refactor

docs/user/ptychography/lamni.md

@@ -41,13 +41,13 @@ With LamNI it can be difficult to relocate the sample between rotations. To keep
 `lamni.xrayeye_alignment_start(keep_shutter_open=True)`
 
 To manually reload the fit parameters after the procedure has completed:  
-`lamni.align.read_xray_eye_correction_from_gui()`  
+`lamni.read_xray_eye_correction_from_gui()`  
 **Note:** this reads from the live GUI widget via the `omny_xray_gui` device. It only works as long as the XRayEye GUI window remains open. If the window has been closed, reload from the archived text files instead:  
-`lamni.align.read_xray_eye_correction()`  
+`lamni.read_xray_eye_correction()`  
 (these files are written to `~/Data10/specES1/internal/xrayeye_alignmentvalues` at the end of every alignment run)
 
 The correction is applied at each projection angle via  
-`lamni.align.lamni_compute_additional_correction_xeye_mu(angle)`  
+`lamni.lamni_compute_additional_correction_xeye_mu(angle)`  
 which is called automatically inside `lamni.tomo_scan_projection()`.
 
 To capture a single fresh frame without running the full alignment:  
@@ -68,12 +68,12 @@ The sample fine alignment can be obtained using ptychography. For this a short l
 * Record a last projection for all scans to reconstruct `lamni.tomo_scan_projection(0)` and wait for the reconstructions to be complete
 * Run `SPEC_ptycho_align.m` (in Matlab, **force ptycho=1**, and **correct scan numbers**)
 * Click the sample position in the Matlab GUI and then load the generated file by, for example  
-  `lamni.align.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.align.read_additional_correction_2()`
+  `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()`
 
 #### Shifting the FOV
 
-* `lamni.align.tomo_fovx/y_offset=value` [mm] will shift the field of view. Perform this adjustment from projections collected at **lsamrot 0 degrees**.
+* `lamni.tomo_fovx/y_offset=value` [mm] will shift the field of view. Perform this adjustment from projections collected at **lsamrot 0 degrees**.
 
 ### Laminography scan
 
@@ -89,9 +89,9 @@ Start the laminography scan by
 
 #### Reset corrections
 
-* `lamni.align.reset_correction()`
-* `lamni.align.reset_correction_2()`
-* `lamni.align.reset_xray_eye_correction()`
+* `lamni.reset_correction()`
+* `lamni.reset_correction_2()`
+* `lamni.reset_xray_eye_correction()`
 
 #### Adjusting beam size with feedback running
 
@@ -203,4 +203,4 @@ Following functions exist to move the optics in and out, the naming is self-expl
 * `lamni.loptics_out()`
 * `lamni.losa_in()`
 * `lamni.losa_out()`
-* `lamni.lfzp_in()`
+* `lamni.lfzp_in()`