Core Reference

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

The exchange group is where scientific datasets reside. This group contains one or more array datasets containing n-dimensional data and optional descriptions of the axes (dimension scale datasets). Exactly how this group is used is dependent on the application, however the general idea is that one exchange group contains one cohesive dataset. If, for example, the dataset is processed into some other form, then another exchange group is used to store the derived data.

Multiple exchange groups are numbered consecutively as exchange_N. At a minimum, each exchange group should have a primary dataset named data. The title is optional.

Member

Type

Example

name

string dataset

“absorption_tomography”

description

string dataset

“raw absorption tomo”

data

array dataset

n-dimensional dataset

Table: Exchange Group Members

name

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

Description.
data

The primary scientific dataset. Additional related datasets may have any arbitrary name. Each dataset should have a units and description attribute. Discussion of dimension descriptors and optional axes attribute is covered in Section [sec:multidims].

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/2-BM”

component_1

group

component_2

group

component_n

group

setup

group

Table: Instrument

name

Name of the instrument.
component

List of components part of the instrument. Replace component with the actual item name, source, mirror, etc.
detector

The detectors that compose the instrument.

component

Class describing the component being used.

Member

Type

Example

name

string dataset

“APS”

description

string dataset

“APS”

arbitrary_label_1

string dataset

“what ever”

arbitrary_label_2

string dataset

“what ever”

arbitrary_label_n

string dataset

“what ever”

setup

group

geometry

group

Table: Component Description

name

Name.
arbitrary_label(s)

Date and time source was measured.

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

positioner_x

float

-10.107

positioner_y

float

-17.900

positioner_z

float

-5.950

Table: Setup Group Members

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.

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”

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

setup

group

experiment

group

experimenter

group

Table: Sample Group Members

name

Descriptive name of the sample.
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”

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.

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

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”

actor_1

group

actor_2

group

actor_n

group

table

group

Table: Process Group Members

name

Descriptive process task.
description

Description of the process task.

actor

This is the actor description group. Each entry of the process table will refer to the correspondent actor description.

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: 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 actor.

setup (actor)

Here is where to log the actor setup parameters (static setup values).

Member

Type

Example

parameter_name_1

float

0.0

parameter_name_2

string dataset

“Parzen”

parameter_name_n

float

2.0

module__name_1

string dataset

https://github.com/astra/b9ad87e17

module_name_2

string dataset

https://github.com/tomopy/c9ad87e77

Table: Actor Setup Group

table

Scientific users will not generally be expected to maintain data in this group. The expectation is that the data collection and 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

actor_1

21:15:22

21:15:23

SUCCESS

OK

/process/actor_1

raw data collection

actor_2

21:15:26

21:15:27

RUNNING

OK

/process/actor_2

reconstruct

actor_n

21:17:28

22:15:22

QUEUED

OK

/process/actor_n

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.