Add docs/developer/editing_docs.md documenting the MyST/Sphinx conventions
for this site: page anatomy (cross-reference label + single H1), language-
tagged code fences, admonitions, cross-references, the {download} role for
non-image files, the {figure} directive, and how to add a page to a toctree.
Also covers local preview, the merge-then-RTD-build flow, and pitfalls
(broken refs are warnings, public visibility, placeholder consistency).
Turn the empty developer.md stub into a landing page with a toctree and a
card linking to the new guide.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Migrate the SAXS data-analysis content into the RTD/Sphinx docs as
user/saxs/data_analysis.md, and turn the empty saxs.md stub into a
landing page linking to it.
Source: cSAXS documentation wiki, page "SAXS-data-analysis"
https://gitea.psi.ch/cSAXS/documentation/wiki/SAXS-data-analysis
(git@gitea.psi.ch:cSAXS/documentation.wiki.git, as of 408e535)
Converted Gitea-flavored Markdown to MyST: added cross-reference
labels, bash code fences, and {note} admonitions.
Also bundle the SAXS standards plate datasheet (SAXS_standards_plate.pdf),
previously at cSAXS/documentation/attachments/, linked via the MyST
{download} role so Sphinx copies it into the build.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Fix tomo_parameters() printing the per-sub-tomogram angular step
(self.tomo_angle_stepsize) while labeling it as the final tomogram's
step. At 180° / 2400 total projections this printed 0.6° instead of
the actual combined-tomogram resolution of 0.075°. Both the static
printout and the interactive editor for tomo_type 1 now print and
correctly label both numbers, with explicit parentheses around every
(tomo_angle_range / tomo_angle_stepsize) * 8 expression to remove any
ambiguity. tomo_type 2/3 were already correctly labeled and are
unchanged.
Wire manual_shift_y into sum_offset_y in both tomo_scan_projection
and tomo_acquire_at_angle; it was previously defined and shown in
tomo_parameters() but never applied anywhere. Fix its printed unit
from <mm> to <um>, matching the value it actually holds.
Validate frames_per_trigger on assignment: must be a positive
integer (rejects 0, negative, float, and bool).
Set bec.builtin_actors.scan_interlock (trigger_setting=restart_scan,
enabled=True) at the start of tomo_scan.
Reset estimated_remaining_time at the start of a new tomo_scan, and
add estimated_finish_time (wall-clock projected completion,
stored/reset alongside it). Previously estimated_remaining_time was
never reset between scans, so the progress GUI could display a
leftover estimate from a prior run while the client-side text
printout correctly showed N/A (gated until projection 10).
Also includes: guard tomo_parameters() so stitch_x/stitch_y are
forced to 0 and cannot be set while single_point_instead_of_fermat_scan
is enabled, since stitching is not supported in that mode.
Add optional full-circle (0-360°, inclusive) angular sweep for
tomo_type 1 (equally spaced sub-tomograms), selectable via the new
tomo_angle_range property (180 default, or 360). Fixes the
_tomo_scan_at_angle gate, which previously hardcoded a 180.05° cutoff
and would silently drop any projection beyond 180° without error.
Add an alternative acquisition mode for each projection angle:
tomo_acquire_at_angle moves fsamroy and the alignment-corrected
rtx/rty/rtz position (same offset logic as tomo_scan_projection, no
stitching), runs the existing laser-tracker checks and
move_samx_to_scan_region, then calls scans.acquire instead of
scans.flomni_fermat_scan. Selectable per scan via the new
single_point_instead_of_fermat_scan flag, dispatched from
_at_each_angle, so it applies independently of tomo_type and
tomo_angle_range.
Add frames_per_trigger as a persistent property, used by both
scans.flomni_fermat_scan (already supported it) and the new
scans.acquire call, for burst acquisition.
Surface all three new settings in tomo_parameters()'s printout and
interactive editor. Update write_pdf_report's projection-count
estimate to scale with tomo_angle_range instead of a hardcoded 180.
tomo_alignment_scan and tomo_type 2/3 angle generation remain
unchanged (still 0-180°), as the new range option only applies to
tomo_type 1.
appel_candholler
x12saandholler
menzelandClaude Opus 4.8
wakonig_k
wyzula_jandholler