add astra_plot_geom command and sample s024

Signed-off-by: Tim <tim.elberfeld@uantwerpen.be>

13 files changed, 139 insertions, 151 deletions

diff --git a/matlab/algorithms/plot_geom/__main.m b/matlab/algorithms/plot_geom/__main.m
deleted file mode 100644
index 607a242..0000000
--- a/matlab/algorithms/plot_geom/__main.m
+++ /dev/null
@@ -1,44 +0,0 @@
-%% main.m
-% brief             small tool to render astra geometries in matlab
-%
-% date              20.06.2018
-% author            Tim Elberfeld
-%                   imec VisionLab
-%                   University of Antwerp
-%
-% - last update     09.07.2018
-%%
-% close all;
-
-[h_gui, is_running] = create_gui_figure();
-
-%proj_geom = create_example_cone('vec');
-%proj_geom = create_example_cone('normal');
-%proj_geom = create_example_cone('helix');
-proj_geom = create_example_parallel3d('vec');
-%proj_geom = create_example_fanflat('vec');
-%proj_geom = create_example_fanflat();
-%proj_geom = create_example_parallel3d();
-
-draw_proj_geometry(proj_geom, h_gui);
-hold on;
-
-vol_magn = 10;
-phantom_size = 5;
-phantom_px = 1500;
-vx_size = phantom_size / phantom_px; % voxel size
-vol_geom = astra_create_vol_geom(phantom_px, phantom_px, phantom_px);
-line_width = 1; % line width for phantom
-draw_vol_geom(vol_geom, vx_size, h_gui, 'Magnification', vol_magn,...
-    'LineWidth', line_width, 'Color', 'r');
-
-% this magnification is empirically chosen to fit the stl file
-cad_magn = 350;
-draw_cad_phantom('stl/bunny.stl', cad_magn, h_gui);
-
-proj_geom = create_example_cone('deform_vec');
-draw_proj_geometry(proj_geom, h_gui, 'VectorIdx', 3, 'Color', 'b',...
-    'RotationAxis', [0,0,1]);
-
-hold off;
-axis equal;
diff --git a/matlab/algorithms/plot_geom/create_example_cone.m b/matlab/algorithms/plot_geom/astra_create_example_cone.m
index 598899f..598899f 100644
--- a/matlab/algorithms/plot_geom/create_example_cone.m
+++ b/matlab/algorithms/plot_geom/astra_create_example_cone.m
diff --git a/matlab/algorithms/plot_geom/create_example_fanflat.m b/matlab/algorithms/plot_geom/astra_create_example_fanflat.m
index 703a618..703a618 100644
--- a/matlab/algorithms/plot_geom/create_example_fanflat.m
+++ b/matlab/algorithms/plot_geom/astra_create_example_fanflat.m
diff --git a/matlab/algorithms/plot_geom/create_example_parallel3d.m b/matlab/algorithms/plot_geom/astra_create_example_parallel3d.m
index e6fdf8e..e6fdf8e 100644
--- a/matlab/algorithms/plot_geom/create_example_parallel3d.m
+++ b/matlab/algorithms/plot_geom/astra_create_example_parallel3d.m
diff --git a/matlab/algorithms/plot_geom/draw/create_gui_figure.m b/matlab/algorithms/plot_geom/draw/create_gui_figure.m
deleted file mode 100644
index a9acecf..0000000
--- a/matlab/algorithms/plot_geom/draw/create_gui_figure.m
+++ /dev/null
@@ -1,58 +0,0 @@
-function [h_ax, running] = create_gui_figure()
-%% create_gui_figure.m
-% brief     gui for the geometry drawing functions
-% return    h_ax        axis to draw into with draw_*() functions
-%           running     state of the rotation, needs to be passed so that
-%                       the callback will work
-% date      20.06.2018
-% author    Tim Elberfeld
-%           imec VisionLab
-%           University of Antwerp
-%%
-    h_figure = figure('name', 'geometry render', 'ButtonDownFcn', @toggle_rotation);
-    h_ax = axes(h_figure);
-    
-    set(h_figure,'CloseRequestFcn', @handle_close_fig)
-
-    xlabel('x axis')
-    ylabel('y axis')
-    zlabel('z axis')
-
-    grid on
-    box off
-    axis vis3d
-    axis equal
-    view(0,0)
-
-    running = false;
-    do_rotation();
-
-    function [] = handle_close_fig(h_figure,~)
-        % this is necessary to stop the rotation before closing the figure
-        if running
-            toggle_rotation()
-        end
-        
-        delete(h_figure);
-    end
-
-    function [] = toggle_rotation(~, ~)
-        % toggle rotation state
-        running = ~running;         
-        if running
-            view(0,0)
-            do_rotation();
-        else
-            view(45,45);
-        end
-    end
-
-    function [] = do_rotation()
-        % rotate the rendered geometry around the origin
-        camtarget([0,0,0]); % make origin the camera target and point around which to rotate
-        while running
-            camorbit(0.5,0,'camera')
-            drawnow 
-        end       
-    end
-end
\ No newline at end of file
diff --git a/matlab/algorithms/plot_geom/draw/draw_cad_phantom.m b/matlab/algorithms/plot_geom/draw/draw_cad_phantom.m
index 18873a8..92af844 100644
--- a/matlab/algorithms/plot_geom/draw/draw_cad_phantom.m
+++ b/matlab/algorithms/plot_geom/draw/draw_cad_phantom.m
@@ -1,9 +1,9 @@
-function [] = draw_cad_phantom(filename, magn, h_ax)
+function [] = draw_cad_phantom(filename, magn)
 %% draw_cad_phantom.m
 % brief             render an stl model into a 3d axis object
 % param vol_geom    volume geometry describing the phantom
-% param magn        magnification multiplier of the phantom. default = 1
 % param h_ax        handle to axis to plot into
+% param magn        magnification multiplier of the phantom. default = 1
 %
 % date              02.07.2018
 % author            Alice Presenti
@@ -11,12 +11,10 @@ function [] = draw_cad_phantom(filename, magn, h_ax)
 %                   University of Antwerp
 % Modified by Tim Elberfeld
 %%
+    h_ax = gca;    
     if nargin == 1
         magn = 1;
     end
-    if nargin == 2
-        h_ax = axes(gcf);
-    end    
 
     [v,f,~,~] = stlRead(filename);
     m = mean(v); % to center the CAD model!
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 c1ed5b0..bee83b7 100644
--- a/matlab/algorithms/plot_geom/draw/draw_cone_vec_geom.m
+++ b/matlab/algorithms/plot_geom/draw/draw_cone_vec_geom.m
@@ -34,17 +34,15 @@ function [] = draw_cone_vec_geom(h_ax, geom, options)
     % draw the points and connect with lines
     hold on;
     num_angles = size(vectors, 1);
-    for jj = 1:num_angles
-        s_source = scatter3(h_ax, xray_source(jj, 1), xray_source(jj, 2),...
-            xray_source(jj, 3));
-        s_source.Marker = options.SourceMarker;
-        s_source.MarkerEdgeColor = options.SourceMarkerColor;
-        
-        s_det = scatter3(h_ax, detector_center(jj, 1),...
-            detector_center(jj, 2), detector_center(jj, 3));
-        s_det.MarkerEdgeColor = options.DetectorMarkerColor;
-        s_det.Marker = options.DetectorMarker;
-    end
+    s_source = scatter3(h_ax, xray_source(:, 1), xray_source(:, 2),...
+        xray_source(:, 3));
+    s_source.Marker = options.SourceMarker;
+    s_source.MarkerEdgeColor = options.SourceMarkerColor;
+
+    s_det = scatter3(h_ax, detector_center(:, 1),...
+        detector_center(:, 2), detector_center(:, 3));
+    s_det.MarkerEdgeColor = options.DetectorMarkerColor;
+    s_det.Marker = options.DetectorMarker;
 
     detector = struct;
     detector.u = vectors(options.VectorIdx, 7:9);
@@ -56,10 +54,12 @@ function [] = draw_cone_vec_geom(h_ax, geom, options)
     vertices = draw_detector_vec(h_ax, detector, options);
     connect_source_detector(h_ax, vertices, detector_center, ...
         xray_source, options);
-    distances = eucl_dist3d(detector_center, xray_source);
-    mean_sdd = mean(distances(:)); % mean source detector distance
     
+    % rotation axis will be roughly as long as the source detector distance
+    distances = eucl_dist3d(detector_center, xray_source);
+    mean_sdd = mean(distances(:)); % mean source detector distance    
     draw_rotation_axis(h_ax, mean_sdd, options);
+    
     text(h_ax, xray_source(options.VectorIdx, 1),...
         xray_source(options.VectorIdx, 2),...
         xray_source(options.VectorIdx, 3), 'x-ray source');
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 9f5d620..b8261cf 100644
--- a/matlab/algorithms/plot_geom/draw/draw_fanflat_vec_geom.m
+++ b/matlab/algorithms/plot_geom/draw/draw_fanflat_vec_geom.m
@@ -29,15 +29,13 @@ function [ output_args ] = draw_fanflat_vec_geom( h_ax, geom, options)
     
     % draw the points and connect with lines
     hold on;
-    for jj = 1:num_angles
-        scatter3(h_ax, xray_source(jj, 1), xray_source(jj, 2),...
-            xray_source(jj, 3), options.SourceMarker,...
-            options.SourceMarkerColor);
-        scatter3(h_ax, detector_center(jj, 1),...
-            detector_center(jj, 2), detector_center(jj, 3),...
-            options.DetectorMarker, options.DetectorMarkerColor);
-    end   
-   
+    scatter3(h_ax, xray_source(:, 1), xray_source(:, 2),...
+        xray_source(:, 3), options.SourceMarker,...
+        options.SourceMarkerColor);
+    scatter3(h_ax, detector_center(:, 1),...
+        detector_center(:, 2), detector_center(:, 3),...
+        options.DetectorMarker, options.DetectorMarkerColor);
+       
     detector = struct;
     detector.u = [vectors(options.VectorIdx, 5:6), 0];
     detector.v = fliplr(detector.u);
@@ -49,6 +47,7 @@ function [ output_args ] = draw_fanflat_vec_geom( h_ax, geom, options)
     connect_source_detector(h_ax, vertices, detector_center,...
         xray_source, options);   
     
+    % rotation axis will be roughly as long as the source detector distance
     distances = eucl_dist3d(detector_center, xray_source);
     mean_sdd = mean(distances(:)); % mean source detector distance
     draw_rotation_axis(h_ax, mean_sdd, options);
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 351ec42..ab63e43 100644
--- a/matlab/algorithms/plot_geom/draw/draw_parallel3d_vec_geom.m
+++ b/matlab/algorithms/plot_geom/draw/draw_parallel3d_vec_geom.m
@@ -23,13 +23,11 @@ function [ ] = draw_parallel3d_vec_geom( h_ax, geom, options)
     % draw the points and connect with lines
     hold on;
     num_angles = size(vectors, 1);
-    for jj = 1:num_angles
-        scatter3(h_ax, xray_source(jj, 1), xray_source(jj, 2), xray_source(jj, 3),...
-            options.SourceMarkerColor,...
-            options.SourceMarker);
-        scatter3(h_ax, detector_center(jj, 1), detector_center(jj, 2),...
-            detector_center(jj, 3), 'k.');
-    end
+    scatter3(h_ax, xray_source(:, 1), xray_source(:, 2),...
+        xray_source(:, 3), options.SourceMarkerColor,...
+        options.SourceMarker);
+    scatter3(h_ax, detector_center(:, 1), detector_center(:, 2),...
+        detector_center(:, 3), 'k.');
 
     detector = struct;
     detector.u = vectors(options.VectorIdx, 7:9);
@@ -42,9 +40,11 @@ function [ ] = draw_parallel3d_vec_geom( h_ax, geom, options)
     connect_source_detector(h_ax, detector, detector_center, xray_source,...
         options);
     
+    % rotation axis will be roughly as long as the source detector distance
     distances = eucl_dist3d(detector_center, xray_source);
     mean_sdd = mean(distances(:)); % mean source detector distance
     draw_rotation_axis(h_ax, mean_sdd, options);
+    
     text(h_ax, xray_source(options.VectorIdx, 1),...
         xray_source(options.VectorIdx, 2), ...
         xray_source(options.VectorIdx, 3), 'x-ray source');
diff --git a/matlab/algorithms/plot_geom/draw/draw_proj_geometry.m b/matlab/algorithms/plot_geom/draw/draw_proj_geom.m
index 0d31fa2..c20ddc8 100644
--- a/matlab/algorithms/plot_geom/draw/draw_proj_geometry.m
+++ b/matlab/algorithms/plot_geom/draw/draw_proj_geom.m
@@ -1,9 +1,8 @@
-function [] = draw_proj_geometry(geom, h_ax, varargin)
-%% draw_proj_geometry.m
+function [] = draw_proj_geom(geom, varargin)
+%% draw_proj_geom.m
 % brief                         rendering function for astra geometries.
 % param geom                    the geometry to plot. If geometry type
 %                               is not supported, throws error
-% param h_ax                    handle to axis to plot into
 % ------------------------------
 % optional parameters that can be provided as string value pairs:
 %
@@ -38,10 +37,7 @@ function [] = draw_proj_geometry(geom, h_ax, varargin)
 %
 % - last update                 07.11.2018
 %%
-    if nargin == 1
-        h_ax = axes(gcf);
-    end
-
+    h_ax = gca;
     options = parseoptions(varargin);
 
     switch geom.type
diff --git a/matlab/algorithms/plot_geom/draw/draw_vol_geom.m b/matlab/algorithms/plot_geom/draw/draw_vol_geom.m
index e6d550d..0b4fe2f 100644
--- a/matlab/algorithms/plot_geom/draw/draw_vol_geom.m
+++ b/matlab/algorithms/plot_geom/draw/draw_vol_geom.m
@@ -1,17 +1,17 @@
-function [] = draw_vol_geom( vol_geom, vx_size, h_ax, varargin)
+function [] = draw_vol_geom( vol_geom, varargin)
 %% draw_vol_geom.m
 % brief                 rendering function for astra volume geometries
 %                       describing a phantom.
 % param vol_geom        volume geometry describing the phantom
 % param vx_size         voxel size in unit of preference. must be same unit
 %                       that was used to scale the projection geometry
-% param h_ax            handle to axis to plot into
 % ------------------------------
 % optional parameters that can be provided as string value pairs:
 %
 % param Magnification   magnification factor for the phantom. for small
-%                       phantoms it might be necessary to scale the render up
-%                       as otherwise it won't show up in the plot. Default = 1
+%                       phantoms it might be necessary to scale the render 
+%                       up as otherwise it won't show up in the plot.
+%                       Default = 1
 % param LineWidth       line width for the box wireframe. Default = 2
 % param Color           color of the wireframe. Default = 'r'
 %
@@ -20,12 +20,18 @@ function [] = draw_vol_geom( vol_geom, vx_size, h_ax, varargin)
 %                       imec VisionLab
 %                       University of Antwerp
 %
-% - last update         09.07.2018
+% - last update         16.11.2018
 %%
-    if nargin < 4
-        h_ax = axes(gcf);
-    end
+    h_ax = gca;
 
+    if mod(size(varargin), 2) ~= 0
+        vx_size = varargin{1};
+        varargin = varargin(2:end); % consumed vx_size from arg list
+    else
+        vx_size = 1;
+    end
+    
+    
     options = struct;
     options.Color = 'r';
     options.LineWidth = 2;
diff --git a/matlab/algorithms/plot_geom/stl/bunny.stl b/matlab/algorithms/plot_geom/stl/bunny.stl
deleted file mode 100644
index 0b7fcaa..0000000
--- a/matlab/algorithms/plot_geom/stl/bunny.stl
+++ /dev/null
diff --git a/matlab/tools/astra_plot_geom.m b/matlab/tools/astra_plot_geom.m
new file mode 100644
index 0000000..3a654fd
--- /dev/null
+++ b/matlab/tools/astra_plot_geom.m
@@ -0,0 +1,91 @@
+function [] = astra_plot_geom(geometry, varargin)
+%--------------------------------------------------------------------------
+% [] = astra_plot_geometry(geometry, varargin)
+%
+% plot an astra geometry
+%
+% geometry: any astra geometry, either volume geometry, projection
+%           geometry or an *.stl file (powered by stlRead).
+% varargin: supports a variable number of (ordered and unordered)
+%           arguments.
+%
+%           the remaining arguments depend on the input:
+%           if 'geometry' is
+%           - a volume geometry
+%             vx_size               voxel size in unit of preference. Must
+%                                   be same unit that was used to scale the
+%                                   projection geometry.
+%            and as unorderd string-value-pairs
+%             Magnification         magnification factor for the phantom.
+%                                   For small phantoms it might be
+%                                   necessary to scale the render up as 
+%                                   otherwise it won't show up in the plot.
+%                                   Default = 1
+%             LineWidth             line width for the box wireframe.
+%                                   Default = 2
+%             Color                 color of the wireframe. Default = 'r'
+%                  
+%           - a projection geometry (as unordered string-value-pairs)
+%             RotationAxis          if specified, will change the drawn
+%                                   rotation axis to provided axis.
+%                                   Must be 3-vector. Default value is
+%                                   [NaN, NaN, NaN], (meaning do not draw).
+%             RotationAxisOffset    if specified, will translate the drawn 
+%                                   rotation axis by the provided vector.
+%                                   Default = [0, 0, 0]
+%             VectorIdx             index of the vector to visualize if 
+%                                   vector geometry type. Default = 1
+%             Color                 Color for all markers and lines if not 
+%                                   otherwise specified
+%             DetectorMarker        marker for the detector locations.
+%                                   Default = '.'
+%             DetectorMarkerColor   color specifier for the detector marker.
+%                                   Default = 'k'
+%             DetectorLineColor     color for the lines drawing the 
+%                                   detector outline
+%             DetectorLineWidth     line width of detector rectangle
+%             SourceMarker          marker for the source locations
+%             SourceMarkerColor     color specifier for the source marker
+%             SourceDistance        (only for parallel3d and parallel3d_vec)
+%                                   distance of source to origin
+%             OpticalAxisColor      Color for drawing the optical axis
+%                  
+%           - a path to an *.stl file
+%             magn    -             magnification factor for vertices in
+%                                   CAD file. Default value = 1
+%
+%--------------------------------------------------------------------------
+%--------------------------------------------------------------------------
+% This file is part of the ASTRA Toolbox
+%
+% Copyright: 2010-2018, imec Vision Lab, University of Antwerp
+%            2014-2018, CWI, Amsterdam
+% License: Open Source under GPLv3
+% Contact: astra@astra-toolbox.com
+% Website: http://www.astra-toolbox.com/
+%--------------------------------------------------------------------------
+    addpath(genpath('../algorithms/plot_geom')); % add plot_geom tools to matlab path
+
+    if is_vol_geom(geometry)
+        draw_vol_geom(geometry, varargin{:});
+    elseif is_proj_geom(geometry)
+        draw_proj_geom(geometry, varargin{:});
+    elseif ischar(geometry) % assume 'geometry' is a path to a CAD file
+        draw_cad_phantom(geometry, varargin{:});
+    end
+
+    % ---- helper functions ----
+    function [ res ] = is_vol_geom(geom)
+        res = false;
+        if sum(isfield(geom, {'GridRowCount', 'GridColCount'})) == 2
+            res = true;
+        end
+    end
+
+    function [ res ] = is_proj_geom(geom)
+        res = false;
+        if isfield(geom, 'type')
+            res = true;
+        end
+    end
+end