mitkFileSeriesReader.cpp

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/*============================================================================

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

============================================================================*/

#include "mitkFileSeriesReader.h"
#include <itkImageFileReader.h>
#include <itksys/Directory.hxx>
#include <itksys/SystemTools.hxx>
#include <map>

bool mitk::FileSeriesReader::GenerateFileList()
{
  typedef std::vector<std::string> StringContainer;
  typedef std::map<unsigned int, std::string> SortedStringContainer;

  if (m_FileName == "")
  {
    throw itk::ImageFileReaderException(__FILE__, __LINE__, "FileName must be non-empty");
  }
  // MITK_INFO << "FileName: "<< m_FileName <<", FilePrefix: "<< m_FilePrefix << ", FilePattern: "<< m_FilePattern <<
  // std::endl;

  // determine begin and end idexes of the last digit sequence in the
  // filename from the sample file name
  // Therefore, walk backwards from the end of the filename until
  // a number is found. The string in front of the number is the prefix,
  // the string after the number is the extension.
  std::string basename, path;
  path = itksys::SystemTools::GetFilenamePath(m_FileName);
  basename = itksys::SystemTools::GetFilenameName(m_FileName);

  unsigned int digitBegin = 0;
  unsigned int digitEnd = 0;
  bool digitFound = false;
  for (unsigned int i = basename.length() - 1;; --i)
  {
    char character = basename[i];
    if (character >= '0' && character <= '9')
    {
      if (!digitFound)
      {
        digitEnd = i;
        digitBegin = i;
        digitFound = true;
      }
      else
        digitBegin = i;
    }
    else
    {
      // end of digit series found, jump out of loop!
      if (digitFound)
        break;
    }
    if (i == 0)
      break;
  }

  //
  // if there is no digit in the filename, then we have a problem
  // no matching filenames can be identified!
  //
  if (!digitFound)
  {
    itkWarningMacro("Filename contains no digit!");
    return false;
  }

  //
  // determine prefix and extension start and length
  //
  unsigned int prefixBegin = 0;
  unsigned int prefixLength = digitBegin;
  unsigned int extensionBegin = digitEnd + 1;
  unsigned int extensionLength = (digitEnd == basename.length() - 1 ? 0 : basename.length() - 1 - digitEnd);
  unsigned int numberLength = digitEnd - digitBegin + 1;

  //
  // extract prefix and extension
  //
  std::string prefix = "";
  if (prefixLength != 0)
    prefix = basename.substr(prefixBegin, prefixLength);
  std::string extension = "";
  if (extensionLength != 0)
    extension = basename.substr(extensionBegin, extensionLength);

  //
  // print debug information
  //
  /*
  MITK_INFO << "digitBegin      : " << digitBegin << std::endl;
  MITK_INFO << "digitEnd        : " << digitEnd << std::endl;
  MITK_INFO << "number of digits: " << numberLength << std::endl;
  MITK_INFO << "prefixBegin     : " << prefixBegin << std::endl;
  MITK_INFO << "prefixLength    : " << prefixLength << std::endl;
  MITK_INFO << "prefix          : " << prefix << std::endl;
  MITK_INFO << "extensionBegin  : " << extensionBegin << std::endl;
  MITK_INFO << "extensionLength : " << extensionLength << std::endl;
  MITK_INFO << "extension       : " << extension << std::endl;
  */
  if ((prefixLength + extensionLength + numberLength) != basename.length())
  {
    throw itk::ImageFileReaderException(
      __FILE__, __LINE__, "prefixLength + extensionLength + numberLength != basenameLength");
  }

  //
  // Load Directory
  //
  std::string directory = itksys::SystemTools::GetFilenamePath(m_FileName);
  itksys::Directory itkDir;
  if (!itkDir.Load(directory.c_str()))
  {
    itkWarningMacro(<< "Directory " << directory << " cannot be read!");
    return false;
  }

  //
  // Get a list of all files in the directory
  //
  StringContainer unmatchedFiles;
  // unsigned long i;
  for (unsigned long i = 0; i < itkDir.GetNumberOfFiles(); i++)
  {
    // Only read files
    std::string filename = directory + "/" + itkDir.GetFile(i);
    if (itksys::SystemTools::FileIsDirectory(filename.c_str()))
      continue;

    // store the filenames without path
    unmatchedFiles.push_back(itkDir.GetFile(i));
  }

  //
  // Match the file list against the file prefix and extension,
  // the result should be only the files that should be read
  //
  StringContainer matchedFiles;
  for (auto it = unmatchedFiles.begin(); it != unmatchedFiles.end(); ++it)
  {
    bool prefixMatch = false;
    bool extensionMatch = false;

    // check if the file prefix matches the current file
    if (prefixLength != 0)
      prefixMatch = (it->find(prefix) == prefixBegin); // check if prefix is found
    else
      prefixMatch = (((*it)[0] >= '0') && ((*it)[0] <= '9')); // check if filename begins with digit

    // check if the file extension matches the current file
    if (extensionLength != 0)
      extensionMatch = (it->find(extension) == it->length() - extensionLength); // check if prefix is found
    else
      extensionMatch =
        (((*it)[it->length() - 1] >= '0') && ((*it)[it->length() - 1] <= '9')); // check if filename ends with digit

    if (prefixMatch && extensionMatch)
    {
      matchedFiles.push_back(*it);
    }
  }
  if (matchedFiles.size() == 0)
  {
    itkWarningMacro(<< "Sorry, none of the files matched the prefix!");
    return false;
  }

  //
  // parse the file names from back to front for digits
  // and convert them to a number. Store the filename and number
  // in a SortedStringContainer
  //
  SortedStringContainer sortedFiles;
  for (auto it = matchedFiles.begin(); it != matchedFiles.end(); ++it)
  {
    // parse the filename starting from pos digitBegin until we reach a non-digit
    // or the end of filename
    std::string number = "";
    std::string currentFilename(*it);
    for (unsigned int i = digitBegin; i < currentFilename.length(); ++i)
    {
      char character = currentFilename[i];
      // do we have a digit?
      if (character >= '0' && character <= '9')
        number += character;
      else
        break; // end of digit series found, jump out of loop!
    }
    if (number.length() == 0)
    {
      // The file is not numbered, this is an error!
      // Nevertheless, we try the next files.
      itkWarningMacro(<< "The filename " << *it
                      << "does not contain a valid digit sequence but matches prefix and extension. Skipping file!");
    }
    else
    {
      if ((number.length() + prefix.length() + extension.length()) != it->length())
      {
        itkWarningMacro(
          "The file "
          << *it
          << " matches prefix and extension, but the string in beteen is not a single digit-sequence. Skipping file!");
      }
      else
      {
        // convert the number string into an integer and
        // insert the filname (including directory) into the SortedStringContainer
        unsigned int num = atoi(number.c_str());
        sortedFiles.insert(std::make_pair(num, directory + "/" + *it));
      }
    }
  }
  if (sortedFiles.size() == 0)
  {
    itkWarningMacro(<< "Sorry, no numbered files found, I can't load anything...");
    return false;
  }

  //
  // Convert the sorted string container in a plain sorted vector of strings;
  //
  m_MatchedFileNames.clear();
  m_MatchedFileNames.resize(sortedFiles.size());
  unsigned long index = 0;
  for (auto it = sortedFiles.begin(); it != sortedFiles.end(); ++it, ++index)
  {
    m_MatchedFileNames[index] = it->second;
    MITK_INFO << "Added " << it->second << " to the set of matched files!" << std::endl;
  }
  return true;
}

mitk::FileSeriesReader::MatchedFileNames mitk::FileSeriesReader::GetMatchedFileNames()
{
  return m_MatchedFileNames;
}

mitk::FileSeriesReader::FileSeriesReader() : m_FileName(""), m_FilePrefix(""), m_FilePattern("")
{
}

mitk::FileSeriesReader::~FileSeriesReader()
{
}