diff --git a/csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py b/csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py index 24214bb..743c3c1 100644 --- a/csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py +++ b/csaxs_bec/bec_ipython_client/plugins/LamNI/lamni.py @@ -1069,7 +1069,7 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools ) 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 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 during the alignment, writes them (with angles and the existing 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 scan numbers. """ @@ -1145,7 +1145,7 @@ class LamNI(TomoQueueMixin, LamNIAlignmentMixin, LamNIOpticsMixin, LamniGuiTools umv(dev.lsamrot, 0) 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()." ) diff --git a/docs/user/ptychography/lamni.md b/docs/user/ptychography/lamni.md index 673e01d..4a1b25d 100644 --- a/docs/user/ptychography/lamni.md +++ b/docs/user/ptychography/lamni.md @@ -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_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 `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()`