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fix/correct matlab tool name to BEC_ptycho_align in tomo_alignment_scan

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The tool is called BEC_ptycho_align now, not SPEC_ptycho_align.m as
the previous docs/comments said -- fixes the references introduced in
the previous commit (12b2538) in lamni.py's docstrings/print message
and the user docs.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
This commit is contained in:
x01dc
2026-07-21 13:24:37 +02:00
co-authored by Claude Sonnet 5
parent 12b2538333
commit e3c979a375
2 changed files with 4 additions and 4 deletions
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csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py
+3 -3
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@@ -1069,7 +1069,7 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
) )
def write_alignment_scan_numbers(self, first_scan: int) -> None: def write_alignment_scan_numbers(self, first_scan: int) -> None:
"""Write the scan-number/angle/offset log consumed by SPEC_ptycho_align.m. """Write the scan-number/angle/offset log consumed by BEC_ptycho_align.
Mirrors Flomni.write_alignment_scan_numbers() exactly (same 4-line Mirrors Flomni.write_alignment_scan_numbers() exactly (same 4-line
format), adapted to lamni's own alignment-scan angle set (12 points format), adapted to lamni's own alignment-scan angle set (12 points
@@ -1105,7 +1105,7 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
Flomni.tomo_alignment_scan()). Collects all scan numbers acquired Flomni.tomo_alignment_scan()). Collects all scan numbers acquired
during the alignment, writes them (with angles and the existing during the alignment, writes them (with angles and the existing
x-ray-eye-fit offset at each angle) to x-ray-eye-fit offset at each angle) to
~/data/raw/logs/ptychotomoalign_scannum.txt for SPEC_ptycho_align.m, ~/data/raw/logs/ptychotomoalign_scannum.txt for BEC_ptycho_align,
prints them, and creates a scilog entry summarising the alignment prints them, and creates a scilog entry summarising the alignment
scan numbers. scan numbers.
""" """
@@ -1145,7 +1145,7 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools
umv(dev.lsamrot, 0) umv(dev.lsamrot, 0)
self.OMNYTools.printgreenbold( self.OMNYTools.printgreenbold(
"\n\nAlignment scan finished. Please run SPEC_ptycho_align and load the new fit" "\n\nAlignment scan finished. Please run BEC_ptycho_align and load the new fit"
" by lamni.read_additional_correction()." " by lamni.read_additional_correction()."
) )
docs/user/ptychography/lamni.md
+1 -1
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@@ -64,7 +64,7 @@ The sample fine alignment can be obtained using ptychography. For this a short l
* `lamni.tomo_parameters()` adjust the ptychographic scan parameters for the alignment scan (FOV/step size/counting time) — `tomo_type` and number of projections are ignored, since the alignment scan always runs its own fixed 12 points spread evenly across the full 360 degrees, independent of the main tomogram's settings. * `lamni.tomo_parameters()` adjust the ptychographic scan parameters for the alignment scan (FOV/step size/counting time) — `tomo_type` and number of projections are ignored, since the alignment scan always runs its own fixed 12 points spread evenly across the full 360 degrees, independent of the main tomogram's settings.
* `lamni.tomo_alignment_scan()` perform the alignment scan. Requires x-ray-eye alignment to have already been done — it will abort with a message otherwise. Scan numbers, angles and the existing x-ray-eye-fit offset at each angle are written to `~/data/raw/logs/ptychotomoalign_scannum.txt` and also printed at the end. * `lamni.tomo_alignment_scan()` perform the alignment scan. Requires x-ray-eye alignment to have already been done — it will abort with a message otherwise. Scan numbers, angles and the existing x-ray-eye-fit offset at each angle are written to `~/data/raw/logs/ptychotomoalign_scannum.txt` and also printed at the end.
* Run `SPEC_ptycho_align.m` (in Matlab, **force ptycho=1**, and **correct scan numbers**) using the printed/logged scan numbers. * Run `BEC_ptycho_align` (in Matlab, **force ptycho=1**, and **correct scan numbers**) using the printed/logged scan numbers.
* Click the sample position in the Matlab GUI and then load the generated file by, for example * Click the sample position in the Matlab GUI and then load the generated file by, for example
`lamni.read_additional_correction('/sls/X12SA/data/e20632/Data10/cxs_software/ptycho/correction_lamni_um_S05389_lamni_fit.txt')` `lamni.read_additional_correction('/sls/X12SA/data/e20632/Data10/cxs_software/ptycho/correction_lamni_um_S05389_lamni_fit.txt')`
* With this alignment a second iteration could be performed. To read the second correction file use `lamni.read_additional_correction_2()` * With this alignment a second iteration could be performed. To read the second correction file use `lamni.read_additional_correction_2()`