x01dcandClaude Sonnet 5
12b2538333
Replaces the awkward documented workaround (configure a full tomo_type 1 setup with 96 projections, then launch just sub_tomo_scan(1, 0)) with a dedicated command, ported from flomni's tomo_alignment_scan(): adjust tomo_parameters() (FOV/step/counting time), then call lamni.tomo_alignment_scan() directly -- no tomo_type/sub-tomogram bookkeeping involved, matching flomni's clean two-step workflow. Runs 12 points evenly spaced across the full 360 degrees (lamni has no 180-degree symmetry the way flomni does, so unlike flomni's 5-point/ 180-degree scan, this covers the full circle -- point count matches what the old workaround's docs defaulted to, endpoint=False since 360==0 degrees). Aborts if x-ray-eye alignment hasn't been done yet (tomo_fit_xray_eye unset), mirroring flomni's equivalent guard. write_alignment_scan_numbers() writes the same 4-line scan-number/ angle/offset log flomni's version does, to ~/data/raw/logs/ptychotomoalign_scannum.txt for SPEC_ptycho_align.m, also printed at the console (flomni's own console-print equivalent is dead/commented-out code; lamni's actually prints). Scope note: flomni's version conditionally skips its eye-out/optics-in transition when already in measurement condition with feedback running, to avoid an unneeded interferometer reset -- lamni has no equivalent helpers for that check, so this calls leye_out() unconditionally instead. Left as a possible follow-up, not in scope here. Item 6 of csaxs_bec/bec_ipython_client/plugins/LamNI/AI_docs/ FLOMNI_LAMNI_FEATURE_GAPS_2026-07.md. Documented in docs/user/ptychography/lamni.md's "Fine alignment" section. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Getting Started with Testing using pytest
BEC is using the pytest framework. It can be installed via
pip install pytest
in your python environment.
We note that pytest is part of the optional-dependencies [dev] of the plugin package.
Introduction
Tests in this package should be stored in the tests directory.
We suggest to sort tests of different submodules, i.e. scans or devices in the respective folder structure, and to folow a naming convention of <test_module_name.py>.
It is mandatory for test files to begin with test_ for pytest to discover them.
To run all tests, navigate to the directory of the plugin from the command line, and run the command
pytest -v --random-order ./tests
Note, the python environment needs to be active.
The additional arg -v allows pytest to run in verbose mode which provides more detailed information about the tests being run.
The argument --random-order instructs pytest to run the tests in random order, which is the default in the CI pipelines.
Test examples
Writing tests can be quite specific for the given function. We recommend writing tests as isolated as possible, i.e. try to test single functions instead of full classes. A very useful class to enable isolated testing is MagicMock. In addition, we also recommend to take a look at the How-to guides from pytest.