Reorganize functions into packages/private functions

This also replaces modifying the path with a request to the user to modify the path.

35 files changed, 31 insertions, 64 deletions

diff --git a/matlab/algorithms/plot_geom/draw/draw_cad_phantom.m b/matlab/algorithms/plot_geom/+draw/draw_cad_phantom.m
index 92af844..55dedc4 100644
--- a/matlab/algorithms/plot_geom/draw/draw_cad_phantom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_cad_phantom.m
@@ -16,7 +16,7 @@ function [] = draw_cad_phantom(filename, magn)
         magn = 1;
     end
 
-    [v,f,~,~] = stlRead(filename);
+    [v,f,~,~] = stlTools.stlRead(filename);
     m = mean(v); % to center the CAD model!
     for i=1:3
         v(:,i) = (v(:,i)- m(i)) .* magn;
diff --git a/matlab/algorithms/plot_geom/draw/draw_cone_geom.m b/matlab/algorithms/plot_geom/+draw/draw_cone_geom.m
index ae98294..ae98294 100644
--- a/matlab/algorithms/plot_geom/draw/draw_cone_geom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_cone_geom.m
diff --git a/matlab/algorithms/plot_geom/draw/draw_cone_vec_geom.m b/matlab/algorithms/plot_geom/+draw/draw_cone_vec_geom.m
index bee83b7..dac7410 100644
--- a/matlab/algorithms/plot_geom/draw/draw_cone_vec_geom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_cone_vec_geom.m
@@ -51,7 +51,7 @@ function [] = draw_cone_vec_geom(h_ax, geom, options)
     detector.width = geom.DetectorRowCount;
     detector.origin = detector_center(options.VectorIdx, :);
 
-    vertices = draw_detector_vec(h_ax, detector, options);
+    vertices = draw.draw_detector_vec(h_ax, detector, options);
     connect_source_detector(h_ax, vertices, detector_center, ...
         xray_source, options);
     
diff --git a/matlab/algorithms/plot_geom/draw/draw_detector_vec.m b/matlab/algorithms/plot_geom/+draw/draw_detector_vec.m
index 5c293d4..5c293d4 100644
--- a/matlab/algorithms/plot_geom/draw/draw_detector_vec.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_detector_vec.m
diff --git a/matlab/algorithms/plot_geom/draw/draw_fanflat_geom.m b/matlab/algorithms/plot_geom/+draw/draw_fanflat_geom.m
index 5c97d80..a5f28ea 100644
--- a/matlab/algorithms/plot_geom/draw/draw_fanflat_geom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_fanflat_geom.m
@@ -20,6 +20,6 @@ function [] = draw_fanflat_geom( h_ax, geom, options)
         geom.DetectorWidth, 1, geom.DetectorCount, geom.ProjectionAngles,...
         geom.DistanceOriginSource, geom.DistanceOriginDetector);
     
-    draw_cone_geom(h_ax, cone_geom, options);
+    draw.draw_cone_geom(h_ax, cone_geom, options);
 end
 
diff --git a/matlab/algorithms/plot_geom/draw/draw_fanflat_vec_geom.m b/matlab/algorithms/plot_geom/+draw/draw_fanflat_vec_geom.m
index b8261cf..761d96a 100644
--- a/matlab/algorithms/plot_geom/draw/draw_fanflat_vec_geom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_fanflat_vec_geom.m
@@ -43,7 +43,7 @@ function [ output_args ] = draw_fanflat_vec_geom( h_ax, geom, options)
     detector.width = geom.DetectorCount;
     detector.origin = detector_center(options.VectorIdx, :);
     
-    vertices = draw_detector_vec(h_ax, detector, options);        
+    vertices = draw.draw_detector_vec(h_ax, detector, options);        
     connect_source_detector(h_ax, vertices, detector_center,...
         xray_source, options);   
     
diff --git a/matlab/algorithms/plot_geom/draw/draw_parallel3d_geom.m b/matlab/algorithms/plot_geom/+draw/draw_parallel3d_geom.m
index 45a8d60..45a8d60 100644
--- a/matlab/algorithms/plot_geom/draw/draw_parallel3d_geom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_parallel3d_geom.m
diff --git a/matlab/algorithms/plot_geom/draw/draw_parallel3d_vec_geom.m b/matlab/algorithms/plot_geom/+draw/draw_parallel3d_vec_geom.m
index ab63e43..e59fa91 100644
--- a/matlab/algorithms/plot_geom/draw/draw_parallel3d_vec_geom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_parallel3d_vec_geom.m
@@ -35,7 +35,7 @@ function [ ] = draw_parallel3d_vec_geom( h_ax, geom, options)
     detector.height = geom.DetectorColCount;
     detector.width = geom.DetectorRowCount;
     detector.origin = detector_center(options.VectorIdx, :);
-    detector.vertices = draw_detector_vec(h_ax, detector, options);
+    detector.vertices = draw.draw_detector_vec(h_ax, detector, options);
 
     connect_source_detector(h_ax, detector, detector_center, xray_source,...
         options);
diff --git a/matlab/algorithms/plot_geom/draw/draw_proj_geom.m b/matlab/algorithms/plot_geom/+draw/draw_proj_geom.m
index c20ddc8..9691448 100644
--- a/matlab/algorithms/plot_geom/draw/draw_proj_geom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_proj_geom.m
@@ -53,14 +53,14 @@ function [] = draw_proj_geom(geom, varargin)
             disp('DistanceOriginDetector inf');
             disp('DistanceOriginSource inf');
 
-            draw_parallel3d_geom(h_ax, geom, options);
+            draw.draw_parallel3d_geom(h_ax, geom, options);
         case 'parallel3d_vec'
             disp('type: parallel3d_vec')
             disp(['detector px: [' num2str(geom.DetectorRowCount), ', '...
                 num2str(geom.DetectorColCount) ']']);
             disp(['# angles: ' num2str(size(geom.Vectors, 1))]);
 
-            draw_parallel3d_vec_geom(h_ax, geom, options);
+            draw.draw_parallel3d_vec_geom(h_ax, geom, options);
         case 'cone'
             disp('type: cone');
             disp(['detector spacing: [' num2str(geom.DetectorSpacingX), ', '...
@@ -73,14 +73,14 @@ function [] = draw_proj_geom(geom, varargin)
             disp(['DistanceOriginDetector ' num2str(geom.DistanceOriginDetector)]);
             disp(['DistanceOriginSource ' num2str(geom.DistanceOriginSource)]);
 
-            draw_cone_geom(h_ax, geom, options);
+            draw.draw_cone_geom(h_ax, geom, options);
         case 'cone_vec'
             disp('type: cone_vec');
             disp(['detector px: [' num2str(geom.DetectorRowCount), ', ' ...
                 num2str(geom.DetectorColCount) ']']);
             disp(['# angles: ' num2str(size(geom.Vectors, 1))]);
 
-            draw_cone_vec_geom(h_ax, geom, options);
+            draw.draw_cone_vec_geom(h_ax, geom, options);
         case 'fanflat'
             disp('type: fanflat');
             disp(['detector px: ' num2str(geom.DetectorCount)]);
@@ -92,13 +92,13 @@ function [] = draw_proj_geom(geom, varargin)
             disp(['DistanceOriginSource '...
                 num2str(geom.DistanceOriginSource)]);
 
-            draw_fanflat_geom(h_ax, geom, options);
+            draw.draw_fanflat_geom(h_ax, geom, options);
         case 'fanflat_vec'
             disp('type: fanflat_vec');
             disp(['detector px: ' num2str(geom.DetectorCount)]);
             disp(['# angles: ' num2str(size(geom.Vectors, 1))]);
 
-            draw_fanflat_vec_geom(h_ax, geom, options);
+            draw.draw_fanflat_vec_geom(h_ax, geom, options);
         otherwise
             error(['Unknown geometry type ' geom.type])
     end
@@ -119,7 +119,7 @@ function [] = draw_proj_geom(geom, varargin)
         options.SourceMarkerColor = '';
         options.SourceDistance = 100;
         options.OpticalAxisColor = '';
-        options = parseargs(options, input_args{:});
+        options = parseargs.parseargs(options, input_args{:});
 
         % if the color is still empty, replace by global color
         if strcmpi(options.DetectorMarkerColor , '')
diff --git a/matlab/algorithms/plot_geom/draw/draw_vol_geom.m b/matlab/algorithms/plot_geom/+draw/draw_vol_geom.m
index 0b4fe2f..65126c2 100644
--- a/matlab/algorithms/plot_geom/draw/draw_vol_geom.m
+++ b/matlab/algorithms/plot_geom/+draw/draw_vol_geom.m
@@ -36,7 +36,7 @@ function [] = draw_vol_geom( vol_geom, varargin)
     options.Color = 'r';
     options.LineWidth = 2;
     options.Magnification = 1;
-    options = parseargs(options, varargin{:});
+    options = parseargs.parseargs(options, varargin{:});
 
     hold on;
     phantom_height = vol_geom.GridRowCount * vx_size;
diff --git a/matlab/algorithms/plot_geom/util/eucl_dist3d.m b/matlab/algorithms/plot_geom/+draw/private/eucl_dist3d.m
index 57d6cb4..57d6cb4 100644
--- a/matlab/algorithms/plot_geom/util/eucl_dist3d.m
+++ b/matlab/algorithms/plot_geom/+draw/private/eucl_dist3d.m
diff --git a/matlab/algorithms/plot_geom/util/parseargs/license.txt b/matlab/algorithms/plot_geom/+parseargs/license.txt
index cae4cd5..cae4cd5 100644
--- a/matlab/algorithms/plot_geom/util/parseargs/license.txt
+++ b/matlab/algorithms/plot_geom/+parseargs/license.txt
diff --git a/matlab/algorithms/plot_geom/util/parseargs/parseargs.m b/matlab/algorithms/plot_geom/+parseargs/parseargs.m
index 05ad613..05ad613 100644
--- a/matlab/algorithms/plot_geom/util/parseargs/parseargs.m
+++ b/matlab/algorithms/plot_geom/+parseargs/parseargs.m
diff --git a/matlab/algorithms/plot_geom/util/stlTools/license.txt b/matlab/algorithms/plot_geom/+stlTools/license.txt
index b2d00b0..b2d00b0 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/license.txt
+++ b/matlab/algorithms/plot_geom/+stlTools/license.txt
diff --git a/matlab/algorithms/plot_geom/util/stlTools/readme.txt b/matlab/algorithms/plot_geom/+stlTools/readme.txt
index b8037d6..b8037d6 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/readme.txt
+++ b/matlab/algorithms/plot_geom/+stlTools/readme.txt
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlAddVerts.m b/matlab/algorithms/plot_geom/+stlTools/stlAddVerts.m
index bc4ecbc..1894cd7 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlAddVerts.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlAddVerts.m
@@ -6,6 +6,8 @@ function [vnew, fnew] = stlAddVerts(v, f, list)
 %VNEW is the new array of vertices
 %FNEW is the new array of faces
 
+import stlTools.*
+
 % triangulation just with the slice
 faces = delaunay(list(:,1),list(:,2)); % calculate new faces
 % update object
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlDelVerts.m b/matlab/algorithms/plot_geom/+stlTools/stlDelVerts.m
index 718ac53..718ac53 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlDelVerts.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlDelVerts.m
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlDemo.m b/matlab/algorithms/plot_geom/+stlTools/stlDemo.m
index e82d8db..af46315 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlDemo.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlDemo.m
@@ -1,5 +1,7 @@
 %% STLDEMO shows how to use the functions included in the toolbox STLTOOLS
 
+import stlTools.*
+
 %% EXAMPLE 1.- How to cut a sphere and close the base to get a semisphere
 
 % load an ascii STL sample file (STLGETFORMAT and STLREADASCII)
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlGetFormat.m b/matlab/algorithms/plot_geom/+stlTools/stlGetFormat.m
index 6901b26..6901b26 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlGetFormat.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlGetFormat.m
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlGetVerts.m b/matlab/algorithms/plot_geom/+stlTools/stlGetVerts.m
index 179eff3..179eff3 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlGetVerts.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlGetVerts.m
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlPlot.m b/matlab/algorithms/plot_geom/+stlTools/stlPlot.m
index e9f17c5..e9f17c5 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlPlot.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlPlot.m
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlRead.m b/matlab/algorithms/plot_geom/+stlTools/stlRead.m
index 8803516..5775e50 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlRead.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlRead.m
@@ -5,6 +5,8 @@ function [v, f, n, name] = stlRead(fileName)
 %N are the normals
 %NAME is the name of the STL object (NOT the name of the STL file)
 
+import stlTools.*
+
 format = stlGetFormat(fileName);
 if strcmp(format,'ascii')
   [v,f,n,name] = stlReadAscii(fileName);
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlReadAscii.m b/matlab/algorithms/plot_geom/+stlTools/stlReadAscii.m
index 4490662..b035aa8 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlReadAscii.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlReadAscii.m
@@ -5,6 +5,8 @@ function [v, f, n, name] = stlReadAscii(fileName)
 %N are the normals
 %NAME is the name of the STL object (NOT the name of the STL file)
 
+import stlTools.*
+
 %======================
 % STL ascii file format
 %======================
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlReadBinary.m b/matlab/algorithms/plot_geom/+stlTools/stlReadBinary.m
index 314455d..3e04f7a 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlReadBinary.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlReadBinary.m
@@ -5,6 +5,8 @@ function [v, f, n, name] = stlReadBinary(fileName)
 %N are the normals
 %NAME is the name of the STL object (NOT the name of the STL file)
 
+import stlTools.*
+
 %=======================
 % STL binary file format
 %=======================
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlSlimVerts.m b/matlab/algorithms/plot_geom/+stlTools/stlSlimVerts.m
index 2781067..2781067 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlSlimVerts.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlSlimVerts.m
diff --git a/matlab/algorithms/plot_geom/util/stlTools/stlWrite.m b/matlab/algorithms/plot_geom/+stlTools/stlWrite.m
index 0ce5d46..0ce5d46 100644
--- a/matlab/algorithms/plot_geom/util/stlTools/stlWrite.m
+++ b/matlab/algorithms/plot_geom/+stlTools/stlWrite.m
diff --git a/matlab/algorithms/plot_geom/astra_create_example_fanflat.m b/matlab/algorithms/plot_geom/astra_create_example_fanflat.m
index 703a618..251cb47 100644
--- a/matlab/algorithms/plot_geom/astra_create_example_fanflat.m
+++ b/matlab/algorithms/plot_geom/astra_create_example_fanflat.m
@@ -19,8 +19,8 @@ function [ geom ] = create_example_fanflat( type )
     if strcmpi(type, 'normal')
          geom = make_normal_geometry();
     elseif strcmpi(type, 'vec')
-        geom = create_example_fanflat('normal');
-        geom = fanflat_to_fanflat_vec(geom);
+        geom = astra_create_example_fanflat('normal');
+        geom = astra_geom_2vec(geom);
         
     else
         geom = make_normal_geometry();
diff --git a/matlab/algorithms/plot_geom/util/magnify_proj.m b/matlab/algorithms/plot_geom/private/magnify_proj.m
index 73e892a..73e892a 100644
--- a/matlab/algorithms/plot_geom/util/magnify_proj.m
+++ b/matlab/algorithms/plot_geom/private/magnify_proj.m
diff --git a/matlab/algorithms/plot_geom/util/rotate_around3d.m b/matlab/algorithms/plot_geom/private/rotate_around3d.m
index e9f152b..e9f152b 100644
--- a/matlab/algorithms/plot_geom/util/rotate_around3d.m
+++ b/matlab/algorithms/plot_geom/private/rotate_around3d.m
diff --git a/matlab/algorithms/plot_geom/util/rotate_detector.m b/matlab/algorithms/plot_geom/private/rotate_detector.m
index 019f92a..019f92a 100644
--- a/matlab/algorithms/plot_geom/util/rotate_detector.m
+++ b/matlab/algorithms/plot_geom/private/rotate_detector.m
diff --git a/matlab/algorithms/plot_geom/util/rotate_euler3d.m b/matlab/algorithms/plot_geom/private/rotate_euler3d.m
index 6fddb57..6fddb57 100644
--- a/matlab/algorithms/plot_geom/util/rotate_euler3d.m
+++ b/matlab/algorithms/plot_geom/private/rotate_euler3d.m
diff --git a/matlab/algorithms/plot_geom/util/translate_3d.m b/matlab/algorithms/plot_geom/private/translate_3d.m
index bd51485..bd51485 100644
--- a/matlab/algorithms/plot_geom/util/translate_3d.m
+++ b/matlab/algorithms/plot_geom/private/translate_3d.m
diff --git a/matlab/algorithms/plot_geom/util/cone_to_cone_vec.m b/matlab/algorithms/plot_geom/util/cone_to_cone_vec.m
deleted file mode 100644
index 0075db9..0000000
--- a/matlab/algorithms/plot_geom/util/cone_to_cone_vec.m
+++ /dev/null
@@ -1,41 +0,0 @@
-function [ cone_vec_geom] = cone_to_cone_vec( cone_geom )
-%% cone_to_cone_vec.m
-% brief                 convert a cone beam projection geometry into a 
-%                       cone_vec geometry according to:
-%   http://www.astra-toolbox.com/docs/geom3d.html#projection-geometries
-%
-% param cone_geom       the cone beam geometry to convert
-% return cone_vec_geom  the converted geometry
-% 
-% date      21.06.2018
-% author    Tim Elberfeld
-%           imec VisionLab
-%           University of Antwerp
-%%
-    num_angles = numel(cone_geom.ProjectionAngles);
-    vectors = zeros(num_angles, 12);
-
-    for idx = 1:num_angles
-        % source
-        vectors(idx, 1) = sin(cone_geom.ProjectionAngles(idx)) * cone_geom.DistanceOriginSource;
-        vectors(idx, 2) = -cos(cone_geom.ProjectionAngles(idx)) * cone_geom.DistanceOriginSource;
-        vectors(idx, 3) = 0;
-
-        % center of detector
-        vectors(idx, 4) = -sin(cone_geom.ProjectionAngles(idx)) * cone_geom.DistanceOriginDetector;
-        vectors(idx, 5) = cos(cone_geom.ProjectionAngles(idx)) * cone_geom.DistanceOriginDetector;
-        vectors(idx, 6) = 0;
-
-        % vector from detector pixel (0,0) to (0,1)
-        vectors(idx, 7) = cos(cone_geom.ProjectionAngles(idx)) * cone_geom.DetectorSpacingX;
-        vectors(idx, 8) = sin(cone_geom.ProjectionAngles(idx)) * cone_geom.DetectorSpacingX;
-        vectors(idx, 9) = 0;
-
-        % vector from detector pixel (0,0) to (1,0)
-        vectors(idx, 10) = 0;
-        vectors(idx, 11) = 0;
-        vectors(idx, 12) = cone_geom.DetectorSpacingY;
-    end
-    
-    cone_vec_geom = astra_create_proj_geom('cone_vec', cone_geom.DetectorRowCount, cone_geom.DetectorColCount, vectors);
-end
diff --git a/matlab/algorithms/plot_geom/util/fanflat_to_fanflat_vec.m b/matlab/algorithms/plot_geom/util/fanflat_to_fanflat_vec.m
deleted file mode 100644
index 9707592..0000000
--- a/matlab/algorithms/plot_geom/util/fanflat_to_fanflat_vec.m
+++ /dev/null
@@ -1,4 +0,0 @@
-function [ vec_geom] = fanflat_to_fanflat_vec( geom )
-    vec_geom = astra_geom_2vec(geom);
-end
-
diff --git a/matlab/tools/astra_plot_geom.m b/matlab/tools/astra_plot_geom.m
index 3a654fd..62eed79 100644
--- a/matlab/tools/astra_plot_geom.m
+++ b/matlab/tools/astra_plot_geom.m
@@ -64,14 +64,16 @@ function [] = astra_plot_geom(geometry, varargin)
 % Contact: astra@astra-toolbox.com
 % Website: http://www.astra-toolbox.com/
 %--------------------------------------------------------------------------
-    addpath(genpath('../algorithms/plot_geom')); % add plot_geom tools to matlab path
+    if exist('astra_create_example_cone') ~= 2
+        error('Please add astra/algorithms/plot_geom to your path to use this function')
+    end
 
     if is_vol_geom(geometry)
-        draw_vol_geom(geometry, varargin{:});
+        draw.draw_vol_geom(geometry, varargin{:});
     elseif is_proj_geom(geometry)
-        draw_proj_geom(geometry, varargin{:});
+        draw.draw_proj_geom(geometry, varargin{:});
     elseif ischar(geometry) % assume 'geometry' is a path to a CAD file
-        draw_cad_phantom(geometry, varargin{:});
+        draw.draw_cad_phantom(geometry, varargin{:});
     end
 
     % ---- helper functions ----