Test get_material

Also fix changes from material -> get_material

examples/scan_shepp_logan.m

@@ -2,7 +2,7 @@
 vox_arr_center = zeros(3, 1); 
 phantom_size = 500; 
 voxel_size = 1;
-water = material("water");
+water = get_material("water");
 
 % Create voxel array
 voxel_generator = voxel_shepp_logan(vox_arr_center, phantom_size, voxel_size);

src/detectors/detector.m

@@ -96,7 +96,7 @@
         function scan = air_scan(self)
             % air_scan  Generate a scan of air
             dtd = self.dist_to_detector;
-            air = material("air");
+            air = get_material("air");
             air_cylinder = @(i,j,k,e) air.get_mu(e);
             array = voxel_array(zeros(3, 1), zeros(3,1)+dtd*2, dtd/100, air_cylinder);
             scan = zeros(self.ny_pixels, self.nz_pixels, self.num_rotations);

src/get_material.m

@@ -1,15 +1,18 @@
-classdef material
+classdef get_material
     %MATERIAL A class to represent a material and its properties necessary 
     % for ray tracing and scattering
 
     properties
+        get_mu
+    end
+
+    properties (Access=protected)
         atomic_numbers
         mass_fractions
-        get_mu
         density
     end
 
-    properties (Access=private)
+    properties (Access=private, Constant)
         known_materials = {'air','blood','bone','lung','muscle','water'};
         known_densitys = [1.205E-03, 1.06, 1.92, 1.05, 1.05, 1.00];
         known_atomic_numbers = {...
@@ -47,7 +50,7 @@
     end
 
     methods
-        function self = material(varargin)
+        function self = get_material(varargin)
             %MATERIAL Construct a material object
             %   material("material_name") creates a material object with the properties of the given material, if it is available
             %   material(atomic_numbers, mass_fractions, density) creates a material object with the given properties, using the PhotonAttenuation package
@@ -56,30 +59,28 @@
                 error(aac, 'MATLAB:notEnoughInputs', 'Not enough input arguments.') 
             elseif nargin == 1
                 material_name = varargin{1};
-                assert(isstring(material_name), 'When only one input is given, it should be a string with the name of the material');
+                assert(isstring(material_name), 'assert:failure', 'When only one input is given, it should be a string with the name of the material.');
                 material_index = find(self.known_materials == lower(material_name));
                 if any(material_index)
                     self.atomic_numbers = self.known_atomic_numbers{material_index};
                     self.mass_fractions = self.known_mass_fractions{material_index};
                     self.density = self.known_densitys(material_index);
                 else
-                    aac = matlab.lang.correction.AppendArgumentsCorrection('"blood"');
-                    list_available_materials = strjoin(self.known_materials, ', ');
-                    error(aac, 'MATLAB:invalidMaterial', ...
+                    error('MATLAB:invalidMaterial', ...
                         'The material %s is not available. Available materials are: %s', ...
-                        material_name, list_available_materials);
+                        material_name, strjoin(self.known_materials, ', '));
                 end
             elseif nargin == 3
                 self.atomic_numbers = varargin{1};
                 self.mass_fractions = varargin{2};
-                self.mass_fractions = self.mass_fractions / sum(self.mass_fractions); 
                 self.density = varargin{3};
-                assert(isnumeric(self.density) && isscalar(self.density), 'The density should be a scalar number');
-                assert(isvector(self.atomic_numbers), 'The atomic numbers should be a vector');
-                assert(isvector(self.mass_fractions), 'The mass fractions should be a vector');
-                assert(length(self.atomic_numbers) == length(self.mass_fractions), 'The atomic numbers and mass fractions should have the same length');
+                assert(isvector(self.atomic_numbers), 'assert:failure', 'The atomic numbers should be a vector.');
+                assert(isvector(self.mass_fractions), 'assert:failure', 'The mass fractions should be a vector.');
+                assert(length(self.atomic_numbers) == length(self.mass_fractions), 'assert:failure', 'The atomic numbers and mass fractions should have the same length.');
+                assert(isnumeric(self.density) && isscalar(self.density), 'assert:failure', 'The density should be a scalar number.');
+                self.mass_fractions = self.mass_fractions / sum(self.mass_fractions); 
             else
-                error('MATLAB:invalidInput', 'Invalid number of input arguments');
+                error('MATLAB:invalidInput', 'Invalid number of input arguments.');
             end
             self.get_mu = @(E) sum(PhotonAttenuationQ(self.atomic_numbers, E, 1) .* self.mass_fractions) * self.density;
         end

tests/attenuation_tests.m

@@ -1,9 +1,32 @@
 classdef attenuation_tests < matlab.unittest.TestCase
     methods(Test)
         % Test methods
+
+        function test_constructor(tc)
+            % Test the constructor
+            tc.verifyError(@() get_material(), 'MATLAB:notEnoughInputs', 'Not enough input arguments.');
+            tc.verifyError(@() get_material("water", 2), 'MATLAB:invalidInput', 'Invalid number of input arguments.');
+            tc.verifyError(@() get_material(1, 2, 3, 4), 'MATLAB:invalidInput', 'Invalid number of input arguments.');
+            tc.verifyError(@() get_material(1), 'assert:failure', 'When only one input is given, it should be a string with the name of the material.');
+            tc.verifyError(@() get_material('water'), 'assert:failure', 'When only one input is given, it should be a string with the name of the material.');
+            tc.verifyError(@() get_material("wat"), 'MATLAB:invalidMaterial', 'The material wat is not available. Available materials are: air, blood, bone, lung, muscle, water.');
+            tc.verifyError(@() get_material([1, 8], [0.111898, 0.888102], [0, 1]), 'assert:failure', 'The density should be a scalar number.');
+            tc.verifyError(@() get_material([1, 8], [0.1, 0.2], "1"), 'assert:failure', 'The density should be a scalar number.');
+            tc.verifyError(@() get_material([1, 2;1, 2], [0.111898, 0.888102], 1), 'assert:failure', 'The atomic numbers should be a vector.');
+            tc.verifyError(@() get_material([1, 8], [0.1, 0.2; 0.3, 0.4], 1), 'assert:failure', 'The mass fractions should be a vector.');
+            tc.verifyError(@() get_material(1, [0.1, 0.2], 1), 'assert:failure', 'The atomic numbers and mass fractions should have the same length.');
+        end
 
         function test_water_by_z(tc)
-            water_mat = material("water");
+            water_mat = get_material("water");
+            water = @water_mat.get_mu;
+            tc.verifyEqual(water(1e-3  ), 4.078E+03, "RelTol", 1e-3)
+            tc.verifyEqual(water(1.5e-2), 1.673E+00, "RelTol", 1e-3)
+            tc.verifyEqual(water(8e-2  ), 1.837E-01, "RelTol", 1e-3)
+            tc.verifyEqual(water(1.25  ), 6.323E-02, "RelTol", 1e-3)
+            tc.verifyEqual(water(2e1   ), 1.813E-02, "RelTol", 1e-3)
+
+            water_mat = get_material([1, 8], [0.111898, 0.888102], 1);
             water = @water_mat.get_mu;
             tc.verifyEqual(water(1e-3  ), 4.078E+03, "RelTol", 1e-3)
             tc.verifyEqual(water(1.5e-2), 1.673E+00, "RelTol", 1e-3)
@@ -13,7 +36,7 @@ function test_water_by_z(tc)
         end
 
         function test_bone_by_z(tc)
-            bone_mat = material("bone");
+            bone_mat = get_material("bone");
             bone = @bone_mat.get_mu;
             tc.verifyEqual(bone(1e-3     ), 3.781E+03 * 1.92, "RelTol", 1e-3)
             tc.verifyEqual(bone(1.305E-03), 1.873E+03 * 1.92, "RelTol", 1e-2)% Check this is because of the absorption edge
@@ -27,7 +50,7 @@ function test_bone_by_z(tc)
         end
 
         function test_blood_by_z(tc)
-            blood_mat = material("blood");
+            blood_mat = get_material("blood");
             blood = @blood_mat.get_mu;
             tc.verifyEqual(blood(1e-3      ), 3.806E+03 * 1.06, "RelTol", 1e-3)
             tc.verifyEqual(blood(1.5e-3    ), 1.282E+03 * 1.06, "RelTol", 1e-3)
@@ -42,7 +65,7 @@ function test_blood_by_z(tc)
         end
 
         function test_lung_by_z(tc)
-            lung_mat = material("lung");    
+            lung_mat = get_material("lung");    
             lung = @lung_mat.get_mu;            
             tc.verifyEqual(lung(1e-3      ), 3.803E+03 * 1.050, "RelTol", 1e-3)
             tc.verifyEqual(lung(1.5e-3    ), 1.283E+03 * 1.050, "RelTol", 1e-3)
@@ -56,7 +79,7 @@ function test_lung_by_z(tc)
         end
 
         function test_muscle_by_z(tc)
-            muscle_mat = material("muscle");
+            muscle_mat = get_material("muscle");
             muscle = @muscle_mat.get_mu;
             tc.verifyEqual(muscle(1e-3      ), 3.719E+03 * 1.050, "RelTol", 1e-3)
             tc.verifyEqual(muscle(1.5e-3    ), 1.251E+03 * 1.050, "RelTol", 1e-3) 

tests/detector_tests.m

@@ -117,7 +117,7 @@ function test_get_scan_angles(tc)
 
         function test_generate_image(tc)
             detector = parallel_detector(10, [1, 1], [5, 1], 4);
-            mat = material("water"); mat.get_mu = @(e) 1;
+            mat = get_material("water"); mat.get_mu = @(e) 1;
             my_box = voxel_box([0;0;0], [3;3;3], mat);
             array = voxel_array(zeros(3, 1), [5; 5; 5], 1, my_box);
             sq2 = sqrt(2);
@@ -137,7 +137,7 @@ function test_generate_image(tc)
 
         function test_generate_image_p(tc)
             detector = parallel_detector(10, [1, 1], [5, 1], 4);
-            my_mat = material("water"); my_mat.get_mu = @(e) 1;
+            my_mat = get_material("water"); my_mat.get_mu = @(e) 1;
             my_box = voxel_box([0;0;0], [3;3;3], my_mat);
             array = voxel_array(zeros(3, 1), [5; 5; 5], 1, my_box);
             sq2 = sqrt(2);
@@ -154,7 +154,7 @@ function test_curved_generate_image_p(tc)
             dist_to_detector = 10;
             num_rotations = 16;
             detector = curved_detector(dist_to_detector, [pi/500, 0.01], [25, 10], num_rotations);
-            my_mat = material("water"); my_mat.get_mu = @(e) 1;
+            my_mat = get_material("water"); my_mat.get_mu = @(e) 1;
             my_box = voxel_box([0;0;0], [3;3;3], my_mat);
             array = voxel_array(zeros(3, 1), [5; 5; 5], 1, my_box);
             image = detector.generate_image(array);

tests/ray_tests.m

@@ -84,7 +84,7 @@ function test_siddon_ray(tc)
         end
 
         function test_calculate_mu(tc)
-            water = material("water");
+            water = get_material("water");
             my_box = voxel_box([0;0;0], [3;3;3], water);
             array = voxel_array(zeros(3, 1), [5; 5; 5], 1, my_box);
             voxel_attenuation = water.get_mu(100/1000); % Default value of ray

tests/voxel_shapes_tests.m

@@ -14,7 +14,7 @@
         function test_cylinder(tc)
             radius = 1;
             width = 2;
-            water= material("water");
+            water= get_material("water");
             my_cyl = voxel_cylinder([0, 0, 0], radius, width, water);
             for x = -2:0.25:2
                 if x ^ 2 <= radius ^ 2
@@ -59,7 +59,7 @@ function test_cylinder(tc)
         end
 
         function box(tc)
-            water = material("water");
+            water = get_material("water");
             my_box = voxel_box([0,0,0], 100, water);
             res = my_box(-100:0.5:100, -100:0.5:100, -100:0.5:100, 10);
             exp = cat(2,zeros(1, 100), zeros(1, 201)+water.get_mu(10), zeros(1, 100)); %101 includes 0
@@ -85,11 +85,11 @@ function shepp_logan(tc)
         end
 
         function test_collection(tc)
-            mat1 = material("water"); mat1.get_mu = @(e) 10;
+            mat1 = get_material("water"); mat1.get_mu = @(e) 10;
             big_box = voxel_box([0,0,0], 10, mat1);
-            mat2 = material("water"); mat2.get_mu = @(e) 5;
+            mat2 = get_material("water"); mat2.get_mu = @(e) 5;
             med_box = voxel_box([0,0,0], 6, mat2);
-            mat3 = material("water"); mat3.get_mu = @(e) 1;
+            mat3 = get_material("water"); mat3.get_mu = @(e) 1;
             small_box = voxel_box([0,0,0], 2, mat3);
             my_collection = voxel_collection(big_box, med_box, small_box);
             for x = -5:5