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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).Uses lazy loading (see Comment 1).
  1. Data are loaded on the first access request by the next 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.



Parameters


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.
-------------------------------------------------------------------------------------

>>>
ItemParameter nameParameter formatExample(s)Comment(s)
Parameter valueEffect
1preview[ind_0, ind_1,... ind_n]


[ ]To load all n-dimensional data located at data_path.Default value.
[:, :, :]To load all 3d data located at data_path.
[:, s, :] To load from a given 3d dataset only the data of the s-th tomography slice.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 only the data of the p-th sample projection.This particular interpretation applies if data are laid out in the (angle-enumeration, image_height, image_width) format.
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 flats from a dataset located at entry1/instrument/detector/pco1/data in a NeXus scan file named /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).If <path-to-NeXus-file> is not None, then flats are loaded from a dataset found at <path-to-dataset> inside the NeXus file located on the file-system at <path-to-NeXus-file>, and their pixel values are then multiplied by <exposure-time-compensation-factor>.
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 darks from a dataset located at entry1/instrument/detector/pco1/data in a NeXus scan file named /dls/i13/data/2018/cm123-4/raw/6.nxs, and then to multiply their pixel values by 1.If <path-to-NeXus-file> is not None, then darks are loaded from a dataset found at <path-to-dataset> inside the NeXus file located on the file-system at <path-to-NeXus-file>, and their pixel values are then multiplied by <exposure-time-compensation-factor>.
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 series of m batches of flats (each containing however many individual flat-field images).
  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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