
-#         return gonget("readbackBCS")
-
-#     def target_scs(self):
-#         """currently assigned targets for the smargon control system"""
-#         return gonget("targetSCS")
-
-#     def initialize(self):
-#         """initialize the smargon"""
-#         self.set_mode(MODE_UNINITIALIZED)
-#         sleep(0.1)
-#         self.set_mode(MODE_INITIALIZING)
-
-#     def set_mode(self, mode: int):
-#         """put smargon control system in a given mode
-#         MODE_UNINITIALIZED = 0
-#         MODE_INITIALIZING = 1
-#         MODE_READY = 2
-#         MODE_ERROR = 99
-#         """
-#         gonput(f"mode?mode={mode}")
-
-#     def enable_correction(self):
-#         """enable calibration based corrections"""
-#         gonput("corr_type?corr_type=1")
-
-#     def disable_correction(self):
-#         """disable calibration based corrections"""
-#         gonput("corr_type?corr_type=0")
-
-#     def chi(self, val=None, wait=False):
-#         if val is None:
-#             return self.readback_scs()["CHI"]
-#         scsput(CHI=val)
-#         if wait:
-#             timeout = 10 + time()
-#             while time() < timeout:
-#                 if abs(val - self.readback_scs()["CHI"]) < 0.1:
-#                     break
-#             if time() > timeout:
-#                 raise RuntimeError(f"SmarGon CHI did not reach requested target {val} in time")
-
-#     def phi(self, val=None, wait=False):
-#         if val is None:
-#             return self.readback_scs()["PHI"]
-#         scsput(PHI=val)
-#         if wait:
-#             timeout = 70 + time()
-#             while time() < timeout:
-#                 if abs(val - self.readback_scs()["PHI"]) < 0.1:
-#                     break
-#             if time() > timeout:
-#                 raise RuntimeError(f"SmarGon PHI did not reach requested target {val} in time")
-
-#     def wait(self, timeout=60.0):
-#         """waits up to `timeout` seconds for smargon to reach target"""
-#         target = {
-#             k.upper(): v
-#             for k, v in self.target_scs().items()
-#             if k.lower() in ("shx", "shy", "shz", "chi", "phi")
-#         }
-
-#         timeout = timeout + time()
-#         while time() < timeout:
-#             s = {
-#                 k: (abs(v - target[k]) < 0.01)
-#                 for k, v in self.readback_scs().items()
-#                 if k.upper() in ("SHX", "SHY", "SHZ", "CHI", "PHI")
-#             }
-#             if all(list(s.values())):
-#                 break
-#         if time() > timeout:
-#             raise TimeoutError("timed out waiting for smargon to reach target")
-
-#     def __setattr__(self, key, value):
-#         key = key.lower()
-#         if key == "mode":
-#             self.set_mode(value)
-#         elif key == "correction":
-#             assert value in (
-#                 0,
-#                 1,
-#                 False,
-#                 True,
-#             ), "correction is either 1 or True (enabled) or 0 (disabled)"
-#             gonput(f"corr_type?corr_type?{value}")
-#         elif key == "scs":
-#             scsput(**value)
-#         elif key == "bcs":
-#             bcsput(**value)
-#         elif key == "target":
-#             if not isinstance(value, dict):
-#                 raise Exception(
-#                     f"expected a dict with target axis and values got something else: {value}"
-#                 )
-#             for k in value.keys():
-#                 if k.lower() not in "shx shy shz chi phi ox oy oz".split():
-#                     raise Exception(f'unknown axis in target "{k}"')
-#             scsput(**value)
-#         elif key in "shx shy shz chi phi ox oy oz".split():
-#             scsput(**{key: value})
-#         elif key in "bx by bz".split():
-#             bcs = self.readback_bcs()
-#             bcs[key] = value
-#             bcsput(**bcs)
-#         else:
-#             self.__dict__[key].update(value)
-
-#     def __getattr__(self, key):
-#         key = key.lower()
-#         if key == "mode":
-#             return self.readback_mcs()["mode"]
-#         elif key == "correction":
-#             return gonget("corr_type")
-#         elif key == "bcs":
-#             return self.readback_bcs()
-#         elif key == "mcs":
-#             return self.readback_mcs()
-#         elif key == "scs":
-#             return self.readback_scs()
-#         elif key in "shx shy shz chi phi ox oy oz".split():
-#             return self.readback_scs()[key.upper()]
-#         elif key in "bx by bz".split():
-#             return self.readback_bcs()[key.upper()]
-#         else:
-#             return self.__getattribute__(key)
-
-
-# if __name__ == "__main__":
-#     import argparse
-
-#     parser = argparse.ArgumentParser(description="SmarGon client")
-#     parser.add_argument("-i", "--initialize", help="initialize smargon", action="store_true")
-#     args = parser.parse_args()
-
-#     smargon = SmarGon()
-
-#     if args.initialize:
-#         print("initializing smargon device")
-#         import Aerotech
-
-#         print("moving aerotech back by 50mm")
-#         abr = Aerotech.Abr()
-
-#         abr.incr_x(-50.0, wait=True, velo=100.0)
-
-#         print("issuing init command to smargon")
-#         smargon.initialize()
-#         sleep(0.5)
-
-#         print("waiting for init routine to complete")
-#         while MODE_READY != smargon.mode:
-#             sleep(0.5)
-
-#         print("moving smargon to HOME position")
-#         smargon.move_home()
-
-#         print("moving aerotech to its previous position")
-#         abr.incr_x(50.0, wait=True, velo=100.0)
-#         exit(0)

pxiii_bec/devices/StdDaqPreview.py

@@ -1,206 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Standard DAQ preview image stream module
-
-Created on Thu Jun 27 17:28:43 2024
-
-@author: mohacsi_i
-"""
-import json
-from time import sleep, time
-from threading import Thread
-import zmq
-import numpy as np
-from ophyd import Device, Signal, Component, Kind
-from ophyd_devices.interfaces.base_classes.psi_detector_base import (
-    CustomDetectorMixin,
-    PSIDetectorBase,
-)
-
-from bec_lib import bec_logger
-
-logger = bec_logger.logger
-ZMQ_TOPIC_FILTER = b""
-
-
-class StdDaqPreviewMixin(CustomDetectorMixin):
-    """Setup class for the standard DAQ preview stream
-
-    Parent class: CustomDetectorMixin
-    """
-
-    _mon = None
-
-    def on_stage(self):
-        """Start listening for preview data stream"""
-        if self._mon is not None:
-            self.parent.unstage()
-            sleep(0.5)
-
-        logger.info(f"[{self.parent.name}] Attaching monitor to {self.parent.url.get()}")
-        self.parent.connect()
-        self._stop_polling = False
-        self._mon = Thread(target=self.poll, daemon=True)
-        self._mon.start()
-
-    def on_unstage(self):
-        """Stop a running preview"""
-        if self._mon is not None:
-            self._stop_polling = True
-            # Might hang on recv_multipart
-            self._mon.join(timeout=1)
-            # So also disconnect the socket
-            try:
-                # pylint: disable=protected-access
-                self.parent._socket.disconnect(self.parent.url.get())
-            except zmq.error.ZMQError:
-                # Might be already closed
-                pass
-
-    def on_stop(self):
-        """Stop a running preview"""
-        self.on_unstage()
-
-    def poll(self):
-        """Collect streamed updates"""
-        try:
-            t_last = time()
-            while True:
-                try:
-                    # Exit loop and finish monitoring
-                    if self._stop_polling:
-                        logger.info(f"[{self.parent.name}]\tDetaching monitor")
-                        break
-
-                    # pylint: disable=no-member
-                    # pylint: disable=protected-access
-                    r = self.parent._socket.recv_multipart(flags=zmq.NOBLOCK)
-
-                    # Length and throtling checks
-                    if len(r) != 2:
-                        logger.warning(
-                            f"[{self.parent.name}] Received malformed array of length {len(r)}"
-                        )
-                    t_curr = time()
-                    t_elapsed = t_curr - t_last
-                    if t_elapsed < self.parent.throttle.get():
-                        sleep(0.1)
-                        continue
-
-                    # Unpack the Array V1 reply to metadata and array data
-                    meta, data = r
-
-                    # Update image and update subscribers
-                    header = json.loads(meta)
-                    image = np.frombuffer(data, dtype=header["type"])
-                    if image.size != np.prod(header["shape"]):
-                        err = f"Unexpected array size of {image.size} for header: {header}"
-                        raise ValueError(err)
-                    image = image.reshape(header["shape"])
-
-                    # Update image and update subscribers
-                    self.parent.array_counter.put(header["frame"], force=True)
-                    self.parent.ndimensions.put(len(header["shape"]), force=True)
-                    self.parent.array_size.put(header["shape"], force=True)
-                    # self.parent.array_data.put(data, force=True)
-                    self.parent.shaped_image.put(image, force=True)
-
-                    # pylint: disable=protected-access
-                    self.parent._last_image = image
-                    self.parent._run_subs(sub_type=self.parent.SUB_MONITOR, value=image)
-                    t_last = t_curr
-                    logger.info(
-                        f"[{self.parent.name}] Updated frame {header['frame']}\t"
-                        f"Shape: {header['shape']}\tMean: {np.mean(image):.3f}"
-                    )
-                except ValueError:
-                    # Happens when ZMQ partially delivers the multipart message
-                    pass
-                except zmq.error.Again:
-                    # Happens when receive queue is empty
-                    sleep(0.1)
-        except Exception as ex:
-            logger.info(f"[{self.parent.name}]\t{str(ex)}")
-            raise
-        finally:
-            self._mon = None
-            logger.info(f"[{self.parent.name}]\tDetaching monitor")
-
-
-class StdDaqPreviewDetector(PSIDetectorBase):
-    """Detector wrapper class around the StdDaq preview image stream.
-
-    This was meant to provide live image stream directly from the StdDAQ but
-    also works with other ARRAY v1 streamers, like the AreaDetector ZMQ plugin.
-    Note that the preview stream must be already throtled in order to cope with
-    the incoming data and the python class might throttle it further.
-
-    NOTE: As an explicit request, it does not record the image data.
-
-    You can add a preview widget to the dock by:
-    cam_widget = gui.add_dock('cam_dock1').add_widget('BECFigure').image('daq_stream1')
-    """
-
-    # Subscriptions for plotting image
-    USER_ACCESS = ["image", "savemode"]
-    SUB_MONITOR = "device_monitor_2d"
-    _default_sub = SUB_MONITOR
-
-    custom_prepare_cls = StdDaqPreviewMixin
-
-    # Configuration attributes
-    url = Component(Signal, kind=Kind.config, metadata={"write_access": False})
-    throttle = Component(Signal, value=0.25, kind=Kind.config)
-    # Streamed data status
-    array_counter = Component(Signal, kind=Kind.hinted, metadata={"write_access": False})
-    ndimensions = Component(Signal, kind=Kind.normal, metadata={"write_access": False})
-    array_size = Component(Signal, kind=Kind.normal, metadata={"write_access": False})
-    # array_data = Component(Signal, kind=Kind.omitted, metadata={"write_access": False})
-    shaped_image = Component(Signal, kind=Kind.omitted, metadata={"write_access": False})
-    _last_image = None
-
-    def __init__(
-        self, *args, url: str = "tcp://129.129.95.38:20000", parent: Device = None, **kwargs
-    ) -> None:
-        super().__init__(*args, parent=parent, **kwargs)
-        self.url.set(url, force=True).wait()
-        # Connect to the DAQ
-        self.connect()
-
-    def connect(self):
-        """Connect to te StDAQs PUB-SUB streaming interface
-
-        StdDAQ may reject connection for a few seconds when it restarts,
-        so if it fails, wait a bit and try to connect again.
-        """
-        # pylint: disable=no-member
-        # Socket to talk to server
-        context = zmq.Context()
-        self._socket = context.socket(zmq.SUB)
-        self._socket.setsockopt(zmq.SUBSCRIBE, ZMQ_TOPIC_FILTER)
-        try:
-            self._socket.connect(self.url.get())
-        except ConnectionRefusedError:
-            sleep(1)
-            self._socket.connect(self.url.get())
-
-    def savemode(self, save=False):
-        """Toggle save mode for the shaped image"""
-        # pylint: disable=protected-access
-        if save:
-            self.shaped_image._kind = Kind.normal
-        else:
-            self.shaped_image._kind = Kind.omitted
-
-    def image(self):
-        """
-        Gets the last image as an attribute in case image must be abandoned
-        due to some caching on the BEC.
-        """
-        return self._last_image
-
-
-# Automatically connect to MicroSAXS testbench if directly invoked
-if __name__ == "__main__":
-    daq = StdDaqPreviewDetector(url="tcp://129.129.95.111:20000", name="preview")
-    daq.wait_for_connection()

pxiii_bec/devices/__init__.py

@@ -1,14 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Ophyd devices for the PX III beamline, including the MX specific Aerotech A3200 stage.
-
-@author: mohacsi_i
-"""
-from .A3200 import AerotechAbrStage
-from .A3200utils import A3200Axis
-from .SmarGonA import SmarGonAxis as SmarGonAxisA
-from .SmarGonB import SmarGonAxis as SmarGonAxisB
-from .StdDaqPreview import StdDaqPreviewDetector
-from .NDArrayPreview import NDArrayPreview
-from .SamCamDetector import SamCamDetector
-from .PneumaticValve import PneumaticValve

pxiii_bec/devices/device_list.md

@@ -1,11 +0,0 @@
-// This file was autogenerated. Do not edit it manually.
-## Device List
-### pxiii_bec 
-| Device | Documentation | Module |
-| :----- | :------------- | :------ |
-| A3200Axis | Positioner wrapper for A3200 axes<br><br><br>    Positioner wrapper for motors on the Aerotech A3200 controller. As the IOC<br>    does not provide a motor record, this class simply wraps axes into a<br>    standard Ophyd positioner for the BEC. It also has some additional<br>    functionality for error checking and diagnostics.<br><br>    Examples<br>    --------<br>    omega = A3200Axis('X06DA-ES-DF1:OMEGA', base_pv='X06DA-ES')<br><br>    Parameters<br>    ----------<br>    prefix : str<br>        Axis PV name root.<br>    base_pv : str (situational)<br>        IOC PV name root, i.e. X06DA-ES if standalone class.<br>     | [pxiii_bec.devices.A3200utils](https://gitlab.psi.ch/bec/pxiii_bec/-/blob/main/pxiii_bec/devices/A3200utils.py) |
-| AerotechAbrStage | Standard PX stage on A3200 controller<br><br>    This is the wrapper class for the standard rotation stage layout for the PX<br>    beamlines at SLS. It wraps the main rotation axis OMEGA (Aerotech ABR)and<br>    the associated motion axes GMX, GMY and GMZ. The ophyd class associates to<br>    the general PX measurement procedure, which is that the actual scan script<br>    is running as an AeroBasic program on the controller and we communicate to<br>    it via 10+1 global variables.<br>     | [pxiii_bec.devices.A3200](https://gitlab.psi.ch/bec/pxiii_bec/-/blob/main/pxiii_bec/devices/A3200.py) |
-| NDArrayPreview | Wrapper class around AreaDetector's NDStdArray plugins<br><br>    This is a standalone class to display images from AreaDetector's<br>    ImagePlugin without using a parent device. It also offers BEC exposed<br>    methods to transfer image and change image array Kind-ness.<br><br>    NOTE: As an explicit request, it can toggle data recording<br>     | [pxiii_bec.devices.NDArrayPreview](https://gitlab.psi.ch/bec/pxiii_bec/-/blob/main/pxiii_bec/devices/NDArrayPreview.py) |
-| SamCamDetector | Sample camera device<br><br>    The SAMCAM continously streams images to the GUI and sample alignment<br>    scripts via ZMQ.<br>     | [pxiii_bec.devices.SamCamDetector](https://gitlab.psi.ch/bec/pxiii_bec/-/blob/main/pxiii_bec/devices/SamCamDetector.py) |
-| SmarGonAxis | SmarGon client deice<br><br>    This class controls the SmarGon goniometer via the REST interface. All<br>    SmarGon axes share a common mutex to manage actual HW access.<br>     | [pxiii_bec.devices.SmarGonB](https://gitlab.psi.ch/bec/pxiii_bec/-/blob/main/pxiii_bec/devices/SmarGonB.py) |
-| StdDaqPreviewDetector | Detector wrapper class around the StdDaq preview image stream.<br><br>    This was meant to provide live image stream directly from the StdDAQ but<br>    also works with other ARRAY v1 streamers, like the AreaDetector ZMQ plugin.<br>    Note that the preview stream must be already throtled in order to cope with<br>    the incoming data and the python class might throttle it further.<br><br>    NOTE: As an explicit request, it does not record the image data.<br><br>    You can add a preview widget to the dock by:<br>    cam_widget = gui.add_dock('cam_dock1').add_widget('BECFigure').image('daq_stream1')<br>     | [pxiii_bec.devices.StdDaqPreview](https://gitlab.psi.ch/bec/pxiii_bec/-/blob/main/pxiii_bec/devices/StdDaqPreview.py) |

pxiii_bec/macros/README.md

@@ -1,6 +0,0 @@
-# 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 pxiii_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

pxiii_bec/macros/calculator.py

@@ -1,357 +0,0 @@
-"""Utility functions for calculating energy, wavelength, and Bragg angle."""
-
-from dataclasses import dataclass
-import numpy as np
-# from pxii_parameters import (EnergyDefaults, CamConversion)
-
-
-@dataclass(frozen=True)
-class Constants:
-    """Constants used in energy calculations"""
-
-    # # Physical Constants from https://physics.nist.gov/cuu/Constants/index.html
-    ANGSTROM_CONVERSION = 1e10  # Convert meters to angstrom
-    PLANCK_CONST_EV = 4.135667696e-15  # eV/Hz
-    SPEED_OF_LIGHT = 299792458  # m/s
-
-    # d-spacings
-    d_spacing = {120: 3.13481, 298: 3.13562}
-
-
-def speed_of_light_ang():
-    """
-    Calculate the speed of light in angstroms per second.
-
-    Returns:
-        float: The speed of light converted to angstroms per second.
-    """
-    return Constants.SPEED_OF_LIGHT * Constants.ANGSTROM_CONVERSION
-
-
-def en_wav_factor():
-    """
-    Calculate the energy wavelength factor.
-
-    This function computes a constant factor used to calculate energy
-    values in relation to wavelength by combining Planck's constant,
-    in eV/Hz, and the speed of light in angstrom.
-
-    Returns:
-        float: The computed energy wavelength factor.
-    """
-    return Constants.PLANCK_CONST_EV * speed_of_light_ang()
-
-
-# Helper Functions
-def convert_to_degrees(angle_mrad: float) -> float:
-    """
-    Convert an angle from milliradians to degrees.
-
-    Args:
-        angle_mrad: The angle value in milliradians.
-
-    Returns:
-        The angle converted into degrees as a float.
-    """
-    return np.rad2deg(angle_mrad / 1000)
-
-
-def create_conversion_result(
-    energy_ev: float, wavelength: float, bragg_angle_mrad: float
-) -> dict:
-    """
-    Creates a dictionary containing converted values of energy and angles.
-
-    This function takes the energy in electron-volts, the wavelength,
-    and the Bragg angle in milliradians as input. It computes and
-    returns a dictionary containing the energy in both electron-volts
-    and kiloelectron-volts, the wavelength, the Bragg angle in milliradians,
-    and the Bragg angle converted to degrees.
-
-    Args:
-        energy_ev: Energy value in electron-volts.
-        wavelength: Wavelength value.
-        bragg_angle_mrad: Bragg angle in milliradians.
-
-    Returns:
-        dict: A dictionary containing the following keys:
-            - "energy_kev": Energy value in kiloelectron-volts.
-            - "energy_ev": Energy value in electron-volts.
-            - "wavelength": Wavelength value.
-            - "bragg_angle_mrad": Bragg angle in milliradians.
-            - "bragg_angle_deg": Bragg angle in degrees.
-    """
-    return {
-        "energy_kev": energy_ev / 1000,
-        "energy_ev": energy_ev,
-        "wavelength": wavelength,
-        "bragg_angle_mrad": float(bragg_angle_mrad),
-        "bragg_angle_deg": float(convert_to_degrees(bragg_angle_mrad)),
-    }
-
-
-def print_conversion_result(result: dict) -> None:
-    """
-    Prints the energy-related conversion results to the console.
-    """
-
-    line = (
-        f"energy: {result['energy_ev']:.6g} eV, energy: {result['energy_kev']:.6g} keV, "
-        f"wavelength: {result['wavelength']:.4g} Å, "
-        f"bragg angle: {result['bragg_angle_mrad']:.5g} mrad, {result['bragg_angle_deg']:.4g} deg"
-    )
-    print(line)
-
-
-# Conversion Functions
-def calculate_wavelength_from_angle(bragg_angle_mrad: float, temp=120) -> float:
-    """
-    calculate_wavelength_from_angle(bragg_angle_mrad: float) -> float
-
-    Arguments:
-        bragg_angle_mrad: The Bragg angle in milliradians, used to compute the
-                          sine value required for the wavelength calculation.
-
-    Returns:
-        The calculated wavelength as a float value.
-    """
-    d = Constants.d_spacing[temp]
-    return 2 * d * np.sin(bragg_angle_mrad / 1000)
-
-
-def calculate_energy_from_wavelength(wavelength: float) -> float:
-    """
-    Calculates the energy of a photon based on its wavelength.
-
-    Args:
-        wavelength: The wavelength of the photon in angstrom.
-
-    Returns:
-        The energy of the photon in eV.
-    """
-    return en_wav_factor() / wavelength
-
-
-def calculate_wavelength_from_energy(energy_ev: float) -> float:
-    """
-    Calculates the wavelength of a photon from its energy.
-
-    Arguments:
-        energy_ev: float
-            The energy of the photon in electronvolts (eV).
-
-    Returns:
-        float
-            The calculated wavelength of the photon in angstrom.
-    """
-    return en_wav_factor() / energy_ev
-
-
-def calculate_bragg_angle_from_wavelength(wavelength: float, temp=120) -> float:
-    """
-    Calculate the Bragg angle in milliradians for a given wavelength.
-
-    Args:
-        wavelength: The wavelength in angstrom.
-
-    Returns:
-        The Bragg angle in milliradians as a float.
-    """
-    d = Constants.d_spacing[temp]
-    angle_rad = np.arcsin(wavelength / (2 * d))
-    return angle_rad * 1000
-
-
-def convert_input_angle_to_mrad(bragg_angle: float) -> float:
-    """
-    Convert input angle into milliradians (mrad).
-
-    This function takes an angle as input and determines its likely unit,
-    converting it to milliradians (mrad) if necessary. If the input value
-    is less than 1, it is assumed to be in radians and is converted to
-    mrad. If the input value falls between predefined minimum and
-    maximum values for mrad, it is assumed to be in degrees and thus
-    converted to mrad using the degrees-to-radians conversion factor.
-
-    For input values that don't match these scenarios, it assumes
-    that the input is already in mrad and returns it unchanged.
-
-    Arguments:
-        bragg_angle (float): The input Bragg angle, which can be in
-        radians, degrees, or milliradians.
-
-    Returns:
-        float: The Bragg angle converted into milliradians (mrad).
-    """
-    if bragg_angle < 1:  # Likely the input angle is in radians
-        return bragg_angle * 1000
-    if 3 < bragg_angle < 25:  # Likely input angle is in degrees
-        return np.deg2rad(bragg_angle) * 1000
-    return bragg_angle  # Already in mrad
-
-
-# Core Functions
-def validate_energy(energy_ev):
-    """
-    Validates the energy value to ensure it falls within the acceptable range. The function
-    converts the provided energy from keV to eV if the input value is less than 1/1000 of the
-    maximum energy value. It then checks whether the energy is within the defined bounds.
-    If the energy value is outside the acceptable range, the function raises a ValueError.
-
-    Args:
-        energy_ev (float): The energy value in eV or keV to be validated. If this value is
-            smaller than 1/1000 of the maximum allowed energy (in eV), it will be multiplied
-            by 1000 to convert it from keV to eV.
-
-    Returns:
-        float: The validated energy value in eV that falls within the acceptable range.
-
-    Raises:
-        ValueError: If the energy value is outside the defined range of
-            [MIN_ENERGY_EV, MAX_ENERGY_EV].
-    """
-    if energy_ev < EnergyDefaults.max_energy_ev / 1000:  # Assuming the input is in keV.
-        energy_ev *= 1000
-    if not EnergyDefaults.min_energy_ev <= energy_ev <= EnergyDefaults.max_energy_ev:
-        raise ValueError(
-            f"Energy of {energy_ev} eV is outside the valid range "
-            f"({EnergyDefaults.min_energy_ev} eV to {EnergyDefaults.max_energy_ev} eV)"
-        )
-    return energy_ev
-
-
-def convert_from_bragg(
-    bragg_angle_mrad: float, temp=120, print_result: bool = False
-) -> dict:
-    """
-    Convert the Bragg angle to wavelength and energy, returning the result as a dictionary.
-
-    This function converts a given Bragg angle (in milliradians) into the corresponding
-    wavelength and energy values, and returns them in a dictionary format. The function
-    also supports optional printing of the calculated results.
-
-    Args:
-        bragg_angle_mrad (float): The Bragg angle in milliradians to be converted.
-        print_result (bool): Whether to print the conversion result. Defaults to False.
-
-    Returns:
-        dict: A dictionary containing the following keys:
-            - 'energy_ev': Energy in electronvolts.
-            - 'wavelength': Wavelength corresponding to the input angle.
-            - 'bragg_angle_mrad': Input Bragg angle in milliradians.
-    """
-    bragg_angle_mrad = convert_input_angle_to_mrad(bragg_angle_mrad)
-    wavelength = float(calculate_wavelength_from_angle(bragg_angle_mrad, temp=temp))
-    energy_ev = float(calculate_energy_from_wavelength(wavelength))
-    result = create_conversion_result(energy_ev, wavelength, bragg_angle_mrad)
-    if print_result:
-        print_conversion_result(result)
-    return result
-
-
-def convert_from_energy(energy_ev: float, temp=120, print_result: bool = False) -> dict:
-    """
-    Convert energy in electron volts (eV) to  wavelength and Bragg angle in milliradians
-    (mrad). This method validates the given energy, calculates corresponding properties,
-    and optionally prints the result.
-
-    Args:
-        energy_ev: Energy value in electron volts (float) to be converted.
-        print_result: Flag indicating whether to print the resulting
-            conversion details (bool). Defaults to False.
-
-    Returns:
-        A dictionary containing the following key-value pairs:
-            - "energy_ev" (float): Validated energy in eV.
-            - "wavelength" (float): Calculated wavelength in meters.
-            - "bragg_angle_mrad" (float): Calculated Bragg angle in mrad.
-    """
-    energy_ev = validate_energy(energy_ev)
-    wavelength = calculate_wavelength_from_energy(energy_ev)
-    bragg_angle_mrad = float(
-        calculate_bragg_angle_from_wavelength(wavelength, temp=temp)
-    )
-    result = create_conversion_result(energy_ev, wavelength, bragg_angle_mrad)
-    if print_result:
-        print_conversion_result(result)
-    return result
-
-
-def convert_from_wavelength(
-    wavelength: float,
-    temp: float = 120,
-    print_result: bool = False,
-) -> dict:
-    """
-    Convert a given wavelength value into corresponding energy, Bragg angle, and
-    generate a result dictionary.
-
-    The function processes a wavelength value, checks its validity against a
-    permitted range, calculates corresponding energy and Bragg angle, and
-    formats the results into a dictionary. Optionally, the function can print
-    the result.
-
-    Parameters:
-        wavelength: float
-            The input wavelength value in Angstroms to be converted. Should
-            fall within the permitted wavelength range.
-        print_result: bool
-            Optional flag indicating whether to print the conversion result.
-            Default is False.
-
-    Returns:
-        dict
-            A dictionary containing the energy (electron-volts), wavelength
-            (Angstroms), and Bragg angle (milliradians). If the wavelength is
-            outside of the permitted range, returns None.
-    """
-    energy_ev = calculate_energy_from_wavelength(wavelength)
-    bragg_angle_mrad = float(
-        calculate_bragg_angle_from_wavelength(wavelength, temp=temp)
-    )
-    result = create_conversion_result(energy_ev, wavelength, bragg_angle_mrad)
-    if print_result:
-        print_conversion_result(result)
-    return result
-
-
-def calc_perp_position(
-    energy_ev: float,
-    print_result: bool = False,
-) -> float:
-    """
-    Calculate the perpendicular motor position based on provided energy in electron-volts (eV).
-
-    This function computes the perpendicular motor position using the given energy value in
-    electron-volts. The calculation is based on the Bragg angle derived from the energy. An optional
-    parameter allows printing the result during execution.
-
-    Parameters:
-        energy_ev (float): The energy value in electron-volts used for the calculation.
-        print_result (bool): Flag to determine whether to print the computed perpendicular offset.
-            Default is False.
-
-    Returns:
-        float: The computed perpendicular position.
-
-    Raises:
-        None
-    """
-    result = convert_from_energy(energy_ev, print_result=False)
-    bragg_angle_rad = result["bragg_angle_mrad"] / 1000
-    perp_offset = float(EnergyDefaults.beam_offset / (2 * np.cos(bragg_angle_rad))) - 3
-    if print_result:
-        print(f"Perp = {perp_offset: .4f}")
-    return perp_offset
-
-def calc_scam_microns(pixels, zoom = 1000):
-    return pixels/(0.5208 * np.exp(0.002586 * zoom))
-
-def calc_scam_microns(pixels, zoom=1000):
-    """Convert pixels to microns for the sample camera"""
-    return float(pixels / (CamConversion.a * np.exp(CamConversion.b * zoom)))
-
-def calc_bsccam_microns(pixels):
-    """Convert pixels to microns for the BSC camera"""
-    return pixels*20
-

pxiii_bec/macros/check.py

@@ -1,495 +0,0 @@
-from dataclasses import dataclass, field
-from enum import Enum
-from typing import Any, Callable
-from datetime import datetime
-
-from bec_lib.device import Signal, Positioner
-
-
-# -------------------------------------------------------------------
-# Status Enum
-# -------------------------------------------------------------------
-
-
-class Status(Enum):
-    OK = 0
-    WARNING = 1
-    ERROR = 2
-    UNKNOWN = 3
-
-    @property
-    def color(self):
-        return {
-            Status.OK: "green",
-            Status.WARNING: "yellow",
-            Status.ERROR: "red",
-            Status.UNKNOWN: "blue",
-        }[self]
-    
-    @property
-    def color_scilog(self):
-        return {
-            Status.OK: "green",
-            Status.WARNING: "",
-            Status.ERROR: "red",
-            Status.UNKNOWN: "",
-        }[self]
-
-
-# -------------------------------------------------------------------
-# Health Result Object
-# -------------------------------------------------------------------
-
-
-@dataclass
-class HealthCheckResult:
-
-    name: str
-    description: str 
-    status: Status
-
-    value: Any = None
-
-    message: str = ""
-
-    category: str = "general"
-
-    def __str__(self):
-
-        if self.status == Status.OK:
-            return f"[{self.status.name}] {self.description}"
-
-        return (
-            f"[{self.status.name}] "
-            f"{self.description}: {self.message}"
-        )
-    
-    def formatted_message(self):
-        if self.status == Status.OK:
-            return f"[{self.status.name}] {self.name}"
-        
-        return (
-            f"[{self.status.name}] "
-            f"{self.description}: {self.message}"
-        )
-
-# -------------------------------------------------------------------
-# Send to SciLog
-# -------------------------------------------------------------------
-
-def send_to_scilog(results):
-
-    counts = {
-        Status.OK: 0,
-        Status.WARNING: 0,
-        Status.ERROR: 0,
-        Status.UNKNOWN: 0,
-    }
-
-    for result in results:
-        counts[result.status] += 1
-    timestamp = datetime.now().strftime("%Y/%m/%d %H:%M")
-
-    msg = bec.messaging.scilog.new()
-
-    msg.add_text(
-        f"Beamline Health Summary {timestamp}",
-        bold = True
-    )
-
-    msg.add_text("\n")
-    for status, count in counts.items():
-        msg.add_text(
-            f"{status.name:<10}: {count}",
-            bold=True,
-        )
-    msg.add_text("\n")
-
-    for result in results:
-        msg.add_text(
-            result.formatted_message(),
-            # bold=result.status != Status.OK,
-            color = result.status.color_scilog
-        )
-        msg.add_text("\n")
-    msg.add_tags(["beamline health check"])
-    msg.send()
-
-
-# -------------------------------------------------------------------
-# Configuration
-# -------------------------------------------------------------------
-
-@dataclass
-class BeamlineHealthConfig:
-
-    signal_rules: dict[str, Callable] = field(
-        default_factory=lambda: {
-            "cam": lambda x: x != 0,
-            "bpm": lambda x: x != 0,
-        }
-    )
-
-    motor_tolerances: dict[str, float] = field(
-        default_factory=lambda: {
-            # examples
-            # "mono_theta": 0.001,
-            # "detector_z": 0.1,
-        }
-    )
-
-    default_motor_tolerance: float = 0.02
-
-
-# -------------------------------------------------------------------
-# Device Collection
-# -------------------------------------------------------------------
-
-
-def get_devices():
-    return list(dev.items())
-
-
-# -------------------------------------------------------------------
-# Signal Checks
-# -------------------------------------------------------------------
-
-
-def check_signals(devices, config: BeamlineHealthConfig):
-
-    results = []
-
-    signal_devices = [
-        (name, obj)
-        for name, obj in devices
-        if isinstance(obj, Signal)
-    ]
-
-    for name, obj in signal_devices:
-
-        try:
-            data = obj.read()
-            actual = data[name]["value"]
-            description = obj.description
-
-        except Exception as e:
-
-            results.append(
-                HealthCheckResult(
-                    name=name,
-                    description=name,
-                    status=Status.UNKNOWN,
-                    message=f"Failed to read signal: {e}",
-                    category="signals",
-                )
-            )
-
-            continue
-
-        matched = False
-
-        for keyword, rule in config.signal_rules.items():
-
-            if keyword in name:
-
-                matched = True
-
-                try:
-                    passed = rule(actual)
-
-                except Exception as e:
-
-                    results.append(
-                        HealthCheckResult(
-                            name=name,
-                            description=name,
-                            status=Status.UNKNOWN,
-                            value=actual,
-                            message=f"Rule evaluation failed: {e}",
-                            category="signals",
-                        )
-                    )
-
-                    break
-
-                if passed:
-
-                    results.append(
-                        HealthCheckResult(
-                            name=name,
-                            description=description,
-                            status=Status.OK,
-                            value=actual,
-                            category="signals",
-                        )
-                    )
-
-                else:
-
-                    results.append(
-                        HealthCheckResult(
-                            name=name,
-                            description=description,
-                            status=Status.ERROR,
-                            value=actual,
-                            message=f"Signal value {actual} failed validation",
-                            category="signals",
-                        )
-                    )
-                break
-
-        if not matched:
-            continue
-
-    return results
-
-
-# -------------------------------------------------------------------
-# Motor Checks
-# -------------------------------------------------------------------
-
-
-def check_motors(devices, config: BeamlineHealthConfig):
-
-    results = []
-
-    motor_devices = [
-        (name, obj)
-        for name, obj in devices
-        if isinstance(obj, Positioner)
-    ]
-
-    for name, obj in motor_devices:
-
-        try:
-
-            data = obj.read()
-
-            description = obj.description
-
-            actual = data[name]["value"]
-
-            error_code = obj.motor_status.get()
-
-            move_state = obj.motor_is_moving.get()
-
-        except Exception as e:
-
-            results.append(
-                HealthCheckResult(
-                    name=name,
-                    description=name,
-                    status=Status.UNKNOWN,
-                    message=f"Failed to read motor: {e}",
-                    category="motors",
-                )
-            )
-
-            continue
-
-        # -----------------------------------------------------------
-        # Error state
-        # -----------------------------------------------------------
-
-        if error_code != 0:
-
-            results.append(
-                HealthCheckResult(
-                    name=name,
-                    description=description,
-                    status=Status.ERROR,
-                    value=error_code,
-                    message=f"motor error code: {error_code}",
-                    category="motors",
-                )
-            )
-
-            continue
-
-        # -----------------------------------------------------------
-        # Moving state
-        # -----------------------------------------------------------
-
-        if move_state != 0:
-
-            results.append(
-                HealthCheckResult(
-                    name=name,
-                    description=description,
-                    status=Status.WARNING,
-                    value=move_state,
-                    message="motor is currently moving",
-                    category="motors",
-                )
-            )
-
-            continue
-
-        # -----------------------------------------------------------
-        # Setpoint comparison
-        # -----------------------------------------------------------
-
-        sp_key = f"{name}_user_setpoint"
-
-        if sp_key in data:
-
-            setpoint = data[sp_key]["value"]
-
-            diff = abs(actual - setpoint)
-
-            tolerance = config.motor_tolerances.get(
-                name,
-                config.default_motor_tolerance,
-            )
-
-            if diff > tolerance:
-
-                results.append(
-                    HealthCheckResult(
-                        name=name,
-                        description=description,
-                        status=Status.WARNING,
-                        value=diff,
-                        message=(
-                            f"Setpoint {setpoint:.5g} differs "
-                            f"from readback {actual:.5g} "
-                            f"by {diff:.4g}"
-                        ),
-                        category="motors",
-                    )
-                )
-
-            else:
-
-                results.append(
-                    HealthCheckResult(
-                        name=name,
-                        description=description,
-                        status=Status.OK,
-                        value=actual,
-                        category="motors",
-                    )
-                )
-
-        else:
-
-            results.append(
-                HealthCheckResult(
-                    name=name,
-                    description=description,
-                    status=Status.UNKNOWN,
-                    message="No setpoint available",
-                    category="motors",
-                )
-            )
-
-    return results
-
-
-# -------------------------------------------------------------------
-# Main Check Entry Point
-# -------------------------------------------------------------------
-
-
-def check2(config: BeamlineHealthConfig | None = None):
-    if config is None:
-        config = BeamlineHealthConfig()
-
-    devices = get_devices()
-
-    results = []
-
-    results.extend(check_signals(devices, config))
-
-    results.extend(check_motors(devices, config))
-
-    # ---------------------------------------------------------------
-    # Sort by severity
-    # ---------------------------------------------------------------
-
-    results.sort(
-        key=lambda r: r.status.value,
-    )
-
-    return results
-
-
-# -------------------------------------------------------------------
-# Summary Printer
-# -------------------------------------------------------------------
-
-
-def summary_text(results):
-
-    timestamp = datetime.now().strftime("%Y-%m-%d %H:%M")
-
-
-    n_ok = sum(r.status == Status.OK for r in results)
-
-    n_warn = sum(r.status == Status.WARNING for r in results)
-
-    n_err = sum(r.status == Status.ERROR for r in results)
-
-    n_unknown = sum(r.status == Status.UNKNOWN for r in results)
-
-    return (
-        f"==========================================\n"
-        f"Beamline Health Check at {timestamp}\n"
-        f"==========================================\n"
-        f"OK       : {n_ok}\n"
-        f"WARNING  : {n_warn}\n"
-        f"ERROR    : {n_err}\n"
-        f"UNKNOWN  : {n_unknown}\n"
-        "==========================================\n"
-    )
-    # return "\n".join(lines)
-
-
-# -------------------------------------------------------------------
-# Filter results
-# -------------------------------------------------------------------
-def filter_results(results, statuses = None):
-    if statuses is None:
-        return results
-    
-    return [
-        r for r in results
-        if r.status in statuses
-    ]
-
-# -------------------------------------------------------------------
-# CLI Entry Point
-# -------------------------------------------------------------------
-
-
-def run_check(show_all= False):
-
-    results = check2()
-
-    print(summary_text(results))
-
-    problem_results = filter_results(
-        results,
-        statuses={
-            Status.WARNING,
-            Status.ERROR,
-            Status.UNKNOWN,
-        }
-    )
-    send_to_scilog(results)
-    
-    if not show_all:
-        results = filter_results(
-            results,
-            statuses={
-                Status.WARNING,
-                Status.ERROR,
-                Status.UNKNOWN
-            }
-        )
-    for result in results:
-        print(result)
-
-
-
-

pxiii_bec/macros/mx_basics.py

@@ -1,252 +0,0 @@
-"""Get data from an h5 file or BEC history and perform fitting."""
-
-import numpy as np
-from lmfit.models import (
-    GaussianModel,
-    LorentzianModel,
-    VoigtModel,
-    ConstantModel,
-    LinearModel,
-)
-from scipy.ndimage import gaussian_filter1d
-import h5py
-import matplotlib.pyplot as plt
-
-
-def create_fit_parameters(
-    deriv: bool = False,
-    model: str = "Voigt",
-    baseline: str = "Linear",
-    smoothing: None = None,
-):
-    """Store the fit parameters in a dictionary."""
-    # map input model to lmfit model name
-    model_mappings = {
-        "Gaussian": GaussianModel,
-        "Lorentzian": LorentzianModel,
-        "Voigt": VoigtModel,
-        "Constant": ConstantModel,
-        "Linear": LinearModel,
-    }
-    return {
-        "deriv": deriv,
-        "model": model_mappings[model],
-        "baseline": model_mappings[baseline],
-        "smoothing": smoothing,
-    }
-
-
-def get_data_from_h5(signal_name: str = "lu_bpmsum"):
-    """Get data from an h5 file."""
-    with h5py.File("scan_676.h5", "r") as f:
-        entry = f["entry"]["collection"]
-        y_data = entry["devices"][signal_name][signal_name]["value"][:]
-        motor_data = entry["metadata"]["bec"]
-        motor_name = motor_data["scan_motors"][0].decode()
-        scan_number = motor_data["scan_number"][()]
-        x_data = entry["devices"][motor_name][motor_name]["value"][:]
-    return {
-        "x_data": x_data,
-        "y_data": y_data,
-        "signal_name": signal_name,
-        "motor_name": motor_name,
-        "scan_number": str(scan_number),
-    }
-
-
-def get_data_from_history(
-    history_index: int,
-    signal_name: str = "lu_bpmsum",
-):
-    """Read data from the BEC history and return the X and Y data as arrays."""
-    scan = bec.history[history_index]
-    md = scan.metadata["bec"]
-    motor_name = md["scan_motors"][0].decode()
-    scan_number = md["scan_number"]
-    x_data = scan.devices[motor_name][motor_name].read()["value"]
-    y_data = scan.devices[signal_name][signal_name].read()["value"]
-    return {
-        "signal_name": signal_name,
-        "x_data": x_data,
-        "y_data": y_data,
-        "motor_name": motor_name,
-        "scan_number": scan_number,
-    }
-
-
-def process_data(data, fit_params):
-    """
-    Process the signal data for fitting based on derivative or smoothing.
-    """
-    smoothing, deriv = fit_params["smoothing"], fit_params["deriv"]
-    signal_name = data["signal_name"]
-    y_data = data["y_data"]
-
-    if deriv:
-        if smoothing:
-            y_smooth = gaussian_filter1d(y_data, smoothing)
-            fitting_data = np.gradient(y_smooth)
-            signal_name = f"Derivative of smoothed {signal_name}"
-        else:
-            fitting_data = np.gradient(y_data)
-            signal_name = f"Derivative of {signal_name}"
-    elif smoothing and smoothing > 0.01:
-        fitting_data = gaussian_filter1d(y_data, smoothing)
-        signal_name = f"Smoothed {signal_name}"
-    else:
-        fitting_data = y_data
-
-    updated_data = {
-        "y_to_fit": fitting_data,
-        "signal_name": signal_name,
-    }
-    data.update(updated_data)
-    return data
-
-
-def fit(data, fit_params):
-    """Fit a signal to a model and return the fitting results."""
-    # Create the model
-    peak_model = fit_params["model"](prefix="peak_")
-    baseline_model = fit_params["baseline"](prefix="base_")
-    full_model = peak_model + baseline_model
-
-    # Prepare data
-    processed_data = process_data(data, fit_params)
-    params = full_model.make_params()
-    y_min = np.min(processed_data["y_to_fit"])
-
-    # Configure baseline parameters
-    if fit_params["baseline"] == ConstantModel:
-        params["base_c"].set(value=y_min)
-    elif fit_params["baseline"] == LinearModel:
-        params["base_intercept"].set(value=y_min)
-        params["base_slope"].set(value=0)
-
-    # Add peak-specific parameters
-    params.update(
-        peak_model.guess(processed_data["y_to_fit"], x=processed_data["x_data"])
-    )
-
-    # Perform the fitting
-    lmfit_result = full_model.fit(
-        processed_data["y_to_fit"], params, x=processed_data["x_data"]
-    )
-
-    # Find the X that gives the max Y
-    max_index = np.argmax(processed_data["y_to_fit"])
-    x_max = processed_data["x_data"][max_index]
-
-    # Generate data for a smoothed fit curve
-    fit_xdata = np.linspace(np.min(data["x_data"]), np.max(data["x_data"]), 500)
-    fit_ydata = lmfit_result.eval(x=fit_xdata, params=lmfit_result.params)
-
-    # Collect results
-    return {
-        "model": fit_params["model"].__name__,
-        "fwhm": lmfit_result.params["peak_fwhm"].value,
-        "centre": lmfit_result.best_values["peak_center"],
-        "height": lmfit_result.params["peak_height"].value,
-        "chi_sq": lmfit_result.chisqr,
-        "lmfit_result": lmfit_result,
-        "x_max": x_max,
-        "fit_xdata": fit_xdata,
-        "fit_ydata": fit_ydata,
-    }
-
-
-def plot_fitted_data(data, fit_result):
-    """Plot the original data and the fitted model."""
-    plt.plot(data["x_data"], data["y_to_fit"], label="Data")
-    plt.plot(fit_result['fit_xdata'], fit_result['fit_ydata'], label="Fit")
-    plt.xlabel(data["motor_name"])
-    plt.ylabel(data["signal_name"])
-    plt.title(f"Scan {data['scan_number']}, fitted with {fit_result['model']}")
-    plt.grid(True)
-    plt.legend()
-    plt.show()
-
-
-def select_bec_window(dock_area_name="Fitting"):
-    """Check to see if the fitting results dock is already open and re-create it if not"""
-    open_docks = bec.gui.windows
-    if open_docks.get(dock_area_name) is None:
-        dock_area = bec.gui.new(dock_area_name)
-        # wf = dock_area.new("Plot").new(bec.gui.available_widgets.Waveform)
-        wf = dock_area.new(widget='Waveform', object_name='Plot')
-        text_box = dock_area.new(widget='TextBox', object_name="Results", where="bottom")
-    else:
-        wf = bec.gui.Fitting.Plot
-        text_box = bec.gui.Fitting.Results
-    return wf, text_box
-
-
-def plot_live_data_bec(
-    motor_name,
-    signal_name,
-    window_name="Fitting"
-):
-    """
-    Plotting live data for motor and signal using BEC.
-
-    This function plots live data from a specified motor and signal.
-    It clears the current plot window, sets its title, labels the axes
-    with the provided motor and signal names, and initializes live plotting
-    on the given signal against the motor.
-
-    Args:
-        motor_name (str): The name of the motor to be used as the x-axis.
-        signal_name (str): The name of the signal to be used as the y-axis.
-
-    Returns:
-        None
-    """
-    wf, text_box = select_bec_window(window_name)
-    text_box.set_plain_text("Plotting live data")
-    wf.clear_all()
-    wf.title = "Scan: Live scan"
-    wf.x_label = motor_name
-    wf.y_label = signal_name
-    wf.plot(device_x=motor_name, device_y=signal_name)
-
-
-def plot_fitted_data_bec(
-    data,
-    fit_result,
-):
-    """
-    Plot fitted data and display fitting parameters in the specified window.
-
-    This function selects a BEC window and plots the original data along with the
-    fitted function. Additionally, it displays the fitting results in a text
-    box within the same window for better visualization of the fit results.
-
-    Parameters:
-    data : dict
-        Dictionary containing the original dataset, where 'x_data' and 'y_to_fit'
-        hold the independent variable and the dependent variable, respectively,
-        'scan_number' represents the scan number, 'motor_name' and 'signal_name'
-        provide axis labels.
-    fit_result : dict
-        Dictionary containing the results of the fit, including parameters such
-        as 'centre', 'fwhm', 'height', and the fitted model stored under
-        'lmfit_result', with its 'best_fit' attribute representing the fitted data.
-    """
-    wf, text_box = select_bec_window()
-    fit_text = (
-        f"Fit parameters: Centre = {fit_result['centre']:.4f}, "
-        f"FWHM = {fit_result['fwhm']:.3f}, "
-        f"Height = {fit_result['height']:.4f}\n"
-        f"Model = {fit_result['model']}\n"
-        f"Chi sq = {fit_result['chi_sq']:.3g}"
-    )
-    text_box.set_plain_text(fit_text)
-    wf.clear_all()
-    wf.title = f"Scan: {data['scan_number']}"
-    wf.x_label = data["motor_name"]
-    wf.y_label = data["signal_name"]
-    wf.plot(x=data["x_data"], y=data["y_to_fit"], label="Data")
-    wf.plot(x=fit_result["fit_xdata"], y=fit_result["fit_ydata"], label="Fit")
-    # wf.Fit.set(symbol_size = 0)
-    wf.get_curve('Fit').set(symbol_size=0)
-

pxiii_bec/macros/mx_methods.py

@@ -1,321 +0,0 @@
-"""Use the methods in mx_basics to perform:
-1) a go_to_peak scan, that scans a motor, finds the peak position and moves to peak
-2) fits data from a bec history file
-"""
-
-from dataclasses import dataclass
-import numpy as np
-
-# from pxiii_parameters import FitDefaults, BPMScans, MirrorConfig
-
-# from mx_basics import (
-#     create_fit_parameters,
-#     get_data_from_history,
-#     fit,
-#     plot_fitted_data_bec,
-#     plot_live_data_bec,
-# )
-
-
-# Method functions
-def calculate_step_size(start: float, stop: float, steps: int) -> float:
-    """
-    Provides the function to calculate the step size for dividing a specified range
-    into a given number of steps.
-
-    Args:
-        start: The starting value of the range.
-        stop: The stopping value of the range.
-        steps: The number of steps to divide the range into. Must be at least 1.
-
-    Raises:
-        ValueError: If the steps value is less than 1.
-
-    Returns:
-        The calculated step size as a float, rounded to three decimal places.
-    """
-    if steps < 1:
-        raise ValueError("Number of steps must be at least 1.")
-    return round((stop - start) / steps, 3)
-
-
-def move_to_position(motor_device, motor_name: str, position: float, data: dict):
-    """
-    Function to move a specified motor device to a given position.
-
-    The function verifies if the requested position is within the scan range of the
-    motor device provided. If the position is outside the range, the motor is
-    moved to the center of its scan range, an error message is raised, and the
-    operation is halted. If the position is valid, the motor is moved to the
-    specified position.
-
-    Parameters:
-        motor_device: The motor device to be moved.
-        motor_name: str
-            The name of the motor as a string
-        position: float
-            The desired position to move the motor to. Position should be within
-            the scan range of the motor determined by the provided data.
-        data: dict
-            A dictionary containing "x_data", which is used to determine the
-            scan range of the motor.
-
-    Raises:
-        ValueError: Raised if the specified position is outside the valid scan
-        range determined by "x_data" in the data dictionary. The motor will
-        return to the center of its scan range in this case.
-    """
-
-    motor_min = np.min(data["x_data"])
-    motor_max = np.max(data["x_data"])
-    motor_centre = (motor_max + motor_min) / 2
-
-    if not motor_min <= position <= motor_max:
-        scans.umv(motor_device, motor_centre, relative=False)
-        msg = (
-            f"Position {position: .2f} is outside the scan range of "
-            f"{motor_min: .2f} to {motor_max: .2f}. "
-            f"Returning to centre of scan range {motor_centre: .3f}."
-        )
-        raise ValueError(msg)
-    motor_position = round(position, 4)
-    scans.umv(motor_device, motor_position, relative=False)
-    print(f"\n Moving {motor_name} to position {motor_position: .3f}")
-
-
-# @dataclass(frozen=True)
-# class FitDefaults:
-#     """Default values for fitting routines"""
-
-#     # Constants for default models, baselines, and parameters
-#     MODEL = "Voigt"
-#     BASELINE = "Linear"
-#     SETTLE_TIME = 0.1
-#     RELATIVE_MODE = True
-
-
-def go_to_peak(
-    motor_device,
-    signal_device,
-    start: float,
-    stop: float,
-    steps: int,
-    relative: bool = FitDefaults.RELATIVE_MODE,
-    plot: bool = True,
-    settle: float = FitDefaults.SETTLE_TIME,
-    confirm: bool = True,
-    gomax: bool = False,
-):
-    """
-    Go to the peak of a signal by scanning a motor within a specified range and
-    identifying the optimal position based on signal peak data.
-
-    Parameters:
-        motor_device: The motor device to be scanned.
-        signal_device: The signal device to monitor during the scan.
-        start (float): The starting position of the scan. Ignored if `relative` is True.
-        stop (float): The ending position of the scan. Ignored if `relative` is True.
-        steps (int): The number of steps to divide the scan range into.
-        relative (bool, optional): If True, interpret `start` and `stop` as relative to
-            the current motor position. Defaults to RELATIVE_MODE constant.
-        plot (bool, optional): If True, plot the scan data and the fitted results.
-            Defaults to True.
-        settle (float, optional): The time in seconds to wait after each step for the
-            signal to stabilize. Defaults to DEFAULT_SETTLE_TIME constant.
-        confirm (bool, optional): If True, ask for user confirmation before starting
-            the scan. Defaults to True.
-
-    Raises:
-        Exception: Raises exceptions potentially raised by dependent functions or
-            operations such as plotting, fitting, or motor movement.
-
-    Returns:
-        None
-    """
-    motor_name = motor_device.name
-    signal_name = signal_device.name
-    # wf.plot(x_name=motor_name, y_name=signal_name)
-    if plot:
-        plot_live_data_bec(motor_name, signal_name)
-
-    # Validate and calculate step size
-    step_size = calculate_step_size(start, stop, steps)
-
-    # Confirm the scan range
-    # current_motor_position = motor_device.user_readback.get()
-    current_motor_position = motor_device.read()[motor_name]["value"]
-    if confirm:
-        if relative:
-            scan_start = current_motor_position + start
-            scan_end = current_motor_position + stop
-            print(
-                f"\nScanning from {scan_start: .6g} to {scan_end: .6g} in "
-                f"{steps} steps of size {step_size}"
-            )
-            print(f"Relative mode = {relative}")
-        else:
-            print(
-                f"\nScanning from {start: .5g} to {stop: .5g} in {steps} steps of size {step_size}"
-            )
-            print(f"Relative mode = {relative}")
-        input("Press Enter to continue...")
-    # Perform the scan
-    scan_result = scans.line_scan(
-        motor_device, start, stop, steps=steps, relative=relative, settling_time=settle
-    )
-    motor_data = scan_result.scan.live_data[motor_name][motor_name].val
-    signal_data = scan_result.scan.live_data[signal_name][signal_name].val
-    scan_number = "Current"
-
-    data = {
-        "x_data": np.array(motor_data),
-        "y_data": np.array(signal_data),
-        "motor_name": motor_name,
-        "signal_name": signal_name,
-        "motor_device": motor_device,
-        "scan_number": scan_number,
-    }
-
-    # Define and fit model to scan data
-    fit_params = create_fit_parameters(False, FitDefaults.MODEL, FitDefaults.BASELINE)
-    fit_result = fit(data, fit_params)
-
-    # Plot the fitted data if plot = True
-    if plot:
-        plot_fitted_data_bec(data, fit_result)
-
-    # If gomax is set then move to the maximum value, rather than the fit centre
-    if gomax:
-        value = fit_result["x_max"]
-        print(f"Max position is at {value}")
-        move_to_position(data["motor_device"], data["motor_name"], fit_result["x_max"], data)
-    else:
-        # Safely move the motor to the peak position
-        move_to_position(data["motor_device"], data["motor_name"], fit_result["centre"], data)
-
-
-def fit_history(
-    history_index: int,
-    signal_name: str,
-    deriv: bool = False,
-    model: str = FitDefaults.MODEL,
-    move_to_peak: bool = False,
-):
-    """
-    Retrieve and analyze historical data by fitting a model, optionally moving to
-    a peak position.
-
-    Parameters:
-        history_index (int): Index of the historical data set to retrieve.
-        signal_name (str): Name of the signal to fit.
-        deriv (bool, optional): Whether to include the derivative in the fitting
-            procedure. Defaults to False.
-        model (str, optional): Name of the model to use for fitting. Defaults to
-            DEFAULT_MODEL.
-        move_to_peak (bool, optional): Whether to move the motor to the peak position
-            after fitting. Defaults to False.
-
-    Raises:
-        KeyError: If required keys are not found in the retrieved data dictionary.
-        ValueError: If the fitting process fails or produces invalid results.
-
-    Returns:
-        None
-    """
-    # Retrieve historical data
-    data = get_data_from_history(history_index, signal_name)
-
-    # Define fitting parameters
-    fit_params = create_fit_parameters(deriv, model, FitDefaults.BASELINE)
-
-    # Perform fit and plot the data
-    fit_result = fit(data, fit_params)
-    plot_fitted_data_bec(data, fit_result)
-
-    # Optionally move the motor to the peak position
-    if move_to_peak:
-        move_to_position(data["motor_device"], data["motor_name"], fit_result["centre"], data)
-
-
-def scan_bpm(bpmname):
-    """
-    Runs a grid scan of a BPM in x and y,  and plots each channel
-    as a heatmap.
-
-    Parameters:
-        bpmname: the name of the bpm to be scanned e.g. "fe"
-
-    """
-
-    # Open a dock area and set up the heatmaps
-    dock_area = bec.gui.new("XBPM_Scan")
-    wf5 = dock_area.new("Sum").new(bec.gui.available_widgets.Heatmap)
-    wf1 = dock_area.new("Ch1", relative_to="Sum", position="bottom").new(
-        bec.gui.available_widgets.Heatmap
-    )
-    wf3 = dock_area.new("Ch3", relative_to="Ch1", position="right").new(
-        bec.gui.available_widgets.Heatmap
-    )
-    wf4 = dock_area.new("Ch4", relative_to="Ch3", position="bottom").new(
-        bec.gui.available_widgets.Heatmap
-    )
-    wf2 = dock_area.new("Ch2", relative_to="Ch1", position="bottom").new(
-        bec.gui.available_widgets.Heatmap
-    )
-    wfscan = dock_area.new("ScanControl").new(bec.gui.available_widgets.ScanControl)
-
-    cfg = getattr(BPMScans, bpmname)
-
-    wf1.x_label = cfg["x_name"]
-    wf1.y_label = cfg["y_name"]
-    wf1.plot(x_name=cfg["x_name"], y_name=cfg["y_name"], z_name=cfg["z1_name"], color_map="plasma")
-
-    wf2.x_label = cfg["x_name"]
-    wf2.y_label = cfg["y_name"]
-    wf2.plot(x_name=cfg["x_name"], y_name=cfg["y_name"], z_name=cfg["z2_name"], color_map="plasma")
-
-    wf3.x_label = cfg["x_name"]
-    wf3.y_label = cfg["y_name"]
-    wf3.plot(x_name=cfg["x_name"], y_name=cfg["y_name"], z_name=cfg["z3_name"], color_map="plasma")
-
-    wf4.x_label = cfg["x_name"]
-    wf4.y_label = cfg["y_name"]
-    wf4.plot(x_name=cfg["x_name"], y_name=cfg["y_name"], z_name=cfg["z4_name"], color_map="plasma")
-
-    wf5.x_label = cfg["x_name"]
-    wf5.y_label = cfg["y_name"]
-    wf5.plot(x_name=cfg["x_name"], y_name=cfg["y_name"], z_name=cfg["z5_name"], color_map="plasma")
-    # Run the scan
-    x_mot = cfg["x_device"]
-    y_mot = cfg["y_device"]
-    # scans.grid_scan(x_mot, -0.5, 0.5, 20, y_mot, -0.5, 0.5, 20,
-    #                     exp_time=0.5, relative=False, snaked=True)
-
-
-def optimise_kb(mirror):
-    """
-    Runs a grid scan of a the upstream and downstream benders,
-    and plots a heatmap of the sample camera x or y sigma.
-
-    Parameters:
-        mirror: either "hfm" or :vfm"
-
-    """
-
-    # Open a dock area and set up the heatmaps
-    dock_area = bec.gui.new(mirror)
-    wf1 = dock_area.new("Heatmap").new(bec.gui.available_widgets.Heatmap)
-
-    wfscan = dock_area.new("ScanControl").new(bec.gui.available_widgets.ScanControl)
-
-    cfg = getattr(MirrorConfig, mirror)
-
-    wf1.x_label = cfg["bu_name"]
-    wf1.y_label = cfg["bd_name"]
-    wf1.plot(x_name=cfg["bu_name"], y_name=cfg["bd_name"], z_name=cfg["z_name"], color_map="plasma")
-
-    # Run the scan
-    x_mot = cfg["x_device"]
-    y_mot = cfg["y_device"]
-    # scans.grid_scan(x_mot, -0.02, 0.02, 11, y_mot, -0.02, 0.02, 11,
-    #                     exp_time=0.5, relative=True, snaked=True)

pxiii_bec/macros/pxiii_energy.py

@@ -1,251 +0,0 @@
-"""Script to change energy at PXIII by setting DCCM motors and mirror stripe
-
-Moving DCCM motors - implemented for dccm_theta1 and dccm_theta2
-Mirrors - change of mirror stripe is not yet implemented
-Plotting optional
-
-"""
-
-import pandas as pd
-import numpy as np
-# from mx_methods import go_to_peak
-# from pxiii_parameters import EnergyDefaults
-
-# from calculator import (
-#     validate_energy,
-#     convert_from_bragg,
-#     convert_from_energy,
-# )
-
-
-def get_current_energy():
-    """
-    Returns the energy in eV from the current bragg angle.
-    """
-    # current_bragg_angle = dev.dccm_theta1.user_readback.get()
-    current_bragg_angle = -EnergyDefaults.energy.user_readback.get()
-    current_energy = convert_from_bragg(current_bragg_angle, print_result=False)[
-        "energy_ev"
-    ]
-    return current_energy
-
-
-# Functions below are common to all beamlines
-def calculate_energy_difference(current_energy, target_energy):
-    """
-    Calculate the absolute difference in energy between the current energy level
-    and the target energy level.
-    """
-    return abs(target_energy - current_energy)
-
-
-def interpolate_column(energy_ev, x_values, y_values):
-    """
-    Perform interpolation for a specific column of data.
-
-    This function uses numpy's interpolation method to perform linear
-    interpolation. It calculates the interpolated y-values corresponding
-    to the given energy in electron-volts (energy_ev), based on specified
-    x-values and y-values.
-
-    Parameters:
-        energy_ev (array-like): Array of energy values in electron-volts
-            at which interpolation is needed.
-        x_values (array-like): Array of x-values corresponding to known
-            data points.
-        y_values (array-like): Array of y-values corresponding to known
-            data points.
-
-    Returns:
-        numpy.ndarray: Interpolated y-values computed for the energy_ev
-            input.
-    """
-    return np.interp(energy_ev, x_values, y_values)
-
-
-def get_value_from_lut(energy_ev):
-    """
-    Retrieve interpolated values from a Lookup Table (LUT) based on the provided energy
-    in electron volts (eV).
-
-    This function reads a CSV file containing energy lookup data and processes the LUT
-    to return interpolated values for specified relevant columns. The interpolation is
-    performed for the provided energy value using the LUT's energy and data values.
-
-    Args:
-        energy_ev (float): The energy value in electron volts for which the interpolated data is
-            required.
-
-    Returns:
-        dict: A dictionary where the keys are the relevant column names from the LUT, and the values
-            are the interpolated values as floats.
-    """
-
-    energy_lookup_data = pd.read_csv(EnergyDefaults.LUT_table)
-    column_names = energy_lookup_data.columns.tolist()
-    lut_values = energy_lookup_data.values.astype(float).T
-
-    # Filter relevant columns for interpolation
-    relevant_columns = {"dccm_pitch"}
-    int_values = {}
-
-    for i, col_name in enumerate(column_names):
-        if col_name in relevant_columns:
-            int_values[col_name] = float(
-                interpolate_column(energy_ev, lut_values[0], lut_values[i])
-            )
-    return int_values
-
-
-def get_mirror_stripe(energy_ev):
-    """
-    Determines the mirror stripe material based on the energy level provided.
-
-    This function evaluates the given energy level in electron volts (eV) and
-    identifies the material type that corresponds to the specified thresholds
-    for silicon, rhodium, and, if applicable, platinum.
-
-    Args:
-        energy_ev (float): Energy level in electron volts, used to determine
-            the corresponding material type.
-
-    Returns:
-        str: A string indicating the material type corresponding to the provided
-            energy level. Possible values are "silicon", "rhodium", or "platinum".
-    """
-    if energy_ev <= EnergyDefaults.stripe_thresholds["silicon"]:
-        return "silicon"
-    if (
-        EnergyDefaults.stripe_thresholds["silicon"]
-        < energy_ev
-        <= EnergyDefaults.stripe_thresholds["rhodium"]
-    ):
-        return "rhodium"
-    return "platinum"
-
-
-def set_mirror_stripe(energy_ev):
-    """
-    Selects and sets the appropriate mirror stripe based on the given energy value
-    in electron volts (eV). Prints the selected mirror stripe.
-
-    Args:
-        energy_ev (float): The energy value in electron volts used to determine
-                           the appropriate mirror stripe.
-
-    Returns:
-        None
-    """
-    selected_stripe = get_mirror_stripe(energy_ev)
-    print(f"Selected mirror stripe: {selected_stripe}")
-
-
-def mono_pitch_scan(plot=True):
-    """Scan the monochromator pitch and move to the peak."""
-
-    if plot:
-        print("Scanning monochromator pitch and moving to peak, with plotting.")
-        go_to_peak(
-            EnergyDefaults.mono_pitch,
-            EnergyDefaults.signals["sig1"],
-            -EnergyDefaults.pitch_scan["halfwidth"],
-            EnergyDefaults.pitch_scan["halfwidth"],
-            steps=EnergyDefaults.pitch_scan["steps"],
-            relative=True,
-            settle=0.01,
-            plot=True,
-            confirm=False,
-        )
-    else:
-        print("Scanning monochromator pitch and moving to peak, without plotting.")
-        go_to_peak(
-            EnergyDefaults.mono_pitch,
-            EnergyDefaults.signals["sig1"],
-            -EnergyDefaults.pitch_scan["halfwidth"],
-            EnergyDefaults.pitch_scan["halfwidth"],
-            steps=EnergyDefaults.pitch_scan["steps"],
-            relative=True,
-            settle=0.01,
-            plot=False,
-            confirm=False,
-        )
-
-
-
-def get_dccm_motors_positions(energy_ev):
-    """
-    Retrieve the positions of DCCM motors based on given energy value.
-    The function returns a dictionary containing all
-    calculated motor positions.
-
-    Arguments:
-        energy_ev (float): The energy value in electron volts for which the
-                           DCCM motor positions are to be calculated.
-
-    Returns:
-        dict: A dictionary containing the calculated DCCM motor positions
-              including values retrieved from the lookup table, if applicable.
-    """
-    # dccm_motor_values = get_value_from_lut(energy_ev)
-    th1_angle = -convert_from_energy(energy_ev, print_result=False)["bragg_angle_deg"]
-    th2_angle = convert_from_energy(energy_ev, temp=298, print_result=False)["bragg_angle_deg"]
-    # dccm_motor_values.update({"theta1_angle": th1_angle, "theta2_angle": th2_angle})
-    dccm_motor_values = {"theta1_angle": th1_angle, "theta2_angle": th2_angle}
-    return dccm_motor_values
-
-
-def move_dccm_motors(energy_ev):
-    """
-    Move the DCCM theta1 and theta2 motors to the required positions
-    for the given energy in eV.
-
-    """
-    dccm_pos = get_dccm_motors_positions(energy_ev)
-    print(
-        f"Moving DCCM theta1: {dccm_pos['theta1_angle']: .5g} deg, theta2: {dccm_pos['theta2_angle']: .5g} deg, "
-        # f"DCM pitch: {dcm_pos['dcm_pitch']: .5g} mrad, "
-    )
-    umv(EnergyDefaults.energy, dccm_pos["theta1_angle"], 
-    EnergyDefaults.mono_pitch, dccm_pos["theta2_angle"])
-
-
-
-def bl_energy(energy_ev, plot=True):
-    """
-    Adjusts the beamline's energy to the specified energy in electron volts (eV).
-    The function validates the target energy, checks the current energy, and makes
-    adjustments only if the energy difference is significant enough. It performs
-    necessary operations including changing DCCM motors, updating
-    the mirror stripe, and scanning to find the optimal DCCM pitch of 2nd crystal..
-
-    Args:
-        energy_ev: Target energy in electron volts to which the beamline should be adjusted.
-        plot: Boolean flag indicating whether to plot the DCCM pitch scan for finding the peak.
-
-    Returns:
-        None
-    """
-    energy_ev = validate_energy(energy_ev)  # Ensure energy is valid.
-
-    # Check current energy to avoid unnecessary adjustments.
-
-    current_energy = get_current_energy()
-    energy_diff = calculate_energy_difference(current_energy, energy_ev)
-
-    if energy_diff <= EnergyDefaults.min_energy_change:
-        print(
-            f"Energy change of {energy_diff:.2f} eV is too small, not changing energy."
-        )
-        return
-
-    # Step 1: Move and set the DCCM motors.
-    move_dccm_motors(energy_ev)
-
-    # Step 2: Update the mirror stripe.
-    set_mirror_stripe(energy_ev)
-
-    # Step 3: Perform DCCM pitch scan and move to peak.
-    if plot:
-        mono_pitch_scan(plot=True)
-    else:
-        mono_pitch_scan(plot=False)

pxiii_bec/macros/pxiii_parameters.py

@@ -1,80 +0,0 @@
-"""File to store beamline parameters and defaults"""
-
-from dataclasses import dataclass
-import numpy as np
-
-
-@dataclass(frozen=True)
-class FitDefaults:
-    """Default values for fitting routines"""
-
-    # Constants for default models, baselines, and parameters
-    MODEL = "Voigt"
-    BASELINE = "Linear"
-    SETTLE_TIME = 0.1
-    RELATIVE_MODE = True
-
-
-@dataclass(frozen=True)
-class EnergyDefaults:
-    """Parameters for PXIII energy changes"""
-
-    min_energy_change = 1
-    min_energy_ev = 4500
-    max_energy_ev = 15000
-    signals = {
-        "sig1": dev.dccm_di_top,
-        "sig2": dev.dccm_bpmsum,
-        "sig3": dev.ss_bpmsum,
-        # "sig4": dev.xbox_xbpm,
-    }
-    energy = dev.dccm_theta1
-    mono_pitch = dev.dccm_theta2
-    # LUT_table = "luts/energy_lut.csv"
-    stripe_thresholds = {"silicon": 9000, "rhodium": 40000}
-    pitch_scan = {"halfwidth": 0.15, "steps": 30}
-
-
-@dataclass(frozen=True)
-class CamConversion:
-    """Convert pixels to microns for sam cam"""
-
-    a = 0.5208
-    b = 0.002586
-
-
-@dataclass(frozen=True)
-class BPMScans:
-    """Define the names of the motors and bpm channels"""
-
-    ss = {
-        "x_name": dev.ss_bpm_x.name,
-        "y_name": dev.ss_bpm_y.name,
-        "z1_name": dev.ss_bpm1.name,
-        "z2_name": dev.ss_bpm2.name,
-        "z3_name": dev.ss_bpm3.name,
-        "z4_name": dev.ss_bpm3.name,
-        "z5_name": dev.ss_bpmsum.name,
-        "x_device": dev.ss_bpm_x,
-        "y_device": dev.ss_bpm_y,
-    }
-
-
-# @dataclass(frozen=True)
-# class MirrorConfig:
-#     """Define the names of the mirror channels"""
-
-#     hfm = {
-#         "bu_name": dev.hfm_bu.name,
-#         "bd_name": dev.hfm_bd.name,
-#         "z_name": dev.samcam_xsig.name,
-#         "x_device": dev.hfm_bu,
-#         "y_device": dev.hfm_bd,
-#     }
-#     vfm = {
-#         "bu_name": dev.vfm_bu.name,
-#         "bd_name": dev.vfm_bd.name,
-#         "z_name": dev.samcam_ysig.name,
-#         "x_device": dev.vfm_bu,
-#         "y_device": dev.vfm_bd,
-#     }

pxiii_bec/scans/__init__.py

@@ -1,8 +0,0 @@
-from .mx_measurements import (
-    MeasureStandardWedge,
-    MeasureVerticalLine,
-    MeasureRasterSimple,
-    MeasureScreening,
-    MeasureHelical,
-    MeasureHelical2,
-)

pxiii_bec/scans/metadata_schema/metadata_schema_registry.py

@@ -1,12 +0,0 @@
-# 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

pxiii_bec/scans/metadata_schema/metadata_schema_template.py

@@ -1,34 +0,0 @@
-# # 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.

pxiii_bec/scans/mx_measurements.py

@@ -1,473 +0,0 @@
-"""MX measurements module
-
-Scan primitives for standard BEC scans at the PX beamlines at SLS.
-Theese scans define the event model and can be called from higher levels.
-"""
-
-import time
-import numpy as np
-from bec_lib import bec_logger
-from bec_server.scan_server.scans import AsyncFlyScanBase
-
-logger = bec_logger.logger
-
-
-class AbrCmd:
-    """Valid Aerotech ABR scan commands from the AeroBasic files"""
-
-    NONE = 0
-    RASTER_SCAN_SIMPLE = 1
-    MEASURE_STANDARD = 2
-    VERTICAL_LINE_SCAN = 3
-    SCREENING = 4
-    # SUPER_FAST_OMEGA = 5            # Some Japanese measured samples in capilaries at high RPMs
-    # STILL_WEDGE = 6                 # NOTE: Unused    Step scan
-    # STILLS = 7                      # NOTE: Unused    Just send triggers to detector
-    # REPEAT_SINGLE_OSCILLATION = 8   # NOTE: Unused
-    # SINGLE_OSCILLATION = 9
-    # OLD_FASHIONED = 10              # NOTE: Unused
-    # RASTER_SCAN = 11
-    # JET_ROTATION = 12               # NOTE: Unused
-    # X_HELICAL = 13                  # NOTE: Unused
-    # X_RUNSEQ = 14                   # NOTE: Unused
-    # JUNGFRAU = 15
-    # MSOX = 16                       # NOTE: Unused
-    # SLIT_SCAN = 17                  # NOTE: Unused
-    # RASTER_SCAN_STILL = 18
-    # SCAN_SASTT = 19
-    # SCAN_SASTT_V2 = 20
-    # SCAN_SASTT_V3 = 21
-
-
-class AerotechFlyscanBase(AsyncFlyScanBase):
-    """Base class for MX flyscans
-
-    Low-level base class for standard scans at the PX beamlines at SLS. Theese
-    scans use the A3200 rotation stage and the actual experiment is performed
-    using an AeroBasic script controlled via global variables. The base class
-    has some basic safety features like checking status then sets globals and
-    fires off the scan. Implementations can choose to set the corresponding
-    configurations in child classes or pass it as command line parameters.
-
-    IMPORTANT: The AeroBasic scripts take care of the PSO configuration.
-
-    Parameters:
-    -----------
-    abr_complete : bool
-        Wait for the launched ABR task to complete.
-    """
-
-    scan_type = "fly"
-    scan_report_hint = "table"
-    arg_input = {}
-    arg_bundle_size = {"bundle": len(arg_input), "min": None, "max": None}
-
-    # Aerotech stage config
-    abr_raster_reset = False
-    abr_complete = False
-    abr_timeout = None
-    pointID = 0
-    num_pos = 0
-
-    def __init__(self, *args, parameter: dict = None, **kwargs):
-        """Just set num_pos=0 to avoid hanging and override defaults if explicitly set from
-        parameters.
-        """
-        super().__init__(parameter=parameter, **kwargs)
-        if "abr_raster_reset" in self.caller_kwargs:
-            self.abr_raster_reset = self.caller_kwargs.get("abr_raster_reset")
-        if "abr_complete" in self.caller_kwargs:
-            self.abr_complete = self.caller_kwargs.get("abr_complete")
-        if "abr_timeout" in self.caller_kwargs:
-            self.abr_timeout = self.caller_kwargs.get("abr_timeout")
-
-    def pre_scan(self):
-        """Mostly just checking if ABR stage is ok..."""
-        # TODO: Move roughly to start position???
-
-        # ABR status checking
-        stat = yield from self.stubs.send_rpc_and_wait("abr", "status.get")
-        if stat not in (0, "OK"):
-            raise RuntimeError("Aerotech ABR seems to be in error state {stat}, please reset")
-        task = yield from self.stubs.send_rpc_and_wait("abr", "task1.get")
-        # From what I got values are copied to local vars at the start of scan,
-        # so only kickoff should be forbidden.
-        if task not in (1, "OK"):
-            raise RuntimeError("Aerotech ABR task #1 seems to busy")
-
-        # Reset the raster scan engine
-        if self.abr_raster_reset:
-            yield from self.stubs.send_rpc_and_wait("abr", "raster_scan_done.set", 0)
-
-        # Call super
-        yield from super().pre_scan()
-
-    def scan_core(self):
-        """The actual scan logic comes here."""
-        # Kick off the run
-        yield from self.stubs.send_rpc_and_wait("abr", "bluekickoff")
-        logger.info("Measurement launched on the ABR stage...")
-
-        # Wait for grid scanner to finish
-        if self.abr_complete:
-            if self.abr_timeout is not None:
-                st = yield from self.stubs.send_rpc_and_wait("abr", "complete", self.abr_timeout)
-                st.wait()
-            else:
-                st = yield from self.stubs.send_rpc_and_wait("abr", "complete")
-                st.wait()
-
-    def cleanup(self):
-        """Set scan progress to 1 to finish the scan"""
-        self.num_pos = 1
-        return super().cleanup()
-
-
-class MeasureStandardWedge(AerotechFlyscanBase):
-    """Standard wedge scan using the OMEGA motor
-
-    Measure an absolute continous line scan from `start` to `start` + `range`
-    during `move_time` on the Omega axis with PSO output.
-
-    The scan itself is executed by the scan service running on the Aerotech
-    controller. Ophyd just configures, launches it and waits for completion.
-
-    Example
-    -------
-        >>> scans.standard_wedge(start=42, range=10, move_time=20)
-
-    Parameters
-    ----------
-    start : (float, float)
-        Scan start position of the axis.
-    range : (float, float)
-        Scan range of the axis.
-    move_time : (float)
-        Total travel time for the movement [s].
-    ready_rate : float, optional
-        No clue what is this... (default=500)
-    """
-
-    scan_name = "standardscan"
-    required_kwargs = ["start", "range", "move_time"]
-
-
-class MeasureVerticalLine(AerotechFlyscanBase):
-    """Vertical line scan using the GMY motor
-
-    Simple relative continous line scan that records a single vertical line
-    with PSO output. There's no actual stepping, it's only used for velocity
-    calculation.
-
-    The scan itself is executed by the scan service running on the Aerotech
-    controller. Ophyd just configures, launches it and waits for completion.
-
-    Example
-    -------
-        >>> scans.measure_vline(range_y=12, steps_y=40, exp_time=0.1)
-
-    Parameters
-    ----------
-    range : float
-        Step size [mm].
-    steps : int
-        Scan range of the axis.
-    exp_time : float
-        Eeffective exposure time per step [s]
-    """
-
-    scan_name = "vlinescan"
-    required_kwargs = ["exp_time", "range", "steps"]
-
-
-class MeasureRasterSimple(AerotechFlyscanBase):
-    """Simple raster scan
-
-    Measure a simplified relative zigzag raster scan in the X-Y plane.
-    The scan is relative assumes the goniometer is currently at the CENTER of
-    the first cell (i.e. TOP-LEFT). Each line is executed as a single continous
-    movement, i.e. there's no actual stepping in the X direction.
-
-    The scan itself is executed by the scan service running on the Aerotech
-    controller. Ophyd just configures, launches it and waits for completion.
-
-    Example
-    -------
-        >>> scans.raster_simple(exp_time=0.1, range_x=4, range_y=4, steps_x=80, steps_y=80)
-
-    Parameters
-    ----------
-    exp_time : float
-        Effective exposure time for each cell along the X axis [s].
-    range_x : float
-        Scan step size [mm].
-    range_y : float
-        Scan step size [mm].
-    steps_x : int
-        Number of scan steps in X (fast). Only used for velocity calculation.
-    steps_y : int
-        Number of scan steps in Y (slow).
-    """
-
-    scan_name = "rasterscan"
-    required_kwargs = ["exp_time", "range_x", "range_y", "steps_x", "steps_y"]
-
-
-class MeasureScreening(AerotechFlyscanBase):
-    """Sample screening scan
-
-    Sample screening scan that scans intervals on the rotation axis taking
-    1 image/interval. This makes sure that we hit diffraction peaks if there
-    are any crystals.
-
-    The scan itself is executed by the scan service running on the Aerotech
-    controller. Ophyd just configures, launches it and waits for completion.
-
-    Example
-    -------
-        >>> scans.measure_screening(start=42, range=180, steps=18, exp_time=0.1, oscrange=2.0)
-
-    Parameters
-    ----------
-        start : float
-            Absolute scan start position of the omega axis [deg].
-        range : float
-            Total screened range of the omega axis relative to 'start' [deg].
-        steps : int
-            Number of blurred intervals.
-        exp_time : float
-            Exposure time per blurred interval [s].
-        oscrange : float
-            Motion blurring of each interval [deg]
-        delta : float
-            Safety margin for sub-range movements (default: 0.5) [deg].
-    """
-
-    scan_name = "screeningscan"
-    required_kwargs = ["start", "range", "steps", "exp_time", "oscrange"]
-
-
-class MeasureHelical(AerotechFlyscanBase):
-    """Helical scan using the OMEGA motor
-
-    Measure an absolute continous line scan from `start` to `start` + `range`
-    during `move_time` on the Omega axis with PSO output.
-
-    The scan itself is executed by the scan service running on the Aerotech
-    controller. Ophyd just configures, launches it and waits for completion.
-
-    Example
-    -------
-        >>> scans.standard_wedge(start=42, range=10, move_time=20)
-
-    Parameters
-    ----------
-    start : float
-        Scan start position of the axis.
-    range : float
-        Scan range of the axis.
-    move_time : float
-        Total travel time for the movement [s].
-    ready_rate : float, optional
-        No clue what is this... (default=500)
-    sg_start : (float, float, float, float, float)
-        Complete SmarGon coordinate in tuple form.
-    sg_end : (float, float, float, float, float)
-        Complete SmarGon coordinate in tuple form.
-    sg_steps : int
-        Number of steps with SmarGon.
-    """
-
-    scan_name = "helicalscan"
-    required_kwargs = ["start", "range", "move_time", "sg_start", "sg_end", "sg_steps"]
-
-    def pre_scan(self):
-        """Mostly just checking if ABR stage is ok..."""
-
-        # Smargon has no velocity control
-        self.smargon_start = np.array(self.caller_kwargs.get("sg_start"))
-        self.smargon_end = np.array(self.caller_kwargs.get("sg_end"))
-        self.smargon_steps = self.caller_kwargs.get("sg_steps")
-        self.smargon_range = self.smargon_end - self.smargon_start
-        self.smargon_step_size = self.smargon_range / self.smargon_steps
-        self.smargon_step_time = self.caller_kwargs.get("move_time") / self.smargon_steps
-
-        logger.info(f"Start:\t{self.smargon_start}")
-        logger.info(f"End:\t{self.smargon_end}")
-        logger.info(f"Steps:\t{self.smargon_steps}")
-        logger.info(f"Range:\t{self.smargon_range}")
-        logger.info(f"StepSize:\t{self.smargon_step_size}")
-        logger.info(f"StepTime:\t{self.smargon_step_time}")
-
-        # TODO: Move roughly to start position???
-        st0 = yield from self.stubs.send_rpc("shx", "omove", self.smargon_start[0])
-        st1 = yield from self.stubs.send_rpc("shy", "omove", self.smargon_start[1])
-        st2 = yield from self.stubs.send_rpc("shz", "omove", self.smargon_start[2])
-        st3 = yield from self.stubs.send_rpc("chi", "omove", self.smargon_start[3])
-        st4 = yield from self.stubs.send_rpc("phi", "omove", self.smargon_start[4])
-        st0.wait()
-        st1.wait()
-        st2.wait()
-        st3.wait()
-        st4.wait()
-
-        # Call super
-        yield from super().pre_scan()
-
-    def scan_core(self):
-        """The actual scan logic comes here."""
-        # Kick off the run
-        yield from self.stubs.send_rpc_and_wait("abr", "kickoff")
-        logger.info("Measurement launched on the ABR stage...")
-
-        logger.info("Performing SmarGon stepping...")
-        for ss in range(self.smargon_steps):
-            sg_pos = self.smargon_start + ss * self.smargon_step_size
-            # Move to position but don't care
-            st0 = yield from self.stubs.send_rpc("shx", "omove", sg_pos[0])
-            st1 = yield from self.stubs.send_rpc("shy", "omove", sg_pos[1])
-            st2 = yield from self.stubs.send_rpc("shz", "omove", sg_pos[2])
-            st3 = yield from self.stubs.send_rpc("chi", "omove", sg_pos[3])
-            st4 = yield from self.stubs.send_rpc("phi", "omove", sg_pos[4])
-            t_start = time.time()
-            st0.wait()
-            st1.wait()
-            st2.wait()
-            st3.wait()
-            st4.wait()
-            t_end = time.time()
-            t_elapsed = t_end - t_start
-            time.sleep(max(self.smargon_step_time - t_elapsed, 0))
-
-        # Wait for scan task to finish
-        if self.abr_complete:
-            if self.abr_timeout is not None:
-                st = yield from self.stubs.send_rpc_and_wait("abr", "complete", self.abr_timeout)
-                st.wait()
-            else:
-                st = yield from self.stubs.send_rpc_and_wait("abr", "complete")
-                st.wait()
-
-
-class MeasureHelical2(AerotechFlyscanBase):
-    """Helical scan using the OMEGA motor
-
-    Measure an absolute continous line scan from `start` to `start` + `range`
-    during `move_time` on the Omega axis with PSO output.
-
-    The scan itself is executed by the scan service running on the Aerotech
-    controller. Ophyd just configures, launches it and waits for completion.
-
-    Example
-    -------
-        >>> scans.standard_wedge(start=42, range=10, move_time=20)
-
-    Parameters
-    ----------
-    start : float
-        Scan start position of the axis.
-    range : float
-        Scan range of the axis.
-    move_time : float
-        Total travel time for the movement [s].
-    ready_rate : float, optional
-        No clue what is this... (default=500)
-    sg_start : (float, float, float, float, float)
-        Complete SmarGon coordinate in tuple form.
-    sg_end : (float, float, float, float, float)
-        Complete SmarGon coordinate in tuple form.
-    sg_steps : int
-        Number of steps with SmarGon.
-    """
-
-    scan_name = "helicalscan2"
-    required_kwargs = ["start", "range", "move_time", "sg_start", "sg_end", "sg_steps"]
-    point_id = 0
-
-    # def __init__(self, *args, parameter: dict = None, **kwargs):
-    #     """Just set num_pos=0 to avoid hanging and override defaults if explicitly set from
-    #     parameters.
-    #     """
-    #     self.num_pos = kwargs["sg_steps"]
-    #     super().__init__(*args, parameter=parameter, **kwargs)
-
-    def prepare_positions(self):
-        # Smargon has no velocity control
-        self.smargon_start = np.array(self.caller_kwargs.get("sg_start"))
-        self.smargon_end = np.array(self.caller_kwargs.get("sg_end"))
-        self.smargon_steps = self.caller_kwargs.get("sg_steps")
-        self.smargon_range = self.smargon_end - self.smargon_start
-        self.smargon_step_size = self.smargon_range / self.smargon_steps
-        self.smargon_step_time = self.caller_kwargs.get("move_time") / self.smargon_steps
-
-        logger.info(f"Start:\t{self.smargon_start}")
-        logger.info(f"End:\t{self.smargon_end}")
-        logger.info(f"Steps:\t{self.smargon_steps}")
-        logger.info(f"Range:\t{self.smargon_range}")
-        logger.info(f"StepSize:\t{self.smargon_step_size}")
-        logger.info(f"StepTime:\t{self.smargon_step_time}")
-
-        self.num_pos = self.smargon_steps
-        self.positions = np.linspace(self.smargon_start, self.smargon_end, self.smargon_steps)
-        self.start_pos = self.positions[0, :]
-        # Call super
-        yield from super().prepare_positions()
-
-    # def update_scan_motors(self):
-    #     """ Update step scan motors"""
-    #     self.scan_motors = ['shx', 'shy', 'shz', 'chi', 'phi']
-
-    def pre_scan(self):
-        """Mostly just checking if ABR stage is ok..."""
-        # Move roughly to start position
-        st0 = yield from self.stubs.send_rpc("shx", "omove", self.start_pos[0])
-        st1 = yield from self.stubs.send_rpc("shy", "omove", self.start_pos[1])
-        st2 = yield from self.stubs.send_rpc("shz", "omove", self.start_pos[2])
-        st3 = yield from self.stubs.send_rpc("chi", "omove", self.start_pos[3])
-        st4 = yield from self.stubs.send_rpc("phi", "omove", self.start_pos[4])
-        st0.wait()
-        st1.wait()
-        st2.wait()
-        st3.wait()
-        st4.wait()
-
-        # print(f"\n\n{self.readout_priority}\n\n")
-
-        # Call super
-        yield from super().pre_scan()
-
-    def scan_core(self):
-        """The actual scan logic comes here."""
-        # Kick off the run
-        yield from self.stubs.send_rpc_and_wait("abr", "kickoff")
-        logger.info("Measurement launched on the ABR stage...")
-
-        logger.info("Performing SmarGon stepping...")
-        for _, sg_pos in enumerate(self.positions):
-            # sg_pos = self.smargon_start + ss * self.smargon_step_size
-            # Move to position but don't care
-            st0 = yield from self.stubs.send_rpc("shx", "omove", sg_pos[0])
-            st1 = yield from self.stubs.send_rpc("shy", "omove", sg_pos[1])
-            st2 = yield from self.stubs.send_rpc("shz", "omove", sg_pos[2])
-            st3 = yield from self.stubs.send_rpc("chi", "omove", sg_pos[3])
-            st4 = yield from self.stubs.send_rpc("phi", "omove", sg_pos[4])
-            t_start = time.time()
-            st0.wait()
-            st1.wait()
-            st2.wait()
-            st3.wait()
-            st4.wait()
-            t_end = time.time()
-            t_elapsed = t_end - t_start
-            time.sleep(max(self.smargon_step_time - t_elapsed, 0))
-            yield from self.stubs.read(group="monitored", point_id=self.point_id)
-            self.point_id += 1
-
-        # Wait for scan task to finish
-        if self.abr_complete:
-            if self.abr_timeout is not None:
-                st = yield from self.stubs.send_rpc_and_wait("abr", "complete", self.abr_timeout)
-                st.wait()
-            else:
-                st = yield from self.stubs.send_rpc_and_wait("abr", "complete")
-                st.wait()

pxiii_bec/scans/scan_customization/scan_components.py

@@ -1,12 +0,0 @@
-"""
-Scan components for pxiii_bec.
-
-The scan components module allows you to define custom components that can be used in your scans.
-These components can be used to encapsulate reusable logic, interact with devices, or perform specific actions during the scan lifecycle.
-"""
-
-from bec_server.scan_server.scans.scan_components import ScanComponents
-
-
-class PxiiiBecScanComponents(ScanComponents):
-    """Scan components for pxiii_bec."""

pxiii_bec/scans/scan_customization/scan_modifier.py

@@ -1,33 +0,0 @@
-"""
-Scan modifier plugin for pxiii_bec.
-
-The scan modifier allows you to modify the scan lifecycle and run custom actions before or after the scan hook or replace the scan hook entirely.
-Note that the scan_modifier module must be registered as a plugin in the pyproject.toml file for it to be recognized by the BEC framework and that
-there can only be one scan_modifier plugin registered at a time. If you need to run multiple scan modifiers, you can create a single scan
-modifier plugin that runs multiple actions in sequence with conditional logic to determine which actions to run based on the scan context.
-"""
-
-from bec_server.scan_server.scans.scan_modifier import ScanModifier, scan_hook_impl
-
-
-class PxiiiBecScanModifier(ScanModifier):
-    """
-    Scan modifier for pxiii_bec.
-    
-    By inheriting from the ScanModifier base class, you get access to currently running scan (self.scan), the devices (self.dev), the scan info (self.scan_info),
-    the scan components (self.components) and the scan actions (self.actions).
-    """
-
-    def __init__(self, **kwargs):
-        """Initialize the scan modifier."""
-        super().__init__(**kwargs)
-
-    # Example of running code before the scan stage for a specific scan
-    # @scan_hook_impl("stage", "before")
-    # def before_stage(self):
-    #     """Run before the stage hook."""
-    #     self.actions.send_client_info("Custom stage logic executed by ScanModifier.")
-    #     if self.scan_info.scan_name == "example_scan":
-    #         self.dev.samx.set(20)
-
-    

pxiii_bec/scripts/alignment_fit.py

@@ -1,50 +0,0 @@
-import numpy as np
-from scipy.ndimage import gaussian_filter1d
-from lmfit.models import GaussianModel
-
-
-def alignment_fit_and_plot(
-    history_index: int,
-    device_name: str,
-    signal_name: str | None = None,
-    smoothing_sigma: float = 2.0,
-):
-    """
-    Get data for a completed scan from the BEC history, apply smoothing, gaussian fit,
-    gradient, and plot all the results.
-
-    Args:
-        history_index (int): scan to fetch, e.g. -1 for the most recent scan
-        device_name (str): the device for which to get the monitoring data
-        signal_name (str | None): the signal to plot, if different from the device name.
-        smoothing_sigma (float): the sigma for the Gaussian smoothing filter
-    """
-    # Fetch scan data from the history
-    # by default, signal = device name, unless otherwise specified
-    signal = signal_name or device_name
-    scan = bec.history[history_index]
-    md = scan.metadata["bec"]
-    data = scan.devices[device_name][signal].read()["value"]
-    # motor name is a bytes object in the metadata, so make a string
-    motor_name = md["scan_motors"][0].decode()
-
-    # Create a plot and a text box to display results
-    dock_area = bec.gui.new()
-    wf = dock_area.new(bec.gui.available_widgets.Waveform)
-    wf.title = f"Scan {md['scan_number']}: {md['scan_name']} of {motor_name}"
-    text = dock_area.new(bec.gui.available_widgets.TextBox, where="right")
-
-    # Calculate some processed data and add everything to the plot
-    wf.plot(data, label="Raw data")
-    smoothed_data = gaussian_filter1d(data, smoothing_sigma)
-    wf.plot(smoothed_data, label="Smoothed")
-    gradient = np.gradient(smoothed_data)
-    wf.plot(gradient, label="gradient")
-
-    # Fit a Gaussian model to the smoothed data and show the fitting parameters in the textbox
-    x_data = scan.devices[motor_name][motor_name].read()["value"]
-    model = GaussianModel()
-    result = model.fit(smoothed_data, x=x_data)
-    text.set_plain_text(f"Fit parameters: \n{result.params.pretty_repr()}")
-
-    return result

pxiii_bec/scripts/beamlinescripts.py

@@ -1,85 +0,0 @@
-# pylint: disable=undefined-variable
-# import bec
-# import bec_lib.devicemanager.DeviceContainer as dev
-
-import time
-
-
-def _device_name(device):
-    return device.name if hasattr(device, "name") else str(device)
-
-
-def _get_or_create_scan_window(name="CurrentScan"):
-    window = bec.gui.windows.get(name)
-    if window is None:
-        return bec.gui.new(name)
-    window.delete_all()
-    return window
-
-
-def rock(steps, exp_time, scan_start=None, scan_end=None, datasource=None, visual=True, **kwargs):
-    """Demo step scan with plotting
-
-    This is a simple user-space demo step scan with the BEC. It be a
-    standard BEC scan, while still setting up the environment.
-
-    Example:
-    --------
-    ascan(dev.dccm_energy, 12,13, steps=21, exp_time=0.1, datasource=dev.dccm_xbpm)
-    """
-    # Dummy method to check beamline status
-    if not bl_check_beam():
-        raise RuntimeError("Beamline is not in ready state")
-
-    motor = dev.dccm_theta2
-    if scan_start is None:
-        scan_start = -0.05 / dev.dccm_energy.user_readback.get()
-    if scan_end is None:
-        scan_end = 0.05 / dev.dccm_energy.user_readback.get()
-
-    if visual:
-        # Get or create scan specific window.
-        window = _get_or_create_scan_window("CurrentScan")
-        motor_name = _device_name(motor)
-        datasource_name = _device_name(datasource)
-
-        # Draw a waveform plot in the window.
-        plt1 = window.new(
-            bec.gui.available_widgets.Waveform, object_name=f"ScanDisplay_{motor_name}"
-        )
-        plt1.plot(device_x=motor_name, device_y=datasource_name, dap="LinearModel")
-        plt1.x_label = motor_name
-        plt1.y_label = datasource_name
-        window.show()
-
-    print("Handing over to 'scans.line_scan'")
-    s = scans.line_scan(
-        motor,
-        scan_start,
-        scan_end,
-        steps=steps,
-        exp_time=exp_time,
-        datasource=datasource,
-        relative=True,
-        **kwargs,
-    )
-
-    if visual:
-        # If fitting via GUI
-        firt_par = plt1.get_dap_params()
-    else:
-        # Without GUI
-        firt_par = bec.dap.LinearModel.fit(
-            s, motor.name, motor.name, datasource.name, datasource.name
-        )
-
-    # TODO: Validate fitted position
-    # TODO: Move to fitted maximum
-
-    return s, firt_par
-
-
-def monitor(device, steps, t=1):
-    for _ in range(steps):
-        print(device.read())
-        time.sleep(t)

pxiii_bec/scripts/kat.py

@@ -1,29 +0,0 @@
-def scan_theta2(scan_start, scan_end, stepno, exp):
-    # Save the motor starting position
-    start_value = dev.dccm_theta2.read()['dccm_theta2']['value']
-    print(f"Motor position is {start_value}")
-
-    # Run the scan
-    s = scans.line_scan(dev.dccm_theta2, scan_start, scan_end, steps=stepno, exp_time=exp, relative=True)
-
-   # data = s.devices[dccm_xbpm][dccm_xbpm].read()["value"]
-
-    # Move motor back to starting position and print XBPM reading
-    umv(dev.dccm_theta2, start_value)
-    xbpm_reading = dev.dccm_xbpm.read()['dccm_xbpm']['value']
-    print(f"Moving dccm_theta2 back to start position of where XBPM Reading is {xbpm_reading}")
-    end_value = dev.dccm_theta2.read()['dccm_theta2']['value']
-    print(f"Motor was at {start_value} before the scan, now at {end_value}")
-
-    # # Create a plot to display the results
-    dock_area = bec.gui.new()
-    wf = dock_area.new(bec.gui.available_widgets.Waveform)
-    wf.title = f"Scan of DCCM_theta2"
-    wf.plot(device_x="dccm_theta2", device_y="dccm_xbpm", label="dccm_xbpm-dccm_xbpm")
-    dap_xbpm = wf.add_dap_curve(device_label="dccm_xbpm-dccm_xbpm", dap_name="GaussianModel")
-    print(dap_xbpm.dap_params)
-
-
-
-
-

pxiii_bec/scripts/scanwrappers.py

@@ -1,77 +0,0 @@
-# pylint: disable=undefined-variable
-
-
-def bl_check_beam():
-    """Check beamline status before scan"""
-    return True
-
-
-def _device_name(device):
-    return device.name if hasattr(device, "name") else str(device)
-
-
-def _get_or_create_scan_window(name="CurrentScan"):
-    window = bec.gui.windows.get(name)
-    if window is None:
-        return bec.gui.new(name)
-    window.delete_all()
-    return window
-
-
-def ascan(
-    motor, scan_start, scan_end, steps, exp_time, plot=None, visual=True, relative=False, **kwargs
-):
-    """Demo step scan with plotting
-
-    This is a simple user-space demo step scan with the BEC. It be a
-    standard BEC scan, while still setting up the environment.
-
-    Example:
-    --------
-    ascan(dev.dccm_energy, 12,13, steps=21, exp_time=0.1, datasource=dev.dccm_xbpm)
-    """
-    # Dummy method to check beamline status
-    if not bl_check_beam():
-        raise RuntimeError("Beamline is not in ready state")
-
-    if visual:
-        # Get or create scan specific window.
-        window = _get_or_create_scan_window("CurrentScan")
-        motor_name = _device_name(motor)
-        plot_name = _device_name(plot)
-
-        # Draw a waveform plot in the window.
-        plt1 = window.new(
-            bec.gui.available_widgets.Waveform, object_name=f"ScanDisplay_{motor_name}"
-        )
-        plt1.plot(device_x=motor_name, device_y=plot_name, dap="LinearModel")
-        plt1.x_label = motor_name
-        plt1.y_label = plot_name
-        window.show()
-
-    print("Handing over to 'scans.line_scan'")
-    s = scans.line_scan(
-        motor,
-        scan_start,
-        scan_end,
-        steps=steps,
-        exp_time=exp_time,
-        plot=plot,
-        relative=relative,
-        **kwargs,
-    )
-
-    if visual:
-        # Fitting via GUI
-        firt_par = plt1.get_dap_params()
-    else:
-        # Fitting without GUI
-        firt_par = bec.dap.LinearModel.fit(s, motor.name, motor.name, plot.name, plot.name)
-
-    # # Some basic fit
-    # dkey = datasource.full_name
-    # NOTE: s.scan.data == bec.history[-1]
-    # datapoints = bec.history[-1].devices[dkey].read()[dkey]['value']
-    # positions
-
-    return s, firt_par

pyproject.toml

@@ -1,93 +0,0 @@
-[build-system]
-requires = ["hatchling"]
-build-backend = "hatchling.build"
-
-[project]
-name = "pxiii_bec"
-version = "0.0.0"
-description = "A plugin repository for BEC"
-requires-python = ">=3.11"
-classifiers = [
-    "Development Status :: 3 - Alpha",
-    "Programming Language :: Python :: 3",
-    "Topic :: Scientific/Engineering",
-]
-dependencies = [
-    "bec_ipython_client",
-    "bec_lib",
-    "bec_server",
-    "bec_widgets",
-    "ophyd_devices",
-    "std_daq_client",
-    "rich",
-    "pyepics",
-    "pandas~=2.0",
-    "matplotlib",
-    "zmq",
-]
-
-[project.optional-dependencies]
-dev = [
-    "black",
-    "copier",
-    "isort",
-    "coverage",
-    "pylint",
-    "pytest",
-    "pytest-random-order",
-    "ophyd_devices",
-    "bec_server",
-]
-
-[project.entry-points."bec"]
-plugin_bec = "pxiii_bec"
-
-[project.entry-points."bec.deployment.device_server"]
-plugin_ds_startup = "pxiii_bec.deployments.device_server.startup:run"
-
-[project.entry-points."bec.file_writer"]
-plugin_file_writer = "pxiii_bec.file_writer"
-
-[project.entry-points."bec.scans"]
-plugin_scans = "pxiii_bec.scans"
-
-[project.entry-points."bec.scans.scan_modifier"]
-plugin_scan_modifier = "pxiii_bec.scans.scan_customization.scan_modifier"
-
-[project.entry-points."bec.scans.metadata_schema"]
-plugin_metadata_schema = "pxiii_bec.scans.metadata_schema"
-
-[project.entry-points."bec.ipython_client_startup"]
-plugin_ipython_client_pre = "pxiii_bec.bec_ipython_client.startup.pre_startup"
-plugin_ipython_client_post = "pxiii_bec.bec_ipython_client.startup"
-
-[project.entry-points."bec.widgets.auto_updates"]
-plugin_widgets_update = "pxiii_bec.bec_widgets.auto_updates"
-
-[project.entry-points."bec.widgets.user_widgets"]
-plugin_widgets = "pxiii_bec.bec_widgets.widgets"
-
-[tool.hatch.build.targets.wheel]
-include = ["*"]
-
-[tool.isort]
-profile = "black"
-line_length = 100
-multi_line_output = 3
-include_trailing_comma = true
-
-[tool.black]
-line-length = 100
-skip-magic-trailing-comma = true
-
-[tool.pylint.basic]
-# Good variable names regexes, separated by a comma. If names match any regex,
-# they will always be accepted
-good-names-rgxs = [
-    ".*scanID.*",
-    ".*RID.*",
-    ".*pointID.*",
-    ".*ID.*",
-    ".*_2D.*",
-    ".*_1D.*",
-]

setup.cfg

@@ -0,0 +1,21 @@
+[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 = .

setup.py

@@ -0,0 +1,7 @@
+from setuptools import setup
+
+if __name__ == "__main__":
+    setup(
+        install_requires=[],
+        extras_require={"dev": ["pytest", "pytest-random-order", "coverage"]},
+    )

tests/tests_bec_ipython_client/README.md

@@ -1,34 +0,0 @@
-# Getting Started with Testing using pytest
-
-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_.
-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
-
-```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.
-
-## Test examples
-
-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).

tests/tests_bec_widgets/README.md

@@ -1,34 +0,0 @@
-# Getting Started with Testing using pytest
-
-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_.
-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
-
-```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.
-
-## Test examples
-
-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).

tests/tests_dap_services/README.md

@@ -1,34 +0,0 @@
-# Getting Started with Testing using pytest
-
-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_.
-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
-
-```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.
-
-## Test examples
-
-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).

tests/tests_devices/README.md

@@ -1,34 +0,0 @@
-# Getting Started with Testing using pytest
-
-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_.
-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
-
-```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.
-
-## Test examples
-
-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).

tests/tests_file_writer/README.md

@@ -1,34 +0,0 @@
-# Getting Started with Testing using pytest
-
-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_.
-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
-
-```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.
-
-## Test examples
-
-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).

tests/tests_scans/README.md

@@ -1,34 +0,0 @@
-# Getting Started with Testing using pytest
-
-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_.
-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
-
-```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.
-
-## Test examples
-
-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).