mitkdump.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 "mitkDICOMFileReaderSelector.h"
#include "mitkDICOMImageFrameInfo.h"
#include "mitkDICOMReaderConfigurator.h"

using mitk::DICOMTag;

std::string buildDateString()
{
  std::time_t rawtime;
  std::tm *timeinfo;
  char buffer[80];

  std::time(&rawtime);
  timeinfo = std::localtime(&rawtime);

  std::strftime(buffer, 80, "%Y%m%d-%H%M%S", timeinfo);

  return std::string(buffer);
}

void gen_random(char *s, const int len)
{
  static const char alphanum[] = "0123456789"
                                 "ABCDEFGHIJKLMNOPQRSTUVWXYZ";

  for (int i = 0; i < len; ++i)
  {
    s[i] = alphanum[rand() % (sizeof(alphanum) - 1)];
  }

  s[len] = 0;
}

std::string gen_random(const int len)
{
  if (len > 0 && len < 100)
  {
    char retval[100];
    gen_random(retval, len);
    return std::string(retval);
  }
  else
  {
    return std::string("");
  }
}

std::string removeUnsafeChars(const std::string &str)
{
  std::string retval;
  for (std::string::const_iterator it = str.begin(); it != str.end(); ++it)
  {
    const char &c = *it;
    if ((c >= '0' && c <= '9') || (c >= 'A' && c <= 'Z') || (c >= 'a' && c <= 'z') || (c == '.') || (c == '-') ||
        (c == '_'))
    {
      retval += c;
    }
  }
  return retval;
}

std::string extractDirString(const std::string &dirString)
{
  std::string wholeprefix = dirString.substr(0, dirString.find_last_of("/\\"));
  std::string lastDirectoryPart = wholeprefix.substr(wholeprefix.find_last_of("/\\") + 1);
  std::string cleanLastDirectoryPart = removeUnsafeChars(lastDirectoryPart);
  if (!cleanLastDirectoryPart.empty())
  {
    return cleanLastDirectoryPart;
  }
  else
  {
    std::stringstream emptydirname;
    emptydirname << "noname_" << gen_random(6);

    return emptydirname.str();
  }
}

int main(int argc, char *argv[])
{
  bool fileDetails(false);
  bool loadimage(false);
  int firstFileIndex = 1;

  // see if we got the '-v' flag to output file details
  if (argc > 1 && std::string(argv[firstFileIndex]) == "-v")
  {
    fileDetails = true;
    ++firstFileIndex;
  }

  // see if we got the '-l' flag
  if (argc > 1 && std::string(argv[firstFileIndex]) == "-l")
  {
    loadimage = true;
    ++firstFileIndex;
  }

  // analyze files from argv
  mitk::StringList inputFiles;
  for (int a = firstFileIndex; a < argc; ++a)
  {
    inputFiles.push_back(std::string(argv[a]));
  }

  if (inputFiles.empty())
  {
    MITK_INFO << "0 input files given, exiting...";
    return EXIT_SUCCESS;
  }

  mitk::DICOMFileReaderSelector::Pointer configSelector = mitk::DICOMFileReaderSelector::New();
  configSelector->LoadBuiltIn3DConfigs(); // a set of compiled in ressources with standard configurations that work well
  configSelector->SetInputFiles(inputFiles);
  mitk::DICOMFileReader::Pointer reader = configSelector->GetFirstReaderWithMinimumNumberOfOutputImages();
  if (reader.IsNull())
  {
    MITK_ERROR << "Could not configure any DICOM reader.. Exiting...";
    return EXIT_FAILURE;
  }

  // output best reader result
  MITK_INFO << "---- Best reader configuration '" << reader->GetConfigurationLabel() << "' with "
            << reader->GetNumberOfOutputs() << " outputs";
  if (fileDetails)
  {
    reader->PrintOutputs(std::cout, fileDetails);
  }

  // construct the name of a log file
  std::string datestring = buildDateString();
  ;
  std::string dirString = extractDirString(argv[firstFileIndex]);
  std::string logfilename = datestring + "_dir_" + dirString + ".mitkdump";
  MITK_INFO << "Logfile " << logfilename;

  // write output to file for later analysis
  std::ofstream fs;
  fs.open(logfilename.c_str());
  fs << "---- " << dirString << ": Best reader configuration '" << reader->GetConfigurationLabel() << "' with "
     << reader->GetNumberOfOutputs() << " outputs" << std::endl;
  reader->PrintOutputs(fs, true); // always verbose in log file
  fs.close();

  // serialize, deserialize, analyze again, verify result!
  mitk::DICOMReaderConfigurator::Pointer serializer = mitk::DICOMReaderConfigurator::New();
  std::string readerSerialization = serializer->CreateConfigStringFromReader(reader.GetPointer());

  bool outputError(false);
  for (unsigned int outputIndex = 0; outputIndex < reader->GetNumberOfOutputs(); ++outputIndex)
  {
    const mitk::DICOMImageBlockDescriptor &outputDescriptor = reader->GetOutput(outputIndex);

    mitk::StringList filenamesOfThisGroup;
    const mitk::DICOMImageFrameList &frames = outputDescriptor.GetImageFrameList();
    for (auto fIter = frames.begin(); fIter != frames.end(); ++fIter)
    {
      filenamesOfThisGroup.push_back((*fIter)->Filename);
    }

    mitk::DICOMReaderConfigurator::Pointer readerConfigurator = mitk::DICOMReaderConfigurator::New();
    mitk::DICOMFileReader::Pointer dicomReader = readerConfigurator->CreateFromUTF8ConfigString(readerSerialization);
    dicomReader->SetInputFiles(filenamesOfThisGroup);
    dicomReader->AnalyzeInputFiles();
    if (dicomReader->GetNumberOfOutputs() != 1)
    {
      MITK_ERROR << "****** Re-analyzing files of output group " << outputIndex << " yields "
                 << dicomReader->GetNumberOfOutputs() << " groups";
      outputError = true;

      for (auto fIter = frames.begin(); fIter != frames.end(); ++fIter)
      {
        MITK_INFO << "filename group " << outputIndex << ": " << (*fIter)->Filename;
      }
    }
    else
    {
      MITK_INFO << "Re-analyzing files of output group " << outputIndex << " yields "
                << dicomReader->GetNumberOfOutputs() << " groups";
    }
  }

  if (outputError)
  {
    std::stringstream es;
    es << "Original reader configuration: " << std::endl;
    reader->PrintConfiguration(es);
    es << std::endl;
    mitk::DICOMReaderConfigurator::Pointer readerConfigurator = mitk::DICOMReaderConfigurator::New();
    mitk::DICOMFileReader::Pointer dicomReader = readerConfigurator->CreateFromUTF8ConfigString(readerSerialization);
    es << "New reader configuration: " << std::endl;
    dicomReader->PrintConfiguration(es);
    es << std::endl;

    es << "Original XML: \n" << readerSerialization << std::endl;
    std::string newSerialization = serializer->CreateConfigStringFromReader(dicomReader.GetPointer());
    es << "New XML: \n" << newSerialization << std::endl;
    MITK_ERROR << es.str();
  }

  if (loadimage)
  {
    MITK_INFO << "Loading...";
    reader->LoadImages();
    mitk::Image::Pointer image = reader->GetOutput(0).GetMitkImage();
    MITK_INFO << "---- Output image:";
    mitk::BaseGeometry::Pointer geo3D = image->GetGeometry();
    if (geo3D.IsNotNull())
    {
      mitk::SlicedGeometry3D::Pointer sg = dynamic_cast<mitk::SlicedGeometry3D *>(geo3D.GetPointer());
      if (sg.IsNotNull())
      {
        unsigned int nos = sg->GetSlices();
        mitk::PlaneGeometry::ConstPointer first = sg->GetPlaneGeometry(0);
        mitk::PlaneGeometry::ConstPointer last = sg->GetPlaneGeometry(nos - 1);

        mitk::Point3D firstOrigin = first->GetOrigin();
        mitk::Point3D lastOrigin = last->GetOrigin();
        MITK_INFO << "Geometry says: First slice at " << firstOrigin << ", last slice at " << lastOrigin;

        mitk::StringLookupTableProperty::Pointer sliceLocations =
          dynamic_cast<mitk::StringLookupTableProperty *>(image->GetProperty("dicom.image.0020.1041").GetPointer());
        if (sliceLocations.IsNotNull())
        {
          std::string firstSliceLocation = sliceLocations->GetValue().GetTableValue(0);
          std::string lastSliceLocation = sliceLocations->GetValue().GetTableValue(nos - 1);
          MITK_INFO << "Image properties says: first slice location at " << firstSliceLocation
                    << ", last slice location at " << lastSliceLocation;
        }

        mitk::StringLookupTableProperty::Pointer instanceNumbers =
          dynamic_cast<mitk::StringLookupTableProperty *>(image->GetProperty("dicom.image.0020.0013").GetPointer());
        if (instanceNumbers.IsNotNull())
        {
          std::string firstInstanceNumber = instanceNumbers->GetValue().GetTableValue(0);
          std::string lastInstanceNumber = instanceNumbers->GetValue().GetTableValue(nos - 1);
          MITK_INFO << "Image properties says: first instance number at " << firstInstanceNumber
                    << ", last instance number at " << lastInstanceNumber;
        }
      }
    }
    MITK_INFO << "---- End of output";
  }

  // if we got so far, everything is fine
  return EXIT_SUCCESS;
}