Merge branch 'master' into parvec

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