function [out,status] = amt_extern(environment, directory, module, input, outstruct)
%AMT_EXTERN Process a function from an external environment
%   Usage:
%     output = amt_extern(environment, directory, module, input, outstruct);
%
%   Input parameters:
%
%     environment  : String selecting the environment to be used.
%                    Currently must be Python.
%     directory    : Diretory inside the environment.
%                    For example, verhulst2018 for the model from
%                    Verhulst et al. (2018).
%     module       : Module name to be called within the environment.
%                    For example, run_cochlear_model.py for the model
%                    from Verhulst et al. (2018).
%     input        : Structure with the input parameters. All fields
%                    will be saved in the directory out within the
%                    directory in the file input.mat.
%     outstruct    : Structure defining the output parameters. Each field's
%                    name defines the variable name to be read from a file
%                    named by the field with the ending .np in the
%                    out directory. Each field must contain a vector
%                    defining the size of the variable to be read. Up to
%                    three dimensions are handled.
%
%   Output parameters:
%
%     out          : Structure with the output defined by outstruct. The
%                    fields of out will have names as in outstruct. Each
%                    field will have size as given by the corresponding
%                    vector in outstruct.
%     status       : Structure with the status and results, see system.
%
%   See also: verhulst2012 verhulst2018
%
%   Url: http://amtoolbox.org/amt-1.6.0/doc/core/amt_extern.php


%   #Author: Piotr Majdak (2021): programmed for the AMT 1.0
%   #Author: Alejandro Osses (2023): compatible with AMT paths containing spaces (on Unix)
%   #Author: Piotr Majdak (2023): adapted for various python evironments based on amt_configuration

% This file is licensed unter the GNU General Public License (GPL) either
% version 3 of the license, or any later version as published by the Free Software
% Foundation. Details of the GPLv3 can be found in the AMT directory "licences" and
% at <https://www.gnu.org/licenses/gpl-3.0.html>.
% You can redistribute this file and/or modify it under the terms of the GPLv3.
% This file is distributed without any warranty; without even the implied warranty
% of merchantability or fitness for a particular purpose.



switch environment
  case 'Python'
    [~,kv]=amt_configuration; % get the command to run python
    if isempty(kv.pythoncmd)
      error('Python Environment not available. Probed commands: python, python3');
    end
      % change to directory
    act_path=pwd;

    cd(fullfile(amt_basepath,'environments', directory));
      % input parameters
    if ~isempty(input)
      save(fullfile('out','input.mat'), '-struct', 'input', '-v7');
    end
      % call
    [stat,res]=system([kv.pythoncmd ' ' module]);
      % check the status
    status.status=stat;
    status.res=res;
    if stat ~= 0
        amt_disp();
        amt_disp(res);
        error('AMT_EXTERN: Something went wrong calling Python (see message above)');
    end
      % collect the output
    if isempty(outstruct)
      out=[]; % no output requested
    else
      fn=fieldnames(outstruct);
      for ii=1:length(fn)
          varname=fn{ii};
          var=outstruct.(varname);
          dim1=var(1);
          if length(var)<2, dim2=1; else dim2=var(2); end
          if length(var)<3, dim3=1; else dim3=var(3); end
          for jj=1:dim3
            filename=fullfile(amt_basepath,'environments', directory, 'out',[varname int2str(jj) '.np']);
            f=fopen(filename,'r');
            out.(varname)(:,:,jj)=fread(f,[dim1 dim2],'double','n');
            fclose(f);
            delete(filename);
          end
      end
    end
      % clean up
    if ~isempty(input), delete(fullfile('out','input.mat')); end
    cd(act_path);
  otherwise
    error(['Environment ' environment ' is not supported']);
end