csaxs_bec/docs/user/ptychography/flomni.md

(user.ptychography.flomni)=
# flOMNI

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 

… a step-by-step guide for users

(user.ptychography.flomni.transfer)=
### Sample storage and transfer

Print the current usage of the sample storage  
`flomni.ftransfer_show_all()`

flOMNI has to know about the loaded positions and sample names. To modify use  
`flomni.ftransfer_modify_storage(<position>, 0 (=free) / 1 (=used))`  
positions `<1> .. <20>` are available slots in the tray.
Special position: `0 = sample stage`, `100 = gripper`.
You will be asked to enter a sample name. 

To load a new sample in the sample stage, in principle only one command is needed  
`flomni.ftransfer_sample_change(<position new sample>)`  
You will be asked where the previous sample should go with a suggestion for an empty position in the tray.

To remove the current sample from the sample stage __without__ mounting a new one, use  
`flomni.ftransfer_sample_change(-1)`  
You will be asked where to stow the removed sample, same as above.
Other commands:  
`ftransfer_tray_in /_out	 (not yet implemented).`

__If something goes wrong__, there are additional commands to perform a manual operation of the gripper.

| command | explanation |
| --- | --- |
| `flomni.ftransfer_get_sample(<position>)`  | Pick sample from <position> |
| `flomni.ftransfer_put_sample(<position>)`  | Mount sample at <position> |
| `flomni.ftransfer_flomni_stage_in()`       | stage to measurement position |
| `flomni.ftransfer_flomni_stage_out()`      | stage to the sample change position |

Manual operation of the gripper (do not leave it too long in open state)  
`flomni.ftransfer_gripper_open()`  
`flomni.ftransfer_gripper_close()`

Manually move the gripper to a transfer position
`flomni.ftransfer_gripper_move(<position>)`

### Alignment of samples

#### Coarse alignment

After the sample transfer the sample stage moved to the measurement position with your new sample. The Xray eye will automatically move in, the alignment GUI opens and shows a current snapshot.
If you see your sample already at the approximately correct height:

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 its height and then angles of 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.

Otherwise adjust the height manually:

1. `flomni.umvr_fsamy_tracked(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

#### Fine alignment

After the xrayeyealign, a fine alignment needs to be performed using ptychography.
_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.
1. `flomni.tomo_alignment_scan()` perform the alignment scan. When the first scan is running, switch to a matlab session and run `BEC_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, up (positive) or down (negative). After adjusting the numbers, type again `flomni.tomo_parameters()` and verify that they are correct. For the "8 sub-tomograms" mode, an optional 0-deg reference shot can be enabled at the start of every odd sub-tomogram and once more at the end, useful for tracking radiation damage over the course of a long measurement.
1. `flomni.tomo_scan_projection(angle)` perform a ptychographic scan at the rotation angle <angle>. Launch the tomographic measurement by `flomni.tomo_scan()`. During the scan a live progress report is printed, including an estimated time of completion. Unusually long gaps (e.g. a beamline interruption) are detected automatically and excluded from the estimate, and the total time lost to such gaps is reported once the scan finishes.
1. Before changing sample, verify that all subtomograms were completely acquired using the tomo_reconstruction matlab script.

#### Queueing multiple scans

Several parameter sets can be queued and run one after another automatically, e.g. a fast overview scan followed by a higher resolution scan on the same sample, without having to wait around to start the next one by hand.
1. `flomni.tomo_parameters()` set up the first parameter set, then `flomni.tomo_queue_add("label")` to add it to the queue.
1. Repeat for further parameter sets.
1. `flomni.tomo_queue_show()` review the queue before starting.
1. `flomni.tomo_queue_execute()` run all queued scans in sequence.

If a queued scan is interrupted, the next call to `flomni.tomo_queue_execute()` resumes it automatically rather than starting over, then continues with the remaining entries.

The same queue can also hold **command jobs** that reconfigure the beamline between scans (e.g. change energy, then re-peak the undulator gap) instead of running a tomogram, so "scan A, reconfigure, scan B" runs unattended as one queue. A queued tomogram can also run custom code at each projection angle (e.g. moving a polarizer in and out between two exposures) via a registered **at_each_angle hook**. See [Tomography](user.ptychography.flomni.tomography) below for the full command reference, including command jobs and hooks.

#### If something went wrong…

A __single projection__ is to be repeated use
`flomni.tomo_scan_projection(<angle>)`. The target angle of scans can be found in the second column of the file in 
`~/data/raw/logs/tomography_scannumbers.txt`

To continue an __interrupted tomography scan__, run  
`flomni.tomo_scan_resume()`  
It picks up automatically from wherever the scan was interrupted, no need to look up the exact subtomogram/angle by hand. Do not use this command when running from the tomo queuing system. Instead use `flomni.tomo_queue_execute()`.

Alternatively, the same kind of parameters used internally by `tomo_scan_resume()` can be given to `flomni.tomo_scan()` directly, e.g. to resume from a different point than where it actually stopped:
| tomo type | parameters and their defaults |
| --- | --- |
| 8 sub-tomograms | subtomo_start=1, start_angle=None |
| Golden ratio tomography (sorted in bunches) | projection_number=None |
| Equally spaced with golden starting angle | projection_number=None |

### GUI tools

During operation the BEC GUI will show the relevant cameras or progress information. To manually switch view TAB completion on 'flomni.flomnigui_' will show all options to control the GUI. Most useful
'flomni.flomnigui_show_cameras()' will show the cameras for sample transfer and interior overview
'flomni.flomnigui_show_progress()' will show the measurement progress GUI
'flomnigui_show_xeyealign()' will show the XrayEye alignment GUI


## How to setup flOMNI (software)

This part of the manual is intended for beamline staff and expert users

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 written on the physical machine.
1. `cd OMNY/flOMNI/`
1. `./startflOMNI`

Once the loop has started, it is possible to start bec with the flOMNI configuration file.

Starting bec with session will load the scripts
`bec --session flomni`

The flOMNI scripts can be loaded manually by  
`from csaxs_bec.bec_ipython_client.plugins.flomni import Flomni`  
`flomni =  Flomni(bec)`

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")`



If the realtime system is restarted, bec will lose communication. To restart:  
`flomni.rt_off()` … then wait a few seconds  
`flomni.rt_on()`

### Initialization of the stages

The stages of flOMNI are referenced in respect to their endswitches. The stages have to be initialized at the beginning of a run or when the Galil motor controllers have been reset or restarted. To see the status of the stages following commands are available:

Show the status of all galil controllers (all stepper motors and the UPR rotation stage)  
`dev.fsamx.controller.galil_show_all()`

The same holds true for the Smaract stages which control the OSA position.  Their status can be checked by  
`dev.fosax.controller.show_all()`

In case referencing of the flOMNI stages is required, run  
`flomni.flomni_init_stages()`  
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.

### X-ray optics alignment

The positions of the optics stages are stored as stage parameters and are thus linked to the configuration file.  
Example: The OSAx “in” position can be reviewed by `dev.fosax.user_parameter`  
Update the value by (example "fosax", "in") by `dev.fosax.update_user_parameter({"in":value})`
Important note: if these values are changed, they are not automatically stored to the config file and will only be available in the current session.
Note: The minimal position of the motor foptz is 14, and the minimal reachable distance FZP to sample is 36 mm.

`flomni.ffzp_info()` shows info about the available FZPs at the current energy of the beamline. Optional parameter is the photon _energy_ in keV.  
Example: `flomni.ffzp_info(6.2)`

Documents about availabe optics can be accessed by
`flomni.flomnigui_docs`

The [laser feedback](user.ptychography.flomni.laser_feedback) will be disabled and fine alignment lost if foptx/y are moved!

Following functions exist to move the optics in and out, with self-explaining naming.
- `flomni.ffzp_in()`
- `flomni.foptics_in()`
- `flomni.foptics_out()`
- `flomni.fosa_in()`
- `flomni.fosa_out()`

### Interferometer

The position feedback in flOMNI is controlled in closed loop to an interferometric position measurement. To show the signal of the interferometers:
`flomni.show_signal_strength_interferometer()`  
Typical values with proper alignment, sample stage at the measurement position and laser tracker running are in the range of
|    Axis   |       Value        |
| --- | --- |
|     0     |      13681.0       |
|     1     |      12383.0       |
|     2     |      10716.0       |
|     3     |      11032.0       |


#### Laser tracker commands

The horizontal interferometer is built according to the [tracking interferometer](https://www.dora.lib4ri.ch/psi/islandora/object/psi:7524). The tracker can be controlled by following commands. During commissioning of the setup it is worthy to check the status, but during general operation these commands should not be required.

- `flomni.laser_tracker_show_all()`
- `flomni.laser_tracker_on()`
- `flomni.laser_tracker_off()`

(user.ptychography.flomni.laser_feedback)=
#### Interferometer feedback commands

The closed loop control of the Piezo stages can be controlled by  
- `flomni.feedback_feedback_enable_with_reset()`.  
_There is also an enable without reset, which is used during tomography scans, when using coarse stages to increase the scan range. It should not be required to use manually._  
- `flomni.feedback_disable()`
- `flomni.feedback_status()`

### Scanning in 2D and sample alignment

#### flOMNI Fermat scan

The basic scan function can be called by `scans.flomni_fermat_scan()` and offers a detailed doc string for further details (`scans.flomni_fermat_scan?`). A prerequisite for scanning is a running feedback system. The scan has following parameters.

| Parameters |  |
| --- | --- |
| fovx (float) | Fov in the piezo plane (i.e. piezo range). Max 200 um |
| fovy (float) | Fov in the piezo plane (i.e. piezo range). Max 100 um |
| cenx (float) | center position in x |
| ceny (float) | center position in y |
| exp_time (float) | exposure time per frame |
| frames_per_trigger(int) | Number of burst frames per position |
| step (float) | stepsize |
| zshift (float) | shift in z |
| angle (float) | rotation angle (will rotate first) |
| corridor_size (float) | corridor size for the corridor optimization. Default 3 um |

Example:  
`scans.flomni_fermat_scan(fovx=20, fovy=25, cenx=0.02, ceny=0, zshift=0, angle=0, step=0.5, exp_time=0.01, frames_per_trigger=1)`

#### Overview of the alignment steps

There are several corrections applied to maintain the sample in the FOV:
1. Mirror calibration
1. X-ray eye alignment
1. Ptychography fine alignment (improvement of the X-ray eye alignment step)
1. Vertical shifts from tomography reconstruction (for very small vertical FOV)

#### XrayEye and sample alignment

The XrayEye can be moved in and out by  
`flomni.feye_in()`  
`flomni.feye_out()`

The _in_ and _out_ positions are stored as user parameters in the stage definition. Get the values by  
`dev.feyex.user_parameter`  
`dev.feyey.user_parameter`

Update the values by, example for feyex and in position,  
`dev.feyex.update_user_parameter({"in":value})`

To refresh the frame of the xray eye windows software  
`flomni.xrayeye_update_frame()`

This command can also be called to keep the shutter open and live view active
`flomni.xrayeye_update_frame(keep_shutter_open=True)`

To start the xray eye alignment (and clear any previous alignment)  
`flomni.xrayeye_alignment_start()`

This command can also be called to keep the shutter open and live view active. Warning: The dose to the sample will be significantly higher.
`flomni.xrayeye_update_frame(keep_shutter_open=True)`

To load the fit parameters from directory _dir_path_ computed by _BEC_ptycho_align.m_ in Matlab run  
`flomni.read_alignment_offset(dir_path='')`  
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`.

At each projection, the angular dependent is computed by  
`flomni.get_alignment_offset(angle)`, with _angle_ in degrees.

The alignment can be cleared by  
`flomni.reset_tomo_alignment_fit()`

#### Fine alignment

The alginment obtained by the X-ray eye can be refinde by recording ptychography projections at 45 deg. intervals. For this, adjust the tomo parameters by  
`flomni.tomo_parameters()`

Next, run the alignment scan by
`flomni.tomo_alignment_scan()`

Reconstruct the scan and use BEC_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:  
`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  
`flomni.compute_additional_correction_y(angle)`  
`flomni.compute_additional_correction_y2(angle)`

The additional correct can be __reset__ by  
`flomni.reset_correction()`  
It will automatically load the default mirror correction file as primary correction! To reset and not load any correction, which might be useful to obtain a new default correction file, run  
`flomni.reset_correction(use_default_correction=False)`

#### Scanning of projections

At any stage of the alignment process it is possible to scan a projection.

Define the scan parameters by `flomni.tomo_parameters()`

Run a scan at _angle_ (in degrees) by `flomni.tomo_scan_projection(angle)`

(user.ptychography.flomni.tomography)=
### Tomography

The tomo parameters have to be set by  
`flomni.tomo_parameters()`

Once satisfied with the alignment, the tomography scan can be started by  
`flomni.tomo_scan()`

During the scan, a live progress report is printed (subtomogram/projection counters and an estimated time of completion). Gaps significantly longer than a normal acquisition cycle (e.g. a beamline-down interruption, or a crash followed by a restart) are detected automatically from the time between consecutive projections and excluded from the time estimate; the total time lost to such gaps is printed once the scan finishes.

Three modes for angular sampling are implemented and they have different optional parameters for the tomo_scan method:
| tomography mode | parameters and defaults |
| --- | --- |
| 8 sub-tomograms | subtomo_start=1, start_angle=None |
| Golden ratio tomography (sorted in bunches) | projection_number=None |
| Equally spaced with golden starting angle | projection_number=None |

For the "8 sub-tomograms" mode, `flomni.tomo_parameters()` also offers a `zero_deg_reference_at_each_subtomo` option: when enabled, an additional reference projection at exactly 0 degrees is acquired at the start of every odd (forward) sub-tomogram and once more after the final sub-tomogram, useful for tracking radiation damage across the full measurement.

The parameters above can be used to __restart an interrupted acquisition__ manually, or - more conveniently - by running  
`flomni.tomo_scan_resume()`  
which reads the last recorded progress and resumes automatically at the exact point (subtomogram/angle, or projection for the golden ratio modes) the scan was interrupted at, without needing to look up the values by hand. When running from the tomo scan queuing system use `flomni.tomo_queue_execute()` instead!

In case of eight equally spaced sub-tomograms, an individual sub tomogram can be scanned by flomni.sub_tomo_scan(subtomo_number, start_angle). If the start angle is not specified, it will be computed depending on the subtomo_number, which is ranging from 1 to 8.

#### Queueing multiple scans

Several tomo parameter sets can be queued and run sequentially on the same sample, without having to start each one by hand.

| command | explanation |
| --- | --- |
| `flomni.tomo_queue_add(label=None)` | Snapshot the currently set tomo parameters and add them as a new job to the queue. Returns the job's index. |
| `flomni.tomo_queue_show()` | Print and return the current queue, with status per job. |
| `flomni.tomo_queue_delete(*indices)` | Delete one or more jobs by index. |
| `flomni.tomo_queue_clear()` | Empty the queue. |
| `flomni.tomo_queue_execute(start_index=0)` | Run all pending jobs in sequence, on the current sample. |
| `flomni.tomo_queue_resume(start_index=0)` | Alias for `tomo_queue_execute()` — identical behavior, just a name that matches `tomo_scan_resume()`. |

The queue is persisted (it survives a BEC client restart). Each job's status is one of `pending`, `running`, `incomplete`, or `done`. A job that did not run to completion (an exception was caught, or the BEC client itself crashed mid-scan) is automatically resumed - rather than restarted - the next time `flomni.tomo_queue_execute()` is called.

If the process running the queue dies hard enough that it never gets to write a status update at all (a kernel restart, a Ctrl-C during a blocking prompt) a job can be left stuck showing `running` with nothing actually running. `flomni.tomo_queue_delete(index)` has no status guard and works on a stuck row regardless; you can also fix the status directly with `flomni._tomo_queue_proxy.update_by_id(job_id, status="incomplete")` (to make it resumable) or `status="done"` (to skip it). The GUI's Delete/Clear normally refuse to touch a `running` row, but detect a stale one (no recent scan heartbeat) and offer to proceed anyway with an explicit confirmation instead of blocking forever.

Example:
```
flomni.tomo_parameters()                  # set up parameter set #1
flomni.tomo_queue_add("fast overview")
flomni.tomo_parameters()                  # set up parameter set #2
flomni.tomo_queue_add("hires scan")
flomni.tomo_queue_show()
flomni.tomo_queue_execute()               # runs both, in order, on this sample
```

**GUI: reusing an earlier job's settings.** In the ☰ Queue control… dialog, select a
single tomo job (not a command job — those have no scan parameters) and click
**"Load into editor"** to pull its saved settings into the params panel's editor,
as if you'd just clicked Edit. Nothing is written yet — review or tweak the fields,
then Submit (writes live, blocked while the beamline is busy) or "Add to queue" (always
allowed) as usual. If you already had an edit in progress, it asks before discarding it.

**GUI: two different "Add to queue" buttons.** The params panel's own **"Add to
queue"** (visible in edit mode) queues whatever you've typed, unsubmitted. The ☰
Queue control… window's **"Add current params to queue"** is a different button on a
different window — it always queues the *live* parameters, regardless of any edit
open in the panel. If you have an unsaved edit open and click the queue window's
button instead of the panel's, it warns and names the correct one before proceeding,
since it would otherwise queue your last-submitted values, not what you just typed.

**Reacquiring from an earlier projection.** A resumed job normally picks up
exactly where it stopped. If a beamline problem means earlier projections need
redoing too — even in a job that's already marked `done` — use:

`flomni.tomo_queue_reacquire(job_index, projection_number)`

`job_index` is the job's position, same indexing as `tomo_queue_show()`.
`projection_number` is a flat, 0-indexed projection count that works the same
way for all three tomography modes — for "8 sub-tomograms" it counts straight
through all 8 in order (subtomogram 1's projections first, then subtomogram
2's, ...), exactly matching the running `projection` counter already shown in
the live progress report / `flomni.progress["projection"]`; for the
golden-ratio modes it's the same projection number those already use. This
reopens the job at that point and resets every job queued *after* it —
tomograms and command jobs alike, regardless of their own current status — to
`pending`, so the next `flomni.tomo_queue_resume()` (or `tomo_queue_execute()`)
call re-runs everything from there forward, in order. It does not run
anything itself.

Example — job 0 already finished, but its last few projections (and the jobs
queued after it) need redoing:
```
flomni.tomo_queue_show()               # find the job index and the projection number to restart at
flomni.tomo_queue_reacquire(0, 130)    # reopen job 0 at projection 130; jobs 1+ reset to pending
flomni.tomo_queue_resume()             # actually re-run, in order
```

Refuses (raises) if `job_index` points at a command job (nothing to
reacquire), or if some *other* job in the queue is already `incomplete`/
`running` — only one job's progress can be tracked at a time, so resolve that
one first (or pass its own index instead).

#### Command jobs — reconfiguring the beamline between scans

In addition to tomogram jobs, the same queue can hold **command jobs**: an ordered
list of beamline reconfiguration steps (move a device, ...) that run instead of a
scan. This is what lets one queue express *"tomogram A, then reconfigure, then
tomogram B"* unattended, e.g. change energy and re-peak the undulator gap between
two tomograms on the same sample.

`flomni.tomo_queue_add_command(steps, label=None, idempotent=None)`

- `steps`: a single `{"action": ..., "kwargs": {...}}` dict, or a list of them run in
  sequence within that one job.
- `label`: optional name shown by `tomo_queue_show()`, same as for `tomo_queue_add()`.
- `idempotent`: normally inferred (safe to blindly re-run after a crash only if every
  step is); override explicitly if needed.

Only actions from a fixed, reviewed registry can be queued — not arbitrary code:

| action | does | parameters |
| --- | --- | --- |
| `move` | Move device(s) to absolute position(s). Only devices on the allow-list below can be targeted. | `positions`: `{device: target}`, e.g. `{"mokev": 6.2}` |
| `optimize_idgap` | Scan the undulator gap over a range and move to the peak. **Not yet implemented (no-op stub).** | `search_range`: mm, default 0.5, range 0–2 |

Devices allowed for `move`: `mokev` (energy, keV), `idgap` (undulator gap, mm). A
`move` naming any other device is rejected, both when the job is added and again when
it actually runs.

Example — change energy, then re-peak idgap, before the next tomogram:
```
flomni.tomo_queue_add_command(
    [{"action": "move", "kwargs": {"positions": {"mokev": 6.2}}},
     {"action": "optimize_idgap", "kwargs": {"search_range": 0.5}}],
    label="reconfigure to 6.2 keV",
)
```

`tomo_queue_show()` lists command jobs alongside tomogram jobs, e.g.:
```
[2]    pending  reconfigure to 6.2 keV  CMD move{'positions': {'mokev': 6.2}} > optimize_idgap{'search_range': 0.5}  [idem]
```

If a command job is interrupted by a crash, there is no per-step resume point — the
whole job is either safe to redo from the top or it isn't:
- If every step is idempotent (the usual case — an absolute move is harmless to
  repeat), `flomni.tomo_queue_execute()` silently re-runs the whole job from the top.
- If any step is not idempotent, you are asked whether to re-run the job from the top
  or mark it done as-is.

#### Custom behavior at each projection angle

By default, every projection in a tomo scan is a single ptychography scan at that
angle. For cases that need something more — e.g. record a projection, move a
polarizer in, record again, move it back out, at every angle — write a small Python
function and register it as an **at_each_angle hook**. Once registered, it can be
selected per tomo-queue job, so the whole modulated tomogram runs unattended along
with any other queued jobs.

A hook is a function `func(flomni, angle)`, called once per projection angle instead
of the normal acquisition. Acquire the actual projection(s) inside it the same way
`tomo_scan()` would on its own — `tomo_scan_projection(angle)` for a normal
(Fermat-scan) measurement, or `tomo_acquire_at_angle(angle)` if `tomo_parameters()`
has single-point mode enabled for this job (see the warning below for why it matters
which one you call):
```python
def polarizer_modulation(flomni, angle):
    flomni.tomo_scan_projection(angle)
    umv(dev.polarizer, "in")
    flomni.tomo_scan_projection(angle)
    umv(dev.polarizer, "out")
```

| command | explanation |
| --- | --- |
| `flomni.register_at_each_angle_hook("name", func)` | Load a hook function under `name`. |
| `flomni.at_each_angle_hook = "name"` | Activate it — the next tomo-queue job added will use it. |
| `flomni.at_each_angle_hook = None` | Deactivate it — back to normal projections for the next job. |
| `flomni.list_at_each_angle_hooks()` | Print the names of all currently registered hooks (the active one is marked). |
| `flomni.unregister_at_each_angle_hook("name")` | Remove a hook by name. |

Example — queue a polarizer-modulated tomogram, then a normal one:
```python
flomni.register_at_each_angle_hook("polarizer_mod", polarizer_modulation)

flomni.tomo_parameters()                        # set up the scan parameters as usual
flomni.at_each_angle_hook = "polarizer_mod"      # activate the hook
flomni.tomo_queue_add("polarizer run")

flomni.at_each_angle_hook = None                 # back to normal -- do not skip this!
flomni.tomo_queue_add("plain follow-up scan")

flomni.tomo_queue_execute()                      # runs both, hook active only for the first
```
**Do not forget to reset `flomni.at_each_angle_hook = None`** before adding a job
that should run normally — each queued job remembers whatever `at_each_angle_hook`
was set to at the moment it was added (like every other tomo parameter), so a job
added right after a hook-using one without resetting it first will silently run with
that hook still active.

Registered hooks are **session-only** — they live in memory and do not survive a
kernel restart. If `tomo_queue_execute()` reaches a job whose `at_each_angle_hook`
isn't registered in the current session (e.g. after restarting BEC), it stops with a
clear error rather than silently running a plain scan; re-run
`register_at_each_angle_hook()` for that hook, then call `tomo_queue_execute()`
again to resume.

**Editing a hook after registering it:** `register_at_each_angle_hook()` stores
whichever function object you pass it at that moment — it is not a live link to the
function's name. If you edit the function's source and re-run the `def` (in a cell,
or reload the file it's defined in — see below), the change is picked up
automatically the next time the hook runs, and a note is printed telling you so.
You don't need to call `register_at_each_angle_hook()` again after an edit.

**Recommended: define hooks in a file, not inline in the shell.** For anything
beyond a quick one-off, put the hook function in a `.py` file — ideally together
with the `tomo_queue_add()`/`at_each_angle_hook` calls that use it, so the file is a
single, compact record of exactly what ran during the experiment. Load it with
`import myhooks` (or `from myhooks import my_hook`) and, after editing, reload with
`importlib.reload(myhooks)` — the automatic pick-up described above still works,
because it detects the change via the module's own namespace, not the local name
you imported it under. `%run -i myhooks.py` also works (runs in the current
namespace, same as a cell). **Avoid plain `%run myhooks.py`** (without `-i`): it
executes in a fresh, throwaway namespace each time, so an edit-and-rerun is *not*
picked up automatically and the old version keeps running silently.

**`tomo_scan_projection()` vs `tomo_acquire_at_angle()`:** these are not
interchangeable. `tomo_scan_projection(angle)` always runs a full Fermat-scan
projection; `tomo_acquire_at_angle(angle)` always runs a single-point acquisition.
Use whichever matches how `tomo_parameters()` has this job configured
(`single_point_instead_of_fermat_scan`) — calling the wrong one for the job's mode
produces the wrong kind of data, and calling `tomo_scan_projection()` directly while
single-point mode is on prints a warning and asks for confirmation. **Declining that
confirmation now fails the job** (raises, rather than silently skipping that
projection) — inside a custom hook or the normal tomo flow this correctly marks the
queue job `incomplete` and pauses the queue, instead of quietly acquiring fewer
projections than expected with no trace, or (if you get asked at every angle and
eventually give up and hit Ctrl-C) leaving a job stuck at status `running` forever
with nothing actually running. If you hit this, use `tomo_acquire_at_angle(angle)`
in your hook instead, or fix the queue entry via `flomni.tomo_queue_delete(index)`
(no status guard, works even on a stuck `running` row) or by marking it done/
incomplete directly: `flomni._tomo_queue_proxy.update_by_id(job_id, status=...)`.
A reminder of which one to use fires the moment you switch single-point mode on
(`flomni.single_point_instead_of_fermat_scan = True`), and again any time you check
`flomni.tomo_parameters()` while it's on; the params panel (GUI) shows the same
reminder as a visible note whenever "Single-point scan" is checked.

**GUI:** the tomo parameters panel has an "At-each-angle hook" dropdown, listing
whatever is currently registered from the CLI (`register_at_each_angle_hook()`) —
the GUI process can't register hooks itself, only select one by name for the job
you're about to submit or add to the queue. Pick "None (default)" for a normal scan.
If a job's stored hook isn't currently registered anywhere, it still shows up in the
dropdown labeled "(not registered in this session)" so it's never silently hidden.
A queued job's active hook (if any) also appears on the status webpage (queue detail
and "Current measurement"), the ☰ Queue control… table's Details column, and the
`flomnigui_show_progress()` ring's center label.

**Unregistering does not clear `at_each_angle_hook`.** `unregister_at_each_angle_hook()`
only removes the function from this session's registry — if `at_each_angle_hook` (or a
queued job) still names it, that reference is untouched; it just becomes an
unregistered name, flagged as such wherever it's shown (CLI, GUI dropdown, webpage,
Details column). Set `flomni.at_each_angle_hook = None` (or the GUI dropdown's "None
(default)") explicitly if you want to actually clear the selection, not just remove
the hook it points to.

**Where the hook shows up in the permanent record:** `flomni.tomo_parameters()`,
the end-of-scan scilog entry, and `write_pdf_report()` all show the active hook's
name (flagged if unregistered) — and, when it's still registered, its full **source
code** too (scilog entry and PDF report only, not the console print), so what a
tomogram actually did is part of the log even if the hook itself is edited or
removed later.

### Sample storage and transfer

[See short version](user.ptychography.flomni.transfer)

### Heater

The [heater](https://www.dora.lib4ri.ch/psi/islandora/object/psi:45302) can be moved up and down by
flomni.move_fheater_down()
flomni.move_fheater_up()

The functions are safe in the sense that no collisions should occur. E.g. the OSA will be moved back before a movement of the heater.

__The heater still needs commissioning in BEC!!!__