From d100af542946fffbe622a38290b904bfdf33ba18 Mon Sep 17 00:00:00 2001 From: x12sa Date: Sun, 13 Sep 2026 21:54:42 +0200 Subject: [PATCH] docs(flomni): document manual tomo_alignment_fit offset nudge Add a snippet to the XrayEye alignment section showing how to patch the constant x/y offset terms of tomo_alignment_fit directly on the command line, for a quick few-micron correction (e.g. after moving foptz) without recording a new fit. Co-Authored-By: Claude Sonnet 5 Claude-Session: https://claude.ai/code/session_01FFeiCHv3qUxxssmP9Qzhom --- docs/user/ptychography/flomni.md | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/docs/user/ptychography/flomni.md b/docs/user/ptychography/flomni.md index 5796480b..82c89415 100644 --- a/docs/user/ptychography/flomni.md +++ b/docs/user/ptychography/flomni.md @@ -272,6 +272,22 @@ The loading routine uses default values for the vertical alignment. This behavio At each projection, the angular dependent is computed by `flomni.get_alignment_offset(angle)`, with _angle_ in degrees. +To manually nudge the alignment by a few microns without recording a new fit +(e.g. to compensate for a small shift introduced by moving `foptz`), edit the +constant offset term of the currently loaded fit directly: +```python +fit = flomni.client.get_global_var("tomo_alignment_fit") +fit[0][2] += 5.0 # x offset, microns +fit[1][2] += 3.0 # y offset, microns +flomni.client.set_global_var("tomo_alignment_fit", fit) +``` +`tomo_alignment_fit` is a 2x5 list (row 0 = x, row 1 = y); column 2 in each +row is the constant offset of the sinusoidal fit +(`correction = A*sin(angle + phase) + offset [+ 3rd-order term for y]`), so +changing it shifts the correction by that amount at every angle without +touching the fitted amplitude/phase. Check the result with +`flomni.get_alignment_offset(angle)`. + The alignment can be cleared by `flomni.reset_tomo_alignment_fit()`