Acquisition

Conditions containing the parameters used for the acquisition of the data.

Constants

Raster modes

pyhmsa.spec.condition.acquisition.RASTER_MODE_STAGE

pyhmsa.spec.condition.acquisition.RASTER_MODE_BEAM

Z raster modes

pyhmsa.spec.condition.acquisition.RASTER_MODE_Z_FIB

Position locations

pyhmsa.spec.condition.acquisition.POSITION_LOCATION_START

pyhmsa.spec.condition.acquisition.POSITION_LOCATION_CENTER

pyhmsa.spec.condition.acquisition.POSITION_LOCATION_END

Classes

class pyhmsa.spec.condition.acquisition.AcquisitionPoint(position, dwell_time=None, total_time=None, dwell_time_live=None)

Defines the position and duration for a singular measurement of the specimen.

Parameters:

• position – physical location on (or in) the specimen (required)
• dwell_time – uniform real time taken for each individual measurement (optional)
• total_time – total real time taken to collect all measurements (optional)
• dwell_time_live – analogous detector live time for each individual measurement (optional)

CLASS = 'Point'

TEMPLATE = 'Acquisition'

dwell_time

uniform real time taken for each individual measurement

dwell_time_live

analogous detector live time for each individual measurement

get_dwell_time(instance)

get_dwell_time_live(instance)

get_position(instance)

get_total_time(instance)

position

physical location on (or in) the specimen

set_dwell_time(instance, value, unit=None)

set_dwell_time_live(instance, value, unit=None)

set_position(instance, value)

set_total_time(instance, value, unit=None)

total_time

total real time taken to collect all measurements

class pyhmsa.spec.condition.acquisition.AcquisitionMultipoint(positions=None, dwell_time=None, total_time=None, dwell_time_live=None)

Defines the position and duration of an irregular sequence of measurements of the specimen.

Parameters:

• positions – iterable of specimen positions (optional)
• dwell_time – uniform real time taken for each individual measurement (optional)
• total_time – total real time taken to collect all measurements (optional)
• dwell_time_live – analogous detector live time for each individual measurement (optional)

CLASS = 'Multipoint'

TEMPLATE = 'Acquisition'

dwell_time

uniform real time taken for each individual measurement

dwell_time_live

analogous detector live time for each individual measurement

get_dwell_time(instance)

get_dwell_time_live(instance)

get_positions(instance)

get_total_time(instance)

positions

specimen positions

set_dwell_time(instance, value, unit=None)

set_dwell_time_live(instance, value, unit=None)

set_total_time(instance, value, unit=None)

total_time

total real time taken to collect all measurements

class pyhmsa.spec.condition.acquisition.AcquisitionRasterLinescan(step_count, step_size=None, frame_count=None, position_start=None, position_end=None, raster_mode=None, dwell_time=None, total_time=None, dwell_time_live=None)

Defines the position and duration of a one-dimensional raster over the specimen. Applies only to a linear sequence of steps, using equal step sizes and dwell times for each measurement. For irregular step sizes, refer to AcquisitionMultiPoint

Parameters:

• step_count – number of steps (required)
• step_size – dimension of each step (optional)
• position_start – start position (optional)
• position_end – end position (optional)
• raster_mode – mode of rastering, RASTER_MODE_STAGE or RASTER_MODE_BEAM (optional)
• dwell_time – uniform real time taken for each individual measurement (optional)
• total_time – total real time taken to collect all measurements (optional)
• dwell_time_live – analogous detector live time for each individual measurement (optional)

CLASS = 'Raster/Linescan'

TEMPLATE = 'Acquisition'

dwell_time

uniform real time taken for each individual measurement

dwell_time_live

analogous detector live time for each individual measurement

frame_count

number of accumulated frames

get_dwell_time(instance)

get_dwell_time_live(instance)

get_frame_count(instance)

get_position_end()

Returns the end position.

Returns:end position Return type:SpecimenPosition

get_position_start()

Returns the start position.

Returns:start position Return type:SpecimenPosition

get_positions(instance)

get_raster_mode(instance)

get_step_count(instance)

get_step_size(instance)

get_total_time(instance)

position_end

End position

position_start

Start position

positions

defined physical location(s) of the raster

raster_mode

mode of rastering

set_dwell_time(instance, value, unit=None)

set_dwell_time_live(instance, value, unit=None)

set_frame_count(instance, value, unit=None)

set_position_end(value)

Sets the end position.

Parameters:value (SpecimenPosition) – end position

set_position_start(value)

Sets the start position.

Parameters:value (SpecimenPosition) – start position

set_raster_mode(instance, value)

set_step_count(instance, value, unit=None)

set_step_size(instance, value, unit=None)

set_total_time(instance, value, unit=None)

step_count

number of steps

step_size

dimension of each step

total_time

total real time taken to collect all measurements

class pyhmsa.spec.condition.acquisition.AcquisitionRasterXY(step_count_x, step_count_y, step_size_x=None, step_size_y=None, frame_count=None, position=None, raster_mode=None, dwell_time=None, total_time=None, dwell_time_live=None)

Defines the position and duration of a two-dimensional X/Y raster over the specimen.

Parameters:

• step_count_x – number of steps in x direction (required)
• step_count_y – number of steps in y direction (required)
• step_size_x – dimension of each step in x direction (optional)
• step_size_y – dimension of each step in y direction (optional)
• frame_count – number of accumulated frames (optional)
• position – specimen position (optional)
• raster_mode – mode of rastering, RASTER_MODE_STAGE or RASTER_MODE_BEAM (optional)
• dwell_time – uniform real time taken for each individual measurement (optional)
• total_time – total real time taken to collect all measurements (optional)
• dwell_time_live – analogous detector live time for each individual measurement (optional)

CLASS = 'Raster/XY'

TEMPLATE = 'Acquisition'

dwell_time

uniform real time taken for each individual measurement

dwell_time_live

analogous detector live time for each individual measurement

frame_count

number of accumulated frames

get_dwell_time(instance)

get_dwell_time_live(instance)

get_frame_count(instance)

get_position(include_location=False)

Returns the physical location on (or in) the specimen.

Returns:specimen position Return type:SpecimenPosition

get_positions(instance)

get_raster_mode(instance)

get_step_count_x(instance)

get_step_count_y(instance)

get_step_size_x(instance)

get_step_size_y(instance)

get_total_time(instance)

position

Physical location on (or in) the specimen

positions

defined physical location(s) of the raster

raster_mode

mode of rastering

set_dwell_time(instance, value, unit=None)

set_dwell_time_live(instance, value, unit=None)

set_frame_count(instance, value, unit=None)

set_position(value, loc=None)

Sets the physical location on (or in) the specimen.

Parameters:

• value (SpecimenPosition) – specimen position
• loc – location, either POSITION_LOCATION_START or POSITION_LOCATION_CENTER

set_raster_mode(instance, value)

set_step_count_x(instance, value, unit=None)

set_step_count_y(instance, value, unit=None)

set_step_size_x(instance, value, unit=None)

set_step_size_y(instance, value, unit=None)

set_total_time(instance, value, unit=None)

step_count_x

number of steps in x direction

step_count_y

number of steps in y direction

step_size_x

dimension of each step in x direction

step_size_y

dimension of each step in y direction

total_time

total real time taken to collect all measurements

class pyhmsa.spec.condition.acquisition.AcquisitionRasterXYZ(step_count_x, step_count_y, step_count_z, step_size_x=None, step_size_y=None, step_size_z=None, position=None, raster_mode_z=None, raster_mode=None, dwell_time=None, total_time=None, dwell_time_live=None)

Defines the position and duration of a three-dimensional X/Y/Z raster over the specimen.

Parameters:

• step_count_x – number of steps in x direction (required)
• step_count_y – number of steps in y direction (required)
• step_count_z – number of steps in z direction (required)
• step_size_x – dimension of each step in x direction (optional)
• step_size_y – dimension of each step in y direction (optional)
• step_size_z – dimension of each step in z direction (optional)
• position – specimen position (optional)
• raster_mode_z – mode of rastering in z direction, RASTER_MODE_Z_FIB (optional)
• raster_mode – mode of rastering, RASTER_MODE_STAGE or RASTER_MODE_BEAM (optional)
• dwell_time – uniform real time taken for each individual measurement (optional)
• total_time – total real time taken to collect all measurements (optional)
• dwell_time_live – analogous detector live time for each individual measurement (optional)

CLASS = 'Raster/XYZ'

TEMPLATE = 'Acquisition'

dwell_time

uniform real time taken for each individual measurement

dwell_time_live

analogous detector live time for each individual measurement

get_dwell_time(instance)

get_dwell_time_live(instance)

get_position(include_location=False)

Returns the physical location on (or in) the specimen.

Returns:specimen position Return type:SpecimenPosition

get_positions(instance)

get_raster_mode(instance)

get_raster_mode_z(instance)

get_step_count_x(instance)

get_step_count_y(instance)

get_step_count_z(instance)

get_step_size_x(instance)

get_step_size_y(instance)

get_step_size_z(instance)

get_total_time(instance)

position

Physical location on (or in) the specimen

positions

defined physical location(s) of the raster

raster_mode

mode of rastering

raster_mode_z

mode of rastering in z direction

set_dwell_time(instance, value, unit=None)

set_dwell_time_live(instance, value, unit=None)

set_position(value, loc=None)

Sets the physical location on (or in) the specimen.

Parameters:

• value (SpecimenPosition) – specimen position
• loc – location, either POSITION_LOCATION_START or POSITION_LOCATION_CENTER

set_raster_mode(instance, value)

set_raster_mode_z(instance, value)

set_step_count_x(instance, value, unit=None)

set_step_count_y(instance, value, unit=None)

set_step_count_z(instance, value, unit=None)

set_step_size_x(instance, value, unit=None)

set_step_size_y(instance, value, unit=None)

set_step_size_z(instance, value, unit=None)

set_total_time(instance, value, unit=None)

step_count_x

number of steps in x direction

step_count_y

number of steps in y direction

step_count_z

number of steps in z direction

step_size_x

dimension of each step in x direction

step_size_y

dimension of each step in y direction

step_size_z

dimension of each step in z direction

total_time

total real time taken to collect all measurements