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-rw-r--r--matlab/tools/astra_create_fbp_reconstruction.m1
-rw-r--r--matlab/tools/astra_create_projector.m9
-rw-r--r--matlab/tools/astra_create_reconstruction_cuda.m2
-rw-r--r--matlab/tools/astra_create_vol_geom.m15
-rw-r--r--matlab/tools/astra_mex_direct.m24
-rw-r--r--matlab/tools/astra_mex_plugin.m24
-rw-r--r--matlab/tools/opTomo.m79
7 files changed, 100 insertions, 54 deletions
diff --git a/matlab/tools/astra_create_fbp_reconstruction.m b/matlab/tools/astra_create_fbp_reconstruction.m
index 5540f27..a2561b7 100644
--- a/matlab/tools/astra_create_fbp_reconstruction.m
+++ b/matlab/tools/astra_create_fbp_reconstruction.m
@@ -19,6 +19,7 @@ cfg.ProjectorId = proj_id;
cfg.Options.GPUindex = 0;
alg_id = astra_mex_algorithm('create', cfg);
astra_mex_algorithm('run', alg_id);
+astra_mex_algorithm('delete', alg_id);
if numel(sinogram) ~= 1
astra_mex_data2d('delete', sinogram_id);
diff --git a/matlab/tools/astra_create_projector.m b/matlab/tools/astra_create_projector.m
index da9c083..9bbef9e 100644
--- a/matlab/tools/astra_create_projector.m
+++ b/matlab/tools/astra_create_projector.m
@@ -1,7 +1,7 @@
-function proj_id = astra_create_projector(type, proj_geom, vol_geom)
+function proj_id = astra_create_projector(type, proj_geom, vol_geom, options)
%--------------------------------------------------------------------------
-% proj_id = astra_create_projector(type, proj_geom, vol_geom)
+% proj_id = astra_create_projector(type, proj_geom, vol_geom, options)
%
% Create a new projector object based on projection and volume geometry.
% Used when the default values of each projector are sufficient.
@@ -9,6 +9,7 @@ function proj_id = astra_create_projector(type, proj_geom, vol_geom)
% type: type of the projector. 'blob', 'line', 'linear' 'strip', ... See API for more information.
% proj_geom: MATLAB struct containing the projection geometry.
% vol_geom: MATLAB struct containing the volume geometry.
+% options: Optional MATLAB struct containing projector options (like: 'GPUindex', 'DetectorSuperSampling', and 'VoxelSuperSampling')
% proj_id: identifier of the projector as it is now stored in the astra-library.
%--------------------------------------------------------------------------
%--------------------------------------------------------------------------
@@ -38,6 +39,10 @@ if strcmp(type,'blob')
cfg_proj.Kernel.KernelValues = blob_values;
end
+if exist('options', 'var')
+ cfg_proj.options = options;
+end
+
if strcmp(type,'linear3d') || strcmp(type,'linearcone') || strcmp(type,'cuda3d')
proj_id = astra_mex_projector3d('create', cfg_proj);
else
diff --git a/matlab/tools/astra_create_reconstruction_cuda.m b/matlab/tools/astra_create_reconstruction_cuda.m
index 7d9e1dd..7d0421c 100644
--- a/matlab/tools/astra_create_reconstruction_cuda.m
+++ b/matlab/tools/astra_create_reconstruction_cuda.m
@@ -45,7 +45,7 @@ if strcmp(rec_type,'')
end
% configure
-cfg = astra_struct('SIRT_CUDA');
+cfg = astra_struct(rec_type);
cfg.ProjectionGeometry = proj_geom;
cfg.ReconstructionGeometry = vol_geom;
cfg.ProjectionDataId = sinogram_id;
diff --git a/matlab/tools/astra_create_vol_geom.m b/matlab/tools/astra_create_vol_geom.m
index ea975e6..a3ba7de 100644
--- a/matlab/tools/astra_create_vol_geom.m
+++ b/matlab/tools/astra_create_vol_geom.m
@@ -15,6 +15,7 @@ function vol_geom = astra_create_vol_geom(varargin)
% vol_geom: MATLAB struct containing all information of the geometry.
%--------------------------------------------------------------------------
% vol_geom = astra_create_vol_geom(row_count, col_count, slice_count);
+% vol_geom = astra_create_vol_geom(row_count, col_count, slice_count, min_x, max_x, min_y, max_y, min_z, max_z);
%
% Create a 3D volume geometry. See the API for more information.
% row_count: number of rows.
@@ -93,4 +94,18 @@ elseif numel(varargin) == 3
vol_geom.GridRowCount = varargin{1};
vol_geom.GridColCount = varargin{2};
vol_geom.GridSliceCount = varargin{3};
+
+% astra_create_vol_geom(row_count, col_count, slice_count, min_x, max_x, min_y, max_y, min_z, max_z)
+elseif numel(varargin) == 9
+ vol_geom = struct();
+ vol_geom.GridRowCount = varargin{1};
+ vol_geom.GridColCount = varargin{2};
+ vol_geom.GridSliceCount = varargin{3};
+ vol_geom.option.WindowMinX = varargin{4};
+ vol_geom.option.WindowMaxX = varargin{5};
+ vol_geom.option.WindowMinY = varargin{6};
+ vol_geom.option.WindowMaxY = varargin{7};
+ vol_geom.option.WindowMinZ = varargin{8};
+ vol_geom.option.WindowMaxZ = varargin{9};
+
end
diff --git a/matlab/tools/astra_mex_direct.m b/matlab/tools/astra_mex_direct.m
new file mode 100644
index 0000000..58c4fd2
--- /dev/null
+++ b/matlab/tools/astra_mex_direct.m
@@ -0,0 +1,24 @@
+function [varargout] = astra_mex_direct(varargin)
+%------------------------------------------------------------------------
+% Reference page in Help browser
+% <a href="matlab:docsearch('astra_mex_direct' )">astra_mex_data3d</a>.
+%------------------------------------------------------------------------
+%------------------------------------------------------------------------
+% This file is part of the ASTRA Toolbox
+%
+% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
+% 2014-2015, CWI, Amsterdam
+% License: Open Source under GPLv3
+% Contact: astra@uantwerpen.be
+% Website: http://sf.net/projects/astra-toolbox
+%------------------------------------------------------------------------
+% $Id$
+if nargout == 0
+ astra_mex_direct_c(varargin{:});
+ if exist('ans','var')
+ varargout{1} = ans;
+ end
+else
+ varargout = cell(1,nargout);
+ [varargout{:}] = astra_mex_direct_c(varargin{:});
+end
diff --git a/matlab/tools/astra_mex_plugin.m b/matlab/tools/astra_mex_plugin.m
new file mode 100644
index 0000000..4159365
--- /dev/null
+++ b/matlab/tools/astra_mex_plugin.m
@@ -0,0 +1,24 @@
+function [varargout] = astra_mex_plugin(varargin)
+%------------------------------------------------------------------------
+% Reference page in Help browser
+% <a href="matlab:docsearch('astra_mex_plugin' )">astra_mex_plugin</a>.
+%------------------------------------------------------------------------
+%------------------------------------------------------------------------
+% This file is part of the ASTRA Toolbox
+%
+% Copyright: 2010-2015, iMinds-Vision Lab, University of Antwerp
+% 2014-2015, CWI, Amsterdam
+% License: Open Source under GPLv3
+% Contact: astra@uantwerpen.be
+% Website: http://sf.net/projects/astra-toolbox
+%------------------------------------------------------------------------
+% $Id$
+if nargout == 0
+ astra_mex_plugin_c(varargin{:});
+ if exist('ans','var')
+ varargout{1} = ans;
+ end
+else
+ varargout = cell(1,nargout);
+ [varargout{:}] = astra_mex_plugin_c(varargin{:});
+end \ No newline at end of file
diff --git a/matlab/tools/opTomo.m b/matlab/tools/opTomo.m
index 14128d2..04b3634 100644
--- a/matlab/tools/opTomo.m
+++ b/matlab/tools/opTomo.m
@@ -44,11 +44,9 @@ classdef opTomo < opSpot
vol_id
fp_alg_id
bp_alg_id
+ proj_id
% ASTRA IDs handle
astra_handle
- % geometries
- proj_geom;
- vol_geom;
end % properties
properties ( SetAccess = private, GetAccess = public )
@@ -139,6 +137,17 @@ classdef opTomo < opSpot
error(['Only type ' 39 'cuda' 39 ' is supported ' ...
'for 3D geometries.'])
end
+
+ % setup projector
+ cfg = astra_struct('cuda3d');
+ cfg.ProjectionGeometry = proj_geom;
+ cfg.VolumeGeometry = vol_geom;
+ cfg.option.GPUindex = gpu_index;
+
+ % create projector
+ op.proj_id = astra_mex_projector3d('create', cfg);
+ % create handle to ASTRA object, for cleaning up
+ op.astra_handle = opTomo_helper_handle(op.proj_id);
% create a function handle
op.funHandle = @opTomo_intrnl3D;
@@ -148,8 +157,6 @@ classdef opTomo < opSpot
% pass object properties
op.proj_size = proj_size;
op.vol_size = vol_size;
- op.proj_geom = proj_geom;
- op.vol_geom = vol_geom;
op.cflag = false;
op.sweepflag = false;
@@ -169,10 +176,12 @@ classdef opTomo < opSpot
if issparse(x)
x = full(x);
end
-
- % convert input to single
- if isa(x, 'single') == false
+
+ if isa(x, 'double')
+ isdouble = true;
x = single(x);
+ else
+ isdouble = false;
end
% the multiplication
@@ -180,6 +189,10 @@ classdef opTomo < opSpot
% make sure output is column vector
y = y(:);
+
+ if isdouble
+ y = double(y);
+ end
end % multiply
@@ -194,7 +207,7 @@ classdef opTomo < opSpot
function y = opTomo_intrnl2D(op,x,mode)
if mode == 1
- % X is passed as a vector, reshape it into an image.
+ % x is passed as a vector, reshape it into an image.
x = reshape(x, op.vol_size);
% Matlab data copied to ASTRA data
@@ -206,7 +219,7 @@ classdef opTomo < opSpot
% retrieve Matlab array
y = astra_mex_data2d('get_single', op.sino_id);
else
- % X is passed as a vector, reshape it into a sinogram.
+ % x is passed as a vector, reshape it into a sinogram.
x = reshape(x, op.proj_size);
% Matlab data copied to ASTRA data
@@ -218,6 +231,7 @@ classdef opTomo < opSpot
% retrieve Matlab array
y = astra_mex_data2d('get_single', op.vol_id);
end
+
end % opTomo_intrnl2D
@@ -225,53 +239,16 @@ classdef opTomo < opSpot
function y = opTomo_intrnl3D(op,x,mode)
if mode == 1
- % X is passed as a vector, reshape it into an image
+ % x is passed as a vector, reshape it into an image
x = reshape(x, op.vol_size);
- % initialize output
- y = zeros(op.proj_size, 'single');
-
- % link matlab array to ASTRA
- vol_id = astra_mex_data3d_c('link', '-vol', op.vol_geom, x, 0);
- sino_id = astra_mex_data3d_c('link', '-sino', op.proj_geom, y, 1);
-
- % initialize fp algorithm
- cfg = astra_struct('FP3D_CUDA');
- cfg.ProjectionDataId = sino_id;
- cfg.VolumeDataId = vol_id;
-
- alg_id = astra_mex_algorithm('create', cfg);
-
% forward projection
- astra_mex_algorithm('iterate', alg_id);
-
- % cleanup
- astra_mex_data3d('delete', vol_id);
- astra_mex_data3d('delete', sino_id);
+ y = astra_mex_direct('FP3D', op.proj_id, x);
else
- % X is passed as a vector, reshape it into projection data
+ % x is passed as a vector, reshape it into projection data
x = reshape(x, op.proj_size);
-
- % initialize output
- y = zeros(op.vol_size,'single');
-
- % link matlab array to ASTRA
- vol_id = astra_mex_data3d_c('link', '-vol', op.vol_geom, y, 1);
- sino_id = astra_mex_data3d_c('link', '-sino', op.proj_geom, x, 0);
- % initialize bp algorithm
- cfg = astra_struct('BP3D_CUDA');
- cfg.ProjectionDataId = sino_id;
- cfg.ReconstructionDataId = vol_id;
-
- alg_id = astra_mex_algorithm('create', cfg);
-
- % backprojection
- astra_mex_algorithm('iterate', alg_id);
-
- % cleanup
- astra_mex_data3d('delete', vol_id);
- astra_mex_data3d('delete', sino_id);
+ y = astra_mex_direct('BP3D', op.proj_id, x);
end
end % opTomo_intrnl3D
generated by cgit v1.2.3 (git 2.25.1) at 2024-09-21 14:10:33 +0000