tidy more files: tumor_cell.h

Author: salva24

clang_output.txt

@@ -28,6 +28,7 @@
 #include "core/behavior/behavior.h"
 #include "core/diffusion/diffusion_grid.h"
 #include "core/container/math_array.h"
+#include "core/agent/new_agent_event.h"
 #include "core/real_t.h"
 #include "core/interaction_force.h"
 #include "tumor_cell.h"

src/cart_cell.h

@@ -115,9 +115,7 @@ int Simulate(int argc, const char** argv) {
   }
 
   // OutputSummary operation
-  auto* summary_op = new bdm::Operation("OutputSummary");
-  // Set the interval for outputting CSV files
-  summary_op->frequency_ = kOutputCsvInterval;
+  auto* summary_op = new bdm::Operation("OutputSummary", kOutputCsvInterval);
   summary_op->AddOperationImpl(bdm::kCpu, new bdm::OutputSummary());
   scheduler->ScheduleOp(summary_op);
 

src/cart_tumor.cc

@@ -164,12 +164,15 @@ class DiffusionThomasAlgorithm : public DiffusionGrid {
   std::vector<real_t> thomas_c_z_;
 
   /// Index jump for i-direction (x-axis)
+  // NOLINTNEXTLINE(readability-identifier-naming)
   int jump_i_;
 
   /// Index jump for j-direction (y-axis)
+  // NOLINTNEXTLINE(readability-identifier-naming)
   int jump_j_;
 
   /// Index jump for k-direction (z-axis)
+  // NOLINTNEXTLINE(readability-identifier-naming)
   int jump_k_;
 
 

src/diffusion_thomas_algorithm.h

@@ -22,7 +22,17 @@
 #ifndef TUMOR_CELL_H_
 #define TUMOR_CELL_H_
 
-#include "biodynamo.h"
+#include "core/util/root.h"
+#include "core/agent/agent.h"
+#include "core/agent/agent.h"  // Ensure bdm::Agent is directly included
+#include "core/agent/cell.h"
+#include "core/behavior/behavior.h"
+#include "core/diffusion/diffusion_grid.h"
+#include "core/agent/new_agent_event.h"
+#include "core/real_t.h"
+#include "core/interaction_force.h"
+#include "core/resource_manager.h"
+#include "core/scheduler.h"
 #include "core/container/math_array.h"
 
 namespace bdm {
@@ -59,15 +69,40 @@ enum class TumorCellState : int {
 /// - Displacement computation applying pushing/adhesive forces between cells
 /// - Oncoprotein expression levels
 /// - Interactions with CAR-T cells
+
 class TumorCell : public Cell {
   BDM_AGENT_HEADER(TumorCell, Cell, 1);
 
  public:
-  TumorCell() {}
+  TumorCell()
+      : state_(TumorCellState::kAlive),
+        timer_state_(0),
+        oxygen_dgrid_(nullptr),
+        immunostimulatory_factor_dgrid_(nullptr),
+        oncoproteine_level_(0.0),
+        transformation_random_rate_(0.0),
+        attached_to_cart_(false),
+        fluid_fraction_(0.0),
+        nuclear_volume_(0.0),
+        target_cytoplasm_solid_(0.0),
+        target_nucleus_solid_(0.0),
+        target_fraction_fluid_(0.0),
+        target_relation_cytoplasm_nucleus_(0.0),
+        type_(0),
+        oxygen_consumption_rate_(0.0),
+        immunostimulatory_factor_secretion_rate_(0.0),
+        constant1_oxygen_(0.0),
+        constant2_oxygen_(0.0),
+        constant1_immunostimulatory_factor_(0.0),
+        constant2_immunostimulatory_factor_(0.0) {}
 
   explicit TumorCell(const Real3& position);
 
-  virtual ~TumorCell() {}
+  // Special member functions
+  TumorCell(const TumorCell&) = default;
+  TumorCell(TumorCell&&) = default;
+
+  ~TumorCell() override = default;
 
   /// Called when a new agent is created (after cell division)
   /// @param event The new agent event containing initialization data
@@ -198,76 +233,97 @@ class TumorCell : public Cell {
 
  private:
   /// Current state of the tumor cell
-  TumorCellState state_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  TumorCellState state_ = TumorCellState::kAlive;
 
   /// Timer to track time in the current state (in minutes)
-  int timer_state_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  int timer_state_ = 0;
 
   /// Pointer to the oxygen diffusion grid
-  DiffusionGrid* oxygen_dgrid_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  DiffusionGrid* oxygen_dgrid_ = nullptr;
 
   /// Pointer to the immunostimulatory factor diffusion grid
-  DiffusionGrid* immunostimulatory_factor_dgrid_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  DiffusionGrid* immunostimulatory_factor_dgrid_ = nullptr;
 
   /// Level of oncoprotein expression
-  real_t oncoproteine_level_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t oncoproteine_level_ = 0.0;
 
   /// Transition random rate between states:
   /// Affects the probability of transitioning and depends on the individual
   /// cell. This rate is kept constant during the cell's lifetime.
-  real_t transformation_random_rate_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t transformation_random_rate_ = 0.0;
 
   /// Flag indicating if the cell is attached to a CAR-T cell
-  bool attached_to_cart_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  bool attached_to_cart_ = false;
 
   /// Fluid fraction of the cell volume
-  real_t fluid_fraction_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t fluid_fraction_ = 0.0;
 
   /// Volume of the nucleus
-  real_t nuclear_volume_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t nuclear_volume_ = 0.0;
 
   /// Target cytoplasm solid volume for exponential relaxation
   ///
   /// Used for growing or shrinking tumor cells. The volume change follows
   /// an exponential relaxation equation toward this target volume.
-  real_t target_cytoplasm_solid_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t target_cytoplasm_solid_ = 0.0;
 
   /// Target nucleus solid volume for exponential relaxation
-  real_t target_nucleus_solid_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t target_nucleus_solid_ = 0.0;
 
   /// Target fluid fraction for exponential relaxation
-  real_t target_fraction_fluid_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t target_fraction_fluid_ = 0.0;
 
   /// Target relation between cytoplasm and nucleus volumes
-  real_t target_relation_cytoplasm_nucleus_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t target_relation_cytoplasm_nucleus_ = 0.0;
 
   /// Cell type according to oncoprotein level:
   /// Types 1-4: 1 is the most mutated and proliferative type, 4 is the least
   /// aggressive. Type 5 means the cell is dead.
-  int type_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  int type_ = 0;
 
   /// Velocity of the cell in the previous time step
-  Real3 older_velocity_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  Real3 older_velocity_ = {};
 
   /// Rate of oxygen consumption by the cell
-  real_t oxygen_consumption_rate_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t oxygen_consumption_rate_ = 0.0;
 
   /// Rate of immunostimulatory factor secretion by the cell
-  real_t immunostimulatory_factor_secretion_rate_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t immunostimulatory_factor_secretion_rate_ = 0.0;
 
   /// Constant 1 for oxygen consumption/secretion differential equation solution
-  real_t constant1_oxygen_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t constant1_oxygen_ = 0.0;
 
   /// Constant 2 for oxygen consumption/secretion differential equation solution
-  real_t constant2_oxygen_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t constant2_oxygen_ = 0.0;
 
   /// Constant 1 for immunostimulatory factor consumption/secretion differential
   /// equation solution
-  real_t constant1_immunostimulatory_factor_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t constant1_immunostimulatory_factor_ = 0.0;
 
   /// Constant 2 for immunostimulatory factor consumption/secretion differential
   /// equation solution
-  real_t constant2_immunostimulatory_factor_;
+  // NOLINTNEXTLINE(readability-identifier-naming)
+  real_t constant2_immunostimulatory_factor_ = 0.0;
 };
 
 /// Behavior class for controlling tumor cell state transitions and growth
@@ -276,12 +332,19 @@ class TumorCell : public Cell {
 /// transitions between different cell states, growth, proliferation, and death
 /// processes. It includes logic for determining when cells should enter
 /// necrosis based on oxygen levels and other environmental factors.
+
 struct StateControlGrowProliferate : public Behavior {
   BDM_BEHAVIOR_HEADER(StateControlGrowProliferate, Behavior, 1);
 
   StateControlGrowProliferate() { AlwaysCopyToNew(); }
 
-  virtual ~StateControlGrowProliferate() {}
+  // Special member functions
+  StateControlGrowProliferate(const StateControlGrowProliferate&) = default;
+  StateControlGrowProliferate& operator=(const StateControlGrowProliferate&) = default;
+  StateControlGrowProliferate(StateControlGrowProliferate&&) = default;
+  StateControlGrowProliferate& operator=(StateControlGrowProliferate&&) = default;
+
+  ~StateControlGrowProliferate() override = default;
 
   /// Execute the state control and growth behavior
   void Run(Agent* agent) override;

src/tumor_cell.h

@@ -23,10 +23,13 @@
 #define CORE_UTIL_UTILS_AUX_H_
 
 #include <cstdint>
+#include <cstddef>
 #include <tuple>
 #include <vector>
-#include "biodynamo.h"
+#include "core/real_t.h"
 #include "core/container/math_array.h"
+#include "core/operation/operation.h"
+#include "core/operation/operation_registry.h"
 
 namespace bdm {
 /// Forward declaration of TumorCell class
@@ -77,8 +80,15 @@ ComputeNumberTumorCellsAndRadius();
 struct OutputSummary : public StandaloneOperationImpl {
   BDM_OP_HEADER(OutputSummary);
 
-  /// Frequency of output (every N simulation steps)
-  uint64_t frequency_ = 1;
+  public:
+    void SetFrequency(uint64_t frequency) { frequency_ = frequency; }
+    uint64_t GetFrequency() const { return frequency_; }
+
+  private:
+    /// Frequency of output (every N simulation steps)
+    // NOLINTNEXTLINE(readability-identifier-naming)
+    uint64_t frequency_ = 1;
+
 
   /// Collects current simulation data and writes it to CSV files
   ///