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@@ -1,264 +1,173 @@
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(user.ptychography.lamni)=
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# LamNI
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The LamNI part needs to be written. This is a mix from LamNI and flomni
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This manual is intended for beamline staff and expert users
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LamNI is an instrument for 3D ptychography via ptychographic X-ray computed lamninography (PyXL). The instrument is described in detail [here](https://www.dora.lib4ri.ch/psi/islandora/object/psi:33067).
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Start the bec server and client as documented elsewhere
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## How to LamNI
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Loading the configuration, if not done by default
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… a step-by-step guide for _beamline staff and expert users_.
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bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/lamni_config.yaml")
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### Sample change and alignment
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Loading the LamNI scripts
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The access to the sample region is blocked by the flight tube during measurement. To get the flight tube out of the way use
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`lamni.leye_in()`.
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Mount the new sample. The X-ray eye is already in, but the X-ray optics needs to be moved out of the beam path by
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`lamni.loptics_out()`. Potentially a larger area needs to be illuminated to properly see the sample, which can be done by
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`open slits`.
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from csaxs_bec.bec_ipython_client.plugins.LamNI import LamNI
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lamni = LamNI(bec)
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#### Coarse axis alignment
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## Initialization of the stages
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To see the status of the stages following commands are available:
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The effective position of the axis of rotation shifts with sample thickness or mounting position of the sample along the axis of rotation. The position of the axis of rotation is controlled by user parameters __center__ of the __lsamx__ and __lsamy__ stages. To observe the axis of rotation obtain the position of the Fresnel zone plate on the X-ray eye, possibly in the _ueye gui_ by:
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1. `lamni.lfzp_in()`, move the FZP in
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1. `dev.rtx.controller.feedback_disable()`, disable feedback to allow lsam movements
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1. `fshopen()`, open the shutter
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1. `umv(dev.lsamrot,90)` to rotate the sample. One might observe the center of rotation at 0 and 180 degress.
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1. `umvr(dev.lsamx,0.01)` to move lsamx and lsamy such that the center of rotation is at the center of the X-ray beam
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1. `dev.lsamx` and `dev.lsamy` will print current position and the center value. Update the center value by
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`dev.lsamx.update_user_parameter({'center':8.69})`
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`dev.lsamy.update_user_parameter({'center':8.69})`
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1. close the shutter: `fshclose()`
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Show the status of all galil controllers (all stepper motor and rotation stage)
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dev.lsamx.controller.galil_show_all()
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#### X-ray eye alignment
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For the smaract stages (OSA stages)
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dev.losax.controller.show_all()
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The GUI on the windows computer is used to obtain a coarse sample alignment. Start the alignment process (and clear any previous alignment) by
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`lamni.align.align()`. With LamNI it can be very difficult to follow a region of interest as the sample rotates. Therefore the X-ray shutter will be open during the entire process. Therefore the windows software has to be set on __FORCE__ to continuously update frames and not freeze frames after rotation.
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- run `SPEC_ptycho_align.m` (in matlab, use __force_ptychography = 0__)
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- `lamni.align.read_xray_eye_correction()` to read the alignment parameters. The correction is based on sinusoidal fits in x and y direction. The values are computed by
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`lamni_compute_additional_correction_xeye_mu(angle)`
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- If slits were opened during alignment, close the slits `slits 1 to around 0.3`
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- `lamni.leye_out()` remove the X-ray eye and move the flight tube in
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- _possibly check slit0wh, idgap_
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To only see one frame on the Windows GUI run `lamni.align.update_frame()`
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To reference the stages of LamNI call
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lamni.init.lamni_init_stages()
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#### Fine alignment
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This script will first verify that the stages are not in an initialized state, and then reference all stages in a safe way.
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The sample fine alignment can be obtained using ptychography. For this a short laminogram has to be recorded.
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- `lamni.tomo_parameters()` adjust the parameters for a coarse scan: A large step size and large FOV. Especially select __FOV offset = 0__ and __number of projections = 96__ (only one sub-laminogram will be recorded).
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- `lamni.sub_tomo_scan(1,0)` record one sub-laminogram
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- use the corresponding scan numbers in `SPEC_ptycho_align.m`
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- Record a last projection for all scans to reconstruct `lamni.tomo_scan_projection(0)` and wait for the reconstructions to be complete
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- Run `SPEC_ptycho_align.m` (in Matlab, __force ptycho=1__, and __correct scan numbers__)
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- Click the sample position in the Matlab GUI and then load the generated file by, for example
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`lamni.align.read_additional_correction('/sls/X12SA/data/e20632/Data10/cxs_software/ptycho/correction_lamni_um_S05389_lamni_fit.txt')`
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- With this alignment a second iteration could be performed. To read the second correction file use `lamni.align.read_additional_correction_2()`
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## Interferometer
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If the realtime system is restarted, bec will lose communication. To restart:
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#### Shifting the FOV
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flomni.rt_off() … then wait a few seconds
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flomni.rt_on()
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- `lamni.align.tomo_fovx/y_offset=value` [mm] will shift the field of view. Perform this adjustment from projections collected at __lsamrot 0 degrees__.
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To show the signal of the interferometers:
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flomni.show_signal_strength_interferometer()
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### Laminography scan
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### Interferometer feedback commands
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Start the laminography scan by
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1. `lamni.tomo_parameters()` adjust the parameters to the desired settings.
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1. for test scans run
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`lamni.tomo_scan_projection(angle)`
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`lamni.tomo_reconstruct()`
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1. `lamni.tomo_scan()` to start the lamninography scan
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dev.rtx.feedback_enable_with_reset()
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dev.rtx.feedback_disable()
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dev.rtx.feedback_enable_without_reset() *is only used by functions
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if reset of angle interferometer is required
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dev.rtx.feedback_disable_and_even_reset_lamni_angle_interferometer
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dev.rtx.feedback_enable_with_reset()
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### Tips and Tricks
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Todo Feedback status might be helpful. Plus make accessible via lamni.feedback…
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#### Reset corrections
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### LamNI Fermat scan
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- `lamni.align.reset_correction()`
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- `lamni.align.reset_correction_2()`
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- `lamni.align.reset_xray_eye_correction()`
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The underlying scan function can be called as
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scans.lamni_fermat_scan()
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#### Adjusting beam size with feedback running
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Use
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scans.lamni_fermat_scan?
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If the beam size needs to be changed with feedback running, e.g. to switch from near-field to far-field ptychography, following steps can be taken:
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1. `dev.loptz.enable_set=True` to enable loptz movements with feedback running
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1. `umvr(dev.lopz,_value_)` move loptz to the desired position.
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1. `lamni._manual_shift_x/y = _value_` correct the stage run out from motion along the optical axis (units of um). The exact value can be checked by comparing feature positions in projections before/after adjusting loptz.
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1. Potentially correct the alignment of the OSA
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for detailed information. A prerequisite for scanning is a running feedback system.
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#### BEC tips
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### Alignment overview
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Print all global variables `bec.global_vars()`
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There are several corrections applied to get the sample to the FOV:
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`dev.lsamx/y.wm` or `dev.lsamx/y` prints a motor position
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## How to setup LamNI (software)
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### XrayEye and sample alignment
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The XrayEye can be moved in and out by
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lamni.leye_in()
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lamni.leye_out()
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This part of the manual describes the software structure in more detail.
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The in and out positions are stored as user parameters in the stage. Get the values by
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dev.leyex.user_parameter
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dev.leyey.user_parameter
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### start the realtime feedback loop and BEC with OMNY
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Update the values by example for leyex and in position
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dev.leyex.update_user_parameter({"in":value})
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The nano-positioning is controlled by a feedback loop running on a real-time linux based computer. With all related hardware connected, this loop has to be started manually.
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To refresh the frame of the xray eye windows software
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lamni.align.update_frame()
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1. Login to the computer by `ssh control@mpc2680`. The password is "engine".
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1. `cd OMNY/lamni/`
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1. `./startLAMNI`
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To start the xray eye alignment (and clear any previous alignment)
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lamni.align.align()
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Once the loop has started, it is possible to start bec with the LamNI configuration file.
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The alignment is based on the center values of the lsamx and lsamy stages, and are stored as user parameters. To get the current values
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dev.lsamx.user_parameter
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dev.lsamy.user_parameter
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Loading the LamNI configuration (this command will load the LamNI configuration only - isolated from the beamline)
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`bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/lamni_config.yaml")`
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To change the values
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dev.lsamx.update_user_parameter({"center":value})
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dev.lsamy.update_user_parameter({"center":value})
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Loading the LamNI scripts
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`from csaxs_bec.bec_ipython_client.plugins.LamNI import LamNI`
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`lamni = LamNI(bec)`
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After running SPEC_ptycho_align the alignment data can be loaded by
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lamni.align.read_xray_eye_correction()
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If the realtime system is restarted, BEC will lose communication. To restart:
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`lamni.rt_off()` … then wait a 10 seconds
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`lamni.rt_on()`
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The correction is based on sinusoidal fits in x and y direction. The values are computed by
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lamni_compute_additional_correction_xeye_mu(angle)
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### Initialization of the stages
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The stages of LamNI are referenced in respect to their endswitches or reference marks. The stages have to be initialized at the beginning of a run or when the Galil motor controller has been reset or restarted. To see the status of the stages following commands are available:
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To load from a specific directory, specify it as parameter. Example:
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dir_path='/afs/psi.ch/user/h/holler/Data10/specES1/internal/'
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Show the status of all galil controllers (all stepper motors and the UPR rotation stage)
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`dev.lsamx.controller.galil_show_all()`
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The loading routine uses default values for the vertical alignment. This behavior can be changed (e.g. for getting new default values) by the parameter use_vertical_default_values=False
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The same holds true for the Smaract stages which control the OSA position. Their status can be checked by
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`dev.losax.controller.show_all()`
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The alignment offset is computed by
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flomni.get_alignment_offset(angle)
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In case referencing of the LamNI stages is required, run
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`lamni.init.lamni_init_stages()`
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This script will first verify that the stages are not in an initialized state, and then reference all stages in a safe way. The user will be warned in case of a potentially risky situation. This mainly involves a collision risk upstream with the exposure box exit window. It might be worth to check clearance prior to calling the init skript.
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The alignment can be cleared by
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flomni.reset_tomo_alignment_fit()
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### Interferometer
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The position feedback in LamNI is controlled in closed loop to an interferometric position measurement. To show the signal of the interferometers:
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`lamni.show_signal_strength_interferometer()`
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Typical values with proper alignment are
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_TODO_
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#### Interferometer feedback commands
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### Fine alignment
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Recording ptychography projections at 45 deg. intervals allow replacing the X-ray eye alignment by more accurate parameters.
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Adjust the tomo parameters by
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flomni.tomo_parameters()
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- `dev.rtx.feedback_enable_with_reset()`
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- `dev.rtx.feedback_disable()`
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- `dev.rtx.feedback_enable_without_reset()` *is only used internally by lamni methods
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- if reset of angle interferometer is required
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`dev.rtx.feedback_disable_and_even_reset_lamni_angle_interferometer()`
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- `dev.rtx.feedback_enable_with_reset()`
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And run the alignment scan by
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flomni.tomo_alignment_scan()
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_ToDo Feedback status might be helpful. Plus make accessible via lamni.methods…_
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The updated fit from SPEC_ptycho_align can be loaded by
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flomni.read_alignment_offset()
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### Scanning in 2D and sample alignment
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For very fine vertical alignment based on output of an initial tomography reconstruction (for very tight vertical field of view) alignment, the data file can be loaded by
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read_additional_correction_y(), careful a default mirror correction is loaded automatically, so likely do not use this function. One can load a second iteration instead:
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read_additional_correction_y2()
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The underlying scan function can be called as
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`scans.lamni_fermat_scan()`
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The scan offsets are computed by
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compute_additional_correction_y(angle)
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compute_additional_correction_y2(angle)
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Use `scans.lamni_fermat_scan?`for detailed information. A prerequisite for scanning is a running feedback system.
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The additional correct can be reset by
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flomni.reset_correction()
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It will load the default primary correction! To run without any correction run (which might be useful to obtain a new default correction file)
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flomni.reset_correction(use_default_correction=False)
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### X-ray optics alignment
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The positions of the optics stages are stored as stage parameters and are thus linked to the configuration file.
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Example: The OSAx “in” position can be reviewed by `dev.losax.user_parameter`
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Update the value by (example "losax", "in") by `dev.losax.update_user_parameter({"in":value})`
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### Scanning of projections
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At any stage it is possible to scan a projection by
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`lamni.lfzp_info()` shows info about the available FZPs at the current energy of the beamline. Optional parameter is the photon _energy_ in keV.
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Example: `lamni.lfzp_info(6.2)`
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Defining scan parameters by running
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flomni.tomo_parameters()
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A scan can be performed at projection <angle> by running
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flomni.tomo_scan_projection(angle)
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### Tomography
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The tomo parameters have to be set by
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flomni.tomo_parameters()
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The tomography can be started by
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tomo_scan()
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Three modes for angular sampling are implemented and they have different optional parameters:
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8 sub-tomograms
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Parameters and their defaults: subtomo_start=1, start_angle=None
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Golden ratio tomography (sorted in bunches)
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Parameters and their defaults: projection_number=None
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Equally spaced with golden starting angle
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Parameters and their defaults: projection_number=None
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The following parameters can be used to restart an interrupted acquisition.
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In case of eight equally spaced sub-tomograms, an individual sub tomogram can be scanned by
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flomni.sub_tomo_scan(subtomo_number, start_angle).
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If the start angle is not specified, it will be computed depending on the subtomo_number, which is ranging from 1 to 8.
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Optics alignment
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The positions of the optics stages are stored as parameters to the stages.
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Example: The OSAx “in” position can be seen by
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dev.fosax.user_parameter
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Update the value by (example "fosax", "in")
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dev.fosax.update_user_parameter({"in":value})
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ffzp_info()
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Shows info about the available FZPs at the current energy of the beamline.
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Optional parameter energy in keV to get values at a different energy.
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Example: flomni.ffzp_info(6.2)
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Feedback will be disabled and fine alignment lost if foptx/y are moved!
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The laser feedback will be disabled and fine alignment lost if foptx/y are moved!
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Following functions exist to move the optics in and out, the naming is self-explaining.
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ffzp_in()
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foptics_in()
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foptics_out()
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flomni.fosa_in()
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flomni.fosa_out()
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- `lamni.lfzp_in()`
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- `lamni.loptics_in()`
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- `lamni.loptics_out()`
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- `lamni.losa_in()`
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- `lamni.losa_out()`
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- `lamni.lfzp_in()`
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### quick description
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This is a description of how to start a laminography measurement in bec
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Created Apr 13 2023
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This document is a replica of the Howto LamNI - short version
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THis version v02 was done on 18th April 2023
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Sample change and alignment
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- lamni.leye_in(); lamni.loptics_out() to get space for mounting
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- mount the sample
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- maybe open slits1 (still in spec) for a larger illuminated area
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To do in case the rotation center is off:
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If the rotation center is far off, it needs to be adjusted using the ueye gui:
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- fshopen() open the shutter
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- lamni.loptics_out
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- lamni.lfzp_in()
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- dev.rtx.controller.feedback_disable()
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- to rotate umv(dev.lsamrot,90) [go to 0 and 180 deg, for example, to see where the center is]
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- to move lsamx/y umvr(dev.lsamx,0.01)
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- once the position is found update the center values
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dev.lsamx will print current position and center value
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set it by
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dev.lsamx/y.update_user_parameter({'center':8.69})
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- close the shutter: fshclose()
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- lamni.align.align() starts the xrayeye align. Use the windows GUI. It has to be on 'FORCE', shutter will b
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e open all the time during alignment
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- run SPEC_ptycho_align.m (in matlab, force ptychography = 0)
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- lamni.align.read_xray_eye_correction() read the alignment parameters
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- maybe close slits 1 again to around 0.3
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- lamni.leye_out()
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- possibly check slit0wh, idgap in SPEC
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Sample fine alignment
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- lamni.tomo_parameters()
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make FOV offset 0
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select a large step and large FOV. Number of projections 96
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- important: set the exposure time in spec if changed to match!
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_rtscan_pointbypoint_setup_ddg <exptime>
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- record a sub-laminogram and use these scan numbers in SPECalign
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- lamni.sub_tomo_scan(1,0)
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- lamni.tomo_scan_projection(0)
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- Wait for the wrapper to reconstruct
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- Run SPEC_ptycho_align.m (in Matlab, force ptycho=1, and correct scan numbers)
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- Click the sample position in the GUI and then load the generated file by, for example
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lamni.align.read_additional_correction('/sls/X12SA/data/e20632/Data10/cxs_software/ptycho/correction_lamni_um_S05389_lamni_fit.txt')
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- For a second correction lamni.align.read_additional_correction_2()
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Shifting the FOV
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- lamni.align.tomo_fovx/y_offset=value [mm] do this from a pojection collected at 0 degrees
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Start the laminography scans
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- lamni.tomo_parameters()
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- for test scans run
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lamni.tomo_scan_projection(angle)
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lamni.tomo_reconstruct()
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lamni.tomo_scan_projection(angle)
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- start the lamni scan
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lamni.tomo_scan()
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Resetting corrections - to be done earlier, need to ask Mirko
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- lamni.align.reset_correction()
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- lamni.align.reset_correction_2()
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- lamni.align.reset_xray_eye_correction()
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Print all global variables
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bec.global_vars()
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dev.lsamx/y.wm or dev.lsamx/y to print a motor position
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ctrl+c twice to break a scan. and issue an %abort and %reset after
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Switching to between farfield and nearfield geometries
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From FF to NF (undo these changes as required to return to FF)
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- dev.loptz.enable_set=True This enables the loptz motor so that it can be used to move the focal position upstream
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- umvr(dev.lopz,-5) A motion of 5 mm is about right for a 20 um beam, depending on the exact geometery required
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- lamni._manual_shift_x/y = 21/6 Correct the stage run out from motion along the optical axis (units of um). The exact value can be checked by comparing feature positions in projections before/after swich to NF.
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- dev.losax/y.update_user_parameter({'in':-1.442+0.004/-0.171-0.004}) Correct the alignment of the osa in x/y
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Mirko Holler