| Table of Contents |
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Summary
| NxtomoLoader | |||||
| Process category | Brief description | Computational demand for typical tomography data (low, medium, high) | Comment(s) | Reference(s) | Common alternative process(es) |
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| loader | To load raw data from input file(s). | Low |
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Parameters
Brief description |
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| Code Block | ||
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>>> 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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>>> |
Additional notes |
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| Item | Parameter name | Parameter format | Example(s) | Comment(s) | |
|---|---|---|---|---|---|
| Parameter value | Effect | ||||
| 1 | preview | [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). |
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| 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). |
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| 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. |
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