csaxs_bec.bec_ipython_client.plugins.flomni.flomni.Flomni#

class Flomni(client)[source]#

Bases: FlomniInitStagesMixin, FlomniSampleTransferMixin, FlomniAlignmentMixin, FlomniOpticsMixin, cSAXSBeamlineChecks, flomniGuiTools

Methods

`add_sample_database`	Add a sample to the omny sample database.
`axis_id_to_numeric`
`check_all_axes_of_fomni_referenced`
`check_position_is_valid`
`check_sensor_connected`
`check_tray_in`
`compute_additional_correction_y`
`compute_additional_correction_y_2`
`drive_axis_to_limit`
`ensure_fheater_up`
`ensure_gripper_up`
`ensure_osa_back`
`feedback_disable`
`feedback_enable_with_reset`
`feedback_enable_without_reset`
`feedback_status`
`feye_in`
`feye_out`
`ffzp_in`	move in the flomni zone plate.
`ffzp_info`
`flomni_init_stages`
`flomni_modify_storage_non_interactive`
`flomnigui_docs`
`flomnigui_idle`
`flomnigui_raise`
`flomnigui_remove_all_docks`
`flomnigui_show_cameras`
`flomnigui_show_gui`
`flomnigui_show_progress`
`flomnigui_show_xeyealign`
`flomnigui_show_xeyealign_fittab`
`flomnigui_stop_gui`
`foptics_in`	Move in the flomni optics, including the FZP and the OSA.
`foptics_out`	Move out the flomni optics
`fosa_in`
`fosa_out`
`ftransfer_confirm`
`ftransfer_controller_disable_mount_mode`
`ftransfer_controller_enable_mount_mode`
`ftransfer_controller_in_mount_mode`
`ftransfer_flomni_stage_in`
`ftransfer_flomni_stage_out`
`ftransfer_get_sample`
`ftransfer_gripper_close`
`ftransfer_gripper_is_open`
`ftransfer_gripper_move`
`ftransfer_gripper_open`
`ftransfer_modify_storage`
`ftransfer_put_sample`
`ftransfer_sample_change`
`ftransfer_show_all`
`get_alignment_offset`	Compute the alignment offset for the given angle.
`get_beamline_checks_enabled`
`laser_tracker_off`
`laser_tracker_on`
`laser_tracker_show_all`
`lights_off`
`lights_on`
`move_fheater_down`
`move_fheater_up`
`read_additional_correction_y`
`read_additional_correction_y_2`
`read_alignment_offset`
`remove_special_angles`	Remove the special angles and set the number of repeats to 1
`reset_correction`	Reset the correction to the default values.
`reset_tomo_alignment_fit`
`rt_off`
`rt_on`
`sample_get_name`	Get the name of the sample currently in the given position.
`set_client`
`set_limits`
`set_special_angles`	Set the special angles for a tomo
`set_web_password`	Set the web password for the current BEC account.
`show_signal_strength_interferometer`
`start_x_ray_eye_alignment`
`sub_tomo_scan`	Performs a sub tomogram scan.
`tomo_acquire_at_angle`	Move fsamroy to angle, then move rtx/rty/rtz to the alignment-corrected scan center (same alignment-offset logic as tomo_scan_projection, but without stitching), and acquire a single frame or a burst via scans.acquire instead of running a fermat scan.
`tomo_alignment_scan`	Performs a tomogram alignment scan.
`tomo_parameters`	print and update the tomo parameters
`tomo_reconstruct`	write the tomo reconstruct file for the reconstruction queue
`tomo_scan`	start a tomo scan
`tomo_scan_projection`
`write_alignment_scan_numbers`
`write_pdf_report`	create and write the pdf report with the current flomni settings
`xrayeye_alignment_start`
`xrayeye_update_frame`

Attributes

`beamline_checks_enabled`
`corridor_size`
`csaxs_bec_basepath`
`default_correction_file`
`default_correction_file_rel`
`fovx`
`fovy`
`frames_per_trigger`	Number of burst frames acquired per point/projection.
`golden_max_number_of_projections`
`golden_projections_at_0_deg_for_damage_estimation`
`golden_ratio_bunch_size`
`manual_shift_y`
`progress`	Proxy dict backed by the BEC global variable `tomo_progress`.
`ptycho_reconstruct_foldername`
`sample_name`
`single_point_instead_of_fermat_scan`	If True, tomo_scan acquires a single point (or burst) at each angle via scans.acquire instead of running scans.flomni_fermat_scan.
`stitch_x`
`stitch_y`
`tomo_angle_range`	Total angular sweep in degrees for tomo_type 1 (equally spaced sub-tomograms), inclusive of the upper bound.
`tomo_angle_stepsize`
`tomo_countingtime`
`tomo_shellstep`
`tomo_stitch_overlap`
`tomo_type`

add_sample_database(samplename, date, eaccount, scan_number, setup, sample_additional_info, user)[source]#: Add a sample to the omny sample database. This also retrieves the tomo id.

ffzp_in()#: move in the flomni zone plate. This will disable rt feedback, move the FZP and re-enabled the feedback.

foptics_in()#: Move in the flomni optics, including the FZP and the OSA.

foptics_out()#: Move out the flomni optics

property frames_per_trigger#: Number of burst frames acquired per point/projection. Used both by scans.flomni_fermat_scan (via tomo_scan_projection) and by tomo_acquire_at_angle (scans.acquire).

get_alignment_offset(angle: float)#

Compute the alignment offset for the given angle.

Parameters:: angle (float) – The angle to compute the alignment offset for.
Returns:: The alignment offset in x, y and z direction.
Return type:: tuple

property progress: _ProgressProxy#

Proxy dict backed by the BEC global variable tomo_progress.

Readable from any BEC client session via:

client.get_global_var("tomo_progress")

Individual fields can be read and written just like a regular dict:

flomni.progress["projection"]          # read
flomni.progress["projection"] = 42     # write (persists immediately)

To update multiple fields atomically use _ProgressProxy.update():

flomni.progress.update(projection=42, angle=90.0)

To reset all fields to their defaults:

flomni.progress.reset()

remove_special_angles()[source]#: Remove the special angles and set the number of repeats to 1

reset_correction(use_default_correction=True)#

Reset the correction to the default values. If use_default_correction is False, the correction will be set to empty values. Otherwise the default values will be loaded.

Parameters:: use_default_correction (bool, optional) – If set to true, a call reset the correction to the default values. Defaults to True.

sample_get_name(position: int = 0) → str#: Get the name of the sample currently in the given position.

set_special_angles(angles: list, repeats: int = 20, tolerance: float = 0.5)[source]#

Set the special angles for a tomo

Parameters:

angles (list) – List of special angles
repeats (int, optional) – Number of repeats at a special angle. Defaults to 20.
tolerance (float, optional) – Number of repeats at a special angle. Defaults to 0.5.

set_web_password(password: str) → None[source]#: Set the web password for the current BEC account.

property single_point_instead_of_fermat_scan#: If True, tomo_scan acquires a single point (or burst) at each angle via scans.acquire instead of running scans.flomni_fermat_scan. Applies to all tomo_types, since it only changes how a given angle is acquired, not which angles are visited.

sub_tomo_scan(subtomo_number, start_angle=None)[source]#: Performs a sub tomogram scan. :param subtomo_number: The sub tomogram number. :type subtomo_number: int :param start_angle: The start angle of the scan. Defaults to None. :type start_angle: float, optional

tomo_acquire_at_angle(angle: float, frames_per_trigger: int | None = None)[source]#

Move fsamroy to angle, then move rtx/rty/rtz to the alignment-corrected scan center (same alignment-offset logic as tomo_scan_projection, but without stitching), and acquire a single frame or a burst via scans.acquire instead of running a fermat scan.

This mirrors the positioning sequence used internally by flomni_fermat_scan (rotation, then rtx/rty/rtz with laser-tracker on/check/move-to-region), but executes it as plain blocking client-side calls, since this runs in the BEC client, not on the scan server.

Parameters:

angle (float) – rotation angle [deg] to move fsamroy to.
frames_per_trigger (int, optional) – number of burst frames for this acquisition. Defaults to self.frames_per_trigger.

tomo_alignment_scan()[source]#: Performs a tomogram alignment scan. Collects all scan numbers acquired during the alignment, prints them at the end, and creates a BEC scilog text entry summarising the alignment scan numbers.

property tomo_angle_range#: Total angular sweep in degrees for tomo_type 1 (equally spaced sub-tomograms), inclusive of the upper bound. Either 180 (default, original behaviour) or 360.

tomo_parameters()[source]#: print and update the tomo parameters

tomo_reconstruct(base_path='~/data/raw/logs/reconstruction_queue')[source]#: write the tomo reconstruct file for the reconstruction queue

tomo_scan(subtomo_start=1, start_angle=None, projection_number=None)[source]#: start a tomo scan

write_pdf_report()[source]#: create and write the pdf report with the current flomni settings