dxfile

Subclasses the h5py module for interacting with Data Exchange files.

Functions:

File
Entry(**kwargs)	Interact with Data Exchange files.

dxfile.dxtomo.File

class dxfile.dxtomo.Entry(**kwargs)

Bases: object

Interact with Data Exchange files.

_entry_definitions(self)

Contains the archetypes for Data Exchange file entries.

_generate_classes(self)

This method is used to turn the Entry._entry_definitions into generate_classes which can be instantitated for hold data.

class acquisition(**kwargs)

Bases: object

docstring = 'Tomography specific tag to store dynamic (per image) parameters.'

end_date = {'units': 'text', 'docstring': 'Date and time measurement ends.', 'value': None}

entry_name = 'acquisition'

image_date = {'units': 'time', 'docstring': 'Vector containing the date/time each image was acquired in iso 8601.', 'value': None}

image_exposure_time = {'units': None, 'docstring': 'Vector containin for each image the the measured exposure time in 1e-7 seconds (0.1us)', 'value': None}

image_is_complete = {'units': None, 'docstring': 'Vector containin for each image the boolen status of: is any pixel data missing?', 'value': None}

image_number = {'units': None, 'docstring': 'Vector containin for each image the the image serial number as assigned by the camera. Unique for each individual scan. Always starts at 0.', 'value': None}

image_theta = {'units': 'degree', 'docstring': 'Vector containing the rotary stage angular position read from the encoder at each image.', 'value': None}

image_type = {'units': None, 'docstring': 'Vector containin for each image contained in /exchange/data 0 for white, 1 for projection and 2 for dark', 'value': None}

root = '/process'

sample_image_shift_x = {'units': 'pixels', 'docstring': 'Vector containing the shift of the sample axis x at each projection on the detector plane.', 'value': None}

sample_image_shift_y = {'units': 'pixels', 'docstring': 'Vector containing the shift of the sample axis y at each projection on the detector plane.', 'value': None}

sample_position_x = {'units': 'mm', 'docstring': 'Vector containing the position of the sample axis x at each projection image collection.', 'value': None}

sample_position_y = {'units': 'mm', 'docstring': 'Vector containing the position of the sample axis y at each projection image collection.', 'value': None}

sample_position_z = {'units': 'mm', 'docstring': 'Vector containing the position of the sample axis z at each projection image collection.', 'value': None}

scan_date = {'units': None, 'docstring': 'Vector containing for each image the wall date/time at start of scan in iso 8601.', 'value': None}

scan_index = {'units': None, 'docstring': 'Vector containin for each image the identifier assigned by beamline controls to each individual series of images or scan.', 'value': None}

shutter = {'units': None, 'docstring': 'Vector containin for each image the beamline shutter status: 0 for closed, 1 for open', 'value': None}

start_date = {'units': 'text', 'docstring': 'Date and time measurement starts.', 'value': None}

time_stamp = {'units': None, 'docstring': 'Vector containin for each image the relative time since scan_date in 1e-7 seconds.', 'value': None}

acquisition_setup

alias of setup

class attenuator(**kwargs)

Bases: object

description = {'units': 'text', 'docstring': 'Description or composition of attenuator.', 'value': None}

docstring = 'X-ray beam attenuator.'

entry_name = 'attenuator'

name = {'units': 'text', 'docstring': 'Name of the attenuator.', 'value': None}

root = '/measurement/instrument'

thickness = {'units': 'm', 'docstring': 'Thickness of attenuator along beam direction.', 'value': None}

transmission = {'units': 'None', 'docstring': 'The nominal amount of the beam that gets through (transmitted intensity)/(incident intensity)', 'value': None}

data

class detector(**kwargs)

Bases: object

actual_pixel_size_x = {'units': 'm', 'docstring': 'Pixel size on the sample plane (m).', 'value': None}

actual_pixel_size_y = {'units': 'm', 'docstring': 'Pixel size on the sample plane (m).', 'value': None}

basis_vectors = {'units': 'fps', 'docstring': 'A matrix with the basis vectors of the detector data.', 'value': None}

binning_x = {'units': 'pixels', 'docstring': 'If the data are collected binning the detector x binning and y binning store the binning factor.', 'value': None}

binning_y = {'units': 'dimensionless', 'docstring': 'If the data are collected binning the detector x binning and y binning store the binning factor.', 'value': None}

bit_depth = {'units': 'dimensionless', 'docstring': 'The detector ADC bit depth.', 'value': None}

corner_position = {'units': 'fps', 'docstring': 'The x, y and z coordinates of the corner of the first data element.', 'value': None}

counts_per_joule = {'units': 'counts', 'docstring': 'Number of counts recorded per each joule of energy received by the detector', 'value': None}

delay_time = {'units': 's', 'docstring': 'Detector delay time (s). This is used in combination with a mechanical shutter.', 'value': None}

description = {'units': 'text', 'docstring': 'Description of the detector', 'value': None}

dimension_x = {'units': 'pixels', 'docstring': 'The detector horiz. dimension.', 'value': None}

dimension_y = {'units': 'text', 'docstring': 'The detector vertical dimension.', 'value': None}

docstring = 'X-ray detector.'

entry_name = 'detector'

exposure_time = {'units': 's', 'docstring': 'The set detector exposure time (s).', 'value': None}

firmware_version = {'units': 'text', 'docstring': 'The detector firmware version.', 'value': None}

frame_rate = {'units': 'fps', 'docstring': 'The detector frame rate (fps).', 'value': None}

manufacturer = {'units': 'text', 'docstring': 'The detector manufacturer.', 'value': None}

model = {'units': 'text', 'docstring': 'The detector model', 'value': None}

name = {'units': 'text', 'docstring': 'Name of the detector.', 'value': None}

operating_temperature = {'units': 'dimensionless', 'docstring': 'The detector operating temperature (K).', 'value': None}

output_data = {'units': 'text', 'docstring': 'String HDF5 path to the exchange group where the detector output data is located.', 'value': None}

pixel_size_x = {'units': 'm', 'docstring': 'Physical detector pixel size (m).', 'value': None}

pixel_size_y = {'units': 'm', 'docstring': 'Physical detector pixel size (m).', 'value': None}

root = '/measurement/instrument'

serial_number = {'units': 'text', 'docstring': 'The detector serial number.', 'value': None}

shutter_mode = {'units': 'text', 'docstring': 'The detector shutter mode: global, rolling etc.', 'value': None}

software_version = {'units': 'text', 'docstring': 'The detector software version.', 'value': None}

stabilization_time = {'units': 's', 'docstring': 'Detector delay time (s). This is used during stop and go data collection to allow the sample to stabilize.', 'value': None}

exchange

class experiment(**kwargs)

Bases: object

activity = {'units': 'text', 'docstring': 'Proposal scheduler id. For the APS this is the beamline scheduler activity id.', 'value': None}

docstring = 'This provides references to facility ids for the proposal, scheduled activity, and safety form.'

entry_name = 'experiment'

proposal = {'units': 'text', 'docstring': 'Proposal reference number. For the APS this is the General User Proposal number.', 'value': None}

root = '/measurement/sample'

safety = {'units': 'text', 'docstring': 'Safety reference document. For the APS this is the Experiment Safety Approval Form number.', 'value': None}

title = {'units': 'text', 'docstring': 'Experiment title. For the APS this is the proposal title assigned by the user.', 'value': None}

class experimenter(**kwargs)

Bases: object

address = {'units': 'text', 'docstring': 'User address.', 'value': None}

affiliation = {'units': 'text', 'docstring': 'User affiliation.', 'value': None}

docstring = 'Description of a single experimenter.'

email = {'units': 'text', 'docstring': 'User email address.', 'value': None}

entry_name = 'experimenter'

facility_user_id = {'units': 'text', 'docstring': 'User badge number.', 'value': None}

name = {'units': 'text', 'docstring': 'User name.', 'value': None}

phone = {'units': 'text', 'docstring': 'User phone number.', 'value': None}

role = {'units': 'text', 'docstring': 'User role.', 'value': None}

root = '/measurement/sample'

class instrument(**kwargs)

Bases: object

comment = {'units': 'text', 'docstring': 'comment', 'value': None}

docstring = 'All relevant beamline components status at the beginning of a measurement'

entry_name = 'instrument'

name = {'units': 'text', 'docstring': 'Name of the instrument.', 'value': None}

root = '/measurement'

class interferometer(**kwargs)

Bases: object

description = {'units': 'text', 'docstring': 'Description of the interferometer.', 'value': None}

docstring = 'interferometer name'

entry_name = 'interferometer'

name = {'units': 'text', 'docstring': 'Descriptive name of the interferometer.', 'value': None}

root = '/measurement/instrument/'

interferometer_setup

alias of setup

class mirror(**kwargs)

Bases: object

angle = {'units': 'rad', 'docstring': 'Mirror incident angle', 'value': None}

description = {'units': 'text', 'docstring': 'Description of the mirror', 'value': None}

docstring = 'X-ray beam mirror.'

entry_name = 'mirror'

name = {'units': 'text', 'docstring': 'Name of the mirror.', 'value': None}

root = '/measurement/instrument'

class monochromator(**kwargs)

Bases: object

description = {'units': 'text', 'docstring': 'Description of the monochromator', 'value': None}

docstring = 'X-ray beam monochromator.'

energy = {'units': 'J', 'docstring': 'Peak of the spectrum that the monochromator selects. When units is not defined this field is in J', 'value': None}

energy_error = {'units': 'J', 'docstring': 'Standard deviation of the spectrum that the monochromator selects. When units is not defined this field is in J.', 'value': None}

entry_name = 'monochromator'

mono_stripe = {'units': 'text', 'docstring': 'Type of multilayer coating or crystal.', 'value': None}

name = {'units': 'text', 'docstring': 'Name of the monochromator.', 'value': None}

root = '/measurement/instrument'

class objective(**kwargs)

Bases: object

description = {'units': 'text', 'docstring': 'Lens description', 'value': None}

docstring = 'microscope objective lenses used.'

entry_name = 'objective'

magnification = {'units': 'dimensionless', 'docstring': 'Lens specified magnification', 'value': None}

manufacturer = {'units': 'text', 'docstring': 'Lens manufacturer', 'value': None}

model = {'units': 'text', 'docstring': 'Lens model.', 'value': None}

name = {'units': 'text', 'docstring': 'Lens name', 'value': None}

numerical_aperture = {'units': 'dimensionless', 'docstring': 'The numerical aperture (N.A.) is a measure of the light-gathering characteristics of the lens.', 'value': None}

root = '/measurement/instrument/detection_system'

process

class roi(**kwargs)

Bases: object

description = {'units': 'text', 'docstring': 'ROI description', 'value': None}

docstring = 'region of interest (ROI) of the image actually collected, if smaller than the full CCD.'

entry_name = 'roi'

min_x = {'units': 'pixels', 'docstring': 'Top left x pixel position', 'value': None}

min_y = {'units': 'pixels', 'docstring': 'Top left y pixel position', 'value': None}

name = {'units': 'text', 'docstring': 'ROI name', 'value': None}

root = '/measurement/instrument/detector'

size_x = {'units': 'pixels', 'docstring': 'Horizontal image size', 'value': None}

size_y = {'units': 'pixels', 'docstring': 'Vertical image size', 'value': None}

class sample(**kwargs)

Bases: object

chemical_formula = {'units': 'text', 'docstring': 'Sample chemical formula using the CIF format.', 'value': None}

comment = {'units': 'text', 'docstring': 'comment', 'value': None}

concentration = {'units': 'kgm^-3', 'docstring': 'Mass/volume.', 'value': None}

description = {'units': 'text', 'docstring': 'Description of the sample.', 'value': None}

docstring = 'The sample measured.'

entry_name = 'sample'

environment = {'units': 'text', 'docstring': 'Sample environment.', 'value': None}

fatigue_cycle = {'units': None, 'docstring': 'Sample fatigue cycles.', 'value': None}

mass = {'units': 'kg', 'docstring': 'Mass of the sample.', 'value': None}

name = {'units': 'text', 'docstring': 'Descriptive name of the sample.', 'value': None}

preparation_date = {'units': 'text', 'docstring': 'Date and time the sample was prepared.', 'value': None}

pressure = {'units': 'kPa', 'docstring': 'Sample pressure.', 'value': None}

root = '/measurement'

temperature = {'units': 'kelvin', 'docstring': 'Sample temperature.', 'value': None}

temperature_set = {'units': 'kelvin', 'docstring': 'Sample temperature set point.', 'value': None}

thickness = {'units': 'm', 'docstring': 'Sample thickness.', 'value': None}

tray = {'units': 'text', 'docstring': 'Sample position in the sample changer/robot.', 'value': None}

sample_stack

alias of sample

sample_stack_setup

alias of setup

class scintillator(**kwargs)

Bases: object

description = {'units': 'text', 'docstring': 'Scintillator description', 'value': None}

docstring = 'scintillator used.'

entry_name = 'scintillator'

manufacturer = {'units': 'text', 'docstring': 'Scintillator Manufacturer.', 'value': None}

name = {'units': 'text', 'docstring': 'Scintillator name', 'value': None}

root = '/measurement/instrument/detection_system'

scintillating_thickness = {'units': 'm', 'docstring': 'Scintillator thickness.', 'value': None}

serial_number = {'units': 'text', 'docstring': 'Scintillator serial number.', 'value': None}

substrate_thickness = {'units': 'm', 'docstring': 'Scintillator substrate thickness.', 'value': None}

class source(**kwargs)

Bases: object

beam_intensity_incident = {'units': 'phs^-1', 'docstring': 'Incident beam intensity in (photons per s).', 'value': None}

beam_intensity_transmitted = {'units': 'phs^-1', 'docstring': 'Transmitted beam intensity (photons per s).', 'value': None}

beamline = {'units': 'text', 'docstring': 'Name of the beamline.', 'value': None}

current = {'units': 'A', 'docstring': 'Electron beam current (A).', 'value': None}

datetime = {'units': 'text', 'docstring': 'Date and time source was measured.', 'value': None}

docstring = 'The light source being used'

energy = {'units': 'J', 'docstring': 'Characteristic photon energy of the source (J). For an APS bending magnet this is 30 keV or 4.807e-15 J.', 'value': None}

entry_name = 'source'

mode = {'units': 'text', 'docstring': 'top-up', 'value': None}

name = {'units': 'text', 'docstring': 'Name of the facility.', 'value': None}

pulse_energy = {'units': 'J', 'docstring': 'Sum of the energy of all the photons in the pulse (J).', 'value': None}

pulse_width = {'units': 's', 'docstring': 'Duration of the pulse (s).', 'value': None}

root = '/measurement/instrument'