X-ray Tomography

This section describes extensions and additions to the core Data Exchange format for X-ray Tomography. We begin with the extensions to the exchange and instrument groups, and then describe the possible tomography data collection schemes and corresponding data structures.

Top level (root)

This node represents the top level of the HDF5 file and holds some general information about the file.

Member Type Example
implements string dataset exchange:measurement:process
exchange group  
measurement group  
process group  
implements

A colon separated list that shows which components are present in the file. The only mandatory component is exchange. A more general Data Exchange file also contains measurement and process information, if so these will be declared in implements as exchange:measurement:process
exchange or exchange_N

The data taken from measurements or processing. Dimension descriptors within the group may also serve to describe “positioner” values involved in a scan.
measurement or measurement_N

Description of the sample and instrument as configured for the measurement. This group is appropriate for relatively static metadata. For measurements where there are many “positioner” values (aka a “scan”), it is more sensible to add dimension(s) to the exchange dataset, and describe the “positioner” values as dimension scales rather than record the data via multiple matching measurement and exchange groups. This is a judgement left to the user.
process

The Process group describes all the “work” that has been done. This includes data processing steps that have been applied to the data as well as experimental steps (e.g. data collection strategy etc.) and sample preparation ahead of the experiment and during the measurement (e.g. environment conditions etc.).

exchange

In X-ray tomography, the 3D arrays representing the most basic version of the data include projections, dark, and white fields. It is mandatory that there is at least one dataset named data in each exchange group. Most data analysis and plotting programs will primarily focus in this group.

Member Type Example/Attributes
name string dataset “absorption_tomography”
description string dataset “raw absorption tomo”
data 3D dataset axes: theta:y:x
theta 1D dataset units: “deg”
data_dark 3D dataset axes: theta_dark:y:x
theta_dark 1D dataset units: “deg”
data_white 3D dataset axes: theta_white:y:x
theta_white 1D dataset units: “deg”
data_shift_x relative x shift of data at each angular position  
data_shift_y relative y shift of data at each angular position  

Table: Exchange Group Members for Tomography

name

Descriptive name for data dataset. Current types include: absorption_tomography, phase_tomography, dpc_tomography
description

Description.
data

A tomographic data set consists of a series of projections (data), dark field (data_dark), and white field (data_white) images. The dark and white fields must have the same projection image dimensions and can be collected at any time before, after or during the projection data collection. The angular position of the tomographic rotation axis, theta, can be used to keep track of when the dark and white images are collected. These datasets are saved in 3D arrays using, by default, the natural HDF5 order of a multidimensional array (rotation axis, ccd y, ccd x), i.e. with the fastest changing dimension being the last dimension, and the slowest changing dimension being the first dimension. If using the default dimension order, the axes attribute theta:y:x can be omitted. The attribute is mandatory if the 3D arrays use a different axes order. This could be the case when, for example, the arrays are optimized for sinogram read ( = y:theta:x). As no units are specified the data is assumed to be in counts with the axes (x, y) in pixels.
data_dark, data_white

The dark field and white fields must have the same dimensions as the projection images and can be collected at any time before, during, or after the projection data collection. To specify where dark and white images were taken, specify the axes attribute with “theta_dark:y:x” and “theta_white:y:x” and provide theta_dark and theta_white vector datasets that specify the rotation angles where they were collected.
theta, theta dark, theta_white

Theta is a vector dataset storing the projection angular positions. If theta is not defined the projections are assumed to be collected at equally spaced angular interval between 0 and 180 degree. The dark field and white fields can be collected at any time before, during, or after the projection data. theta_dark, and theta_white store the position of the tomographic rotation axis when the corresponding dark and white images are collected. If theta_dark and theta_white are missing the corresponding data_dark and data_white are assumed to be collected all at the beginning or at the end of the projection data collection.
data_shift_x, data_shift_y

Data_shift_x and data_shift_y are the vectors storing at each projection angular positions the image relative shift in x and y. These vectors are used in high resolution CT when at each angular position the sample x and y are moved to keep the sample in the field of view based on a pre-calibration of rotary stage runout. If the unit is not defined are assumed to be in pixels.

Attribute

Description and units can be added as attribute to any data, both array or values, inside a data exchange file. If units is omitted default is SI.

Member Type Example
description string attribute “transmission”
units string attribute counts

Table: data attributes

measurement

This group holds sample and instrument information. These groups are designed to hold relatively static data about the sample and instrument configuration at the time of the measurement. Rapidly changing positioner values (aka scan) are better represented in the exchange group dataset.

Member Type Example
instrument group  
sample group  

Table: Measurement Group Members

instrument

The instrument used to collect this data.
sample

The sample measured.

instrument

The instrument group stores all relevant beamline components status at the beginning of a measurement. While all these fields are optional, if you do intend to include them they should appear within this parentage of groups.

Member Type Example
name string dataset “XSD/32-ID/TXM”
description string dataset “X-ray Microscope”
attenuator group  
beam_monitor group  
beam_stop group  
bertrand_lens group  
condenser group  
crl group  
detection_system group  
detector group  
diffuser group  
flight_tube group  
interferometer group  
mirror group  
monochromator group  
pin_hole group  
samplee group  
shutter group  
source group  
slits group  
table group  
zone_plate group  
setup group  

Table: Instrument Group for Tomography

name

Name of the instrument.
source

The source used by the instrument.
shutter

The shutter(s) used by the instrument.
attenuator

The attenuators that are part of the instrument.
monochromator

The monochromator used by the instrument.
detector

The detectors that compose the instrument.

attenuator

This class describes the beamline attenuator(s) used during data collection. If more than one attenuators are used they will be named as attenuator_1, attenuator_2 etc.

Member Type Example
name string dataset “Filter Set 1”
description string dataset “Al”
thickness float dataset 1e-3
transmission float dataset unit-less
geometry group  
setup group  

Table: Attenuator Group Members

name

Name.
description

Description.
thickness

Thickness of attenuator along beam direction.
attenuator_transmission

The nominal amount of the beam that gets through (transmitted
intensity)/(incident intensity).
description

Type or composition of attenuator.

beam_monitor

Class describing the beam monitor being used, if there is more than one append _##

Member Type Example
name string dataset “Beam Monitor”
description string dataset “optional”
geometry group  
setup group  

Table: Beam Monitor Group Members

beam_stop

Class describing the beam stop being used, if there is more than one append _##

Member Type Example
name string dataset “Beam Stop”
description string dataset “optional”
geometry group  
setup group  

Table: Beam Stop Group Members

bertrand_lens

Class describing the Bertrand lens being used, if there is more than one append _##

Member Type Example
name string dataset “Bertrand Lens”
description string dataset “optional”
geometry group  
setup group  

Table: Bertrand Lens Group Members

condenser

Class describing the condenser being used, if there is more than one append _##

Member Type Example
name string dataset “Condenser”
description string dataset “optional”
geometry group  
setup group  

Table: Condenser Group Members

crl

Class describing the compound refractive lenses being used, if there is more than one append _##

Member Type Example
name string dataset “CRL”
description string dataset “optional”
geometry group  
setup group  

Table: CRL Group Members

detection_system

In full field imaging the detector consists of microscope objective and a scintillator screen.

Member Type Example
name string dataset “Detection 1”
description string dataset “Standard microCT”
objective group  
scintillator group  

Table: Detection System Group Members

name

Name.
description

Description.
objective_N

List of the visible light objectives mounted between the detector and the scintillator screen.
scintillator

Scintillator screen

detector

This class holds information about the detector used during the experiment. If more than one detector are used they will be all listed as detector_N. In full field imaging the detector consists of a CCD camera, microscope objective and a scintillator screen. Raw data recorded by a detector as well as its position and geometry should be stored in this class.

Member Type Example
name string dataset “DIMAX 1”
description string dataset “description”
manufacturer string dataset “CooKe Corporation”
model string dataset “pco dimax”
serial_number string dataset “1234XW2”
firmware_version string dataset “3.7.9”
software_version string dataset “1.3.14”
bit_depth integer 12
pixel_size_x float 6.7e-6
pixel_size_y float 6.7e-6
actual_pixel_size_x float 1.2e-6
actual_pixel_size_y float 1.2e-6
dimension_x integer 2048
dimension_y integer 2048
binning_x integer 1
binning_y integer 1
operating_temperature float 270
exposure_time float 1.7e-3
delay_time float 1.7e-3
stabilization_time float 1.7e-3
frame_rate integer 2
output_data string dataset “/exchange”
roi group  
counts_per_joule float unitless
basis_vectors float array length
corner_position 3 floats length
geometry group  
setup group  

Table: Detector Group Members for Tomography

name

Name.
description

Description.
manufacturer

The detector manufacturer.
model

The detector model.
serial_number

The detector serial number .
bit_depth

The detector bit depth.
pixel_size_x, pixel_size_y

Physical detector pixel size (m).
dimension_x, dimension_y

The detector horiz./vertical dimension.
actual_pixel_size_x, actual_pixel_size_y

Actual pixel size on the sample plane.
binning_x, binning_y

If the data are collected binning the detector binning_x and binning_y store the binning factor.
operating_temperature

The detector operating temperature (K).
exposure_time

The detector exposure time (s).
delay_time

Delay time between projections when using a mechanical shutter to reduce radiation damage of the sample (s).
stabilization_time

Time required by the sample to stabilize (s).
frame_rate

The detector frame rate (fps). This parameter is set for fly scan.
roi

The detector selected Region Of Interest (ROI).
counts_per_joule

Number of counts recorded per each joule of energy received by the detector. The number of incident photons can then be calculated by:
basis_vectors

A matrix with the basis vectors of the detector data.
corner_position

The x, y and z coordinates of the corner of the first data element.
geometry

Position and orientation of the center of mass of the detector. This should only be specified for non pixel detectors. For pixel detectors use basis_vectors and corner_position.

diffuser

Class describing the diffuser being used, if there is more than one append _##

Member Type Example
name string dataset “Diffuser”
description string dataset “optional”
geometry group  
setup group  

Table: Diffuser Group Members

flight_tube

Class describing the flight tube being used, if there is more than one append _##

Member Type Example
name string dataset “Flight Tube”
description string dataset “optional”
geometry group  
setup group  

Table: Flight Tube Group Members

interferometer

This group stores the interferometer parameters.

Member Type Example
name string dataset “Inter 1”
description string dataset “description”
grid_start float 1.8
grid_end float 3.51
number_of_grid_periods int 1
number_of_grid_steps int 6
geometry group  
setup group  

Table: Interferometer Group Members

name

Name.
description

Description.
start_angle

Interferometer start angle.
grid_start

Interferometer grid start angle.
grid_end

Interferometer grid end angle.
grid_position_for_scan

Interferometer grid position for scan.
number_of_grid_steps

Number of grid steps.

mirror

Class describing the mirror being used, if there is more than one append _##

Member Type Example
name string dataset “M1”
description string dataset “optional”
angle float “optional”
geometry group  
setup group  

Table: Mirror Group Members

monochromator

Define the monochromator used in the instrument.

Member Type Example
name string dataset “Mono 1”
description string dataset “Multilayer”
energy float dataset 1.602e-15
energy_error float dataset 1.602e-17
mono_stripe string dataset “Ru/C”
geometry group  
setup group  

Table: Monochromator Group Members

name

Name.
description

Description.
energy

Peak of the spectrum that the monochromator selects. Since units
is not defined this field is in J and corresponds to 10 keV.
energy_error

Standard deviation of the spectrum that the monochromator selects.
Since units is not defined this field is in J.
mono_stripe

Type of multilayer coating or crystal.

pin_hole

Class describing the pin hole being used, if there is more than one append _##

Member Type Example
name string dataset “Pin Hole”
description string dataset “optional”
geometry group  
setup group  

Table: Pin Hole Group Members

shutter

Class describing the shutter being used.

Member Type Example
name string dataset “Front End Shutter 1”
description string dataset “optional”
status string dataset “OPEN”
geometry group  
setup group  

Table: Shutter Group Members

name

Name.
description

Description.
status

“OPEN” or “CLOSED”

sample

Class describing the sample stage stack being used.

Member Type Example
name string dataset “TXM sample stack”
description string dataset “optional”
detector_distance string dataset “optional”
geometry group  
setup group  

Table: Sample stage stack Group Members

source

Class describing the light source being used.

Member Type Example
name string dataset “APS”
description float dataset “optional”
datetime string dataset (ISO 8601) “2011-07-15T15:10Z”
beamline string dataset “2-BM”
current float dataset 0.094
energy float dataset 4.807e-15
pulse_energy float dataset 1.602e-15
pulse_width float dataset 15e-11
mode string dataset “TOPUP”
beam_intensity_incident float dataset 55.93
beam_intensity_transmitted float dataset 100.0
geometry group  
setup group  

Table: Source

name

Name.
description

Description.
datetime

Date and time source was measured.
beamline

Name of the beamline.
current

Electron beam current (A).
energy

Characteristic photon energy of the source (J). For an APS bending
magnet this is 30 keV or 4.807e-15 J.
pulse_energy

Sum of the energy of all the photons in the pulse (J). pulse_width
Duration of the pulse (s).
mode

Beam mode: TOP-UP.
beam_intensity_incident

Incident beam intensity in (photons per s).
beam_intensity_transmitted

Transmitted beam intensity (photons per s).

slists

Class describing the slits being used.

Member Type Example
name string dataset “A slits”
description string dataset “Horizontal Slits”
geometry group  
setup group  

Table: Slits Group Members

name

Name.
description

Description.

table

Class describing the zone plate being used, if there is more than one append _##

Member Type Example
name string dataset “Optical Table”
description string dataset “optional”
geometry group  
setup group  

Table: Optical Table Group Members

zone_plate

Class describing the zone plate being used, if there is more than one append _##

Member Type Example
name string dataset “Zone Plate”
description string dataset “optional”
geometry group  
setup group  

Table: Zone Plate Group Members

roi

Group describing the region of interest (ROI) of the image actually collected, if smaller than the full CCD.

Member Type Example
name string dataset “ROI 04”
description string dataset “center third”
min_x integer 256
size_x integer 256
min_y integer 1792
size_y integer 1792

Table: ROI Group Members

name

Name.
description

Description.
min_x, min_y

Top Left pixel x and y position.
size_x, size_y

x and y image size.
objective

Group describing the microscope objective lenses used.

Member Type Example
name string dataset “Lens 01”
description string dataset “ZeissAx”
manufacturer string dataset “Zeiss”
model string dataset “Axioplan”
magnification float dataset 5
numerical_aperture float dataset 0.8
geometry group  
setup group  

Table: Objective Group Members

name

Name.
description

Description.
manufacturer

Lens manufacturer.
model

Lens model.
magnification

Lens specified magnification.
numerical_aperture

The numerical aperture (N.A.) is a measure of the light-gathering characteristics of the lens.
scintillator

Group describing the visible light scintillator coupled to the CCD camera objective lens.

Member Type Example
name string dataset “Yag polished”
description string dataset “Yag on Yag”
manufacturer string dataset “Crytur”
serial_number string dataset “12”
scintillating_thickness float dataset 5e-6
substrate_thickness float dataset 1e-4
geometry group  
setup group  

Table: Scintillator Group Members

name

Scintillator name.
description

Scintillator description.
manufacturer

Scintillator Manufacturer.
serial_number

Scintillator serial number.
scintillating_thickness

Scintillator thickness.
substrate_thickness

Scintillator substrate thickness.

setup

Logging instrument and beamline component setup parameters (static setup values) is not defined by Data Exchange because is specific and different for each instrument and beamline. To capture this information Data Exchange requires to set a setup group under each beamline component and leaves each facility free to store what is relevant for each component (list of motor positions etc.). Ideally each component in the instrument list (source, shutter, attenuator etc.) should have included its setup group. For setup values not associated with a specific beamline component a setup group in the instrument group should be created.

Member Type Example
motor_x float -10.107
motor_y float -17.900
motor_z float -5.950
motor_xx float -1.559
motor_zz float 1.307

sample

This group holds basic information about the sample, its geometry, properties, the sample owner (user) and sample proposal information. While all these fields are optional, if you do intend to include them they should appear within this parentage of groups.

Member Type Example
name string dataset “cells sample 1”
description string dataset “malaria cells”
file_path string dataset “/2016-03/tst/”
preparation_date string dataset (ISO 8601) “2012-07-31T21:15:22+0600”
chemical_formula string dataset (abbr. CIF format) “(Cd 2+)3, 2(H2 O)”
mass float dataset 0.25
concentration float dataset 0.4
environment string dataset “air”
temperature float dataset 25.4
temperature_set float dataset 26.0
pressure float dataset 101325
thickness float dataset 0.001
position string dataset “2D” APS robot coord.
geometry group  
experiment group  
experimenter group  

Table: Sample Group Members

name

Descriptive name of the sample.
file_path

Directory path where the data were originally saved.
description

Description of the sample.
preparation_date

Date and time the sample was prepared.
chemical_formula

Sample chemical formula using the CIF format.
mass

Mass of the sample.
concentration

Mass/volume.
environment

Sample environment.
temperature

Sample temperature.
temperature_set

Sample temperature set point.
pressure

Sample pressure.
thickness

Sample thickness.
position

Sample position in the sample changer/robot.
geometry

Sample center of mass position and orientation.
experiment

Facility experiment identifiers.
experimenter

Experimenter identifiers.

experiment

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

Member Type Example
proposal string dataset “1234”
activity string dataset “9876”
safety string dataset “9876”
title string dataset “Al 4D dynamic tomo”

Table: Experiment Group Members

proposal

Proposal reference number. For the APS this is the General User
Proposal number.
activity

Proposal scheduler id. For the APS this is the beamline scheduler activity id.
safety

Safety reference document. For the APS this is the Experiment
Safety Approval Form number.
title

Proposal title.

experimenter

Description of a single experimenter. Multiple experimenters can be represented through numbered entries such as experimenter_1, experimenter_2.

Member Type Example
name string dataset “John Doe”
role string dataset “Project PI”
affiliation string dataset “University of California, Berkeley”
address string dataset “EPS UC Berkeley CA 94720 4767 USA”
phone string dataset “+1 123 456 0000”
email string dataset johndoe@berkeley.edu
facility_user_id string dataset “a123456”

Table: Experimenter Group Members

name: User name.

role: User role.

affiliation: User affiliation.

address: User address.

phoen: User phone number.

email: User e-mail address

facility_user_id: User badge number

geometry

The geometry group is common to many of the subgroups under measurement. The intent is to describe the translation and rotation (orientation) of the sample or instrument component relative to some coordinate system. Since we believe it is not possible to determine all possible uses at this time, we leave the precise definition of geometry up to the technique. We do encourage the use of separate translation and orientation subgroups within geometry. As such, we do not describe geometry further here. This class holds the general position and orientation of a component.

Member Type Example
translation group  
orientation group  
translation

The position of the object with respect to the origin of your coordinate system.
orientation

The rotation of the object with respect to your coordinate system.
translation

This is the description for the general spatial location of a component for tomography.

Member Type Example
distances 3 float array dataset (0, 0.001, 0)
distances

The x, y and z components of the translation of the origin of the object
relative to the origin of the global coordinate system (the place where
the X-ray beam meets the sample when the sample is first aligned in the beam).
If distances does not have the attribute units set then the units are in
meters.
orientation

This is the description for the orientation of a component for tomography.

Member Type Example
value 6 float array dataset  
value

Dot products between the local and the global unit vectors. Unitless

The orientation information is stored as direction cosines. The direction cosines will be between the local coordinate directions and the global coordinate directions. The unit vectors in both the local and global coordinates are right-handed and orthonormal.

Calling the local unit vectors (x’, y’,z’) and the reference unit vectors (x, y, z) the six numbers will be

\[[x \cdot x, x' \cdot y, x' \cdot z, y' \cdot x, y' \cdot y, y' \cdot z]\]

where

\[`\cdot`\]

is the scalar dot product (cosine of the angle between the unit vectors).

Notice that this corresponds to the first two rows of the rotation matrix that transforms from the global orientation to the local orientation. The third row can be recovered by using the fact that the basis vectors are orthonormal.

process

Process is the documentation of the data collection strategy (acquisition) steps, all transformations, analyses and interpretations of data performed by a sequence of process functions (actor) as well as any sample preparation step done ahead of the experiment and during the measurement (e.g. environment conditions etc.).

Maintaining this history, also called provenance, allows for reproducible data. The Data Exchange format tracks process by allowing each actor to append process information to a process table.

The process table tracks provenance in the execution order as a series of processing steps by appending sequential actor entries in the process table.

Member Type Example
name string dataset “name”
description string dataset “optional”
acquisition group  
tomo_rec group  
transfer group  
table group  

Table: Process Group Members

name

Descriptive process task.
description

Description of the process task.

acquisition

Logging acquisition parameters (static setup and per-image values) is not defined by Data Exchange because is specific and different for each instrument and beamline. In the table below we present the implementation adopted by the Swiss Light Source and Advanced Photon Source.

Member Type Example
name string dataset “mosaic”
description string dataset “step scan”
output_data string dataset “/exchange”
version string dataset https://github.com/data_collection_scripts/b9ad87e17
sample_position_x 1D array Position of the sample axis x for each image collected
sample_position_y 1D array Position of the sample axis y for each image collected
sample_position_z 1D array Position of the sample axis z for each image collected
sample_image_shift_x 1D array Vector containing the shift of the sample axis x at each projection on the detector plane.
sample_image_shift_y 1D array Vector containing the shift of the sample axis y at each projection on the detector plane.
sample_image_shift_x 1D array Vector containing the shift of the sample axis z at each projection on the detector plane.
image_theta 1D array Vector containing the rotary stage angular position read from the encoder at each image.
scan_index 1D array Vector containin for each image the identifier assigned by beamline controls to each individual series of images or scan.
scan_date 1D array Vector containin for each image the wall date/time at start of scan in iso 8601.
image_date 1D array Vector containing the date/time each image was acquired in iso 8601.
time_stamp 1D array Vector containin for each image the relative time since scan_date
image_number 1D array Vector containin for each image the the image serial number as assigned by the camera. Unique for each individual scan. Always starts at 0.0
image_exposure_time 1D array Vector containin for each image the the measured exposure time
image_is_complete 1D array Vector containin for each image the boolen status of: is any pixel data missing?
image_type 1D array Vector containin for each image contained in /exchange/data 0 for white, 1 for projection and 2 for dark.
set-up group  

Table: Acquisition Group Members

name

Descriptive name for acquisition. Current name include: tomo, interlaced, mosaic.
description

Description.

setup

List of static scan setup values. In the table below we present the implementation adopted by the Swiss Light Source and Advanced Photon Source.

Member Type Example
rotation_start_angle float 0.0
rotation_end_angle float 180.0
rotation_speed float 180.0
angular_step float 0.125
number_of_projections integer 1441
number_of_whites integer 100
number_of_darks integer 32
number_of_inter_whites integer 1
inner_scan_flag integer 1
white_frequency integer 0
sample_in float 0.0
sample_out float 4.0

Table: Static Setup Acquisition Group for Tomography

tomo_rec (APS)

The Reconstruction process description group contains metadata required to run a tomography reconstruction. The specific algorithm is described in a separate group under the reconstruction setup group. Here is where to log the algorithm setup parameters. In the case of tomoPy this can simply be the link to the scrip used to run the reconstruction.

Member Type Example
name string dataset “test rec”
description string dataset “optional”
version string dataset https://github.com/tomopy_scripts/b9ad87e17
input_data string dataset “/exchange”
output_data string dataset “/exchange_1”
set_up group  

Table: Reconstruction Actor Group Members

name

Descriptive actor task.
description

Description of the actor task.
version

Version of the actor task.

If available this can be the repository link to the actor version used
input_data, output_data

Origin and destination of the data processed by the reconstruction task.

setup (APS)

Here is where to log the algorithms used by the reconstruction actor.

Member Type Example
astra string dataset https://github.com/astra/b9ad87e17
tomopy string dataset https://github.com/tomopy/c9ad87e77

Table: Reconstruction Setup Group Members

tomo_rec (SLS)

The reconstruction process description group contains metadata required to run a tomography reconstruction. The specific algorithm is described in a separate group under the reconstruction setup group. Here is where to log the algorithm setup parameters.

Member Type Example
name string dataset “sls rec”
description string dataset “optional”
version string dataset https://github.com/sls_scripts/b9ad87e17
input_data string dataset “/exchange”
output_data string dataset “/exchange_1”
set_up_sls group  

Table: Reconstruction Actor Group Members

name

Descriptive actor task.
description

Description of the actor task.
version

Version of the actor task.

If available this can be the repository link to the actor version used
input_data, output_data

Origin and destination of the data processed by the reconstruction task.

setup (SLS)

Here is where to log the algorithms used by the reconstruction actor.

Member Type Example
reconstruction_slice_start int dataset 1000
reconstruction_slice_end int dataset 1030
rotation_center Float dataset 1048.50
algorithm-sls Group  

Table: Reconstruction Setup SLS Group Members

reconstruction_slice_start

First reconstruction slice.
reconstruction_slice_end

Last reconstruction slice.
rotation_center

Center of rotation in pixels.
algorithm

Algorithm group describing reconstruction algorithm parameters.
algorithm (SLS iterative)

The Algorithm group contains information required to run a tomography reconstruction algorithm.

Member Type Example
name string dataset “SART”
version string dataset “1.0”
implementation string dataset “GPU”
number_of_nodes int dataset 16
type string dataset “Iterative”
stop_condition string dataset “iteration_max”
iteration_max int dataset 200
projection_threshold float dataset  
difference_threshold_percent float dataset  
difference_threshold_value float dataset  
regularization_type string dataset “total_variation”
regularization_parameter float dataset  
step_size float dataset 0.3
sampling_step_size float dataset 0.2

Table: Algorithm Group Members

name

Reconstruction method name: SART, EM, FBP.
version

Algorithm version.
implementation

CPU or GPU.
number_of_nodes

Number of nodes to use on cluster. This parameter is set when the reconstruction is parallelized and run on a cluster.
type

Tomography reconstruction method: iterative.
stop_condition

iteration_max, projection_threshold, difference_threshold_percent, difference_threshold_value.
iteration_max

Maximum number of iterations.
projection_threshold

The threshold of projection difference to stop the iterations as
\[\begin{split}| y - Ax_{\mathrm{n}}| < p\end{split}\]
difference_threshold_percent

The threshold of reconstruction difference to stop the iterations as
\[\begin{split}| x_{\mathrm{n+1}}|/ |x_{\mathrm{n}}| < p\end{split}\]
difference_threshold_value

The threshold of reconstruction difference to stop the iterations as:
\[\begin{split}| x_{\mathrm{n+1}}| - |x_{\mathrm{n}}| < p\end{split}\]
regularization_type

total_variation, none.
regularization_parameter


step_size

Step size between iterations in iterative methods
sampling_step_size

Step size used for forward projection calculation in iterative methods.
algorithm (SLS analytic)

The Algorithm group contains information required to run a tomography reconstruction algorithm.

Member Type Example
name string dataset “gridrec”
version string dataset “1.0”
implementation string dataset “CPU”
number_of_nodes int dataset 16
type string dataset “analytic”
filter string dataset “Parzen”
padding float dataset 0.50

Table: Algorithm Group Members

name

Reconstruction method name: GridRec.
version

Algorithm version.
implementation

CPU or GPU.
number_of_nodes

Number of nodes to use on cluster. This parameter is set when the reconstruction is parallelized and run on a cluster.
type

Tomography reconstruction method: analytic.
filter

Filter type.

padding

transfer

The transfer process description group contains metadata required to trasfer data from source (data analysis machine) to destination (data distribution server).

Member Type Example
name string dataset “Globus”
description string dataset “data distribution to users”
version string dataset https://github.com/globus/b9ad87e17
input_data string dataset “gsiftp://host1/path”
output_data string dataset “gsiftp://host2/path”
setup group  

Table: Transfer Actor Group Members

name

Descriptive actor task.
description

Description of the actor task.
version

Version of the actor task.

If available this can be the repository link to the actor version used
input_data, output_data

Origin and destination of the data processed by the trasnfer task.
setup

Group containing the specific data transfer protocol paramenters.

table

Scientific users will not generally be expected to maintain data in this group. The expectation is that analysis pipeline tools will automatically record process steps using this group. In addition, it is possible to re-run an analysis using the information provided here.

actor start_time end_time status message reference description
acquisition 21:15:22 21:15:23 FAILED beamline off line /process/acquisition raw data collection
acquisition 21:15:26 21:15:27 FAILED beamline off line /process/acquisition raw data collection
acquisition 21:17:28 22:15:22 SUCCESS OK /process/acquisition raw data collection
tomo_rec 22:30:23 22:50:22 SUCCESS OK /process/tomo_rec reconstruct
transfer     QUEUED   /process/transfer transfer data to user

Table: Process table to log actors activity

actor

Name of the process in the pipeline stage that is executed at this step.
start_time

Time the process started.
end_time

TIme the process ended.
status

Current process status. May be one of the following: QUEUED,
RUNNING, FAILED, or SUCCESS.
message

A process specific message generated by the process. It may be a
confirmation that the process was successful, or a detailed error
message, for example.
reference

Path to the actor description group. The process description group
contains all metadata to perform the specific process. This
reference is simply the HDF5 path within this file of the
technique specific process description group. The process
description group should contain all parameters necessary to run
the process, including the name and version of any external
analysis tool used to process the data. It should also contain
input and output references that point to the
exchange_N groups that contain the input and output
datasets of the process.
description

Process description.