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SAVU documentation is found here |
Automatic reconstruction
Savu process lists are added during the scan configuration stageImaging data is stored as an H5 file
Automatic reconstruction
During your beamtime, a Savu process lists will be automatically run after each scan completes. This will usually be discussed with you during your beamtime.
Savu lists are usually stored in:
<visit folder>/xml/tomography/Savu
An example of the standard lists we use:
...
Each list is named with each process that is being applied. for example
full_fd_rr_vo_pag_AST_tiff.nxs
will run:
Full reconstruction
Flat/Darkfield correction
Ring removal
Vo centering (Nghia Vo’s centering method)
Paganin filter
Astra reconstruction
Output tiff files
The result of autoprocessing goes into the Processedfolder and will look like:
...
The result of the autoprocess will be named with Savu (indicating its a Savu process), the file name and the process list that was applied. The inside of this folder looks like:
...
The nxs file will give you a simple way to visualise all the output data. If you prefer then the reconstructed data lives in the file with astra_recon_gpu.h5 or as individual tiffs in the folder labeled TiffSaver*.
The run_log folder contains some log files and a copy of the process list that was run.
...
Manual reconstruction
If you are not happy with your reconstructions you can always send them off manually with your own configured process lists. This guide is for manual reconstructions using Diamond workstations.
To load Savu on Wilson:
Open terminal
Config the process list to make sure you are happy. BL scientist may do this for you.
To submit savu jobs to the cluster use:
...
An example process list is shown here:
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1) NxtomoLoader
--basic----------------------------------------------------------------------------------------
1) preview : [:, 300, :]
2) data_path : /entry/imaging/data
3) dark : [None, None, 1.0]
4) flat : [None, None, 1.0]
--intermediate---------------------------------------------------------------------------------
5) name : tomo
6) image_key_path : /entry/instrument/imaging/image_key
7) angles : None
8) 3d_to_4d : False
9) ignore_flats : None
2) DezingerGpu
--basic----------------------------------------------------------------------------------------
1) kernel_size : 2
2) outlier_mu : 0.1
--datasets-------------------------------------------------------------------------------------
3) in_datasets : []
4) out_datasets : []
3) DarkFlatFieldCorrection
--basic----------------------------------------------------------------------------------------
1) pattern : PROJECTION
--intermediate---------------------------------------------------------------------------------
2) lower_bound : None
3) upper_bound : None
4) warn_proportion : 0.05
--datasets-------------------------------------------------------------------------------------
5) in_datasets : []
6) out_datasets : []
4) PaganinFilter
--basic----------------------------------------------------------------------------------------
1) Ratio : 0.5
2) Energy : 22.0
3) Distance : 0.14875
4) Resolution : 0.54
--intermediate---------------------------------------------------------------------------------
5) Padtopbottom : 100
6) Padleftright : 100
7) Padmethod : edge
8) increment : 0.0
--datasets-------------------------------------------------------------------------------------
9) in_datasets : []
10) out_datasets : []
5) RemoveLargeRings
--basic----------------------------------------------------------------------------------------
1) size : 71
2) snr : 10.0
--datasets-------------------------------------------------------------------------------------
3) in_datasets : []
4) out_datasets : []
***OFF*** 6) RemoveAllRings
--basic----------------------------------------------------------------------------------------
1) sm_size : 31
2) la_size : 71
3) snr : 100.0
--datasets-------------------------------------------------------------------------------------
4) in_datasets : []
5) out_datasets : []
***OFF*** 7) VoCentering
--basic----------------------------------------------------------------------------------------
1) preview : []
2) search_area : [-50, 50]
--intermediate---------------------------------------------------------------------------------
3) start_pixel : None
4) ratio : 0.5
5) search_radius : 6
6) step : 0.5
7) datasets_to_populate : []
--advanced-------------------------------------------------------------------------------------
8) broadcast_method : median
9) row_drop : 20
10) average_radius : 5
--datasets-------------------------------------------------------------------------------------
11) in_datasets : []
12) out_datasets : [cor_preview, cor_broadcast]
8) AstraReconGpu
--basic----------------------------------------------------------------------------------------
1) centre_of_rotation : 1295.0
2) algorithm : FBP_CUDA
--intermediate---------------------------------------------------------------------------------
3) init_vol : None
4) log : False
5) preview : []
6) force_zero : [None, None]
7) ratio : 0.95
8) vol_shape : fixed
9) outer_pad : False
10) centre_pad : False
11) FBP_filter : ram-lak
--advanced-------------------------------------------------------------------------------------
12) log_func : np.nan_to_num(-np.log(sino))
--datasets-------------------------------------------------------------------------------------
13) in_datasets : []
14) out_datasets : []
***********************************************************************************************
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