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%--------------------------------------------------------------------------
% This file is part of the ASTRA Toolbox
%
% Copyright: 2010-2016, iMinds-Vision Lab, University of Antwerp
% 2014-2016, CWI, Amsterdam
% License: Open Source under GPLv3
% Contact: astra@uantwerpen.be
% Website: http://www.astra-toolbox.com/
%--------------------------------------------------------------------------
classdef MaskingDefault < matlab.mixin.Copyable
% Default policy class for masking for DART.
%----------------------------------------------------------------------
properties (Access=public)
radius = 1; % SETTING: Radius of masking kernel.
conn = 8; % SETTING: Connectivity window. For 2D: 4 or 8. For 3D: 6 or 26.
edge_threshold = 1; % SETTING: Number of pixels in the window that should be different.
random = 0.1; % SETTING: Percentage of random points. Between 0 and 1.
gpu = 'yes'; % SETTING: Use gpu? {'yes', 'no'}
gpu_core = 0; % SETTING: Which gpu core to use, only when gpu='yes'.
end
%----------------------------------------------------------------------
methods (Access=public)
%------------------------------------------------------------------
function settings = getsettings(this)
% Returns a structure containing all settings of this object.
% >> settings = DART.masking.getsettings();
settings.radius = this.radius;
settings.conn = this.conn;
settings.edge_threshold = this.edge_threshold;
settings.random = this.random;
end
%------------------------------------------------------------------
function Mask = apply(this, ~, S)
% Applies masking.
% >> Mask = DART.segmentation.apply(DART, S);
% 2D, one slice
if size(S,3) == 1
if strcmp(this.gpu,'yes')
Mask = this.apply_2D_gpu(S);
else
Mask = this.apply_2D(S);
end
% 3D, slice by slice
elseif this.conn == 4 || this.conn == 8
Mask = zeros(size(S));
for slice = 1:size(S,3)
if strcmp(this.gpu,'yes')
Mask(:,:,slice) = this.apply_2D_gpu(S(:,:,slice));
else
Mask(:,:,slice) = this.apply_2D(S(:,:,slice));
end
end
% 3D, full
else
if strcmp(this.gpu,'yes')
Mask = this.apply_3D_gpu(S);
else
Mask = this.apply_3D(S);
end
end
end
end
%----------------------------------------------------------------------
methods (Access=protected)
%------------------------------------------------------------------
function Mask = apply_2D_gpu(this, S)
vol_geom = astra_create_vol_geom(size(S));
data_id = astra_mex_data2d('create', '-vol', vol_geom, S);
mask_id = astra_mex_data2d('create', '-vol', vol_geom, 0);
cfg = astra_struct('DARTMASK_CUDA');
cfg.SegmentationDataId = data_id;
cfg.MaskDataId = mask_id;
cfg.option.GPUindex = this.gpu_core;
cfg.option.Connectivity = this.conn;
cfg.option.Threshold = this.edge_threshold;
cfg.option.Radius = this.radius;
alg_id = astra_mex_algorithm('create',cfg);
astra_mex_algorithm('iterate',alg_id,1);
Mask = astra_mex_data2d('get', mask_id);
astra_mex_algorithm('delete', alg_id);
astra_mex_data2d('delete', data_id, mask_id);
% random
RandomField = double(rand(size(S)) < this.random);
% combine
Mask = or(Mask, RandomField);
end
%------------------------------------------------------------------
function Mask = apply_2D(this, S)
r = this.radius;
w = 2 * r + 1;
kernel = Kernels.BinaryPixelKernel(r, this.conn);
% edges
Xlarge = zeros(size(S,1)+w-1, size(S,2)+w-1);
Xlarge(1+r:end-r, 1+r:end-r) = S;
Edges = zeros(size(S));
for s = -r:r
for t = -r:r
if kernel(s+r+1, t+r+1) == 0
continue
end
Temp = abs(Xlarge(1+r:end-r, 1+r:end-r) - Xlarge(1+r+s:end-r+s, 1+r+t:end-r+t));
Edges(Temp > eps) = Edges(Temp > eps) + 1;
end
end
Edges = Edges > this.edge_threshold;
% random
RandomField = double(rand(size(S)) < this.random);
% combine
Mask = or(Edges, RandomField);
end
%------------------------------------------------------------------
function Mask = apply_3D(this, S)
r = this.radius;
w = 2 * r + 1;
kernel = Kernels.BinaryPixelKernel(r, this.conn);
% edges
Xlarge = zeros(size(S,1)+w-1, size(S,2)+w-1, size(S,3)+w-1);
Xlarge(1+r:end-r, 1+r:end-r, 1+r:end-r) = S;
Edges = zeros(size(S));
for s = -r:r
for t = -r:r
for u = -r:r
if kernel(s+r+1, t+r+1, u+r+1) == 0
continue
end
Temp = abs(Xlarge(1+r:end-r, 1+r:end-r, 1+r:end-r) - Xlarge(1+r+s:end-r+s, 1+r+t:end-r+t, 1+r+u:end-r+u));
Edges(Temp > eps) = 1;
end
end
end
clear Xlarge;
% random
RandomField = double(rand(size(S)) < this.random);
% combine
Mask = or(Edges, RandomField);
end
%------------------------------------------------------------------
function Mask = apply_3D_gpu(this, S)
vol_geom = astra_create_vol_geom(size(S,2), size(S,1), size(S,3));
data_id = astra_mex_data3d('create', '-vol', vol_geom, S);
cfg = astra_struct('DARTMASK3D_CUDA');
cfg.SegmentationDataId = data_id;
cfg.MaskDataId = data_id;
cfg.option.GPUindex = this.gpu_core;
cfg.option.Connectivity = this.conn;
cfg.option.Threshold = this.edge_threshold;
cfg.option.Radius = this.radius;
alg_id = astra_mex_algorithm('create',cfg);
astra_mex_algorithm('iterate',alg_id,1);
Mask = astra_mex_data3d('get', data_id);
astra_mex_algorithm('delete', alg_id);
astra_mex_data3d('delete', data_id);
% random
RandomField = double(rand(size(S)) < this.random);
% combine
Mask = or(Mask, RandomField);
end
%------------------------------------------------------------------
end
end
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