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SAVU documentation is found here |
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Automatic reconstruction
Savu process lists are added during the scan configuration stage.
Manual reconstruction
If you are not happy with your reconstructions you can always send them off manually with your own configured process lists.
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:
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ssh wilson
module load savu/4.2-slurm
savu_mpi <IN_FILE> <PROCESS_LIST> <OUT_FOLDER> -d <TMP_FOLDER> -p |
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This will leave you with a terminal that can submit savu jobs to DIAD’s nodes on the cluster.
To configure your SAVU process lists. In a new terminal
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module load savu
// Will load savu in cwd and allow you to create processlists. You cannot submit to cluster using this module.
// This should be done in a normal terminal, do not ssh into wilson
savu_config - i xxxxx.nxs
// Where "xxxx.nxs" is the path of your process list (ie. 3x_fd_vo_AST_tiff.nxs).
// This command will open up the savu config with this process list.
// You can omit -i xxxx.nxs to open config with an empty list. You will then need to populate savu with each process |
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You can then use these commands to create and edit the process lists.
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list
disp -a
// This will display each process module and the parameters that you can change.
// Use -avv for more detailed information.
fg /ctrl + z
// Will bring savu config to foreground / Send config to background to allow you to run savu_mpi in the same terminal window
add RemoveAllRings 2
// will add the module RemoveAllRings to position 2 in the process list. If no number is included it will add to the end.
rem 2
// will remove module at position 2 in the list |
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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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