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Summary


NxtomoLoader
Process categoryBrief description

Computational demand

for typical tomography data

(low, medium, high)

Comment(s)Reference(s)Common alternative process(es)
loaderTo load raw data from input file(s).Low
  1. Implements lazy loading, i. e. loading of data is delayed until the first genuine access by another process in the process list - loading times depend on data chunking of source dataset(s).
  2. Capable of handling the case of dark- and flat-field images being supplied in datasets stored in individual NeXus datasets.
  1. NeXus NXtomo application definition
  2. NeXus file format
  3. HDF5 data model & file format



Parameters


Brief description

Savu Configurator command
>>> disp 1 -avv

-------------------------------------------------------------------------------------
 1) NxtomoLoader(savu.plugins.loaders.full_field_loaders.nxtomo_loader)              
  A class for loading standard tomography data in Nexus format                       
    1)                preview : []
    A slice list of required frames.
    2)         image_key_path : entry1/tomo_entry/instrument/detector/image_key
    Path to the image key entry inside the nxs file.
    3)                   name : tomo
    The name assigned to the dataset.
    4)               3d_to_4d : False
    Set to true if this reshape is required.
    5)                   flat : [None, None, 1]
    Optional Path to the flat field data file, nxs path and scale value.
    6)              data_path : entry1/tomo_entry/data/data
    Path to the data inside the file.
    7)                   dark : [None, None, 1]
    Optional path to the dark field data file, nxs path and scale value.
    8)                 angles : None
    A python statement to be evaluated or a file.
    9)           ignore_flats : None
    List of batch numbers of flats (start at 1) to ignore.
-------------------------------------------------------------------------------------

>>>

Additional notes

ItemParameter nameParameter formatExample(s)Comment(s)
Parameter valueEffect
1preview[ind_0, ind_1,... ind_(n-1)]


[ ]To load the entire n-dimensional dataset, stored at location specified by the data_path parameter.Default value.
[:, :, :]To load the entire 3d data dataset, stored at location specified by the data_path parameter.
[:, s, :] To load from a given 3d dataset (stored at the data_path location) only a subset of data corresponding to the s-th sinogram.This particular interpretation applies if data are laid out in the (angle_enumeration, image_height, image_width) format.
[p, :, :]To load from a given 3d dataset (stored at data_path location) only a subset of data corresponding to the p-th projection.This particular interpretation applies if data are laid out in the (angle_enumeration, image_height, image_width) format.
[:, :, 123:-123]To load from a given 3d dataset (stored at the data_path location) only a subset of data generated by cropping the width of each projection by 123 pixels on either side.This particular interpretation applies if data are laid out in the (angle_enumeration, image_height, image_width) format.
[:, mid - 1:mid + 2, :]To load from a given 3d dataset (stored at the data_path location) only a subset of data corresponding to the middle 2 sinograms.mid is one of Savu keywords (with an obvious meaning).
[0:end:2, :, :]To load from a given 3d dataset (stored at the data_path location) only a subset of data corresponding to every other projection.end is one of Savu keywords (with an obvious meaning).
[:, 0:end:2, :]To load from a given 3d dataset (stored at the data_path location) only a subset of data corresponding to every other sinogram.
2

image_key_path




Mandatory dataset.
3

name





4

3d_to_4d





5

flat

[<path-to-NeXus-file>, <path-to-dataset>, <exposure-time-compensation-factor>][/dls/i13/data/2018/cm123-4/raw/5.nxs, entry1/instrument/detector/pco1/data, 1.25]To load all flats from the flats-only dataset found at entry1/instrument/detector/pco1/data inside a NeXus scan file, located on the file system at /dls/i13/data/2018/cm123-4/raw/5.nxs, and then to multiply their pixel values by 1.25 (to compensate for the flat-field exposure time being 0.8 times shorter than the sample-projection exposure time).
  1. If <path-to-NeXus-file> is not None, then flats are loaded from a dataset found at <path-to-dataset> inside a NeXus file, located on the file-system at <path-to-NeXus-file>, and their pixel values are then multiplied by <exposure-time-compensation-factor>.
  2. Specify this parameter only if your flats are not stored in the same dataset as your sample projections.
6

data_path




Mandatory dataset.
7

dark

[<path-to-NeXus-file>, <path-to-dataset>, <exposure-time-compensation-factor>][/dls/i13/data/2018/cm123-4/raw/6.nxs, entry1/instrument/detector/pco1/data, 1]To load all darks from the darks-only dataset found at entry1/instrument/detector/pco1/data inside a NeXus scan file, located on the file system at /dls/i13/data/2018/cm123-4/raw/6.nxs, and then to multiply their pixel values by 1 (no change to intensities).
  1. If <path-to-NeXus-file> is not None, then darks are loaded from a dataset found at <path-to-dataset> inside a NeXus file, located on the file-system at <path-to-NeXus-file>, and their pixel values are then multiplied by <exposure-time-compensation-factor>.
  2. Specify this parameter only if your darks are not stored in the same dataset as your sample projections.
8

angles




If the angles parameter is set to None, then this loader attempts to find them in a default dataset, located at entry1/tomo_entry/data/rotation_angle in the input NeXus scan file.
9

ignore_flats

[ind_1, ind_2,... ind_m][1, r]To ignore the initial and the r-th batch in a given series of batches of flats (each containing however many individual flat-field images), stored in the same dataset as darks and sample projections.
  1. Useful for excluding compromised flats for scans containing multiple batches of mid-scan flats.
  2. In the ignore_flats list, batch indexing starts from 1 (not 0).


Usage

How to load dark- and flat-field data from individual NeXus datasets?

Any standard tomography NeXus scan file, generated by GDA, stores all the images (i.e. sample projections as well as dark- and flat-field images) in a single dataset located at entry1/tomo_entry/data/data, which is accompanied by another dataset containing the corresponding image-key information, located at entry1/tomo_entry/instrument/detector/image_key in the same file. The default values of NxtomoLoader's parameters have been selected to reflect this scenario. However, NxtomoLoader can be used to load dark- and flat-field data from individual NeXus datasets, if required. This can be done by modifying the flat and dark parameters appropriately (see the table above for more details).





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