#+TITLE: Matlab Functions used for the NASS Project
:DRAWER:
#+STARTUP: overview

#+LANGUAGE: en
#+EMAIL: dehaeze.thomas@gmail.com
#+AUTHOR: Dehaeze Thomas

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#+PROPERTY: header-args:matlab  :session *MATLAB*
#+PROPERTY: header-args:matlab+ :comments org
#+PROPERTY: header-args:matlab+ :results none
#+PROPERTY: header-args:matlab+ :exports both
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:END:

* Functions
<<sec:functions>>
** computePsdDispl
:PROPERTIES:
:header-args:matlab+: :tangle ../src/computePsdDispl.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:computePsdDispl>>

This Matlab function is accessible [[file:../src/computePsdDispl.m][here]].

#+begin_src matlab
  function [psd_object] = computePsdDispl(sys_data, t_init, n_av)
      i_init = find(sys_data.time > t_init, 1);

      han_win = hanning(ceil(length(sys_data.Dx(i_init:end, :))/n_av));
      Fs = 1/sys_data.time(2);

      [pdx, f] = pwelch(sys_data.Dx(i_init:end, :), han_win, [], [], Fs);
      [pdy, ~] = pwelch(sys_data.Dy(i_init:end, :), han_win, [], [], Fs);
      [pdz, ~] = pwelch(sys_data.Dz(i_init:end, :), han_win, [], [], Fs);

      [prx, ~] = pwelch(sys_data.Rx(i_init:end, :), han_win, [], [], Fs);
      [pry, ~] = pwelch(sys_data.Ry(i_init:end, :), han_win, [], [], Fs);
      [prz, ~] = pwelch(sys_data.Rz(i_init:end, :), han_win, [], [], Fs);

      psd_object = struct(...
          'f',  f,   ...
          'dx', pdx, ...
          'dy', pdy, ...
          'dz', pdz, ...
          'rx', prx, ...
          'ry', pry, ...
          'rz', prz);
  end
#+end_src

** computeSetpoint
:PROPERTIES:
:header-args:matlab+: :tangle ../src/computeSetpoint.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:computeSetpoint>>

This Matlab function is accessible [[file:../src/computeSetpoint.m][here]].

#+begin_src matlab
  function setpoint = computeSetpoint(ty, ry, rz)
  %%
  setpoint = zeros(6, 1);

  %% Ty
  Ty = [1 0 0 0  ;
        0 1 0 ty ;
        0 0 1 0  ;
        0 0 0 1 ];

  % Tyinv = [1 0 0  0  ;
  %          0 1 0 -ty ;
  %          0 0 1  0  ;
  %          0 0 0  1 ];

  %% Ry
  Ry = [ cos(ry) 0 sin(ry) 0 ;
        0       1 0       0 ;
        -sin(ry) 0 cos(ry) 0 ;
        0        0 0       1 ];

  % TMry = Ty*Ry*Tyinv;

  %% Rz
  Rz = [cos(rz) -sin(rz) 0 0 ;
        sin(rz)  cos(rz) 0 0 ;
        0        0       1 0 ;
        0        0       0 1 ];

  % TMrz = Ty*TMry*Rz*TMry'*Tyinv;

  %% All stages
  % TM = TMrz*TMry*Ty;

  TM = Ty*Ry*Rz;

  [thetax, thetay, thetaz] = RM2angle(TM(1:3, 1:3));

  setpoint(1:3) = TM(1:3, 4);
  setpoint(4:6) = [thetax, thetay, thetaz];

  %% Custom Functions
  function [thetax, thetay, thetaz] = RM2angle(R)
      if abs(abs(R(3, 1)) - 1) > 1e-6 % R31 != 1 and R31 != -1
          thetay = -asin(R(3, 1));
          thetax = atan2(R(3, 2)/cos(thetay), R(3, 3)/cos(thetay));
          thetaz = atan2(R(2, 1)/cos(thetay), R(1, 1)/cos(thetay));
      else
          thetaz = 0;
          if abs(R(3, 1)+1) < 1e-6 % R31 = -1
              thetay = pi/2;
              thetax = thetaz + atan2(R(1, 2), R(1, 3));
          else
              thetay = -pi/2;
              thetax = -thetaz + atan2(-R(1, 2), -R(1, 3));
          end
      end
  end
  end
#+end_src

** converErrorBasis
:PROPERTIES:
:header-args:matlab+: :tangle ../src/converErrorBasis.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:converErrorBasis>>

This Matlab function is accessible [[file:../src/converErrorBasis.m][here]].

#+begin_src matlab
  function error_nass = convertErrorBasis(pos, setpoint, ty, ry, rz)
  % convertErrorBasis -
  %
  % Syntax: convertErrorBasis(p_error, ty, ry, rz)
  %
  % Inputs:
  %    - p_error - Position error of the sample w.r.t. the granite [m, rad]
  %    - ty - Measured translation of the Ty stage [m]
  %    - ry - Measured rotation of the Ry stage [rad]
  %    - rz - Measured rotation of the Rz stage [rad]
  %
  % Outputs:
  %    - P_nass - Position error of the sample w.r.t. the NASS base [m]
  %    - R_nass - Rotation error of the sample w.r.t. the NASS base [rad]
  %
  % Example:
  %

  %% If line vector => column vector
  if size(pos, 2) == 6
      pos = pos';
  end

  if size(setpoint, 2) == 6
      setpoint = setpoint';
  end

  %% Position of the sample in the frame fixed to the Granite
  P_granite = [pos(1:3); 1]; % Position [m]
  R_granite = [setpoint(1:3); 1]; % Reference [m]

  %% Transformation matrices of the stages
  % T-y
  TMty = [1 0 0 0  ;
          0 1 0 ty ;
          0 0 1 0  ;
          0 0 0 1 ];

  % R-y
  TMry = [ cos(ry) 0 sin(ry) 0 ;
          0       1 0       0 ;
          -sin(ry) 0 cos(ry) 0 ;
          0        0 0       1 ];

  % R-z
  TMrz = [cos(rz) -sin(rz) 0 0 ;
          sin(rz)  cos(rz) 0 0 ;
          0        0       1 0 ;
          0        0       0 1 ];

  %% Compute Point coordinates in the new reference fixed to the NASS base
  % P_nass = TMrz*TMry*TMty*P_granite;
  P_nass = TMrz\TMry\TMty\P_granite;
  R_nass = TMrz\TMry\TMty\R_granite;

  dx = R_nass(1)-P_nass(1);
  dy = R_nass(2)-P_nass(2);
  dz = R_nass(3)-P_nass(3);

  %% Compute new basis vectors linked to the NASS base
  % ux_nass = TMrz*TMry*TMty*[1; 0; 0; 0];
  % ux_nass = ux_nass(1:3);
  % uy_nass = TMrz*TMry*TMty*[0; 1; 0; 0];
  % uy_nass = uy_nass(1:3);
  % uz_nass = TMrz*TMry*TMty*[0; 0; 1; 0];
  % uz_nass = uz_nass(1:3);

  ux_nass = TMrz\TMry\TMty\[1; 0; 0; 0];
  ux_nass = ux_nass(1:3);
  uy_nass = TMrz\TMry\TMty\[0; 1; 0; 0];
  uy_nass = uy_nass(1:3);
  uz_nass = TMrz\TMry\TMty\[0; 0; 1; 0];
  uz_nass = uz_nass(1:3);

  %% Rotations error w.r.t. granite Frame
  % Rotations error w.r.t. granite Frame
  rx_nass = pos(4);
  ry_nass = pos(5);
  rz_nass = pos(6);

  % Rotation matrices of the Sample w.r.t. the Granite
  Mrx_error = [1 0              0 ;
              0 cos(-rx_nass) -sin(-rx_nass) ;
              0 sin(-rx_nass)  cos(-rx_nass)];

  Mry_error = [ cos(-ry_nass) 0 sin(-ry_nass) ;
                0             1 0 ;
              -sin(-ry_nass) 0 cos(-ry_nass)];

  Mrz_error = [cos(-rz_nass) -sin(-rz_nass) 0 ;
              sin(-rz_nass)  cos(-rz_nass) 0 ;
              0              0             1];

  % Rotation matrix of the Sample w.r.t. the Granite
  Mr_error = Mrz_error*Mry_error*Mrx_error;

  %% Use matrix to solve
  R = Mr_error/[ux_nass, uy_nass, uz_nass]; % Rotation matrix from NASS base to Sample

  [thetax, thetay, thetaz] = RM2angle(R);

  error_nass = [dx; dy; dz; thetax; thetay; thetaz];

  %% Custom Functions
  function [thetax, thetay, thetaz] = RM2angle(R)
      if abs(abs(R(3, 1)) - 1) > 1e-6 % R31 != 1 and R31 != -1
          thetay = -asin(R(3, 1));
          % thetaybis = pi-thetay;
          thetax = atan2(R(3, 2)/cos(thetay), R(3, 3)/cos(thetay));
          % thetaxbis = atan2(R(3, 2)/cos(thetaybis), R(3, 3)/cos(thetaybis));
          thetaz = atan2(R(2, 1)/cos(thetay), R(1, 1)/cos(thetay));
          % thetazbis = atan2(R(2, 1)/cos(thetaybis), R(1, 1)/cos(thetaybis));
      else
          thetaz = 0;
          if abs(R(3, 1)+1) < 1e-6 % R31 = -1
              thetay = pi/2;
              thetax = thetaz + atan2(R(1, 2), R(1, 3));
          else
              thetay = -pi/2;
              thetax = -thetaz + atan2(-R(1, 2), -R(1, 3));
          end
      end
  end

  end
#+end_src

** generateDiagPidControl
:PROPERTIES:
:header-args:matlab+: :tangle ../src/generateDiagPidControl.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:generateDiagPidControl>>

This Matlab function is accessible [[file:../src/generateDiagPidControl.m][here]].

#+begin_src matlab
  function [K] = generateDiagPidControl(G, fs)
      %%
      pid_opts = pidtuneOptions(...
          'PhaseMargin', 50, ...
          'DesignFocus', 'disturbance-rejection');

      %%
      K = tf(zeros(6));

      for i = 1:6
          input_name = G.InputName(i);
          output_name = G.OutputName(i);
          K(i, i) = tf(pidtune(minreal(G(output_name, input_name)), 'PIDF', 2*pi*fs, pid_opts));
      end

      K.InputName = G.OutputName;
      K.OutputName = G.InputName;
  end
#+end_src

** identifyPlant
:PROPERTIES:
:header-args:matlab+: :tangle ../src/identifyPlant.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:identifyPlant>>

This Matlab function is accessible [[file:../src/identifyPlant.m][here]].

#+begin_src matlab
  function [sys] = identifyPlant(opts_param)
      %% Default values for opts
      opts = struct();

      %% Populate opts with input parameters
      if exist('opts_param','var')
          for opt = fieldnames(opts_param)'
              opts.(opt{1}) = opts_param.(opt{1});
          end
      end

      %% Options for Linearized
      options = linearizeOptions;
      options.SampleTime = 0;

      %% Name of the Simulink File
      mdl = 'sim_nano_station_id';

      %% Input/Output definition
      io(1)  = linio([mdl, '/Fn'],   1, 'input');  % Cartesian forces applied by NASS
      io(2)  = linio([mdl, '/Dw'],   1, 'input');  % Ground Motion
      io(3)  = linio([mdl, '/Fs'],   1, 'input');  % External forces on the sample
      io(4)  = linio([mdl, '/Fnl'],  1, 'input');  % Forces applied on the NASS's legs
      io(5)  = linio([mdl, '/Fd'],   1, 'input');  % Disturbance Forces
      io(6)  = linio([mdl, '/Dsm'],  1, 'output'); % Displacement of the sample
      io(7)  = linio([mdl, '/Fnlm'], 1, 'output'); % Force sensor in NASS's legs
      io(8)  = linio([mdl, '/Dnlm'], 1, 'output'); % Displacement of NASS's legs
      io(9)  = linio([mdl, '/Es'],   1, 'output'); % Position Error w.r.t. NASS base
      io(10) = linio([mdl, '/Vlm'],  1, 'output'); % Measured absolute velocity of the legs

      %% Run the linearization
      G = linearize(mdl, io, options);
      G.InputName  = {'Fnx', 'Fny', 'Fnz', 'Mnx', 'Mny', 'Mnz', ...
                      'Dgx', 'Dgy', 'Dgz', ...
                      'Fsx', 'Fsy', 'Fsz', 'Msx', 'Msy', 'Msz', ...
                      'F1', 'F2', 'F3', 'F4', 'F5', 'F6', ...
                      'Frzz', 'Ftyx', 'Ftyz'};
      G.OutputName = {'Dx', 'Dy', 'Dz', 'Rx', 'Ry', 'Rz', ...
                      'Fm1', 'Fm2', 'Fm3', 'Fm4', 'Fm5', 'Fm6', ...
                      'Dm1', 'Dm2', 'Dm3', 'Dm4', 'Dm5', 'Dm6', ...
                      'Edx', 'Edy', 'Edz', 'Erx', 'Ery', 'Erz', ...
                      'Vm1', 'Vm2', 'Vm3', 'Vm4', 'Vm5', 'Vm6'};

      %% Create the sub transfer functions
      minreal_tol = sqrt(eps);
      % From forces applied in the cartesian frame to displacement of the sample in the cartesian frame
      sys.G_cart  = minreal(G({'Dx', 'Dy', 'Dz', 'Rx', 'Ry', 'Rz'}, {'Fnx', 'Fny', 'Fnz', 'Mnx', 'Mny', 'Mnz'}), minreal_tol, false);
      % From ground motion to Sample displacement
      sys.G_gm    = minreal(G({'Dx', 'Dy', 'Dz', 'Rx', 'Ry', 'Rz'}, {'Dgx', 'Dgy', 'Dgz'}), minreal_tol, false);
      % From direct forces applied on the sample to displacement of the sample
      sys.G_fs    = minreal(G({'Dx', 'Dy', 'Dz', 'Rx', 'Ry', 'Rz'}, {'Fsx', 'Fsy', 'Fsz', 'Msx', 'Msy', 'Msz'}), minreal_tol, false);
      % From forces applied on NASS's legs to force sensor in each leg
      sys.G_iff   = minreal(G({'Fm1', 'Fm2', 'Fm3', 'Fm4', 'Fm5', 'Fm6'}, {'F1', 'F2', 'F3', 'F4', 'F5', 'F6'}), minreal_tol, false);
      % From forces applied on NASS's legs to displacement of each leg
      sys.G_dleg  = minreal(G({'Dm1', 'Dm2', 'Dm3', 'Dm4', 'Dm5', 'Dm6'}, {'F1', 'F2', 'F3', 'F4', 'F5', 'F6'}), minreal_tol, false);
      % From forces/torques applied by the NASS to position error
      sys.G_plant = minreal(G({'Edx', 'Edy', 'Edz', 'Erx', 'Ery', 'Erz'}, {'Fnx', 'Fny', 'Fnz', 'Mnx', 'Mny', 'Mnz'}), minreal_tol, false);
      % From forces/torques applied by the NASS to velocity of the actuator
      sys.G_geoph = minreal(G({'Vm1', 'Vm2', 'Vm3', 'Vm4', 'Vm5', 'Vm6'}, {'F1', 'F2', 'F3', 'F4', 'F5', 'F6'}), minreal_tol, false);
      % From various disturbance forces to position error
      sys.G_dist = minreal(G({'Dx', 'Dy', 'Dz', 'Rx', 'Ry', 'Rz'}, {'Frzz', 'Ftyx', 'Ftyz'}), minreal_tol, false);

      %% We remove low frequency and high frequency dynamics that are usually unstable
      % using =freqsep= is risky as it may change the shape of the transfer functions
      % f_min = 0.1; % [Hz]
      % f_max = 1e4; % [Hz]

      % [~, sys.G_cart]  = freqsep(freqsep(sys.G_cart,  2*pi*f_max), 2*pi*f_min);
      % [~, sys.G_gm]    = freqsep(freqsep(sys.G_gm,    2*pi*f_max), 2*pi*f_min);
      % [~, sys.G_fs]    = freqsep(freqsep(sys.G_fs,    2*pi*f_max), 2*pi*f_min);
      % [~, sys.G_iff]   = freqsep(freqsep(sys.G_iff,   2*pi*f_max), 2*pi*f_min);
      % [~, sys.G_dleg]  = freqsep(freqsep(sys.G_dleg,  2*pi*f_max), 2*pi*f_min);
      % [~, sys.G_plant] = freqsep(freqsep(sys.G_plant, 2*pi*f_max), 2*pi*f_min);

      %% We finally verify that the system is stable
      if ~isstable(sys.G_cart) || ~isstable(sys.G_gm) || ~isstable(sys.G_fs) || ~isstable(sys.G_iff) || ~isstable(sys.G_dleg) || ~isstable(sys.G_plant)
        warning('One of the identified system is unstable');
      end
  end
#+end_src

** runSimulation
:PROPERTIES:
:header-args:matlab+: :tangle ../src/runSimulation.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:runSimulation>>

This Matlab function is accessible [[file:../src/runSimulation.m][here]].

#+begin_src matlab
  function [] = runSimulation(sys_name, sys_mass, ctrl_type, act_damp)
      %% Load the controller and save it for the simulation
      if strcmp(ctrl_type, 'cl') && strcmp(act_damp, 'none')
        K_obj = load('./mat/K_fb.mat');
        K = K_obj.(sprintf('K_%s_%s', sys_mass, sys_name)); %#ok
        save('./mat/controllers.mat', 'K');
      elseif strcmp(ctrl_type, 'cl') && strcmp(act_damp, 'iff')
        K_obj = load('./mat/K_fb_iff.mat');
        K = K_obj.(sprintf('K_%s_%s_iff', sys_mass, sys_name)); %#ok
        save('./mat/controllers.mat', 'K');
      elseif strcmp(ctrl_type, 'ol')
        K = tf(zeros(6)); %#ok
        save('./mat/controllers.mat', 'K');
      else
        error('ctrl_type should be cl or ol');
      end

      %% Active Damping
      if strcmp(act_damp, 'iff')
        K_iff_crit = load('./mat/K_iff_crit.mat');
        K_iff = K_iff_crit.(sprintf('K_iff_%s_%s', sys_mass, sys_name)); %#ok
        save('./mat/controllers.mat', 'K_iff', '-append');
      elseif strcmp(act_damp, 'none')
        K_iff = tf(zeros(6)); %#ok
        save('./mat/controllers.mat', 'K_iff', '-append');
      end

      %%
      if strcmp(sys_name, 'pz')
        initializeNanoHexapod(struct('actuator', 'piezo'));
      elseif strcmp(sys_name, 'vc')
        initializeNanoHexapod(struct('actuator', 'lorentz'));
      else
        error('sys_name should be pz or vc');
      end

      if strcmp(sys_mass, 'light')
        initializeSample(struct('mass', 1));
      elseif strcmp(sys_mass, 'heavy')
        initializeSample(struct('mass', 50));
      else
        error('sys_mass should be light or heavy');
      end

      %% Run the simulation
      sim('sim_nano_station_ctrl.slx');

      %% Split the Dsample matrix into vectors
      [Dx, Dy, Dz, Rx, Ry, Rz] = matSplit(Es.Data, 1); %#ok
      time = Dsample.Time; %#ok

      %% Save the result
      filename = sprintf('sim_%s_%s_%s_%s', sys_mass, sys_name, ctrl_type, act_damp);
      save(sprintf('./mat/%s.mat', filename), ...
          'time', 'Dx', 'Dy', 'Dz', 'Rx', 'Ry', 'Rz', 'K');
  end
#+end_src

** Inverse Kinematics of the Hexapod
:PROPERTIES:
:header-args:matlab+: :tangle ../src/inverseKinematicsHexapod.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:inverseKinematicsHexapod>>

This Matlab function is accessible [[file:src/inverseKinematicsHexapod.m][here]].

#+begin_src matlab
  function [L] = inverseKinematicsHexapod(hexapod, AP, ARB)
  % inverseKinematicsHexapod - Compute the initial position of each leg to have the wanted Hexapod's position
  %
  % Syntax: inverseKinematicsHexapod(hexapod, AP, ARB)
  %
  % Inputs:
  %    - hexapod - Hexapod object containing the geometry of the hexapod
  %    - AP - Position vector of point OB expressed in frame {A} in [m]
  %    - ARB - Rotation Matrix expressed in frame {A}

    % Wanted Length of the hexapod's legs [m]
    L = zeros(6, 1);

    for i = 1:length(L)
      Bbi = hexapod.pos_top_tranform(i, :)' - 1e-3*[0 ; 0 ; hexapod.TP.thickness+hexapod.Leg.sphere.top+hexapod.SP.thickness.top+hexapod.jacobian]; % [m]
      Aai = hexapod.pos_base(i, :)' + 1e-3*[0 ; 0 ; hexapod.BP.thickness+hexapod.Leg.sphere.bottom+hexapod.SP.thickness.bottom-hexapod.h-hexapod.jacobian]; % [m]

      L(i) = sqrt(AP'*AP + Bbi'*Bbi + Aai'*Aai - 2*AP'*Aai + 2*AP'*(ARB*Bbi) - 2*(ARB*Bbi)'*Aai);
    end
  end
#+end_src