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AstraReconGpu

AstraReconGpu


Summary


AstraReconGpu
Process categoryBrief description

Computational demand

for typical tomography data

(low, medium, high)

Comment(s)Reference(s)Common alternative process(es)
reconstructor

To reconstruct normalised and conditioned data.

Depends on the reconstruction algorithm selected.Uses GPU resources. The Astra Toolbox
  1. AstraReconCpu
  2. TomopyRecon


Parameters


Brief description

Savu Configurator command
>>> disp -avv

-------------------------------------------------------------------------------------
 8) AstraReconGpu(savu.plugins.reconstructions.astra_recons.astra_recon_gpu)         
  Wrapper around the Astra toolbox for gpu reconstruction.                           
    1)               init_vol : None
    Dataset to use as volume initialiser (doesn't currently work with preview).
    2)                preview : []
    A slice list of required frames.
    3)                    log : True
    Take the log of the data before reconstruction (True or False).
    4)              algorithm : FBP_CUDA
    Reconstruction type (FBP_CUDA|SIRT_CUDA| SART_CUDA (not currently
    working)|CGLS_CUDA|FP_CUDA|BP_CUDA| SIRT3D_CUDA|CGLS3D_CUDA).
    5)           n_iterations : 1
    Number of Iterations - only valid for iterative algorithms.
    6)               res_norm : False
    Output the residual norm at each iteration (Error in the solution - iterative
    solvers only).
    7)     centre_of_rotation : 0.0
    Centre of rotation to use for the reconstruction.
    8)             FBP_filter : ram-lak
    The FBP reconstruction filter type (none|ram-lak| shepp-
    logan|cosine|hamming|hann|tukey|lanczos|triangular|gaussian| barlett-
    hann|blackman|nuttall|blackman-harris|blackman-nuttall| flat-top|kaiser|parzen).
    9)            in_datasets : []
    Create a list of the dataset(s) to process.
   10)                  ratio : 0.95
    Ratio of the masks diameter in pixels to the smallest edge size along given axis.
   11)           out_datasets : []
    Create a list of the dataset(s) to create.
   12)             centre_pad : False
    Pad the sinogram to centre it in order to fill the reconstructed volume ROI for
    asthetic purposes. NB: Only available for selected algorithms and will be ignored
    otherwise. WARNING: This will significantly increase the size of the data and the
    time to compute the reconstruction).
   13)              outer_pad : False
    Pad the sinogram width to fill the reconstructed volume for asthetic purposes.
    Choose from True (defaults to sqrt(2)), False or float <= 2.1. NB: Only available
    for selected algorithms and will be ignored otherwise. WARNING: This will
    increase the size of the data and the time to compute the reconstruction).
   14)               log_func : np.nan_to_num(-np.log(sino))
    Override the default log function.
   15)             force_zero : [None, None]
    Set any values in the reconstructed image outside of this range to zero.
-------------------------------------------------------------------------------------

>>> 

Additional notes

For basic information on this process, please use the disp -av (or disp -avv or disp -v[v] <process index>) command in Savu Configurator (see above). The table below is intended to provide some additional notes on a number of selected topics:

ItemParameter nameParameter formatExample(s)Comment(s)
Parameter valueEffect
1

init_vol





2

preview





3

log




The log parameter needs to be set to False, if PaganinFilter is applied beforehand.
4algorithm



5n_iterations



6res_norm



7

centre_of_rotation




The default value of the centre_of_rotation parameter is 0.0, which normally needs to be manually modified  to a more appropriate value or, if VoCentering is used beforehand in the process chain, then this parameter is automatically set to a value determined by this auto-centring process.
8FBP_filter



9

in_datasets





10ratio



11out_datasets



12

centre_pad





13outer_pad



14force_zero





Usage

TBC.




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