.. auto-generated by script ../../../../utils/nxdl2rst.py from the NXDL source NXtomophase.nxdl.xml

.. index::
    ! NXtomophase (application definition)
    ! tomophase (application definition)
    see: tomophase (application definition); NXtomophase

.. _NXtomophase:

===========
NXtomophase
===========

**Status**:

  application definition, extends :ref:`NXobject`, version 1.0b

**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**:
  :ref:`NXdata`, :ref:`NXdetector`, :ref:`NXentry`, :ref:`NXinstrument`, :ref:`NXmonitor`, :ref:`NXsample`, :ref:`NXsource`

.. index:: NXentry (base class); used in application definition, NXinstrument (base class); used in application definition, NXsource (base class); used in application definition, NXdetector (base class); used in application definition, NXsample (base class); used in application definition, NXmonitor (base class); used in application definition, NXdata (base class); used in application definition

**Structure**:

  **entry**: :ref:`NXentry`


    .. index:: title (field)

    **title**: :ref:`NX_CHAR <NX_CHAR>`


    .. index:: start time (field)

    **start_time**: :ref:`NX_DATE_TIME <NX_DATE_TIME>`


    .. index:: end time (field)

    **end_time**: :ref:`NX_DATE_TIME <NX_DATE_TIME>`


    .. index:: definition (field)

    **definition**: :ref:`NX_CHAR <NX_CHAR>`

      Official NeXus NXDL schema to which this file conforms

      Obligatory value:  ``NXtomophase``

    **instrument**: :ref:`NXinstrument`


      **(source)**: :ref:`NXsource`


        .. index:: type (field)

        **type**: :ref:`NX_CHAR <NX_CHAR>`


        .. index:: name (field)

        **name**: :ref:`NX_CHAR <NX_CHAR>`


        .. index:: probe (field)

        **probe**: :ref:`NX_CHAR <NX_CHAR>`


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

      **bright_field**: :ref:`NXdetector`


        .. index:: data (field)

        **data[nBrightFrames, xsize, ysize]**: :ref:`NX_INT <NX_INT>`


        .. index:: sequence number (field)

        **sequence_number[nBrightFrames]**: :ref:`NX_INT <NX_INT>`


      **dark_field**: :ref:`NXdetector`


        .. index:: data (field)

        **data[nDarkFrames, xsize, ysize]**: :ref:`NX_INT <NX_INT>`


        .. index:: sequence number (field)

        **sequence_number[nDarkFrames]**: :ref:`NX_INT <NX_INT>`


      **sample**: :ref:`NXdetector`


        .. index:: data (field)

        **data[nSampleFrames, nPhase, xsize, ysize]**: :ref:`NX_INT <NX_INT>`


        .. index:: sequence number (field)

        **sequence_number[nSampleFrames, nPhase]**: :ref:`NX_INT <NX_INT>`


        .. index:: x pixel size (field)

        **x_pixel_size**: :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}


        .. index:: y pixel size (field)

        **y_pixel_size**: :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}


        .. index:: distance (field)

        **distance**: :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}

          Distance between detector and sample

    **sample**: :ref:`NXsample`


      .. index:: name (field)

      **name**: :ref:`NX_CHAR <NX_CHAR>`

        Descriptive name of sample

      .. index:: rotation angle (field)

      **rotation_angle[nSampleFrames]**: :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_ANGLE <NX_ANGLE>`}


      .. index:: x translation (field)

      **x_translation[nSampleFrames]**: :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}


      .. index:: y translation (field)

      **y_translation[nSampleFrames]**: :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}


      .. index:: z translation (field)

      **z_translation[nSampleFrames]**: :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_LENGTH <NX_LENGTH>`}


    **control**: :ref:`NXmonitor`


      .. index:: integral (field)

      **integral[nDarkFrames + nBrightFrames + nSampleFrame]**: :ref:`NX_FLOAT <NX_FLOAT>` {units=\ :ref:`NX_ANY <NX_ANY>`}

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

    **data**: :ref:`NXdata`


      **data** --> /NXentry/NXinstrument/sample:NXdetector/data


      **rotation_angle** --> /NXentry/NXsample/rotation_angle


**NXDL Source**:
  https://github.com/nexusformat/definitions/blob/master/applications/NXtomophase.nxdl.xml