xref: /dports/science/InsightToolkit/ITK-5.0.1/Examples/IO/DicomSeriesReadPrintTags.cxx

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 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/

//  Software Guide : BeginLatex
//
//  This example illustrates how to read a DICOM series into a volume and then
//  print most of the DICOM header information. The binary fields are skipped.
//
//  \index{DICOM!Header}
//  \index{DICOM!Tags}
//  \index{DICOM!Printing Tags}
//
//  Software Guide : EndLatex

// Software Guide : BeginLatex
//
// The header files for the series reader and the GDCM classes for image IO and
// name generation should be included first.
//
// Software Guide : EndLatex

// Software Guide : BeginCodeSnippet
#include "itkImageSeriesReader.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
// Software Guide : EndCodeSnippet

int main( int argc, char* argv[] )
{
  if( argc < 2 )
    {
    std::cerr << "Usage: " << argv[0] << " DicomDirectory " << std::endl;
    return EXIT_FAILURE;
    }

  // Software Guide : BeginLatex
  //
  //  Next, we instantiate the type to be used for storing the image once it is
  //  read into memory.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using PixelType = signed short;
  constexpr unsigned int Dimension = 3;

  using ImageType = itk::Image< PixelType, Dimension >;
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We use the image type for instantiating the series reader type and then we
  // construct one object of this class.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ReaderType = itk::ImageSeriesReader< ImageType >;

  ReaderType::Pointer reader = ReaderType::New();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // A GDCMImageIO object is created and assigned to the reader.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using ImageIOType = itk::GDCMImageIO;

  ImageIOType::Pointer dicomIO = ImageIOType::New();

  reader->SetImageIO( dicomIO );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // A GDCMSeriesFileNames is declared in order to generate the names of DICOM
  // slices. We specify the directory with the \code{SetInputDirectory()} method
  // and, in this case, take the directory name from the command line arguments.
  // You could have obtained the directory name from a file dialog in a GUI.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using NamesGeneratorType = itk::GDCMSeriesFileNames;

  NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();

  nameGenerator->SetInputDirectory( argv[1] );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The list of files to read is obtained from the name generator by invoking
  // the \code{GetInputFileNames()} method and receiving the results in a
  // container of strings. The list of filenames is passed to the reader using
  // the \code{SetFileNames()} method.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using FileNamesContainer = std::vector<std::string>;
  FileNamesContainer fileNames = nameGenerator->GetInputFileNames();

  reader->SetFileNames( fileNames );
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We trigger the reader by invoking the \code{Update()} method. This
  // invocation should normally be done inside a \code{try/catch} block given
  // that it may eventually throw exceptions.
  //
  // Software Guide : EndLatex

  try
    {
    // Software Guide : BeginCodeSnippet
    reader->Update();
    // Software Guide : EndCodeSnippet
    }
  catch (itk::ExceptionObject &ex)
    {
    std::cout << ex << std::endl;
    return EXIT_FAILURE;
    }

  // Software Guide : BeginLatex
  //
  // ITK internally queries GDCM and obtains all the DICOM tags from the file
  // headers. The tag values are stored in the \doxygen{MetaDataDictionary}
  // which is a general-purpose container for \{key,value\} pairs. The Metadata
  // dictionary can be recovered from any ImageIO class by invoking the
  // \code{GetMetaDataDictionary()} method.
  //
  // \index{MetaDataDictionary}
  // \index{ImageIO!GetMetaDataDictionary()}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using DictionaryType = itk::MetaDataDictionary;

  const  DictionaryType & dictionary = dicomIO->GetMetaDataDictionary();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // In this example, we are only interested in the DICOM tags that can be
  // represented as strings. Therefore, we declare a \doxygen{MetaDataObject} of
  // string type in order to receive those particular values.
  //
  // \index{MetaDataDictionary!MetaDataObject}
  // \index{MetaDataDictionary!String entries}
  // \index{MetaDataObject!Strings}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  using MetaDataStringType = itk::MetaDataObject< std::string >;
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // The metadata dictionary is organized as a container with its corresponding
  // iterators. We can therefore visit all its entries by first getting access to
  // its \code{Begin()} and \code{End()} methods.
  //
  // \index{MetaDataDictionary!Begin()}
  // \index{MetaDataDictionary!End()}
  // \index{MetaDataDictionary!Iterator}
  // \index{MetaDataDictionary!ConstIterator}
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  auto itr = dictionary.Begin();
  auto end = dictionary.End();
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // We are now ready for walking through the list of DICOM tags. For this
  // purpose we use the iterators that we just declared. At every entry we
  // attempt to convert it into a string entry by using the \code{dynamic\_cast}
  // based on RTTI information\footnote{Run Time Type Information}. The
  // dictionary is organized like a \code{std::map} structure, so we should use
  // the \code{first} and \code{second} members of every entry in order
  // to get access to the \{key,value\} pairs.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  while( itr != end )
    {
    itk::MetaDataObjectBase::Pointer  entry = itr->second;

    MetaDataStringType::Pointer entryvalue =
      dynamic_cast<MetaDataStringType *>( entry.GetPointer() );

    if( entryvalue )
      {
      std::string tagkey   = itr->first;
      std::string tagvalue = entryvalue->GetMetaDataObjectValue();
      std::cout << tagkey <<  " = " << tagvalue << std::endl;
      }

    ++itr;
    }
  // Software Guide : EndCodeSnippet

  //  Software Guide : BeginLatex
  //
  //  It is also possible to query for specific entries instead of reading all of
  //  them as we did above. In this case, the user must provide the tag
  //  identifier using the standard DICOM encoding. The identifier is stored in a
  //  string and used as key in the dictionary.
  //
  //  Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  std::string entryId = "0010|0010";

  auto tagItr = dictionary.Find( entryId );

  if( tagItr == end )
    {
    std::cerr << "Tag " << entryId;
    std::cerr << " not found in the DICOM header" << std::endl;
    return EXIT_FAILURE;
    }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // Since the entry may or may not be of string type we must again use a
  // \code{dynamic\_cast} in order to attempt to convert it to a string dictionary
  // entry. If the conversion is successful, we can then print out its content.
  //
  // Software Guide : EndLatex

  // Software Guide : BeginCodeSnippet
  MetaDataStringType::ConstPointer entryvalue =
    dynamic_cast<const MetaDataStringType *>( tagItr->second.GetPointer() );

  if( entryvalue )
    {
    std::string tagvalue = entryvalue->GetMetaDataObjectValue();
    std::cout << "Patient's Name (" << entryId <<  ") ";
    std::cout << " is: " << tagvalue << std::endl;
    }
  else
    {
    std::cerr << "Entry was not of string type" << std::endl;
    return EXIT_FAILURE;
    }
  // Software Guide : EndCodeSnippet

  // Software Guide : BeginLatex
  //
  // This type of functionality will probably be more useful when provided
  // through a graphical user interface. For a full description of the DICOM
  // dictionary please look at the following file.
  //
  // \code{Insight/Utilities/gdcm/Dicts/dicomV3.dic}
  //
  // Software Guide : EndLatex

  return EXIT_SUCCESS;

}