Merging Sachetto changes/There is a bug in the free memory stage when…

… we use the (update_monodomain_default) function

CMakeLists.txt

@@ -3,10 +3,10 @@ IF(EXISTS "/etc/manjaro-release")
     set(CMAKE_CXX_COMPILER "/opt/cuda/bin/g++")
 ENDIF(EXISTS "/etc/manjaro-release")
 
-IF(EXISTS "/etc/debconf.conf")
-    set(CMAKE_C_COMPILER "/usr/bin/gcc-6")
-    set(CMAKE_CXX_COMPILER "/usr/bin/g++-6")
-ENDIF(EXISTS "/etc/debconf.conf")
+#IF(EXISTS "/etc/debconf.conf")
+#    set(CMAKE_C_COMPILER "/usr/bin/gcc-6")
+#    set(CMAKE_CXX_COMPILER "/usr/bin/g++-6")
+#ENDIF(EXISTS "/etc/debconf.conf")
 
 
 cmake_minimum_required(VERSION 3.0.1)
@@ -84,7 +84,7 @@ ENDIF(CUDA_FOUND)
 SET(OpenGL_GL_PREFERENCE "GLVND")
 FIND_PACKAGE(OpenGL)
 
-IF(OPENGL_FOUND AND OPENMP_FOUND)
+IF(NOT MSVC AND OPENGL_FOUND AND OPENMP_FOUND)
     SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -DCOMPILE_OPENGL")
 ENDIF()
 
@@ -97,7 +97,7 @@ ADD_SUBDIRECTORY(src/config)
 ADD_SUBDIRECTORY(src/graph)
 ADD_SUBDIRECTORY(src/vtk_utils)
 
-IF(OPENGL_FOUND AND OPENMP_FOUND)
+IF(NOT MSVC AND OPENGL_FOUND AND OPENMP_FOUND)
     set(BUILD_EXAMPLES OFF CACHE BOOL "" FORCE)
     set(BUILD_GAMES    OFF CACHE BOOL "" FORCE)
     ADD_SUBDIRECTORY(src/raylib/src)
@@ -162,7 +162,9 @@ ADD_SUBDIRECTORY(src/linear_system_solver_library)
 ADD_SUBDIRECTORY(src/save_mesh_library)
 ADD_SUBDIRECTORY(src/save_state_library)
 ADD_SUBDIRECTORY(src/restore_state_library)
+ADD_SUBDIRECTORY(src/update_monodomain_library)
 
 SET( CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/tests_bin )
 
 ADD_SUBDIRECTORY(src/tests)
+

ToDo

@@ -1,5 +1,4 @@
 Sachetto
-- Convert my internal libraries to single header libraries
 - Rewrite the flags parsing using: https://github.com/kgabis/kgflags/blob/master/examples/full_api.c
 - Correct the domain version that sets the two scars and the fibrosis from file (maybe the error is on extra-data)
 - Compare the mesh with the mesh from the scientific reports paper

clean_project.sh

@@ -1,3 +1,15 @@
 #!/bin/bash
-cd build; rm -r *; cd ..
-cd bin; rm *
+
+BUILD_DIR="build"
+
+if [[ "$#" -eq 1 ]]; then
+    BUILD_DIR=$1
+fi
+
+if [[ ! -d "${BUILD_DIR}" ]]; then
+  echo "Directory ${BUILD_DIR} does not exist"
+  exit
+fi
+
+rm -fr ${BUILD_DIR}/*
+rm -fr bin/*

example_configs/elnaz_plain_mesh_tentusscher.ini

@@ -1,7 +1,7 @@
 [main]
 num_threads=2
 dt_pde=0.02
-simulation_time=500.0
+simulation_time=10.0
 abort_on_no_activity=false
 use_adaptivity=false
 
@@ -14,6 +14,9 @@ save_pvd=true
 ;//////////////////
 file_prefix=V
 
+[update_monodomain]
+function=update_monodomain_default
+
 [assembly_matrix]
 sigma_x=0.0000176
 sigma_y=0.0001334

example_configs/plain_mesh_ddm_2d.ini

@@ -15,6 +15,8 @@ save_pvd=true
 ;//////////////////
 file_prefix=V
 
+[update_monodomain]
+function=update_monodomain_ddm
 
 [assembly_matrix]
 sigma_x=0.00176

example_configs/simple_purkinje_example.ini

@@ -16,6 +16,9 @@ file_prefix=V
 binary=false
 compress=false
 
+[update_monodomain]
+function=update_monodomain_default
+
 [assembly_matrix]
 sigma_x=0.0000176
 sigma_y=0.0001334

recompile_project.sh

@@ -1,2 +1,21 @@
 #!/bin/bash
-cd build; cmake ..; make
+
+BUILD_DIR="build"
+BUILD_TYPE="Release"
+
+if [[ "$#" -eq 1 ]]; then
+    BUILD_DIR=$1
+fi
+
+if [[ "$#" -eq 2 ]]; then
+    BUILD_DIR=$1
+    BUILD_TYPE=$2
+fi
+
+
+if [[ ! -d "${BUILD_DIR}" ]]; then
+  echo "Directory ${BUILD_DIR} does not exist. Creating."
+  mkdir ${BUILD_DIR}
+fi
+
+cd ${BUILD_DIR}; cmake -DCMAKE_BUILD_TYPE=${BUILD_TYPE} ..; make

scripts/animations/convert_png_to_mp4.sh

@@ -12,4 +12,4 @@ OUTPUT_VIDEO_FILENAME="video/ddm_3d"
 RESOLUTION="1020x720"
 
 # Execute the converting command using FFMPEG
-ffmpeg -r $FRAME_RATE -f image2 -s $RESOLUTION -start_number 1 -i $FILENAME.%04d.png -vframes $END_FRAME -vcodec libx264 -crf 25  -pix_fmt yuv420p $OUTPUT_VIDEO_FILENAME.mp4
+ffmpeg -r ${FRAME_RATE} -f image2 -s ${RESOLUTION} -start_number 1 -i ${FILENAME}.%04d.png -vframes ${END_FRAME} -vcodec libx264 -crf 25  -pix_fmt yuv420p ${OUTPUT_VIDEO_FILENAME}.mp4

scripts/calc_APD.py

@@ -1,15 +1,16 @@
 import sys
 
+
 def forwarddiff(y, h):
     n = len(y)
     res = []
-    i = 1
 
-    for i in range(1,n):
-        res.append((y[i] - y[i-1]) / h);
+    for i in range(1, n):
+        res.append((y[i] - y[i-1]) / h)
 
     return res
 
+
 def slope_start(data, start=0, epsilon=0.0001, h=1.0):
 
     d = data[start:]
@@ -19,6 +20,7 @@ def slope_start(data, start=0, epsilon=0.0001, h=1.0):
         if abs(d[i] - d[i-1]/h) > epsilon:
             return i+start
 
+
 def slope_end(data, start=0, epsilon=0.0001, h=1.0):
 
     d = data[start:]
@@ -40,11 +42,12 @@ def max_index(data, start, end):
 
     return max_index
 
+
 def index_activation(data, start=0):
     d = data[start:]
 
     for i, v in enumerate(d):
-        if d[i+start] < 0.0 and d[i+start+1] > 0.0:
+        if d[i + start] < 0.0 < d[i + start + 1]:
             return i+start
 
 def main ():

scripts/getAps.sh

@@ -1,10 +1,11 @@
+#!/usr/bin/env bash
 AP_DIR=$1
 AP_PREFIX=$2
 AP_LINE=$3
 AP_OUT=$4
 CELL_ID=$5
 
-if [ "$#" -ne 5 ]; then
+if [[ "$#" -ne 5 ]]; then
     echo "-------------------------------------------------------------------"
     echo "Usage:> $0 <AP_DIR> <AP_PREFIX> <AP_LINE> <AP_OUT> <CELL_ID>"
     echo "-------------------------------------------------------------------"

scripts/get_number_lines_from_file_in_vtk_folder.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-if [ "$#" -ne 2 ]; then
+if [[ "$#" -ne 2 ]]; then
     echo "-------------------------------------------------------------------"
     echo "Usage:> $0 <AP_DIR> <AP_PREFIX>"
     echo "-------------------------------------------------------------------"
@@ -17,7 +17,7 @@ AP_DIR=$1
 AP_PREFIX=$2
 
 FIRST_FILE=$(ls -1v ${AP_DIR}/${AP_PREFIX}_it_0_*)
-NUMBER_OF_LINES=$(wc $FIRST_FILE | awk -F ' ' '{print $1}')
+NUMBER_OF_LINES=$(wc ${FIRST_FILE} | awk -F ' ' '{print $1}')
 NUMBER_OF_LINES=$((NUMBER_OF_LINES+1))
-echo $NUMBER_OF_LINES
+echo ${NUMBER_OF_LINES}
 

scripts/plot_potential.py

@@ -1,8 +1,8 @@
-import os
 import sys
 import numpy as np
 import matplotlib.pyplot as plt
 
+
 def read_transmembrane_potential (input_file,dt,print_rate):
 	data = np.genfromtxt(input_file)
 	n = len(data)
@@ -12,19 +12,20 @@ def read_transmembrane_potential (input_file,dt,print_rate):
 
 	return timesteps, vms
 
+
 def plot_transmembrane_potential (t,v):
 	plt.grid()
-	plt.plot(t,v,label="Vm",c="black",linewidth=3.0)
+	plt.plot(t, v, label="Vm", c="black", linewidth=3.0)
 	plt.xlabel("t (ms)",fontsize=15)
 	plt.ylabel("V (mV)",fontsize=15)
 	plt.title("Action potential",fontsize=14)
 	plt.legend(loc=2,fontsize=14)
 	plt.show()
-    #plt.savefig("ap.pdf")
+
 
 def main ():
 
-	if (len(sys.argv) != 4):
+	if len(sys.argv) != 4:
 		print("-------------------------------------------------------------------------")
 		print("Usage:> python %s <input_file> <dt> <print_rate>" % sys.argv[0])
 		print("-------------------------------------------------------------------------")
@@ -41,6 +42,7 @@ def main ():
 	t, vm = read_transmembrane_potential(input_file,dt,print_rate)
 
 	plot_transmembrane_potential(t,vm)
-
+
+
 if __name__ == "__main__":
 	main()

scripts/run_valgrind.sh

@@ -1 +1,2 @@
+#!/usr/bin/env bash
 valgrind --xml=yes --xml-file=val.xml --suppressions=scripts/valgrind.supp  --leak-check=full --leak-check=yes $@

src/alg/grid/grid.c

@@ -230,9 +230,9 @@ void clean_grid(struct grid *the_grid) {
 
     struct cell_node *grid_cell = NULL;
 
-    // TODO: Think about this function
+    // TODO: Think about this function when the coupling happens ...
     // Delete nodes from the Purkinje network
-    if (the_grid->the_purkinje_network->list_nodes == NULL) 
+    if (the_grid->the_purkinje_network->list_nodes != NULL) 
     {
 
         // First free the Purkinje mesh structure
@@ -293,12 +293,12 @@ void clean_grid(struct grid *the_grid) {
 
     if(the_grid->refined_this_step) 
     {
-        arrsetlen(the_grid->refined_this_step, 0);
+        arrreset(the_grid->refined_this_step);
     }
 
     if(the_grid->free_sv_positions) 
     {
-        arrsetlen(the_grid->free_sv_positions, 0);
+        arrreset(the_grid->free_sv_positions);
     }
 }
 

src/alg/grid/grid.h

@@ -27,7 +27,7 @@ struct grid {
     uint32_t *free_sv_positions;
     uint32_t *refined_this_step;
 
-    struct cell_node* *active_cells;
+    struct cell_node **active_cells;
     bool adaptive;
 
     struct graph *the_purkinje_network;

src/alg/grid/grid_refinement.c

@@ -42,7 +42,7 @@ bool refine_grid_with_bound(struct grid *the_grid, double refinement_bound, doub
 
     uint32_t *free_sv_pos = the_grid->free_sv_positions;
 
-    arrsetlen(the_grid->refined_this_step, 0);
+    arrreset(the_grid->refined_this_step);
 
     while(continue_refining) {
         continue_refining = false;

src/config/CMakeLists.txt

@@ -10,6 +10,7 @@ set(SOURCE_FILES_CONFIG
 		save_mesh_config.c save_mesh_config.h
 		save_state_config.c save_state_config.h
 		restore_state_config.c restore_state_config.h
+		update_monodomain_config.c update_monodomain_config.h
         )
 
 ADD_LIBRARY(config STATIC ${SOURCE_FILES_CONFIG})
@@ -18,5 +19,4 @@ IF(MSVC)
 	TARGET_LINK_LIBRARIES(config string getopt utils dl)
 ELSE()
 	TARGET_LINK_LIBRARIES(config string utils dl)
-
 ENDIF()

src/config/config_common.c

@@ -4,7 +4,11 @@
 
 #include <stddef.h>
 #include "config_common.h"
+#ifdef _MSC_VER
+#include "../dlfcn-win32/dlfcn.h"
+#else
 #include <dlfcn.h>
+#endif
 
 #include "../single_file_libraries/stb_ds.h"
 

src/config/config_parser.c

@@ -46,6 +46,7 @@ static const struct option long_options[] = {
     {"save_state", required_argument, NULL, SAVE_STATE_OPT}, //Complex option
     {"restore_state", required_argument, NULL, RESTORE_STATE_OPT}, //Complex option
     {"linear_system_solver", required_argument, NULL, LINEAR_SYSTEM_SOLVER_OPT}, //Complex option
+    {"update_monodomain", required_argument, NULL, UPDATE_MONODOMAIN_SOLVER_OPT}, //Complex option
     {"visualize", no_argument, NULL, DRAW_OPT},
     {"visualization_max_v", required_argument, NULL, MAX_V_OPT},
     {"visualization_min_v", required_argument, NULL, MIN_V_OPT},
@@ -195,6 +196,7 @@ struct user_options *new_user_options() {
     user_args->save_mesh_config = NULL;
     user_args->save_state_config = NULL;
     user_args->restore_state_config = NULL;
+    user_args->update_monodomain_config = NULL;
 
     user_args->draw = false;
     user_args->max_v = 40.0f;
@@ -785,6 +787,13 @@ void parse_options(int argc, char **argv, struct user_options *user_args) {
             }
             set_config(optarg, user_args->linear_system_solver_config, user_args->config_file, "linear_system_solver");
             break;
+        case UPDATE_MONODOMAIN_SOLVER_OPT:
+            if(user_args->update_monodomain_config == NULL) {
+                print_to_stdout_and_file("Creating new update_monodomain config from command line!\n");
+                user_args->update_monodomain_config = new_update_monodomain_config();
+            }
+            set_config(optarg, user_args->update_monodomain_config, user_args->config_file, "update_monodomain");
+            break;
         case EXTRA_DATA_OPT:
             if(user_args->extra_data_config == NULL) {
                 print_to_stdout_and_file("Creating new extra data config from command line!\n");
@@ -1069,7 +1078,25 @@ int parse_config_file(void *user, const char *section, const char *name, const c
         } else {
             shput(pconfig->assembly_matrix_config->config_data.config, name, strdup(value));
         }
-    } else if(MATCH_SECTION(LINEAR_SYSTEM_SOLVER_SECTION)) {
+    }
+    else if(MATCH_SECTION(UPDATE_MONODOMAIN_SECTION)) {
+
+        if(pconfig->update_monodomain_config == NULL) {
+            pconfig->update_monodomain_config = new_update_monodomain_config();
+        }
+
+        if(MATCH_NAME("function")) {
+            pconfig->update_monodomain_config->config_data.function_name = strdup(value);
+            pconfig->update_monodomain_config->config_data.function_name_was_set = true;
+
+        } else if(MATCH_NAME("library_file")) {
+            pconfig->update_monodomain_config->config_data.library_file_path = strdup(value);
+            pconfig->update_monodomain_config->config_data.library_file_path_was_set = true;
+        } else {
+            shput(pconfig->update_monodomain_config->config_data.config, name, strdup(value));
+        }
+    }
+    else if(MATCH_SECTION(LINEAR_SYSTEM_SOLVER_SECTION)) {
 
         if(pconfig->linear_system_solver_config == NULL) {
             pconfig->linear_system_solver_config = new_linear_system_solver_config();
@@ -1201,5 +1228,8 @@ void free_user_options(struct user_options *s) {
     if(s->save_state_config)
         free_save_state_config(s->save_state_config);
 
+    if(s->update_monodomain_config)
+        free_update_monodomain_config(s->update_monodomain_config);
+
     free(s);
 }