csaxs_bec.bec_ipython_client.plugins.omny.omny.OMNY#

class OMNY(client)[source]#

Bases: OMNYInitStagesMixin, OMNYSampleTransferMixin, OMNYAlignmentMixin, OMNYOpticsMixin, cSAXSBeamlineChecks, OMNY_rt_client, OMNYGuiTools

Methods

`add_sample_database`	Add a sample to the omny sample database.
`axis_id_to_numeric`
`check_all_axes_of_OMNY_referenced`
`compute_additional_correction_x`
`compute_additional_correction_y`
`compute_additional_correction_y_2`
`dewar_show_all`
`enable_all_devices`
`feedback_disable`
`feedback_enable_with_reset`
`feedback_status`
`get_alignment_offset`	Compute the alignment offset for the given angle.
`get_beamline_checks_enabled`
`interferometer_tweak_otrack`
`interferometer_tweaking`
`laser_tracker_check_and_wait_for_signalstrength`
`laser_tracker_off`
`laser_tracker_on`
`laser_tracker_show_all`
`oeye_cam_in`
`oeye_out`
`oeye_xray_in`
`ofzp_in`
`ofzp_info`
`ofzp_out`
`omny_init_smaract`
`omny_init_stages`
`omny_interferometer_align_incoupling_angle`
`omny_interferometer_align_tracking`
`omnygui_idle`
`omnygui_remove_all_docks`
`omnygui_show_gui`
`omnygui_show_omnycam_parking`
`omnygui_show_omnycam_samplestage`
`omnygui_show_progress`
`omnygui_stop_gui`
`ooptics_in`
`oosa_in`
`oosa_move_out_of_shield`
`oosa_out`
`otransfer_get_sample`
`otransfer_help`
`otransfer_park_loadlock_slot`
`otransfer_park_slot`
`otransfer_put_sample`
`otransfer_storage`
`read_additional_correction_x`
`read_additional_correction_y`
`read_additional_correction_y_2`
`read_alignment_offset`	Read the alignment offset from the given directory and set the global parameter tomo_alignment_fit.
`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`
`set_special_angles`	Set the special angles for a tomo
`show_signal_strength_interferometer`
`start_x_ray_eye_alignment`
`sub_tomo_scan`	Performs a sub tomogram scan.
`temperatures_show_all`
`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`
`vcs_show_all`
`vcs_valves_in_measurement_position`
`write_pdf_report`	create and write the pdf report with the current OMNY settings
`write_to_scilog`
`xrayeye_alignment_start`
`xrayeye_update_frame`

Attributes

`beamline_checks_enabled`
`corridor_size`
`default_correction_file`
`default_correction_file_x`
`fovx`
`fovy`
`golden_max_number_of_projections`
`golden_projections_at_0_deg_for_damage_estimation`
`golden_ratio_bunch_size`
`manual_shift_y`
`near_field`
`ptycho_reconstruct_foldername`
`sample_name`
`stitch_x`
`stitch_y`
`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.

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

read_alignment_offset(dir_path='/home/docs/Data10/specES1/internal/', setup='omny', use_vertical_default_values=True)#

Read the alignment offset from the given directory and set the global parameter tomo_alignment_fit.

Parameters:: dir_path (str, optional) – The directory to read the alignment offset from. Defaults to os.path.expanduser(“~/Data10/specES1/internal/”).

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.

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.

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_alignment_scan()[source]#: Performs a tomogram alignment scan.

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

tomo_reconstruct(base_path='~/Data10/specES1')[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 OMNY settings