NXtomophase

Status:

application definition, extends NXobject

Description:

This is the application definition for x-ray or neutron tomography raw data with phase contrast variation at each point.

In tomography first some dark field images are measured, some bright field images and, of course the sample. In order to properly sort the order of the images taken, a sequence number is stored with each image.

Symbols:

These symbols will be used below to coordinate datasets with the same shape.

nBrightFrames: Number of bright frames

nDarkFrames: Number of dark frames

nSampleFrames: Number of image (sample) frames

nPhase: Number of phase settings

xSize: Number of pixels in X direction

ySize: Number of pixels in Y direction

Groups cited:

NXdata, NXdetector, NXentry, NXinstrument, NXmonitor, NXsample, NXsource

Structure:

entry: (required) NXentry

title: (required) NX_CHAR

start_time: (required) NX_DATE_TIME

end_time: (required) NX_DATE_TIME

definition: (required) NX_CHAR

Official NeXus NXDL schema to which this file conforms

Obligatory value: NXtomophase

instrument: (required) NXinstrument

SOURCE: (required) NXsource

type: (required) NX_CHAR

name: (required) NX_CHAR

probe: (required) NX_CHAR

Any of these values: neutron | x-ray | electron

bright_field: (required) NXdetector

data: (required) NX_INT (Rank: 3, Dimensions: [nBrightFrames, xSize, ySize])

sequence_number: (required) NX_INT (Rank: 1, Dimensions: [nBrightFrames])

dark_field: (required) NXdetector

data: (required) NX_INT (Rank: 3, Dimensions: [nDarkFrames, xSize, ySize])

sequence_number: (required) NX_INT (Rank: 1, Dimensions: [nDarkFrames])

sample: (required) NXdetector

data: (required) NX_INT (Rank: 4, Dimensions: [nSampleFrames, nPhase, xSize, ySize])

sequence_number: (required) NX_INT (Rank: 2, Dimensions: [nSampleFrames, nPhase])

x_pixel_size: (required) NX_FLOAT {units=NX_LENGTH}

y_pixel_size: (required) NX_FLOAT {units=NX_LENGTH}

distance: (required) NX_FLOAT {units=NX_LENGTH}

Distance between detector and sample

sample: (required) NXsample

name: (required) NX_CHAR

Descriptive name of sample

rotation_angle: (required) NX_FLOAT (Rank: 1, Dimensions: [nSampleFrames]) {units=NX_ANGLE}

x_translation: (required) NX_FLOAT (Rank: 1, Dimensions: [nSampleFrames]) {units=NX_LENGTH}

y_translation: (required) NX_FLOAT (Rank: 1, Dimensions: [nSampleFrames]) {units=NX_LENGTH}

z_translation: (required) NX_FLOAT (Rank: 1, Dimensions: [nSampleFrames]) {units=NX_LENGTH}

control: (required) NXmonitor

integral: (required) NX_FLOAT (Rank: 1, Dimensions: [nDarkFrames + nBrightFrames + nSampleFrame]) {units=NX_ANY}

Total integral monitor counts for each measured frame. Allows a correction for fluctuations in the beam between frames.

data: (required) NXdata

data: link (suggested target: /NXentry/NXinstrument/sample:NXdetector/data)

rotation_angle: link (suggested target: /NXentry/NXsample/rotation_angle)

Hypertext Anchors

List of hypertext anchors for all groups, fields, attributes, and links defined in this class.

NXDL Source:

https://github.com/FAIRmat-Experimental/nexus_definitions/tree/fairmat/applications/NXtomophase.nxdl.xml