added backbone script to produce markers. So far it starts from (R,z,E,pitch)...

added backbone script to produce markers. So far it starts from (R,z,E,pitch) and computes (x,y) assuming phi=0. Computes also vpara, vperp, vtot."

matlab/IMAS/ids_fill_markers.m

+function [ids_distributions] = ids_fill_markers(markers_in)
+%
+%  [ids_distributions, varargout] = ids_fill_markers(markers_in);
+%
+% Function to fill the distributions.distribution.markers fields
+% So far the input markers_in must contain at least (E,pitch,R,z) fields
+%
+% M. Vallar - 03/2022
+ids_distributions = ids_empty_distributions();
+
+allowed_fields = {'E', 'pitch','R','z'};
+%% Checking if all the fields needed are present
+for i=1:numel(allowed_fields)
+  if ~isfield(markers_in, allowed_fields{i})
+    error('Cannot continue without field %s \nExit \n', allowed_fields{i})
+  end
+end
+fprintf('All needed quantities present in input structure \n');
+markers2ids = markers_in;
+
+%% if no mass can be detected, assume mass is the one of deuterium
+mass = 2*1.6e-27;
+%% Making names compliant to ids names
+if isfield(markers_in, 'E')
+  markers2ids.energy_kinetic = markers2ids.E;
+  markers2ids = rmfield(markers2ids, 'E');
+end
+if isfield(markers_in, 'R')
+  markers2ids.r = markers2ids.R;
+  markers2ids = rmfield(markers2ids, 'R');
+end
+%% Computing x,y,z coordinates giving phi=0
+markers2ids.phi = zeros(size(markers2ids.energy_kinetic));
+markers2ids.x = markers2ids.r.*cos(markers2ids.phi);
+markers2ids.y = markers2ids.r.*sin(markers2ids.phi);
+%% Computing vpara, vperp 
+%Converting energy to J, if needed
+if any(markers2ids.energy_kinetic)>1000
+  markers2ids.energy_kinetic = markers2ids.energy_kinetic*1.602e-19;
+end
+markers2ids.velocity = sqrt(2.*markers2ids.energy_kinetic./mass);
+markers2ids.velocity_parallel = markers2ids.velocity.*markers2ids.pitch;
+markers2ids.velocity_perpendicular = sqrt(markers2ids.velocity.^2-markers2ids.velocity_parallel.^2);
+markers2ids.pitch_angle = acos(markers2ids.pitch);
+
+%% Assigning markers into ids structure
+ids_distributions.distribution{1}.markers{1} = markers2ids;
+end
\ No newline at end of file