refactor: changes for new plugin structure

.gitignore

@@ -1,8 +1,177 @@
-**/venv
+**/*_venv
 **/.idea
 *.log
 **/__pycache__
-.DS_Store
+**/.DS_Store
 **/out
 **/.vscode
 **/.pytest_cache
+**/*.egg*
+
+# file writer data
+**.h5
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/**/_build/
+docs/**/autodoc/
+docs/**/_autosummary/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+**.prof
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "bec"]
-	path = bec
-	url = https://gitlab.psi.ch/bec/bec.git

bec_plugins/plugins/scan_server/scan_plugins/LamNIFermatScan.py

@@ -13,7 +13,7 @@ but they are executed in a specific order:
 - self.open_scan                         # send an open_scan message including the scan name, the number of points and the scan motor names
 - self.stage                             # stage all devices for the upcoming acquisiton
 - self.run_baseline_readings             # read all devices to get a baseline for the upcoming scan
-- self.scan_core                         # run a loop over all position 
+- self.scan_core                         # run a loop over all position
     - self._at_each_point(ind, pos)      # called at each position with the current index and the target positions as arguments
 - self.finalize                          # clean up the scan, e.g. move back to the start position; wait everything to finish
 - self.unstage                           # unstage all devices that have been staged before
@@ -23,8 +23,8 @@ but they are executed in a specific order:
 import time
 
 import numpy as np
-from bec_utils import BECMessage, MessageEndpoints, bec_logger
-
+from bec_lib.core import BECMessage, MessageEndpoints, bec_logger
+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))
@@ -243,17 +243,30 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
         self.fov_circular = scan_kwargs.get("fov_circular", 0)
         self.stitch_overlap = scan_kwargs.get("stitch_overlap", 1)
         # self.keep_plot = scan_kwargs.get("keep_plot", 0)
-        # self.optim_trajectory = scan_kwargs.get("optim_trajectory", "corridor")
+        self.optim_trajectory = scan_kwargs.get("optim_trajectory", "corridor")
+        self.optim_trajectory_corridor = scan_kwargs.get("optim_trajectory_corridor")
 
     def initialize(self):
         self.scan_motors = ["rtx", "rty"]
 
+    def _optimize_trajectory(self):
+        self.positions = self.optimize_corridor(
+            self.positions, corridor_size=self.optim_trajectory_corridor
+        )
+
     def prepare_positions(self):
         self._calculate_positions()
         self._optimize_trajectory()
         # self._sort_positions()
 
         self.num_pos = len(self.positions)
+        self._check_min_positions()
+
+    def _check_min_positions(self):
+        if self.num_pos < 20:
+            raise ScanAbortion(
+                f"The number of positions must exceed 20. Currently: {self.num_pos}."
+            )
 
     def _lamni_check_pos_in_fov_range_and_circ_fov(self, x, y) -> bool:
         # this function checks if positions are reachable in a scan
@@ -411,6 +424,16 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
             logger.info("No rotation required")
         else:
             logger.info("Rotating to requested angle")
+            yield from self.stubs.scan_report_instruction(
+                {
+                    "readback": {
+                        "RID": self.metadata["RID"],
+                        "devices": ["lsamrot"],
+                        "start": [lsamrot_current_setpoint],
+                        "end": [angle],
+                    }
+                }
+            )
             yield from self.stubs.set_and_wait(device=["lsamrot"], positions=[angle])
 
     def scan_core(self):
@@ -428,10 +451,14 @@ class LamNIFermatScan(ScanBase, LamNIMixin):
                 msg = self.device_manager.producer.get(MessageEndpoints.device_status("rt_scan"))
                 if msg:
                     status = BECMessage.DeviceStatusMessage.loads(msg)
-                    if status.content.get("status", 1) == 0 and self.metadata.get(
-                        "RID"
-                    ) == status.metadata.get("RID"):
+                    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(
+                            f"An error occured during the LamNI readout: {status.metadata.get('error')}"
+                        )
 
                 time.sleep(1)
                 logger.debug("reading monitors")

setup.cfg

@@ -0,0 +1,21 @@
+[metadata]
+name = bec_plugins
+description = BEC plugins to modify the behaviour of services within the BEC framework
+long_description = file: README.md
+long_description_content_type = text/markdown
+url = https://gitlab.psi.ch/bec/bec
+project_urls =
+    Bug Tracker = https://gitlab.psi.ch/bec/bec/issues
+classifiers =
+    Programming Language :: Python :: 3
+    Development Status :: 3 - Alpha
+    Topic :: Scientific/Engineering
+
+[options]
+package_dir =
+    = .
+packages = find:
+python_requires = >=3.8
+
+[options.packages.find]
+where = .

setup.py

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