minor

Author: aghaeifar

docs/source/create_phantom.rst

@@ -0,0 +1,3 @@
+##############
+Create Phantom
+##############

docs/source/file format.rst

@@ -12,5 +12,6 @@ Welcome to SpinWalk's documentation!
 
    installation
    tutorial
-   file format
+   io_file
+   create_phantom 
    View on GitHub <https://github.com/aghaeifar/SpinWalk>

docs/source/index.rst

@@ -0,0 +1,3 @@
+###############
+Data Structures
+###############

docs/source/io_file.rst

@@ -1,2 +1,3 @@
+########
 Tutorial
-*********
+########

docs/source/tutorial.rst

@@ -168,9 +168,10 @@ void cylinder::generate_mask_fieldmap()
     int32_t cyl_rad_vox, cyl_pnt_vox[3];
 
     std::cout<<"B0 direction: ["<<B0[0]<<", "<<B0[1]<<", "<<B0[2]<<"]\n";
-    std::cout<<"Allocating memory..."<<std::endl;
+    std::cout<<"Allocating memory...";
     m_fieldmap.resize(m_calc_fieldmap ? res3:0, 0.f);
     m_mask.resize(res3, 0);
+    std::cout<<"Done!\n";
     float v_size = m_fov / m_resolution;
 
     float cyl_dir[3] = {0.0, 0.0, 1.0};
@@ -181,6 +182,7 @@ void cylinder::generate_mask_fieldmap()
     theta_c2 = theta_c * theta_c;
     theta_s2 = 1. - theta_c2; // sin^2(theta)
 
+    std::cout<<"Generating...\n";
     ProgressBar bar{option::ShowPercentage{true}, option::Start{"["}, option::Fill{"="}, option::Lead{">"}, option::End{"]"}};
     auto start = std::chrono::high_resolution_clock::now();
     for (size_t c = 0; c < m_cylinder_radii.size(); c++)

src/shapes/cylinder.cu

@@ -109,11 +109,13 @@ void sphere::generate_mask_fieldmap()
     int32_t x_min, x_max, y_min, y_max, z_min, z_max;
     int32_t sph_rad_vox, sph_center_vox[3];
 
-    std::cout<<"Allocating memory..."<<std::endl;
+    std::cout<<"Allocating memory...";
     m_fieldmap.resize(m_calc_fieldmap ? res3:0, 0.f);
     m_mask.resize(res3, 0);
+    std::cout<<"Done!\n";
     float v_size = m_fov / m_resolution;
 
+    std::cout << "Generating...\n";
     ProgressBar bar{option::ShowPercentage{true}, option::Start{"["}, option::Fill{"="}, option::Lead{">"}, option::End{"]"}, option::FontStyles{std::vector<FontStyle>{FontStyle::bold}}};
     auto start = std::chrono::high_resolution_clock::now();
     for (size_t c = 0; c < m_sphere_radii.size(); c++)