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.
This node represents the top level of the HDF5 file and holds some general information about the file.
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- 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.).
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.
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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.
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.
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description |
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“transmission” |
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Table: data attributes
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.
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Table: Measurement Group Members
- instrument
The instrument used to collect this data.- sample
The sample measured.
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.
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"XSD/32-ID/TXM" |
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"X-ray Microscope" |
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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.
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.
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name |
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description |
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thickness |
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transmission |
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geometry |
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setup |
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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.
Class describing the beam monitor being used, if there is more than one append _##
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Table: Beam Monitor Group Members
Class describing the beam stop being used, if there is more than one append _##
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Table: Beam Stop Group Members
Class describing the Bertrand lens being used, if there is more than one append _##
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Table: Bertrand Lens Group Members
Class describing the condenser being used, if there is more than one append _##
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Table: Condenser Group Members
Class describing the compound refractive lenses being used, if there is more than one append _##
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Table: CRL Group Members
In full field imaging the detector consists of microscope objective and a scintillator screen.
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string dataset |
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string dataset |
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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
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.
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string dataset |
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string dataset |
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string dataset |
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string dataset |
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string dataset |
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string dataset |
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string dataset |
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string dataset |
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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.
Class describing the diffuser being used, if there is more than one append _##
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Table: Diffuser Group Members
Class describing the flight tube being used, if there is more than one append _##
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Table: Flight Tube Group Members
This group stores the interferometer parameters.
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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.
Class describing the mirror being used, if there is more than one append _##
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Table: Mirror Group Members
Define the monochromator used in the instrument.
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description |
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energy |
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energy_error |
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mono_stripe |
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geometry |
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setup |
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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.
Class describing the pin hole being used, if there is more than one append _##
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Table: Pin Hole Group Members
Class describing the shutter being used.
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Table: Shutter Group Members
- name
Name.- description
Description.- status
“OPEN” or “CLOSED”
Class describing the sample stage stack being used.
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detector_distance |
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Table: Sample stage stack Group Members
Class describing the light source being used.
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name |
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description |
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datetime |
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beamline |
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current |
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energy |
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pulse_energy |
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pulse_width |
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mode |
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beam_intensity_incident |
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beam_intensity_transmitted |
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geometry |
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setup |
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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).
Class describing the slits being used.
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Table: Slits Group Members
- name
Name.- description
Description.
Class describing the zone plate being used, if there is more than one append _##
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Table: Optical Table Group Members
Class describing the zone plate being used, if there is more than one append _##
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Table: Zone Plate Group Members
Group describing the region of interest (ROI) of the image actually collected, if smaller than the full CCD.
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string dataset | "ROI 04" |
description | string dataset | "center third" |
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integer |
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integer |
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integer |
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integer |
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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.
Group describing the microscope objective lenses used.
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name | string dataset |
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description | string dataset |
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manufacturer | string dataset |
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model | string dataset |
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magnification | float dataset |
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numerical_aperture | float dataset |
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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.
Group describing the visible light scintillator coupled to the CCD camera objective lens.
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string dataset |
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string dataset |
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string dataset |
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string dataset |
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float dataset |
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float dataset |
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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.
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.
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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.
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string dataset (abbr. CIF format) |
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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.
This provides references to facility ids for the proposal, scheduled activity, and safety form.
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proposal |
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activity |
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safety |
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title |
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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.
Description of a single experimenter. Multiple experimenters can be represented through numbered entries such as experimenter_1, experimenter_2.
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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
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.
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- 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.
This is the description for the general spatial location of a component for tomography.
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3 float array dataset |
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- 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.
This is the description for the orientation of a component for tomography.
Member | Type | Example |
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- 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 ⋅ x, x′ ⋅ y, x′ ⋅ z, y′ ⋅ x, y′ ⋅ y, y′ ⋅ z]
where
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 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.
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Table: Process Group Members
- name
Descriptive process task.- description
Description of the process task.
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.
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string dataset |
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string dataset |
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string dataset |
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string dataset | |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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1D array |
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group |
Table: Acquisition Group Members
- name
Descriptive name for acquisition. Current name include: tomo, interlaced, mosaic.- description
Description.
List of static scan setup values. In the table below we present the implementation adopted by the Swiss Light Source and Advanced Photon Source.
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Table: Static Setup Acquisition Group for Tomography
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.
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https://github.com/tomopy_scripts/b9ad87e17 |
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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
https://github.com/tomopy_scripts/b9ad87e17- input_data, output_data
Origin and destination of the data processed by the reconstruction task.
Here is where to log the algorithms used by the reconstruction actor.
Member | Type | Example |
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https://github.com/astra/b9ad87e17 |
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https://github.com/tomopy/c9ad87e77 |
Table: Reconstruction Setup Group Members
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.
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https://github.com/sls_scripts/b9ad87e17 |
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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
https://github.com/tomopy_scripts/b9ad87e17- input_data, output_data
Origin and destination of the data processed by the reconstruction task.
Here is where to log the algorithms used by the reconstruction actor.
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int dataset |
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int dataset |
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Float dataset |
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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.
The Algorithm group contains information required to run a tomography reconstruction algorithm.
Member | Type | Example |
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string dataset | "SART" |
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string dataset | "1.0" |
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string dataset | "GPU" |
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int dataset | 16 |
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string dataset | "Iterative" |
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string dataset | "iteration_max" |
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int dataset | 200 |
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float dataset | |
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float dataset | |
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float dataset | |
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string dataset | "total_variation" |
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float dataset | |
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float dataset | 0.3 |
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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
|y − Axn| < p
- difference_threshold_percent
The threshold of reconstruction difference to stop the iterations as
|xn + 1|/|xn| < p
- difference_threshold_value
The threshold of reconstruction difference to stop the iterations as:
|xn + 1| − |xn| < p
- regularization_type
total_variation, none.- regularization_parameter
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- step_size
Step size between iterations in iterative methods- sampling_step_size
Step size used for forward projection calculation in iterative methods.
The Algorithm group contains information required to run a tomography reconstruction algorithm.
Member | Type | Example |
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string dataset | "gridrec" |
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string dataset | "1.0" |
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string dataset | "CPU" |
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int dataset | 16 |
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string dataset | "analytic" |
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string dataset | "Parzen" |
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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
The transfer process description group contains metadata required to trasfer data from source (data analysis machine) to destination (data distribution server).
Member | Type | Example |
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https://github.com/globus/b9ad87e17 |
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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
https://github.com/globus/b9ad87e17- input_data, output_data
Origin and destination of the data processed by the trasnfer task.- setup
Group containing the specific data transfer protocol paramenters.
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 |
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acquisition |
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acquisition |
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acquisition |
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tomo_rec |
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transfer |
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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.