refactor: converted to new plugin structure

.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: v1.2.2
-_src_path: https://github.com/bec-project/plugin_copier_template.git
-make_commit: false
-project_name: csaxs_bec
-widget_plugins_input: []

.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 +1,2 @@
-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')
+black --line-length=100 $(git diff --cached --name-only --diff-filter=ACM)
+git add $(git diff --cached --name-only --diff-filter=ACM)

.gitea/workflows/ci.yml

@@ -1,85 +0,0 @@
-name: CI for csaxs_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: "3.11"
-
-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: "${{ inputs.PYTHON_VERSION || '3.11' }}"
-
-      - name: Checkout BEC Core
-        run: git clone --depth 1 --branch "${{ inputs.BEC_CORE_BRANCH || 'main' }}" https://github.com/bec-project/bec.git ./bec
-
-      - name: Checkout Ophyd Devices
-        run: git clone --depth 1 --branch "${{ inputs.OPHYD_DEVICES_BRANCH || 'main' }}" https://github.com/bec-project/ophyd_devices.git ./ophyd_devices
-
-      - name: Checkout BEC Widgets
-        run: git clone --depth 1 --branch "${{ inputs.BEC_WIDGETS_BRANCH || 'main' }}" https://github.com/bec-project/bec_widgets.git ./bec_widgets
-
-      - name: Checkout BEC Plugin Repository
-        uses: actions/checkout@v4
-        with:
-          repository: bec/csaxs_bec
-          ref: "${{ inputs.BEC_PLUGIN_REPO_BRANCH || github.head_ref || github.sha }}"
-          path: ./csaxs_bec
-
-      - 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 ./csaxs_bec
-
-      - name: Run Pytest with Coverage
-        id: coverage
-        run: pytest --random-order --cov=./csaxs_bec --cov-config=./csaxs_bec/pyproject.toml --cov-branch --cov-report=xml --no-cov-on-fail ./csaxs_bec/tests/ || test $? -eq 5

.gitignore

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

.gitlab-ci.yml

@@ -1,20 +0,0 @@
-include:
-  - project: bec/awi_utils
-    file: /templates/plugin-repo-template.yml
-    inputs:
-      name: "csaxs"
-      target: "csaxs_bec"
-      branch: $CHILD_PIPELINE_BRANCH
-
-pages:
-  stage: Deploy
-  needs: []
-  variables:
-    TARGET_BRANCH: $CI_COMMIT_REF_NAME
-  rules:
-    - if: "$CI_COMMIT_TAG != null"
-      variables:
-        TARGET_BRANCH: $CI_COMMIT_TAG
-    - if: '$CI_COMMIT_REF_NAME == "main" && $CI_PROJECT_PATH == "bec/csaxs_bec"'
-  script:
-    - curl -X POST -d "branches=$CI_COMMIT_REF_NAME" -d "token=$RTD_TOKEN" https://readthedocs.org/api/v2/webhook/sls-csaxs/270162/

.readthedocs.yaml

@@ -1,29 +0,0 @@
-# .readthedocs.yaml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-version: 2
-
-# Set the version of Python and other tools you might need
-build:
-  os: ubuntu-20.04
-  tools:
-    python: "3.10"
-  jobs:
-    pre_install:
-      - pip install .
-
-
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-   configuration: docs/conf.py
-
-# If using Sphinx, optionally build your docs in additional formats such as PDF
-# formats:
-#    - pdf
-
-# Optionally declare the Python requirements required to build your docs
-python:
-   install:
-   - requirements: docs/requirements.txt
-

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.

README.md

@@ -6,12 +6,15 @@ You might want to run cSAXS copy scripts before in case you want to have the for
 
 ## Overview
 
-- Clone cSAXS BEC repository into e-account (e.g. into ~/Data10/software/.)
-- Start Epics iocs 
-- Start BEC, BEC server and load/modify the device config with relevant hardware
-- BEC commands
+1. Clone cSAXS BEC repository into e-account (e.g. into ~/Data10/software/.)
+2. Install BEC
+3. Start Epics iocs 
+4. Start BEC, BEC server and load/modify the device config with relevant hardware
+5. BEC commands
+6. Start BEC widgets (GUI for motor control, eiger live plot)
+7. Troubleshooting and common problems
 
-## Clone cSAXS BEC repository
+## 1. Clone cSAXS BEC repository
 
 Clone the current cSAXS BEC repository from GIT into the new e-account.
 Create directory
@@ -21,9 +24,19 @@ cd ~/Data10/software
 ```
 Clone repository
 ```bash
-git clone https://gitlab.psi.ch/bec/csaxs_bec.git
+git clone https://gitlab.psi.ch/bec/csaxs-bec.git
 ```
-## Start epics iocs
+
+## 2. Install BEC
+
+There is a bash sript in the followin directory. 
+Go to the directory and run the script on pc15543 logged in as the e-account (BEC server):
+```bash
+ssh pc15543
+cd ~/Data10/software/csaxs-bec/bin/
+./setup_bec.sh
+```
+## 3. Start epics iocs
 
 You can start up the iocs while the *./setup_bec.sh* script is running. Be aware though that the scripts requires you to interact with it.
 
@@ -81,7 +94,7 @@ iocsh -7.0.6 startup.script
 ```
 Be aware -7.0.6 is referring to the current epics version and might change in future (SLS 2.0)
 
-## Start BEC, BEC server and load device config
+## 4. Start BEC, BEC server and load device config
 
 Step 1 needs to have finished for continuing with these steps. 
 What remains now is to start the bec server. Connect to pc15543 and open a new terminal to run:
@@ -114,7 +127,7 @@ bec.config.save_current_session('~/Data10/software/current_config.yaml')
 ```
 The second command is helpful if you adjust limits of motors, which will then be stored in the config and loaded if a reload of the configuration is needed.
 
-## BEC commands
+## 5. BEC commands
 
 A number of commands that are useful:
 
@@ -134,3 +147,41 @@ scans.line_scan(dev.samx, -1, 1, dev.samy, -1, 1, steps=20, exp_time=0.5, readou
 scans.sgalil_grid(start_y = , end_y = , interval_y = , start_x=, end_x=, interval_x =, exp_time=0.5, readout_time=3e-3, relative=True)
 ```
 
+## 6. Start BEC widgets (GUI for motor control, eiger live plot)
+
+To start the BEC widgets, the first step is to make the bec_widgets_venv using the start startup script. 
+Follow the commands below:
+``` bash
+cd ~/Data10/software/csaxs-bec/bin
+./setup_bec_widgets.sh
+```
+Afterwards, activate the environment on either cons-01 comp-1/2
+``` bash
+cd ~/Data10/software/
+source activate bec_widgets_venv/bin/activate
+```
+Each Plot needs their own shell with activate environment
+
+1. Eiger Plot
+``` bash
+cd ~/Data10/software/bec-widgets/bec_widgets/examples/eiger_plot
+python eiger_plot.py
+```
+2. Motor Controller
+``` bash
+cd ~/Data10/software/bec-widgets/bec_widgets/examples/motor_movement
+python motor_example.py --config csaxs_config.yaml
+```
+
+## 7. Troubleshooting and common problems
+
+Sometimes the data backend for the Eiger gets stuck or misses frames, this will result in an error
+``` python
+raise EigerTimeoutError(
+ophyd_devices.epics.devices.eiger9m_csaxs.EigerTimeoutError: Reached timeout with detector state 1, std_daq state FINISHED and received frames of 100 for the file writer)
+```
+This happens more likely after CTRL C of a scan. To recover from this more reliably, perform the an acquisition in burst mode with 100 frames, little exposure until no error message is raised after. This can be up to 3 times from former experience.
+``` bash
+scans.acquire(exp_time=0.02, frames_per_trigger=100, readout_time= 3e-3)
+```
+Afterwards, you should be good to continue with 2D gridscans.

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/high_level_interface/spec_hli.py

@@ -0,0 +1,245 @@
+from bec_lib.devicemanager import Device
+from bec_lib.scan_report import ScanReport
+
+# 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/plugins/LamNI/__init__.py

@@ -0,0 +1,2 @@
+from .load_additional_correction import lamni_read_additional_correction
+from .x_ray_eye_align import LamNI, XrayEyeAlign, MagLamNI, DataDrivenLamNI

bec_plugins/bec_client/plugins/LamNI/bl_show_all.mac

@@ -0,0 +1,269 @@
+def bl_show_all '{
+  local gap
+
+  printf("beamline status at %s:\n",date())
+
+  if (!_bl_hall_temperature_ok()) {
+    bl_hall_temperature
+    printf("\n")
+  }
+
+  if (_bl_sls_status_unusual()) {
+    bl_sls_status
+  } else {
+    bl_ring_current
+  }
+  bl_chk_beam _show
+  printf("\n")
+
+  printf("U19 ID gap                         : ",gap)
+  gap = _id_get_gap_mm()
+  if (gap >= 8) {
+    text_bf
+  }
+  printf("%.3f mm\n",gap)
+  text_non_bf
+
+  if (!_id_loss_rate_ok()) {
+    id_loss_rate
+  }
+
+  bl_shutter_status
+
+  if (_bl_cvd_filter_open()) {
+    text_bf
+    printf("CVD diamond filter                 : open / out\n")
+    text_non_bf
+  }
+
+  if (!_bl_xbox_valve_es1_open()) {
+    bl_xbox_valve_es1 _show
+  }
+
+  if (_bl_ln2_non_standard()) {
+    text_bf
+    printf("\nNon standard liquid nitrogen cooling-warning parameters occur. Please report this to your local contact.\n")
+    text_non_bf
+    printf("The macro bl_ln2_warn can be used to control this e-mail warning feature.\n")
+    bl_ln2_warn "show"
+    printf("\n")
+  }
+
+  printf("\n")
+  bl_flight_tube_pressure
+  printf("\n")
+
+  bl_attended _show
+
+  _bl_check_alarm_records(1,1)
+
+  printf("\n")
+  bl_op_msg
+}'
+
+
+def _bl_hall_temperature_ok() '{
+  local temp_ok
+  local stat
+
+  temp_ok = 1
+
+  # EH T02 average temperature
+  stat = epics_get("ILUUL-02AV:TEMP")
+  if ((stat < 23.0) || (stat > 26.0)) {
+    temp_ok = 0
+  }
+
+  # EH T02 temperature at T0204 axis 16
+  stat = epics_get("ILUUL-0200-EB104:TEMP")
+  if ((stat < 23.0) || (stat > 26.0)) {
+    temp_ok = 0
+  }
+
+  # EH T02 temperature at T0205 axis 18
+  stat = epics_get("ILUUL-0200-EB105:TEMP")
+  if ((stat < 23.0) || (stat > 26.0)) {
+    temp_ok = 0
+  }
+
+  return (temp_ok)
+}'
+
+
+# ----------------------------------------------------------------------
+def bl_hall_temperature '{
+  local stat
+
+  stat = epics_get("ILUUL-02AV:TEMP")
+  printf("hall T02 average temperature       : ")
+  if ((stat < 23.0) || (stat > 25.0)) {
+    text_bf
+  }
+  printf("%.2f deg.C\n",stat)
+  text_non_bf
+
+  stat = epics_get("ILUUL-0200-EB104:TEMP")
+  printf("hall temperature at T0204 axis 16  : ")
+  if ((stat < 23) || (stat > 25)) {
+    text_bf
+  }
+  printf("%.2f deg.C\n",stat)
+  text_non_bf
+
+  stat = epics_get("ILUUL-0200-EB105:TEMP")
+  printf("hall temperature at T0205 axis 18  : ")
+  if ((stat < 23) || (stat > 25)) {
+    text_bf
+  }
+  printf("%.2f deg.C\n",stat)
+  text_non_bf
+
+#   stat = epics_get("ILUUL-0300-EB102:TEMP")
+#   printf("EH T03 temperature at T0302 axis 21: ")
+#   if ((stat < 23) || (stat > 25)) {
+#     text_bf
+#   }
+#   printf("%.2f deg.C\n",stat)
+#   text_non_bf
+
+}'
+
+def _bl_sls_status_unusual() '{
+  local unusual
+  local stat
+
+  unusual = 0
+
+  stat = epics_get("X12SA-SR-VAC:SETPOINT")
+  if (stat != "OK") {
+    unusual = 1
+  }
+
+  stat = epics_get("ACOAU-ACCU:OP-MODE.VAL")
+  if ((stat != "Light Available") && (stat != "Light-Available")) {
+    unusual = 1
+  }
+
+  stat = epics_get("ALIRF-GUN:INJ-MODE")
+  if (stat != "TOP-UP") {
+    unusual = 1
+  }
+
+  # current threshold
+  stat = epics_get("ALIRF-GUN:CUR-LOWLIM")
+  if (stat < 350) {
+    unusual = 1
+  }
+
+  # current deadband
+  stat = epics_get("ALIRF-GUN:CUR-DBAND")
+  if (stat > 2) {
+    unusual = 1
+  }
+
+  # orbit feedback mode
+  stat = epics_get("ARIDI-BPM:OFB-MODE")
+  if (stat != "fast") {
+    unusual = 1
+  }
+
+  # fast orbit feedback
+  stat = epics_get("ARIDI-BPM:FOFBSTATUS-G")
+  if (stat != "running") {
+    unusual = 1
+  }
+
+  return(unusual)
+}'
+
+def bl_sls_status '{
+  local stat
+
+  stat = epics_get("ACOAU-ACCU:OP-MODE.VAL")
+  printf("SLS status                         : ")
+  if ((stat != "Light Available") && (stat != "Light-Available")) {
+    text_bf
+  }
+  printf("%s\n",stat)
+  text_non_bf
+
+  stat = epics_get("ALIRF-GUN:INJ-MODE")
+  printf("SLS injection mode                 : ")
+  if (stat != "TOP-UP") {
+    text_bf
+  }
+  printf("%s\n",stat)
+  text_non_bf
+
+  stat = epics_get("ALIRF-GUN:CUR-LOWLIM")
+  printf("SLS current threshold              : ")
+  if (stat < 350) {
+    text_bf
+  }
+  printf("%7.3f\n",stat)
+  text_non_bf
+
+  stat = epics_get("ALIRF-GUN:CUR-DBAND")
+  printf("SLS current deadband               : ")
+  if (stat > 2) {
+    text_bf
+  }
+  printf("%7.3f\n",stat)
+  text_non_bf
+
+  stat = epics_get("ACORF-FILL:PAT-SELECT")
+  printf("SLS filling pattern                : ")
+  printf("%s\n",stat)
+
+  bl_ring_current
+
+  stat = epics_get("ARIDI-PCT:TAU-HOUR")
+  printf("SLS filling life time              : ")
+  printf("%.2f h\n",stat)
+
+  stat = epics_get("ARIDI-BPM:OFB-MODE")
+  printf("orbit feedback mode                : ")
+  if (stat != "fast") {
+    text_bf
+  }
+  printf("%s\n",stat)
+  text_non_bf
+
+  stat = epics_get("ARIDI-BPM:FOFBSTATUS-G")
+  printf("fast orbit feedback                : ")
+  if (stat != "running") {
+    text_bf
+  }
+  printf("%s\n",stat)
+  text_non_bf
+
+}'
+
+def _bl_get_ring_current() '{
+  return epics_get("ARIDI-PCT:CURRENT")
+}'
+
+
+# ----------------------------------------------------------------------
+def _bl_no_ring_current() '{
+  # set an arbitrary current limit of 100mA as no-beam limit
+  if (_bl_get_ring_current() < 100) {
+    return 1
+  } else {
+    return 0
+  }
+}'
+
+
+# ----------------------------------------------------------------------
+def bl_ring_current '{
+  local curr
+
+  curr = _bl_get_ring_current()
+
+  if (curr < 300) {
+    text_bf
+  }
+  printf("SLS ring current                   : %.3f mA\n",curr)
+  text_non_bf
+}'

bec_plugins/bec_client/plugins/LamNI/lamni_optics_mixin.py

@@ -0,0 +1,161 @@
+import builtins
+import time
+
+from rich import box
+from rich.console import Console
+from rich.table import Table
+
+from bec_client.plugins.cSAXS import epics_get, epics_put, fshclose
+
+# import builtins to avoid linter errors
+dev = builtins.__dict__.get("dev")
+umv = builtins.__dict__.get("umv")
+bec = builtins.__dict__.get("bec")
+
+
+class LamNIOpticsMixin:
+    @staticmethod
+    def _get_user_param_safe(device, var):
+        param = dev[device].user_parameter
+        if not param or param.get(var) is None:
+            raise ValueError(f"Device {device} has no user parameter definition for {var}.")
+        return param.get(var)
+
+    def leye_out(self):
+        self.loptics_in()
+        fshclose()
+        leyey_out = self._get_user_param_safe("leyey", "out")
+        umv(dev.leyey, leyey_out)
+
+        epics_put("XOMNYI-XEYE-ACQ:0", 2)
+        # move rotation stage to zero to avoid problems with wires
+        umv(dev.lsamrot, 0)
+        umv(dev.dttrz, 5854, dev.fttrz, 2395)
+
+    def leye_in(self):
+        bec.queue.next_dataset_number += 1
+        # move rotation stage to zero to avoid problems with wires
+        umv(dev.lsamrot, 0)
+        umv(dev.dttrz, 6419.677, dev.fttrz, 2959.979)
+        while True:
+            moved_out = (input("Did the flight tube move out? (Y/n)") or "y").lower()
+            if moved_out == "y":
+                break
+            if moved_out == "n":
+                return
+        leyex_in = self._get_user_param_safe("leyex", "in")
+        leyey_in = self._get_user_param_safe("leyey", "in")
+        umv(dev.leyex, leyex_in, dev.leyey, leyey_in)
+        self.align.update_frame()
+
+    def _lfzp_in(self):
+        loptx_in = self._get_user_param_safe("loptx", "in")
+        lopty_in = self._get_user_param_safe("lopty", "in")
+        umv(
+            dev.loptx, loptx_in, dev.lopty, lopty_in
+        )  # for 7.2567 keV and 150 mu, 60 nm fzp, loptz 83.6000 for propagation 1.4 mm
+
+    def lfzp_in(self):
+        """
+        move in the lamni zone plate.
+        This will disable rt feedback, move the FZP and re-enabled the feedback.
+        """
+        if "rtx" in dev and dev.rtx.enabled:
+            dev.rtx.controller.feedback_disable()
+
+        self._lfzp_in()
+
+        if "rtx" in dev and dev.rtx.enabled:
+            dev.rtx.controller.feedback_enable_with_reset()
+
+    def loptics_in(self):
+        """
+        Move in the lamni optics, including the FZP and the OSA.
+        """
+        self.lfzp_in()
+        self.losa_in()
+
+    def loptics_out(self):
+        """Move out the lamni optics"""
+        if "rtx" in dev and dev.rtx.enabled:
+            dev.rtx.controller.feedback_disable()
+
+        # self.lcs_out()
+        self.losa_out()
+        loptx_out = self._get_user_param_safe("loptx", "out")
+        lopty_out = self._get_user_param_safe("lopty", "out")
+        umv(dev.loptx, loptx_out, dev.lopty, lopty_out)
+
+        if "rtx" in dev and dev.rtx.enabled:
+            time.sleep(1)
+            dev.rtx.controller.feedback_enable_with_reset()
+
+    def lcs_in(self):
+        # umv lcsx -1.852 lcsy -0.095
+        pass
+
+    def lcs_out(self):
+        umv(dev.lcsy, 3)
+
+    def losa_in(self):
+        # 6.2 keV, 170 um FZP
+        # umv(dev.losax, -1.4450000, dev.losay, -0.1800)
+        # umv(dev.losaz, -1)
+        # 6.7, 170
+        # umv(dev.losax, -1.4850, dev.losay, -0.1930)
+        # umv(dev.losaz, 1.0000)
+        # 7.2, 150
+        losax_in = self._get_user_param_safe("losax", "in")
+        losay_in = self._get_user_param_safe("losay", "in")
+        losaz_in = self._get_user_param_safe("losaz", "in")
+        umv(dev.losax, losax_in, dev.losay, losay_in)
+        umv(dev.losaz, losaz_in)
+        # 11 kev
+        # umv(dev.losax, -1.161000, dev.losay, -0.196)
+        # umv(dev.losaz, 1.0000)
+
+    def losa_out(self):
+        losay_out = self._get_user_param_safe("losay", "out")
+        losaz_out = self._get_user_param_safe("losaz", "out")
+        umv(dev.losaz, losaz_out)
+        umv(dev.losay, losay_out)
+
+    def lfzp_info(self):
+        loptz_val = dev.loptz.read()["loptz"]["value"]
+        distance = -loptz_val + 85.6 + 52
+        print(f"The sample is in a distance of {distance:.1f} mm from the FZP.")
+
+        diameters = [80e-6, 100e-6, 120e-6, 150e-6, 170e-6, 200e-6, 220e-6, 250e-6]
+
+        mokev_val = dev.mokev.read()["mokev"]["value"]
+        console = Console()
+        table = Table(
+            title=f"At the current energy of {mokev_val:.4f} keV we have following options:",
+            box=box.SQUARE,
+        )
+        table.add_column("Diameter", justify="center")
+        table.add_column("Focal distance", justify="center")
+        table.add_column("Current beam size", justify="center")
+
+        wavelength = 1.2398e-9 / mokev_val
+
+        for diameter in diameters:
+            outermost_zonewidth = 60e-9
+            focal_distance = diameter * outermost_zonewidth / wavelength
+            beam_size = (
+                -diameter / (focal_distance * 1000) * (focal_distance * 1000 - distance) * 1e6
+            )
+            table.add_row(
+                f"{diameter*1e6:.2f} microns",
+                f"{focal_distance:.2f} mm",
+                f"{beam_size:.2f} microns",
+            )
+
+        console.print(table)
+
+        print("OSA Information:")
+        # print(f"Current losaz %.1f\n", A[losaz])
+        # print("The OSA will collide with the sample plane at %.1f\n\n", 89.3-A[loptz])
+        print(
+            "The numbers presented here are for a sample in the plane of the lamni sample holder.\n"
+        )

bec_plugins/bec_client/plugins/LamNI/load_additional_correction.py

@@ -1,6 +1,7 @@
 def lamni_read_additional_correction():
     # "additional_correction_shift"
     # [0][] x , [1][] y, [2][] angle, [3][0] number of elements
+    import numpy as np
 
     with open("correction_lamni_um_S01405_.txt", "r") as f:
         num_elements = f.readline()

bec_plugins/bec_client/plugins/LamNI/x_ray_eye_align.py

@@ -9,14 +9,13 @@ from pathlib import Path
 
 import h5py
 import numpy as np
+from bec_client.plugins.cSAXS import epics_get, epics_put, fshclose, fshopen
 from bec_lib import bec_logger
 from bec_lib.alarm_handler import AlarmBase
 from bec_lib.pdf_writer import PDFWriter
 from typeguard import typechecked
 
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen
-
-from .lamni_optics_mixin import LaMNIInitStagesMixin, LamNIOpticsMixin
+from .lamni_optics_mixin import LamNIOpticsMixin
 
 logger = bec_logger.logger
 bec = builtins.__dict__.get("bec")
@@ -32,7 +31,7 @@ class XrayEyeAlign:
         self.lamni = lamni
         self.device_manager = client.device_manager
         self.scans = client.scans
-        # self.xeye = self.device_manager.devices.xeye
+        self.xeye = self.device_manager.devices.xeye
         self.alignment_values = defaultdict(list)
         self._reset_init_values()
         self.corr_pos_x = []
@@ -189,8 +188,7 @@ class XrayEyeAlign:
                 val_y = epics_get(f"XOMNYI-XEYE-YVAL_Y:{k}") * self.PIXEL_CALIBRATION  # in mm
                 self.alignment_values[k] = [val_x, val_y]
                 print(
-                    f"Clicked position {k}: x {self.alignment_values[k][0]}, y"
-                    f" {self.alignment_values[k][1]}"
+                    f"Clicked position {k}: x {self.alignment_values[k][0]}, y {self.alignment_values[k][1]}"
                 )
 
                 if k == 0:  # received center value of FZP
@@ -215,10 +213,7 @@ class XrayEyeAlign:
                 elif (
                     k == 1
                 ):  # received sample center value at samroy 0 ie the final base shift values
-                    msg = (
-                        f"Base shift values from movement are x {self.shift_xy[0]}, y"
-                        f" {self.shift_xy[1]}"
-                    )
+                    msg = f"Base shift values from movement are x {self.shift_xy[0]}, y {self.shift_xy[1]}"
                     print(msg)
                     logger.info(msg)
                     self.shift_xy[0] += (
@@ -228,12 +223,13 @@ class XrayEyeAlign:
                         self.alignment_values[1][1] - self.alignment_values[0][1]
                     ) * 1000
                     print(
-                        "Base shift values from movement and clicked position are x"
-                        f" {self.shift_xy[0]}, y {self.shift_xy[1]}"
+                        f"Base shift values from movement and clicked position are x {self.shift_xy[0]}, y {self.shift_xy[1]}"
                     )
 
                     self.scans.lamni_move_to_scan_center(
-                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                        self.shift_xy[0] / 1000,
+                        self.shift_xy[1] / 1000,
+                        self.get_tomo_angle(),
                     ).wait()
 
                     self.send_message("please wait ...")
@@ -242,7 +238,9 @@ class XrayEyeAlign:
                     time.sleep(1)
 
                     self.scans.lamni_move_to_scan_center(
-                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                        self.shift_xy[0] / 1000,
+                        self.shift_xy[1] / 1000,
+                        self.get_tomo_angle(),
                     ).wait()
 
                     epics_put("XOMNYI-XEYE-ANGLE:0", self.get_tomo_angle())
@@ -259,12 +257,16 @@ class XrayEyeAlign:
                     self._disable_rt_feedback()
                     self.tomo_rotate((k - 1) * 45 - 45 / 2)
                     self.scans.lamni_move_to_scan_center(
-                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                        self.shift_xy[0] / 1000,
+                        self.shift_xy[1] / 1000,
+                        self.get_tomo_angle(),
                     ).wait()
                     self._disable_rt_feedback()
                     self.tomo_rotate((k - 1) * 45)
                     self.scans.lamni_move_to_scan_center(
-                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                        self.shift_xy[0] / 1000,
+                        self.shift_xy[1] / 1000,
+                        self.get_tomo_angle(),
                     ).wait()
 
                     epics_put("XOMNYI-XEYE-ANGLE:0", self.get_tomo_angle())
@@ -291,7 +293,9 @@ class XrayEyeAlign:
                     self.shift_xy[0] = self.shift_xy[0] + _xrayeyalignmvx
                     self.shift_xy[1] = self.shift_xy[1] + _xrayeyalignmvy
                     self.scans.lamni_move_to_scan_center(
-                        self.shift_xy[0] / 1000, self.shift_xy[1] / 1000, self.get_tomo_angle()
+                        self.shift_xy[0] / 1000,
+                        self.shift_xy[1] / 1000,
+                        self.get_tomo_angle(),
                     ).wait()
                     print(
                         f"Current center horizontal {self.shift_xy[0]} vertical {self.shift_xy[1]}"
@@ -306,14 +310,12 @@ class XrayEyeAlign:
         fovx = self._xray_fov_xy[0] * self.PIXEL_CALIBRATION * 1000 / 2
         fovy = self._xray_fov_xy[1] * self.PIXEL_CALIBRATION * 1000 / 2
         print(
-            f"The largest field of view from the xrayeyealign was \nfovx = {fovx:.0f} microns, fovy"
-            f" = {fovy:.0f} microns"
+            f"The largest field of view from the xrayeyealign was \nfovx = {fovx:.0f} microns, fovy = {fovy:.0f} microns"
         )
         print("Use matlab routine to fit the current alignment...")
 
         print(
-            "This additional shift is applied to the base shift values\n which are x"
-            f" {self.shift_xy[0]}, y {self.shift_xy[1]}"
+            f"This additional shift is applied to the base shift values\n which are x {self.shift_xy[0]}, y {self.shift_xy[1]}"
         )
 
         self._disable_rt_feedback()
@@ -321,8 +323,7 @@ class XrayEyeAlign:
         self.tomo_rotate(0)
 
         print(
-            "\n\nNEXT LOAD ALIGNMENT PARAMETERS\nby running"
-            " lamni.align.read_xray_eye_correction()\n"
+            "\n\nNEXT LOAD ALIGNMENT PARAMETERS\nby running lamni.align.read_xray_eye_correction()\n"
         )
 
         self.client.set_global_var("tomo_fov_offset", self.shift_xy)
@@ -331,13 +332,12 @@ class XrayEyeAlign:
         with open(
             os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues"), "w"
         ) as alignment_values_file:
-            alignment_values_file.write("angle\thorizontal\tvertical\n")
+            alignment_values_file.write(f"angle\thorizontal\tvertical\n")
             for k in range(2, 11):
                 fovx_offset = (self.alignment_values[0][0] - self.alignment_values[k][0]) * 1000
                 fovy_offset = (self.alignment_values[k][1] - self.alignment_values[0][1]) * 1000
                 print(
-                    f"Writing to file new alignment: number {k}, value x {fovx_offset}, y"
-                    f" {fovy_offset}"
+                    f"Writing to file new alignment: number {k}, value x {fovx_offset}, y {fovy_offset}"
                 )
                 alignment_values_file.write(f"{(k-2)*45}\t{fovx_offset}\t{fovy_offset}\n")
 
@@ -422,8 +422,7 @@ class XrayEyeAlign:
             additional_correction_shift_x = self.corr_pos_x[-1]
             additional_correction_shift_y = self.corr_pos_y[-1]
         print(
-            "Additional correction shifts:"
-            f" {additional_correction_shift_x} {additional_correction_shift_y}"
+            f"Additional correction shifts: {additional_correction_shift_x} {additional_correction_shift_y}"
         )
         return (additional_correction_shift_x, additional_correction_shift_y)
 
@@ -477,8 +476,7 @@ class XrayEyeAlign:
             additional_correction_shift_x = self.corr_pos_x_2[-1]
             additional_correction_shift_y = self.corr_pos_y_2[-1]
         print(
-            "Additional correction shifts 2:"
-            f" {additional_correction_shift_x} {additional_correction_shift_y}"
+            f"Additional correction shifts 2: {additional_correction_shift_x} {additional_correction_shift_y}"
         )
         return (additional_correction_shift_x, additional_correction_shift_y)
 
@@ -511,7 +509,7 @@ class LamNI(LamNIOpticsMixin):
         super().__init__()
         self.client = client
         self.align = XrayEyeAlign(client, self)
-        self.init = LaMNIInitStagesMixin()
+
         self.check_shutter = True
         self.check_light_available = True
         self.check_fofb = True
@@ -527,8 +525,7 @@ class LamNI(LamNIOpticsMixin):
 
     def get_beamline_checks_enabled(self):
         print(
-            f"Shutter: {self.check_shutter}\nFOFB: {self.check_fofb}\nLight available:"
-            f" {self.check_light_available}"
+            f"Shutter: {self.check_shutter}\nFOFB: {self.check_fofb}\nLight available: {self.check_light_available}"
         )
 
     @property
@@ -586,27 +583,6 @@ class LamNI(LamNIOpticsMixin):
     def tomo_circfov(self, val: float):
         self.client.set_global_var("tomo_circfov", val)
 
-    @property
-    def tomo_type(self):
-        val = self.client.get_global_var("tomo_type")
-        if val is None:
-            return 1
-        return val
-
-    @tomo_type.setter
-    def tomo_type(self, val: float):
-        if val == 1:
-            # equally spaced tomography with 8 sub tomograms
-            self.client.set_global_var("tomo_type", val)
-        # elif val == 2:
-        #    # golden ratio tomography (sorted bunches)
-        #    self.client.set_global_var("tomo_type", val)
-        # elif val == 3:
-        #    # equally spaced tomography with starting angles shifted by golden ratio
-        #    self.client.set_global_var("tomo_type", val)
-        else:
-            raise ValueError("Unknown tomo_type.")
-
     @property
     def tomo_countingtime(self):
         val = self.client.get_global_var("tomo_countingtime")
@@ -790,18 +766,13 @@ class LamNI(LamNIOpticsMixin):
                 # pylint: disable=undefined-variable
                 self._current_scan_list.append(bec.queue.next_scan_number)
                 logger.info(
-                    f"scans.lamni_fermat_scan(fov_size=[{self.lamni_piezo_range_x},{self.lamni_piezo_range_y}],"
-                    f" step={self.tomo_shellstep}, stitch_x={0}, stitch_y={0},"
-                    f" stitch_overlap={1},center_x={self.align.tomo_fovx_offset},"
-                    f" center_y={self.align.tomo_fovy_offset},"
-                    f" shift_x={self.manual_shift_x+correction_xeye_mu[0]-additional_correction[0]-additional_correction_2[0]},"
-                    f" shift_y={self.manual_shift_y+correction_xeye_mu[1]-additional_correction[1]-additional_correction_2[1]},"
-                    f" fov_circular={self.tomo_circfov}, angle={angle}, scan_type='fly')"
-                )
-                log_message = (
-                    f"{str(datetime.datetime.now())}: LamNI scan projection at angle {angle}, scan"
-                    f" number {bec.queue.next_scan_number}.\n"
+                    f"scans.lamni_fermat_scan(fov_size=[{self.lamni_piezo_range_x},{self.lamni_piezo_range_y}], step={self.tomo_shellstep}, stitch_x={0}, stitch_y={0}, stitch_overlap={1},"
+                    f"center_x={self.align.tomo_fovx_offset}, center_y={self.align.tomo_fovy_offset}, "
+                    f"shift_x={self.manual_shift_x+correction_xeye_mu[0]-additional_correction[0]-additional_correction_2[0]}, "
+                    f"shift_y={self.manual_shift_y+correction_xeye_mu[1]-additional_correction[1]-additional_correction_2[1]}, "
+                    f"fov_circular={self.tomo_circfov}, angle={angle}, scan_type='fly')"
                 )
+                log_message = f"{str(datetime.datetime.now())}: LamNI scan projection at angle {angle}, scan number {bec.queue.next_scan_number}.\n"
                 self.write_to_spec_log(log_message)
                 # self.write_to_scilog(log_message, ["BEC_scans", self.sample_name])
                 corridor_size = self.corridor_size if self.corridor_size > 0 else None
@@ -843,7 +814,10 @@ class LamNI(LamNIOpticsMixin):
                     msgs.append("Check beam failed: Shutter is closed.")
             if self.check_light_available:
                 machine_status = dev.sls_machine_status.read(cached=True)
-                if machine_status["value"] not in ["Light Available", "Light-Available"]:
+                if machine_status["value"] not in [
+                    "Light Available",
+                    "Light-Available",
+                ]:
                     self._beam_is_okay = False
                     msgs.append("Check beam failed: Light not available.")
             if self.check_fofb:
@@ -884,8 +858,7 @@ class LamNI(LamNIOpticsMixin):
         try:
             msg = bec.logbook.LogbookMessage()
             msg.add_text(
-                "<p><mark class='pen-red'><strong>Beamline checks failed at"
-                f" {str(datetime.datetime.now())}: {''.join(self._check_msgs)}</strong></mark></p>"
+                f"<p><mark class='pen-red'><strong>Beamline checks failed at {str(datetime.datetime.now())}: {''.join(self._check_msgs)}</strong></mark></p>"
             ).add_tag(["BEC", "beam_check"])
             self.client.logbook.send_logbook_message(msg)
         except Exception:
@@ -902,20 +875,25 @@ class LamNI(LamNIOpticsMixin):
         try:
             msg = bec.logbook.LogbookMessage()
             msg.add_text(
-                "<p><mark class='pen-red'><strong>Operation resumed at"
-                f" {str(datetime.datetime.now())}.</strong></mark></p>"
+                f"<p><mark class='pen-red'><strong>Operation resumed at {str(datetime.datetime.now())}.</strong></mark></p>"
             ).add_tag(["BEC", "beam_check"])
             self.client.logbook.send_logbook_message(msg)
         except Exception:
             logger.warning("Failed to send update to SciLog.")
 
     def add_sample_database(
-        self, samplename, date, eaccount, scan_number, setup, sample_additional_info, user
+        self,
+        samplename,
+        date,
+        eaccount,
+        scan_number,
+        setup,
+        sample_additional_info,
+        user,
     ):
         """Add a sample to the omny sample database. This also retrieves the tomo id."""
         subprocess.run(
-            "wget --user=omny --password=samples -q -O /tmp/currsamplesnr.txt"
-            f" 'https://omny.web.psi.ch/samples/newmeasurement.php?sample={samplename}&date={date}&eaccount={eaccount}&scannr={scan_number}&setup={setup}&additional={sample_additional_info}&user={user}'",
+            f"wget --user=omny --password=samples -q -O /tmp/currsamplesnr.txt 'https://omny.web.psi.ch/samples/newmeasurement.php?sample={samplename}&date={date}&eaccount={eaccount}&scannr={scan_number}&setup={setup}&additional={sample_additional_info}&user={user}'",
             shell=True,
         )
         with open("/tmp/currsamplesnr.txt") as tomo_number_file:
@@ -969,63 +947,25 @@ class LamNI(LamNIOpticsMixin):
         # _tomo_shift_angles (potential global variable)
         _tomo_shift_angles = 0
         angle_end = start_angle + 360
-        angles = np.linspace(
+        for angle in np.linspace(
             start_angle + _tomo_shift_angles,
             angle_end,
             num=int(360 / self.tomo_angle_stepsize) + 1,
             endpoint=True,
-        )
-
-        # reverse even sub-tomograms
-        if not (subtomo_number % 2):
-            angles = np.flip(angles)
-        for angle in angles:
-            self.progress["subtomo"] = subtomo_number
-            self.progress["subtomo_projection"] = angles.index(angle)
-            self.progress["subtomo_total_projections"] = 180 / self.tomo_angle_stepsize
-            self.progress["projection"] = (subtomo_number - 1) * self.progress[
-                "subtomo_total_projections"
-            ] + self.progress["subtomo_projection"]
-            self.progress["total_projections"] = 180 / self.tomo_angle_stepsize * 8
-            self.progress["angle"] = angle
-            self._tomo_scan_at_angle(angle, subtomo_number)
-
-    def _print_progress(self):
-        print("\x1b[95mProgress report:")
-        print(f"Tomo type: ....................... {self.progress['tomo_type']}")
-        print(f"Projection: ...................... {self.progress['projection']}")
-        print(f"Total projections expected ....... {self.progress['total_projections']}")
-        print(f"Angle: ........................... {self.progress['angle']}")
-        print(f"Current subtomo: ................. {self.progress['subtomo']}")
-        print(f"Current projection within subtomo: {self.progress['subtomo_projection']}\x1b[0m")
-
-    def _tomo_scan_at_angle(self, angle, subtomo_number):
-        successful = False
-        error_caught = False
-        if 0 <= angle < 360.05:
-            print(f"Starting LamNI scan for angle {angle} in subtomo {subtomo_number}")
-            self._print_progress()
-            while not successful:
-                self._start_beam_check()
-                if not self.special_angles:
-                    self._current_special_angles = []
-                if self._current_special_angles:
-                    next_special_angle = self._current_special_angles[0]
-                    if np.isclose(angle, next_special_angle, atol=0.5):
-                        self._current_special_angles.pop(0)
-                        num_repeats = self.special_angle_repeats
-                else:
-                    num_repeats = 1
-                try:
-                    start_scan_number = bec.queue.next_scan_number
-                    for i in range(num_repeats):
-                        self._at_each_angle(angle)
-                    error_caught = False
-                except AlarmBase as exc:
-                    if exc.alarm_type == "TimeoutError":
-                        bec.queue.request_queue_reset()
-                        time.sleep(2)
-                        error_caught = True
+        ):
+            successful = False
+            error_caught = False
+            if 0 <= angle < 360.05:
+                print(f"Starting LamNI scan for angle {angle}")
+                while not successful:
+                    self._start_beam_check()
+                    if not self.special_angles:
+                        self._current_special_angles = []
+                    if self._current_special_angles:
+                        next_special_angle = self._current_special_angles[0]
+                        if np.isclose(angle, next_special_angle, atol=0.5):
+                            self._current_special_angles.pop(0)
+                            num_repeats = self.special_angle_repeats
                     else:
                         num_repeats = 1
                     try:
@@ -1065,7 +1005,7 @@ class LamNI(LamNIOpticsMixin):
         scans = builtins.__dict__.get("scans")
         self._current_special_angles = self.special_angles.copy()
 
-        if self.tomo_type == 1 and subtomo_start == 1 and start_angle is None:
+        if subtomo_start == 1 and start_angle is None:
             # pylint: disable=undefined-variable
             self.tomo_id = self.add_sample_database(
                 self.sample_name,
@@ -1088,16 +1028,14 @@ class LamNI(LamNIOpticsMixin):
         print(f"Counting time           <ctime>  =  {self.tomo_countingtime} s")
         print(f"Stepsize microns         <step>  =  {self.tomo_shellstep}")
         print(
-            f"Piezo range (max 80)  <microns>  =  {self.lamni_piezo_range_x},"
-            f" {self.lamni_piezo_range_y}"
+            f"Piezo range (max 80)  <microns>  =  {self.lamni_piezo_range_x}, {self.lamni_piezo_range_y}"
         )
         print(f"Stitching number x,y             =  {self.lamni_stitch_x}, {self.lamni_stitch_y}")
         print(f"Stitching overlap                =  {self.tomo_stitch_overlap}")
         print(f"Circuilar FOV diam    <microns>  =  {self.tomo_circfov}")
         print(f"Reconstruction queue name        =  {self.ptycho_reconstruct_foldername}")
         print(
-            "For information, fov offset is rotating and finding the ROI, manual shift moves"
-            " rotation center"
+            "For information, fov offset is rotating and finding the ROI, manual shift moves rotation center"
         )
         print(f"   _tomo_fovx_offset       <mm>  =  {self.align.tomo_fovx_offset}")
         print(f"   _tomo_fovy_offset       <mm>  =  {self.align.tomo_fovy_offset}")
@@ -1153,7 +1091,7 @@ class LamNI(LamNIOpticsMixin):
         with open(ptycho_queue_file, "w") as queue_file:
             scans = " ".join([str(scan) for scan in self._current_scan_list])
             queue_file.write(f"p.scan_number {scans}\n")
-            queue_file.write("p.check_nextscan_started 1\n")
+            queue_file.write(f"p.check_nextscan_started 1\n")
 
     def write_pdf_report(self):
         """create and write the pdf report with the current LamNI settings"""
@@ -1178,25 +1116,17 @@ class LamNI(LamNIOpticsMixin):
             f"{'Dataset ID:':<{padding}}{dataset_id:>{padding}}\n",
             f"{'Sample Info:':<{padding}}{'Sample Info':>{padding}}\n",
             f"{'e-account:':<{padding}}{str(self.client.username):>{padding}}\n",
-            (
-                f"{'Number of projections:':<{padding}}{int(360 / self.tomo_angle_stepsize * 8):>{padding}}\n"
-            ),
+            f"{'Number of projections:':<{padding}}{int(360 / self.tomo_angle_stepsize * 8):>{padding}}\n",
             f"{'First scan number:':<{padding}}{self.client.queue.next_scan_number:>{padding}}\n",
-            (
-                f"{'Last scan number approx.:':<{padding}}{self.client.queue.next_scan_number + int(360 / self.tomo_angle_stepsize * 8) + 10:>{padding}}\n"
-            ),
-            (
-                f"{'Current photon energy:':<{padding}}{dev.mokev.read(cached=True)['value']:>{padding}.4f}\n"
-            ),
+            f"{'Last scan number approx.:':<{padding}}{self.client.queue.next_scan_number + int(360 / self.tomo_angle_stepsize * 8) + 10:>{padding}}\n",
+            f"{'Current photon energy:':<{padding}}{dev.mokev.read(cached=True)['value']:>{padding}.4f}\n",
             f"{'Exposure time:':<{padding}}{self.tomo_countingtime:>{padding}.2f}\n",
             f"{'Fermat spiral step size:':<{padding}}{self.tomo_shellstep:>{padding}.2f}\n",
             f"{'Piezo range (FOV sample plane):':<{padding}}{piezo_range:>{padding}}\n",
             f"{'Restriction to circular FOV:':<{padding}}{self.tomo_circfov:>{padding}.2f}\n",
             f"{'Stitching:':<{padding}}{stitching:>{padding}}\n",
             f"{'Number of individual sub-tomograms:':<{padding}}{8:>{padding}}\n",
-            (
-                f"{'Angular step within sub-tomogram:':<{padding}}{self.tomo_angle_stepsize:>{padding}.2f}\n"
-            ),
+            f"{'Angular step within sub-tomogram:':<{padding}}{self.tomo_angle_stepsize:>{padding}.2f}\n",
         ]
         content = "".join(content)
         user_target = os.path.expanduser(f"~/Data10/documentation/tomo_scan_ID_{self.tomo_id}.pdf")
@@ -1204,13 +1134,20 @@ class LamNI(LamNIOpticsMixin):
             file.write(header)
             file.write(content)
         subprocess.run(
-            "xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &", shell=True
+            "xterm /work/sls/spec/local/XOMNY/bin/upload/upload_last_pon.sh &",
+            shell=True,
         )
         # status = subprocess.run(f"cp /tmp/spec-e20131-specES1.pdf {user_target}", shell=True)
         msg = bec.logbook.LogbookMessage()
         logo_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), "LamNI_logo.png")
         msg.add_file(logo_path).add_text("".join(content).replace("\n", "</p><p>")).add_tag(
-            ["BEC", "tomo_parameters", f"dataset_id_{dataset_id}", "LamNI", self.sample_name]
+            [
+                "BEC",
+                "tomo_parameters",
+                f"dataset_id_{dataset_id}",
+                "LamNI",
+                self.sample_name,
+            ]
         )
         self.client.logbook.send_logbook_message(msg)
 
@@ -1295,12 +1232,16 @@ class DataDrivenLamNI(LamNI):
 
     def sub_tomo_scan(self):
         raise NotImplementedError(
-            "Cannot run sub_tomo_scan with data-driven LamNI. Please use"
-            " lamni.tomo_scan(subtomo_start=<START_NUM>) instead."
+            "Cannot run sub_tomo_scan with data-driven LamNI. Please use lamni.tomo_scan(subtomo_start=<START_NUM>) instead."
         )
 
     def _at_each_angle(
-        self, angle=None, stepsize=None, loptz_pos=None, manual_shift_x=0, manual_shift_y=0
+        self,
+        angle=None,
+        stepsize=None,
+        loptz_pos=None,
+        manual_shift_x=0,
+        manual_shift_y=0,
     ):
         # Do something...
         # self.tomo_parameters

bec_plugins/bec_client/plugins/__init__.py

@@ -0,0 +1,3 @@
+from .cSAXS import *
+
+# from .LamNI import *

bec_plugins/bec_client/plugins/cSAXS/__init__.py

@@ -0,0 +1 @@
+from .cSAXS_beamline import fshopen, fshclose, fshstatus, epics_get, epics_put

bec_plugins/bec_client/plugins/cSAXS/beamline_info.py

@@ -1,9 +1,10 @@
 import builtins
 
-from bec_ipython_client.beamline_mixin import BeamlineShowInfo
 from rich import box
 from rich.table import Table
 
+from bec_client.beamline_mixin import BeamlineShowInfo
+
 
 class BeamlineInfo(BeamlineShowInfo):
     def show(self):

bec_plugins/bec_client/startup/post_startup.py

@@ -16,13 +16,14 @@ 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
 
@@ -30,39 +31,46 @@ logger = bec_logger.logger
 
 logger.info("Using the cSAXS startup script.")
 
-# pylint: disable=import-error
-_args = _main_dict["args"]
+parser = argparse.ArgumentParser()
+parser.add_argument("--session", help="Session name", type=str, default="cSAXS")
+args = parser.parse_args()
 
-_session_name = "cSAXS"
-if _args.session.lower() == "lamni":
-    from csaxs_bec.bec_ipython_client.plugins.cSAXS import *
-    from csaxs_bec.bec_ipython_client.plugins.LamNI import *
+if args.session == "LamNI":
+    print("Loading LamNI session")
+    from bec_plugins.bec_client.plugins.cSAXS import *
+    from bec_plugins.bec_client.plugins.LamNI import *
 
-    _session_name = "LamNI"
     lamni = LamNI(bec)
-    logger.success("LamNI session loaded.")
 
-elif _args.session.lower() == "csaxs":
+elif args.session == "cSAXS":
     print("Loading cSAXS session")
-    from csaxs_bec.bec_ipython_client.plugins.cSAXS import *
-
-    logger.success("cSAXS session loaded.")
-
-from csaxs_bec.bec_ipython_client.plugins.tool_box.debug_tools import DebugTools
-
-debug = DebugTools()
-logger.success("Debug tools loaded. Use 'debug' to access them.")
+    from bec_plugins.bec_client.plugins.cSAXS import *
 
 
 # SETUP BEAMLINE INFO
-from bec_ipython_client.plugins.SLS.sls_info import OperatorInfo, SLSInfo
+from bec_client.plugins.SLS.sls_info import OperatorInfo, SLSInfo
 
-from csaxs_bec.bec_ipython_client.plugins.cSAXS.beamline_info import BeamlineInfo
+from bec_plugins.bec_client.plugins.cSAXS.beamline_info import BeamlineInfo
 
 bec._beamline_mixin._bl_info_register(BeamlineInfo)
 bec._beamline_mixin._bl_info_register(SLSInfo)
 bec._beamline_mixin._bl_info_register(OperatorInfo)
 
 # SETUP PROMPTS
-bec._ip.prompts.session_name = _session_name
+bec._ip.prompts.username = args.session
 bec._ip.prompts.status = 1
+
+
+# REGISTER BEAMLINE CHECKS
+from bec_lib.bl_conditions import (
+    FastOrbitFeedbackCondition,
+    LightAvailableCondition,
+    ShutterCondition,
+)
+
+# _fast_orbit_feedback_condition = FastOrbitFeedbackCondition(dev.sls_fast_orbit_feedback)
+_light_available_condition = LightAvailableCondition(dev.sls_machine_status)
+_shutter_condition = ShutterCondition(dev.x12sa_es1_shutter_status)
+# bec.bl_checks.register(_fast_orbit_feedback_condition)
+bec.bl_checks.register(_light_available_condition)
+bec.bl_checks.register(_shutter_condition)

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 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/device_configs/lamni_config.py

@@ -0,0 +1,152 @@
+import yaml
+
+# TODO: fix imports, those classes are located in .../bec/scibec/init_scibec/configs/config.py
+# (see also lamni_config.py in bec repository)
+from .config import DemoConfig, X12SAConfig
+
+
+class LamNIConfig(DemoConfig, X12SAConfig):
+    def run(self):
+        # self.write_galil_motors()
+        # self.write_rt_motors()
+        # self.write_smaract_motors()
+        # self.write_eiger1p5m()
+        self.write_x12sa_status()
+        self.write_sls_status()
+        self.load_csaxs_config()
+        # self.write_sim_user_motors()
+        # self.write_sim_beamline_motors()
+        # self.write_sim_beamline_monitors()
+
+    def write_galil_motors(self):
+        lamni_galil_motors = [
+            ("lsamx", "A", -1, 0.5, {"center": 8.768000}),
+            ("lsamy", "B", 1, 0.5, {"center": 10.041000}),
+            ("lsamrot", "C", 1, 0.5, {}),
+            ("loptz", "D", -1, 0.5, {}),
+            ("loptx", "E", 1, 0.5, {"in": -0.8380, "out": -0.699}),
+            ("lopty", "F", 1, 0.5, {"in": 3.3540, "out": 3.53}),
+            ("leyex", "G", -1, 0.001, {"in": 14.117000}),
+            ("leyey", "H", -1, 0.001, {"in": 48.069000, "out": 0.5}),
+        ]
+        out = {}
+        for m in lamni_galil_motors:
+            out[m[0]] = dict(
+                {
+                    "status": {"enabled": True, "enabled_set": True},
+                    "deviceClass": "GalilMotor",
+                    "deviceConfig": {
+                        "axis_Id": m[1],
+                        "name": m[0],
+                        "labels": m[0],
+                        "host": "mpc2680.psi.ch",
+                        "port": 8081,
+                        "sign": m[2],
+                        "limits": [0, 0],
+                        "tolerance": m[3],
+                        "device_access": True,
+                        "device_mapping": {"rt": "rtx"},
+                    },
+                    "acquisitionConfig": {
+                        "schedule": "sync",
+                        "acquisitionGroup": "motor",
+                        "readoutPriority": "baseline",
+                    },
+                    "deviceTags": ["lamni"],
+                }
+            )
+            if m[4]:
+                out[m[0]]["userParameter"] = m[4]
+        self.write_section(out, "LamNI Galil motors")
+
+    def write_rt_motors(self):
+        lamni_rt_motors = [
+            ("rtx", "A", 1),
+            ("rty", "B", 1),
+        ]
+        out = dict()
+        for m in lamni_rt_motors:
+            out[m[0]] = dict(
+                {
+                    "status": {"enabled": True, "enabled_set": True},
+                    "deviceClass": "RtLamniMotor",
+                    "deviceConfig": {
+                        "axis_Id": m[1],
+                        "name": m[0],
+                        "labels": m[0],
+                        "host": "mpc2680.psi.ch",
+                        "port": 3333,
+                        "limits": [0, 0],
+                        "sign": m[2],
+                        "device_access": True,
+                    },
+                    "acquisitionConfig": {
+                        "schedule": "sync",
+                        "acquisitionGroup": "motor",
+                        "readoutPriority": "baseline",
+                    },
+                    "deviceTags": ["lamni"],
+                }
+            )
+        self.write_section(out, "LamNI RT")
+
+    def write_smaract_motors(self):
+        lamni_smaract_motors = [
+            ("losax", "A", -1, {"in": -0.848000}),
+            ("losay", "B", -1, {"in": 0.135000, "out": 3.8}),
+            ("losaz", "C", 1, {"in": -1, "out": -3}),
+            ("lcsx", "D", -1, {}),
+            ("lcsy", "E", -1, {}),
+        ]
+        out = dict()
+        for m in lamni_smaract_motors:
+            out[m[0]] = dict(
+                {
+                    "status": {"enabled": True, "enabled_set": True},
+                    "deviceClass": "SmaractMotor",
+                    "deviceConfig": {
+                        "axis_Id": m[1],
+                        "name": m[0],
+                        "labels": m[0],
+                        "host": "mpc2680.psi.ch",
+                        "port": 8085,
+                        "limits": [0, 0],
+                        "sign": m[2],
+                        "tolerance": 0.05,
+                    },
+                    "acquisitionConfig": {
+                        "schedule": "sync",
+                        "acquisitionGroup": "motor",
+                        "readoutPriority": "baseline",
+                    },
+                    "deviceTags": ["lamni"],
+                }
+            )
+            if m[3]:
+                out[m[0]]["userParameter"] = m[3]
+        self.write_section(out, "LamNI SmarAct motors")
+
+    def write_eiger1p5m(self):
+        out = {
+            "eiger1p5m": {
+                "description": "Eiger 1.5M in vacuum detector, in-house developed, PSI",
+                "status": {"enabled": True, "enabled_set": True},
+                "deviceClass": "Eiger1p5MDetector",
+                "deviceConfig": {"device_access": True, "name": "eiger1p5m"},
+                "acquisitionConfig": {
+                    "schedule": "sync",
+                    "acquisitionGroup": "detector",
+                    "readoutPriority": "monitored",
+                },
+                "deviceTags": ["detector"],
+            }
+        }
+        self.write_section(out, "LamNI Eiger 1.5M in vacuum")
+
+    def load_csaxs_config(self):
+        CONFIG_PATH = "./init_scibec/configs/test_config_cSAXS.yaml"
+        content = {}
+        with open(CONFIG_PATH, "r") as csaxs_config_file:
+            content = yaml.safe_load(csaxs_config_file.read())
+
+        self.write_section(content, "Default cSAXS config")

bec_plugins/device_server/startup.py

@@ -0,0 +1,11 @@
+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()

bec_plugins/scan_server/scan_plugins/LamNIFermatScan.py

@@ -23,10 +23,9 @@ but they are executed in a specific order:
 import time
 
 import numpy as np
-from bec_lib import bec_logger
-from bec_lib.endpoints import MessageEndpoints
-from bec_server.scan_server.errors import ScanAbortion
-from bec_server.scan_server.scans import RequestBase, ScanArgType, ScanBase
+from bec_lib import MessageEndpoints, bec_logger, messages
+from scan_server.errors import ScanAbortion
+from scan_server.scans import RequestBase, ScanArgType, ScanBase
 
 MOVEMENT_SCALE_X = np.sin(np.radians(15)) * np.cos(np.radians(30))
 MOVEMENT_SCALE_Y = np.cos(np.radians(15))
@@ -97,8 +96,8 @@ class LamNIMixin:
         coarse_move_req_x = np.abs(lsamx_current - move_x)
         coarse_move_req_y = np.abs(lsamy_current - move_y)
 
-        self.device_manager.devices.lsamx.read_only = False
-        self.device_manager.devices.lsamy.read_only = False
+        self.device_manager.devices.lsamx.enabled_set = True
+        self.device_manager.devices.lsamy.enabled_set = True
 
         if (
             np.abs(y_drift) > 150
@@ -110,8 +109,9 @@ class LamNIMixin:
             logger.info(
                 f"Compensating {[val/1000 for val in lamni_to_stage_coordinates(x_drift,y_drift)]}"
             )
-            yield from self.stubs.set(device="lsamx", value=move_x)
-            yield from self.stubs.set(device="lsamy", value=move_y)
+            yield from self.stubs.set_and_wait(
+                device=["lsamx", "lsamy"], positions=[move_x, move_y]
+            )
 
         time.sleep(0.01)
         rtx_current = yield from self.stubs.send_rpc_and_wait("rtx", "readback.get")
@@ -126,14 +126,12 @@ class LamNIMixin:
         x_drift2 = x_center_expect * 1000 - rtx_current
         y_drift2 = y_center_expect * 1000 - rty_current
         logger.info(
-            f"Uncompensated drift of setup after first iteration is x={x_drift2:.3f},"
-            f" y={y_drift2:.3f}"
+            f"Uncompensated drift of setup after first iteration is x={x_drift2:.3f}, y={y_drift2:.3f}"
         )
 
         if np.abs(x_drift2) > 5 or np.abs(y_drift2) > 5:
             logger.info(
-                "Compensating second iteration"
-                f" {[val/1000 for val in lamni_to_stage_coordinates(x_drift2,y_drift2)]}"
+                f"Compensating second iteration {[val/1000 for val in lamni_to_stage_coordinates(x_drift2,y_drift2)]}"
             )
             move_x = (
                 x_stage
@@ -147,28 +145,26 @@ class LamNIMixin:
                 + lamni_to_stage_coordinates(x_drift, y_drift)[1] / 1000
                 + lamni_to_stage_coordinates(x_drift2, y_drift2)[1] / 1000
             )
-            yield from self.stubs.set(device="lsamx", value=move_x)
-            yield from self.stubs.set(device="lsamy", value=move_y)
-
+            yield from self.stubs.set_and_wait(
+                device=["lsamx", "lsamy"], positions=[move_x, move_y]
+            )
             time.sleep(0.01)
             rtx_current = yield from self.stubs.send_rpc_and_wait("rtx", "readback.get")
             rty_current = yield from self.stubs.send_rpc_and_wait("rty", "readback.get")
 
             logger.info(
-                f"New scan center interferometer after second iteration {rtx_current:.3f},"
-                f" {rty_current:.3f} microns"
+                f"New scan center interferometer after second iteration {rtx_current:.3f}, {rty_current:.3f} microns"
             )
             x_drift2 = x_center_expect * 1000 - rtx_current
             y_drift2 = y_center_expect * 1000 - rty_current
             logger.info(
-                f"Uncompensated drift of setup after second iteration is x={x_drift2:.3f},"
-                f" y={y_drift2:.3f}"
+                f"Uncompensated drift of setup after second iteration is x={x_drift2:.3f}, y={y_drift2:.3f}"
             )
         else:
             logger.info("No second iteration required")
 
-        self.device_manager.devices.lsamx.read_only = True
-        self.device_manager.devices.lsamy.read_only = True
+        self.device_manager.devices.lsamx.enabled_set = False
+        self.device_manager.devices.lsamy.enabled_set = False
 
         yield from self.stubs.send_rpc_and_wait("rtx", "controller.feedback_enable_without_reset")
 
@@ -178,12 +174,8 @@ class LamNIMoveToScanCenter(RequestBase, LamNIMixin):
     scan_report_hint = None
     scan_type = "step"
     required_kwargs = []
-    arg_input = {
-        "shift_x": ScanArgType.FLOAT,
-        "shift_y": ScanArgType.FLOAT,
-        "angle": ScanArgType.FLOAT,
-    }
-    arg_bundle_size = {"bundle": len(arg_input), "min": 1, "max": 1}
+    arg_input = [ScanArgType.FLOAT, ScanArgType.FLOAT, ScanArgType.FLOAT]
+    arg_bundle_size = None
 
     def __init__(self, *args, parameter=None, **kwargs):
         """
@@ -207,10 +199,10 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
     scan_report_hint = "table"
     scan_type = "step"
     required_kwargs = ["fov_size", "exp_time", "step", "angle"]
-    arg_input = {}
-    arg_bundle_size = {"bundle": len(arg_input), "min": None, "max": None}
+    arg_input = []
+    arg_bundle_size = None
 
-    def __init__(self, *args, parameter: dict = None, **kwargs):
+    def __init__(self, *args, parameter=None, **kwargs):
         """
         A LamNI scan following Fermat's spiral.
 
@@ -365,8 +357,7 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
             self.stitch_x, self.stitch_y, self.angle
         )
         logger.info(
-            f"Total shift [mm] {_shfitx+x_stitch_shift/1000+self.shift_x},"
-            f" {_shfity+y_stitch_shift/1000+self.shift_y}"
+            f"Total shift [mm] {_shfitx+x_stitch_shift/1000+self.shift_x}, {_shfity+y_stitch_shift/1000+self.shift_y}"
         )
         return (
             _shfitx + x_stitch_shift / 1000 + self.shift_x,
@@ -443,7 +434,7 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
                     }
                 }
             )
-            yield from self.stubs.set(device="lsamrot", value=angle)
+            yield from self.stubs.set_and_wait(device=["lsamrot"], positions=[angle])
 
     def scan_core(self):
         if self.scan_type == "step":
@@ -456,18 +447,17 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
             # scan ID before sending the message to the device server
             yield from self.stubs.kickoff(device="rtx")
             while True:
-                yield from self.stubs.read(group="monitored")
-                msg = self.device_manager.connector.get(MessageEndpoints.device_status("rt_scan"))
+                yield from self.stubs.read_and_wait(group="primary", wait_group="readout_primary")
+                msg = self.device_manager.producer.get(MessageEndpoints.device_status("rt_scan"))
                 if msg:
-                    status = msg
+                    status = messages.DeviceStatusMessage.loads(msg)
                     status_id = status.content.get("status", 1)
                     request_id = status.metadata.get("RID")
                     if status_id == 0 and self.metadata.get("RID") == request_id:
                         break
                     if status_id == 2 and self.metadata.get("RID") == request_id:
                         raise ScanAbortion(
-                            "An error occured during the LamNI readout:"
-                            f" {status.metadata.get('error')}"
+                            f"An error occured during the LamNI readout: {status.metadata.get('error')}"
                         )
 
                 time.sleep(1)

bec_plugins/scan_server/scan_plugins/scan_plugin_template.py

@@ -25,9 +25,8 @@ but they are executed in a specific order:
 
 # import numpy as np
 
-# from bec_lib import bec_logger, messages
-# from bec_lib.endpoints import MessageEndpoints
-# from bec_server.scan_server.errors import ScanAbortion
-# from bec_server.scan_server.scans import FlyScanBase, RequestBase, ScanArgType, ScanBase
+# from bec_lib import MessageEndpoints, bec_logger, messages
+# from scan_server.errors import ScanAbortion
+# from scan_server.scans import FlyScanBase, RequestBase, ScanArgType, ScanBase
 
 # logger = bec_logger.logger

bec_plugins/utils/csaxs_post_archive.py

@@ -0,0 +1,182 @@
+import os
+import json
+import subprocess
+import requests
+
+from bec_lib.file_utils import FileWriterMixin
+#from bec_lib.bec_service import SERVICE_CONFIG
+
+
+class csaxs_archiver:
+    """Class to archive data from a beamtime.
+    To run this script from a shell, go to discovery.psi.ch and copy your token.
+    Complement the information in user_input below in the if __name__ == __main__ part of the script.
+    Afterwards, get a Keberos token (kinit) for yourself in the shell.
+    Activate the bec_venv by doing "source bec_venv/bin/activate" and then run this code via  python $filename.
+    As a last step, adjust the dictionary below in if __name__ == '__main__' with your token as well as information about the experiment
+    """
+
+    def __init__(
+        self,
+        start_scan: int,
+        stop_scan: int,
+        base_path: str,
+        log_path: str,
+        eacc: str,
+        pi: str,
+        pi_email: str,
+        token: str,
+        type: str = "raw",
+        overwrite: bool = False,
+        online: bool = True,
+    ):
+        self.start_scan = start_scan
+        self.stop_scan = stop_scan
+        self.log_path = os.path.expanduser(log_path)
+        self.eacc = eacc
+        self.pi = pi
+        self.pi_email = pi_email
+        self.token = token
+        self.type = type
+        self.overwrite = overwrite
+        self.online = online
+
+        #from bec_lib.bec_service import SERVICE_CONFIG
+        #SERVICE_CONFIG.config["service_config"]["file_writer"]
+        self._load_datacatalogue_module()
+        self._create_directory(base_path)
+        self._disable_mail_confirmation()
+
+        self.service_cfg = {'base_path' : f'{self.base_path}'}
+
+        self.file_writer = FileWriterMixin(self.service_cfg)
+
+    def _disable_mail_confirmation(self):
+        # Define the URL and payload
+        url = "https://dacat.psi.ch/api/v3/Policies/updatewhere"
+        payload = {
+            "ownerGroupList": f'p{self.eacc[1:]}',
+            "data": '{"archiveEmailNotification": false, "accessGroups": ["slscsaxs"]}'
+        }
+
+        # Define headers
+        headers = {
+            "Content-Type": "application/x-www-form-urlencoded",
+            "Accept": "application/json",
+        }
+
+        # Add the access_token to the URL
+        url += "?access_token=" + self.token
+
+        # Make a POST request
+        print(url, payload, headers)
+        response = requests.post(url, data=payload, headers=headers)
+
+        # Check the response
+        if response.status_code == 200:
+            print("Request was successful.")
+            print(response.json())
+        else:
+            print("Request failed with status code:", response.status_code)
+            print(response.text)
+
+    def _create_directory(self, base_path: str) -> None:
+        if self.online:
+            self.base_path = os.path.expanduser("~/Data10")
+        else:
+            self.base_path = base_path
+
+        if not os.path.exists(self.log_path):
+            os.makedirs(self.log_path)
+
+    def _load_datacatalogue_module(self):
+        command = 'module add datacatalog/1.1.9'
+        os.popen(command)
+        # result = subprocess.run(
+        #     command,
+        #     shell=False,
+        #     stdout=subprocess.PIPE,
+        #     stderr=subprocess.PIPE,
+        #     universal_newlines=True,
+        # )
+        # if result.returncode == 0:
+        #     print(f"Command {command} was succesful")
+        # else:
+        #     print(f"Failed to run command {command} with return message {result.returncode}")
+
+    def prep_metadata(self, scannr: int) -> dict:
+        user_metadata = {}
+        user_metadata.update(
+            {
+                "principalInvestigator": self.pi_email,
+                "owner": self.pi,
+                "ownerEmail": self.pi_email,
+                "sourceFolder": self.base_path,
+                "creationLocation": "/PSI/SLS/CSAXS",
+                "type": "raw",
+                "ownerGroup": f"p{self.eacc.strip('e')}",
+                "datasetName": f"S{scannr:05d}",
+            }
+        )
+        return user_metadata
+
+    def _write_ingestion_log(self, scannr: int) -> None:
+        ...
+
+    def run_for_all_scans(self):
+        for scan in range(self.start_scan, self.stop_scan + 1):
+            print(f"Start ingestion for scan {scan}")
+            fname = os.path.join(os.path.expanduser(self.log_path), f"ingestion_log_S{scan:05d}")
+            self.datafile_name = f"{fname}.txt"
+            if os.path.isfile(self.datafile_name) and not self.overwrite == True:
+                print(
+                    f"Skipping scan {scan}, already ingested due to logs, moving on to next scan {scan+1}"
+                )
+                continue
+
+            user_metadata = self.prep_metadata(scan)
+
+            # Write metadata file in json file
+            self.metadata_file = f"{fname}.json"
+            with open(self.metadata_file, "w") as file:
+                json.dump(user_metadata, file)
+
+            # Compile datapath based on structure a cSAXS
+            datadir_path = os.path.join('data', self.file_writer.get_scan_directory(scan, 1000, 5))
+            print(f"Archiving directory {datadir_path}")
+            if not os.path.isdir(os.path.join(self.base_path, datadir_path)):
+                print(f"Did not find directory {datadir_path}, skipping scan {scan}")
+                continue
+
+            # Create datafile path for archiving
+            with open(self.datafile_name, "w") as file:
+                file.write(datadir_path)
+
+            print(f"Starting ingestion for S#{scan}")
+            command = f'datasetIngestor -allowexistingsource -ingest -autoarchive -noninteractive -token {self.token} {self.metadata_file} {self.datafile_name}'
+            rtr = os.popen(command)
+
+            #with open(os.path.join(fname,'_log.txt'), "w") as file:
+            #    print(f'Writing reponse to file')
+            #    file.write(rtr.read())
+            # result = subprocess.run(command, shell=False, stdout = subprocess.PIPE, stderr = subprocess.PIPE, universal_newlines=True)
+            # if result.returncode == 0:
+            #     print(f"Command {command} was succesful")
+            # else:
+            #     print(f"Failed to run command {command} with return message {result.returncode}")
+
+
+if __name__ == "__main__":
+    # Generate dictionary with user input.
+    user_input = {
+        "base_path": "~/Data10",
+        "eacc": "e20638",
+        "pi": "Emma Sparr",
+        "pi_email": "emma.sparr@fkem1.lu.se",
+        'log_path' : '~/Data10/documentation/ingestion_logs/',
+        'token' : 'YK8gkmQmEVxVxjiA57D6tVmpBVs7T235nWEuBT0behN9BPM2BdWARWPPgEsQVrPe',
+        'start_scan' : 1,
+        'stop_scan' : 450,
+    }
+    archiver = csaxs_archiver(**user_input)
+    archiver.run_for_all_scans()

bec_plugins/utils/saxs_params.py

@@ -0,0 +1,88 @@
+import csv
+import os
+from collections import defaultdict
+from collections.abc import Callable
+
+import numpy as np
+
+
+class ScanItem:
+    def __init__(self, offset_xy: Callable) -> None:
+        self.start_entry = None
+        self.end_entry = None
+        self.offset_xy = offset_xy
+
+    def to_scan_params(self) -> dict:
+        scan_params = {
+            "start_x": float(self.start_entry["X"]) + self.offset_xy()[0],
+            "start_y": float(self.start_entry["Y"]) + self.offset_xy()[1],
+            "end_x": float(self.end_entry["X"]) + self.offset_xy()[0],
+            "end_y": float(self.end_entry["Y"]) + self.offset_xy()[1],
+            "interval_x": int(
+                np.round(
+                    np.abs(float(self.start_entry["X"]) - float(self.end_entry["X"]))
+                    / (float(self.start_entry["step_x [mu]"]) * 1e-3)
+                )
+            ),
+            "interval_y": int(
+                np.round(
+                    np.abs(float(self.start_entry["Y"]) - float(self.end_entry["Y"]))
+                    / (float(self.start_entry["step_y [mu]"]) * 1e-3)
+                )
+            ),
+            "exp_time": float(self.start_entry["exp_time [s]"]),
+            "readout_time": 3e-3,
+            "md": {"sample_name": self.start_entry["sample name"]},
+        }
+        if scan_params["interval_x"] < 1 or scan_params["interval_x"] < 1:
+            raise ValueError("Bugger off...")
+        return scan_params
+
+
+class SAXSParams:
+    def __init__(self, offset: Callable):
+        self.offset_xy = offset
+        self.data = defaultdict(lambda: ScanItem(offset))
+
+    def load_from_csv(self, file_path: str) -> None:
+        """
+        Load the acquisition parameter from a csv file.
+        """
+
+        if not os.path.exists(file_path):
+            raise FileNotFoundError(
+                f"The specified CSV file could not be found. Please check that the given path is correct: {file_path}."
+            )
+
+        data_transposed = defaultdict(lambda: [])
+        with open(os.path.expanduser(file_path), "r") as file:
+            csv_reader = csv.DictReader(file)
+            for row in csv_reader:
+                for key, val in row.items():
+                    data_transposed[key].append(val)
+                if int(row["start"]):
+                    self.data[row["sample name"]].start_entry = row
+                else:
+                    self.data[row["sample name"]].end_entry = row
+        self._check_params(dict(data_transposed))
+
+    def _check_params(self, data_transposed: dict) -> dict:
+        sample_names = set(data_transposed["sample name"])
+        if len(data_transposed["start"]) != len(sample_names) * 2:
+            raise ValueError(
+                f"The given params file does not provide N*2 start/stop positions. Found {len(sample_names)} samples and {len(data_transposed['start'])} start/stop positions."
+            )
+
+
+if __name__ == "__main__":
+    from pprint import pprint
+
+    INPUT_FILE = "/sls/X12SA/data/e21206/Data10/software/test_script.csv"
+
+    def my_offset():
+        return [0, 0]
+
+    params = SAXSParams(my_offset)
+    params.load_from_csv(INPUT_FILE)
+    for key in params.data:
+        pprint(params.data[key].to_scan_params())

bec_plugins/utils/saxs_params_start_stop.py

@@ -1,7 +1,3 @@
-""" Script used for parsing scan parameters from a CSV file as created by the motormap GUI.
-This needs to be reviewed and tested during the deployment phase."""
-
-# pylint: skip-file
 import csv
 import os
 from collections import defaultdict

bec_plugins/utils/service_config.py

@@ -0,0 +1,13 @@
+import yaml
+
+CONFIG_PATH = "/sls/X12SA/data/gac-x12saop/bec/config/bec_service_config.yaml"
+
+
+def load_service_config() -> dict:
+    """Load the service configuration from the YAML file."""
+    with open(CONFIG_PATH, "r", encoding="utf-8") as stream:
+        try:
+            config = yaml.safe_load(stream)
+        except yaml.YAMLError as exc:
+            print(exc)
+    return config

bin/.gitignore

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

bin/cbf_converter/cbf_converter.py

@@ -3,9 +3,8 @@ from __future__ import annotations
 import os
 import subprocess
 
-from bec_lib import bec_logger, messages
-from bec_lib.endpoints import MessageEndpoints
-from bec_lib.redis_connector import MessageObject, RedisConnector
+from bec_lib import MessageEndpoints, RedisConnector, bec_logger, messages
+from bec_lib.redis_connector import MessageObject
 
 logger = bec_logger.logger
 
@@ -13,6 +12,7 @@ logger = bec_logger.logger
 class PilatusConverter:
     def __init__(self, host: str, port: int) -> None:
         self._connector = RedisConnector(f"{host}:{port}")
+        self._producer = self._connector.producer()
 
     def start(self) -> None:
         """start the consumer"""
@@ -27,7 +27,7 @@ class PilatusConverter:
             message (MessageObject): Message object
             parent (PilatusConverter): Parent object
         """
-        msg = message.value
+        msg = messages.MessageReader.loads(message.value)
         print(msg)
         if not msg:
             return
@@ -56,9 +56,10 @@ class PilatusConverter:
         """
         Start the consumer.
         """
-        self._connector.register(
+        file_consumer = self._connector.consumer(
             MessageEndpoints.file_event("pilatus_2"), cb=self.on_new_message, parent=self
         )
+        file_consumer.start()
 
 
 if __name__ == "__main__":

bin/open_tunnel.sh

@@ -0,0 +1,5 @@
+
+for i in `seq 1 8`
+do
+  ssh -N -R 6379:localhost:6379 x12sa-cn-$i &
+done

bin/setup_bec.sh

@@ -0,0 +1,48 @@
+
+if [ "pc15543.psi.ch" != "$(hostname)" ]; then
+    echo "Please run this script on pc15543"
+    exit 1
+fi
+
+module use unstable
+module add psi-python311/2024.02
+echo module add tmux/3.2 >> ~/.bashrc
+echo module add redis/7.0.12 >> ~/.bashrc
+
+source ~/.bashrc
+
+cd ~/Data10
+mkdir -p software/
+mkdir -p ~/bec/scripts
+cd software
+
+git clone https://gitlab.psi.ch/bec/bec.git
+git clone https://gitlab.psi.ch/bec/ophyd_devices.git
+git clone https://gitlab.psi.ch/bec/bec-widgets.git
+
+python -m venv ./bec_venv
+source ./bec_venv/bin/activate
+
+cd bec
+git checkout sastt-online-changes
+pip install -e ./bec_server[dev]
+
+cd ../csaxs-bec
+pip install -e .[dev]
+
+#redis-server --protected-mode no &
+
+read -p "Do you want to set the current BEC account to $(whoami)? (yes/no) " yn
+
+val=$(whoami)
+
+case $yn in
+	yes ) echo ok, setting account to $val;
+    redis-cli SET internal/account:val $val;;
+	no ) echo ;;
+	* ) echo invalid response;
+		exit 1;;
+esac
+
+
+$(pwd)/open_tunnel.sh

bin/setup_bec_widgets.sh

@@ -0,0 +1,17 @@
+module use unstable
+module add psi-python311/2024.02
+
+cd ~/Data10/software
+python -m venv ./bec_widgets_venv
+source ./bec_widgets_venv/bin/activate
+pip install --upgrade pip
+cd ~/Data10/software/bec/bec_lib
+pip install -e .
+
+cd ~/Data10/software/csaxs-bec
+pip install -e .
+
+cd ~/Data10/software/bec-widgets
+pip install -e .
+
+echo "For the moment widgets only run on beamline consoles comp1/2 and cons1"

csaxs_bec/bec_ipython_client/plugins/LamNI/__init__.py

@@ -1,2 +0,0 @@
-from .load_additional_correction import lamni_read_additional_correction
-from .x_ray_eye_align import DataDrivenLamNI, LamNI, MagLamNI, XrayEyeAlign

csaxs_bec/bec_ipython_client/plugins/LamNI/lamni_optics_mixin.py

@@ -1,329 +0,0 @@
-import builtins
-import time
-
-from rich import box
-from rich.console import Console
-from rich.table import Table
-
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put, fshclose
-
-# import builtins to avoid linter errors
-dev = builtins.__dict__.get("dev")
-umv = builtins.__dict__.get("umv")
-bec = builtins.__dict__.get("bec")
-
-
-class LamNIInitError(Exception):
-    pass
-
-
-class LaMNIInitStagesMixin:
-    def lamni_init_stages(self):
-        user_input = input("Starting initialization of LamNI stages. OK? [y/n]")
-        if user_input == "y":
-            print("staring...")
-            dev.lsamrot.enabled = True
-        else:
-            return
-
-        if self.check_all_axes_of_lamni_referenced():
-            user_input = input("Continue anyways? [y/n]")
-            if user_input == "y":
-                print("ok then...")
-            else:
-                return
-
-        axis_id_lsamrot = dev.lsamrot._config["deviceConfig"].get("axis_Id")
-        if dev.lsamrot.controller.get_motor_limit_switch(axis_id_lsamrot)[1] == False:
-            user_input = input("The rotation stage will be moved to one limit [y/n]")
-            if user_input == "y":
-                print("starting...")
-            else:
-                return
-
-            self.drive_axis_to_limit(dev.lsamrot, "forward")
-            dev.lsamrot.enabled = False
-            print("Now hard reboot the controller and run the initialization routine again.")
-            print("The controller will be disabled in bec. To enable dev.lsamrot.enabled=True")
-            return
-
-        user_input = input(
-            "Init of loptz. Can the stage move to the upstream limit without collision?? [y/n]"
-        )
-        if user_input == "y":
-            print("ok then...")
-        else:
-            return
-
-        print("Referencing loptz")
-        self.drive_axis_to_limit(dev.loptz, "forward")
-        self.find_reference_mark(dev.loptz)
-
-        print("Referencing loptx")
-        self.drive_axis_to_limit(dev.loptx, "reverse")
-        self.find_reference_mark(dev.loptx)
-
-        print("Referencing lopty")
-        self.drive_axis_to_limit(dev.lopty, "forward")
-        self.find_reference_mark(dev.lopty)
-
-        print("Referencing lsamx")
-        self.drive_axis_to_limit(dev.lsamx, "forward")
-        self.find_reference_mark(dev.lsamx)
-
-        print("Referencing lsamy")
-        self.drive_axis_to_limit(dev.lsamy, "reverse")
-        self.find_reference_mark(dev.lsamy)
-
-        # the dual encoder requires the reference mark to pass on both encoders
-        print("Referencing lsamrot")
-        self.drive_axis_to_limit(dev.lsamrot, "reverse")
-        time.sleep(0.1)
-        self.find_reference_mark(dev.lsamrot)
-
-        user_input = input("Init of leye. Can the stage move to -x limit without collision? [y/n]")
-        if user_input == "y":
-            print("starting...")
-        else:
-            return
-
-        print("Referencing leyex")
-        self.drive_axis_to_limit(dev.leyex, "forward")
-        print("Referencing leyey")
-        self.drive_axis_to_limit(dev.leyey, "forward")
-
-        # set_lm lsamx 6 14
-        # set_lm lsamy 6 14
-        # set_lm lsamrot -3 362
-        # set_lm loptx -1 -0.2
-        # set_lm lopty 3.0 3.6
-        # set_lm loptz 82 87
-        # set_lm leyex 0 25
-        # set_lm leyey 0.5 50
-
-        print("Init of Smaract stages")
-        dev.losax.controller.find_reference_mark(2, 0, 1000, 1)
-        time.sleep(1)
-        dev.losax.controller.find_reference_mark(0, 0, 1000, 1)
-        time.sleep(1)
-        dev.losax.controller.find_reference_mark(1, 0, 1000, 1)
-        time.sleep(1)
-        # dev.losax.controller.find_reference_mark(3, 1, 1000, 1)
-        # time.sleep(1)
-        # dev.losax.controller.find_reference_mark(4, 1, 1000, 1)
-        # time.sleep(1)
-
-        # set_lm losax -1.5 0.25
-        # set_lm losay -2.5 4.1
-        # set_lm losaz -4.1 -0.5
-        # set_lm lcsy -1.5 5
-
-        self._align_setup()
-
-    def find_reference_mark(self, device):
-        axis_id = device._config["deviceConfig"].get("axis_Id")
-        axis_id_numeric = self.axis_id_to_numeric(axis_id)
-        device.controller.find_reference(axis_id_numeric)
-
-    def drive_axis_to_limit(self, device, direction):
-        axis_id = device._config["deviceConfig"].get("axis_Id")
-        axis_id_numeric = self.axis_id_to_numeric(axis_id)
-        device.controller.drive_axis_to_limit(axis_id_numeric, direction)
-
-    def axis_id_to_numeric(self, axis_id) -> int:
-        return ord(axis_id.lower()) - 97
-
-    def _align_setup(self):
-        user_input = input("Start moving stages to default initial positions? [y/n]")
-        if user_input == "y":
-            print("Start moving stages...")
-        else:
-            print("Stopping.")
-            return
-
-        lsamx_center = dev.lsamx.user_parameter.get("center")
-        if lsamx_center is None:
-            raise LamNIInitError(
-                "Could not find a lsamx center position. Please check your device config."
-            )
-        lsamy_center = dev.lsamy.user_parameter.get("center")
-        if lsamy_center is None:
-            raise LamNIInitError(
-                "Could not find a lsamy center position. Please check your device config."
-            )
-        umv(dev.lsamx, lsamx_center, dev.lsamy, lsamy_center, dev.loptx, -0.3, dev.lopty, 0)
-        umv(dev.losax, -1)
-        umv(dev.loptz, 82.25)
-        umv(dev.lsamrot, -1)
-        umv(dev.lsamrot, 0)
-
-        time.sleep(2)
-        dev.rtx.controller.feedback_disable_and_even_reset_lamni_angle_interferometer()
-
-    def check_all_axes_of_lamni_referenced(self):
-        if (
-            dev.losax.controller.axis_is_referenced(0)
-            & dev.losax.controller.axis_is_referenced(1)
-            & dev.losax.controller.axis_is_referenced(2)
-            & dev.lsamx.controller.all_axes_referenced()
-        ):
-            print("All axes of LamNI are referenced.")
-            return True
-        else:
-            return False
-
-
-class LamNIOpticsMixin:
-    @staticmethod
-    def _get_user_param_safe(device, var):
-        param = dev[device].user_parameter
-        if not param or param.get(var) is None:
-            raise ValueError(f"Device {device} has no user parameter definition for {var}.")
-        return param.get(var)
-
-    def leye_out(self):
-        self.loptics_in()
-        fshclose()
-        leyey_out = self._get_user_param_safe("leyey", "out")
-        umv(dev.leyey, leyey_out)
-
-        epics_put("XOMNYI-XEYE-ACQ:0", 2)
-        # move rotation stage to zero to avoid problems with wires
-        umv(dev.lsamrot, 0)
-        umv(dev.dttrz, 5854, dev.fttrz, 2395)
-
-    def leye_in(self):
-        bec.queue.next_dataset_number += 1
-        # move rotation stage to zero to avoid problems with wires
-        umv(dev.lsamrot, 0)
-        umv(dev.dttrz, 6419.677, dev.fttrz, 2959.979)
-        while True:
-            moved_out = (input("Did the flight tube move out? (Y/n)") or "y").lower()
-            if moved_out == "y":
-                break
-            if moved_out == "n":
-                return
-        leyex_in = self._get_user_param_safe("leyex", "in")
-        leyey_in = self._get_user_param_safe("leyey", "in")
-        umv(dev.leyex, leyex_in, dev.leyey, leyey_in)
-        self.align.update_frame()
-
-    def _lfzp_in(self):
-        loptx_in = self._get_user_param_safe("loptx", "in")
-        lopty_in = self._get_user_param_safe("lopty", "in")
-        umv(
-            dev.loptx, loptx_in, dev.lopty, lopty_in
-        )  # for 7.2567 keV and 150 mu, 60 nm fzp, loptz 83.6000 for propagation 1.4 mm
-
-    def lfzp_in(self):
-        """
-        move in the lamni zone plate.
-        This will disable rt feedback, move the FZP and re-enabled the feedback.
-        """
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_disable()
-
-        self._lfzp_in()
-
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_enable_with_reset()
-
-    def loptics_in(self):
-        """
-        Move in the lamni optics, including the FZP and the OSA.
-        """
-        self.lfzp_in()
-        self.losa_in()
-
-    def loptics_out(self):
-        """Move out the lamni optics"""
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_disable()
-
-        # self.lcs_out()
-        self.losa_out()
-        loptx_out = self._get_user_param_safe("loptx", "out")
-        lopty_out = self._get_user_param_safe("lopty", "out")
-        umv(dev.loptx, loptx_out, dev.lopty, lopty_out)
-
-        if "rtx" in dev and dev.rtx.enabled:
-            time.sleep(1)
-            dev.rtx.controller.feedback_enable_with_reset()
-
-    def lcs_in(self):
-        # umv lcsx -1.852 lcsy -0.095
-        pass
-
-    def lcs_out(self):
-        umv(dev.lcsy, 3)
-
-    def losa_in(self):
-        # 6.2 keV, 170 um FZP
-        # umv(dev.losax, -1.4450000, dev.losay, -0.1800)
-        # umv(dev.losaz, -1)
-        # 6.7, 170
-        # umv(dev.losax, -1.4850, dev.losay, -0.1930)
-        # umv(dev.losaz, 1.0000)
-        # 7.2, 150
-        losax_in = self._get_user_param_safe("losax", "in")
-        losay_in = self._get_user_param_safe("losay", "in")
-        losaz_in = self._get_user_param_safe("losaz", "in")
-        umv(dev.losax, losax_in, dev.losay, losay_in)
-        umv(dev.losaz, losaz_in)
-        # 11 kev
-        # umv(dev.losax, -1.161000, dev.losay, -0.196)
-        # umv(dev.losaz, 1.0000)
-
-    def losa_out(self):
-        losay_out = self._get_user_param_safe("losay", "out")
-        losaz_out = self._get_user_param_safe("losaz", "out")
-        umv(dev.losaz, losaz_out)
-        umv(dev.losay, losay_out)
-
-    def lfzp_info(self, mokev_val=-1):
-
-        if mokev_val == -1:
-            try:
-                mokev_val = dev.mokev.readback.get()
-            except:
-                print(
-                    "Device mokev does not exist. You can specify the energy in keV as an argument instead."
-                )
-                return
-        loptz_val = dev.loptz.read()["loptz"]["value"]
-        distance = -loptz_val + 85.6 + 52
-        print(f"The sample is in a distance of {distance:.1f} mm from the FZP.")
-
-        diameters = [80e-6, 100e-6, 120e-6, 150e-6, 170e-6, 200e-6, 220e-6, 250e-6]
-
-        console = Console()
-        table = Table(
-            title=f"At the current energy of {mokev_val:.4f} keV we have following options:",
-            box=box.SQUARE,
-        )
-        table.add_column("Diameter", justify="center")
-        table.add_column("Focal distance", justify="center")
-        table.add_column("Current beam size", justify="center")
-
-        wavelength = 1.2398e-9 / mokev_val
-
-        for diameter in diameters:
-            outermost_zonewidth = 60e-9
-            focal_distance = diameter * outermost_zonewidth / wavelength
-            beam_size = (
-                -diameter / (focal_distance * 1000) * (focal_distance * 1000 - distance) * 1e6
-            )
-            table.add_row(
-                f"{diameter*1e6:.2f} microns",
-                f"{focal_distance:.2f} mm",
-                f"{beam_size:.2f} microns",
-            )
-
-        console.print(table)
-
-        print("OSA Information:")
-        # print(f"Current losaz %.1f\n", A[losaz])
-        # print("The OSA will collide with the sample plane at %.1f\n\n", 89.3-A[loptz])
-        print(
-            "The numbers presented here are for a sample in the plane of the lamni sample holder.\n"
-        )

csaxs_bec/bec_ipython_client/plugins/cSAXS/__init__.py

@@ -1,2 +0,0 @@
-from .cSAXS_beamline import epics_get, epics_put, fshclose, fshopen, fshstatus
-from .csaxs_bl_checks import cSAXSBeamlineChecks

csaxs_bec/bec_ipython_client/plugins/cSAXS/cSAXS.py

@@ -1,41 +0,0 @@
-# import builtins
-# import datetime
-# import os
-# import subprocess
-# import time
-# from pathlib import Path
-
-# import numpy as np
-from bec_lib import bec_logger
-# from bec_lib.alarm_handler import AlarmBase
-# from bec_lib.pdf_writer import PDFWriter
-from typeguard import typechecked
-
-
-from csaxs_bec.bec_ipython_client.plugins.cSAXS.smaract import cSAXSInitSmaractStages
-from csaxs_bec.bec_ipython_client.plugins.cSAXS.smaract import cSAXSSmaract
-from csaxs_bec.bec_ipython_client.plugins.omny.omny_general_tools import OMNYTools
-from csaxs_bec.bec_ipython_client.plugins.cSAXS.filter_transmission import cSAXSFilterTransmission
-class cSAXSError(Exception):
-    pass
-
-class cSAXS(
-    cSAXSInitSmaractStages,
-    cSAXSSmaract,
-    cSAXSFilterTransmission,
-):
-    def __init__(self, client):
-        self.client = client
-        self.device_manager = client.device_manager
-        self.OMNYTools = OMNYTools(self.client)
-        super().__init__(client=client)
-
-
-# this is the csaxs master file that imports all routines from csaxs
-# can be imported in the bec client by
-# run in bec from folder /sls/x12sa/config/bec/production/csaxs_bec
-# from csaxs_bec.bec_ipython_client.plugins.cSAXS.cSAXS import cSAXS
-# csaxs = cSAXS(bec)
-#
-# then all commands can be accessed by for example
-# csaxs._cSAXS_smaract_stages_.....

csaxs_bec/bec_ipython_client/plugins/cSAXS/csaxs_bl_checks.py

@@ -1,122 +0,0 @@
-import builtins
-import datetime
-import threading
-import time
-
-from bec_lib import bec_logger
-
-logger = bec_logger.logger
-
-if builtins.__dict__.get("bec"):
-    bec = builtins.__dict__.get("bec")
-
-
-class cSAXSBeamlineChecks:
-
-    def __init__(self, *args, **kwargs):
-        super().__init__(*args, **kwargs)
-        self.check_shutter = True
-        self.check_light_available = True
-        self.check_fofb = True
-        self._check_msgs = []
-        self._beam_is_okay = True
-        self._stop_beam_check_event = None
-        self.beam_check_thread = None
-
-    def get_beamline_checks_enabled(self):
-        print(
-            f"Shutter: {self.check_shutter}\nFOFB: {self.check_fofb}\nLight available:"
-            f" {self.check_light_available}"
-        )
-
-    @property
-    def beamline_checks_enabled(self):
-        return {
-            "shutter": self.check_shutter,
-            "fofb": self.check_fofb,
-            "light available": self.check_light_available,
-        }
-
-    @beamline_checks_enabled.setter
-    def beamline_checks_enabled(self, val: bool):
-        self.check_shutter = val
-        self.check_light_available = val
-        self.check_fofb = val
-        self.get_beamline_checks_enabled()
-
-    def _run_beamline_checks(self):
-        msgs = []
-        dev = builtins.__dict__.get("dev")
-        try:
-            if self.check_shutter:
-                shutter_val = dev.x12sa_es1_shutter_status.read(cached=True)
-                if shutter_val["value"].lower() != "open":
-                    self._beam_is_okay = False
-                    msgs.append("Check beam failed: Shutter is closed.")
-            if self.check_light_available:
-                machine_status = dev.sls_machine_status.read(cached=True)
-                if machine_status["value"] not in ["Light Available", "Light-Available"]:
-                    self._beam_is_okay = False
-                    msgs.append("Check beam failed: Light not available.")
-            if self.check_fofb:
-                fast_orbit_feedback = dev.sls_fast_orbit_feedback.read(cached=True)
-                if fast_orbit_feedback["value"] != "running":
-                    self._beam_is_okay = False
-                    msgs.append("Check beam failed: Fast orbit feedback is not running.")
-        except Exception:
-            logger.warning("Failed to check beam.")
-        return msgs
-
-    def _check_beam(self):
-        while not self._stop_beam_check_event.is_set():
-            self._check_msgs = self._run_beamline_checks()
-
-            if not self._beam_is_okay:
-                self._stop_beam_check_event.set()
-            time.sleep(1)
-
-    def _start_beam_check(self):
-        self._beam_is_okay = True
-        self._stop_beam_check_event = threading.Event()
-
-        self.beam_check_thread = threading.Thread(target=self._check_beam, daemon=True)
-        self.beam_check_thread.start()
-
-    def _was_beam_okay(self):
-        self._stop_beam_check_event.set()
-        self.beam_check_thread.join()
-        return self._beam_is_okay
-
-    def _print_beamline_checks(self):
-        for msg in self._check_msgs:
-            logger.warning(msg)
-
-    def _wait_for_beamline_checks(self):
-        self._print_beamline_checks()
-        try:
-            msg = bec.logbook.LogbookMessage()
-            msg.add_text(
-                "<p><mark class='pen-red'><strong>Beamline checks failed at"
-                f" {str(datetime.datetime.now())}: {''.join(self._check_msgs)}</strong></mark></p>"
-            ).add_tag(["BEC", "beam_check"])
-            bec.logbook.send_logbook_message(msg)
-        except Exception:
-            logger.warning("Failed to send update to SciLog.")
-
-        while True:
-            self._beam_is_okay = True
-            self._check_msgs = self._run_beamline_checks()
-            if self._beam_is_okay:
-                break
-            self._print_beamline_checks()
-            time.sleep(1)
-
-        try:
-            msg = bec.logbook.LogbookMessage()
-            msg.add_text(
-                "<p><mark class='pen-red'><strong>Operation resumed at"
-                f" {str(datetime.datetime.now())}.</strong></mark></p>"
-            ).add_tag(["BEC", "beam_check"])
-            bec.logbook.send_logbook_message(msg)
-        except Exception:
-            logger.warning("Failed to send update to SciLog.")

csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_data/filter_attenuation-length_al.txt

@@ -1,601 +0,0 @@
-   4000.00  10.5509
-   4012.90  10.6470
-   4025.83  10.7440
-   4038.81  10.8418
-   4051.83  10.9406
-   4064.90  11.0404
-   4078.00  11.1410
-   4091.15  11.2426
-   4104.34  11.3451
-   4117.57  11.4487
-   4130.85  11.5532
-   4144.17  11.6587
-   4157.53  11.7652
-   4170.93  11.8726
-   4184.38  11.9811
-   4197.87  12.0906
-   4211.41  12.2011
-   4224.98  12.3126
-   4238.60  12.4252
-   4252.27  12.5389
-   4265.98  12.6536
-   4279.73  12.7694
-   4293.53  12.8863
-   4307.37  13.0042
-   4321.26  13.1234
-   4335.19  13.2436
-   4349.17  13.3650
-   4363.19  13.4875
-   4377.26  13.6111
-   4391.37  13.7360
-   4405.53  13.8620
-   4419.73  13.9892
-   4433.98  14.1175
-   4448.28  14.2470
-   4462.62  14.3779
-   4477.01  14.5099
-   4491.44  14.6432
-   4505.92  14.7777
-   4520.45  14.9135
-   4535.02  15.0507
-   4549.65  15.1891
-   4564.31  15.3289
-   4579.03  15.4699
-   4593.79  15.6123
-   4608.60  15.7560
-   4623.46  15.9010
-   4638.37  16.0473
-   4653.32  16.1950
-   4668.33  16.3442
-   4683.38  16.4948
-   4698.48  16.6468
-   4713.62  16.8002
-   4728.82  16.9551
-   4744.07  17.1114
-   4759.36  17.2693
-   4774.71  17.4287
-   4790.10  17.5895
-   4805.54  17.7519
-   4821.04  17.9157
-   4836.58  18.0811
-   4852.17  18.2481
-   4867.82  18.4166
-   4883.51  18.5866
-   4899.26  18.7583
-   4915.05  18.9317
-   4930.90  19.1069
-   4946.80  19.2836
-   4962.75  19.4619
-   4978.75  19.6419
-   4994.80  19.8237
-   5010.90  20.0072
-   5027.06  20.1924
-   5043.26  20.3793
-   5059.52  20.5680
-   5075.84  20.7585
-   5092.20  20.9507
-   5108.62  21.1448
-   5125.09  21.3406
-   5141.61  21.5384
-   5158.19  21.7383
-   5174.82  21.9400
-   5191.50  22.1436
-   5208.24  22.3491
-   5225.03  22.5565
-   5241.88  22.7659
-   5258.78  22.9772
-   5275.73  23.1905
-   5292.74  23.4057
-   5309.81  23.6231
-   5326.93  23.8425
-   5344.10  24.0641
-   5361.33  24.2876
-   5378.62  24.5133
-   5395.96  24.7411
-   5413.35  24.9712
-   5430.81  25.2034
-   5448.32  25.4377
-   5465.88  25.6742
-   5483.50  25.9131
-   5501.18  26.1546
-   5518.92  26.3982
-   5536.71  26.6441
-   5554.56  26.8923
-   5572.47  27.1429
-   5590.44  27.3957
-   5608.46  27.6508
-   5626.54  27.9084
-   5644.68  28.1683
-   5662.88  28.4308
-   5681.14  28.6958
-   5699.46  28.9633
-   5717.83  29.2334
-   5736.27  29.5059
-   5754.76  29.7811
-   5773.31  30.0590
-   5791.93  30.3395
-   5810.60  30.6226
-   5829.33  30.9083
-   5848.13  31.1968
-   5866.98  31.4883
-   5885.90  31.7823
-   5904.88  32.0791
-   5923.91  32.3787
-   5943.01  32.6814
-   5962.17  32.9873
-   5981.40  33.2960
-   6000.68  33.6076
-   6020.03  33.9221
-   6039.44  34.2394
-   6058.91  34.5595
-   6078.44  34.8826
-   6098.04  35.2086
-   6117.70  35.5378
-   6137.42  35.8704
-   6157.21  36.2065
-   6177.06  36.5457
-   6196.98  36.8881
-   6216.96  37.2338
-   6237.00  37.5828
-   6257.11  37.9350
-   6277.28  38.2906
-   6297.52  38.6496
-   6317.82  39.0118
-   6338.19  39.3777
-   6358.63  39.7471
-   6379.13  40.1200
-   6399.69  40.4964
-   6420.33  40.8763
-   6441.03  41.2599
-   6461.79  41.6472
-   6482.63  42.0382
-   6503.53  42.4328
-   6524.49  42.8311
-   6545.53  43.2333
-   6566.63  43.6396
-   6587.80  44.0496
-   6609.04  44.4635
-   6630.35  44.8813
-   6651.73  45.3031
-   6673.17  45.7289
-   6694.69  46.1588
-   6716.27  46.5926
-   6737.93  47.0306
-   6759.65  47.4730
-   6781.44  47.9197
-   6803.31  48.3706
-   6825.24  48.8258
-   6847.25  49.2852
-   6869.32  49.7491
-   6891.47  50.2174
-   6913.69  50.6902
-   6935.98  51.1675
-   6958.34  51.6491
-   6980.77  52.1356
-   7003.28  52.6268
-   7025.86  53.1226
-   7048.51  53.6231
-   7071.24  54.1282
-   7094.03  54.6384
-   7116.91  55.1537
-   7139.85  55.6736
-   7162.87  56.1985
-   7185.96  56.7283
-   7209.13  57.2635
-   7232.38  57.8038
-   7255.69  58.3491
-   7279.09  58.8996
-   7302.55  59.4554
-   7326.10  60.0165
-   7349.72  60.5832
-   7373.41  61.1551
-   7397.19  61.7324
-   7421.03  62.3153
-   7444.96  62.9039
-   7468.96  63.4982
-   7493.04  64.0981
-   7517.20  64.7037
-   7541.44  65.3149
-   7565.75  65.9323
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-   7614.62  67.1849
-   7639.17  67.8201
-   7663.79  68.4612
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-   7788.14  71.7608
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-   7863.71  73.8182
-   7889.06  74.5170
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-   7940.01  75.9348
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-   7991.29  77.3796
-   8017.06  78.1123
-   8042.91  78.8520
-   8068.84  79.5991
-   8094.85  80.3534
-   8120.95  81.1149
-   8147.13  81.8836
-   8173.40  82.6595
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-   8279.32  85.8404
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-   8332.79  87.4766
-   8359.65  88.3065
-   8386.60  89.1443
-   8413.64  89.9900
-   8440.77  90.8436
-   8467.98  91.7062
-   8495.29  92.5774
-   8522.67  93.4567
-   8550.15  94.3443
-   8577.72  95.2403
-   8605.37  96.1451
-   8633.12  97.0584
-   8660.95  97.9803
-   8688.87  98.9109
-   8716.89  99.8503
-   8744.99  100.799
-   8773.19  101.757
-   8801.47  102.724
-   8829.85  103.700
-   8858.32  104.686
-   8886.88  105.681
-   8915.53  106.687
-   8944.27  107.701
-   8973.11  108.726
-   9002.04  109.760
-   9031.06  110.804
-   9060.18  111.859
-   9089.39  112.924
-   9118.69  113.998
-   9148.09  115.083
-   9177.59  116.179
-   9207.18  117.285
-   9236.86  118.401
-   9266.64  119.529
-   9296.52  120.666
-   9326.49  121.816
-   9356.56  122.976
-   9386.72  124.148
-   9416.99  125.330
-   9447.35  126.524
-   9477.81  127.730
-   9508.37  128.946
-   9539.02  130.174
-   9569.78  131.414
-   9600.63  132.666
-   9631.58  133.931
-   9662.63  135.209
-   9693.79  136.498
-   9725.04  137.800
-   9756.39  139.115
-   9787.85  140.441
-   9819.41  141.780
-   9851.07  143.131
-   9882.83  144.496
-   9914.69  145.873
-   9946.65  147.265
-   9978.72  148.671
-   10010.9  150.090
-   10043.2  151.522
-   10075.5  152.968
-   10108.0  154.429
-   10140.6  155.904
-   10173.3  157.393
-   10206.1  158.896
-   10239.0  160.413
-   10272.0  161.946
-   10305.2  163.493
-   10338.4  165.055
-   10371.7  166.632
-   10405.1  168.224
-   10438.7  169.832
-   10472.3  171.455
-   10506.1  173.093
-   10540.0  174.747
-   10574.0  176.417
-   10608.1  178.104
-   10642.3  179.808
-   10676.6  181.527
-   10711.0  183.263
-   10745.5  185.015
-   10780.2  186.785
-   10814.9  188.572
-   10849.8  190.376
-   10884.8  192.197
-   10919.9  194.035
-   10955.1  195.892
-   10990.4  197.767
-   11025.8  199.659
-   11061.4  201.570
-   11097.0  203.498
-   11132.8  205.447
-   11168.7  207.414
-   11204.7  209.400
-   11240.8  211.405
-   11277.1  213.429
-   11313.4  215.474
-   11349.9  217.538
-   11386.5  219.622
-   11423.2  221.725
-   11460.0  223.849
-   11497.0  225.994
-   11534.1  228.159
-   11571.2  230.344
-   11608.6  232.550
-   11646.0  234.778
-   11683.5  237.028
-   11721.2  239.300
-   11759.0  241.593
-   11796.9  243.908
-   11834.9  246.246
-   11873.1  248.607
-   11911.4  250.991
-   11949.8  253.398
-   11988.3  255.827
-   12026.9  258.280
-   12065.7  260.757
-   12104.6  263.257
-   12143.7  265.781
-   12182.8  268.329
-   12222.1  270.902
-   12261.5  273.502
-   12301.0  276.126
-   12340.7  278.776
-   12380.5  281.450
-   12420.4  284.150
-   12460.4  286.877
-   12500.6  289.629
-   12540.9  292.408
-   12581.3  295.212
-   12621.9  298.045
-   12662.6  300.906
-   12703.4  303.794
-   12744.4  306.709
-   12785.5  309.653
-   12826.7  312.624
-   12868.0  315.625
-   12909.5  318.655
-   12951.1  321.713
-   12992.9  324.800
-   13034.8  327.917
-   13076.8  331.067
-   13119.0  334.246
-   13161.3  337.456
-   13203.7  340.696
-   13246.3  343.968
-   13289.0  347.271
-   13331.8  350.607
-   13374.8  353.973
-   13417.9  357.371
-   13461.2  360.802
-   13504.6  364.269
-   13548.1  367.769
-   13591.8  371.301
-   13635.6  374.867
-   13679.6  378.467
-   13723.7  382.103
-   13767.9  385.773
-   13812.3  389.478
-   13856.9  393.217
-   13901.5  396.994
-   13946.4  400.809
-   13991.3  404.660
-   14036.4  408.548
-   14081.7  412.472
-   14127.1  416.434
-   14172.6  420.436
-   14218.3  424.475
-   14264.2  428.552
-   14310.2  432.668
-   14356.3  436.824
-   14402.6  441.022
-   14449.0  445.260
-   14495.6  449.539
-   14542.3  453.858
-   14589.2  458.217
-   14636.2  462.619
-   14683.4  467.064
-   14730.8  471.549
-   14778.3  476.076
-   14825.9  480.648
-   14873.7  485.268
-   14921.7  489.931
-   14969.8  494.637
-   15018.0  499.389
-   15066.5  504.191
-   15115.0  509.040
-   15163.8  513.935
-   15212.7  518.876
-   15261.7  523.864
-   15310.9  528.901
-   15360.3  533.988
-   15409.8  539.123
-   15459.5  544.306
-   15509.3  549.539
-   15559.3  554.823
-   15609.5  560.159
-   15659.8  565.546
-   15710.3  570.984
-   15761.0  576.473
-   15811.8  582.014
-   15862.7  587.611
-   15913.9  593.262
-   15965.2  598.964
-   16016.7  604.719
-   16068.3  610.531
-   16120.1  616.402
-   16172.1  622.326
-   16224.2  628.306
-   16276.5  634.342
-   16329.0  640.437
-   16381.7  646.596
-   16434.5  652.811
-   16487.5  659.084
-   16540.6  665.416
-   16593.9  671.811
-   16647.4  678.268
-   16701.1  684.786
-   16755.0  691.364
-   16809.0  698.004
-   16863.2  704.710
-   16917.5  711.482
-   16972.1  718.318
-   17026.8  725.217
-   17081.7  732.182
-   17136.8  739.214
-   17192.0  746.315
-   17247.4  753.482
-   17303.1  760.717
-   17358.8  768.018
-   17414.8  775.391
-   17470.9  782.836
-   17527.3  790.351
-   17583.8  797.934
-   17640.5  805.587
-   17697.4  813.318
-   17754.4  821.128
-   17811.6  829.008
-   17869.1  836.961
-   17926.7  844.987
-   17984.5  853.094
-   18042.5  861.278
-   18100.6  869.538
-   18159.0  877.874
-   18217.5  886.286
-   18276.3  894.784
-   18335.2  903.364
-   18394.3  912.023
-   18453.6  920.761
-   18513.1  929.582
-   18572.8  938.489
-   18632.7  947.484
-   18692.8  956.561
-   18753.0  965.723
-   18813.5  974.967
-   18874.1  984.303
-   18935.0  993.729
-   18996.0  1003.24
-   19057.3  1012.84
-   19118.7  1022.53
-   19180.4  1032.31
-   19242.2  1042.19
-   19304.2  1052.16
-   19366.5  1062.22
-   19428.9  1072.37
-   19491.6  1082.63
-   19554.4  1092.98
-   19617.4  1103.42
-   19680.7  1113.96
-   19744.1  1124.59
-   19807.8  1135.38
-   19871.7  1146.29
-   19935.7  1157.29
-   20000.0  1168.40
-   20081.3  1182.56
-   20162.8  1196.82
-   20244.8  1211.23
-   20327.0  1225.81
-   20409.6  1240.55
-   20492.5  1255.47
-   20575.8  1270.57
-   20659.4  1285.83
-   20743.3  1301.26
-   20827.6  1316.88
-   20912.2  1332.67
-   20997.2  1348.64
-   21082.5  1364.79
-   21168.1  1381.13
-   21254.1  1397.65
-   21340.5  1414.36
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-   21689.4  1483.11
-   21777.6  1500.78
-   21866.0  1518.66
-   21954.9  1536.73
-   22044.1  1555.01
-   22133.6  1573.50
-   22223.6  1592.19
-   22313.9  1611.09
-   22404.5  1630.19
-   22495.5  1649.51
-   22586.9  1669.05
-   22678.7  1688.80
-   22770.8  1708.77
-   22863.4  1728.96
-   22956.3  1749.38
-   23049.5  1770.02
-   23143.2  1790.88
-   23237.2  1811.97
-   23331.6  1833.30
-   23426.4  1854.85
-   23521.6  1876.64
-   23617.1  1898.66
-   23713.1  1920.93
-   23809.4  1943.44
-   23906.2  1966.19
-   24003.3  1989.19
-   24100.8  2012.43
-   24198.7  2035.93
-   24297.1  2059.67
-   24395.8  2083.67
-   24494.9  2107.92
-   24594.4  2132.44
-   24694.3  2157.20
-   24794.7  2182.24
-   24895.4  2207.53
-   24996.6  2233.09
-   25098.1  2258.92
-   25200.1  2285.02
-   25302.5  2311.40
-   25405.3  2338.05
-   25508.5  2364.98
-   25612.1  2392.19
-   25716.2  2419.68
-   25820.7  2447.45
-   25925.6  2475.50
-   26030.9  2503.85
-   26136.7  2532.50
-   26242.9  2561.42
-   26349.5  2590.64
-   26456.5  2620.16
-   26564.0  2649.97
-   26672.0  2680.08
-   26780.3  2710.49
-   26889.1  2741.21
-   26998.4  2772.24
-   27108.1  2803.57
-   27218.2  2835.21
-   27328.8  2867.17
-   27439.8  2899.44
-   27551.3  2932.02
-   27663.2  2964.91
-   27775.6  2998.14
-   27888.5  3031.69
-   28001.8  3065.56
-   28115.6  3099.75
-   28229.8  3134.27
-   28344.5  3169.12
-   28459.6  3204.30
-   28575.3  3239.80
-   28691.4  3275.66
-   28807.9  3311.85
-   28925.0  3348.37
-   29042.5  3385.23
-   29160.5  3422.44
-   29279.0  3459.98
-   29397.9  3497.87
-   29517.4  3536.09
-   29637.3  3574.69
-   29757.7  3613.62
-   29878.6  3652.90
-   30000.0  3692.52

csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_data/filter_attenuation-length_cr.txt

@@ -1,713 +0,0 @@
- cr Density=7.19, Angle=90.deg
- Photon Energy (eV), Atten Length (microns)
-   4000.00  7.36948
-   4012.90  7.43487
-   4025.83  7.50083
-   4038.81  7.56737
-   4051.83  7.63450
-   4064.90  7.70224
-   4078.00  7.77057
-   4091.15  7.83951
-   4104.34  7.90905
-   4117.57  7.97916
-   4130.85  8.04989
-   4144.17  8.12124
-   4157.53  8.19322
-   4170.93  8.26584
-   4184.38  8.33903
-   4197.87  8.41287
-   4211.41  8.48736
-   4224.98  8.56251
-   4238.60  8.63834
-   4252.27  8.71478
-   4265.98  8.79189
-   4279.73  8.86969
-   4293.53  8.94819
-   4307.37  9.02737
-   4321.26  9.10723
-   4335.19  9.18779
-   4349.17  9.26908
-   4363.19  9.35108
-   4377.26  9.43379
-   4391.37  9.51723
-   4405.53  9.60141
-   4419.73  9.68634
-   4433.98  9.77201
-   4448.28  9.85842
-   4462.62  9.94550
-   4477.01  10.0334
-   4491.44  10.1220
-   4505.92  10.2114
-   4520.45  10.3016
-   4535.02  10.3923
-   4549.65  10.4839
-   4564.31  10.5763
-   4579.03  10.6695
-   4593.79  10.7635
-   4608.60  10.8584
-   4623.46  10.9541
-   4638.37  11.0507
-   4653.32  11.1481
-   4668.33  11.2464
-   4683.38  11.3454
-   4698.48  11.4454
-   4713.62  11.5462
-   4728.82  11.6479
-   4744.07  11.7504
-   4759.36  11.8538
-   4774.71  11.9581
-   4790.10  12.0633
-   4805.54  12.1694
-   4821.04  12.2764
-   4836.58  12.3843
-   4852.17  12.4932
-   4867.82  12.6031
-   4883.51  12.7139
-   4899.26  12.8256
-   4915.05  12.9381
-   4930.90  13.0516
-   4946.80  13.1662
-   4962.75  13.2817
-   4978.75  13.3982
-   4994.80  13.5157
-   5010.90  13.6342
-   5027.06  13.7537
-   5043.26  13.8743
-   5059.52  13.9959
-   5075.84  14.1184
-   5092.20  14.2419
-   5108.62  14.3665
-   5125.09  14.4922
-   5141.61  14.6190
-   5158.19  14.7468
-   5174.82  14.8758
-   5191.50  15.0059
-   5208.24  15.1371
-   5225.03  15.2694
-   5241.88  15.4027
-   5258.78  15.5371
-   5275.73  15.6728
-   5292.74  15.8096
-   5309.81  15.9475
-   5326.93  16.0865
-   5344.10  16.2268
-   5361.33  16.3682
-   5378.62  16.5109
-   5395.96  16.6547
-   5413.35  16.7997
-   5430.81  16.9460
-   5448.32  17.0935
-   5465.88  17.2423
-   5483.50  17.3923
-   5501.18  17.5434
-   5518.92  17.6959
-   5536.71  17.8497
-   5554.56  18.0048
-   5572.47  18.1612
-   5590.44  18.3188
-   5608.46  18.4778
-   5626.54  18.6382
-   5644.68  18.7999
-   5662.88  18.9630
-   5681.14  19.1272
-   5699.46  19.2929
-   5717.83  19.4600
-   5736.27  19.6286
-   5754.76  19.7984
-   5773.31  19.9696
-   5791.93  20.1423
-   5810.60  20.3164
-   5829.33  20.4921
-   5848.13  20.6691
-   5866.98  20.8476
-   5885.90  21.0276
-   5904.88  21.2091
-   5923.91  21.3922
-   5943.01  21.5768
-   5962.17  21.7631
-   5981.40  21.9510
-   5985.00  21.9863
-   5985.10  21.9873
-   5985.20  21.9883
-   5985.30  21.9892
-   5985.40  21.9902
-   5985.50  21.9912
-   5985.60  21.9922
-   5985.70  21.9932
-   5985.80  21.9941
-   5985.90  21.9951
-   5986.00  21.9961
-   5986.10  21.9971
-   5986.20  21.9981
-   5986.30  21.9990
-   5986.40  22.0000
-   5986.50  22.0010
-   5986.60  22.0020
-   5986.70  22.0030
-   5986.80  22.0040
-   5986.90  22.0049
-   5987.00  22.0059
-   5987.10  22.0069
-   5987.20  22.0079
-   5987.30  22.0088
-   5987.40  22.0098
-   5987.50  22.0108
-   5987.60  22.0118
-   5987.70  22.0128
-   5987.80  22.0138
-   5987.90  22.0147
-   5988.00  22.0157
-   5988.10  22.0167
-   5988.20  22.0177
-   5988.30  22.0187
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csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_data/filter_attenuation-length_cu.txt

@@ -1,636 +0,0 @@
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csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_data/filter_attenuation-length_diamond.txt

@@ -1,601 +0,0 @@
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csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_data/filter_attenuation-length_ge.txt

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csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_data/filter_attenuation-length_si.txt

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csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_data/filter_attenuation-length_ti.txt

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csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_data/filter_attenuation-length_zr.txt

@@ -1,901 +0,0 @@
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csaxs_bec/bec_ipython_client/plugins/cSAXS/filter_transmission.py

@@ -1,672 +0,0 @@
-
-"""
-cSAXS exposure-box filter transmission utilities.
-
-This method has been created based on previous spec implementations
-The translation was mainly done by copilot AI.
-
-Implements fil_trans physics:
-- Per-material attenuation-length tables loaded from package 'filter_data/'.
-- Linear interpolation of attenuation length vs. energy (eV).
-- Transmission T = exp(-t / lambda), t in micrometers.
-- Enumeration of all enabled combinations across 4 units x 6 positions.
-- Selection of the combination with transmission closest to a target.
-
-Motion is executed using provided position tables for each filter_array_*_x stage.
-"""
-
-
-#todo
-#check dmm is off
-#X12SA-OP-DMM-EMLS-3010:THRU translation THROUGH
-#X12SA-OP-DMM-EMLS-3030:THRU bragg through
-#X12SA-OP-CCM1:ENERGY-GET > 1
-
-from __future__ import annotations
-
-import math
-from typing import Dict, List, Optional, Tuple
-
-from importlib import resources
-# Resolve the filter_data/ folder via importlib.resources
-import csaxs_bec.bec_ipython_client.plugins.cSAXS.filter_transmission as ft_pkg
-
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get
-
-from bec_lib import bec_logger
-
-import builtins
-
-
-if builtins.__dict__.get("bec") is not None:
-    bec = builtins.__dict__.get("bec")
-    dev = builtins.__dict__.get("dev")
-    umv = builtins.__dict__.get("umv")
-    umvr = builtins.__dict__.get("umvr")
-
-class cSAXSFilterTransmission:
-    """
-    Mixin providing the fil_trans command.
-    Assumes self.client and self.OMNYTools exist.
-
-    Example:
-        csaxs.fil_trans(0.10, energy_kev=6.2)  # dry-run first, then asks to execute
-    """
-
-    # -----------------------------
-    # Material naming & file mapping
-    # -----------------------------
-    _MATERIAL_FILES: Dict[str, Optional[str]] = {
-        "none": None,
-        "diam": "filter_attenuation-length_diamond.txt",
-        "al":   "filter_attenuation-length_al.txt",
-        "si":   "filter_attenuation-length_si.txt",
-        "ti":   "filter_attenuation-length_ti.txt",
-        "cu":   "filter_attenuation-length_cu.txt",
-        "ge":   "filter_attenuation-length_ge.txt",
-        "zr":   "filter_attenuation-length_zr.txt",
-        # optional; provide file if you enable Fe5
-        "fe":   "filter_attenuation-length_fe.txt",
-    }
-
-    # -----------------------------------------
-    # Exposure-box filter configuration (4 x 6)
-    #
-    # Current hardware (per your message):
-    # Unit 1 (filter_array_1_x): out, Si400, Ge300, Ti800, Zr20
-    # Unit 2 (filter_array_2_x): out, Si200, Si3200, Ti400, Cu20
-    # Unit 3 (filter_array_3_x): out, Si100, Si1600, Ti200, Ti3200, Fe5
-    # Unit 4 (filter_array_4_x): out, Si50,  Si800,  Ti100, Ti1600, Ti20
-    #
-    # Positions 1..6 = [out, m1, m2, m3, m4, m5]
-    # Each entry: ((mat1, th1_um), (mat2, th2_um), enabled_bool)
-    # -----------------------------------------
-    _FILTERS: List[Tuple[Tuple[str, float], Tuple[str, float], bool]] = [
-        # Unit 1
-        (("none", 0.0),   ("none", 0.0),  True),   # out
-        (("si",   400.0), ("none", 0.0),  True),   # Si400
-        (("ge",   300.0), ("none", 0.0),  True),   # Ge300
-        (("ti",   800.0), ("none", 0.0),  True),   # Ti800
-        (("zr",    20.0), ("none", 0.0),  True),   # Zr20
-        (("none",  0.0),  ("none", 0.0),  False),  # unused
-
-        # Unit 2
-        (("none", 0.0),   ("none", 0.0),  True),   # out
-        (("si",   200.0), ("none", 0.0),  True),   # Si200
-        (("si",  3200.0), ("none", 0.0),  True),   # Si3200
-        (("ti",   400.0), ("none", 0.0),  True),   # Ti400
-        (("cu",    20.0), ("none", 0.0),  True),   # Cu20
-        (("none",  0.0),  ("none", 0.0),  False),  # unused
-
-        # Unit 3
-        (("none", 0.0),   ("none", 0.0),  True),   # out
-        (("si",   100.0), ("none", 0.0),  True),   # Si100
-        (("si",  1600.0), ("none", 0.0),  True),   # Si1600
-        (("ti",   200.0), ("none", 0.0),  True),   # Ti200
-        (("ti",  3200.0), ("none", 0.0),  True),   # Ti3200
-        (("fe",     5.0), ("none", 0.0),  False),  # Fe5 (disabled unless data file provided)
-
-        # Unit 4
-        (("none", 0.0),   ("none", 0.0),  True),   # out
-        (("si",    50.0), ("none", 0.0),  True),   # Si50
-        (("si",   800.0), ("none", 0.0),  True),   # Si800
-        (("ti",   100.0), ("none", 0.0),  True),   # Ti100
-        (("ti",  1600.0), ("none", 0.0),  True),   # Ti1600
-        (("ti",    20.0), ("none", 0.0),  True),   # Ti20
-    ]
-
-    _UNITS = 4
-    _PER_UNIT = 6
-
-    # -----------------------------------------
-    # Motion mapping: user-scale coordinates
-    # [out, m1, m2, m3, m4, m5]
-    # -----------------------------------------
-    _POSITIONS_USER: List[List[Optional[float]]] = [
-        # Unit 1 (filter_array_1_x)
-        [25.0, 17.9, 7.9, -2.3, -12.1, None],
-        # Unit 2 (filter_array_2_x)
-        [25.5, 17.6, 7.8, -2.3, -12.3, None],
-        # Unit 3 (filter_array_3_x)
-        [25.8, 17.6, 7.8, -2.2, -12.3, -22.3],  # Fe5 at -22.3
-        # Unit 4 (filter_array_4_x)
-        [25.0, 17.5, 7.5, -2.2, -12.4, -22.2],
-    ]
-
-    # Device axis names (adjust if different)
-    _AXES: List[str] = [
-        "filter_array_1_x",
-        "filter_array_2_x",
-        "filter_array_3_x",
-        "filter_array_4_x",
-    ]
-
-    # -----------------------------
-    # Construction / Internals
-    # -----------------------------
-    def __init__(self, **kwargs):
-        super().__init__(**kwargs)
-        # In multiple-inheritance setups our __init__ might be skipped; guard lazily too.
-        self._attlen_cache: Dict[str, Tuple[List[float], List[float]]] = {}
-
-    def _ensure_internal_state(self):
-        """Lazy guard for robustness if __init__ wasn’t called."""
-        if not hasattr(self, "_attlen_cache"):
-            self._attlen_cache = {}
-
-    # -----------------------------
-    # Public API
-    # -----------------------------
-    def fil_trans(
-        self,
-        transmission: Optional[float] = None,
-        energy_kev: Optional[float] = None,
-        print_only: bool = True,
-    ) -> Optional[None]:
-        """
-        Set exposure-box filters to achieve a target transmission.
-
-        If called without 'transmission', prints usage and current status.
-
-        Safety:
-        - fil_trans(1) is always allowed.
-        - fil_trans(<1) is only allowed if:
-            - epics_get("X12SA-OP-DMM-EMLS-3010:THRU") == 1  (DMM translation THROUGH)
-            - epics_get("X12SA-OP-DMM-EMLS-3030:THRU") == 1  (DMM rotation THROUGH)
-            - epics_get("X12SA-OP-CCM1:ENERGY-GET") > 1      (CCM active, energy in keV)
-        Otherwise, prompt with default NO.
-        """
-
-        # --- No-arg usage helper ---
-        if transmission is None:
-            print("\nUsage example:")
-            print("  csaxs.fil_trans(0.10, energy_kev=6.2)")
-            print("  First parameter is the transmission factor requested.")
-            print("  If energy is not specified it will be read from the CCM energy PV.")
-            print("\nCurrent filter transmission:")
-            self._fil_trans_report(energy_kev=energy_kev)
-            return None
-
-        # --- Validation of transmission ---
-        try:
-            transmission = float(transmission)
-        except Exception:
-            raise ValueError("Transmission must be numeric.")
-
-        if not (0.0 < transmission <= 1.0):
-            raise ValueError("Transmission must be between 0 and 1.")
-
-        # -------------------------------------------------------
-        # SAFETY CHECK (before any calculation/motion):
-        # Only allow fil_trans < 1 when DMM is in THROUGH (both)
-        # and CCM energy > 1 keV. fil_trans(1) is always allowed.
-        # -------------------------------------------------------
-        if transmission < 1.0:
-            try:
-                dmm_trans = float(epics_get("X12SA-OP-DMM-EMLS-3010:THRU"))
-            except Exception:
-                dmm_trans = -1
-            try:
-                dmm_rot = float(epics_get("X12SA-OP-DMM-EMLS-3030:THRU"))
-            except Exception:
-                dmm_rot = -1
-            try:
-                ccm_energy = float(epics_get("X12SA-OP-CCM1:ENERGY-GET"))
-            except Exception:
-                ccm_energy = -1
-
-            allowed = (dmm_trans == 1) and (dmm_rot == 1) and (ccm_energy > 1)
-
-            if not allowed:
-                print("\n⚠️  SAFETY WARNING: Reducing transmission (< 1) typically requires:")
-                print("   - DMM translation in THROUGH (THRU == 1)")
-                print("   - DMM rotation in THROUGH (THRU == 1)")
-                print("   - CCM energy > 1 keV")
-                print("\nCurrent state:")
-                print(f"   DMM translation THRU : {dmm_trans}")
-                print(f"   DMM rotation THRU    : {dmm_rot}")
-                print(f"   CCM energy (keV)     : {ccm_energy}")
-
-                # Ask user (default = NO)
-                if hasattr(self, "OMNYTools") and hasattr(self.OMNYTools, "yesno"):
-                    proceed = self.OMNYTools.yesno(
-                        "Conditions not satisfied. Proceed anyway?",
-                        default="n",
-                    )
-                else:
-                    # Safe fallback
-                    proceed = False
-
-                if not proceed:
-                    print("Aborted. Transmission unchanged.")
-                    return None
-        
-        # --- Energy handling (EPICS only) ---
-        if energy_kev is None:
-            try:
-                energy_kev = float(epics_get("X12SA-OP-CCM1:ENERGY-GET"))
-            except Exception as exc:
-                raise RuntimeError(
-                    "Energy not specified and could not read EPICS PV "
-                    "'X12SA-OP-CCM1:ENERGY-GET'."
-                ) from exc
-        else:
-            energy_kev = float(energy_kev)
-
-
-        # --- Summary header ---
-        print("\nExposure-box filter transmission request")
-        print("-" * 60)
-        print(f"Target transmission : {transmission:.6e}")
-        print(f"Photon energy       : {energy_kev:.3f} keV")
-        print(f"Mode                : {'PRINT ONLY' if print_only else 'EXECUTE'}")
-        print("-" * 60)
-
-        # --- Compute best combination ---
-        best = self._find_best_combination(transmission, energy_kev)
-
-        # --- Report selected combination ---
-        self._print_combination(best, energy_kev, header="Selected combination")
-
-        # Nearby: print only code + transmission
-        neighbors = self._neighbors_around_best(transmission, energy_kev, span=5)
-        if neighbors:
-            print("\nNearby combinations (by transmission proximity):")
-            for row in neighbors:
-                print(f"{row['transmission']:9.3e}")
-
-        # --- Dry run prompt ---
-        if print_only:
-            print("\n[DRY RUN] No motion executed yet.")
-            if hasattr(self, "OMNYTools") and hasattr(self.OMNYTools, "yesno"):
-                if self.OMNYTools.yesno(
-                    "Execute motion to the selected filter combination now?",
-                    "y",  # default YES
-                ):
-                    self._execute_combination(best, energy_kev)
-                else:
-                    print("Execution skipped.")
-            else:
-                # If yesno not available, default to 'skip' on print_only
-                print("No interactive prompt available. Execution skipped (print_only=True).")
-            return None
-
-        # --- Execute motion directly ---
-        self._execute_combination(best, energy_kev)
-        return None
-
-    # -----------------------------
-    # Physics helpers
-    # -----------------------------
-    def _load_attlen(self, material: str) -> Tuple[List[float], List[float]]:
-        """
-        Load and cache attenuation-length table for a material from package resources.
-
-        Returns:
-            energies_eV (list), attlen_um (list)
-        """
-        self._ensure_internal_state()
-
-        material = material.lower()
-        if material in self._attlen_cache:
-            return self._attlen_cache[material]
-
-        fname = self._MATERIAL_FILES.get(material)
-        if not fname:
-            # 'none' or unsupported mapped to empty
-            self._attlen_cache[material] = ([], [])
-            return ([], [])
-
-        energies_eV: List[float] = []
-        attlen_um: List[float] = []
-
-        # Load from installed package: <this_module>/filter_data/<fname>
-        res = resources.files(ft_pkg) / "filter_data" / fname
-        try:
-            # as_file yields a concrete filesystem path even if package is zipped
-            with resources.as_file(res) as p:
-                with p.open("r") as f:
-                    for line in f:
-                        line = line.strip()
-                        if not line:
-                            continue
-                        parts = line.split()
-                        if len(parts) < 2:
-                            continue
-                        energies_eV.append(float(parts[0]))
-                        attlen_um.append(float(parts[1]))
-        except FileNotFoundError as e:
-            raise FileNotFoundError(
-                f"Attenuation data file not found for '{material}': {fname} "
-                f"(looked in package filter_data)"
-            ) from e
-
-        if not energies_eV:
-            raise ValueError(
-                f"Attenuation data for material '{material}' is empty or invalid: {fname}"
-            )
-
-        self._attlen_cache[material] = (energies_eV, attlen_um)
-        return energies_eV, attlen_um
-
-    def _attenuation_length_um(self, energy_kev: float, material: str) -> float:
-        """
-        Linear interpolation of attenuation length λ(energy) in µm.
-        Input energy in keV; tables are in eV.
-        """
-        material = material.lower()
-        if material == "none":
-            return float("inf")  # No attenuation
-
-        energies_eV, attlen_um = self._load_attlen(material)
-        if not energies_eV:
-            # unsupported mapped above
-            raise ValueError(f"Unsupported material or missing data: '{material}'")
-
-        e_ev = energy_kev * 1000.0
-
-        # Clip to the nearest edge for practicality
-        if e_ev <= energies_eV[0]:
-            bec_logger.logger.warning(
-                f"[cSAXS] energy {energy_kev:.3f} keV below table range for {material}; "
-                f"clipping to {energies_eV[0]/1000.0:.3f} keV."
-            )
-            return attlen_um[0]
-        if e_ev >= energies_eV[-1]:
-            bec_logger.logger.warning(
-                f"[cSAXS] energy {energy_kev:.3f} keV above table range for {material}; "
-                f"clipping to {energies_eV[-1]/1000.0:.3f} keV."
-            )
-            return attlen_um[-1]
-
-        # Binary search for interval
-        lo, hi = 0, len(energies_eV) - 1
-        while hi - lo > 1:
-            mid = (lo + hi) // 2
-            if energies_eV[mid] >= e_ev:
-                hi = mid
-            else:
-                lo = mid
-
-        e_lo, e_hi = energies_eV[lo], energies_eV[hi]
-        lam_lo, lam_hi = attlen_um[lo], attlen_um[hi]
-        lam = (e_ev - e_lo) / (e_hi - e_lo) * (lam_hi - lam_lo) + lam_lo
-        return lam
-
-    def _position_transmission(
-        self,
-        pos_entry: Tuple[Tuple[str, float], Tuple[str, float], bool],
-        energy_kev: float,
-    ) -> Optional[float]:
-        """Transmission for a single position (possibly two layers)."""
-        (mat1, th1), (mat2, th2), enabled = pos_entry
-        if not enabled:
-            return None
-        T1 = 1.0
-        T2 = 1.0
-        if mat1 != "none" and th1 > 0.0:
-            lam1 = self._attenuation_length_um(energy_kev, mat1)
-            T1 = math.exp(-th1 / lam1)
-        if mat2 != "none" and th2 > 0.0:
-            lam2 = self._attenuation_length_um(energy_kev, mat2)
-            T2 = math.exp(-th2 / lam2)
-        return T1 * T2
-
-    def _all_combinations(self, energy_kev: float) -> List[dict]:
-        """
-        Enumerate all enabled combinations across 4 units.
-        Returns a list of dicts sorted by transmission ascending:
-            {
-                'code': 'abcd'  # positions 1..6 per unit
-                'indices': [i0, i1, i2, i3],  # 0..5
-                'materials': [ ((m1,t1), (m2,t2)|None ), ... for 4 units ]
-                'transmission': float
-            }
-        """
-        # Slice filters per unit
-        units = [
-            self._FILTERS[u * self._PER_UNIT : (u + 1) * self._PER_UNIT]
-            for u in range(self._UNITS)
-        ]
-
-        # Precompute per-position transmissions
-        per_pos_T: List[List[Optional[float]]] = [
-            [self._position_transmission(pos_entry, energy_kev) for pos_entry in unit]
-            for unit in units
-        ]
-
-        combos: List[dict] = []
-        for i0 in range(self._PER_UNIT):
-            T0 = per_pos_T[0][i0]
-            if T0 is None:
-                continue
-            for i1 in range(self._PER_UNIT):
-                T1 = per_pos_T[1][i1]
-                if T1 is None:
-                    continue
-                for i2 in range(self._PER_UNIT):
-                    T2 = per_pos_T[2][i2]
-                    if T2 is None:
-                        continue
-                    for i3 in range(self._PER_UNIT):
-                        T3 = per_pos_T[3][i3]
-                        if T3 is None:
-                            continue
-
-                        T = T0 * T1 * T2 * T3
-                        indices = [i0, i1, i2, i3]
-                        code = "".join(str(i + 1) for i in indices)
-
-                        # Collect materials/thickness for reporting
-                        mats = []
-                        for u, idx in enumerate(indices):
-                            (m1, t1), (m2, t2), _ = units[u][idx]
-                            mats.append(((m1, t1), (m2, t2) if (m2 != "none" and t2 > 0.0) else None))
-
-                        combos.append(
-                            {
-                                "code": code,
-                                "indices": indices,
-                                "materials": mats,
-                                "transmission": T,
-                            }
-                        )
-
-        combos.sort(key=lambda c: c["transmission"])  # ascending
-        return combos
-
-    def _find_best_combination(self, target_T: float, energy_kev: float) -> dict:
-        """Pick combination with transmission closest to target."""
-        combos = self._all_combinations(energy_kev)
-        best = min(combos, key=lambda c: abs(c["transmission"] - target_T))
-        return best
-
-    def _neighbors_around_best(
-        self, target_T: float, energy_kev: float, span: int = 5
-    ) -> List[dict]:
-        """Return a few combinations around the best, by proximity in transmission."""
-        combos = self._all_combinations(energy_kev)
-        ranked = sorted(combos, key=lambda c: abs(c["transmission"] - target_T))
-        return ranked[1 : 1 + span]  # exclude best itself
-
-    # -----------------------------
-    # Formatting & motion
-    # -----------------------------
-    def _print_combination(self, comb: dict, energy_kev: float, header: Optional[str] = None):
-        if header:
-            print(f"\n{header}:")
-        code = comb["code"]
-        T = comb["transmission"]
-        print(f"  Filters {code}  transmission at {energy_kev:.3f} keV = {T:9.3e}")
-        # Per-unit detail for the selected combination only
-        for u, matinfo in enumerate(comb["materials"], start=1):
-            first, second = matinfo
-            (m1, t1) = first
-            pos = int(code[u - 1])
-            if second is not None:
-                (m2, t2) = second
-                print(
-                    f"    unit {u}: #{pos}  "
-                    f"{t1:4.0f} mu {m1:<4} + {t2:4.0f} mu {m2:<4}"
-                )
-            else:
-                if m1 != "none" and t1 > 0.0:
-                    print(f"    unit {u}: #{pos}  {t1:4.0f} mu {m1:<4}")
-                else:
-                    print(f"    unit {u}: #{pos}  ----- out")
-
-
-
-    def _execute_combination(self, comb: dict, energy_kev: float):
-        """
-        Execute motion to the indices encoded in 'comb["code"]'.
-
-        Mapping:
-        - code 'abcd' → per-unit index (a,b,c,d) ∈ {1..6}
-        - positions are looked up from _POSITIONS_USER
-        - axes are defined in _AXES
-
-        Motion uses: umv(dev.axis, position, dev.axis2, position2, ...)
-        """
-
-        indices = comb["indices"]  # 0-based per unit
-        move_args = []  # Collect (device, position) pairs
-
-        print("\nExecuting combined motion:")
-        for unit_idx, pos_idx in enumerate(indices):
-            pos_list = self._POSITIONS_USER[unit_idx]
-            target_pos = pos_list[pos_idx]
-            if target_pos is None:
-                raise RuntimeError(
-                    f"Unit {unit_idx+1} position {pos_idx+1} has no defined coordinate."
-                )
-
-            axis_name = self._AXES[unit_idx]
-            axis_obj = getattr(dev, axis_name)
-            print(f"  {axis_name} → {target_pos:.3f}")
-            move_args.extend([axis_obj, target_pos])
-
-        umv(*move_args)
-
-        print("\nVerifying final positions:")
-        for unit_idx in range(self._UNITS):
-            axis_name = self._AXES[unit_idx]
-            axis_obj = getattr(dev, axis_name)
-            try:
-                actual = float(axis_obj.readback.get())
-                print(f"  {axis_name} = {actual:.3f}")
-            except Exception:
-                print(f"  {axis_name}: readback unavailable")
-
-        achieved_T = comb["transmission"]
-        print(f"\nAchieved transmission (approx.): {achieved_T:9.3e} at {energy_kev:.3f} keV")
-
-
-
-    def _fil_trans_report(self, tol: float = 0.1, energy_kev: Optional[float] = None) -> None:
-        """
-        Report the currently active exposure‑box filter combination.
-        Determines stage positions via dev.<axis>.readback.get()
-        with a tolerance window of ±tol relative to nominal positions.
-
-        Parameters
-        ----------
-        tol : float
-            Tolerance for matching positions.
-        energy_kev : float, optional
-            Photon energy in keV. If None, tries to read from dev.mokev or defaults to 6.2 keV.
-        """
-
-        # Ensure global dev is available
-        if dev is None:
-            print("ERROR: Global 'dev' object not found.")
-            return
-
-        # --- Energy handling (EPICS only) ---
-        if energy_kev is None:
-            try:
-                energy_kev = float(epics_get("X12SA-OP-CCM1:ENERGY-GET"))
-            except Exception as exc:
-                raise RuntimeError(
-                    "Energy not specified and could not read EPICS PV "
-                    "'X12SA-OP-CCM1:ENERGY-GET'."
-                ) from exc
-        else:
-            energy_kev = float(energy_kev)
-
-
-        print("\nCurrent filter transmission report")
-        print("-" * 60)
-        print(f"Photon energy : {energy_kev:.3f} keV")
-
-        indices = []  # 0–5 per unit
-
-        for unit_idx, axis_name in enumerate(self._AXES):
-            axis_obj = getattr(dev, axis_name, None)
-            if axis_obj is None:
-                print(f"ERROR: Device axis '{axis_name}' not found.")
-                return
-
-            try:
-                rb = float(axis_obj.readback.get())
-            except Exception:
-                print(f"ERROR: readback unavailable for axis {axis_name}")
-                return
-
-            # Match readback to nearest nominal
-            pos_list = self._POSITIONS_USER[unit_idx]
-            best_idx = None
-            for i, nominal in enumerate(pos_list):
-                if nominal is None:
-                    continue
-                if abs(rb - nominal) <= tol:
-                    best_idx = i
-                    break
-
-            if best_idx is None:
-                print(f"Unit {unit_idx+1}: readback {rb:.3f} does not match any known position.")
-                return
-
-            indices.append(best_idx)
-
-        # Build combination code
-        code = "".join(str(i + 1) for i in indices)
-        print(f"Matched filter code: {code}")
-
-        # Compute transmission and materials
-        units = [
-            self._FILTERS[u * self._PER_UNIT : (u + 1) * self._PER_UNIT]
-            for u in range(self._UNITS)
-        ]
-
-        materials = []
-        total_T = 1.0
-
-        for u, pos_idx in enumerate(indices):
-            (m1, t1), (m2, t2), enabled = units[u][pos_idx]
-            T = self._position_transmission(units[u][pos_idx], energy_kev)
-            if T is None:
-                print(f"Unit {u+1}: position disabled")
-                T = 1.0
-            total_T *= T
-
-            if m2 != "none" and t2 > 0:
-                materials.append(((m1, t1), (m2, t2)))
-            else:
-                materials.append(((m1, t1), None))
-
-        # Print detailed report
-        self.OMNYTools.printgreenbold(f"Total transmission: {total_T:.6e}")
-        print("-" * 60)
-
-        for u, matinfo in enumerate(materials, start=1):
-            (m1, t1), second = matinfo
-            pos = indices[u - 1] + 1
-            if second:
-                m2, t2 = second
-                print(f" unit {u}: #{pos} {t1:4.0f} µm {m1:<4} + {t2:4.0f} µm {m2:<4}")
-            else:
-                if m1 != "none" and t1 > 0:
-                    print(f" unit {u}: #{pos} {t1:4.0f} µm {m1:<4}")
-                else:
-                    print(f" unit {u}: #{pos} ----- out")

csaxs_bec/bec_ipython_client/plugins/cSAXS/smaract.py

@@ -1,447 +0,0 @@
-
-import builtins
-import time
-
-from bec_lib import bec_logger
-
-# Logger initialization
-logger = bec_logger.logger
-
-# Pull BEC globals if present
-bec = builtins.__dict__.get("bec")
-dev = builtins.__dict__.get("dev")
-umv = builtins.__dict__.get("umv")
-umvr = builtins.__dict__.get("umvr")
-
-
-class cSAXSInitSmaractStagesError(Exception):
-    pass
-
-
-class cSAXSInitSmaractStages:
-    """
-    Runtime SmarAct utilities for referencing and moving to initial positions.
-
-    This class no longer relies on static mappings. Instead, it:
-    - discovers available devices from `list(dev.keys())`
-    - reads the numeric channel/axis from each device's `user_parameter['bl_smar_stage']`
-    - reads `init_position` from `user_parameter['init_position']`
-    """
-
-    def __init__(self, client) -> None:
-        self.client = client
-
-    # ------------------------------
-    # Internal helpers (runtime-based)
-    # ------------------------------
-    def _yesno(self, question: str, default: str = "y") -> bool:
-        """
-        Use OMNYTools.yesno if available; otherwise default to 'yes' (or fallback to input()).
-        """
-        try:
-            if hasattr(self, "OMNYTools") and hasattr(self.OMNYTools, "yesno"):
-                return self.OMNYTools.yesno(question, default)
-        except Exception:
-            pass
-
-        # Fallback: default answer without interaction
-        # (Safe default: 'y' proceeds; adjust if you want interactive input)
-        logger.info(f"[cSAXS] (yesno fallback) {question} -> default '{default}'")
-        return (default or "y").lower().startswith("y")
-
-    def _get_user_param_safe(self, device_name: str, key: str):
-        """
-        Safe access to device user parameters from current BEC session.
-        """
-        try:
-            return dev[device_name].user_parameter.get(key)
-        except Exception:
-            return None
-
-    def _iter_session_devices(self):
-        """
-        Yield device names available in current BEC session.
-        """
-        if dev is None:
-            return
-        for name in list(dev.keys()):
-            yield name
-
-    def _build_session_axis_map(self, selection: set | None = None) -> dict:
-        """
-        Build runtime axis map {device_name: channel} for devices that define 'bl_smar_stage'.
-        If 'selection' is provided, restrict to names in selection.
-        """
-        axis_map = {}
-        missing = []
-        for name in self._iter_session_devices() or []:
-            if selection is not None and name not in selection:
-                continue
-            ch = self._get_user_param_safe(name, "bl_smar_stage")
-            if ch is None:
-                missing.append(name)
-                continue
-            try:
-                axis_map[name] = int(ch)
-            except Exception:
-                missing.append(name)
-
-        if missing and selection is None:
-            logger.info(
-                "[cSAXS] Devices without 'bl_smar_stage' (ignored): " + ", ".join(sorted(missing))
-            )
-        return axis_map
-
-    def _get_device_object(self, device_name: str):
-        """
-        Return the live device object from BEC 'dev'.
-        """
-        try:
-            return getattr(dev, device_name)
-        except Exception:
-            return None
-
-    # ------------------------------
-    # Public API
-    # ------------------------------
-    def smaract_reference_stages(self, force: bool = False, devices_to_reference=None):
-        """
-        Reference SmarAct stages using runtime discovery.
-
-        Parameters
-        ----------
-        force : bool, optional
-            If True, re-reference ALL selected stages.
-            If False (default), only reference stages that are currently NOT referenced.
-
-        devices_to_reference : iterable of str or str, optional
-            If provided, only these devices will be considered for referencing.
-            If None, all devices in the current session that define 'bl_smar_stage' are considered.
-
-        Behavior
-        --------
-        - Runtime-based: reads axis channel from user_parameter['bl_smar_stage'].
-        - If devices_to_reference is given → restrict referencing to those.
-        - If force=False → skip devices already referenced.
-        - If force=True → re-reference selected devices always.
-        - Only newly referenced devices are passed to
-          smaract_components_to_initial_position(devices_to_move=[...]) afterwards.
-
-        Examples
-        --------
-        Reference only stages that are NOT referenced yet (default)
-            csaxs.smaract_reference_stages()
-
-        Force re-reference of all stages
-            csaxs.smaract_reference_stages(force=True)
-
-        Reference only specific stages
-            csaxs.smaract_reference_stages(
-                devices_to_reference=["sl3trxi", "sl3trxo", "xbpm3x"]
-            )
-
-        Reference selected stages and force re-referencing
-            csaxs.smaract_reference_stages(
-                devices_to_reference=["sl4trxi", "sl4trxo"],
-                force=True
-            )
-
-        Reference a single device
-            csaxs.smaract_reference_stages(
-                devices_to_reference="xbimtrx"
-            )
-
-        Reference only the selected devices (skip already-referenced ones)
-            csaxs.smaract_reference_stages(
-                devices_to_reference=["sl3trxi", "sl4trxo", "sl5trxt"]
-            )
-
-        Check referencing status of all stages
-            csaxs.smaract_check_all_referenced()
-        """
-        # Normalize selection
-        if isinstance(devices_to_reference, str):
-            devices_to_reference = [devices_to_reference]
-        selection = set(devices_to_reference) if devices_to_reference else None
-
-        # Build axis map for selected devices (or all devices present)
-        axis_map = self._build_session_axis_map(selection=selection)
-        if selection:
-            unknown = sorted(list(selection - set(axis_map.keys())))
-            if unknown:
-                print(f"Unknown devices requested or missing 'bl_smar_stage' (ignored): {unknown}")
-
-
-        newly_referenced = []
-        already_referenced = []
-        failed = []
-        to_verify = []   # devices that need a final verification
-
-        print("\nStarting SmarAct referencing...\n")
-
-        for dev_name in sorted(axis_map.keys()):
-            ch = axis_map[dev_name]
-            d = self._get_device_object(dev_name)
-
-            if d is None:
-                print(f"{dev_name}: device not accessible, skipping.")
-                failed.append(dev_name)
-                continue
-
-            try:
-                is_ref = d.controller.axis_is_referenced(ch)
-
-                # Skip if already referenced and not forcing
-                if is_ref and not force:
-                    print(f"{dev_name}: already referenced, skipping.")
-                    already_referenced.append(dev_name)
-                    continue
-
-                # Start referencing
-                print(f"{dev_name}: referencing axis...")
-                d.controller.set_closed_loop_move_speed(ch, 1)
-                d.controller.find_reference_mark(ch, 0, 1000, 1)
-                time.sleep(0.1)
-
-                # Add to list for final verification
-                to_verify.append((dev_name, ch, d))
-
-            except Exception as e:
-                print(f"Error referencing {dev_name} (axis {ch}): {e}")
-                failed.append(dev_name)
-
-        time.sleep(1.0)
-
-        print("\nVerifying referencing state...\n")
-
-        for dev_name, ch, d in to_verify:
-            try:
-                if d.controller.axis_is_referenced(ch):
-                    print(f"{dev_name}: successfully referenced.")
-                    newly_referenced.append(dev_name)
-                else:
-                    print(f"{dev_name}: referencing FAILED.")
-                    failed.append(dev_name)
-            except Exception as e:
-                print(f"{dev_name}: verification error: {e}")
-                failed.append(dev_name)
-
-        # --- Summary ---
-        print("\n--- Referencing summary ---")
-        print(f"Newly referenced:          {newly_referenced}")
-        print(f"Already referenced (kept): {already_referenced}")
-        print(f"Failed:                    {failed}")
-        print("-----------------------------------------\n")
-
-        # --- Move newly referenced only ---
-        if newly_referenced:
-            print("Moving newly referenced stages to initial positions...")
-            self.smaract_components_to_initial_position(devices_to_move=newly_referenced)
-        else:
-            print("No newly referenced stages.")
-
-    def smaract_check_all_referenced(self):
-        """
-        Check reference state for all SmarAct devices that define 'bl_smar_stage'.
-        """
-        axis_map = self._build_session_axis_map(selection=None)
-        for dev_name in sorted(axis_map.keys()):
-            ch = axis_map[dev_name]
-            d = self._get_device_object(dev_name)
-            if d is None:
-                print(f"{dev_name}: device not accessible or unsupported.")
-                continue
-            try:
-                if d.controller.axis_is_referenced(ch):
-                    print(f"{dev_name} (axis {ch}) is referenced.")
-                else:
-                    print(f"{dev_name} (axis {ch}) is NOT referenced.")
-            except Exception as e:
-                print(f"Error checking {dev_name} (axis {ch}): {e}")
-
-    def smaract_components_to_initial_position(self, devices_to_move=None):
-        """
-        Move selected (or all) SmarAct-based components to their configured init_position.
-
-        Parameters
-        ----------
-        devices_to_move : iterable of str or str, optional
-            Specific device names to move (e.g. ["xbpm3x", "sl3trxi"]).
-            If None, all devices in the current session that define 'bl_smar_stage' are considered.
-
-        Behavior
-        --------
-        - Runtime-based: uses user_parameter['bl_smar_stage'] (numeric channel) and 'init_position'.
-        - Only axes that are referenced will be moved.
-        - Unreferenced axes are skipped with a WARNING; the operation continues.
-        - Devices missing `init_position` are skipped and listed.
-        - At the end, a summary warns if some stages could not be moved because they were not referenced.
-        """
-        # Normalize selection
-        if isinstance(devices_to_move, str):
-            devices_to_move = [devices_to_move]
-        selection = set(devices_to_move) if devices_to_move else None
-
-        # Resolve axis map based on selection
-        axis_map = self._build_session_axis_map(selection=selection)
-        unknown_requested = []
-        if selection:
-            unknown_requested = sorted(list(selection - set(axis_map.keys())))
-            if unknown_requested:
-                logger.warning(
-                    "[cSAXS] Requested devices unknown or missing 'bl_smar_stage': "
-                    + ", ".join(unknown_requested)
-                )
-
-        # First confirmation: intent
-        scope_desc = "all SmarAct-based components" if selection is None else "the selected SmarAct-based components"
-        if not self._yesno(
-            f"Do you want to move {scope_desc} to the init position as defined in the config file?",
-            "y",
-        ):
-            return
-
-        planned_moves = []
-        not_referenced = []
-        missing_params = []
-        inaccessible_devices = []
-
-        # --- Pre-check phase ---
-        for dev_name in sorted(axis_map.keys()):
-            d = self._get_device_object(dev_name)
-            if d is None:
-                logger.warning(f"[cSAXS] Device {dev_name} not accessible, skipping.")
-                inaccessible_devices.append(dev_name)
-                continue
-
-            ch = axis_map[dev_name]
-            try:
-                # Reference check
-                if not d.controller.axis_is_referenced(ch):
-                    not_referenced.append(dev_name)
-                    continue
-
-                # Fetch init_position (from user parameters)
-                init_pos = self._get_user_param_safe(dev_name, "init_position")
-                if init_pos is None:
-                    missing_params.append(dev_name)
-                    continue
-
-                planned_moves.append((dev_name, float(init_pos)))
-
-            except Exception as exc:
-                logger.error(f"[cSAXS] Error during pre-check for {dev_name}: {exc}")
-
-        if not planned_moves:
-            # Nothing to move—still summarize why.
-            header = "\nNo motions planned. Summary of issues:"
-            lines = []
-            if not_referenced:
-                lines.append(" - Not referenced: " + ", ".join(sorted(not_referenced)))
-            if missing_params:
-                lines.append(" - Missing init_position: " + ", ".join(sorted(missing_params)))
-            if inaccessible_devices:
-                lines.append(" - Not accessible: " + ", ".join(sorted(inaccessible_devices)))
-            if unknown_requested:
-                lines.append(" - Unknown requested: " + ", ".join(sorted(unknown_requested)))
-            if not lines:
-                lines.append(" - (No eligible devices or nothing to do.)")
-
-            print(header)
-            for line in lines:
-                print(line)
-            logger.warning("[cSAXS] Nothing to do.")
-            return
-
-        # --- Summary table ---
-        print("\nPlanned SmarAct motions to initial position:")
-        print("-" * 60)
-        print(f"{'Device':<35} {'Init position':>20}")
-        print("-" * 60)
-        for dev_name, init_pos in planned_moves:
-            print(f"{dev_name:<35} {init_pos:>20.6g}")
-        print("-" * 60)
-
-        # Notes / diagnostics
-        if selection is not None:
-            print("\nNote: Only the following devices were requested to move:")
-            print(", ".join(sorted(selection)))
-        if unknown_requested:
-            print("\nNote: The following requested devices are unknown and were ignored:")
-            print(", ".join(unknown_requested))
-        if not_referenced:
-            print("\nNote: The following devices are NOT referenced and will be skipped:")
-            print(", ".join(sorted(not_referenced)))
-        if missing_params:
-            print("\nNote: The following devices have no init_position defined and will be skipped:")
-            print(", ".join(sorted(missing_params)))
-        if inaccessible_devices:
-            print("\nNote: The following devices were not accessible and will be skipped:")
-            print(", ".join(sorted(inaccessible_devices)))
-
-        # Second confirmation: execution
-        if not self._yesno("Proceed with the motions listed above?", "y"):
-            logger.info("[cSAXS] Motion to initial position aborted by user.")
-            return
-
-        # --- Execution phase (SIMULTANEOUS MOTION) ---
-        if umv is None:
-            logger.error("[cSAXS] 'umv' is not available in this session.")
-            return
-
-        # Build a flat argument list: [dev1, pos1, dev2, pos2, ...]
-        move_args = []
-        for dev_name, init_pos in planned_moves:
-            d = self._get_device_object(dev_name)
-            if d is None:
-                logger.error(f"[cSAXS] Could not access {dev_name}, skipping.")
-                continue
-            move_args.append(d)
-            move_args.append(init_pos)
-            logger.info(f"[cSAXS] Preparing move: {dev_name} -> {init_pos}")
-
-        if not move_args:
-            logger.warning("[cSAXS] No valid devices left for simultaneous motion.")
-            return
-
-        # Trigger simultaneous move
-        try:
-            logger.info(f"[cSAXS] Starting simultaneous motion of {len(planned_moves)} devices.")
-            umv(*move_args)  # simultaneous move
-        except Exception as exc:
-            logger.error(f"[cSAXS] Simultaneous motion failed: {exc}")
-            return
-
-        logger.info("[cSAXS] Simultaneous SmarAct motion to initial positions completed.")
-
-        # Final warning summary about unreferenced devices
-        if not_referenced:
-            logger.warning(
-                "[cSAXS] Some stages were NOT moved because they are not referenced:\n"
-                + ", ".join(sorted(not_referenced))
-                + "\nPlease reference these axes and re-run if needed."
-            )
-
-
-class cSAXSSmaract:
-    def __init__(self, client) -> None:
-        self.client = client
-
-    def _get_user_param_safe(self, device_name: str, key: str):
-        try:
-            return dev[device_name].user_parameter.get(key)
-        except Exception:
-            return None
-
-    def fshn1in(self):
-        """
-        Move fast shutter n1 to its 'in' position defined in user parameters.
-        """
-        in_pos = self._get_user_param_safe("fast_shutter_n1_x", "in")
-        if in_pos is None:
-            logger.error("[cSAXS] No 'in' position defined for fast_shutter_n1_x.")
-            return
-        if umv is None:
-            logger.error("[cSAXS] 'umv' is not available in this session.")
-            return
-        umv(dev.fast_shutter_n1_x, in_pos)

csaxs_bec/bec_ipython_client/plugins/flomni/__init__.py

@@ -1 +0,0 @@
-from .flomni import Flomni

csaxs_bec/bec_ipython_client/plugins/flomni/correction_flomni_20210300_360deg.txt

@@ -1,351 +0,0 @@
-corr_elements = 175 
-corr_angle[0] = 0.100000 
-corr_angle[1] = 1.001000 
-corr_angle[2] = 1.902000 
-corr_angle[3] = 2.798000 
-corr_angle[4] = 7.305000 
-corr_angle[5] = 8.204000 
-corr_angle[6] = 9.104000 
-corr_angle[7] = 10.005000 
-corr_angle[8] = 14.504000 
-corr_angle[9] = 15.404000 
-corr_angle[10] = 16.304000 
-corr_angle[11] = 17.204000 
-corr_angle[12] = 21.704000 
-corr_angle[13] = 22.604000 
-corr_angle[14] = 23.504000 
-corr_angle[15] = 24.404000 
-corr_angle[16] = 28.904000 
-corr_angle[17] = 29.804000 
-corr_angle[18] = 30.704000 
-corr_angle[19] = 31.604000 
-corr_angle[20] = 36.104000 
-corr_angle[21] = 37.004000 
-corr_angle[22] = 37.904000 
-corr_angle[23] = 38.804000 
-corr_angle[24] = 43.305000 
-corr_angle[25] = 44.205000 
-corr_angle[26] = 45.104000 
-corr_angle[27] = 46.005000 
-corr_angle[28] = 50.504000 
-corr_angle[29] = 51.404000 
-corr_angle[30] = 52.305000 
-corr_angle[31] = 53.205000 
-corr_angle[32] = 57.705000 
-corr_angle[33] = 58.605000 
-corr_angle[34] = 59.505000 
-corr_angle[35] = 60.405000 
-corr_angle[36] = 64.904000 
-corr_angle[37] = 65.804000 
-corr_angle[38] = 66.704000 
-corr_angle[39] = 67.604000 
-corr_angle[40] = 72.104000 
-corr_angle[41] = 73.004000 
-corr_angle[42] = 73.904000 
-corr_angle[43] = 74.804000 
-corr_angle[44] = 79.304000 
-corr_angle[45] = 80.204000 
-corr_angle[46] = 81.104000 
-corr_angle[47] = 82.005000 
-corr_angle[48] = 86.505000 
-corr_angle[49] = 87.404000 
-corr_angle[50] = 88.304000 
-corr_angle[51] = 89.205000 
-corr_angle[52] = 93.704000 
-corr_angle[53] = 94.604000 
-corr_angle[54] = 95.505000 
-corr_angle[55] = 96.404000 
-corr_angle[56] = 100.904000 
-corr_angle[57] = 101.804000 
-corr_angle[58] = 102.704000 
-corr_angle[59] = 103.604000 
-corr_angle[60] = 108.104000 
-corr_angle[61] = 109.004000 
-corr_angle[62] = 109.904000 
-corr_angle[63] = 110.804000 
-corr_angle[64] = 115.304000 
-corr_angle[65] = 116.204000 
-corr_angle[66] = 117.104000 
-corr_angle[67] = 118.004000 
-corr_angle[68] = 122.504000 
-corr_angle[69] = 123.404000 
-corr_angle[70] = 124.304000 
-corr_angle[71] = 125.204000 
-corr_angle[72] = 129.704000 
-corr_angle[73] = 130.604000 
-corr_angle[74] = 131.504000 
-corr_angle[75] = 132.404000 
-corr_angle[76] = 136.904000 
-corr_angle[77] = 137.804000 
-corr_angle[78] = 138.701000 
-corr_angle[79] = 139.604000 
-corr_angle[80] = 144.104000 
-corr_angle[81] = 145.004000 
-corr_angle[82] = 145.904000 
-corr_angle[83] = 146.804000 
-corr_angle[84] = 151.304000 
-corr_angle[85] = 152.204000 
-corr_angle[86] = 153.104000 
-corr_angle[87] = 154.004000 
-corr_angle[88] = 158.504000 
-corr_angle[89] = 159.404000 
-corr_angle[90] = 160.304000 
-corr_angle[91] = 161.204000 
-corr_angle[92] = 165.704000 
-corr_angle[93] = 166.604000 
-corr_angle[94] = 167.504000 
-corr_angle[95] = 168.404000 
-corr_angle[96] = 172.904000 
-corr_angle[97] = 173.805000 
-corr_angle[98] = 174.704000 
-corr_angle[99] = 180.104000 
-corr_angle[100] = 183.704000 
-corr_angle[101] = 184.603000 
-corr_angle[102] = 185.504000 
-corr_angle[103] = 190.904000 
-corr_angle[104] = 191.805000 
-corr_angle[105] = 192.704000 
-corr_angle[106] = 198.104000 
-corr_angle[107] = 199.004000 
-corr_angle[108] = 199.904000 
-corr_angle[109] = 205.304000 
-corr_angle[110] = 206.204000 
-corr_angle[111] = 207.104000 
-corr_angle[112] = 212.504000 
-corr_angle[113] = 213.404000 
-corr_angle[114] = 214.304000 
-corr_angle[115] = 219.704000 
-corr_angle[116] = 220.604000 
-corr_angle[117] = 221.504000 
-corr_angle[118] = 226.904000 
-corr_angle[119] = 227.804000 
-corr_angle[120] = 228.704000 
-corr_angle[121] = 234.104000 
-corr_angle[122] = 235.004000 
-corr_angle[123] = 235.904000 
-corr_angle[124] = 241.304000 
-corr_angle[125] = 242.204000 
-corr_angle[126] = 243.104000 
-corr_angle[127] = 248.504000 
-corr_angle[128] = 249.404000 
-corr_angle[129] = 250.304000 
-corr_angle[130] = 255.704000 
-corr_angle[131] = 256.604000 
-corr_angle[132] = 257.504000 
-corr_angle[133] = 262.904000 
-corr_angle[134] = 263.804000 
-corr_angle[135] = 264.704000 
-corr_angle[136] = 270.104000 
-corr_angle[137] = 271.004000 
-corr_angle[138] = 271.904000 
-corr_angle[139] = 277.304000 
-corr_angle[140] = 278.205000 
-corr_angle[141] = 279.104000 
-corr_angle[142] = 284.504000 
-corr_angle[143] = 285.405000 
-corr_angle[144] = 286.304000 
-corr_angle[145] = 291.703000 
-corr_angle[146] = 292.604000 
-corr_angle[147] = 293.504000 
-corr_angle[148] = 298.904000 
-corr_angle[149] = 299.804000 
-corr_angle[150] = 300.704000 
-corr_angle[151] = 306.104000 
-corr_angle[152] = 307.004000 
-corr_angle[153] = 307.904000 
-corr_angle[154] = 313.304000 
-corr_angle[155] = 314.204000 
-corr_angle[156] = 315.104000 
-corr_angle[157] = 320.504000 
-corr_angle[158] = 321.404000 
-corr_angle[159] = 322.304000 
-corr_angle[160] = 327.704000 
-corr_angle[161] = 328.605000 
-corr_angle[162] = 329.504000 
-corr_angle[163] = 334.904000 
-corr_angle[164] = 335.804000 
-corr_angle[165] = 336.705000 
-corr_angle[166] = 342.104000 
-corr_angle[167] = 343.004000 
-corr_angle[168] = 343.904000 
-corr_angle[169] = 349.304000 
-corr_angle[170] = 350.204000 
-corr_angle[171] = 351.104000 
-corr_angle[172] = 356.504000 
-corr_angle[173] = 357.404000 
-corr_angle[174] = 358.304000 
-corr_pos[0] = 0.012330 
-corr_pos[1] = 0.024870 
-corr_pos[2] = 0.037262 
-corr_pos[3] = 0.049438 
-corr_pos[4] = 0.108462 
-corr_pos[5] = 0.119791 
-corr_pos[6] = 0.130986 
-corr_pos[7] = 0.142044 
-corr_pos[8] = 0.195045 
-corr_pos[9] = 0.205834 
-corr_pos[10] = 0.216589 
-corr_pos[11] = 0.226402 
-corr_pos[12] = 0.271931 
-corr_pos[13] = 0.281684 
-corr_pos[14] = 0.290769 
-corr_pos[15] = 0.299392 
-corr_pos[16] = 0.337986 
-corr_pos[17] = 0.345178 
-corr_pos[18] = 0.352253 
-corr_pos[19] = 0.358528 
-corr_pos[20] = 0.379520 
-corr_pos[21] = 0.382947 
-corr_pos[22] = 0.386110 
-corr_pos[23] = 0.388887 
-corr_pos[24] = 0.395645 
-corr_pos[25] = 0.396154 
-corr_pos[26] = 0.396679 
-corr_pos[27] = 0.396367 
-corr_pos[28] = 0.392400 
-corr_pos[29] = 0.392530 
-corr_pos[30] = 0.391826 
-corr_pos[31] = 0.391325 
-corr_pos[32] = 0.379188 
-corr_pos[33] = 0.376449 
-corr_pos[34] = 0.373195 
-corr_pos[35] = 0.369588 
-corr_pos[36] = 0.343021 
-corr_pos[37] = 0.336754 
-corr_pos[38] = 0.330310 
-corr_pos[39] = 0.323447 
-corr_pos[40] = 0.281171 
-corr_pos[41] = 0.272735 
-corr_pos[42] = 0.263888 
-corr_pos[43] = 0.254469 
-corr_pos[44] = 0.203024 
-corr_pos[45] = 0.192980 
-corr_pos[46] = 0.182359 
-corr_pos[47] = 0.170780 
-corr_pos[48] = 0.111580 
-corr_pos[49] = 0.101222 
-corr_pos[50] = 0.090051 
-corr_pos[51] = 0.077918 
-corr_pos[52] = 0.015225 
-corr_pos[53] = 0.003876 
-corr_pos[54] = -0.007756 
-corr_pos[55] = -0.020383 
-corr_pos[56] = -0.084910 
-corr_pos[57] = -0.096848 
-corr_pos[58] = -0.108732 
-corr_pos[59] = -0.121432 
-corr_pos[60] = -0.184349 
-corr_pos[61] = -0.195904 
-corr_pos[62] = -0.207113 
-corr_pos[63] = -0.219319 
-corr_pos[64] = -0.274799 
-corr_pos[65] = -0.284942 
-corr_pos[66] = -0.294809 
-corr_pos[67] = -0.305437 
-corr_pos[68] = -0.352114 
-corr_pos[69] = -0.359689 
-corr_pos[70] = -0.367451 
-corr_pos[71] = -0.375629 
-corr_pos[72] = -0.404347 
-corr_pos[73] = -0.407683 
-corr_pos[74] = -0.410857 
-corr_pos[75] = -0.414904 
-corr_pos[76] = -0.424625 
-corr_pos[77] = -0.424357 
-corr_pos[78] = -0.424411 
-corr_pos[79] = -0.424615 
-corr_pos[80] = -0.421392 
-corr_pos[81] = -0.419977 
-corr_pos[82] = -0.417860 
-corr_pos[83] = -0.416400 
-corr_pos[84] = -0.398108 
-corr_pos[85] = -0.392613 
-corr_pos[86] = -0.386455 
-corr_pos[87] = -0.380338 
-corr_pos[88] = -0.341288 
-corr_pos[89] = -0.332298 
-corr_pos[90] = -0.322767 
-corr_pos[91] = -0.311630 
-corr_pos[92] = -0.256798 
-corr_pos[93] = -0.244808 
-corr_pos[94] = -0.232932 
-corr_pos[95] = -0.219785 
-corr_pos[96] = -0.158685 
-corr_pos[97] = -0.146198 
-corr_pos[98] = -0.130743 
-corr_pos[99] = -0.054066 
-corr_pos[100] = -0.001498 
-corr_pos[101] = 0.012010 
-corr_pos[102] = 0.025195 
-corr_pos[103] = 0.094982 
-corr_pos[104] = 0.109235 
-corr_pos[105] = 0.120813 
-corr_pos[106] = 0.179893 
-corr_pos[107] = 0.192147 
-corr_pos[108] = 0.201902 
-corr_pos[109] = 0.245092 
-corr_pos[110] = 0.250501 
-corr_pos[111] = 0.255536 
-corr_pos[112] = 0.280598 
-corr_pos[113] = 0.280673 
-corr_pos[114] = 0.282529 
-corr_pos[115] = 0.293286 
-corr_pos[116] = 0.292713 
-corr_pos[117] = 0.291123 
-corr_pos[118] = 0.288721 
-corr_pos[119] = 0.288260 
-corr_pos[120] = 0.286480 
-corr_pos[121] = 0.271630 
-corr_pos[122] = 0.268004 
-corr_pos[123] = 0.265418 
-corr_pos[124] = 0.239187 
-corr_pos[125] = 0.233224 
-corr_pos[126] = 0.226652 
-corr_pos[127] = 0.189034 
-corr_pos[128] = 0.180302 
-corr_pos[129] = 0.170931 
-corr_pos[130] = 0.125760 
-corr_pos[131] = 0.116433 
-corr_pos[132] = 0.106845 
-corr_pos[133] = 0.057551 
-corr_pos[134] = 0.048531 
-corr_pos[135] = 0.038276 
-corr_pos[136] = -0.012292 
-corr_pos[137] = -0.021223 
-corr_pos[138] = -0.030046 
-corr_pos[139] = -0.077647 
-corr_pos[140] = -0.085863 
-corr_pos[141] = -0.093816 
-corr_pos[142] = -0.138532 
-corr_pos[143] = -0.145584 
-corr_pos[144] = -0.152699 
-corr_pos[145] = -0.192594 
-corr_pos[146] = -0.200980 
-corr_pos[147] = -0.208816 
-corr_pos[148] = -0.241983 
-corr_pos[149] = -0.248319 
-corr_pos[150] = -0.253789 
-corr_pos[151] = -0.276869 
-corr_pos[152] = -0.279240 
-corr_pos[153] = -0.281538 
-corr_pos[154] = -0.294317 
-corr_pos[155] = -0.295586 
-corr_pos[156] = -0.296029 
-corr_pos[157] = -0.297443 
-corr_pos[158] = -0.297185 
-corr_pos[159] = -0.295946 
-corr_pos[160] = -0.284463 
-corr_pos[161] = -0.282598 
-corr_pos[162] = -0.281260 
-corr_pos[163] = -0.256509 
-corr_pos[164] = -0.250326 
-corr_pos[165] = -0.244372 
-corr_pos[166] = -0.204043 
-corr_pos[167] = -0.196147 
-corr_pos[168] = -0.187928 
-corr_pos[169] = -0.131831 
-corr_pos[170] = -0.121351 
-corr_pos[171] = -0.110548 
-corr_pos[172] = -0.038951 
-corr_pos[173] = -0.025887 
-corr_pos[174] = -0.012501 

csaxs_bec/bec_ipython_client/plugins/flomni/flomni_optics_mixin.py

@@ -1,177 +0,0 @@
-import time
-
-from rich import box
-from rich.console import Console
-from rich.table import Table
-
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put, fshclose
-
-
-class FlomniOpticsMixin:
-    @staticmethod
-    def _get_user_param_safe(device, var):
-        param = dev[device].user_parameter
-        if not param or param.get(var) is None:
-            raise ValueError(f"Device {device} has no user parameter definition for {var}.")
-        return param.get(var)
-
-    def feye_out(self):
-        fshclose()
-        self.foptics_in()
-        feyex_out = self._get_user_param_safe("feyex", "out")
-        umv(dev.feyex, feyex_out)
-
-        epics_put("XOMNYI-XEYE-ACQ:0", 2)
-        # move rotation stage to zero to avoid problems with wires
-        umv(dev.fsamroy, 0)
-        # umv(dev.fttrx1, 9.2)
-
-    def feye_in(self):
-        bec.queue.next_dataset_number += 1
-        # umv(dev.fttrx1, -17)
-
-        feyex_in = self._get_user_param_safe("feyex", "in")
-        feyey_in = self._get_user_param_safe("feyey", "in")
-        umv(dev.feyex, feyex_in, dev.feyey, feyey_in)
-        #self.align.update_frame()
-
-    def _ffzp_in(self):
-        foptx_in = self._get_user_param_safe("foptx", "in")
-        fopty_in = self._get_user_param_safe("fopty", "in")
-        umv(dev.foptx, foptx_in)
-        umv(
-            dev.fopty, fopty_in
-        )  # for 7.2567 keV and 150 mu, 60 nm fzp, loptz 83.6000 for propagation 1.4 mm
-
-    def ffzp_in(self):
-        """
-        move in the flomni zone plate.
-        This will disable rt feedback, move the FZP and re-enabled the feedback.
-        """
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_disable()
-
-        self._ffzp_in()
-
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_enable_with_reset()
-
-    def foptics_in(self):
-        """
-        Move in the flomni optics, including the FZP and the OSA.
-        """
-        self.ffzp_in()
-        self.fosa_in()
-
-    def foptics_out(self):
-        """Move out the flomni optics"""
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_disable()
-
-        self.fosa_out()
-        fopty_out = self._get_user_param_safe("fopty", "out")
-        umv(dev.fopty, fopty_out)
-
-        if "rtx" in dev and dev.rtx.enabled:
-            time.sleep(1)
-            dev.rtx.controller.feedback_enable_with_reset()
-
-    def fosa_in(self):
-        # 6.2 keV, 170 um FZP
-        # umv(dev.losax, -1.4450000, dev.losay, -0.1800)
-        # umv(dev.losaz, -1)
-        # 6.7, 170
-        # umv(dev.losax, -1.4850, dev.losay, -0.1930)
-        # umv(dev.losaz, 1.0000)
-        # 7.2, 150
-        fosax_in = self._get_user_param_safe("fosax", "in")
-        fosay_in = self._get_user_param_safe("fosay", "in")
-        fosaz_in = self._get_user_param_safe("fosaz", "in")
-        dev.fosax.limits = [fosax_in - 0.1, fosax_in + 0.1]
-        dev.fosay.limits = [fosay_in - 0.1, fosay_in + 0.1]
-        dev.fosaz.limits = [fosaz_in - 0.1, fosaz_in + 0.1]
-        umv(dev.fosax, fosax_in, dev.fosay, fosay_in)
-        umv(dev.fosaz, fosaz_in)
-
-        # 11 kev
-        # umv(dev.losax, -1.161000, dev.losay, -0.196)
-        # umv(dev.losaz, 1.0000)
-
-    def fosa_out(self):
-        self.ensure_fheater_up()
-        curtain_is_triggered = dev.foptz.controller.fosaz_light_curtain_is_triggered()
-        if not curtain_is_triggered:
-            fosaz_out = self._get_user_param_safe("fosaz", "out")
-            dev.fosaz.limits = [fosaz_out - 0.1, fosaz_out + 0.1]
-            umv(dev.fosaz, fosaz_out)
-        fosax_out = self._get_user_param_safe("fosax", "out")
-        dev.fosax.limits = [fosax_out - 0.1, fosax_out + 0.1]
-        umv(dev.fosax, fosax_out)
-
-    def ffzp_info(self, mokev_val=-1):
-
-        if mokev_val == -1:
-            try:
-                mokev_val = dev.mokev.readback.get()
-            except:
-                print(
-                    "Device mokev does not exist. You can specify the energy in keV as an argument instead."
-                )
-                return
-        foptz_val = dev.foptz.readback.get()
-        distance = -foptz_val + 43.15 + 36.7
-        print(f"\nThe sample is in a distance of \033[1m{distance:.1f} mm\033[0m from the FZP.\n")
-        print(f"At the current energy of {mokev_val:.4f} keV we have following options:\n")
-
-        diameters = [80e-6, 100e-6, 120e-6, 150e-6, 170e-6, 200e-6, 220e-6, 250e-6]
-
-        console = Console()
-        table = Table(title="Outermost zone width \033[1m60 nm\033[0m", box=box.SQUARE)
-        table.add_column("Diameter", justify="center")
-        table.add_column("Focal distance", justify="center")
-        table.add_column("Current beam size", justify="center")
-
-        wavelength = 1.2398e-9 / mokev_val
-
-        for diameter in diameters:
-            outermost_zonewidth = 60e-9
-            focal_distance = diameter * outermost_zonewidth / wavelength * 1000
-            beam_size = -diameter / (focal_distance * 1000) * (focal_distance - distance) * 1e9
-            table.add_row(
-                f"{diameter*1e6:.2f} microns",
-                f"{focal_distance:.2f} mm",
-                f"{beam_size:.2f} microns",
-            )
-
-        console.print(table)
-
-        diameters = [150e-6, 250e-6]
-
-        console = Console()
-        table = Table(title="Outermost zone width \033[1m30 nm\033[0m", box=box.SQUARE)
-        table.add_column("Diameter", justify="center")
-        table.add_column("Focal distance", justify="center")
-        table.add_column("Current beam size", justify="center")
-
-        wavelength = 1.2398e-9 / mokev_val
-
-        for diameter in diameters:
-            outermost_zonewidth = 30e-9
-            focal_distance = diameter * outermost_zonewidth / wavelength * 1000
-            beam_size = -diameter / (focal_distance * 1000) * (focal_distance - distance) * 1e9
-            table.add_row(
-                f"{diameter*1e6:.2f} microns",
-                f"{focal_distance:.2f} mm",
-                f"{beam_size:.2f} microns",
-            )
-
-        console.print(table)
-
-        fosaz_val = dev.fosaz.readback.get()
-
-        print("\nOSA Information:")
-        print(f"  Current fosaz {fosaz_val:.1f}")
-        print(
-            f"  The OSA will collide with a normal OMNY pin at fosaz \033[1m{(33-fosaz_val):.1f}\033[0m"
-        )
-        print(f"  Remaining space: \033[1m{-fosaz_val+(33-foptz_val):.1f}\033[0m")

csaxs_bec/bec_ipython_client/plugins/flomni/gui_tools.py

@@ -1,225 +0,0 @@
-import builtins
-
-from bec_widgets.cli.client import BECDockArea
-
-# from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
-
-if builtins.__dict__.get("bec") is not None:
-    bec = builtins.__dict__.get("bec")
-    dev = builtins.__dict__.get("dev")
-    umv = builtins.__dict__.get("umv")
-    umvr = builtins.__dict__.get("umvr")
-
-
-class flomniGuiToolsError(Exception):
-    pass
-
-
-class flomniGuiTools:
-
-    def __init__(self):
-        self.text_box = None
-        self.progressbar = None
-
-    def set_client(self, client):
-        self.client = client
-        self.gui = self.client.gui
-
-    def flomnigui_show_gui(self):
-        if "flomni" in self.gui.windows:
-            self.gui.flomni.show()
-        else:
-            self.gui.new("flomni")
-
-    def flomnigui_stop_gui(self):
-        self.gui.flomni.hide()
-
-    def flomnigui_raise(self):
-        self.gui.flomni.raise_window()
-
-    # def flomnigui_show_xeyealign(self):
-    #     self.flomnigui_show_gui()
-    #     if self.xeyegui is None:
-    #         self.flomnigui_remove_all_docks()
-    #         self.xeyegui = self.gui.flomni.new("xeyegui").new("XRayEye")
-    #         # start live
-    #         if not dev.cam_xeye.live_mode:
-    #             dev.cam_xeye.live_mode = True
-
-    def flomnigui_show_xeyealign(self):
-        self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("xeyegui"):
-            self.flomnigui_remove_all_docks()
-            self.xeyegui = self.gui.flomni.new("xeyegui").new("XRayEye")
-            # start live
-            if not dev.cam_xeye.live_mode:
-                dev.cam_xeye.live_mode = True
-
-
-    def _flomnigui_check_attribute_not_exists(self, attribute_name):
-        if hasattr(self.gui,"flomni"):
-            if hasattr(self.gui.flomni,attribute_name):
-                return False
-        return True
-
-
-    def flomnigui_show_cameras(self):
-        self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("camera_gripper") or self._flomnigui_check_attribute_not_exists("camera_overview"):
-            self.flomnigui_remove_all_docks()
-            camera_gripper_image = self.gui.flomni.new("camera_gripper").new("Image")
-            if self._flomnicam_check_device_exists(dev.cam_flomni_gripper):
-                camera_gripper_image.image(("cam_flomni_gripper", "preview"))
-                camera_gripper_image.lock_aspect_ratio = True
-                camera_gripper_image.enable_fps_monitor = True
-                camera_gripper_image.enable_toolbar = False
-                camera_gripper_image.outer_axes = False
-                camera_gripper_image.inner_axes = False
-                dev.cam_flomni_gripper.start_live_mode()
-            else:
-                print("Cannot open camera_gripper. Device does not exist.")
-            camera_overview_image = self.gui.flomni.new("camera_overview").new("Image")
-            if self._flomnicam_check_device_exists(dev.cam_flomni_overview):
-                camera_overview_image.image(("cam_flomni_overview", "preview"))
-                camera_overview_image.lock_aspect_ratio = True
-                camera_overview_image.enable_fps_monitor = True
-                camera_overview_image.enable_toolbar = False
-                camera_overview_image.outer_axes = False
-                camera_overview_image.inner_axes = False
-                dev.cam_flomni_overview.start_live_mode()
-            else:
-                print("Cannot open camera_overview. Device does not exist.")
-
-    def flomnigui_remove_all_docks(self):
-        #dev.cam_flomni_overview.stop_live_mode()
-        #dev.cam_flomni_gripper.stop_live_mode()
-        #dev.cam_xeye.live_mode = False
-        self.gui.flomni.delete_all() 
-        self.progressbar = None
-        self.text_box = None
-
-    def flomnigui_idle(self):
-        self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("idle_text_box"):
-            self.flomnigui_remove_all_docks()
-            idle_text_box = self.gui.flomni.new("idle_textbox").new("TextBox")
-        text = (
-            "<pre>"
-            + " ,---.,--. ,-----. ,--.   ,--.,--.  ,--.,--. \n"
-            + "/  .-'|  |'  .-.  '|   `.'   ||  ,'.|  ||  | \n"
-            + "|  `-,|  ||  | |  ||  |'.'|  ||  |' '  ||  | \n"
-            + "|  .-'|  |'  '-'  '|  |   |  ||  | `   ||  | \n"
-            + "`--'  `--' `-----' `--'   `--'`--'  `--'`--' \n"
-            + "</pre>"
-        )
-        idle_text_box.set_html_text(text)
-
-    def flomnigui_docs(self, filename: str | None = None):
-        import csaxs_bec
-        from pathlib import Path
-
-        print("The general flOMNI documentation is at \nhttps://sls-csaxs.readthedocs.io/en/latest/user/ptychography/flomni.html#user-ptychography-flomni")
-
-        csaxs_bec_basepath = Path(csaxs_bec.__file__).parent
-        docs_folder = (
-            csaxs_bec_basepath /
-            "bec_ipython_client" / "plugins" / "flomni" / "docs"
-        )
-
-        if not docs_folder.is_dir():
-            raise NotADirectoryError(f"Docs folder not found: {docs_folder}")
-
-        pdfs = sorted(docs_folder.glob("*.pdf"))
-        if not pdfs:
-            raise FileNotFoundError(f"No PDF files found in {docs_folder}")
-
-        # --- Resolve PDF ------------------------------------------------------
-        if filename is not None:
-            pdf_file = docs_folder / filename
-            if not pdf_file.exists():
-                raise FileNotFoundError(f"Requested file not found: {filename}")
-        else:
-            print("\nAvailable flOMNI documentation PDFs:\n")
-            for i, pdf in enumerate(pdfs, start=1):
-                print(f"  {i:2d}) {pdf.name}")
-            print()
-
-            while True:
-                try:
-                    choice = int(input(f"Select a file (1–{len(pdfs)}): "))
-                    if 1 <= choice <= len(pdfs):
-                        pdf_file = pdfs[choice - 1]
-                        break
-                    print(f"Enter a number between 1 and {len(pdfs)}.")
-                except ValueError:
-                    print("Invalid input. Please enter a number.")
-
-        # --- GUI handling (active existence check) ----------------------------
-        self.flomnigui_show_gui()
-
-        if self._flomnigui_check_attribute_not_exists("PdfViewerWidget"):
-            self.flomnigui_remove_all_docks()
-            self.pdf_viewer = self.gui.flomni.new(widget="PdfViewerWidget")
-
-        # --- Load PDF ---------------------------------------------------------
-        self.pdf_viewer.PdfViewerWidget.load_pdf(str(pdf_file.resolve()))
-        print(f"\nLoaded: {pdf_file.name}\n")
-
-
-    def _flomnicam_check_device_exists(self, device):
-        try:
-            device
-        except:
-            return False
-        else:
-            return True
-
-    def flomnigui_show_progress(self):
-        self.flomnigui_show_gui()
-        if self._flomnigui_check_attribute_not_exists("progressbar"):
-            self.flomnigui_remove_all_docks()
-            # Add a new dock with a RingProgressBar widget
-            self.progressbar = self.gui.flomni.new("progressbar").new("RingProgressBar")
-            # Customize the size of the progress ring
-            self.progressbar.set_line_widths(20)
-            # Disable automatic updates and manually set the self.progressbar value
-            self.progressbar.enable_auto_updates(False)
-            # Set precision for the self.progressbar display
-            self.progressbar.set_precision(1)  # Display self.progressbar with one decimal places
-            # Setting multiple rigns with different values
-            self.progressbar.set_number_of_bars(3)
-            self.progressbar.rings[0].set_update("manual")
-            self.progressbar.rings[1].set_update("manual")
-            self.progressbar.rings[2].set_update("scan")
-            # Set the values of the rings to 50, 75, and 25 from outer to inner ring
-            # self.progressbar.set_value([50, 75])
-            # Add a new dock with a TextBox widget
-            self.text_box = self.gui.flomni.new(name="progress_text").new("TextBox")
-
-        self._flomnigui_update_progress()
-
-    def _flomnigui_update_progress(self):
-        if self.progressbar is not None:
-            progress = self.progress["projection"] / self.progress["total_projections"] * 100
-            subtomo_progress = (
-                self.progress["subtomo_projection"]
-                / self.progress["subtomo_total_projections"]
-                * 100
-            )
-            self.progressbar.set_value([progress, subtomo_progress, 0])
-            if self.text_box is not None:
-                text = f"Progress report:\n Tomo type: ....................... {self.progress['tomo_type']}\n Projection: ...................... {self.progress['projection']:.0f}\n Total projections expected ....... {self.progress['total_projections']}\n Angle: ........................... {self.progress['angle']}\n Current subtomo: ................. {self.progress['subtomo']}\n Current projection within subtomo: {self.progress['subtomo_projection']}\n Total projections per subtomo: ... {self.progress['subtomo_total_projections']}"
-                self.text_box.set_plain_text(text)
-
-
-if __name__ == "__main__":
-    from bec_lib.client import BECClient
-    from bec_widgets.cli.client_utils import BECGuiClient
-
-    client = BECClient()
-    client.start()
-    client.gui = BECGuiClient()
-
-    flomni_gui = flomniGuiTools(client)
-    flomni_gui.flomnigui_show_gui()
-    flomni_gui.flomnigui_show_progress()

csaxs_bec/bec_ipython_client/plugins/flomni/x_ray_eye_align.py

@@ -1,277 +0,0 @@
-from __future__ import annotations
-
-import builtins
-import os
-import time
-from typing import TYPE_CHECKING
-
-from bec_lib import bec_logger
-
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
-
-logger = bec_logger.logger
-# import builtins to avoid linter errors
-bec = builtins.__dict__.get("bec")
-dev = builtins.__dict__.get("dev")
-umv = builtins.__dict__.get("umv")
-umvr = builtins.__dict__.get("umvr")
-
-if TYPE_CHECKING:
-    from bec_ipython_client.plugins.flomni import Flomni
-
-
-class XrayEyeAlign:
-    # pixel calibration, multiply to get mm
-    labview=False
-    PIXEL_CALIBRATION = 0.1 / 113  # .2 with binning
-
-    def __init__(self, client, flomni: Flomni) -> None:
-        self.client = client
-        self.flomni = flomni
-        self.device_manager = client.device_manager
-        self.scans = client.scans
-        self.alignment_values = {}
-        self.flomni.reset_correction()
-        self.flomni.reset_tomo_alignment_fit()
-
-    def _reset_init_values(self):
-        self.shift_xy = [0, 0]
-        self._xray_fov_xy = [0, 0]
-
-    def save_frame(self):
-        epics_put("XOMNYI-XEYE-SAVFRAME:0", 1)
-
-    def update_frame(self,keep_shutter_open=False):
-        if self.labview:
-            epics_put("XOMNYI-XEYE-ACQDONE:0", 0)
-            
-        if not self.labview:
-            self.flomni.flomnigui_show_xeyealign()
-            if not dev.cam_xeye.live_mode:
-                dev.cam_xeye.live_mode = True
-
-        epics_put("XOMNYI-XEYE-ACQ:0", 1)
-        if self.labview:
-            # wait for start live
-            while epics_get("XOMNYI-XEYE-ACQDONE:0") == 0:
-                time.sleep(0.5)
-                print("waiting for live view to start...")
-
-        fshopen()
-
-        if self.labview:
-            epics_put("XOMNYI-XEYE-ACQDONE:0", 0)
-
-            while epics_get("XOMNYI-XEYE-ACQDONE:0") == 0:
-                print("waiting for new frame...")
-                time.sleep(0.5)
-
-        time.sleep(0.5)
-        # stop live view
-        if not keep_shutter_open:
-            epics_put("XOMNYI-XEYE-ACQ:0", 0)
-            time.sleep(0.1)
-            fshclose()
-            print("got new frame")
-        else:
-            print("Staying in live view, shutter is and remains open!")
-
-    def tomo_rotate(self, val: float):
-        # pylint: disable=undefined-variable
-        umv(self.device_manager.devices.fsamroy, val)
-
-    def get_tomo_angle(self):
-        return self.device_manager.devices.fsamroy.readback.get()
-
-    def update_fov(self, k: int):
-        self._xray_fov_xy[0] = max(epics_get(f"XOMNYI-XEYE-XWIDTH_X:{k}"), self._xray_fov_xy[0])
-        self._xray_fov_xy[1] = max(0, self._xray_fov_xy[0])
-
-    @property
-    def movement_buttons_enabled(self):
-        return [epics_get("XOMNYI-XEYE-ENAMVX:0"), epics_get("XOMNYI-XEYE-ENAMVY:0")]
-
-    @movement_buttons_enabled.setter
-    def movement_buttons_enabled(self, enabled: bool):
-        enabled = int(enabled)
-        epics_put("XOMNYI-XEYE-ENAMVX:0", enabled)
-        epics_put("XOMNYI-XEYE-ENAMVY:0", enabled)
-
-    def send_message(self, msg: str):
-        epics_put("XOMNYI-XEYE-MESSAGE:0.DESC", msg)
-
-    def align(self,keep_shutter_open=False):
-        if not keep_shutter_open:
-            print("This routine can be called with paramter keep_shutter_open=True to keep the shutter always open")
-        self.send_message("Getting things ready. Please wait...")
-
-        #potential unresolved movement requests to zero
-        epics_put("XOMNYI-XEYE-MVX:0", 0)
-        epics_put("XOMNYI-XEYE-MVY:0", 0)
-
-        # reset shift xy and fov params
-        self._reset_init_values()
-
-        self.flomni.lights_off()
-
-        self.flomni.flomnigui_show_xeyealign()
-        self.flomni.flomnigui_raise()
-
-        self.tomo_rotate(0)
-        epics_put("XOMNYI-XEYE-ANGLE:0", 0)
-
-        self.flomni.feye_in()
-
-        self.flomni.laser_tracker_on()
-
-        self.flomni.feedback_enable_with_reset()
-
-        # disable movement buttons
-        self.movement_buttons_enabled = False
-
-        sample_name = self.flomni.sample_get_name(0)
-        epics_put("XOMNYI-XEYE-SAMPLENAME:0.DESC", sample_name)
-
-        # this makes sure we are in a defined state
-        self.flomni.feedback_disable()
-
-        epics_put("XOMNYI-XEYE-PIXELSIZE:0", self.PIXEL_CALIBRATION)
-
-        self.flomni.fosa_out()
-
-        fsamx_in = self.flomni._get_user_param_safe("fsamx", "in")
-        umv(dev.fsamx, fsamx_in - 0.25)
-
-        self.flomni.ffzp_in()
-        self.update_frame(keep_shutter_open)
-
-        # enable submit buttons
-        self.movement_buttons_enabled = False
-        epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
-        epics_put("XOMNYI-XEYE-STEP:0", 0)
-        self.send_message("Submit center value of FZP.")
-
-        k = 0
-        while True:
-            if epics_get("XOMNYI-XEYE-SUBMIT:0") == 1:
-                val_x = epics_get(f"XOMNYI-XEYE-XVAL_X:{k}") / 2 * self.PIXEL_CALIBRATION  # in mm
-                self.alignment_values[k] = val_x
-                print(f"Clicked position {k}: x {self.alignment_values[k]}")
-                rtx_position = dev.rtx.readback.get() / 1000
-                print(f"Current rtx position {rtx_position}")
-                self.alignment_values[k] -= rtx_position
-                print(f"Corrected position {k}: x {self.alignment_values[k]}")
-
-                if k == 0:  # received center value of FZP
-                    self.send_message("please wait ...")
-                    self.movement_buttons_enabled = False
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)  # disable submit button
-
-                    self.flomni.feedback_disable()
-                    fsamx_in = self.flomni._get_user_param_safe("fsamx", "in")
-                    umv(dev.fsamx, fsamx_in)
-
-                    self.flomni.foptics_out()
-
-                    self.flomni.feedback_disable()
-                    umv(dev.fsamx, fsamx_in - 0.25)
-
-                    if self.labview:
-                        self.update_frame(keep_shutter_open)
-                        epics_put("XOMNYI-XEYE-RECBG:0", 1)
-                        while epics_get("XOMNYI-XEYE-RECBG:0") == 1:
-                            time.sleep(0.5)
-                            print("waiting for background frame...")
-
-                    umv(dev.fsamx, fsamx_in)
-                    time.sleep(0.5)
-                    self.flomni.feedback_enable_with_reset()
-
-                    self.update_frame(keep_shutter_open)
-                    self.send_message("Adjust sample height and submit center")
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
-                    self.movement_buttons_enabled = True
-
-                elif 1 <= k < 5:  # received sample center value at samroy 0 ... 315
-                    self.send_message("please wait ...")
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)
-                    self.movement_buttons_enabled = False
-
-                    umv(dev.rtx, 0)
-                    self.tomo_rotate(k * 45)
-                    epics_put("XOMNYI-XEYE-ANGLE:0", self.get_tomo_angle())
-                    self.update_frame(keep_shutter_open)
-                    self.send_message("Submit sample center")
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
-                    epics_put("XOMNYI-XEYE-ENAMVX:0", 1)
-                    self.update_fov(k)
-
-                elif k == 5:  # received sample center value at samroy 270 and done
-                    self.send_message("done...")
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)  # disable submit button
-                    self.movement_buttons_enabled = False
-                    self.update_fov(k)
-                    break
-
-                k += 1
-                epics_put("XOMNYI-XEYE-STEP:0", k)
-
-            _xrayeyalignmvx = epics_get("XOMNYI-XEYE-MVX:0")
-            if _xrayeyalignmvx != 0:
-                umvr(dev.rtx, _xrayeyalignmvx)
-                print(f"Current rtx position {dev.rtx.readback.get() / 1000}")
-                epics_put("XOMNYI-XEYE-MVX:0", 0)
-                if k > 0:
-                    epics_put(f"XOMNYI-XEYE-STAGEPOSX:{k}", dev.rtx.readback.get() / 1000)
-                time.sleep(3)
-                self.update_frame(keep_shutter_open)
-
-            if k < 2:
-                # allow movements, store movements to calculate center
-                _xrayeyalignmvy = epics_get("XOMNYI-XEYE-MVY:0")
-                if _xrayeyalignmvy != 0:
-                    self.flomni.feedback_disable()
-                    umvr(dev.fsamy, _xrayeyalignmvy / 1000)
-                    time.sleep(2)
-                    epics_put("XOMNYI-XEYE-MVY:0", 0)
-                    self.flomni.feedback_enable_with_reset()
-                    self.update_frame(keep_shutter_open)
-            time.sleep(0.2)
-
-        self.write_output()
-        fovx = self._xray_fov_xy[0] * self.PIXEL_CALIBRATION * 1000 / 2
-        fovy = self._xray_fov_xy[1] * self.PIXEL_CALIBRATION * 1000 / 2
-
-        self.tomo_rotate(0)
-
-        umv(dev.rtx, 0)
-
-        # free camera        
-        if self.labview:
-            epics_put("XOMNYI-XEYE-ACQ:0", 2)
-        if keep_shutter_open and not self.labview:
-            if self.flomni.OMNYTools.yesno("Close the shutter now?","y"):
-                fshclose()
-                epics_put("XOMNYI-XEYE-ACQ:0", 0)
-        if not self.labview:
-            self.flomni.flomnigui_idle()
-  
-
-        print(
-            f"The largest field of view from the xrayeyealign was \nfovx = {fovx:.0f} microns, fovy"
-            f" = {fovy:.0f} microns"
-        )
-        print("Use the matlab routine to FIT the current alignment...")
-
-        print("Then LOAD ALIGNMENT PARAMETERS by running flomni.read_alignment_offset()\n")
-
-    def write_output(self):
-        file = os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues")
-        if not os.path.exists(file):
-            os.makedirs(os.path.dirname(file), exist_ok=True)
-        with open(file, "w") as alignment_values_file:
-            alignment_values_file.write("angle\thorizontal\n")
-            for k in range(1, 6):
-                fovx_offset = self.alignment_values[0] - self.alignment_values[k]
-                print(f"Writing to file new alignment: number {k}, value x {fovx_offset}")
-                alignment_values_file.write(f"{(k-1)*45}\t{fovx_offset*1000}\n")

csaxs_bec/bec_ipython_client/plugins/omny/__init__.py

@@ -1 +0,0 @@
-from .omny import OMNY

csaxs_bec/bec_ipython_client/plugins/omny/correction_omny_202204.txt

@@ -1,715 +0,0 @@
-corr_elements = 357 
-corr_angle[0] = 0.097400 
-corr_angle[1] = 0.603500 
-corr_angle[2] = 1.134200 
-corr_angle[3] = 1.625000 
-corr_angle[4] = 2.162200 
-corr_angle[5] = 2.700100 
-corr_angle[6] = 3.191600 
-corr_angle[7] = 3.714300 
-corr_angle[8] = 4.223200 
-corr_angle[9] = 4.730900 
-corr_angle[10] = 5.253300 
-corr_angle[11] = 5.743300 
-corr_angle[12] = 6.279200 
-corr_angle[13] = 6.782900 
-corr_angle[14] = 7.301200 
-corr_angle[15] = 7.808100 
-corr_angle[16] = 8.325300 
-corr_angle[17] = 8.859400 
-corr_angle[18] = 9.359400 
-corr_angle[19] = 9.887900 
-corr_angle[20] = 10.395400 
-corr_angle[21] = 10.930700 
-corr_angle[22] = 11.415400 
-corr_angle[23] = 11.928900 
-corr_angle[24] = 12.456900 
-corr_angle[25] = 12.955900 
-corr_angle[26] = 13.479000 
-corr_angle[27] = 13.982700 
-corr_angle[28] = 14.500900 
-corr_angle[29] = 15.016200 
-corr_angle[30] = 15.528000 
-corr_angle[31] = 16.053800 
-corr_angle[32] = 16.562800 
-corr_angle[33] = 17.076600 
-corr_angle[34] = 17.592400 
-corr_angle[35] = 18.094100 
-corr_angle[36] = 18.623800 
-corr_angle[37] = 19.118400 
-corr_angle[38] = 19.655000 
-corr_angle[39] = 20.143900 
-corr_angle[40] = 20.672200 
-corr_angle[41] = 21.171500 
-corr_angle[42] = 21.696300 
-corr_angle[43] = 22.215900 
-corr_angle[44] = 22.728900 
-corr_angle[45] = 23.233100 
-corr_angle[46] = 23.760000 
-corr_angle[47] = 24.267700 
-corr_angle[48] = 24.792100 
-corr_angle[49] = 25.287900 
-corr_angle[50] = 25.824600 
-corr_angle[51] = 26.321900 
-corr_angle[52] = 26.842600 
-corr_angle[53] = 27.337200 
-corr_angle[54] = 27.873500 
-corr_angle[55] = 28.373900 
-corr_angle[56] = 28.895900 
-corr_angle[57] = 29.404900 
-corr_angle[58] = 29.926700 
-corr_angle[59] = 30.439300 
-corr_angle[60] = 30.963700 
-corr_angle[61] = 31.460000 
-corr_angle[62] = 31.989500 
-corr_angle[63] = 32.489700 
-corr_angle[64] = 33.026400 
-corr_angle[65] = 33.516500 
-corr_angle[66] = 34.044000 
-corr_angle[67] = 34.547700 
-corr_angle[68] = 35.070800 
-corr_angle[69] = 35.578400 
-corr_angle[70] = 36.103200 
-corr_angle[71] = 36.603200 
-corr_angle[72] = 37.128200 
-corr_angle[73] = 37.645200 
-corr_angle[74] = 38.164300 
-corr_angle[75] = 38.662100 
-corr_angle[76] = 39.191000 
-corr_angle[77] = 39.693400 
-corr_angle[78] = 40.222500 
-corr_angle[79] = 40.719500 
-corr_angle[80] = 41.247000 
-corr_angle[81] = 41.755700 
-corr_angle[82] = 42.271300 
-corr_angle[83] = 42.767600 
-corr_angle[84] = 43.302200 
-corr_angle[85] = 43.818700 
-corr_angle[86] = 44.330000 
-corr_angle[87] = 44.835300 
-corr_angle[88] = 45.359800 
-corr_angle[89] = 45.867200 
-corr_angle[90] = 46.396200 
-corr_angle[91] = 46.895000 
-corr_angle[92] = 47.411500 
-corr_angle[93] = 47.915200 
-corr_angle[94] = 48.436600 
-corr_angle[95] = 48.946100 
-corr_angle[96] = 49.472300 
-corr_angle[97] = 49.979800 
-corr_angle[98] = 50.503300 
-corr_angle[99] = 51.008700 
-corr_angle[100] = 51.535000 
-corr_angle[101] = 52.036700 
-corr_angle[102] = 52.563700 
-corr_angle[103] = 53.063600 
-corr_angle[104] = 53.591700 
-corr_angle[105] = 54.091200 
-corr_angle[106] = 54.618900 
-corr_angle[107] = 55.116900 
-corr_angle[108] = 55.636100 
-corr_angle[109] = 56.143100 
-corr_angle[110] = 56.672200 
-corr_angle[111] = 57.172900 
-corr_angle[112] = 57.704600 
-corr_angle[113] = 58.204800 
-corr_angle[114] = 58.728600 
-corr_angle[115] = 59.239500 
-corr_angle[116] = 59.768400 
-corr_angle[117] = 60.268300 
-corr_angle[118] = 60.788800 
-corr_angle[119] = 61.289300 
-corr_angle[120] = 61.813300 
-corr_angle[121] = 62.310800 
-corr_angle[122] = 62.836700 
-corr_angle[123] = 63.353700 
-corr_angle[124] = 63.866600 
-corr_angle[125] = 64.377200 
-corr_angle[126] = 64.906600 
-corr_angle[127] = 65.414000 
-corr_angle[128] = 65.937100 
-corr_angle[129] = 66.429400 
-corr_angle[130] = 66.970000 
-corr_angle[131] = 67.459200 
-corr_angle[132] = 67.996400 
-corr_angle[133] = 68.499800 
-corr_angle[134] = 69.014500 
-corr_angle[135] = 69.509500 
-corr_angle[136] = 70.044000 
-corr_angle[137] = 70.543200 
-corr_angle[138] = 71.079400 
-corr_angle[139] = 71.579300 
-corr_angle[140] = 72.103500 
-corr_angle[141] = 72.607000 
-corr_angle[142] = 73.137100 
-corr_angle[143] = 73.633000 
-corr_angle[144] = 74.164500 
-corr_angle[145] = 74.660200 
-corr_angle[146] = 75.180600 
-corr_angle[147] = 75.674200 
-corr_angle[148] = 76.215400 
-corr_angle[149] = 76.718900 
-corr_angle[150] = 77.242300 
-corr_angle[151] = 77.752000 
-corr_angle[152] = 78.279300 
-corr_angle[153] = 78.780500 
-corr_angle[154] = 79.314900 
-corr_angle[155] = 79.424500 
-corr_angle[156] = 79.807000 
-corr_angle[157] = 80.336500 
-corr_angle[158] = 80.338700 
-corr_angle[159] = 80.835300 
-corr_angle[160] = 81.367100 
-corr_angle[161] = 81.376100 
-corr_angle[162] = 81.859000 
-corr_angle[163] = 82.382300 
-corr_angle[164] = 82.384000 
-corr_angle[165] = 82.881100 
-corr_angle[166] = 83.415000 
-corr_angle[167] = 83.421600 
-corr_angle[168] = 83.917100 
-corr_angle[169] = 84.439200 
-corr_angle[170] = 84.439300 
-corr_angle[171] = 84.947400 
-corr_angle[172] = 85.472700 
-corr_angle[173] = 85.987700 
-corr_angle[174] = 86.512400 
-corr_angle[175] = 87.009500 
-corr_angle[176] = 87.536500 
-corr_angle[177] = 88.035600 
-corr_angle[178] = 88.560100 
-corr_angle[179] = 89.057600 
-corr_angle[180] = 89.583200 
-corr_angle[181] = 90.090500 
-corr_angle[182] = 90.614600 
-corr_angle[183] = 91.119900 
-corr_angle[184] = 91.638300 
-corr_angle[185] = 92.153300 
-corr_angle[186] = 92.681600 
-corr_angle[187] = 93.181800 
-corr_angle[188] = 93.710900 
-corr_angle[189] = 94.206100 
-corr_angle[190] = 94.732700 
-corr_angle[191] = 95.226600 
-corr_angle[192] = 95.766400 
-corr_angle[193] = 96.259000 
-corr_angle[194] = 96.783400 
-corr_angle[195] = 97.283100 
-corr_angle[196] = 97.811500 
-corr_angle[197] = 98.323600 
-corr_angle[198] = 98.839400 
-corr_angle[199] = 99.350700 
-corr_angle[200] = 99.880200 
-corr_angle[201] = 100.378100 
-corr_angle[202] = 100.913300 
-corr_angle[203] = 101.405000 
-corr_angle[204] = 101.935700 
-corr_angle[205] = 102.426300 
-corr_angle[206] = 102.957300 
-corr_angle[207] = 103.456500 
-corr_angle[208] = 103.985100 
-corr_angle[209] = 104.490300 
-corr_angle[210] = 105.015100 
-corr_angle[211] = 105.518400 
-corr_angle[212] = 106.047400 
-corr_angle[213] = 106.551100 
-corr_angle[214] = 107.077100 
-corr_angle[215] = 107.575800 
-corr_angle[216] = 108.115200 
-corr_angle[217] = 108.598800 
-corr_angle[218] = 109.129100 
-corr_angle[219] = 109.626200 
-corr_angle[220] = 110.158400 
-corr_angle[221] = 110.661700 
-corr_angle[222] = 111.188600 
-corr_angle[223] = 111.695000 
-corr_angle[224] = 112.216400 
-corr_angle[225] = 112.720000 
-corr_angle[226] = 113.246200 
-corr_angle[227] = 113.757100 
-corr_angle[228] = 114.281900 
-corr_angle[229] = 114.780000 
-corr_angle[230] = 115.306800 
-corr_angle[231] = 115.799800 
-corr_angle[232] = 116.328400 
-corr_angle[233] = 116.829900 
-corr_angle[234] = 117.355400 
-corr_angle[235] = 117.858200 
-corr_angle[236] = 118.380600 
-corr_angle[237] = 118.893200 
-corr_angle[238] = 119.418200 
-corr_angle[239] = 119.921000 
-corr_angle[240] = 120.446100 
-corr_angle[241] = 120.953800 
-corr_angle[242] = 121.480300 
-corr_angle[243] = 121.977600 
-corr_angle[244] = 122.507100 
-corr_angle[245] = 122.996200 
-corr_angle[246] = 123.529600 
-corr_angle[247] = 124.032200 
-corr_angle[248] = 124.554800 
-corr_angle[249] = 125.057800 
-corr_angle[250] = 125.580800 
-corr_angle[251] = 126.090000 
-corr_angle[252] = 126.611600 
-corr_angle[253] = 127.127000 
-corr_angle[254] = 127.650900 
-corr_angle[255] = 128.153700 
-corr_angle[256] = 128.677200 
-corr_angle[257] = 129.170800 
-corr_angle[258] = 129.703000 
-corr_angle[259] = 130.194900 
-corr_angle[260] = 130.733600 
-corr_angle[261] = 131.228300 
-corr_angle[262] = 131.756900 
-corr_angle[263] = 132.263200 
-corr_angle[264] = 132.784700 
-corr_angle[265] = 133.296300 
-corr_angle[266] = 133.818800 
-corr_angle[267] = 134.318900 
-corr_angle[268] = 134.846800 
-corr_angle[269] = 135.344800 
-corr_angle[270] = 135.876000 
-corr_angle[271] = 136.372600 
-corr_angle[272] = 136.902700 
-corr_angle[273] = 137.397800 
-corr_angle[274] = 137.926800 
-corr_angle[275] = 138.428000 
-corr_angle[276] = 138.953700 
-corr_angle[277] = 139.461300 
-corr_angle[278] = 139.987800 
-corr_angle[279] = 140.492600 
-corr_angle[280] = 141.017900 
-corr_angle[281] = 141.524000 
-corr_angle[282] = 142.061200 
-corr_angle[283] = 142.545400 
-corr_angle[284] = 143.069900 
-corr_angle[285] = 143.568700 
-corr_angle[286] = 144.102200 
-corr_angle[287] = 144.596200 
-corr_angle[288] = 145.126400 
-corr_angle[289] = 145.626900 
-corr_angle[290] = 146.158700 
-corr_angle[291] = 146.662200 
-corr_angle[292] = 147.184700 
-corr_angle[293] = 147.692300 
-corr_angle[294] = 148.225900 
-corr_angle[295] = 148.716000 
-corr_angle[296] = 149.243400 
-corr_angle[297] = 149.739400 
-corr_angle[298] = 150.272400 
-corr_angle[299] = 150.762100 
-corr_angle[300] = 151.301800 
-corr_angle[301] = 151.796300 
-corr_angle[302] = 152.333500 
-corr_angle[303] = 152.833100 
-corr_angle[304] = 153.363600 
-corr_angle[305] = 153.862900 
-corr_angle[306] = 154.396100 
-corr_angle[307] = 154.895400 
-corr_angle[308] = 155.417700 
-corr_angle[309] = 155.916900 
-corr_angle[310] = 156.451600 
-corr_angle[311] = 156.942700 
-corr_angle[312] = 157.467600 
-corr_angle[313] = 157.970900 
-corr_angle[314] = 158.501100 
-corr_angle[315] = 158.999600 
-corr_angle[316] = 159.526100 
-corr_angle[317] = 160.028100 
-corr_angle[318] = 160.555800 
-corr_angle[319] = 161.067700 
-corr_angle[320] = 161.597300 
-corr_angle[321] = 162.091300 
-corr_angle[322] = 162.616600 
-corr_angle[323] = 163.107400 
-corr_angle[324] = 163.639100 
-corr_angle[325] = 164.139700 
-corr_angle[326] = 164.672500 
-corr_angle[327] = 165.176800 
-corr_angle[328] = 165.698600 
-corr_angle[329] = 166.205400 
-corr_angle[330] = 166.727300 
-corr_angle[331] = 167.238600 
-corr_angle[332] = 167.771500 
-corr_angle[333] = 168.265000 
-corr_angle[334] = 168.794800 
-corr_angle[335] = 169.293800 
-corr_angle[336] = 169.813300 
-corr_angle[337] = 170.320200 
-corr_angle[338] = 170.845100 
-corr_angle[339] = 171.344000 
-corr_angle[340] = 171.866200 
-corr_angle[341] = 172.375300 
-corr_angle[342] = 172.899400 
-corr_angle[343] = 173.404400 
-corr_angle[344] = 173.928500 
-corr_angle[345] = 174.430800 
-corr_angle[346] = 174.827800 
-corr_angle[347] = 175.460400 
-corr_angle[348] = 175.993100 
-corr_angle[349] = 176.492100 
-corr_angle[350] = 177.014200 
-corr_angle[351] = 177.512100 
-corr_angle[352] = 178.044200 
-corr_angle[353] = 178.643800 
-corr_angle[354] = 179.067200 
-corr_angle[355] = 179.571600 
-corr_angle[356] = 180.093700 
-corr_pos[0] = -0.814519 
-corr_pos[1] = -0.810675 
-corr_pos[2] = -0.806338 
-corr_pos[3] = -0.802047 
-corr_pos[4] = -0.797044 
-corr_pos[5] = -0.791712 
-corr_pos[6] = -0.786558 
-corr_pos[7] = -0.780781 
-corr_pos[8] = -0.774864 
-corr_pos[9] = -0.768674 
-corr_pos[10] = -0.762005 
-corr_pos[11] = -0.755474 
-corr_pos[12] = -0.748024 
-corr_pos[13] = -0.740730 
-corr_pos[14] = -0.732929 
-corr_pos[15] = -0.725011 
-corr_pos[16] = -0.716637 
-corr_pos[17] = -0.707676 
-corr_pos[18] = -0.698861 
-corr_pos[19] = -0.686245 
-corr_pos[20] = -0.676596 
-corr_pos[21] = -0.663643 
-corr_pos[22] = -0.655664 
-corr_pos[23] = -0.642249 
-corr_pos[24] = -0.633516 
-corr_pos[25] = -0.621402 
-corr_pos[26] = -0.612846 
-corr_pos[27] = -0.599978 
-corr_pos[28] = -0.592135 
-corr_pos[29] = -0.577949 
-corr_pos[30] = -0.570695 
-corr_pos[31] = -0.555560 
-corr_pos[32] = -0.549015 
-corr_pos[33] = -0.532162 
-corr_pos[34] = -0.524479 
-corr_pos[35] = -0.507848 
-corr_pos[36] = -0.500301 
-corr_pos[37] = -0.484361 
-corr_pos[38] = -0.477365 
-corr_pos[39] = -0.461751 
-corr_pos[40] = -0.455963 
-corr_pos[41] = -0.439438 
-corr_pos[42] = -0.436103 
-corr_pos[43] = -0.420587 
-corr_pos[44] = -0.417361 
-corr_pos[45] = -0.402270 
-corr_pos[46] = -0.400459 
-corr_pos[47] = -0.384745 
-corr_pos[48] = -0.385280 
-corr_pos[49] = -0.371217 
-corr_pos[50] = -0.373612 
-corr_pos[51] = -0.361838 
-corr_pos[52] = -0.365771 
-corr_pos[53] = -0.354641 
-corr_pos[54] = -0.360647 
-corr_pos[55] = -0.351446 
-corr_pos[56] = -0.359147 
-corr_pos[57] = -0.348696 
-corr_pos[58] = -0.359348 
-corr_pos[59] = -0.349962 
-corr_pos[60] = -0.360782 
-corr_pos[61] = -0.355040 
-corr_pos[62] = -0.367441 
-corr_pos[63] = -0.360511 
-corr_pos[64] = -0.372617 
-corr_pos[65] = -0.366120 
-corr_pos[66] = -0.377568 
-corr_pos[67] = -0.370362 
-corr_pos[68] = -0.380918 
-corr_pos[69] = -0.372553 
-corr_pos[70] = -0.381460 
-corr_pos[71] = -0.371828 
-corr_pos[72] = -0.379428 
-corr_pos[73] = -0.368465 
-corr_pos[74] = -0.374297 
-corr_pos[75] = -0.360340 
-corr_pos[76] = -0.365429 
-corr_pos[77] = -0.349168 
-corr_pos[78] = -0.351544 
-corr_pos[79] = -0.332514 
-corr_pos[80] = -0.333505 
-corr_pos[81] = -0.313316 
-corr_pos[82] = -0.313014 
-corr_pos[83] = -0.291107 
-corr_pos[84] = -0.287807 
-corr_pos[85] = -0.264483 
-corr_pos[86] = -0.260891 
-corr_pos[87] = -0.236646 
-corr_pos[88] = -0.231362 
-corr_pos[89] = -0.205833 
-corr_pos[90] = -0.200663 
-corr_pos[91] = -0.174834 
-corr_pos[92] = -0.171662 
-corr_pos[93] = -0.146200 
-corr_pos[94] = -0.142890 
-corr_pos[95] = -0.118389 
-corr_pos[96] = -0.112895 
-corr_pos[97] = -0.088879 
-corr_pos[98] = -0.084146 
-corr_pos[99] = -0.061625 
-corr_pos[100] = -0.054742 
-corr_pos[101] = -0.032741 
-corr_pos[102] = -0.026725 
-corr_pos[103] = -0.004827 
-corr_pos[104] = 0.002678 
-corr_pos[105] = 0.024418 
-corr_pos[106] = 0.031105 
-corr_pos[107] = 0.052334 
-corr_pos[108] = 0.060072 
-corr_pos[109] = 0.081470 
-corr_pos[110] = 0.088550 
-corr_pos[111] = 0.109685 
-corr_pos[112] = 0.116675 
-corr_pos[113] = 0.136298 
-corr_pos[114] = 0.142152 
-corr_pos[115] = 0.161986 
-corr_pos[116] = 0.166996 
-corr_pos[117] = 0.186466 
-corr_pos[118] = 0.190874 
-corr_pos[119] = 0.208729 
-corr_pos[120] = 0.212714 
-corr_pos[121] = 0.229992 
-corr_pos[122] = 0.232685 
-corr_pos[123] = 0.248748 
-corr_pos[124] = 0.249688 
-corr_pos[125] = 0.264768 
-corr_pos[126] = 0.264432 
-corr_pos[127] = 0.278801 
-corr_pos[128] = 0.278424 
-corr_pos[129] = 0.289656 
-corr_pos[130] = 0.289612 
-corr_pos[131] = 0.299899 
-corr_pos[132] = 0.299782 
-corr_pos[133] = 0.307473 
-corr_pos[134] = 0.309489 
-corr_pos[135] = 0.315999 
-corr_pos[136] = 0.317413 
-corr_pos[137] = 0.325060 
-corr_pos[138] = 0.325931 
-corr_pos[139] = 0.332544 
-corr_pos[140] = 0.332095 
-corr_pos[141] = 0.338738 
-corr_pos[142] = 0.337864 
-corr_pos[143] = 0.343909 
-corr_pos[144] = 0.342973 
-corr_pos[145] = 0.348449 
-corr_pos[146] = 0.346060 
-corr_pos[147] = 0.351949 
-corr_pos[148] = 0.349873 
-corr_pos[149] = 0.354969 
-corr_pos[150] = 0.352375 
-corr_pos[151] = 0.358388 
-corr_pos[152] = 0.354736 
-corr_pos[153] = 0.359539 
-corr_pos[154] = 0.354369 
-corr_pos[155] = 0.358549 
-corr_pos[156] = 0.353217 
-corr_pos[157] = 0.355795 
-corr_pos[158] = 0.351299 
-corr_pos[159] = 0.352922 
-corr_pos[160] = 0.346933 
-corr_pos[161] = 0.350201 
-corr_pos[162] = 0.343937 
-corr_pos[163] = 0.349304 
-corr_pos[164] = 0.344857 
-corr_pos[165] = 0.347471 
-corr_pos[166] = 0.335793 
-corr_pos[167] = 0.341109 
-corr_pos[168] = 0.330453 
-corr_pos[169] = 0.326576 
-corr_pos[170] = 0.320299 
-corr_pos[171] = 0.315348 
-corr_pos[172] = 0.300744 
-corr_pos[173] = 0.294366 
-corr_pos[174] = 0.280438 
-corr_pos[175] = 0.273618 
-corr_pos[176] = 0.259335 
-corr_pos[177] = 0.251464 
-corr_pos[178] = 0.237247 
-corr_pos[179] = 0.229092 
-corr_pos[180] = 0.214882 
-corr_pos[181] = 0.207363 
-corr_pos[182] = 0.193246 
-corr_pos[183] = 0.185868 
-corr_pos[184] = 0.173256 
-corr_pos[185] = 0.165378 
-corr_pos[186] = 0.153853 
-corr_pos[187] = 0.147031 
-corr_pos[188] = 0.135535 
-corr_pos[189] = 0.129435 
-corr_pos[190] = 0.119843 
-corr_pos[191] = 0.115062 
-corr_pos[192] = 0.107115 
-corr_pos[193] = 0.105182 
-corr_pos[194] = 0.099647 
-corr_pos[195] = 0.098162 
-corr_pos[196] = 0.094628 
-corr_pos[197] = 0.095257 
-corr_pos[198] = 0.084490 
-corr_pos[199] = 0.085389 
-corr_pos[200] = 0.074302 
-corr_pos[201] = 0.075265 
-corr_pos[202] = 0.063623 
-corr_pos[203] = 0.064487 
-corr_pos[204] = 0.052841 
-corr_pos[205] = 0.053559 
-corr_pos[206] = 0.042022 
-corr_pos[207] = 0.043321 
-corr_pos[208] = 0.032826 
-corr_pos[209] = 0.032277 
-corr_pos[210] = 0.022169 
-corr_pos[211] = 0.020740 
-corr_pos[212] = 0.010378 
-corr_pos[213] = 0.008668 
-corr_pos[214] = -0.001930 
-corr_pos[215] = -0.003882 
-corr_pos[216] = -0.014694 
-corr_pos[217] = -0.016629 
-corr_pos[218] = -0.026380 
-corr_pos[219] = -0.028069 
-corr_pos[220] = -0.037125 
-corr_pos[221] = -0.039429 
-corr_pos[222] = -0.047773 
-corr_pos[223] = -0.049261 
-corr_pos[224] = -0.056872 
-corr_pos[225] = -0.058756 
-corr_pos[226] = -0.065279 
-corr_pos[227] = -0.066859 
-corr_pos[228] = -0.073027 
-corr_pos[229] = -0.074253 
-corr_pos[230] = -0.079062 
-corr_pos[231] = -0.079800 
-corr_pos[232] = -0.084350 
-corr_pos[233] = -0.084805 
-corr_pos[234] = -0.088621 
-corr_pos[235] = -0.088437 
-corr_pos[236] = -0.092166 
-corr_pos[237] = -0.090769 
-corr_pos[238] = -0.093820 
-corr_pos[239] = -0.091724 
-corr_pos[240] = -0.094152 
-corr_pos[241] = -0.090866 
-corr_pos[242] = -0.092575 
-corr_pos[243] = -0.089239 
-corr_pos[244] = -0.089666 
-corr_pos[245] = -0.086864 
-corr_pos[246] = -0.087183 
-corr_pos[247] = -0.083974 
-corr_pos[248] = -0.083709 
-corr_pos[249] = -0.079848 
-corr_pos[250] = -0.078494 
-corr_pos[251] = -0.072782 
-corr_pos[252] = -0.069638 
-corr_pos[253] = -0.063004 
-corr_pos[254] = -0.058599 
-corr_pos[255] = -0.051737 
-corr_pos[256] = -0.046451 
-corr_pos[257] = -0.040238 
-corr_pos[258] = -0.034071 
-corr_pos[259] = -0.028578 
-corr_pos[260] = -0.021481 
-corr_pos[261] = -0.016346 
-corr_pos[262] = -0.009475 
-corr_pos[263] = -0.004141 
-corr_pos[264] = 0.002780 
-corr_pos[265] = 0.008455 
-corr_pos[266] = 0.015507 
-corr_pos[267] = 0.021672 
-corr_pos[268] = 0.029704 
-corr_pos[269] = 0.036662 
-corr_pos[270] = 0.044794 
-corr_pos[271] = 0.052031 
-corr_pos[272] = 0.061478 
-corr_pos[273] = 0.069150 
-corr_pos[274] = 0.078715 
-corr_pos[275] = 0.087785 
-corr_pos[276] = 0.098593 
-corr_pos[277] = 0.107863 
-corr_pos[278] = 0.118256 
-corr_pos[279] = 0.127631 
-corr_pos[280] = 0.139011 
-corr_pos[281] = 0.150077 
-corr_pos[282] = 0.162154 
-corr_pos[283] = 0.173758 
-corr_pos[284] = 0.186998 
-corr_pos[285] = 0.200111 
-corr_pos[286] = 0.214116 
-corr_pos[287] = 0.227291 
-corr_pos[288] = 0.240662 
-corr_pos[289] = 0.252955 
-corr_pos[290] = 0.265359 
-corr_pos[291] = 0.275995 
-corr_pos[292] = 0.287613 
-corr_pos[293] = 0.295789 
-corr_pos[294] = 0.306424 
-corr_pos[295] = 0.313027 
-corr_pos[296] = 0.322181 
-corr_pos[297] = 0.329313 
-corr_pos[298] = 0.338191 
-corr_pos[299] = 0.345243 
-corr_pos[300] = 0.353316 
-corr_pos[301] = 0.360491 
-corr_pos[302] = 0.367891 
-corr_pos[303] = 0.375027 
-corr_pos[304] = 0.380865 
-corr_pos[305] = 0.388354 
-corr_pos[306] = 0.395257 
-corr_pos[307] = 0.401478 
-corr_pos[308] = 0.408087 
-corr_pos[309] = 0.414083 
-corr_pos[310] = 0.420361 
-corr_pos[311] = 0.424284 
-corr_pos[312] = 0.429614 
-corr_pos[313] = 0.433888 
-corr_pos[314] = 0.438529 
-corr_pos[315] = 0.442302 
-corr_pos[316] = 0.445899 
-corr_pos[317] = 0.449014 
-corr_pos[318] = 0.451693 
-corr_pos[319] = 0.453795 
-corr_pos[320] = 0.455132 
-corr_pos[321] = 0.455438 
-corr_pos[322] = 0.455334 
-corr_pos[323] = 0.454055 
-corr_pos[324] = 0.451146 
-corr_pos[325] = 0.447259 
-corr_pos[326] = 0.442478 
-corr_pos[327] = 0.437520 
-corr_pos[328] = 0.432297 
-corr_pos[329] = 0.426442 
-corr_pos[330] = 0.418918 
-corr_pos[331] = 0.411040 
-corr_pos[332] = 0.402610 
-corr_pos[333] = 0.394491 
-corr_pos[334] = 0.383925 
-corr_pos[335] = 0.374590 
-corr_pos[336] = 0.363650 
-corr_pos[337] = 0.353143 
-corr_pos[338] = 0.339756 
-corr_pos[339] = 0.328074 
-corr_pos[340] = 0.315463 
-corr_pos[341] = 0.302641 
-corr_pos[342] = 0.288898 
-corr_pos[343] = 0.275134 
-corr_pos[344] = 0.260308 
-corr_pos[345] = 0.245582 
-corr_pos[346] = 0.233584 
-corr_pos[347] = 0.213812 
-corr_pos[348] = 0.196540 
-corr_pos[349] = 0.179844 
-corr_pos[350] = 0.161839 
-corr_pos[351] = 0.144160 
-corr_pos[352] = 0.124715 
-corr_pos[353] = 0.102123 
-corr_pos[354] = 0.085736 
-corr_pos[355] = 0.065743 
-corr_pos[356] = 0.044511 

csaxs_bec/bec_ipython_client/plugins/omny/gui_tools.py

@@ -1,171 +0,0 @@
-import builtins
-
-from bec_widgets.cli.client import BECDockArea
-
-# from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
-
-if builtins.__dict__.get("bec") is not None:
-    bec = builtins.__dict__.get("bec")
-    dev = builtins.__dict__.get("dev")
-    umv = builtins.__dict__.get("umv")
-    umvr = builtins.__dict__.get("umvr")
-
-
-class OMNYGuiToolsError(Exception):
-    pass
-
-
-class OMNYGuiTools:
-
-    def __init__(self, client):
-        self.gui = getattr(client, "gui", None)
-        self.gui_window = self.gui.windows['main'].widget
-        self.fig200 = None
-        self.fig201 = None
-        self.fig202 = None
-        self.fig203 = None
-        self.progressbar = None
-        self.text_box = None
-        self.idle_text_box = None
-
-    def omnygui_show_gui(self):
-        self.gui_window.show()
-
-    def omnygui_stop_gui(self):
-        self.gui_window.hide()
-
-    def _omnycam_parking(self):
-        self.omnygui_show_omnycam_parking()
-
-    def omnygui_show_omnycam_parking(self):
-        self.omnygui_show_gui()
-        if self.fig200 is None:
-            self._omnycam_clear()
-            self.fig200 = self.gui_window.add_dock(name="omnycam200").add_widget("BECImageWidget")
-            if self._omnycam_check_device_exists(dev.cam200):
-                fig = self.fig200.image("cam200")
-                fig.set_rotation(deg_90=3)
-                self.fig200.lock_aspect_ratio(True)
-            else:
-                print("Cannot open cam200. Device does not exist.")
-            self.fig203 = self.gui_window.add_dock(name="omnycam203").add_widget("BECImageWidget")
-            if self._omnycam_check_device_exists(dev.cam203):
-                fig = self.fig203.image("cam203")
-                fig.set_rotation(deg_90=3)
-                self.fig203.lock_aspect_ratio(True)
-            else:
-                print("Cannot open cam203. Device does not exist.")
-            try:
-                self.gui_window.remove_dock(name="default_figure")
-            except:
-                pass
-
-    def omnygui_remove_all_docks(self):
-        self.gui_window.clear_all()
-        self.fig200 = None
-        self.fig201 = None
-        self.fig202 = None
-        self.fig203 = None
-        self.progressbar = None
-        self.text_box = None
-        self.idle_text_box = None
-
-    def omnygui_idle(self):
-        self.omnygui_show_gui()
-        if self.idle_text_box is None:
-            self.omnygui_remove_all_docks()
-            self.idle_text_box = self.gui_window.add_dock(name="idle_text").add_widget("TextBox")
-            try:
-                self.gui_window.remove_dock(name="default_figure")
-            except:
-                pass
-        text = (
-            "<pre>"
-            + "    ,o888888o.           ,8.       ,8.          b.             8 `8.`8888.      ,8' \n"
-            + " . 8888     `88.        ,888.     ,888.         888o.          8  `8.`8888.    ,8'  \n"
-            + ",8 8888       `8b      .`8888.   .`8888.        Y88888o.       8   `8.`8888.  ,8'   \n"
-            + "88 8888        `8b    ,8.`8888. ,8.`8888.       .`Y888888o.    8    `8.`8888.,8'    \n"
-            + "88 8888         88   ,8'8.`8888,8^8.`8888.      8o. `Y888888o. 8     `8.`88888'     \n"
-            + "88 8888         88  ,8' `8.`8888' `8.`8888.     8`Y8o. `Y88888o8      `8. 8888      \n"
-            + "88 8888        ,8P ,8'   `8.`88'   `8.`8888.    8   `Y8o. `Y8888       `8 8888      \n"
-            + "`8 8888       ,8P ,8'     `8.`'     `8.`8888.   8      `Y8o. `Y8        8 8888      \n"
-            + " ` 8888     ,88' ,8'       `8        `8.`8888.  8         `Y8o.`        8 8888      \n"
-            + "    `8888888P'  ,8'         `         `8.`8888. 8            `Yo        8 8888      \n"
-            + "</pre>"
-        )
-        self.idle_text_box.set_html_text(text)
-
-    def _omnycam_clear(self):
-        self.omnygui_remove_all_docks()
-
-    def _omnycam_check_device_exists(self, device):
-        try:
-            device
-        except:
-            return False
-        else:
-            return True
-
-    def _omnycam_samplestage(self):
-        self.omnygui_show_omnycam_samplestage()
-
-    def omnygui_show_omnycam_samplestage(self):
-        self.omnygui_show_gui()
-        if self.fig201 is None:
-            self.omnygui_remove_all_docks()
-            self.fig201 = self.gui_window.add_dock(name="omnycam201").add_widget("BECImageWidget")
-            if self._omnycam_check_device_exists(dev.cam201):
-                fig = self.fig201.image("cam201")
-                fig.set_rotation(deg_90=3)
-                self.fig201.lock_aspect_ratio(True)
-            else:
-                print("Cannot open cam201. Device does not exist.")
-            self.fig202 = self.gui_window.add_dock(name="omnycam202").add_widget("BECImageWidget")
-            if self._omnycam_check_device_exists(dev.cam202):
-                fig = self.fig202.image("cam202")
-                fig.set_rotation(deg_90=3)
-                self.fig202.lock_aspect_ratio(True)
-            else:
-                print("Cannot open cam202. Device does not exist.")
-            try:
-                self.gui_window.remove_dock(name="default_figure")
-            except:
-                pass
-
-    def omnygui_show_progress(self):
-        self.omnygui_show_gui()
-        if self.progressbar is None:
-            self.omnygui_remove_all_docks()
-            # Add a new dock with a RingProgressBar widget
-            self.progressbar = self.gui_window.add_dock(name="progress").add_widget("RingProgressBar")
-            # Customize the size of the progress ring
-            self.progressbar.set_line_widths(20)
-            # Disable automatic updates and manually set the self.progressbar value
-            self.progressbar.enable_auto_updates(False)
-            # Set precision for the self.progressbar display
-            self.progressbar.set_precision(1)  # Display self.progressbar with one decimal places
-            # Setting multiple rigns with different values
-            self.progressbar.set_number_of_bars(3)
-            self.progressbar.rings[2].set_update("scan")
-            # Set the values of the rings to 50, 75, and 25 from outer to inner ring
-            # self.progressbar.set_value([50, 75])
-            # Add a new dock with a TextBox widget
-            self.text_box = self.gui_window.add_dock(name="progress_text").add_widget("TextBox")
-            try:
-                self.gui_window.remove_dock(name="default_figure")
-            except:
-                pass
-        self._omnygui_update_progress()
-
-    def _omnygui_update_progress(self):
-        if self.progressbar is not None:
-            progress = self.progress["projection"] / self.progress["total_projections"] * 100
-            subotmo_progress = (
-                self.progress["subtomo_projection"]
-                / self.progress["subtomo_total_projections"]
-                * 100
-            )
-            self.progressbar.set_value([progress, subotmo_progress])
-
-            text = f"Progress report:\n Tomo type: ....................... {self.progress['tomo_type']}\n Projection: ...................... {self.progress['projection']:.0f}\n Total projections expected ....... {self.progress['total_projections']}\n Angle: ........................... {self.progress['angle']}\n Current subtomo: ................. {self.progress['subtomo']}\n Current projection within subtomo: {self.progress['subtomo_projection']}\n Total projections per subtomo: ... {self.progress['subtomo_total_projections']}"
-            self.text_box.set_plain_text(text)

csaxs_bec/bec_ipython_client/plugins/omny/omny_alignment_mixin.py

@@ -1,246 +0,0 @@
-import time
-import numpy as np
-import os
-
-from rich import box
-from rich.console import Console
-from rich.table import Table
-
-from typeguard import typechecked
-from bec_lib import bec_logger
-
-logger = bec_logger.logger
-
-
-class OMNYAlignmentError(Exception):
-    pass
-
-
-class OMNYAlignmentMixin:
-    default_correction_file = "correction_omny_202204.txt"
-    default_correction_file_x = "correction_omny_202204_x.txt"
-
-    def reset_correction(self, use_default_correction=True):
-        """
-        Reset the correction to the default values.
-        If use_default_correction is False, the correction will be set to empty values.
-        Otherwise the default values will be loaded.
-
-        Args:
-            use_default_correction (bool, optional): If set to true, a call reset the correction to the default values. Defaults to True.
-        """
-        self.corr_pos_x = []
-        self.corr_angle_x = []
-        self.corr_pos_y = []
-        self.corr_angle_y = []
-        self.corr_pos_y_2 = []
-        self.corr_angle_y_2 = []
-
-        if use_default_correction:
-            try:
-                self.read_additional_correction_x(self.default_correction_file_x)
-                logger.info(f"Applying default x correction from {self.default_correction_file_x}")
-            except FileNotFoundError:
-                logger.warning(
-                    f"Could not find default correction file {self.default_correction_file_x}."
-                )
-                logger.warning("Not applying any correction.")
-            try:
-                self.read_additional_correction_y(self.default_correction_file)
-                logger.info(f"Applying default y correction from {self.default_correction_file}")
-            except FileNotFoundError:
-                logger.warning(
-                    f"Could not find default correction file {self.default_correction_file}."
-                )
-                logger.warning("Not applying any correction.")
-
-    def reset_tomo_alignment_fit(self):
-        self.client.delete_global_var("tomo_alignment_fit")
-
-    def read_alignment_offset(
-        self,
-        dir_path=os.path.expanduser("~/Data10/specES1/internal/"),
-        setup="omny",
-        use_vertical_default_values=True,
-    ):
-        """
-        Read the alignment offset from the given directory and set the global parameter
-        tomo_alignment_fit.
-
-        Args:
-            dir_path (str, optional): The directory to read the alignment offset from. Defaults to os.path.expanduser("~/Data10/specES1/internal/").
-        """
-        tomo_alignment_fit = np.zeros((2, 5))
-        with open(os.path.join(dir_path, "ptychotomoalign_Ax.txt"), "r") as file:
-            tomo_alignment_fit[0][0] = file.readline()
-
-        with open(os.path.join(dir_path, "ptychotomoalign_Bx.txt"), "r") as file:
-            tomo_alignment_fit[0][1] = file.readline()
-
-        with open(os.path.join(dir_path, "ptychotomoalign_Cx.txt"), "r") as file:
-            tomo_alignment_fit[0][2] = file.readline()
-
-        with open(os.path.join(dir_path, "ptychotomoalign_Ay.txt"), "r") as file:
-            tomo_alignment_fit[1][0] = file.readline()
-
-        with open(os.path.join(dir_path, "ptychotomoalign_By.txt"), "r") as file:
-            tomo_alignment_fit[1][1] = file.readline()
-
-        with open(os.path.join(dir_path, "ptychotomoalign_Cy.txt"), "r") as file:
-            tomo_alignment_fit[1][2] = file.readline()
-
-        with open(os.path.join(dir_path, "ptychotomoalign_Ay3.txt"), "r") as file:
-            tomo_alignment_fit[1][3] = file.readline()
-
-        with open(os.path.join(dir_path, "ptychotomoalign_Cy3.txt"), "r") as file:
-            tomo_alignment_fit[1][4] = file.readline()
-
-        print("New alignment parameters loaded:")
-        print(
-            f"X Amplitude {tomo_alignment_fit[0][0]}, "
-            f"X Phase {tomo_alignment_fit[0][1]}, "
-            f"X Offset {tomo_alignment_fit[0][2]}, "
-            f"Y Amplitude {tomo_alignment_fit[1][0]}, "
-            f"Y Phase {tomo_alignment_fit[1][1]}, "
-            f"Y Offset {tomo_alignment_fit[1][2]}, "
-            f"Y 3rd Order Amplitude {tomo_alignment_fit[1][3]}, "
-            f"Y 3rd Order Phase {tomo_alignment_fit[1][4]} ."
-        )
-
-        if use_vertical_default_values:
-            print(
-                f"Using default values for vertical alignment for setup {setup}. Optional: use_vertical_default_values=False"
-            )
-            if setup == "flomni":
-                tomo_alignment_fit[1][0] = 0
-                tomo_alignment_fit[1][1] = 0
-                tomo_alignment_fit[1][2] = 0
-                tomo_alignment_fit[1][3] = 0
-                tomo_alignment_fit[1][4] = 0
-            elif setup == "omny":
-                tomo_alignment_fit[1][0] = 2.588628
-                tomo_alignment_fit[1][1] = -2.385422
-                tomo_alignment_fit[1][2] = 0
-                tomo_alignment_fit[1][3] = 1.010583
-                tomo_alignment_fit[1][4] = -1.359157
-
-            print("Follwing parameters will be used:")
-            print(
-                f"X Amplitude {tomo_alignment_fit[0][0]}, "
-                f"X Phase {tomo_alignment_fit[0][1]}, "
-                f"X Offset {tomo_alignment_fit[0][2]}, "
-                f"Y Amplitude {tomo_alignment_fit[1][0]}, "
-                f"Y Phase {tomo_alignment_fit[1][1]}, "
-                f"Y Offset {tomo_alignment_fit[1][2]}, "
-                f"Y 3rd Order Amplitude {tomo_alignment_fit[1][3]}, "
-                f"Y 3rd Order Phase {tomo_alignment_fit[1][4]} ."
-            )
-
-        self.client.set_global_var("tomo_alignment_fit", tomo_alignment_fit.tolist())
-        # x amp, phase, offset, y amp, phase, offset, 3rd order amp, 3rd order phase
-        #  0 0    0 1    0 2     1 0    1 1    1 2       1 3           1 4
-
-    def get_alignment_offset(self, angle: float):
-        """
-        Compute the alignment offset for the given angle.
-
-        Args:
-            angle (float): The angle to compute the alignment offset for.
-
-        Returns:
-            tuple: The alignment offset in x, y and z direction.
-        """
-        tomo_alignment_fit = self.client.get_global_var("tomo_alignment_fit")
-        if tomo_alignment_fit is None:
-            print("Not applying any alignment offsets. No tomo alignment fit data available.\n")
-            return (0, 0, 0)
-
-        # x amp, phase, offset, y amp, phase, offset
-        #  0 0    0 1    0 2     1 0    1 1    1 2
-        correction_x = (
-            tomo_alignment_fit[0][0] * np.sin(np.radians(angle) + tomo_alignment_fit[0][1])
-            + tomo_alignment_fit[0][2]
-        )
-        correction_y = (
-            tomo_alignment_fit[1][0] * np.sin(np.radians(angle) + tomo_alignment_fit[1][1])
-            + tomo_alignment_fit[1][2]
-            + tomo_alignment_fit[1][3] * np.sin(3 * np.radians(angle) + tomo_alignment_fit[1][4])
-        )
-        correction_z = tomo_alignment_fit[0][0] * np.sin(
-            np.radians(angle + 90) + tomo_alignment_fit[0][1]
-        )
-
-        print(
-            f"Alignment offset x {correction_x}, y {correction_y}, z {correction_z} for angle"
-            f" {angle}\n"
-        )
-        return (correction_x, correction_y, correction_z)
-
-    def _read_correction_file(self, correction_file: str):
-        with open(correction_file, "r") as f:
-            num_elements = f.readline()
-            int_num_elements = int(num_elements.split(" ")[2])
-            corr_pos = []
-            corr_angle = []
-            for j in range(int_num_elements * 2):
-                line = f.readline()
-                value = line.split(" ")[2]
-                name = line.split(" ")[0].split("[")[0]
-                if name == "corr_pos":
-                    corr_pos.append(float(value))
-                elif name == "corr_angle":
-                    corr_angle.append(float(value))
-        print(
-            f"Loading default mirror correction from file {correction_file} containing {int_num_elements} elements."
-        )
-        # print(corr_pos)
-        return corr_pos, corr_angle
-
-    def read_additional_correction_x(self, correction_file: str):
-        self.corr_pos_x, self.corr_angle_x = self._read_correction_file(correction_file)
-
-    def read_additional_correction_y(self, correction_file: str):
-        self.corr_pos_y, self.corr_angle_y = self._read_correction_file(correction_file)
-
-    def read_additional_correction_y_2(self, correction_file: str):
-        self.corr_pos_y_2, self.corr_angle_y_2 = self._read_correction_file(correction_file)
-
-    def compute_additional_correction_x(self, angle):
-        return self._compute_additional_correction(angle, iteration="x1")
-
-    def compute_additional_correction_y(self, angle):
-        return self._compute_additional_correction(angle, iteration="y1")
-
-    def compute_additional_correction_y_2(self, angle):
-        return self._compute_additional_correction(angle, iteration="y2")
-
-    def _compute_additional_correction(self, angle, iteration="y1"):
-        if iteration == "x1":
-            corr_pos = self.corr_pos_x
-            corr_angle = self.corr_angle_x
-        elif iteration == "y1":
-            corr_pos = self.corr_pos_y
-            corr_angle = self.corr_angle_y
-        elif iteration == "y2":
-            corr_pos = self.corr_pos_y_2
-            corr_angle = self.corr_angle_y_2
-        if not corr_pos:
-            print(f"Not applying any additional correction {iteration}. No data available.\n")
-            return 0
-
-        # find index of closest angle
-        for j, _ in enumerate(corr_pos):
-            newangledelta = np.fabs(corr_angle[j] - angle)
-            if j == 0:
-                angledelta = newangledelta
-                additional_correction_shift = corr_pos[j]
-                continue
-
-            if newangledelta < angledelta:
-                additional_correction_shift = corr_pos[j]
-                angledelta = newangledelta
-
-        if additional_correction_shift == 0 and angle > corr_angle[-1]:
-            additional_correction_shift = corr_pos[-1]
-        print(f"Additional correction shift {iteration}: {additional_correction_shift}")
-        return additional_correction_shift

csaxs_bec/bec_ipython_client/plugins/omny/omny_general_tools.py

@@ -1,153 +0,0 @@
-import time
-import numpy as np
-import sys
-import termios
-import tty
-import fcntl
-import os
-import builtins
-
-from rich import box
-from rich.console import Console
-from rich.table import Table
-
-# from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
-
-if builtins.__dict__.get("bec") is not None:
-    bec = builtins.__dict__.get("bec")
-    dev = builtins.__dict__.get("dev")
-    umv = builtins.__dict__.get("umv")
-    umvr = builtins.__dict__.get("umvr")
-
-
-class OMNYToolsError(Exception):
-    pass
-
-
-class OMNYTools:
-
-    HEADER = "\033[95m"
-    OKBLUE = "\033[94m"
-    OKCYAN = "\033[96m"
-    OKGREEN = "\033[92m"
-    WARNING = "\033[93m"
-    FAIL = "\033[91m"
-    ENDC = "\033[0m"
-    BOLD = "\033[1m"
-    UNDERLINE = "\033[4m"
-
-    def __init__(self, client) -> None:
-        self.client = client
-
-    @staticmethod
-    def _get_user_param_safe(device, var):
-        param = dev[device].user_parameter
-        if not param or param.get(var) is None:
-            raise ValueError(f"Device {device} has no user parameter definition for {var}.")
-        return param.get(var)
-
-    def printgreen(self, string: str):
-        print(self.OKGREEN + string + self.ENDC)
-
-    def printgreenbold(self, string: str):
-        print(self.BOLD + self.OKGREEN + string + self.ENDC)
-
-    def yesno(self, message: str, default="none", autoconfirm=0) -> bool:
-        if autoconfirm and default == "y":
-            self.printgreen(message + " Automatically confirming default: yes")
-            return True
-        elif autoconfirm and default == "n":
-            self.printgreen(message + " Automatically confirming default: no")
-            return False
-        if default == "y":
-            message_ending = " [Y]/n? "
-        elif default == "n":
-            message_ending = " y/[N]? "
-        else:
-            message_ending = " y/n? "
-        while True:
-            user_input = input(self.OKBLUE + message + message_ending + self.ENDC)
-            if (
-                user_input == "Y" or user_input == "y" or user_input == "yes" or user_input == "Yes"
-            ) or (default == "y" and user_input == ""):
-                return True
-            if (
-                user_input == "N" or user_input == "n" or user_input == "no" or user_input == "No"
-            ) or (default == "n" and user_input == ""):
-                return False
-            else:
-                print("Please expicitely confirm y or n.")
-
-    def tweak_cursor(
-        self, dev1, step1: float, dev2="none", step2: float = "0", special_command="none"
-    ):
-        if dev1 not in dev.enabled_devices:
-            print(f"Device 1 {dev} is not in enabled devices.")
-            return
-        if dev2 not in dev.enabled_devices and dev2 != "none":
-            print(f"Device 2 {dev} is not in enabled devices.")
-            return
-        # Save the current terminal settings
-        fd = sys.stdin.fileno()
-        old_term = termios.tcgetattr(fd)
-        try:
-            # Set the terminal to raw mode to capture single key presses
-            tty.setraw(fd)
-            # Set stdin to non-blocking mode
-            old_flags = fcntl.fcntl(fd, fcntl.F_GETFL)
-            fcntl.fcntl(fd, fcntl.F_SETFL, old_flags | os.O_NONBLOCK)
-            print("Tweak Cursor." + self.BOLD + self.OKBLUE + "Press (q) to quit!\r" + self.ENDC)
-            while True:
-                try:
-                    # Read single character input
-                    key = sys.stdin.read(1)
-                    if key == "q":
-                        print("\n\rExiting tweak mode\r")
-                        break
-                    elif key == "\x1b":  # Escape sequences for arrow keys
-                        next1, next2 = sys.stdin.read(2)
-                        if next1 == "[":
-                            if next2 == "A":
-                                # print("up")
-                                if dev2 != "none":
-                                    umvr(dev2, step2)
-                                    if special_command != "none":
-                                        special_command()
-                            elif next2 == "B":
-                                # print(" down")
-                                if dev2 != "none":
-                                    umvr(dev2, -step2)
-                                    if special_command != "none":
-                                        special_command()
-                            elif next2 == "C":
-                                # print("right")
-                                umvr(dev1, step1)
-                                if special_command != "none":
-                                    special_command()
-                            elif next2 == "D":
-                                # print("left")
-                                umvr(dev1, -step1)
-                                if special_command != "none":
-                                    special_command()
-
-                    elif key == "+":
-                        step1 = step1 * 2
-                        if dev2 != "none":
-                            step2 = step2 * 2
-                        print(f"\rDouble step size. New step size: {step1}, {step2}\r")
-                    elif key == "-":
-                        step1 = step1 / 2
-                        if dev2 != "none":
-                            step2 = step2 / 2
-                        print(f"\rHalf step size. New step size: {step1}, {step2}\r")
-                except IOError:
-                    # No input available, keep looping
-                    pass
-
-                # Sleep for a short period to avoid high CPU usage
-                time.sleep(0.02)
-
-        finally:
-            # Restore the terminal to its original state
-            termios.tcsetattr(fd, termios.TCSADRAIN, old_term)
-            fcntl.fcntl(fd, fcntl.F_SETFL, old_flags)

csaxs_bec/bec_ipython_client/plugins/omny/omny_optics_mixin.py

@@ -1,384 +0,0 @@
-import time
-import numpy as np
-
-from rich import box
-from rich.console import Console
-from rich.table import Table
-
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_put, fshclose
-
-
-class OMNYError(Exception):
-    pass
-
-
-class OMNYOpticsMixin:
-    @staticmethod
-    def _get_user_param_safe(device, var):
-        param = dev[device].user_parameter
-        if not param or param.get(var) is None:
-            raise ValueError(f"Device {device} has no user parameter definition for {var}.")
-        return param.get(var)
-
-    def ooptics_in(self):
-        self.ofzp_in()
-        # ocs_in
-        self.oosa_in()
-
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_enable()
-
-        self.align.update_frame()
-
-        user_input = input(
-            "Is the direct beam gone on the xray eye? Do you see the cone of the FZP?"
-        )
-        if user_input == "y":
-            printf("Next oeye_out...\n")
-        else:
-            raise OMNYError("Failed to properly move in the Xray optics")
-
-    def _oeyey_mv(self, position):
-        # direction dependent speeds
-        if dev.oeyez.get().readback < position:
-            dev.oeyez.controller.socket_put_confirmed("axspeed[7]=15000")
-        else:
-            dev.oeyez.controller.socket_put_confirmed("axspeed[7]=10000")
-        umv(dev.oeyey, position)
-        dev.oeyez.controller.socket_put_confirmed("axspeed[7]=10000")
-
-    def oeye_out(self):
-        fshclose()
-        if self.OMNYTools.yesno("Did you move in the optics?"):
-            umv(dev.oeyez, -2)
-            self._oeyey_mv(-60.3)
-            # free camera
-            epics_put("XOMNYI-XEYE-ACQ:0", 2)
-        else:
-            raise OMNYError("The optics were not moved in. Please do so prior to eyey_out")
-        self.OMNYTools.printgreen("Oeye is out.")
-
-    def oeye_cam_in(self):
-        if dev.oeyez.get().readback < -80:
-            umv(dev.oeyez, -50)
-
-        if np.fabs(dev.oeyey.get().readback + 4.8) > 0.1:
-            self._oeyey_mv(-4.8)
-
-        if np.fabs(dev.oeyez.get().readback + 2) > 0.1 or np.fabs(dev.oeyex.get().readback) > 0.1:
-            umv(dev.oeyez, -2, dev.oeyex, 0)
-        # if still too close in z -- safety check
-        if np.fabs(dev.oeyez.get().readback + 2) > 0.1:
-            raise OMNYError("The oeye is too close in z for transfer. ERROR! Aborting.")
-        self.OMNYTools.printgreen("Oeye is at cam position.")
-
-    def _oeye_xray_is_in(self) -> bool:
-        omny_oeye_xray_inx = self._get_user_param_safe("oeyex", "xray_in")
-        omny_oeye_xray_iny = self._get_user_param_safe("oeyey", "xray_in")
-        omny_oeye_currentx = dev.oeyex.get().readback
-        omny_oeye_currenty = dev.oeyey.get().readback
-
-        if (
-            np.fabs(omny_oeye_currentx - omny_oeye_xray_inx) < 0.1
-            and np.fabs(omny_oeye_currenty - omny_oeye_xray_iny) < 0.1
-        ):
-            return True
-        else:
-            return False
-
-    def oeye_xray_in(self):
-        if self._oeye_xray_is_in():
-            pass
-        else:
-            # todo
-            #            self._otransfer_gripper_safe_xray_in_operation()
-            # if(!_oshield_is_ST_closed())
-            # {
-            #  printf("The shield of the sample stage is not closed. Aborting.\n")
-            #  exit
-            # }
-            omny_oeye_xray_inx = self._get_user_param_safe("oeyex", "xray_in")
-            omny_oeye_xray_iny = self._get_user_param_safe("oeyey", "xray_in")
-            omny_oeye_xray_inz = self._get_user_param_safe("oeyez", "xray_in")
-
-            self._oeyey_mv(omny_oeye_xray_iny)
-            omny_oeye_currenty = dev.oeyey.get().readback
-            if np.fabs(omny_oeye_currenty - omny_oeye_xray_iny) > 0.1:
-                raise OMNYError("The oeye did not move up.\n")
-            umv(dev.oeyex, omny_oeye_xray_inx, dev.oeyez, omny_oeye_xray_inz)
-            self.OMNYTools.printgreen("Oeye is at X-ray position.")
-
-            # some notes for the vis microscope:
-            # initial position for the vis light microscope
-            # do not open the shield when the microscope is at the vis mic position
-            # found eoeyx -45.13, z -84.9, y 0.64
-            # for a samy position of 2.8 with delta off
-            # the osa position should be in z around 7.4. in x it seems better
-            # around -0.6, where potentially xrays dont pass anymore
-            #
-
-    def _oosa_check_y(self):
-        omny_oosa_currenty = dev.oosay.get().readback
-        if np.fabs(omny_oosa_currenty - 0.9) > 0.05:
-            umv(dev.oosay, 0.9)
-        omny_oosa_currenty = dev.oosay.get().readback
-        if np.fabs(omny_oosa_currenty - 0.9) > 0.05:
-            raise OMNYError("oosay is not around 0.9. Aborting.")
-
-    def _oosa_to_move_corridor(self):
-        self._oosa_check_y()
-        dev.oosax.limits = [-3, 3.7]  # risk collision with shield
-        umv(dev.oosax, -2)
-        dev.oosax.read(cached=False)
-        omny_oosa_currentx = dev.oosax.get().readback
-        if np.fabs(omny_oosa_currentx + 2) > 0.1:
-            raise OMNYError("oosax did not reach target position. Not moving in z.\n")
-
-    def oosa_in(self):
-        self._oosa_check_y()
-        dev.oshield.read(cached=False)
-        omny_oshield_current = dev.oshield.get().readback
-        if omny_oshield_current < 15:
-            self._oshield_ST_close()
-        if self.near_field == False:
-            x_in_pos = self._get_user_param_safe("oosax", "far_field_in")
-            y_in_pos = self._get_user_param_safe("oosay", "far_field_in")
-            z_in_pos = self._get_user_param_safe("oosaz", "far_field_in")
-            print("OSA movement in far-field mode.")
-            dev.oosaz.read(cached=False)
-            omny_oosa_currentz = dev.oosaz.get().readback
-            if omny_oosa_currentz < 6.4:
-                self._oosa_to_move_corridor()
-            dev.oosaz.limits = [6.4, 6.6]
-            umv(dev.oosaz, z_in_pos)
-            umv(dev.oosax, x_in_pos)
-            umv(dev.oosay, y_in_pos)
-            #### For the 30 nm FZP 220 um we use this part
-            #  umv oosaz 6.5
-            #  umv oosax 3.2453
-            #  umv oosay 0.386015
-
-        if self.near_field == True:
-            x_in_pos = self._get_user_param_safe("oosax", "near_field_in")
-            y_in_pos = self._get_user_param_safe("oosay", "near_field_in")
-            z_in_pos = self._get_user_param_safe("oosaz", "near_field_in")
-            print("OSA movement in near-field mode.")
-            dev.oosaz.read(cached=False)
-            omny_oosa_currentz = dev.oosaz.get().readback
-            if omny_oosa_currentz > 0:
-                self._oosa_to_move_corridor()
-            dev.oosaz.limits = [-0.4, -0.6]
-            umv(dev.oosaz, z_in_pos)
-            umv(dev.oosax, x_in_pos)
-            omny_osamy_current = dev.osamy.get().readback
-            if omny_osamy_current < 3.25:
-                umv(dev.oosay, y_in_pos)
-            else:
-                raise OMNYError("Failed to move oosa in. osamy position is too large.")
-
-        self.OMNYTools.printgreen("OSA is in.")
-
-        # todo
-        # _omny_interferometer_align_tracking
-        # rt_feedback_enable
-
-    def oosa_out(self):
-        self._oosa_check_y()
-        dev.oshield.read(cached=False)
-        omny_oshield_current = dev.oshield.get().readback
-        if omny_oshield_current < 15:
-            self._oshield_ST_close()
-        omny_oosaz_current = dev.oosaz.get().readback
-        if self.near_field == False:
-            print("OSA movement in far-field mode.")
-            if omny_oosaz_current < 6.4:
-                self._oosa_to_move_corridor()
-            dev.oosaz.limits = [6.4, 6.6]
-            umv(dev.oosaz, 6.5)
-            umv(dev.oosax, -2)
-        if self.near_field == True:
-            print("OSA movement in near-field mode.")
-            if omny_oosaz_current > 0:
-                self._oosa_to_move_corridor()
-            dev.oosaz.limits = [-0.4, -0.6]
-            umv(dev.oosaz, -0.45)
-            umv(dev.oosax, -2)
-        # todo _omny_interferometer_align_tracking
-
-        self.OMNYTools.printgreen("OSA is out.")
-
-    def oosa_move_out_of_shield(self):
-        # todo: _omnycam_samplestage
-        self._oosa_check_y()
-        self._oosa_to_move_corridor()
-        omny_osamx_current = dev.osamx.get().readback
-        if np.fabs(omny_osamx_current) > 0.2:
-            umv(dev.osamx, 0)
-        omny_oosaz_current = dev.oosaz.get().readback
-        if omny_oosaz_current > 0.1:
-            dev.oosaz.limits = [-0.1, 0.1]
-            umv(dev.oosaz, 0)
-
-        self.OMNYTools.printgreen("OSA is out of shield.")
-
-    def ofzp_out(self):
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_disable()
-        y_out_pos = self._get_user_param_safe("ofzpy", "out")
-        if np.fabs(dev.ofzpy.get().readback - y_out_pos) > 0.02:
-            umv(dev.ofzpy, y_out_pos)
-        self.OMNYTools.printgreen("FZP at out position")
-
-    def ofzp_in(self):
-        if "rtx" in dev and dev.rtx.enabled:
-            dev.rtx.controller.feedback_disable()
-        x_in_pos = self._get_user_param_safe("ofzpx", "in")
-        y_in_pos = self._get_user_param_safe("ofzpy", "in")
-        if np.fabs(dev.ofzpy.get().readback - y_in_pos) > 0.02:
-            umv(dev.ofzpy, y_in_pos)
-
-        if np.fabs(dev.ofzpx.get().readback - x_in_pos) > 0.02:
-            umv(dev.ofzpx, x_in_pos)
-        self.OMNYTools.printgreen("FZP at in position")
-        # 220 mu FZP at ofzpz 31.8025 for eiger probe (about 2.4 mm propagation after focus)
-        # umv(dev.ofzpy, 0.7944)
-        # if np.fabs(dev.ofzpx.get().readback+0.4317)>0.05:
-        #     umv(dev.ofzpx, -0.4317)
-        # note the 220 fzp also works for near field 6.2 kev by just moving back osa and fzp
-        # ofzpz 24.8 leads to a 9.5 mm propagation distance.
-        # With the 220 mu FZP this gives 100 nm pixel recons
-        # for the oosa macro set near_field=1
-        # 170 mu FZP at 6.2 kev for large beam at ofzpz 31.8025 of about 58 mu diameter
-        # 120 mu FZP at ofzpz 28.1991
-
-        # 250 mu FZP 60 nm at 5.65 keV
-        # ofzpz 29.7 for propagation distance 2.2
-        # umv ofzpx -0.4457
-        # umv ofzpy 0.193630
-
-        # 150 um fzp, 60 nm, ofzpz 33.8 at 8.9 kev for propagation of 1.7 mm after focus
-        # umv ofzpx -0.756678
-        # umv ofzpy 0.193515
-
-        # 250 um 30 nm FZP upper right
-        # small abberrations, seems to give good results in weak objects
-        # ofzpx -0.609240
-        # umv ofzpy 0.118265
-        # 250 um 30 nm FZP lower right very aberated
-        # ofzpx -0.881935
-        # umv ofzpy 0.537050
-
-        # ofzpz 28.4027
-        # 5.30 mm prop at 8.9 keV, 45 nm pixel in near field
-
-        # ofzpz 33.103
-        # 0.6 mm prop at 8.9 kev far field 7 m flight tube at foptz
-
-        # ofzpz 49.4 is reachable just without interferometer swap
-        # which at 6.2 keV and 250 um diam, 30 nm should gives a propagation of 0.8 after focus
-        # and a beam size of 6 microns diamter
-        ###coordinates 30 nm FZP for comparing them
-        # not sure if that is really correct
-        # FZP 1 - FZP 2
-        #   FZP 5
-        # FZP 4 - FZP 1
-
-        # FZP
-        ##upper right
-        # umv ofzpx -0.6154 ofzpy 0.1183
-        # umv ocsx -0.6070 ocsy 0.0540
-
-        # lower right
-        # umv ofzpx -0.8341 ofzpy 0.5683
-        # umv ocsx -0.3880 ocsy -0.3960
-
-        # lower left
-        # umv ofzpx -0.3876 ofzpy 0.7902
-        # umv ocsx -0.8380 ocsy -0.6180
-
-        # upper left
-        # umv ofzpx -0.1678 ofzpy 0.3403
-        # umv ocsx -1.0550 ocsy -0.1680
-
-    def ofzp_info(self, mokev_val=-1, ofzpz_val=-1):
-        print(f"{ofzpz_val}")
-
-        if mokev_val == -1:
-            try:
-                mokev_val = dev.mokev.readback.get()
-            except:
-                print(
-                    "Device mokev does not exist. You can specify the energy in keV as an argument instead."
-                )
-                return
-        if ofzpz_val == -1:
-            ofzpz_val = dev.ofzpz.readback.get()
-        distance = 66 + 2.4 + 31.8025 - ofzpz_val
-        print(
-            f"\nThe sample is in a distance of \033[1m{distance:.1f} mm\033[0m from the 60 nm FZP.\n"
-        )
-        print(f"At the current energy of {mokev_val:.4f} keV we have following options:\n")
-
-        diameters = [80e-6, 100e-6, 120e-6, 150e-6, 170e-6, 200e-6, 220e-6, 250e-6]
-
-        console = Console()
-        table = Table(title="Outermost zone width \033[1m60 nm\033[0m", box=box.SQUARE)
-        table.add_column("Diameter", justify="center")
-        table.add_column("Focal distance", justify="center")
-        table.add_column("Current beam size", justify="center")
-
-        wavelength = 1.2398e-9 / mokev_val
-
-        for diameter in diameters:
-            outermost_zonewidth = 60e-9
-            focal_distance = diameter * outermost_zonewidth / wavelength * 1000
-            beam_size = -diameter / (focal_distance * 1000) * (focal_distance - distance) * 1e9
-            table.add_row(
-                f"{diameter*1e6:.2f} microns",
-                f"{focal_distance:.2f} mm",
-                f"{beam_size:.2f} microns",
-            )
-
-        console.print(table)
-
-        # 30 nm with additional spacer
-        distance = 53.84 + 0.6 + 33.1 - ofzpz_val
-        print(
-            f"\nThe sample is in a distance of \033[1m{distance:.1f} mm\033[0m from the 30 nm FZP.\n"
-        )
-
-        diameters = [150e-6, 250e-6]
-
-        console = Console()
-        table = Table(title="Outermost zone width \033[1m30 nm\033[0m", box=box.SQUARE)
-        table.add_column("Diameter", justify="center")
-        table.add_column("Focal distance", justify="center")
-        table.add_column("Current beam size", justify="center")
-
-        wavelength = 1.2398e-9 / mokev_val
-
-        for diameter in diameters:
-            outermost_zonewidth = 30e-9
-            focal_distance = diameter * outermost_zonewidth / wavelength * 1000
-            beam_size = -diameter / (focal_distance * 1000) * (focal_distance - distance) * 1e9
-            table.add_row(
-                f"{diameter*1e6:.2f} microns",
-                f"{focal_distance:.2f} mm",
-                f"{beam_size:.2f} microns",
-            )
-
-        console.print(table)
-
-        print(
-            "This function can be called with explicit energy and ofzpz position.\n Example: omny.ffzp_info(mokev_val=6.2, ofzpz_val=33.2)"
-        )
-
-        # from flomni
-        # oosaz_val = dev.oosaz.readback.get()
-
-        # print("\nOSA Information:")
-        # print(f"  Current fosaz {fosaz_val:.1f}")
-        # print(
-        #     f"  The OSA will collide with a normal OMNY pin at fosaz \033[1m{(33-fosaz_val):.1f}\033[0m"
-        # )
-        # print(f"  Remaining space: \033[1m{-fosaz_val+(33-foptz_val):.1f}\033[0m")

csaxs_bec/bec_ipython_client/plugins/omny/omny_rt.py

@@ -1,241 +0,0 @@
-import time
-import numpy as np
-import sys
-import termios
-import tty
-import fcntl
-import os
-
-
-from rich import box
-from rich.console import Console
-from rich.table import Table
-
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen, fshclose
-
-
-class OMNY_rt_clientError(Exception):
-    pass
-
-
-class OMNY_rt_client:
-    def __init__(self):
-        self.mirror_channel = -1
-        self.mirror_amplitutde_increase = 0
-        self.mirror_parameters = {}
-        for j in range(1, 9):
-            self.mirror_parameters[j] = dev.rtx.controller.get_mirror_parameters(j)
-
-    @staticmethod
-    def _get_user_param_safe(device, var):
-        param = dev[device].user_parameter
-        if not param or param.get(var) is None:
-            raise OMNY_rt_clientError(
-                f"Device {device} has no user parameter definition for {var}."
-            )
-        return param.get(var)
-
-    def _omny_interferometer_openloop_steps(self, channel, steps, amplitude):
-        dev.rtx.controller._omny_interferometer_openloop_steps(channel, steps, amplitude)
-
-    def interferometer_tweaking(self):
-        self._tweak_interferometer()
-
-    def _tweak_interferometer(self):
-        self.mirror_channel = -1
-
-        # Save the current terminal settings
-        fd = sys.stdin.fileno()
-        old_term = termios.tcgetattr(fd)
-
-        print("Ready to tweak the interferometer. Press q to quit.")
-        print("The arrows adjust directions.")
-        print("Numbers select the mirror aligner.")
-
-        try:
-            # Set the terminal to raw mode to capture single key presses
-            tty.setraw(fd)
-            # Set stdin to non-blocking mode
-            old_flags = fcntl.fcntl(fd, fcntl.F_GETFL)
-            fcntl.fcntl(fd, fcntl.F_SETFL, old_flags | os.O_NONBLOCK)
-            opt_mirrorname = "none"
-            max = 0
-            while True:
-                try:
-                    # Read single character input
-                    key = sys.stdin.read(1)
-
-                    if key == "q":
-                        self.mirror_amplitutde_increase = 0
-                        self.mirror_channel = -1
-                        print("\n\rExiting tweak mode\r")
-                        break
-                    elif key == "\x1b":  # Escape sequences for arrow keys
-                        next1, next2 = sys.stdin.read(2)
-
-                        if next1 == "[":
-                            printit = True
-                            if next2 == "A":
-                                # print("up")
-                                if self.mirror_channel != -1:
-                                    self._omny_interferometer_openloop_steps(
-                                        4,
-                                        -self.mirror_parameters[self.mirror_channel][
-                                            "opt_steps2_neg"
-                                        ],
-                                        self.mirror_parameters[self.mirror_channel][
-                                            "opt_amplitude2_neg"
-                                        ]
-                                        + self.mirror_amplitutde_increase,
-                                    )
-                            elif next2 == "B":
-                                # print(" down")
-                                if self.mirror_channel != -1:
-                                    self._omny_interferometer_openloop_steps(
-                                        4,
-                                        self.mirror_parameters[self.mirror_channel][
-                                            "opt_steps2_pos"
-                                        ],
-                                        self.mirror_parameters[self.mirror_channel][
-                                            "opt_amplitude2_pos"
-                                        ]
-                                        + self.mirror_amplitutde_increase,
-                                    )
-                            elif next2 == "C":
-                                # print("right")
-                                if self.mirror_channel != -1:
-                                    self._omny_interferometer_openloop_steps(
-                                        3,
-                                        -self.mirror_parameters[self.mirror_channel][
-                                            "opt_steps1_neg"
-                                        ],
-                                        self.mirror_parameters[self.mirror_channel][
-                                            "opt_amplitude1_neg"
-                                        ]
-                                        + self.mirror_amplitutde_increase,
-                                    )
-                            elif next2 == "D":
-                                # print("left")
-                                if self.mirror_channel != -1:
-                                    self._omny_interferometer_openloop_steps(
-                                        3,
-                                        self.mirror_parameters[self.mirror_channel][
-                                            "opt_steps1_pos"
-                                        ],
-                                        self.mirror_parameters[self.mirror_channel][
-                                            "opt_amplitude1_pos"
-                                        ]
-                                        + self.mirror_amplitutde_increase,
-                                    )
-                    elif key.isdigit() and 1 <= int(key) <= 8:
-                        self.mirror_channel = int(key)
-                        opt_mirrorname = self.mirror_parameters[self.mirror_channel][
-                            "opt_mirrorname"
-                        ]
-                        autostop = self.mirror_parameters[self.mirror_channel]["opt_signal_stop"]
-                        averaging_time = self.mirror_parameters[self.mirror_channel][
-                            "opt_averaging_time"
-                        ]
-                        print(
-                            f"\nSelected mirror channel {self.mirror_channel}: {opt_mirrorname}. Autostop {autostop}. Signal averaging time: {averaging_time}\r"
-                        )
-                        if int(key) == 6:
-                            dev.rtx.controller.laser_tracker_on()
-                        dev.rtx.controller._omny_interferometer_switch_channel(self.mirror_channel)
-                        max = 0
-                        printit = True
-                    elif key == "+":
-                        print("\nIncreasing voltage amplitudes by 100.\r")
-                        self.mirror_amplitutde_increase += 100
-                    elif key == "-":
-                        print("\nDecreasing voltage amplitudes by 100.\r")
-                        self.mirror_amplitutde_increase -= 100
-                    elif key == "a":
-                        if self.mirror_channel != -1:
-                            dev.rtx.controller._omny_interferometer_optimize(
-                                mirror_channel=self.mirror_channel, channel=3
-                            )
-                            dev.rtx.controller._omny_interferometer_optimize(
-                                mirror_channel=self.mirror_channel, channel=4
-                            )
-                            dev.rtx.controller._omny_interferometer_optimize(
-                                mirror_channel=self.mirror_channel, channel=3
-                            )
-                            dev.rtx.controller._omny_interferometer_optimize(
-                                mirror_channel=self.mirror_channel, channel=4
-                            )
-                    if self.mirror_channel != -1 and printit:
-                        printit = False
-                        signal = dev.rtx.controller._omny_interferometer_get_signalsample(
-                            self.mirror_parameters[self.mirror_channel]["opt_signalchannel"],
-                            self.mirror_parameters[self.mirror_channel]["opt_averaging_time"],
-                        )
-                        if signal > max:
-                            max = signal
-                        info_str = f"Channel {self.mirror_channel}, {opt_mirrorname}, Current signal: {signal:.0f}"
-                        filling = " " * (50 - len(info_str))
-                        # Calculate the number of filled and unfilled segments
-                        length = 30
-                        percentage = signal / max
-                        filled_length = int(length * percentage)
-                        unfilled_length = length - filled_length
-                        bar = "#" * filled_length + "-" * unfilled_length
-                        print(info_str + filling + "0 " + bar + f" {max:.0f}      (q)uit\r", end="")
-
-                except IOError:
-                    # No input available, keep looping
-                    pass
-
-                # Sleep for a short period to avoid high CPU usage
-                time.sleep(0.02)
-
-        finally:
-            # Restore the terminal to its original state
-            termios.tcsetattr(fd, termios.TCSADRAIN, old_term)
-            fcntl.fcntl(fd, fcntl.F_SETFL, old_flags)
-            dev.rtx.controller._omny_interferometer_switch_alloff()
-            self.mirror_channel = -1
-            self.mirror_amplitutde_increase = 0
-            dev.rtx.controller.show_signal_strength_interferometer()
-
-    def show_signal_strength_interferometer(self):
-        dev.rtx.controller.show_signal_strength_interferometer()
-
-    def omny_interferometer_align_incoupling_angle(self):
-        dev.rtx.controller.omny_interferometer_align_incoupling_angle()
-
-    def interferometer_tweak_otrack(self):
-        self.OMNYTools.tweak_cursor(
-            dev.otrackz,
-            0.1,
-            dev.otracky,
-            0.1,
-            special_command=dev.rtx.controller.laser_tracker_print_intensity_for_otrack_tweaking,
-        )
-
-    def feedback_enable_with_reset(self):
-        dev.rtx.controller.feedback_enable_with_reset()
-
-    def feedback_disable(self):
-        dev.rtx.controller.feedback_disable()
-
-    def feedback_status(self):
-        if dev.rtx.controller.feedback_is_running():
-            print("Feedback is running.")
-        else:
-            print("Feedback is NOT running.")
-
-    def laser_tracker_on(self):
-        dev.rtx.controller.laser_tracker_on()
-
-    def laser_tracker_off(self):
-        dev.rtx.controller.laser_tracker_off()
-
-    def laser_tracker_show_all(self):
-        dev.rtx.controller.laser_tracker_show_all()
-
-    def omny_interferometer_align_tracking(self):
-        dev.rtx.controller.omny_interferometer_align_tracking()
-
-    def laser_tracker_check_and_wait_for_signalstrength(self):
-        dev.rtx.controller.laser_tracker_check_and_wait_for_signalstrength()

csaxs_bec/bec_ipython_client/plugins/omny/x_ray_eye_align.py

@@ -1,235 +0,0 @@
-from __future__ import annotations
-
-import builtins
-import os
-import time
-from typing import TYPE_CHECKING
-
-from bec_lib import bec_logger
-
-from csaxs_bec.bec_ipython_client.plugins.cSAXS import epics_get, epics_put, fshopen
-
-logger = bec_logger.logger
-# import builtins to avoid linter errors
-bec = builtins.__dict__.get("bec")
-dev = builtins.__dict__.get("dev")
-umv = builtins.__dict__.get("umv")
-umvr = builtins.__dict__.get("umvr")
-
-if TYPE_CHECKING:
-    from bec_ipython_client.plugins.omny import OMNY
-
-
-class XrayEyeAlign:
-    # pixel calibration, multiply to get mm
-    PIXEL_CALIBRATION = 0.2 / 218  # .2 with binning
-
-    def __init__(self, client, omny: OMNY) -> None:
-        self.client = client
-        self.omny = omny
-        self.device_manager = client.device_manager
-        self.scans = client.scans
-        self.alignment_values = {}
-        self.omny.reset_correction()
-        self.omny.reset_tomo_alignment_fit()
-
-    def _reset_init_values(self):
-        self.shift_xy = [0, 0]
-        self._xray_fov_xy = [0, 0]
-
-    def save_frame(self):
-        epics_put("XOMNYI-XEYE-SAVFRAME:0", 1)
-
-    def update_frame(self):
-        epics_put("XOMNYI-XEYE-ACQDONE:0", 0)
-        # start live
-        epics_put("XOMNYI-XEYE-ACQ:0", 1)
-        # wait for start live
-        while epics_get("XOMNYI-XEYE-ACQDONE:0") == 0:
-            time.sleep(0.5)
-            print("waiting for live view to start...")
-        fshopen()
-
-        epics_put("XOMNYI-XEYE-ACQDONE:0", 0)
-
-        while epics_get("XOMNYI-XEYE-ACQDONE:0") == 0:
-            print("waiting for new frame...")
-            time.sleep(0.5)
-
-        time.sleep(0.5)
-        # stop live view
-        epics_put("XOMNYI-XEYE-ACQ:0", 0)
-        time.sleep(1)
-        # fshclose
-        print("got new frame")
-
-    def tomo_rotate(self, val: float):
-        # pylint: disable=undefined-variable
-        umv(self.device_manager.devices.osamroy, val)
-
-    def get_tomo_angle(self):
-        return self.device_manager.devices.osamroy.readback.get()
-
-    def update_fov(self, k: int):
-        self._xray_fov_xy[0] = max(epics_get(f"XOMNYI-XEYE-XWIDTH_X:{k}"), self._xray_fov_xy[0])
-        self._xray_fov_xy[1] = max(0, self._xray_fov_xy[0])
-
-    @property
-    def movement_buttons_enabled(self):
-        return [epics_get("XOMNYI-XEYE-ENAMVX:0"), epics_get("XOMNYI-XEYE-ENAMVY:0")]
-
-    @movement_buttons_enabled.setter
-    def movement_buttons_enabled(self, enabled: bool):
-        enabled = int(enabled)
-        epics_put("XOMNYI-XEYE-ENAMVX:0", enabled)
-        epics_put("XOMNYI-XEYE-ENAMVY:0", enabled)
-
-    def send_message(self, msg: str):
-        epics_put("XOMNYI-XEYE-MESSAGE:0.DESC", msg)
-
-    def align(self):
-        # reset shift xy and fov params
-        self._reset_init_values()
-
-        self.tomo_rotate(0)
-        epics_put("XOMNYI-XEYE-ANGLE:0", 0)
-
-        self.omny.oeye_xray_in()
-
-        self.omny.feedback_enable_with_reset()
-
-        # disable movement buttons
-        self.movement_buttons_enabled = False
-
-        sample_name = dev.omny_samples.get_sample_name_in_samplestage()
-        epics_put("XOMNYI-XEYE-SAMPLENAME:0.DESC", sample_name)
-
-        # this makes sure we are in a defined state
-        self.omny.feedback_disable()
-
-        epics_put("XOMNYI-XEYE-PIXELSIZE:0", self.PIXEL_CALIBRATION)
-
-        osamx_in = self.omny.OMNYTools._get_user_param_safe("osamx", "in")
-        umv(dev.osamx, osamx_in - 0.35)
-
-        self.omny.ofzp_in()
-        self.update_frame()
-
-        # enable submit buttons
-        self.movement_buttons_enabled = False
-        epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
-        epics_put("XOMNYI-XEYE-STEP:0", 0)
-        self.send_message("Submit center value of FZP.")
-
-        k = 0
-        while True:
-            if epics_get("XOMNYI-XEYE-SUBMIT:0") == 1:
-                val_x = epics_get(f"XOMNYI-XEYE-XVAL_X:{k}") / 2 * self.PIXEL_CALIBRATION  # in mm
-                self.alignment_values[k] = val_x
-                print(f"Clicked position {k}: x {self.alignment_values[k]}")
-                rtx_position = dev.rtx.readback.get() / 1000
-                print(f"Current rtx position {rtx_position}")
-                self.alignment_values[k] -= rtx_position
-                print(f"Corrected position {k}: x {self.alignment_values[k]}")
-
-                if k == 0:  # received center value of FZP
-                    self.send_message("please wait ...")
-                    self.movement_buttons_enabled = False
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)  # disable submit button
-
-                    self.omny.feedback_disable()
-                    osamx_in = self.omny.OMNYTools._get_user_param_safe("osamx", "in")
-                    umv(dev.osamx, osamx_in)
-
-                    self.omny.ofzp_out()
-
-                    self.update_frame()
-                    epics_put("XOMNYI-XEYE-RECBG:0", 1)
-                    while epics_get("XOMNYI-XEYE-RECBG:0") == 1:
-                        time.sleep(0.5)
-                        print("waiting for background frame...")
-
-                    umv(dev.osamx, osamx_in)
-                    time.sleep(0.5)
-                    self.omny.feedback_enable_with_reset()
-
-                    self.update_frame()
-                    self.send_message("Adjust sample height and submit center")
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
-                    self.movement_buttons_enabled = True
-
-                elif 1 <= k < 5:  # received sample center value at samroy 0 ... 315
-                    self.send_message("please wait ...")
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)
-                    self.movement_buttons_enabled = False
-
-                    umv(dev.rtx, 0)
-                    self.tomo_rotate(k * 45)
-                    epics_put("XOMNYI-XEYE-ANGLE:0", self.get_tomo_angle())
-                    self.update_frame()
-                    self.send_message("Submit sample center")
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", 0)
-                    epics_put("XOMNYI-XEYE-ENAMVX:0", 1)
-                    self.update_fov(k)
-
-                elif k == 5:  # received sample center value at samroy 270 and done
-                    self.send_message("done...")
-                    epics_put("XOMNYI-XEYE-SUBMIT:0", -1)  # disable submit button
-                    self.movement_buttons_enabled = False
-                    self.update_fov(k)
-                    break
-
-                k += 1
-                epics_put("XOMNYI-XEYE-STEP:0", k)
-
-            _xrayeyalignmvx = epics_get("XOMNYI-XEYE-MVX:0")
-            if _xrayeyalignmvx != 0:
-                umvr(dev.rtx, _xrayeyalignmvx)
-                print(f"Current rtx position {dev.rtx.readback.get() / 1000}")
-                epics_put("XOMNYI-XEYE-MVX:0", 0)
-                if k > 0:
-                    epics_put(f"XOMNYI-XEYE-STAGEPOSX:{k}", dev.rtx.readback.get() / 1000)
-                time.sleep(3)
-                self.update_frame()
-
-            if k < 2:
-                # allow movements, store movements to calculate center
-                _xrayeyalignmvy = epics_get("XOMNYI-XEYE-MVY:0")
-                if _xrayeyalignmvy != 0:
-                    self.omny.feedback_disable()
-                    umvr(dev.osamy, _xrayeyalignmvy / 1000)
-                    time.sleep(2)
-                    epics_put("XOMNYI-XEYE-MVY:0", 0)
-                    self.omny.feedback_enable_with_reset()
-                    self.update_frame()
-            time.sleep(0.2)
-
-        self.write_output()
-        fovx = self._xray_fov_xy[0] * self.PIXEL_CALIBRATION * 1000 / 2
-        fovy = self._xray_fov_xy[1] * self.PIXEL_CALIBRATION * 1000 / 2
-
-        self.tomo_rotate(0)
-
-        umv(dev.rtx, 0)
-
-        # free camera
-        epics_put("XOMNYI-XEYE-ACQ:0", 2)
-
-        print(
-            f"The largest field of view from the xrayeyealign was \nfovx = {fovx:.0f} microns, fovy"
-            f" = {fovy:.0f} microns"
-        )
-        print("Use the matlab routine to FIT the current alignment...")
-
-        print("Then LOAD ALIGNMENT PARAMETERS by running omny.read_alignment_offset()\n")
-
-    def write_output(self):
-        file = os.path.expanduser("~/Data10/specES1/internal/xrayeye_alignmentvalues")
-        if not os.path.exists(file):
-            os.makedirs(os.path.dirname(file), exist_ok=True)
-        with open(file, "w") as alignment_values_file:
-            alignment_values_file.write("angle\thorizontal\n")
-            for k in range(1, 6):
-                fovx_offset = self.alignment_values[0] - self.alignment_values[k]
-                print(f"Writing to file new alignment: number {k}, value x {fovx_offset}")
-                alignment_values_file.write(f"{(k-1)*45}\t{fovx_offset*1000}\n")

csaxs_bec/bec_ipython_client/plugins/tool_box/debug_tools.py

@@ -1,250 +0,0 @@
-"""Module providing debugging tools for the BEC IPython client at cSAXS."""
-
-from __future__ import annotations
-
-import inspect
-import json
-import os
-import re
-import socket
-from concurrent.futures import ThreadPoolExecutor
-from functools import partial
-from typing import TYPE_CHECKING, Literal
-
-import numpy as np
-from pydantic import BaseModel
-from rich.console import Console
-from rich.panel import Panel
-from rich.table import Table
-from rich.text import Text
-from slugify import slugify
-
-if TYPE_CHECKING:
-    from bec_ipython_client.main import BECIPythonClient
-    from bec_lib.devicemanager import DeviceManagerBase
-    from bec_lib.scans import Scans
-    from bec_widgets.cli.client_utils import BECGuiClient
-
-    scans: Scans  # type: ignore[no-redef]
-
-    bec: BECIPythonClient  # type: ignore[no-redef]
-
-    dev: DeviceManagerBase  # type: ignore[no-redef]
-
-
-class Detector(BaseModel):
-    """Model representing a detector configuration."""
-
-    name: str
-    hostnames: list[str]
-    cfg: dict
-
-
-def to_identifier(text: str) -> str:
-    """
-    Convert an unsafe string into a valid Python identifier.
-    """
-    name = slugify(text.strip(), separator="_")
-    name = re.sub(r"[^a-zA-Z0-9_]", "", name)
-
-    if not name:
-        raise ValueError(f"Cannot convert '{text}' to a valid identifier.")
-
-    if name[0].isdigit():
-        name = f"_{name}"
-
-    return name
-
-
-class DebugTools:
-    """A collection of debugging tools for the BEC IPython client at cSAXS."""
-
-    _PURPOSE = (
-        "Debugging helpers for the cSAXS BEC IPython client. These tools are intended for advanced users "
-        "and developers to diagnose and troubleshoot issues within the BEC environment. "
-        "Below are the available methods together with a brief description of their functionality."
-    )
-
-    ######################
-    ## Internal Methods ##
-    ######################
-
-    def _describe(self) -> None:
-        """Pretty-print a description of this debugging tool."""
-        console = Console()
-
-        # Offset for IPython prompt misplacement
-        console.print("\n\n", end="")
-
-        header = Text("DebugTools", style="bold cyan")
-        purpose = Text(self._PURPOSE, style="dim")
-
-        console.print(Panel(purpose, title=header, expand=False))
-
-        table = Table(show_header=True, header_style="bold magenta")
-        table.add_column("Method", style="bold", no_wrap=True)
-        table.add_column("Description")
-
-        for name, member in inspect.getmembers(self, predicate=inspect.ismethod):
-            if name.startswith("_"):
-                continue
-
-            doc = inspect.getdoc(member)
-            short_doc = doc.splitlines()[0] if doc else ""
-            table.add_row(name, short_doc)
-
-        console.print(table)
-
-    def _repr_pretty_(self, p, cycle: bool) -> None:
-        if cycle:
-            p.text("DebugTools(...)")
-        else:
-            self._describe()
-
-    #####################
-    ### MCS Card Check ###
-    #####################
-
-    def _check_if_device_is_loaded(self, device_name: str):
-        """Check if a device is loaded in the current BEC session."""
-        if device_name not in dev:
-            raise RuntimeError(
-                f"Device {device_name} was not loaded in the current active BEC session."
-            )
-
-    def mcs_test_acquire(
-        self, mode: Literal["high_frame", "medium_frame", "low_frame"] = "high_frame"
-    ):
-        """
-        Method to perform a test acquisition with randomized exposure time, burst frames, and cycles
-        on the MCS card using the DDG trigger setup.
-
-        Args:
-            mode (Literal["high_frame", "medium_frame", "low_frame"]): The mode of the test.
-                - 'high_frame': Tests high frame rates with short exposure times.
-                - 'medium_frame': Tests medium frame rates with moderate exposure times.
-                - 'low_frame': Tests low frame rates with longer exposure times.
-        """
-        self._check_if_device_is_loaded("mcs")
-        self._check_if_device_is_loaded("ddg1")
-        self._check_if_device_is_loaded("ddg2")
-
-        if mode == "high_frame":
-            burst_frames = np.random.randint(10_000, 100_000)  # between 10000 and 100000
-            cycles = np.random.randint(5, 20)  # between 5 and 20
-            exp_time = (
-                np.random.rand() * (0.001 - 0.201e-3) + 0.201e-3
-            )  # between 0.000201 ms and 0.001 s
-        elif mode == "medium_frame":
-            burst_frames = np.random.randint(50, 500)  # between 50 and 500
-            cycles = np.random.randint(1, 10)  # between 1 and 10
-            exp_time = np.random.rand() * (0.01 - 0.001) + 0.001  # between 0.001 ms and 0.01 s
-        elif mode == "low_frame":
-            burst_frames = np.random.randint(5, 20)  # between 5 and 20
-            cycles = np.random.randint(1, 5)  # between 1 and 5
-            exp_time = np.random.rand() * (2 - 0.1) + 0.1  # between 0.1 ms and 2 s
-        else:
-            raise ValueError(f"Invalid mode '{mode}' specified for acquire scan test.")
-        print(
-            f"Starting acquire measurement with exp_time={exp_time:.6f}, burst_frames={burst_frames}, cycles={cycles}"
-        )
-        s = scans.acquire(
-            exp_time=exp_time, frames_per_trigger=burst_frames, burst_at_each_point=cycles
-        )
-        s.wait(file_written=True)
-        print("Acquire measurement finished.")
-        print("Checking MCS data...")
-        scan_data = bec.history.get_by_scan_id(s.scan.scan_id)
-        mcs_data = scan_data.devices.mcs
-        print(mcs_data)
-
-        shape = mcs_data._info["mcs_mca_mca1"]["value"]["shape"]
-        expected_shape = (cycles * burst_frames,)
-        # Assert will raise an error if the shapes do not match
-        assert (
-            shape == expected_shape
-        ), f"MCS data shape {shape} does not match expected shape {expected_shape}."
-
-    ########################
-    ### JFJ/Eiger Checks ###
-    ########################
-
-    def _get_jfj_eiger_config(self) -> dict[str, Detector]:
-        """Retrieve the current JFJ/Eiger detector configuration from the BEC client."""
-        # FIXME: Implement REST API call once ready for use from Leo Sala's team.
-        ret = {}
-        base_path = os.path.dirname(__file__)
-        config_path = os.path.join(base_path, "jfj_config.json")
-        with open(config_path, "r", encoding="utf-8") as fh:
-            cfg = json.load(fh)
-
-            for entry in cfg["detector"]:
-                det = Detector(
-                    name=to_identifier(entry["description"]), hostnames=entry["hostname"], cfg=cfg
-                )
-                ret[det.name] = det
-        return ret
-
-    def list_detectors(self) -> list[str]:
-        """
-        List the names of all JFJ/Eiger detectors configured in the BEC client.
-
-        Returns:
-            list[str]: A list of detector names.
-        """
-        detectors = self._get_jfj_eiger_config()
-        return list(detectors.keys())
-
-    def ping_detector(self, detector_name: str) -> bool:
-        """
-        Ping a JFJ/Eiger detector to check if it is reachable.
-
-        Args:
-            detector_name (str): The name of the detector to ping.
-
-        Returns:
-            bool: True if the detector is reachable, False otherwise.
-        """
-        detectors = self._get_jfj_eiger_config()
-        if detector_name not in detectors:
-            raise ValueError(f"Detector '{detector_name}' not found in configuration.")
-
-        det = detectors[detector_name]
-        results = self._ping_many(det.hostnames)
-
-        table = Table(title=f"Ping results for detector '{detector_name}'")
-        table.add_column("Hostname", style="cyan", no_wrap=True)
-        table.add_column("Status", style="magenta")
-
-        for host, alive in results.items():
-            status = "[green]OK[/green]" if alive else "[red]DOWN[/red]"
-            table.add_row(host, status)
-
-        console = Console()
-        console.print(table)
-
-    def _ping_many(self, hosts: list[str], port=22, timeout=2, max_workers=None):
-        max_workers = max_workers or len(hosts)
-        with ThreadPoolExecutor(max_workers=max_workers) as executor:
-            primed_ping = partial(self._ping, port=port, timeout=timeout)
-            pings = executor.map(primed_ping, hosts)
-            return dict(zip(hosts, pings))
-
-    def _ping(self, host: str, port=23, timeout=2):  # telnet is port 23
-        address = (host, port)
-        try:
-            with socket.create_connection(address, timeout):
-                return True
-        except OSError:
-            return False
-
-    def open_it_service_page(self):
-        """Open the overview of IT services hosted by Science IT Infrastructure and Services for cSAXS."""
-        gui: BECGuiClient = bec.gui
-        dock_area = gui.new()
-        print("Opening IT service page in new dock...")
-        url = "https://metrics.psi.ch/d/saf8mxv/x12sa?orgId=1&from=now-24h&to=now&timezone=browser&var-receiver_hosts=sls-jfjoch-001.psi.ch&var-writer_hosts=xbl-daq-34.psi.ch&var-beamline=X12SA&var-slurm_partitions=csaxs&var-receiver_services=broker&var-writer_services=writer&refresh=15m"
-        # FIXME BEC WIDGETS v3
-        dock = dock_area.new()
-        wb = dock.new(widget=gui.available_widgets.WebsiteWidget)
-        wb.set_url(url)

csaxs_bec/bec_ipython_client/plugins/tool_box/jfj_config.json

@@ -1,162 +0,0 @@
-{
-  "zeromq" : {
-    "image_socket": ["tcp://0.0.0.0:5500"]
-  },
-  "zeromq_preview": {
-    "socket_address": "tcp://0.0.0.0:5400",
-    "enabled": true,
-    "period_ms": 1000
-  },
-  "zeromq_metadata" : {
-   "socket_address": "tcp://0.0.0.0:5600",
-   "enabled": true,
-   "period_ms": 100
-  },
-  "instrument" : {
-    "source_name": "Swiss Light Source",
-    "instrument_name": "cSAXS",
-    "source_type": "Synchrotron X-ray Source"
-  },
-  "detector": [
-    {
-      "description": "EIGER 9M",
-      "serial_number": "E1",
-      "type": "EIGER",
-      "mirror_y": true,
-      "base_data_ipv4_address": "10.10.10.10",
-      "calibration_file":["/opt/jfjoch/calibration/"],
-      "standard_geometry" : {
-        "nmodules": 18,
-        "modules_in_row": 3,
-        "gap_x": 8,
-        "gap_y": 36
-      },
-      "hostname": [
-        "beb101",
-        "beb103",
-        "beb014",
-        "beb078",
-        "beb060",
-        "beb030",
-        "beb092",
-        "beb178",
-        "beb009",
-        "beb038",
-        "beb056",
-        "beb058",
-        "beb033",
-        "beb113",
-        "beb005",
-        "beb017",
-        "beb119",
-        "beb095",
-        "beb186",
-        "beb042",
-        "beb106",
-        "beb059",
-        "beb111",
-        "beb203",
-        "beb100",
-        "beb093",
-        "beb123",
-        "beb061",
-        "beb121",
-        "beb055",
-        "beb004",
-        "beb190",
-        "beb054",
-        "beb189",
-        "beb107",
-        "beb115"
-      ]
-    },
-    {
-      "description": "EIGER 8.5M (tmp)",
-      "serial_number": "E1-tmp",
-      "type": "EIGER",
-      "mirror_y": true,
-      "base_data_ipv4_address": "10.10.10.10",
-      "calibration_file":["/opt/jfjoch/calibration/"],
-      "standard_geometry" : {
-        "nmodules": 17,
-        "modules_in_row": 3,
-        "gap_x": 8,
-        "gap_y": 36
-      },
-      "hostname": [
-        "beb101",
-        "beb103",
-        "beb014",
-        "beb078",
-        "beb060",
-        "beb030",
-        "beb092",
-        "beb178",
-        "beb009",
-        "beb038",
-        "beb056",
-        "beb058",
-        "beb033",
-        "beb113",
-        "beb005",
-        "beb017",
-        "beb119",
-        "beb095",
-        "beb186",
-        "beb042",
-        "beb106",
-        "beb059",
-        "beb100",
-        "beb093",
-        "beb123",
-        "beb061",
-        "beb121",
-        "beb055",
-        "beb004",
-        "beb190",
-        "beb054",
-        "beb189",
-        "beb107",
-        "beb115"
-      ]
-    },
-    {
-      "description": "EIGER 1.5M",
-      "serial_number": "E2",
-      "type": "EIGER",
-      "mirror_y": true,
-      "base_data_ipv4_address": "10.10.11.10",
-      "calibration_file":["/opt/jfjoch/calibration_e1p5m/"],
-      "standard_geometry" : {
-        "nmodules": 3,
-        "modules_in_row": 1,
-        "gap_x": 8,
-        "gap_y": 36
-      },
-      "hostname": ["beb062", "beb026", "beb099", "beb084", "beb120", "beb108"]
-    }
-  ],
-  "frontend_directory": "/usr/share/jfjoch/frontend/",
-  "image_pusher": "ZeroMQ",
-  "numa_policy": "n2g2",
-  "receiver_threads": 64,
-  "image_buffer_MiB": 96000,
-  "pcie": [
-    {
-    "blk": "/dev/jfjoch0",
-    "ipv4": "10.10.10.1"
-    },
-    {
-      "blk": "/dev/jfjoch1",
-      "ipv4": "10.10.10.2"
-    },
-    {
-      "blk": "/dev/jfjoch2",
-      "ipv4": "10.10.10.3"
-    },
-    {
-      "blk": "/dev/jfjoch3",
-      "ipv4": "10.10.10.4"
-    }
-  ]
-}

csaxs_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 csaxs_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="cSAXS")
-
-    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(csaxs_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})

csaxs_bec/bec_widgets/auto_updates/auto_updates.py

@@ -1,63 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING
-
-from bec_widgets.widgets.containers.auto_update.auto_updates import AutoUpdates
-
-if TYPE_CHECKING:  # pragma: no cover
-    from bec_lib.messages import ScanStatusMessage
-
-
-class cSAXSUpdate(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)
-        if 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.
-        """
-
-
-class cSAXSUpdateAlignment(AutoUpdates): ...
-
-
-class cSAXSUpdateScan(AutoUpdates): ...

csaxs_bec/bec_widgets/widgets/client.py

@@ -1,148 +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 = {
-    "OmnyAlignment": "OmnyAlignment",
-    "XRayEye": "XRayEye",
-}
-
-
-class OmnyAlignment(RPCBase):
-    @property
-    @rpc_call
-    def enable_live_view(self):
-        """
-        None
-        """
-
-    @enable_live_view.setter
-    @rpc_call
-    def enable_live_view(self):
-        """
-        None
-        """
-
-    @property
-    @rpc_call
-    def user_message(self):
-        """
-        None
-        """
-
-    @user_message.setter
-    @rpc_call
-    def user_message(self):
-        """
-        None
-        """
-
-    @property
-    @rpc_call
-    def sample_name(self):
-        """
-        None
-        """
-
-    @sample_name.setter
-    @rpc_call
-    def sample_name(self):
-        """
-        None
-        """
-
-    @property
-    @rpc_call
-    def enable_move_buttons(self):
-        """
-        None
-        """
-
-    @enable_move_buttons.setter
-    @rpc_call
-    def enable_move_buttons(self):
-        """
-        None
-        """
-
-
-class XRayEye(RPCBase):
-    @rpc_call
-    def active_roi(self) -> "BaseROI | None":
-        """
-        Return the currently active ROI, or None if no ROI is active.
-        """
-
-    @property
-    @rpc_call
-    def enable_live_view(self):
-        """
-        Get or set the live view enabled state.
-        """
-
-    @enable_live_view.setter
-    @rpc_call
-    def enable_live_view(self):
-        """
-        Get or set the live view enabled state.
-        """
-
-    @property
-    @rpc_call
-    def user_message(self):
-        """
-        None
-        """
-
-    @user_message.setter
-    @rpc_call
-    def user_message(self):
-        """
-        None
-        """
-
-    @property
-    @rpc_call
-    def sample_name(self):
-        """
-        None
-        """
-
-    @sample_name.setter
-    @rpc_call
-    def sample_name(self):
-        """
-        None
-        """
-
-    @property
-    @rpc_call
-    def enable_move_buttons(self):
-        """
-        None
-        """
-
-    @enable_move_buttons.setter
-    @rpc_call
-    def enable_move_buttons(self):
-        """
-        None
-        """
-
-
-class XRayEye2DControl(RPCBase):
-    @rpc_call
-    def remove(self):
-        """
-        Cleanup the BECConnector
-        """

csaxs_bec/bec_widgets/widgets/omny_alignment/omny_alignment.py

@@ -1,140 +0,0 @@
-
-
-from typing import TypedDict
-from bec_widgets.utils.error_popups import SafeSlot
-import os
-from bec_widgets.utils.bec_widget import BECWidget
-from bec_widgets.utils.ui_loader import UILoader
-from qtpy.QtWidgets import QWidget, QPushButton, QLineEdit, QLabel, QVBoxLayout
-from bec_qthemes import material_icon
-from bec_lib.logger import bec_logger
-
-logger = bec_logger.logger 
-
-
-# class OmnyAlignmentUIComponents(TypedDict):
-#     moveRightButton: QPushButton
-#     moveLeftButton: QPushButton
-#     moveUpButton: QPushButton
-#     moveDownButton: QPushButton
-#     image: Image
-
-
-class OmnyAlignment(BECWidget, QWidget):
-    USER_ACCESS = ["enable_live_view", "enable_live_view.setter", "user_message", "user_message.setter","sample_name", "sample_name.setter", "enable_move_buttons", "enable_move_buttons.setter"]
-    PLUGIN = True
-    ui_file = "./omny_alignment.ui"
-
-    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)
-
-        icon_options = {"size": (16, 16), "convert_to_pixmap": False}
-        self.ui.moveRightButton.setText("")
-        self.ui.moveRightButton.setIcon(
-            material_icon(icon_name="keyboard_arrow_right", **icon_options)
-        )
-
-        self.ui.moveLeftButton.setText("")
-        self.ui.moveLeftButton.setIcon(
-            material_icon(icon_name="keyboard_arrow_left", **icon_options)
-        )
-
-        self.ui.moveUpButton.setText("")
-        self.ui.moveUpButton.setIcon(
-            material_icon(icon_name="keyboard_arrow_up", **icon_options)
-        )
-
-        self.ui.moveDownButton.setText("")
-        self.ui.moveDownButton.setIcon(
-            material_icon(icon_name="keyboard_arrow_down", **icon_options)
-        )
-
-        self.ui.confirmButton.setText("OK")
-
-
-        self.ui.liveViewSwitch.enabled.connect(self.on_live_view_enabled)
-
-        # self.ui.moveUpButton.clicked.connect(self.on_move_up)
-
-
-    @property
-    def enable_live_view(self):
-        return self.ui.liveViewSwitch.checked
-    
-    @enable_live_view.setter
-    def enable_live_view(self, enable:bool):
-        self.ui.liveViewSwitch.checked = enable
-
-
-    @property
-    def user_message(self):
-        return self.ui.messageLineEdit.text()
-    
-    @user_message.setter
-    def user_message(self, message:str):
-        self.ui.messageLineEdit.setText(message)
-
-    @property
-    def sample_name(self):
-        return self.ui.sampleLineEdit.text()
-    
-    @sample_name.setter
-    def sample_name(self, message:str):
-        self.ui.sampleLineEdit.setText(message)
-
-
-    @SafeSlot(bool)
-    def on_live_view_enabled(self, enabled:bool):
-        from bec_widgets.widgets.plots.image.image import Image
-        logger.info(f"Live view is enabled: {enabled}")
-        image: Image = self.ui.image
-        if enabled:
-            image.image("cam_xeye")
-            return
-        
-        image.disconnect_monitor("cam_xeye")
-
-
-    @property
-    def enable_move_buttons(self):
-        move_up:QPushButton = self.ui.moveUpButton
-        move_down:QPushButton = self.ui.moveDownButton
-        move_left:QPushButton = self.ui.moveLeftButton
-        move_right:QPushButton = self.ui.moveRightButton
-        return move_up.isEnabled() and move_down.isEnabled() and move_left.isEnabled() and move_right.isEnabled()
-    
-    @enable_move_buttons.setter
-    def enable_move_buttons(self, enabled:bool):
-        move_up:QPushButton = self.ui.moveUpButton
-        move_down:QPushButton = self.ui.moveDownButton
-        move_left:QPushButton = self.ui.moveLeftButton
-        move_right:QPushButton = self.ui.moveRightButton
-
-        move_up.setEnabled(enabled)
-        move_down.setEnabled(enabled)
-        move_left.setEnabled(enabled)
-        move_right.setEnabled(enabled)
-
-        
-
-
-
-
-if __name__ == "__main__":
-    from qtpy.QtWidgets import QApplication
-    import sys
-
-    app = QApplication(sys.argv)
-    widget = OmnyAlignment()
-
-    widget.show()
-    sys.exit(app.exec_())

csaxs_bec/bec_widgets/widgets/omny_alignment/omny_alignment.pyproject

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

csaxs_bec/bec_widgets/widgets/omny_alignment/omny_alignment.ui

@@ -1,125 +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>988</width>
-    <height>821</height>
-   </rect>
-  </property>
-  <property name="windowTitle">
-   <string>Form</string>
-  </property>
-  <layout class="QGridLayout" name="gridLayout_3">
-   <item row="2" column="2">
-    <layout class="QGridLayout" name="gridLayout">
-     <item row="1" column="2">
-      <widget class="QPushButton" name="moveRightButton">
-       <property name="text">
-        <string>PushButton</string>
-       </property>
-      </widget>
-     </item>
-     <item row="1" column="0">
-      <widget class="QPushButton" name="moveLeftButton">
-       <property name="text">
-        <string>PushButton</string>
-       </property>
-      </widget>
-     </item>
-     <item row="0" column="1">
-      <widget class="QPushButton" name="moveUpButton">
-       <property name="text">
-        <string>Up</string>
-       </property>
-      </widget>
-     </item>
-     <item row="2" column="1">
-      <widget class="QPushButton" name="moveDownButton">
-       <property name="text">
-        <string>PushButton</string>
-       </property>
-      </widget>
-     </item>
-     <item row="1" column="1">
-      <widget class="QPushButton" name="confirmButton">
-       <property name="text">
-        <string>PushButton</string>
-       </property>
-      </widget>
-     </item>
-    </layout>
-   </item>
-   <item row="2" column="0">
-    <layout class="QGridLayout" name="gridLayout_2">
-     <item row="0" column="1">
-      <widget class="QLineEdit" name="sampleLineEdit"/>
-     </item>
-     <item row="1" column="1">
-      <widget class="QLineEdit" name="messageLineEdit"/>
-     </item>
-     <item row="0" column="0">
-      <widget class="QLabel" name="label">
-       <property name="text">
-        <string>Sample</string>
-       </property>
-      </widget>
-     </item>
-     <item row="1" column="0">
-      <widget class="QLabel" name="label_2">
-       <property name="text">
-        <string>Message</string>
-       </property>
-      </widget>
-     </item>
-    </layout>
-   </item>
-   <item row="1" column="0" colspan="3">
-    <widget class="Image" name="image">
-     <property name="enable_toolbar" stdset="0">
-      <bool>false</bool>
-     </property>
-     <property name="inner_axes" stdset="0">
-      <bool>false</bool>
-     </property>
-     <property name="monitor" stdset="0">
-      <string>cam_xeye</string>
-     </property>
-     <property name="rotation" stdset="0">
-      <number>3</number>
-     </property>
-    </widget>
-   </item>
-   <item row="0" column="3">
-    <widget class="ToggleSwitch" name="liveViewSwitch"/>
-   </item>
-   <item row="0" column="2">
-    <widget class="QLabel" name="label_3">
-     <property name="text">
-      <string>Live View</string>
-     </property>
-     <property name="alignment">
-      <set>Qt::AlignmentFlag::AlignRight|Qt::AlignmentFlag::AlignTrailing|Qt::AlignmentFlag::AlignVCenter</set>
-     </property>
-    </widget>
-   </item>
-  </layout>
- </widget>
- <customwidgets>
-  <customwidget>
-   <class>Image</class>
-   <extends>QWidget</extends>
-   <header>image</header>
-  </customwidget>
-  <customwidget>
-   <class>ToggleSwitch</class>
-   <extends>QWidget</extends>
-   <header>toggle_switch</header>
-  </customwidget>
- </customwidgets>
- <resources/>
- <connections/>
-</ui>

csaxs_bec/bec_widgets/widgets/omny_alignment/omny_alignment_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 csaxs_bec.bec_widgets.widgets.omny_alignment.omny_alignment import OmnyAlignment
-
-DOM_XML = """
-<ui language='c++'>
-    <widget class='OmnyAlignment' name='omny_alignment'>
-    </widget>
-</ui>
-"""
-
-
-class OmnyAlignmentPlugin(QDesignerCustomWidgetInterface):  # pragma: no cover
-    def __init__(self):
-        super().__init__()
-        self._form_editor = None
-
-    def createWidget(self, parent):
-        t = OmnyAlignment(parent)
-        return t
-
-    def domXml(self):
-        return DOM_XML
-
-    def group(self):
-        return ""
-
-    def icon(self):
-        return designer_material_icon(OmnyAlignment.ICON_NAME)
-
-    def includeFile(self):
-        return "omny_alignment"
-
-    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 "OmnyAlignment"
-
-    def toolTip(self):
-        return "OmnyAlignment"
-
-    def whatsThis(self):
-        return self.toolTip()

csaxs_bec/bec_widgets/widgets/omny_alignment/register_omny_alignment.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 csaxs_bec.bec_widgets.widgets.omny_alignment.omny_alignment_plugin import OmnyAlignmentPlugin
-
-    QPyDesignerCustomWidgetCollection.addCustomWidget(OmnyAlignmentPlugin())
-
-
-if __name__ == "__main__":  # pragma: no cover
-    main()

csaxs_bec/bec_widgets/widgets/xray_eye/register_x_ray_eye.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 csaxs_bec.bec_widgets.widgets.xray_eye.x_ray_eye_plugin import XRayEyePlugin
-
-    QPyDesignerCustomWidgetCollection.addCustomWidget(XRayEyePlugin())
-
-
-if __name__ == "__main__":  # pragma: no cover
-    main()