improvement

Author: aghaeifar

src/file_utils.cpp

@@ -280,7 +280,7 @@ bool file_utils::read_config(std::string config_filename, simulation_parameters
 }
 
 
-bool file_utils::read_fieldmap(std::string fieldmap_filename, std::vector<float> &fieldmap, std::vector<uint8_t> &mask, simulation_parameters *param)
+bool file_utils::read_phantom(std::string fieldmap_filename, std::vector<float> &fieldmap, std::vector<uint8_t> &mask, simulation_parameters *param)
 {
     if(std::filesystem::exists(fieldmap_filename) == false)
     {
@@ -296,9 +296,9 @@ bool file_utils::read_fieldmap(std::string fieldmap_filename, std::vector<float>
         dims = get_size_h5(fieldmap_filename, "fieldmap");
         if (product(dims) != fieldmap.size())
         {
-            BOOST_LOG_TRIVIAL(error) << "Error in reading fieldmap: " << fieldmap_filename;
-            BOOST_LOG_TRIVIAL(error) << "Fieldmap size does not match the expected size: " << product(dims) << " vs " << fieldmap.size() << ". Aborting...!";
-            return false;
+            BOOST_LOG_TRIVIAL(warning) << "Hint in reading fieldmap: " << fieldmap_filename;
+            BOOST_LOG_TRIVIAL(warning) << "Fieldmap size does not match the expected size: " << product(dims) << " vs " << fieldmap.size() << ". resize it...!";
+            fieldmap.resize(product(dims));
         }
         read_h5(fieldmap_filename, fieldmap.data(), "fieldmap", "float");
     }
@@ -309,13 +309,19 @@ bool file_utils::read_fieldmap(std::string fieldmap_filename, std::vector<float>
         dims = get_size_h5(fieldmap_filename, "mask");
         if (product(dims) != mask.size())
         {
-            BOOST_LOG_TRIVIAL(error) << "Error in reading mask: " << fieldmap_filename;
-            BOOST_LOG_TRIVIAL(error) << "Mask size does not match the expected size: " << product(dims) << " vs " << mask.size() << ". Aborting...!";
-            return false;
+            BOOST_LOG_TRIVIAL(warning) << "Hint in reading mask: " << fieldmap_filename;
+            BOOST_LOG_TRIVIAL(warning) << "Mask size does not match the expected size: " << product(dims) << " vs " << mask.size() << ". Aborting...!";
+            mask.resize(product(dims));
         }
         read_h5(fieldmap_filename, mask.data(), "mask", "uint8_t");
     }
 
+    if (param->mask_exist && param->fieldmap_exist && mask.size() != fieldmap.size())
+    {
+        BOOST_LOG_TRIVIAL(error) << "Fieldmap and mask sizes do not match: " << mask.size() << " vs " << fieldmap.size();
+        return false;
+    }    
+
     std::vector<float> fov(3, 0);
     file_utils::read_h5(fieldmap_filename, fov.data(), "fov", "float");
     BOOST_LOG_TRIVIAL(info) << "Size = " << dims[0] << " x " << dims[1] << " x " << dims[2] << std::endl;
@@ -330,6 +336,7 @@ bool file_utils::read_fieldmap(std::string fieldmap_filename, std::vector<float>
     return true;
 }
 
+
 std::vector<size_t> file_utils::get_size_h5(std::string input_filename, std::string dataset_name)
 {
     std::vector<size_t> dims(1,0);
@@ -384,7 +391,11 @@ bool file_utils::read_h5(std::string input_filename, void *data, std::string dat
 
 bool file_utils::save_h5(std::string output_filename, void *data, std::vector<size_t> dims, std::string dataset_name, std::string data_type)
 {
-    BOOST_LOG_TRIVIAL(info) << "Saving " << dataset_name << " to: " << std::filesystem::absolute(output_filename);
+    std::ostringstream oss;
+    for (const auto& elem : dims)
+        oss << elem << " ";
+
+    BOOST_LOG_TRIVIAL(info) << "Saving " << dataset_name << " with size = [" << oss.str() << "] to: " << std::filesystem::absolute(output_filename);
     std::filesystem::path parent_path = std::filesystem::absolute(output_filename).parent_path();
     if (std::filesystem::is_directory(parent_path) == false)
     {

src/file_utils.h

@@ -39,7 +39,7 @@ bool read_config(std::string config_filename, simulation_parameters *param, std:
 //---------------------------------------------------------------------------------------------
 //  
 //---------------------------------------------------------------------------------------------
-bool read_fieldmap(std::string fieldmap_filename, std::vector<float> &fieldmap, std::vector<uint8_t> &mask, simulation_parameters *param);
+bool read_phantom(std::string fieldmap_filename, std::vector<float> &fieldmap, std::vector<uint8_t> &mask, simulation_parameters *param);
 
 //---------------------------------------------------------------------------------------------
 //  

src/simulation_parameters.h

@@ -189,6 +189,11 @@ typedef struct simulation_parameters
         {
             BOOST_LOG_TRIVIAL(warning) << "Off-resonance map is not provided. Simulation will be performed with a perfect homogeneous field.";
         }
+        if(n_fov_scale == 0)
+        {
+            BOOST_LOG_TRIVIAL(error) << "No FoV scale is provided";
+            return false;
+        }
         return true;
     }
 } simulation_parameters;

src/spinwalk.cu

@@ -95,8 +95,15 @@ bool run(simulation_parameters param, std::map<std::string, std::vector<std::str
     {
         // ========== load files (field-maps, xyz0, m0) ==========
         std::cout << "Loading phantom: " << std::filesystem::path(filenames.at("phantom")[fieldmap_no]).filename().string() << "\n";
-        if(file_utils::read_fieldmap(filenames.at("phantom")[fieldmap_no], fieldmap, mask, &param) == false)
+        if(file_utils::read_phantom(filenames.at("phantom")[fieldmap_no], fieldmap, mask, &param) == false)
             return false;
+        param.matrix_length = mask.size(); // update the matrix length based on the mask size from the recent read
+#ifdef __CUDACC__
+        if(d_pMask.size() != mask.size())
+            d_pMask.resize(mask.size());
+        if(d_pFieldMap.size() != fieldmap.size() && param.fieldmap_exist)
+            d_pFieldMap.resize(fieldmap.size());
+#endif
         // convert fieldmap from T to degree per timestep
         float Tesla2deg = param.B0 * param.timestep_us * 1e-6 * GAMMA * RAD2DEG;
         if(param.fieldmap_exist) 
@@ -263,7 +270,7 @@ bool dump_settings(simulation_parameters param, std::map<std::string, std::vecto
         for (int i = 0; i< it->second.size(); i++)
             ss << it->first << "[" << i << "] = " << it->second.at(i) << '\n';
 
-    ss << "\nSample length scale = [";
+    ss << "\nFoV scale = [";
     for (int32_t i = 0; i < param.n_fov_scale; i++)
         ss << fov_scale[i] << ", ";
     ss << "]\n";

src/version.h

@@ -6,7 +6,7 @@
 
 #define SPINWALK_VERSION_MAJOR 1
 #define SPINWALK_VERSION_MINOR 13
-#define SPINWALK_VERSION_PATCH 3
+#define SPINWALK_VERSION_PATCH 4
 
 //---------------------------------------------------------------------------------------------
 //