updated matlab tools

3 files changed, 94 insertions, 31 deletions

diff --git a/matlab/tools/astra_geom_2vec.m b/matlab/tools/astra_geom_2vec.m
index c6dda0d..e563f47 100644
--- a/matlab/tools/astra_geom_2vec.m
+++ b/matlab/tools/astra_geom_2vec.m
@@ -1,7 +1,25 @@
-function proj_geom_out = astra_geom_2vec(proj_geom)
+function proj_geom_vec = astra_geom_2vec(proj_geom)
+%--------------------------------------------------------------------------
+% proj_geom_vec = astra_geom_2vec(proj_geom)
+%
+% Convert a conventional projection geometry to a corresponding vector-base
+% projection geometry
+%
+% proj_geom: input projection geometry (parallel, fanflat, parallel3d, cone)
+% proj_geom_vec: output vector-base projection geometry
+%--------------------------------------------------------------------------
+% 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
+%--------------------------------------------------------------------------
+% $Id$
 
 	% PARALLEL 2D
-	if strcmp(proj_geom.type,'parallel')	
+	if strcmp(proj_geom.type,'parallel')
 
 		vectors = zeros(numel(proj_geom.ProjectionAngles), 6);
 		for i = 1:numel(proj_geom.ProjectionAngles)
@@ -17,10 +35,10 @@ function proj_geom_out = astra_geom_2vec(proj_geom)
 			% vector from detector pixel 0 to 1
 			vectors(i,5) = cos(proj_geom.ProjectionAngles(i)) * proj_geom.DetectorWidth;
 			vectors(i,6) = sin(proj_geom.ProjectionAngles(i)) * proj_geom.DetectorWidth;
-	
+
 		end
 
-		proj_geom_out = astra_create_proj_geom('parallel_vec', proj_geom.DetectorCount, vectors);		
+		proj_geom_vec = astra_create_proj_geom('parallel_vec', proj_geom.DetectorCount, vectors);
 
 	% FANFLAT
 	elseif strcmp(proj_geom.type,'fanflat')
@@ -30,18 +48,18 @@ function proj_geom_out = astra_geom_2vec(proj_geom)
 
 			% source
 			vectors(i,1) = sin(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginSource;
-			vectors(i,2) = -cos(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginSource;	
+			vectors(i,2) = -cos(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginSource;
 
 			% center of detector
 			vectors(i,3) = -sin(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginDetector;
-			vectors(i,4) = cos(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginDetector;	
+			vectors(i,4) = cos(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginDetector;
 
 			% vector from detector pixel 0 to 1
 			vectors(i,5) = cos(proj_geom.ProjectionAngles(i)) * proj_geom.DetectorWidth;
 			vectors(i,6) = sin(proj_geom.ProjectionAngles(i)) * proj_geom.DetectorWidth;
 		end
 
-		proj_geom_out = astra_create_proj_geom('fanflat_vec', proj_geom.DetectorCount, vectors);
+		proj_geom_vec = astra_create_proj_geom('fanflat_vec', proj_geom.DetectorCount, vectors);
 
 	% CONE
 	elseif strcmp(proj_geom.type,'cone')
@@ -51,13 +69,13 @@ function proj_geom_out = astra_geom_2vec(proj_geom)
 
 			% source
 			vectors(i,1) = sin(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginSource;
-			vectors(i,2) = -cos(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginSource;	
-			vectors(i,3) = 0;	
+			vectors(i,2) = -cos(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginSource;
+			vectors(i,3) = 0;
 
 			% center of detector
 			vectors(i,4) = -sin(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginDetector;
-			vectors(i,5) = cos(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginDetector;	
-			vectors(i,6) = 0;	
+			vectors(i,5) = cos(proj_geom.ProjectionAngles(i)) * proj_geom.DistanceOriginDetector;
+			vectors(i,6) = 0;
 
 			% vector from detector pixel (0,0) to (0,1)
 			vectors(i,7) = cos(proj_geom.ProjectionAngles(i)) * proj_geom.DetectorSpacingX;
@@ -67,13 +85,13 @@ function proj_geom_out = astra_geom_2vec(proj_geom)
 			% vector from detector pixel (0,0) to (1,0)
 			vectors(i,10) = 0;
 			vectors(i,11) = 0;
-			vectors(i,12) = proj_geom.DetectorSpacingY;		
+			vectors(i,12) = proj_geom.DetectorSpacingY;
 		end
 
-		proj_geom_out = astra_create_proj_geom('cone_vec', proj_geom.DetectorRowCount, proj_geom.DetectorColCount, vectors);	
+		proj_geom_vec = astra_create_proj_geom('cone_vec', proj_geom.DetectorRowCount, proj_geom.DetectorColCount, vectors);
 
 	% PARALLEL 3D
-	elseif strcmp(proj_geom.type,'parallel3d')	
+	elseif strcmp(proj_geom.type,'parallel3d')
 
 		vectors = zeros(numel(proj_geom.ProjectionAngles), 12);
 		for i = 1:numel(proj_geom.ProjectionAngles)
@@ -81,12 +99,12 @@ function proj_geom_out = astra_geom_2vec(proj_geom)
 			% ray direction
 			vectors(i,1) = sin(proj_geom.ProjectionAngles(i));
 			vectors(i,2) = -cos(proj_geom.ProjectionAngles(i));
-			vectors(i,3) = 0;	
+			vectors(i,3) = 0;
 
 			% center of detector
 			vectors(i,4) = 0;
 			vectors(i,5) = 0;
-			vectors(i,6) = 0;	
+			vectors(i,6) = 0;
 
 			% vector from detector pixel (0,0) to (0,1)
 			vectors(i,7) = cos(proj_geom.ProjectionAngles(i)) * proj_geom.DetectorSpacingX;
@@ -96,11 +114,13 @@ function proj_geom_out = astra_geom_2vec(proj_geom)
 			% vector from detector pixel (0,0) to (1,0)
 			vectors(i,10) = 0;
 			vectors(i,11) = 0;
-			vectors(i,12) = proj_geom.DetectorSpacingY;		
+			vectors(i,12) = proj_geom.DetectorSpacingY;
 		end
 
-		proj_geom_out = astra_create_proj_geom('parallel3d_vec', proj_geom.DetectorRowCount, proj_geom.DetectorColCount, vectors);		
+		proj_geom_vec = astra_create_proj_geom('parallel3d_vec', proj_geom.DetectorRowCount, proj_geom.DetectorColCount, vectors);
 
 	else
 		error(['No suitable vector geometry found for type: ' proj_geom.type])
 	end
+
+end
diff --git a/matlab/tools/astra_geom_postalignment.m b/matlab/tools/astra_geom_postalignment.m
index 4115af2..c16f8ed 100644
--- a/matlab/tools/astra_geom_postalignment.m
+++ b/matlab/tools/astra_geom_postalignment.m
@@ -1,11 +1,36 @@
 function proj_geom = astra_geom_postalignment(proj_geom, factor)
+%--------------------------------------------------------------------------
+% proj_geom = astra_geom_postalignment(proj_geom, factorU)
+% proj_geom = astra_geom_postalignment(proj_geom, [factorU factorV])
+%
+% Apply a postalignment to a vector-based projection geometry.  Can be used to model the rotation axis offset.
+%
+% proj_geom: input projection geometry (vector-based only, use astra_geom_2vec to convert conventional projection geometries)
+% dim (optional): which dimension
+% s: output
+%--------------------------------------------------------------------------
+% 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 strcmp(proj_geom.type,'fanflat_vec') || strcmp(proj_geom.type,'parallel_vec')
+		proj_geom.Vectors(:,3:4) = proj_geom.Vectors(:,3:4) + factor(1) * proj_geom.Vectors(:,5:6);
 
-	if strcmp(proj_geom.type,'fanflat_vec')
-		proj_geom.Vectors(:,3:4) = proj_geom.Vectors(:,3:4) + factor * proj_geom.Vectors(:,5:6);
-		
 	elseif strcmp(proj_geom.type,'cone_vec') || strcmp(proj_geom.type,'parallel3d_vec')
-		proj_geom.Vectors(:,4:6) = proj_geom.Vectors(:,4:6) + factor * proj_geom.Vectors(:,7:9);
+		if numel(factor) == 1
+			proj_geom.Vectors(:,4:6) = proj_geom.Vectors(:,4:6) + factor * proj_geom.Vectors(:,7:9);
+		elseif numel(factor) > 1
+			proj_geom.Vectors(:,4:6) = proj_geom.Vectors(:,4:6) + factor(1) * proj_geom.Vectors(:,7:9) + factor(2) * proj_geom.Vectors(:,10:12);
+		end
 
 	else
 		error('Projection geometry not suited for postalignment correction.')
 	end
+
+end
\ No newline at end of file
diff --git a/matlab/tools/astra_geom_size.m b/matlab/tools/astra_geom_size.m
index 7044515..b3c1522 100644
--- a/matlab/tools/astra_geom_size.m
+++ b/matlab/tools/astra_geom_size.m
@@ -1,4 +1,22 @@
 function s = astra_geom_size(geom, dim)
+%--------------------------------------------------------------------------
+% s = astra_geom_size(geom, dim)
+%
+% Get the size of a volume or projection geometry.
+%
+% geom: volume or projection geometry
+% dim (optional): which dimension
+% s: output
+%--------------------------------------------------------------------------
+% 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 isfield(geom, 'GridSliceCount')
 		% 3D Volume geometry?
@@ -6,23 +24,23 @@ function s = astra_geom_size(geom, dim)
 	elseif isfield(geom, 'GridColCount')
 		% 2D Volume geometry?
 		s = [ geom.GridRowCount, geom.GridColCount ];
-	elseif strcmp(geom.type,'parallel') || strcmp(geom.type,'fanflat') 
+	elseif strcmp(geom.type,'parallel') || strcmp(geom.type,'fanflat')
 		s = [numel(geom.ProjectionAngles), geom.DetectorCount];
-		
-	elseif strcmp(geom.type,'parallel3d') || strcmp(geom.type,'cone') 
+
+	elseif strcmp(geom.type,'parallel3d') || strcmp(geom.type,'cone')
 		s =  [geom.DetectorColCount, numel(geom.ProjectionAngles), geom.DetectorRowCount];
-		
-	elseif strcmp(geom.type,'fanflat_vec')
+
+	elseif strcmp(geom.type,'fanflat_vec') || strcmp(geom.type,'parallel_vec')
 		s = [size(geom.Vectors,1), geom.DetectorCount];
-		
-	elseif strcmp(geom.type,'parallel3d_vec') || strcmp(geom.type,'cone_vec') 		
+
+	elseif strcmp(geom.type,'parallel3d_vec') || strcmp(geom.type,'cone_vec')
 		s = [geom.DetectorColCount, size(geom.Vectors,1), geom.DetectorRowCount];
-		
+
 	end
 
 	if nargin == 2
 		s = s(dim);
 	end
-	
+
 end