/* Copyright (c) 2008-2025 the MRtrix3 contributors.
 *
 * This Source Code Form is subject to the terms of the Mozilla Public
 * License, v. 2.0. If a copy of the MPL was not distributed with this
 * file, You can obtain one at http://mozilla.org/MPL/2.0/.
 *
 * Covered Software is provided under this License on an "as is"
 * basis, without warranty of any kind, either expressed, implied, or
 * statutory, including, without limitation, warranties that the
 * Covered Software is free of defects, merchantable, fit for a
 * particular purpose or non-infringing.
 * See the Mozilla Public License v. 2.0 for more details.
 *
 * For more details, see http://www.mrtrix.org/.
 */
#ifndef __math_stats_import_h__
#define __math_stats_import_h__

#include <fstream>
#include <memory>
#include <string>
#include <vector>

#include "progressbar.h"

#include "file/path.h"

#include "math/stats/typedefs.h"


namespace MR
{
  namespace Math
  {
    namespace Stats
    {



      /** \addtogroup Statistics
      @{ */
      /*! A base class defining the interface for importing subject data
       * This class defines the interface for how subject data is imported
       * into a GLM measurement matrix. Exactly how the subject data is
       * 'vectorised' will depend on the particular type of data being
       * tested; nevertheless, the data for each subject should be stored
       * in a single column within the measurement matrix (or in some
       * cases, within the design matrix).
       */
      class SubjectDataImportBase
      { NOMEMALIGN
        public:
          SubjectDataImportBase (const std::string& path) :
              path (path) { }
          virtual ~SubjectDataImportBase() { }

          /*!
          * @param row the row of a matrix into which the data from this
          * particular file should be loaded
          */
          virtual void operator() (matrix_type::RowXpr column) const = 0;

          /*!
           * @param index extract the data from this file corresponding to a particular
           * row in the measurements vector
           */
          virtual default_type operator[] (const size_t index) const = 0;

          const std::string& name() const { return path; }

          virtual size_t size() const = 0;

        protected:
          const std::string path;

      };
      //! @}



      // During the initial import, the above class can simply be fed one subject at a time
      //   according to per-file path
      // However for use in GLMTTestVariable, a class is needed that stores a list of text files,
      //   where each text file contains a list of file names (one for each subject), and
      //   for each subject a mechanism of data access is spawned & remains open throughout
      //   processing.
      class CohortDataImport
      { NOMEMALIGN
        public:
          CohortDataImport() { }

          // Needs to be its own function rather than the constructor
          //   so that the correct template type can be invoked explicitly
          template <class SubjectDataImport>
          void initialise (const std::string& listpath, const std::string& explicit_from_directory = "");

          /*!
           * @param index for a particular element being tested (data will be acquired for
           * all subjects for that element)
           */
          vector_type operator() (const size_t index) const;

          size_t size() const { return files.size(); }

          std::shared_ptr<SubjectDataImportBase> operator[] (const size_t i) const
          {
            assert (i < files.size());
            return files[i];
          }

          bool allFinite() const;

        protected:
          vector<std::shared_ptr<SubjectDataImportBase>> files;
      };



      template <class SubjectDataImport>
      void CohortDataImport::initialise (const std::string& listpath, const std::string& explicit_from_directory)
      {
        // Read the provided text file one at a time
        // For each file, create an instance of SubjectDataImport
        //   (which must derive from SubjectDataImportBase)

        // - If a directory path is explicitly provided, first try to find
        //   all input files relative to that directory
        // - If that fails, try to find all files relative to
        //   directory in which subject list text file is stored
        // - If that fails, try to find all files relative to
        //   current working directory
        // Only once a directory is selected that contains all inputs listed in the
        //   text file is an attempt made to load all of those files
        vector<std::string> lines;
        {
          std::ifstream ifs (listpath.c_str());
          if (!ifs)
            throw Exception ("Unable to open subject file list \"" + listpath + "\"");
          std::string line;
          while (getline (ifs, line)) {
            size_t p = line.find_last_not_of(" \t");
            if (p != std::string::npos)
              line.erase (p+1);
            if (line.size())
              lines.push_back (line);
          }
        }

        vector<std::string> directories { Path::dirname (listpath) };
        if (directories[0].empty())
          directories[0] = ".";
        else if (directories[0] != ".")
          directories.push_back (".");
        if (explicit_from_directory.size())
          directories.insert (directories.begin(), explicit_from_directory);

        Exception e_nosuccess ("Unable to load all input data from file \"" + listpath + "\"");
        std::string load_from_dir;
        for (const auto& directory : directories) {
          try {
            for (const auto& line : lines) {
              const std::string full_path = Path::join (directory, line);
              if (!Path::is_file (full_path))
                throw Exception ("File \"" + full_path + "\" not found");
            }
            load_from_dir = directory;
            break;
          } catch (Exception& e) {
            e_nosuccess.push_back ("If loading relative to directory \"" + directory + "\": ");
            e_nosuccess.push_back (e);
          }
        }

        if (load_from_dir.empty())
          throw e_nosuccess;

        ProgressBar progress ("Importing data from files listed in \""
                              + Path::basename (listpath)
                              + "\" as found relative to directory \""
                              + load_from_dir + "\"");

        for (const auto& line : lines) {
          try {
            std::shared_ptr<SubjectDataImport> subject (new SubjectDataImport (Path::join (load_from_dir, line)));
            files.emplace_back (subject);
          } catch (Exception& e) {
            throw Exception (e, "Input data not successfully loaded: \"" + line + "\"");
          }
          ++progress;
        }
      }




    }
  }
}


#endif
