Summary
| NxtomoLoader | |||||
| Process category | Brief description | Computational demand (low, medium, high) | Comment(s) | Reference(s) | Common alternative process(es) |
|---|---|---|---|---|---|
| loader | To load raw data from input file(s). | Depends on chunking. | 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
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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.
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>>>
| Item | Parameter name | Parameter format | Example(s) | Comment(s) | |
|---|---|---|---|---|---|
| Parameter value | Effect | ||||
| 1 | preview | [ind_0, ind_1,... ind_n] | [ ] | NxtomoLoader to load all n-dimensional data located at data_path. | Default value. |
| [:, :, :] | NxtomoLoader to load all 3d data located at data_path. | ||||
| [:, s, :] | NxtomoLoader 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, :,:] | NxtomoLoader 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] | NxtomoLoader 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] | NxtomoLoader 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 | ||||
| 9 | ignore_flats | [ind_1, ind_2,... ind_m] | [1, r] | NxtomoLoader 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). |
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Usage
How to load dark- and flat-field data from individual NeXus datasets? |
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Any standard tomography NeXus scan file in DLS 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 with the corresponding image-key information, located at entry1/tomo_entry/instrument/detector/image_key in the same file. Hence, the default values of NxtomoLoader's parameters have been selected to match 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).