compiler-research · salva24 · Oct 26, 2025 · Oct 26, 2025 · Oct 26, 2025 · Oct 26, 2025
diff --git a/CARTopiaX_Simulation_Analysis.ipynb b/CARTopiaX_Simulation_Analysis.ipynb
@@ -26,7 +26,7 @@
     "- **pandas** >= 1.3.0\n",
     "- **matplotlib** >= 3.5.0\n",
     "- **numpy** >= 1.21.0\n",
-    "- **os** - Built-in Python module (no installation required)\n",
+    "\n",
     "\n",
     "### Installation\n",
     "\n",
@@ -145,9 +145,9 @@
     "\n",
     "Shows the absolute count of 5 tumor cell types:\n",
     "- **Type 1** (Dark Red): Most Proliferative Tumor Cells\n",
-    "- **Type 2** (Red): Very Ploliferative Tumor Cells\n",
-    "- **Type 3** (Orange): Less Ploriferative Tumor Cells\n",
-    "- **Type 4** (Yellow): Least Ploriferative Tumor Cells\n",
+    "- **Type 2** (Red): Very Proliferative Tumor Cells\n",
+    "- **Type 3** (Orange): Less Proliferative Tumor Cells\n",
+    "- **Type 4** (Yellow): Least Proliferative Tumor Cells\n",
     "- **Type 5** (Blue): Dead"
    ]
   },

diff --git a/README.md b/README.md
diff --git a/assets/images/CARTopiaXLogo_4x.png b/assets/images/CARTopiaXLogo_4x.png
diff --git a/assets/images/dose_scale1_day0_dose_scale1_day8_num_cells.png b/assets/images/dose_scale1_day0_dose_scale1_day8_num_cells.png
diff --git a/assets/images/dose_scale1_day0_num_cells.png b/assets/images/dose_scale1_day0_num_cells.png
diff --git a/assets/images/dose_scale1_day0_oncoprotein_and_oxygen.png b/assets/images/dose_scale1_day0_oncoprotein_and_oxygen.png
diff --git a/assets/images/dose_scale1_day0_type_of_cells_absolute_numbers.png b/assets/images/dose_scale1_day0_type_of_cells_absolute_numbers.png
diff --git a/assets/images/dose_scale1_day0_type_of_cells_percentage_populations.png b/assets/images/dose_scale1_day0_type_of_cells_percentage_populations.png
diff --git a/assets/images/dose_scale2_day0_dose_scale2_day5_num_cells.png b/assets/images/dose_scale2_day0_dose_scale2_day5_num_cells.png
diff --git a/assets/images/execution_times.png b/assets/images/execution_times.png
diff --git a/assets/images/model_outline.png b/assets/images/model_outline.png
diff --git a/assets/images/no_dose_tumor_evolution_paraview.png b/assets/images/no_dose_tumor_evolution_paraview.png
diff --git a/assets/images/no_doses_num_cells_and_tumor_radius.png b/assets/images/no_doses_num_cells_and_tumor_radius.png
diff --git a/assets/images/no_doses_oncoprotein_and_oxygen.png b/assets/images/no_doses_oncoprotein_and_oxygen.png
diff --git a/assets/images/no_doses_type_of_cells_absolute_numbers.png b/assets/images/no_doses_type_of_cells_absolute_numbers.png
diff --git a/assets/images/shield.png b/assets/images/shield.png
diff --git a/src/utils_aux.cc b/src/utils_aux.cc
@@ -195,7 +195,9 @@ void OutputSummary::operator()() {
   const uint64_t current_step = scheduler->GetSimulatedSteps();
 
   if (current_step % frequency_ == 0) {
-    std::ofstream file("output/final_data.csv", std::ios::app);
+    // Delete csv content current_step == 0 to, otherwise append mode
+    std::ofstream file("output/final_data.csv",
+                       current_step == 0 ? std::ios::trunc : std::ios::app);
     if (file.is_open()) {
       if (current_step == 0) {
         file