From 54bd5902ec1c4a7d7c4f6fe94ea962465dfa8fbc Mon Sep 17 00:00:00 2001
From: Ali Aghaeifar <ali.aghaeifar@tuebingen.mpg.de>
Date: Sat, 13 Jul 2024 12:53:40 +0200
Subject: [PATCH] minor

---
 docs/source/create_phantom.rst | 3 +++
 docs/source/file format.rst    | 2 --
 docs/source/index.rst          | 3 ++-
 docs/source/io_file.rst        | 3 +++
 docs/source/tutorial.rst       | 3 ++-
 src/shapes/cylinder.cu         | 4 +++-
 src/shapes/sphere.cu           | 4 +++-
 7 files changed, 16 insertions(+), 6 deletions(-)
 create mode 100644 docs/source/create_phantom.rst
 delete mode 100644 docs/source/file format.rst
 create mode 100644 docs/source/io_file.rst

diff --git a/docs/source/create_phantom.rst b/docs/source/create_phantom.rst
new file mode 100644
index 0000000..25b3e7b
--- /dev/null
+++ b/docs/source/create_phantom.rst
@@ -0,0 +1,3 @@
+##############
+Create Phantom
+##############
\ No newline at end of file
diff --git a/docs/source/file format.rst b/docs/source/file format.rst
deleted file mode 100644
index ba4f526..0000000
--- a/docs/source/file format.rst	
+++ /dev/null
@@ -1,2 +0,0 @@
-File Format
-***********
\ No newline at end of file
diff --git a/docs/source/index.rst b/docs/source/index.rst
index bd68d72..de71ee1 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.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>
\ No newline at end of file
diff --git a/docs/source/io_file.rst b/docs/source/io_file.rst
new file mode 100644
index 0000000..6e23f8f
--- /dev/null
+++ b/docs/source/io_file.rst
@@ -0,0 +1,3 @@
+###############
+Data Structures
+###############
\ No newline at end of file
diff --git a/docs/source/tutorial.rst b/docs/source/tutorial.rst
index f581052..5037ff6 100644
--- a/docs/source/tutorial.rst
+++ b/docs/source/tutorial.rst
@@ -1,2 +1,3 @@
+########
 Tutorial
-*********
\ No newline at end of file
+########
\ No newline at end of file
diff --git a/src/shapes/cylinder.cu b/src/shapes/cylinder.cu
index e83ed15..cc6eb19 100644
--- a/src/shapes/cylinder.cu
+++ b/src/shapes/cylinder.cu
@@ -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++)
diff --git a/src/shapes/sphere.cu b/src/shapes/sphere.cu
index 3fe5e54..b2ddc56 100644
--- a/src/shapes/sphere.cu
+++ b/src/shapes/sphere.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++)