nxtomomill.converter.hdf5.acquisition.pcotomoacquisition.PCOTomoAcquisition#

class nxtomomill.converter.hdf5.acquisition.pcotomoacquisition.PCOTomoAcquisition(root_url, configuration, detector_sel_callback, start_index)[source]#

Bases: StandardAcquisition

A PCOTomo acquisition is an acquisition that can look like that at bliss side:

scan “descritpion”, title can be tomo:pcotomo for example
Optional scan dark
Optional scan flat
scan “projections”
Optional scan flat

The scan “projections” contains several “tomo” with a parameter evolving with time like heat or pressure. The idea is that we want to split those into several NXtomo. Those NXtomo must duplicate dark and flat scans For example if scan “projections” contains nb_loop = 2 and nb_loop = 3 we must create nb_loop*nb_loop == 6 NXtomo as output.

Split of those can are done in postprocessing on the to_NXtomos function

__init__(root_url, configuration, detector_sel_callback, start_index)[source]#

Methods

`__init__`(root_url, configuration, ...)
`camera_is_valid`(det_name)
`check_tomo_n`()
`get_already_defined_params`(key)
`get_axis_scale_types`()	Return axis display for the detector data to be used by silx view
`get_detector_roi`()
`get_expected_nx_tomo`()	Return the expected number of nxtomo created for this acquisition.
`get_nb_loop`(url)	rtype: int \| None
`get_nb_tomo`(url)	rtype: int \| None
`get_nb_turns`(url)	rtype: int \| None
`get_pcotomo_version`(url)	return the pcotomo version according to the provider version (aka bliss)
`get_translation_z_frm`(root_node, n_frame, ...)
`is_different_sequence`(entry)	Can we have several entries 1.1, 1.2, 1.3.
`is_part_of_same_series`(other)	rtype: `bool`
`parent_root_url`()	rtype: DataUrl \| None
`read_entry`()
`register_step`(url[, entry_type, copy_frames])	type url: DataUrl
`to_NXtomos`(request_input, input_callback[, ...])	rtype: `tuple`
`to_NXtomos_pcotomo_v1`(request_input, ...[, ...])	The first version of 'to_NXtomos' for the first way of storing pcotomo information.
`to_NXtomos_pcotomo_v2`(request_input, ...[, ...])	The second version of 'to_NXtomos' for the second way of storing pcotomo information.
`write_as_nxtomo`(shift_entry, ...[, ...])	This function will dump the acquisition to disk as an NXtomo

Attributes

`configuration`
`data_type`
`dim_1`
`dim_2`
`expo_time`
`image_key_control`
`known_machine_electric_current`	Return the dict of all know machine electric current.
`n_frames`
`n_frames_actual_bliss_scan`
`raise_error_if_issue`	Should we raise an error if we encounter or an issue or should we just log an error message
`root_url`
`rotation_angle`
`sample_x`	Return the '_sample_x' attribute.
`sample_y`	Return the '_sample_y' attribute.
`start_index`	rtype: `int`
`translation_y`
`translation_z`
`x_flipped`
`y_flipped`

get_axis_scale_types()#: Return axis display for the detector data to be used by silx view

get_expected_nx_tomo()[source]#: Return the expected number of nxtomo created for this acquisition. This is required to get consistent entry and file name. At lest for automation

get_pcotomo_version(url)[source]#: return the pcotomo version according to the provider version (aka bliss)

is_different_sequence(entry)#: Can we have several entries 1.1, 1.2, 1.3… to consider.

property known_machine_electric_current: dict | None#

Return the dict of all know machine electric current. Key is the time stamp, value is the electric current

Return type:: dict | None

property raise_error_if_issue#: Should we raise an error if we encounter or an issue or should we just log an error message

register_step(url, entry_type=None, copy_frames=False)#

Parameters:

url (DataUrl) – entry to be registered and contained in the acquisition
entry_type (AcquisitionStep | None) – type of the entry if know. Overwise will be ‘evaluated’

Return type:

None

property sample_x#: Return the ‘_sample_x’ attribute.

property sample_y#: Return the ‘_sample_y’ attribute.

to_NXtomos_pcotomo_v1(request_input, input_callback, check_tomo_n=True)[source]#

The first version of ‘to_NXtomos’ for the first way of storing pcotomo information. In this version we expect to have: * nb_loop: define the number of turn * nb_tomo: define the number of ‘sequence’ per turn. One sequence will generate one NXtomo

Return type:: tuple

to_NXtomos_pcotomo_v2(request_input, input_callback, check_tomo_n=True)[source]#

The second version of ‘to_NXtomos’ for the second way of storing pcotomo information. In this version we expect to have: * nb_turns: number of NXtomo to generate * proj_n: number of projections per NXtomo * scan_range: rotation angle scope

Return type:: tuple

write_as_nxtomo(shift_entry, input_file_path, request_input, divide_into_sub_files, input_callback=None)#

This function will dump the acquisition to disk as an NXtomo

Parameters:

shift_entry (int) – index of the entry to start saving new nxtomos.
input_file_path (str) – output file path
request_input (bool) – if True the conversion can ask user some missing metadata
divide_into_sub_files (bool) – if True then create one file per NXtomo
input_callback – function to call for users to provide missing metadata

Return type:

tuple