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/* Copyright (c) 2008-2022 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
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