docs(lamni): use zensical heading anchors in the quick guide
The docs moved from Sphinx/MyST to zensical on main; replace the MyST (label)= targets with lamni.md#heading links. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01LJWYXx4SS8NgFWog81xjyf
This commit is contained in:
@@ -6,17 +6,16 @@ LamNI is an instrument for 3D ptychography via ptychographic X-ray computed lami
|
||||
|
||||
… a step-by-step guide for *beamline staff and expert users*.
|
||||
|
||||
(user.ptychography.lamni.quick_guide)=
|
||||
### Quick guide
|
||||
|
||||
Only the commands, in the order they are used. Details are in the linked sections below.
|
||||
|
||||
**0. Sample change** ([details](user.ptychography.lamni.sample_change))
|
||||
**0. Sample change** ([details](lamni.md#sample-change-and-alignment))
|
||||
|
||||
- `lamni.leye_in()` moves the flight tube and detector table out and the X-ray eye in, opens slits sl1 and sl6 by 1 mm and reduces the filter transmission to 5 %
|
||||
- mount the sample
|
||||
|
||||
**1. Find the rotation center** ([details](user.ptychography.lamni.rotation_center))
|
||||
**1. Find the rotation center** ([details](lamni.md#coarse-axis-alignment))
|
||||
|
||||
- `lamni.xrayeye_rotation_center_calibration_isolated()` for an isolated particle, or
|
||||
- `lamni.xrayeye_rotation_center_calibration_extended()` for an extended/textured sample
|
||||
@@ -24,14 +23,14 @@ Only the commands, in the order they are used. Details are in the linked section
|
||||
|
||||
Applying a new center erases an existing X-ray eye alignment and fine-alignment correction. You are warned before that happens.
|
||||
|
||||
**2. X-ray eye alignment** ([details](user.ptychography.lamni.xrayeye_alignment))
|
||||
**2. X-ray eye alignment** ([details](lamni.md#x-ray-eye-alignment))
|
||||
|
||||
- `lamni.xrayeye_alignment_start()`, or `lamni.xrayeye_alignment_start(keep_shutter_open=True)` if the sample is hard to find between angles
|
||||
- `lamni.xrayeye_update_frame()` to take a single new frame
|
||||
|
||||
If an alignment already exists, you are asked before it is erased.
|
||||
|
||||
**3. Alignment scan** ([details](user.ptychography.lamni.fine_alignment))
|
||||
**3. Alignment scan** ([details](lamni.md#fine-alignment))
|
||||
|
||||
- `lamni.tomo_parameters()` to set FOV, step size and counting time
|
||||
- `lamni.tomo_alignment_scan()`. This moves the X-ray eye out and the optics in by itself (it calls `lamni.leye_out()`), so no manual step is needed before it.
|
||||
@@ -39,13 +38,12 @@ If an alignment already exists, you are asked before it is erased.
|
||||
- `lamni.read_additional_correction('<file>')`
|
||||
- optional second iteration: `lamni.read_additional_correction_2('<file>')`
|
||||
|
||||
**4. Laminography scan** ([details](user.ptychography.lamni.laminography))
|
||||
**4. Laminography scan** ([details](lamni.md#test-projections-and-laminography-scan))
|
||||
|
||||
- `lamni.tomo_parameters()`
|
||||
- test: `lamni.tomo_scan_projection(angle)` and `lamni.tomo_reconstruct()`
|
||||
- `lamni.tomo_scan()`. This does not move the eye or the optics; it only checks that the eye is out and the optics are in, and asks before continuing otherwise.
|
||||
|
||||
(user.ptychography.lamni.sample_change)=
|
||||
### Sample change and alignment
|
||||
|
||||
The access to the sample region is blocked by the flight tube during measurement. To get the flight tube out of the way use
|
||||
@@ -53,7 +51,6 @@ The access to the sample region is blocked by the flight tube during measurement
|
||||
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
|
||||
`lamni.loptics_out()`. `lamni.leye_in()` also opens slits sl1 and sl6 by 1 mm to illuminate a larger area, and `lamni.leye_out()` restores them. The rotation-center and X-ray eye alignment routines below move the FZP and optics as they need, so `loptics_out()` is only needed for looking at the sample by hand.
|
||||
|
||||
(user.ptychography.lamni.rotation_center)=
|
||||
#### Coarse axis alignment
|
||||
|
||||
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.
|
||||
@@ -100,7 +97,6 @@ To observe the axis of rotation obtain the position of the Fresnel zone plate on
|
||||
|
||||
7. close the shutter: `dev.omnyfsh.fshclose()`
|
||||
|
||||
(user.ptychography.lamni.xrayeye_alignment)=
|
||||
#### X-ray eye alignment
|
||||
|
||||
The BEC GUI is used to obtain a coarse sample alignment. Start the alignment process by
|
||||
@@ -154,7 +150,6 @@ If the drift between coarse stages and interferometer found at the start of the
|
||||
* `lamni.leye_out()` removes the X-ray eye, moves the optics and the flight tube in and restores slits sl1 and sl6 to their size before `leye_in()` (it asks first if they were changed by hand in between). `lamni.tomo_alignment_scan()` calls it by itself.
|
||||
* *possibly check slit1, idgap*
|
||||
|
||||
(user.ptychography.lamni.fine_alignment)=
|
||||
#### Fine alignment
|
||||
|
||||
The sample fine alignment can be obtained using ptychography. For this a short laminogram has to be recorded.
|
||||
|
||||
Reference in New Issue
Block a user