From ef1ab749a9fa4a1c2bdcc8330976baba38536515 Mon Sep 17 00:00:00 2001 From: holler Date: Mon, 2 Dec 2024 13:50:05 +0100 Subject: [PATCH] Update flomni.md --- docs/user/ptychography/flomni.md | 34 ++++++++++++++++---------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/docs/user/ptychography/flomni.md b/docs/user/ptychography/flomni.md index df830dc..453653c 100644 --- a/docs/user/ptychography/flomni.md +++ b/docs/user/ptychography/flomni.md @@ -1,8 +1,9 @@ (user.ptychography.flomni)= # flOMNI -flOMNI is an instrument for tomographic measurements via X-ray ptychography. +flOMNI is an instrument for tomographic measurements via X-ray ptychography. The sample environment is at atmospheric pressure and room temperature (or higher). An early version of the setup is described [here](https://www.dora.lib4ri.ch/psi/islandora/object/psi:12560). Nano positioning is based on closed loop control to a position signal obtained from dedicated [laser interferometry](https://www.dora.lib4ri.ch/psi/islandora/object/psi:7524). For fast scanning a combined motion of the sample (slow axis) and beam defining fresnel zone plate (fast axis) is used. The method is described [here](https://www.dora.lib4ri.ch/psi/islandora/object/psi:21021). The setup is equipped with a [heater](https://www.dora.lib4ri.ch/psi/islandora/object/psi:45302), that can be used to apply hot gas streams to the sample. +Samples are to be mounted on [OMNY pins](https://www.dora.lib4ri.ch/psi/islandora/object/psi:4528). ## How to flOMNI @@ -54,24 +55,25 @@ If you see your sample already at the approximately correct height, you can skip 1. `flomni.rt_feedback_disable()` disable the closed loop operation to allow movement of coarse stages 1. `umvr(dev.fsamy, 0.01)`, attention: unit , move the sample stage relative up (positive) or down (negative) until the sample is approximately vertically centered in xray eye screen 1. `flomni.xrayeye_update_frame()` will update the current image on the xray eye screen -1. `flomni.xrayeye_alignment_start()` start the coarse alignment of the sample by measuring the sample position at 0, 45, 90, 135, 180 degrees. Then use the matlab routine `SPEC_ptycho_align.m` to fit this data. +1. `flomni.xrayeye_alignment_start()` start the coarse alignment of the sample by measuring (clicking in the X-ray eye software) the sample position at 0, 45, 90, 135, 180 degrees. Then use the matlab routine `SPEC_ptycho_align.m` to fit this data. 1. `flomni.read_alignment_offset()` read the generated alignment data. #### Fine alignment -After the xrayeyealign a fine alignment needs to be performed using ptychography. +After the xrayeyealign, a fine alignment needs to be performed using ptychography. _To bypass the fine alignment: `feye_out`_ -1. `flomni.tomo_parameters()` Adjust the ptychographic scan parameters for performing an alignment scan. Typically FOVX = FOVX(Xrayeye)+30 mu, shell step = beamsize/2.5, number of projections and tomo mode are ignored in the alignment scans. +1. `flomni.tomo_parameters()` Adjust the ptychographic scan parameters for performing an alignment scan. Typically FOVX = FOVX(Xrayeye)+20 mu, shell step = beamsize/2.5, number of projections and tomo mode are ignored in the alignment scans. 1. `flomni.tomo_alignment_scan()` perform the alignment scan. When the first scan is running, switch to a matlab session and run `SPEC_ptycho_align` again. Click left and right. The third click can define the height of the scan, but is not needed and ignored by default. The widest horizontal field of view will be printed at the end of the matlab session. 1. `flomni.read_alignment_offset()` Load alignment parameters calculated in matlab. ### Tomographic Measurement Now that the sample is aligned, the tomographic measurement can be performed. -1. `flomni.tomo_parameters()` Adjust the scan parameters for the tomographic scan. This includes the parameters for ptychographic scans of projections plus the strategy for angular sampling. The vertical shift adjusts the field of view from the vertical click up (positive) or down (negative). After adjusting the numbers, type again `flomni.tomo_parameters()` and verify that they are correct. -1. `flomni.tomo_scan_projection(angle)` perform a ptychographic scan at the rotation angle . Launch the tomographic measurement by `flomni.tomo_scan()`. Before changing sample, verify that all subtomograms were completely acquired using the `tomo_recons matlab` script. +1. `flomni.tomo_parameters()` adjust the scan parameters for the tomographic scan. This includes the parameters for ptychographic scans of projections plus the strategy for angular sampling. The vertical shift adjusts the field of view, up (positive) or down (negative). After adjusting the numbers, type again `flomni.tomo_parameters()` and verify that they are correct. +1. `flomni.tomo_scan_projection(angle)` perform a ptychographic scan at the rotation angle . Launch the tomographic measurement by `flomni.tomo_scan()`. +1. Before changing sample, verify that all subtomograms were completely acquired using the `tomo_recons matlab` script. #### If something went wrong… @@ -88,12 +90,10 @@ Depending on the tomo mode following parameters can be given to the `flomni.tomo | Golden ratio tomography (sorted in bunches) | projection_number=None | | Equally spaced with golden starting angle | projection_number=None | -## How to setup flOMNI +## How to setup flOMNI (software) This part of the manual is intended for beamline staff and expert users -### how to start the realtime feedback loop and bec with flOMNI - 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. 1. Login to the computer by `ssh control@mpc2680`. The password is "engine". @@ -102,7 +102,7 @@ The nano-positioning is controlled by a feedback loop running on a real-time lin Once the loop has started, it is possible to start bec with the flOMNI configuration file. -Loading the flOMNI configuration +Loading the flOMNI configuration (this command will load the OMNY configuration only - isolated from the beamline) `bec.config.update_session_with_file("/bec/csaxs_bec/csaxs_bec/device_configs/flomni_config.yaml")` Loading the flOMNI scripts @@ -235,17 +235,17 @@ The alginment obtained by the X-ray eye can be refinde by recording ptychography Next, run the alignment scan by `flomni.tomo_alignment_scan()` -Reconstruct the scand and use SPEC_ptycho_align.m to obtain improved fit parameters. The new parameters can be loaded by +Reconstruct the scan and use SPEC_ptycho_align.m to obtain improved fit parameters. The new parameters can be loaded by `flomni.read_alignment_offset()` For a __very__ tight vertical field of view, a fine vertical alignment based on outputs generated from early tomography reconstructions can be used. A corresponding file can be generated by the tomography reconstruction script and can be loaded by the following two methods: -`read_additional_correction_y()` -`read_additional_correction_y2()` +`flomni.read_additional_correction_y()` +`flomni.read_additional_correction_y2()` One __important__ note: The first method is by default loading a mirror correction file automatically. If the tomogram is using that data, do not overwrite it, use the secondary correction instead. The scan offsets are computed at each projection by -`compute_additional_correction_y(angle)` -`compute_additional_correction_y2(angle)` +`flomni.compute_additional_correction_y(angle)` +`flomni.compute_additional_correction_y2(angle)` The additional correct can be __reset__ by `flomni.reset_correction()` @@ -256,9 +256,9 @@ It will automatically load the default mirror correction file as primary correct At any stage of the alignment process it is possible to scan a projection. -Define the scan parameters by running `flomni.tomo_parameters()` +Define the scan parameters by `flomni.tomo_parameters()` -Run a scan at _angle_ (in degrees) by running `flomni.tomo_scan_projection(angle)` +Run a scan at _angle_ (in degrees) by `flomni.tomo_scan_projection(angle)` ### Tomography