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x12sa
2026-03-17 14:14:14 +01:00
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docs/user/ptychography/flomni.md
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@@ -50,16 +50,15 @@ Manually move the gripper to a transfer position
After the sample transfer the sample stage moved to the measurement position with your new sample. The Xray eye will automatically move in and the shutter will open. You may already see the sample in the omny xeye interface running on the windows computer.
If you see your sample already at the approximately correct height, you can skip steps 1 to 3. Otherwise adjust the height:
1. `flomni.rt_feedback_disable()` disable the closed loop operation to allow movement of coarse stages
1. `flomni.feedback_disable()` disable the closed loop operation to allow movement of coarse stages
1. `umvr(dev.fsamy, 0.01)`, attention: unit <mm>, 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 (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.
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. The GUI will present a fit of this data, which is automatically loaded to BEC for aligning the sample.
#### Fine alignment
After the xrayeyealign, a fine alignment needs to be performed using ptychography.
_To bypass the fine alignment: `feye_out`_
_To bypass the fine alignment: `flomni.feye_out`_
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.
@@ -71,7 +70,7 @@ _To bypass the fine alignment: `feye_out`_
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, 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 <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.
1. Before changing sample, verify that all subtomograms were completely acquired using the tomo_reconstruction matlab script.
#### If something went wrong…