The alignment file

We wish to keep track of the distance from the zone plate (ZP) to the order sorting aperture (OSA) and to the specimen, so as to avoid crashes. We also wish to record the position of the detectors in use in the microscope. For what follows, we will assume that the visible light microscope is used with the $5\times$ objective for recording VLM positions. Tab. 13.1 explains all parameters, that you find in the alignment files (/mnt/x1a/alignment_stxmi.dat, /mnt/x1a/alignment_stxmo.dat). It is possible to change parameters by hand, but usually they are read and written by the sm_scan class.

Table 13.1: Parameters stored in the alignment file. Not shown are the parameters for detector 0, which are analogous to detector 1

Parameter	Description
zp_osa_min_um	Minimum distance between zone plate and OSA
osa_specimen_min_um	Minimum distance between OSA and specimen
d1_specimen_min_um	Minimum distance between the specimen and detector 1
zp_osa_extra_um	Extra distance between the zone plate and OSA beyond the theoretical value of $\texttt{zp\_f\_um}(1-\texttt{zp\_stop\_um}/\texttt{zp\_d\_um})$
d1_d_um	Diameter of detector 1 which should correspond to the illuminated zone plate cone (for example, an angle of (3/2)N.A. from the optical axis)
zp_name	Name/number of the zone plate currently in use.
zp_d_um	Diameter of the ZP.
zp_delta_nm	Outermost zone width in nm.
zp_stop_um	Diameter of the central stop.
osa_d_um	Diameter of the order sorting aperture.
focus_ev	Photon energy at which the alignment was done.
specimen_[x,y]stg_um	[X,Y]STG position at which the specimen stage is inserted
specimen_zstg_um	ZSTG position which puts the specimen in the zone plate focus at focus_eV
stageout_[x,y]stg_um	[X,Y]STG position at which the specimen stage is removed
stageout_zstg_um	ZSTG position at which the specimen stage is removed Redundant: in STXM5 we're actually using the donwstream limit instead
zosa_um	Aligned position of ZOSA motor at focus_ev
vlm_zp_zdet_um	ZDET position which puts the VLM in focus on the zone plate
vlm_[x,y]det_um	[X,Y]DET position which puts the VLM on beam axis
d1_[x,y]det_um	[X,Y]DET position at which detector 1 is inserted
d1_vlm_offset	Z distance between the VLM focus position and the detector 1 inserted position
dremoved_[x,y]det_um	[X,Y]DET position at which the detector stage is removed
laser_[x,y,z]det_um	[X,Y,Z]DET position at which laser is aligned in beam path
photodiode_[x,y,z]det_um	[X,Y,Z]DET position at which photodiode is aligned in beam path
sidet_zmatch	Z alignment factor of segmented detector (size of beam cone relative to quadrant segments) The number is merely informative at this point and not used in the actual alignment. Its value can be changed in SM_GUI
drift_d[x,y]_over_dz	The angle in [X,Y] plane between ZSTG and beam axes (in rad)

Whenever a new set of optics (ZP and OSA) is used, you have to remember to adjust zp_d_um, zp_delta_nm, zp_stop_um, and zp_osa_um. The alignment file is automatically read in at startup of SM_GUI.