I19-2 CLI bugfixes

CHANGELOG.md

@@ -2,10 +2,11 @@
 
 
 
-## 0.#.#
+## 0.8.5
 
 ### Fixed
 - Rotation axis vector for Electron Diffraction.
+- I19 CLI arguments, added number of images, minor bug fixes.
 
 
 ## 0.8.4

docs/api_beamlines.rst

@@ -40,9 +40,10 @@ Some useful type definitions to use with these methods:
     :members:
 
 
+Collection parameters schema for I19-2
 
-.. autoclass:: nexgen.beamlines.I19_2_nxs.CollectionParameters
-    :members:
+.. autopydantic_model:: nexgen.beamlines.I19_2_nxs.CollectionParams
+    :model-show-config-summary: False
 
 
 

docs/beamlines.rst

@@ -211,7 +211,21 @@ Manually generate a NeXus file for a dataset collected on Eiger detector using t
 
 .. code-block:: console
 
-    I19_nexus 2 Expt1_00_meta.h5 eiger 0.02 -tr 100
+    I19_nexus 2 Expt1_00_meta.h5 eiger 0.02 -tr 100 --use-meta
+
+
+If the `--use-meta` flag is not passed, the writer will not look up the axes/beam_center/wavelength information in the meta file.
+This will then need to be passed from the commang line:
+
+.. code-block:: console
+
+    I19_nexus gen Expt1_00_meta.h5 eiger 0.095 -wl 0.485 -bc 989.8 1419 --det-axes det_z --det-start 140 --axes omega phi --ax-start -90 -130.5 --ax-inc 0 0.1 -tr 5 -n 75
+
+
+.. note::
+    Only the goniometer/detector axes that have values and increments different from 0 need to be passed to the command line.
+    If --scan-axis is not passed, it will default to 'phi'.
+    If -bc (beam_center) is not passed, in the absence of a meta file it will default to (0, 0)
 
 
 SSX CLI

docs/conf.py

@@ -38,6 +38,7 @@
     "sphinx.ext.viewcode",
     "sphinx_rtd_theme",
     "sphinx.ext.napoleon",
+    "sphinxcontrib.autodoc_pydantic",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
@@ -103,6 +104,9 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
+# -- Options for pydantic objects
+# autodoc_pydantic_model_show_json = True
+autodoc_pydantic_model_show_config_summary = True
 
 # -- Options for HTMLHelp output ---------------------------------------
 

pyproject.toml

@@ -39,6 +39,7 @@ dev = [
     "pytest-cov",
     "pytest-random-order",
     "sphinx-autobuild",
+    "autodoc_pydantic<2.0.0",     # Needed for pydantic docs
     "bump2version",
     "pipdeptree",
     "ipython",

requirements_doc.txt

@@ -1,5 +1,6 @@
 Sphinx==7.2.6
 sphinx-rtd-theme==2.0.0
+autodoc_pydantic==1.9.0
 numpy==1.26.4
 pint==0.23
 h5py==3.10.0

src/nexgen/beamlines/I19_2_nxs.py

@@ -66,8 +66,18 @@ class ExperimentTypeError(Exception):
 # Useful axis definitions
 axes = namedtuple("axes", ("id", "start", "inc", "end"), defaults=(None, 0.0, 0.0, 0.0))
 axes.__doc__ = """Goniometer axis name, start and end position, increment."""
+axes.id.__doc__ = "Axis name."
+axes.start.__doc__ = "Axis start position. Defaults fo 0.0."
+axes.inc.__doc__ = (
+    "Axis increment value. Defaults fo 0.0. Only needed for the scan axis."
+)
+axes.end.__doc__ = (
+    "Axis end position. Defaults fo 0.0. Only really needed for Tristan collections."
+)
 det_axes = namedtuple("det_axes", ("id", "start"), defaults=(None, 0.0))
 det_axes.__doc__ = """Detector axis name and position."""
+det_axes.id.__doc__ = "Axis name."
+det_axes.start.__doc__ = "Axis position. Defaults to 0.0."
 
 
 def tristan_writer(

src/nexgen/command_line/I19_2_cli.py

@@ -104,14 +104,15 @@
         exposure_time=args.exp_time,
         transmission=args.transmission if args.transmission else None,
         wavelength=args.wavelength if args.wavelength else None,
-        beam_center=args.beam_center if args.beam_center else None,
+        beam_center=args.beam_center if args.beam_center else (0, 0),
         start_time=datetime.strptime(args.start, "%Y-%m-%dT%H:%M:%SZ")
         if args.start
         else None,
         stop_time=datetime.strptime(args.stop, "%Y-%m-%dT%H:%M:%SZ")
         if args.stop
         else None,
-        scan_axis=args.scan_axis if args.scan_axis else None,
+        n_imgs=args.num_imgs if args.num_imgs else None,
+        scan_axis=args.scan_axis if args.scan_axis else "phi",
         gonio_pos=axes_list if args.axes else None,
         det_pos=det_list if args.det_axes else None,
         outdir=args.output if args.output else None,
@@ -131,7 +132,12 @@
 gonioAx_parser.add_argument(
     "--ax-end", type=float, nargs="+", help="Eventual axes ends."
 )
-gonioAx_parser.add_argument("--scan-axis", type=str, help="Identify scan axis.")
+gonioAx_parser.add_argument(
+    "--scan-axis",
+    type=str,
+    default="phi",
+    help="Identify scan axis. If not specified, defaults to phi.",
+)
 
 detAx_parser = argparse.ArgumentParser(add_help=False)
 detAx_parser.add_argument(
@@ -205,6 +211,13 @@
     "detector_name", type=str, help="Detector currently in use on beamline."
 )
 parser_nex.add_argument("exp_time", type=float, help="Exposure time, in s.")
+parser_nex.add_argument(
+    "-n",
+    "--num_imgs",
+    type=int,
+    default=None,
+    help="Number of frames collected. Necessary for eiger if not using meta file.",
+)
 parser_nex.add_argument(
     "-tr",
     "--transmission",