/*******************************************************************************
*
*  McStas, neutron ray-tracing package
*  Copyright(C) 2007 Risoe National Laboratory.
*
* %I
* Written by: Mads Bertelsen
* Date: 20.08.15
* Version: $Revision: 0.1 $
* Origin: University of Copenhagen
*
* Two dimensional spatial logger for the Union components
*
* %D
* Part of the Union components, a set of components that work together and thus
*  sperates geometry and physics within McStas.
* The use of this component requires other components to be used.
*
* 1) One specifies a number of processes using process components
* 2) These are gathered into material definitions using Union_make_material
* 3) Geometries are placed using Union_box/cylinder/sphere, assigned a material
* 4) A Union_master component placed after all of the above
*
* Only in step 4 will any simulation happen, and per default all geometries
*  defined before this master, but after the previous will be simulated here.
*
* There is a dedicated manual available for the Union_components
*
* This logger logs a 2D projection of the position of each scattering in the lab frame.
*
* This logger needs to be placed in space, the position is the center of the histogram.
*
* A logger will log something for scattering events happening to certain volumes,
*  which are specified in the target_geometry string. By leaving it blank, all
*  geometries are logged, even the ones not defined at this point in the
*  instrument file. If a list og target_geometries is selected, one can further
*  narrow the events logged by providing a list of process names in target_process
*  which need to correspond with names of defined Union_process components.
*
* To use the logger_conditional_extend function, set it to some integer value n
*  and make and extend section to the master component that runs the geometry.
* In this extend function, logger_conditional_extend[n] is 1 if the conditional
*  stack evaluated to true, 0 if not. This way one can check what rays is logged
*  using regular McStas monitors. Only works if a conditional is applied to this
*  logger.
*
* %P
* INPUT PARAMETERS:
* D_direction_1:   [string] Direction for first axis ("x", "y" or "z")
* D1_max:          [m]      Histogram boundery, max position value for first axis
* D1_min:          [m]      Histogram boundery, min position value for first axis
* n1:              [1]      Number of bins for first axis
* D_direction_2:   [string] Direction for second axis ("x", "y" or "z")
* D2_max:          [m]      Histogram boundery, max position value for second axis
* D2_min:          [m]      Histogram boundery, min position value for second axis
* n2:              [1]      Number of bins for second axis
* filename:        [string] Filename of produced data file
* target_geometry: [string] Comma seperated list of geometry names that will be logged, leave empty for all volumes (even not defined yet)
* target_process:  [string] Comma seperated names of physical processes, if volumes are selected, one can select Union_process names
* order_total:     [1]      Only log rays that scatter for the n'th time, 0 for all orders
* order_volume:    [1]      Only log rays that scatter for the n'th time in the same geometry
* order_volume_process: [1] Only log rays that scatter for the n'th time in the same geometry, using the same process
* logger_conditional_extend_index: [1] If a conditional is used with this logger, the result of each conditional calculation can be made available in extend as a array called "logger_conditional_extend", and one would then acces logger_conditional_extend[n] if logger_conditional_extend_index is set to n
* init:            [string] Name of Union_init component (typically "init", default)
*
* CALCULATED PARAMETERS:
*
* GLOBAL PARAMETERS:
*
* %L
*
* %E
******************************************************************************/

DEFINE COMPONENT Union_logger_2D_space

SETTING PARAMETERS(string target_geometry="NULL", string target_process="NULL",
                   string D_direction_1="x", D1_min=-5, D1_max=5, n1=90,
                   string D_direction_2="z", D2_min=-5, D2_max=5, n2=90,
                   string filename="NULL", order_total=0, order_volume=0, order_volume_process=0, logger_conditional_extend_index=-1, string init="init")


/* Neutron parameters: (x,y,z,vx,vy,vz,t,sx,sy,sz,p) */

SHARE
%{
#ifndef Union
#error "The Union_init component must be included before this Union_logger_2D_space component"
#endif

struct temp_2DS_data_element_struct {
 int index_1;
 int index_2;
 double weight;
};

struct temp_2DS_data_struct {
  int num_elements;
  int allocated_elements;
  struct temp_2DS_data_element_struct *elements;
};

struct a_2DS_storage_struct {
  struct Detector_2D_struct Detector_2D;
  struct temp_2DS_data_struct temp_2DS_data;
  int dim_1_choice;
  int dim_2_choice;
  int order;
  int order_in_this_volume;
  int order_process_in_this_volume;
  
  Coords position;
  Rotation rotation;
  Rotation t_rotation;
};

// record_to_temp
// Would be nice if x y z, k_new and k_old were all coords
void record_to_temp_2DS(Coords *position, double *k_new, double *k_old, double p, double p_old, double time, int scattered_in_this_volume, int scattered_in_this_volume_by_this_process, int total_number_of_scattering_events, struct logger_struct *logger, struct logger_with_data_struct *logger_with_data_array) {

  struct a_2DS_storage_struct *storage;
  storage = logger->data_union.p_2DS_storage;
  
  int add_point = 1;

  if (storage->order != 0) {
    if (storage->order - 1 == total_number_of_scattering_events)
      add_point = 1;
    else
      add_point = 0;
  }
  
  if (storage->order_in_this_volume != 0) {
    if (storage->order_in_this_volume - 1 == scattered_in_this_volume)
      add_point = 1;
    else
      add_point = 0;
  }
  
  if (storage->order_process_in_this_volume != 0) {
    if (storage->order_process_in_this_volume - 1 == scattered_in_this_volume_by_this_process)
      add_point = 1;
    else
      add_point = 0;
  }

  if (add_point == 1) {

    double p1,p2;

    // dim_1_choice = 0 for x, 1 for y, 2 for z. Done in initialize from input. "x" "y" "z".
    if (storage->dim_1_choice == 0)
      p1 = position->x - storage->position.x;
    else if (storage->dim_1_choice == 1)
      p1 = position->y - storage->position.y;
    else if (storage->dim_1_choice == 2)
      p1 = position->z - storage->position.z;
    
    if (storage->dim_2_choice == 0)
      p2 = position->x - storage->position.x;
    else if (storage->dim_2_choice == 1)
      p2 = position->y - storage->position.y;
    else if (storage->dim_2_choice == 2)
      p2 = position->z - storage->position.z;
  
    int i,j;
  
    // Find bin in histogram
    if (p1>storage->Detector_2D.D1min && p1<storage->Detector_2D.D1max && p2>storage->Detector_2D.D2min && p2<storage->Detector_2D.D2max) {
      i = floor((p1 - storage->Detector_2D.D1min)*storage->Detector_2D.bins_1/(storage->Detector_2D.D1max - storage->Detector_2D.D1min));
      j = floor((p2 - storage->Detector_2D.D2min)*storage->Detector_2D.bins_2/(storage->Detector_2D.D2max - storage->Detector_2D.D2min));
    
      // Save bin in histogram to temp (may need to allocate more memory)
      int index;
      //printf("number of data points used: %d space allocated for %d data points. \n",storage->temp_2DS_data.num_elements,storage->temp_2DS_data.allocated_elements);
  
      if (storage->temp_2DS_data.num_elements < storage->temp_2DS_data.allocated_elements) {
        storage->temp_2DS_data.elements[storage->temp_2DS_data.num_elements].index_1 = i;
        storage->temp_2DS_data.elements[storage->temp_2DS_data.num_elements].index_2 = j;
        storage->temp_2DS_data.elements[storage->temp_2DS_data.num_elements++].weight = p;
      } else {
        // No more space, need to allocate a larger buffer for this logger. Wish I had generics.
    
        // copy current data to temp
        struct temp_2DS_data_struct temporary_storage;
        temporary_storage.num_elements = storage->temp_2DS_data.num_elements;
        temporary_storage.elements = malloc(temporary_storage.num_elements*sizeof(struct temp_2DS_data_element_struct));
    
        for (index=0;index<storage->temp_2DS_data.num_elements;index++) {
          temporary_storage.elements[index].index_1 = storage->temp_2DS_data.elements[index].index_1;
          temporary_storage.elements[index].index_2 = storage->temp_2DS_data.elements[index].index_2;
          temporary_storage.elements[index].weight = storage->temp_2DS_data.elements[index].weight;
        }
      
        // free current data
        free(storage->temp_2DS_data.elements);
    
        // allocate larger array (10 larger)
        storage->temp_2DS_data.allocated_elements = 10 + storage->temp_2DS_data.num_elements;
        storage->temp_2DS_data.elements = malloc(storage->temp_2DS_data.allocated_elements*sizeof(struct temp_2DS_data_element_struct));
    
        // copy back from temp
        for (index=0;index<storage->temp_2DS_data.num_elements;index++) {
          storage->temp_2DS_data.elements[index].index_1 = temporary_storage.elements[index].index_1;
          storage->temp_2DS_data.elements[index].index_2 = temporary_storage.elements[index].index_2;
          storage->temp_2DS_data.elements[index].weight = temporary_storage.elements[index].weight;
        }
    
        // free temporary data
        free(temporary_storage.elements);
    
        // add new data point
        storage->temp_2DS_data.elements[storage->temp_2DS_data.num_elements].index_1 = i;
        storage->temp_2DS_data.elements[storage->temp_2DS_data.num_elements].index_2 = j;
        storage->temp_2DS_data.elements[storage->temp_2DS_data.num_elements++].weight = p;
      }
  
      // If this is the first time this ray is being recorded in this logger, add it to the list of loggers that write to temp and may get it moved to perm
      if (storage->temp_2DS_data.num_elements == 1)
        add_to_logger_with_data(logger_with_data_array,logger);
      
    }
  }
  
}

// clear_temp
void clear_temp_2DS(union logger_data_union *data_union) {
  data_union->p_2DS_storage->temp_2DS_data.num_elements = 0;
}

// record_to_perm
void record_to_perm_2DS(Coords *position, double *k_new, double *k_old, double p, double p_old, double time, int scattered_in_this_volume, int scattered_in_this_volume_by_this_process, int total_number_of_scattering_events, struct logger_struct *logger, struct logger_with_data_struct *logger_with_data_array) {
  
  //printf("In record to permanent \n");
  struct a_2DS_storage_struct *storage;
  storage = logger->data_union.p_2DS_storage;

  int add_point = 1;

  if (storage->order != 0) {
    if (storage->order - 1 == total_number_of_scattering_events)
      add_point = 1;
    else
      add_point = 0;
  }
  
  if (storage->order_in_this_volume != 0) {
    if (storage->order_in_this_volume - 1 == scattered_in_this_volume)
      add_point = 1;
    else
      add_point = 0;
  }
  
  if (storage->order_process_in_this_volume != 0) {
    if (storage->order_process_in_this_volume - 1 == scattered_in_this_volume_by_this_process)
      add_point = 1;
    else
      add_point = 0;
  }

  if (add_point == 1) {
    //printf("storage was set \n");
    double p1,p2;

    // dim_1_choice = 0 for x, 1 for y, 2 for z. Done in initialize from input "x" "y" "z".
    if (storage->dim_1_choice == 0)
      p1 = position->x - storage->position.x;
      //p1 = position->x;
    else if (storage->dim_1_choice == 1)
      p1 = position->y - storage->position.y;
      //p1 = position->y;
    else if (storage->dim_1_choice == 2)
      p1 = position->z - storage->position.z;
      //p1 = position->z;
    
    if (storage->dim_2_choice == 0)
      p2 = position->x - storage->position.x;
      //p2 = position->x;
    else if (storage->dim_2_choice == 1)
      p2 = position->y - storage->position.y;
      //p2 = position->y;
    else if (storage->dim_2_choice == 2)
      p2 = position->z - storage->position.z;
      //p2 = position->z;
  
    int i,j;
  
    // Find bin in histogram
    if (p1>storage->Detector_2D.D1min && p1<storage->Detector_2D.D1max && p2>storage->Detector_2D.D2min && p2<storage->Detector_2D.D2max) {
  
      i = floor((p1 - storage->Detector_2D.D1min)*(double)storage->Detector_2D.bins_1/(storage->Detector_2D.D1max - storage->Detector_2D.D1min));
      j = floor((p2 - storage->Detector_2D.D2min)*(double)storage->Detector_2D.bins_2/(storage->Detector_2D.D2max - storage->Detector_2D.D2min));
    
      //printf("Added to statistics for monitor [%d] [%d] \n",i,j);
      //printf("indicies found\n");
      
      storage->Detector_2D.Array_N[i][j]++;
      storage->Detector_2D.Array_p[i][j] += p;
      storage->Detector_2D.Array_p2[i][j] += p*p;
    
    }
  }

}

// write_temp_to_perm
void write_temp_to_perm_2DS(union logger_data_union *data_union) {
  struct a_2DS_storage_struct *storage;
  storage = data_union->p_2DS_storage;

  int index;
  // Add all data points to the historgram, they are saved as index / weight combinations
  for (index=0;index<storage->temp_2DS_data.num_elements;index++) {
  
    storage->Detector_2D.Array_N[storage->temp_2DS_data.elements[index].index_1][storage->temp_2DS_data.elements[index].index_2]++;
    
    storage->Detector_2D.Array_p[storage->temp_2DS_data.elements[index].index_1][storage->temp_2DS_data.elements[index].index_2] += storage->temp_2DS_data.elements[index].weight;
    
    storage->Detector_2D.Array_p2[storage->temp_2DS_data.elements[index].index_1][storage->temp_2DS_data.elements[index].index_2] += storage->temp_2DS_data.elements[index].weight*storage->temp_2DS_data.elements[index].weight;
  }
  
  clear_temp_2DS(data_union);
}

// write_temp_to_perm_final_p
void write_temp_to_perm_final_p_2DS(union logger_data_union *data_union, double final_weight) {
  struct a_2DS_storage_struct *storage;
  storage = data_union->p_2DS_storage;

  int index;
  // Add all data points to the historgram, they are saved as index / weight combinations
  for (index=0;index<storage->temp_2DS_data.num_elements;index++) {
  
    storage->Detector_2D.Array_N[storage->temp_2DS_data.elements[index].index_1][storage->temp_2DS_data.elements[index].index_2]++;
    
    storage->Detector_2D.Array_p[storage->temp_2DS_data.elements[index].index_1][storage->temp_2DS_data.elements[index].index_2] += final_weight;
    
    storage->Detector_2D.Array_p2[storage->temp_2DS_data.elements[index].index_1][storage->temp_2DS_data.elements[index].index_2] += final_weight*final_weight;
  }
  
  clear_temp_2DS(data_union);
}

// Only need to define linking function for loggers once.
#ifndef UNION_LOGGER
#define UNION_LOGGER Dummy
// Linking function for loggers, finds the indicies of the specified geometries on the global_geometry_list
void manual_linking_function_logger_volumes(char *input_string, struct pointer_to_global_geometry_list *global_geometry_list, struct pointer_to_1d_int_list *accepted_volumes, char *component_name) {
    // Need to check a input_string of text for an occurance of name. If it is in the inputstring, yes return 1, otherwise 0.
   char *token;
   int loop_index;
   char local_string[512];
   
   strcpy(local_string,input_string);
   // get the first token
   token = strtok(local_string,",");
   
   // walk through other tokens
   while( token != NULL ) 
   {
      //printf( " %s\n", token );
      for (loop_index=0;loop_index<global_geometry_list->num_elements;loop_index++) {
        if (strcmp(token,global_geometry_list->elements[loop_index].name) == 0) {
          add_element_to_int_list(accepted_volumes,loop_index);
          break;
        }
        
        if (loop_index == global_geometry_list->num_elements - 1) {
          // All possible geometry names have been looked through, and the break was not executed.
          // Alert the user to this problem by showing the geometry name that was not found and the currently available geometires
            printf("\n");
            printf("ERROR: The target_geometry string \"%s\" in Union logger component \"%s\" had an entry that did not match a specified geometry. \n",input_string,component_name);
            printf("       The unrecoignized geometry name was: \"%s\" \n",token);
            printf("       The geometries available at this point (need to be defined before the logger): \n");
            for (loop_index=0;loop_index<global_geometry_list->num_elements;loop_index++)
              printf("         %s\n",global_geometry_list->elements[loop_index].name);
            exit(1);
        }
      }
      
      // Updates the token
      token = strtok(NULL,",");
   }
}

void manual_linking_function_logger_processes(char *input_string, struct physics_struct *p_physics, struct pointer_to_1d_int_list *accepted_processes, char *component_name, char *Volume_name) {
    // Need to check a input_string of text for an occurance of name. If it is in the inputstring, yes return 1, otherwise 0.
   char *token;
   int loop_index;
   char local_string[256];
   
   strcpy(local_string,input_string);
   // get the first token
   token = strtok(local_string,",");
   
   // walk through other tokens
   while( token != NULL ) 
   {
      //printf( " %s\n", token );
      for (loop_index=0;loop_index<p_physics->number_of_processes;loop_index++) {
        if (strcmp(token,p_physics->p_scattering_array[loop_index].name) == 0) {
          add_element_to_int_list(accepted_processes,loop_index);
          break;
        }
        
        if (loop_index == p_physics->number_of_processes - 1) {
          // All possible process names have been looked through, and the break was not executed.
          // Alert the user to this problem by showing the process name that was not found and the currently available processes
            printf("\n");
            printf("ERROR: The target process string \"%s\" in Union logger \"%s\" had an entry that did not match a specified process in assosiated volume \"%s\". \n",input_string,component_name,Volume_name);
            printf("       The unrecoignized process name was: \"%s\" \n",token);
            printf("       The processes defined in material \"%s\" of which  Volume \"%s\" is made: \n",p_physics->name,Volume_name);
            for (loop_index=0;loop_index<p_physics->number_of_processes;loop_index++)
              printf("         %s\n",p_physics->p_scattering_array[loop_index].name);
            exit(1);
        }
      }
      
      // Updates the token
      token = strtok(NULL,",");
   }
}
#endif

double** allocate2Ddouble_2DS(int count_x, int count_y) {
    // This function is needed to dynamically declare an array
    //  that has continous data as a static array would have,
    //  as that is the format expected by DETECTOR_OUT_2D.
    int i;

    // allocate space for actual data
    double *data = malloc(sizeof(double) * count_x * count_y);

    // create array or pointers to first elem in each 2D row
    double **ptr_array = malloc(sizeof(double*) * count_x);
    for (i = 0; i < count_x; i++) {
        ptr_array[i] = data + (i*count_y);
    }
    return ptr_array;
}

void free2Ddouble_2DS(double** ptr_array) {
    if (!ptr_array) return;
    if (ptr_array[0]) free(ptr_array[0]);
    free(ptr_array);
}

%}

DECLARE
%{
// From make material
// Needed for transport to the main component
//struct global_material_element_struct global_material_element;
//struct physics_struct this_material;

int loop_index;
int found_process;
int specified_processes;
char local_string[256];

// Reused for logger
struct pointer_to_1d_int_list accepted_processes;

struct global_logger_element_struct logger_list_element;

struct pointer_to_1d_int_list accepted_volumes;

struct logger_struct this_logger;
struct a_2DS_storage_struct this_storage;

struct loggers_struct *loggers_on_target_volume;
struct Volume_struct *target_volume;
%}

INITIALIZE
%{

  accepted_processes.elements = NULL;
  accepted_processes.num_elements = 0;
  
  accepted_volumes.elements = NULL;
  accepted_volumes.num_elements = 0;

  // Initialize storage from input
  if (D1_min >= D1_max) {
    printf("ERROR, Union logger \"%s\" had D1_min >= D1_max.\n",NAME_CURRENT_COMP);
    exit(1);
  }
  this_storage.Detector_2D.D1min = D1_min;
  this_storage.Detector_2D.D1max = D1_max;
  
  if (D2_min >= D2_max) {
    printf("ERROR, Union logger \"%s\" had D2_min >= D2_max.\n",NAME_CURRENT_COMP);
    exit(1);
  }
  this_storage.Detector_2D.D2min = D2_min;
  this_storage.Detector_2D.D2max = D2_max;
  
  if (n1 <= 0) {
    printf("ERROR, Union logger \"%s\" had n1 <= 0.\n",NAME_CURRENT_COMP);
    exit(1);
  }
  this_storage.Detector_2D.bins_1 = n1;
  
  if (n2 <= 0) {
    printf("ERROR, Union logger \"%s\" had n2 <= 0.\n",NAME_CURRENT_COMP);
    exit(1);
  }
  this_storage.Detector_2D.bins_2 = n2;
  
  //printf("past input sanitation \n");
  
  
  // Remember to take special care when deallocating this array, use free2Ddouble
  this_storage.Detector_2D.Array_N = allocate2Ddouble_2DS(n1,n2); // Here the n1 double is cast to an int
  this_storage.Detector_2D.Array_p = allocate2Ddouble_2DS(n1,n2);
  this_storage.Detector_2D.Array_p2 = allocate2Ddouble_2DS(n1,n2);
  
  int l1,l2;
  for (l1=0;l1<n1;l1++) { //n1 is technically a double, but this works fine
    for (l2=0;l2<n2;l2++) {
      this_storage.Detector_2D.Array_N[l1][l2] = 0;
      this_storage.Detector_2D.Array_p[l1][l2] = 0;
      this_storage.Detector_2D.Array_p2[l1][l2] = 0;
    }
  }
  
  //printf("past 2D pointer assignment \n");
  
  // Input sanitation for filename apparently done in 2D_detector_out
  
  if (strcmp(D_direction_1,"x") == 0 || strcmp(D_direction_1,"X") == 0) {
      this_storage.dim_1_choice = 0;
      sprintf(this_storage.Detector_2D.string_axis_1,"x [m]");
      sprintf(this_storage.Detector_2D.title_string,"2D position Union logger in plane x");
  } else if (strcmp(D_direction_1,"y") == 0 || strcmp(D_direction_1,"Y") == 0) {
      this_storage.dim_1_choice = 1;
      sprintf(this_storage.Detector_2D.string_axis_1,"y [m]");
      sprintf(this_storage.Detector_2D.title_string,"2D position Union logger in plane y");
  } else if (strcmp(D_direction_1,"z") == 0 || strcmp(D_direction_1,"Z") == 0) {
      this_storage.dim_1_choice = 2;
      sprintf(this_storage.Detector_2D.string_axis_1,"z [m]");
      sprintf(this_storage.Detector_2D.title_string,"2D position Union logger in plane z");
  } else {
      printf("ERROR, Union logger 2DS named \"%s\" has an invalid D_direction_1 string, it should be \"x\",\"y\" or \"z\".\n",NAME_CURRENT_COMP);
      exit(1);
  }
  
  char temp_string[2];
  if (strcmp(D_direction_2,"x") == 0 || strcmp(D_direction_2,"X") == 0) {
      this_storage.dim_2_choice = 0;
      sprintf(this_storage.Detector_2D.string_axis_2,"x [m]");
      sprintf(temp_string,"x");
  } else if (strcmp(D_direction_2,"y") == 0 || strcmp(D_direction_2,"Y") == 0) {
      this_storage.dim_2_choice = 1;
      sprintf(this_storage.Detector_2D.string_axis_2,"y [m]");
      sprintf(temp_string,"y");
  } else if (strcmp(D_direction_2,"z") == 0 || strcmp(D_direction_2,"Z") == 0) {
      this_storage.dim_2_choice = 2;
      sprintf(this_storage.Detector_2D.string_axis_2,"z [m]");
      sprintf(temp_string,"z");
  } else {
      printf("ERROR, Union logger 2DS named \"%s\" has an invalid D_direction_2 string, it should be \"x\",\"y\" or \"z\".\n",NAME_CURRENT_COMP);
      exit(1);
  }
  
  strcat(this_storage.Detector_2D.title_string,temp_string); // Connects the title string started in D_direction_1 part with the ending in D_direction_2 part
  
  sprintf(this_storage.Detector_2D.Filename,"%s",filename);
  
  
  this_storage.order = order_total;
  this_storage.order_in_this_volume = order_volume;
  this_storage.order_process_in_this_volume = order_volume_process;
  this_storage.temp_2DS_data.num_elements=0;
  // Added 17/11/2016, allocating some elements in initialize makes code during trace simpler
  this_storage.temp_2DS_data.allocated_elements = 10;
  this_storage.temp_2DS_data.elements = malloc(this_storage.temp_2DS_data.allocated_elements*sizeof(struct temp_2DS_data_element_struct));


if (_getcomp_index(init) < 0) {
fprintf(stderr,"Union_logger_2D_space:%s: Error identifying Union_init component, %s is not a known component name.\n",
NAME_CURRENT_COMP, init);
exit(-1);
}

struct global_positions_to_transform_list_struct *global_positions_to_transform_list = COMP_GETPAR3(Union_init, init, global_positions_to_transform_list);
  struct global_rotations_to_transform_list_struct *global_rotations_to_transform_list = COMP_GETPAR3(Union_init, init, global_rotations_to_transform_list);
  // Test position and rotation stored in a data storage, and pointers assigned to transform lists
  this_storage.position = POS_A_CURRENT_COMP;
  add_position_pointer_to_list(global_positions_to_transform_list,&this_storage.position);
  
  rot_copy(this_storage.rotation,ROT_A_CURRENT_COMP);
  add_rotation_pointer_to_list(global_rotations_to_transform_list,&this_storage.rotation);
  
  rot_transpose(ROT_A_CURRENT_COMP,this_storage.t_rotation);
  add_rotation_pointer_to_list(global_rotations_to_transform_list,&this_storage.t_rotation);
  
  //printf("past direction choices sanitation \n");
  
  // Book keeping
  this_logger.logger_extend_index = logger_conditional_extend_index;
  this_logger.function_pointers.active_record_function = &record_to_perm_2DS;  // Assume no conditional
  this_logger.function_pointers.inactive_record_function = &record_to_temp_2DS; // If an assume is present, these two pointers are switched
  // Temp to perm functions, and standard identifier
  this_logger.function_pointers.select_t_to_p = 1; // 1: temp_to_perm, 2: temp_to_perm_final_p
  this_logger.function_pointers.temp_to_perm = &write_temp_to_perm_2DS;
  this_logger.function_pointers.temp_to_perm_final_p = &write_temp_to_perm_final_p_2DS;
  this_logger.function_pointers.clear_temp = &clear_temp_2DS;
  // Initializing for conditional
  this_logger.conditional_list.num_elements = 0;
  
  //this_logger.function_pointers.perm_to_disk = &write_perm_to_disk_2DS; //Obsolete
  
  //printf("past this_logger function assignment \n");
  
  this_logger.data_union.p_2DS_storage = &this_storage;
  
  sprintf(this_logger.name,"%s",NAME_CURRENT_COMP);
  
  //printf("past this_logger assignment \n");
  
  sprintf(logger_list_element.name,"%s",NAME_CURRENT_COMP);
  logger_list_element.component_index = INDEX_CURRENT_COMP;
  logger_list_element.logger = &this_logger;
  
  //printf("past logger_list_element assignment \n");
  
  
  struct pointer_to_global_logger_list *global_specific_volumes_logger_list = COMP_GETPAR3(Union_init, init, global_specific_volumes_logger_list);
  struct pointer_to_global_geometry_list *global_geometry_list = COMP_GETPAR3(Union_init, init, global_geometry_list);
  
  // In order to run the logger at the right times, pointers to this logger is stored in each volume it logs,
  //  and additionally for each avaiable process. If a process is not logged, the pointer is simply not stored.
  int process_index;
  // Need to find the volumes for which the processes should have a reference to this logger
  if (target_geometry && strlen(target_geometry) && strcmp(target_geometry,"NULL") && strcmp(target_geometry, "0")) {
    // Certain volumes were selected, find the indicies in the global_geometry_list
    manual_linking_function_logger_volumes(target_geometry, global_geometry_list, &accepted_volumes, NAME_CURRENT_COMP);
    // Add this logger to the global_specific_volumes_logger_list (so that conditionals can affect it)
    add_element_to_logger_list(global_specific_volumes_logger_list,logger_list_element);
    
    for (loop_index=0;loop_index<accepted_volumes.num_elements;loop_index++) {
      target_volume = global_geometry_list->elements[accepted_volumes.elements[loop_index]].Volume;
      // Add an element to its logger list
      add_initialized_logger_in_volume(&target_volume->loggers,target_volume->p_physics->number_of_processes);
    
      if (target_process && strlen(target_process) && strcmp(target_process,"NULL") && strcmp(target_process, "0")) {
        // Unused process pointers should point to NULL
        for (process_index=0;process_index<target_volume->p_physics->number_of_processes;process_index++) {
          target_volume->loggers.p_logger_volume[target_volume->loggers.num_elements-1].p_logger_process[process_index]=NULL;
        }
        // A target_process was set, find it within the volume structure (can be many processes)
        manual_linking_function_logger_processes(target_process, target_volume->p_physics, &accepted_processes, NAME_CURRENT_COMP,target_volume->name);
        for (process_index=0;process_index<accepted_processes.num_elements;process_index++) {
          // Add pointer to this logger for all the accepted processes in this newly added loggers element
          target_volume->loggers.p_logger_volume[target_volume->loggers.num_elements-1].p_logger_process[accepted_processes.elements[process_index]]=&this_logger;
        }
      } else {
        // No target_process was set, attatch the logger to all processes
        for (process_index=0;process_index<target_volume->p_physics->number_of_processes;process_index++) {
          target_volume->loggers.p_logger_volume[target_volume->loggers.num_elements-1].p_logger_process[process_index]=&this_logger;
        }
      }
    }
  } else {
    // Send to global_all_volumes_logger_list
    // Here there is no system for selecting processes as well
    struct pointer_to_global_logger_list *global_all_volume_logger_list = COMP_GETPAR3(Union_init, init, global_all_volume_logger_list);
    add_element_to_logger_list(global_all_volume_logger_list,logger_list_element);
  }
  

 %}

TRACE
%{
%}

SAVE
%{
// Write to disk
DETECTOR_OUT_2D(
 this_storage.Detector_2D.title_string,
 this_storage.Detector_2D.string_axis_1,
 this_storage.Detector_2D.string_axis_2,
 this_storage.Detector_2D.D1min, this_storage.Detector_2D.D1max,
 this_storage.Detector_2D.D2min, this_storage.Detector_2D.D2max,
 this_storage.Detector_2D.bins_1, this_storage.Detector_2D.bins_2,
 *this_storage.Detector_2D.Array_N, *this_storage.Detector_2D.Array_p, *this_storage.Detector_2D.Array_p2,
 this_storage.Detector_2D.Filename);

%}

FINALLY
%{
// Remember to clean up allocated lists
if (this_storage.temp_2DS_data.allocated_elements>0) free(this_storage.temp_2DS_data.elements);

free2Ddouble_2DS(this_storage.Detector_2D.Array_N);
free2Ddouble_2DS(this_storage.Detector_2D.Array_p);
free2Ddouble_2DS(this_storage.Detector_2D.Array_p2);

if (accepted_processes.num_elements > 0) free(accepted_processes.elements);
if (accepted_volumes.num_elements > 0) free(accepted_volumes.elements);

%}

END

