Detach Pupil from MATLAB

tdms/include/arrays/tdms_matrix.h

@@ -89,11 +89,6 @@ class Matrix {
  * definition. */
 typedef Matrix<double> CCoefficientMatrix;
 
-/** TODO: Docstring */
-struct GratingStructure : public Matrix<int> {
-  GratingStructure(const mxArray *ptr, int I_tot);
-};
-
 /**
  * @brief Defines the numerical aperture of the objective, assuming that the
  * lens is centred on the origin of the PSTD simulation.
@@ -105,8 +100,11 @@ struct GratingStructure : public Matrix<int> {
  * Pupil(i, j) thus takes the value 1 for those (i,j) indices within the
  * aperture of the lens.
  */
-struct Pupil : public Matrix<double> {
-  void initialise_from_matlab(const mxArray *ptr, int n_rows, int n_cols);
+typedef Matrix<double> Pupil;
+
+/** TODO: Docstring */
+struct GratingStructure : public Matrix<int> {
+  GratingStructure(const mxArray *ptr, int I_tot);
 };
 
 /**

tdms/src/arrays/tdms_matrix.cpp

@@ -25,24 +25,6 @@ GratingStructure::GratingStructure(const mxArray *ptr, int I_tot) {
   free_cast_matlab_2D_array(matlab_buffer);
 }
 
-void Pupil::initialise_from_matlab(const mxArray *ptr, int n_rows, int n_cols) {
-
-  if (mxIsEmpty(ptr)) { return; }
-
-  auto dims = (int *) mxGetDimensions(ptr);
-
-  if (mxGetNumberOfDimensions(ptr) != 2 || dims[0] != n_rows ||
-      dims[1] != n_cols) {
-    throw runtime_error("Pupil has dimension " + to_string(dims[0]) + "x" +
-                        to_string(dims[1]) + " but it needed to be " +
-                        to_string(n_rows) + "x" + to_string(n_cols));
-  }
-
-  double **matlab_buffer = cast_matlab_2D_array(mxGetPr(ptr), n_rows, n_cols);
-  initialise(matlab_buffer, n_rows, n_cols, true);
-  free_cast_matlab_2D_array(matlab_buffer);
-}
-
 void Vertices::initialise_from_matlab(const mxArray *ptr) {
 
   auto element = ptr_to_matrix_in(ptr, "vertices", "campssample");

tdms/src/simulation_manager/objects_from_infile.cpp

@@ -98,8 +98,7 @@ IndependentObjectsFromInfile::IndependentObjectsFromInfile(
   // if exdetintegral is flagged, setup pupil, D_tilde, and f_vec accordingly
   if (params.exdetintegral) {
     INPUT_FILE.read(f_vec);
-    pupil.initialise_from_matlab(matrices_from_input_file["Pupil"],
-                                 f_vec.x.size(), f_vec.y.size());
+    INPUT_FILE.read("Pupil", pupil);
     D_tilde.initialise(matrices_from_input_file["D_tilde"], f_vec.x.size(),
                        f_vec.y.size());
 

tdms/tests/include/array_test_class.h

@@ -186,19 +186,6 @@ class GratingStructureTest : public AbstractArrayTest {
   std::string get_class_name() override { return "GratingStructure"; }
 };
 
-/** @brief Unit tests for Pupil */
-class PupilTest : public AbstractArrayTest {
-private:
-  const int n_rows = 4, n_cols = 8;
-
-  void test_empty_construction() override;
-  void test_wrong_input_dimensions() override;
-  void test_correct_construction() override;
-
-public:
-  std::string get_class_name() override { return "Pupil"; }
-};
-
 /** @brief Unit tests for Tensor3D */
 class Tensor3DTest : public AbstractArrayTest {
 private:

tdms/tests/unit/array_tests/test_Matrix.cpp

@@ -2,7 +2,7 @@
  * @file test_Matrix.cpp
  * @author William Graham ([email protected])
  * @brief Tests for the Matrix class and its subclasses (Vertices,
- * GratingStructure, Pupil)
+ * GratingStructure)
  */
 #include <catch2/catch_test_macros.hpp>
 #include <spdlog/spdlog.h>
@@ -114,55 +114,8 @@ void GratingStructureTest::test_correct_construction() {
   delete gs;
 }
 
-void PupilTest::test_empty_construction() {
-  Pupil p;
-  dimensions_2d[0] = 0;
-  dimensions_2d[1] = n_cols;
-  create_numeric_array(2, dimensions_2d);
-  // passing in an empty array to initialise() doesn't error, but also doesn't
-  // assign additionally, the rows and columns arguments aren't even used, so
-  // can be garbage
-  p.initialise_from_matlab(matlab_input, 1, 1);
-  REQUIRE(!p.has_elements());// shouldn't have assigned any memory or pointers
-}
-
-void PupilTest::test_wrong_input_dimensions() {
-  Pupil p;
-  SECTION("Wrong number of dimensions (3D)") {
-    dimensions_3d[0] = n_rows;
-    dimensions_3d[1] = n_cols;
-    dimensions_3d[2] = 2;
-    create_numeric_array(3, dimensions_3d);
-    REQUIRE_THROWS_AS(p.initialise_from_matlab(matlab_input, n_rows, n_cols),
-                      std::runtime_error);
-    REQUIRE(!p.has_elements());
-  }
-  SECTION("Wrong dimension size") {
-    dimensions_2d[0] = 2 * n_rows;
-    dimensions_2d[1] = n_cols + 1;
-    create_numeric_array(2, dimensions_2d);
-    REQUIRE_THROWS_AS(p.initialise_from_matlab(matlab_input, n_rows, n_cols),
-                      std::runtime_error);
-    REQUIRE(!p.has_elements());
-  }
-}
-
-void PupilTest::test_correct_construction() {
-  Pupil p;
-  SECTION("Default constructor") { REQUIRE(!p.has_elements()); }
-  SECTION("Overloaded constructor") {
-    dimensions_2d[0] = n_rows;
-    dimensions_2d[1] = n_cols;
-    create_numeric_array(2, dimensions_2d);
-    REQUIRE_NOTHROW(p.initialise_from_matlab(matlab_input, n_rows, n_cols));
-    REQUIRE(p.has_elements());
-  }
-}
-
 TEST_CASE("Matrix") { MatrixTest().run_all_class_tests(); }
 
 TEST_CASE("Vertices") { VerticesTest().run_all_class_tests(); }
 
 TEST_CASE("GratingStructure") { GratingStructureTest().run_all_class_tests(); }
-
-TEST_CASE("Pupil") { PupilTest().run_all_class_tests(); }