dicom-to-nifti.cpp
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/*
* Copyright (c) 2019, NVIDIA CORPORATION. All rights reserved.
*
* Redistribution and use in source and binary forms, with or without
* modification, are permitted provided that the following conditions
* are met:
* * Redistributions of source code must retain the above copyright
* notice, this list of conditions and the following disclaimer.
* * Redistributions in binary form must reproduce the above copyright
* notice, this list of conditions and the following disclaimer in the
* documentation and/or other materials provided with the distribution.
* * Neither the name of NVIDIA CORPORATION nor the names of its
* contributors may be used to endorse or promote products derived
* from this software without specific prior written permission.
*
* THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS ``AS IS'' AND ANY
* EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
* IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
* PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
* CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
* EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
* PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
* PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
* OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
* (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
* OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
*/
#include <itkGDCMImageIO.h>
#include <itkGDCMSeriesFileNames.h>
#include <itkMetaDataObject.h>
#include <itkImageSeriesReader.h>
#include <itkImageFileWriter.h>
#include <iostream>
#include <math.h>
#include <string.h>
#include <stdio.h>
#include <gdcmGlobal.h>
#pragma warning(push, 0)
//The program converts Dicom series to Nifti format with capability of multiple series read and get patient name as output
void trimTrailing(char * str) {
int index, i;
/* Find last index of non-white space character */
i = 0;
while (str[i] != '\0') {
if (str[i] != ' ' && str[i] != '\t' && str[i] != '\n') {
index = i;
}
i++;
}
/* Mark next character to last non-white space character as NULL */
str[index + 1] = '\0';
}
int main(int argc, char * argv[]) {
if (argc < 4) {
std::cerr << "Usage: " << std::endl;
std::cerr << argv[0] << " <DicomDirectory> <outputFileName> <Head Option> (Head Options 0:specified; 1:head with pid+date)" << std::endl;
return EXIT_FAILURE;
}
//ITK settings
const unsigned int Dimension = 3;
typedef int PixelType;
typedef itk::Image<PixelType, Dimension> ImageType;
typedef itk::ImageSeriesReader<ImageType> ReaderType;
typedef itk::GDCMImageIO ImageIOType;
typedef itk::GDCMSeriesFileNames NamesGeneratorType;
typedef itk::ImageFileWriter<ImageType> WriterType;
//Filters
ReaderType::Pointer reader = ReaderType::New();
ImageIOType::Pointer dicomIO = ImageIOType::New();
NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();
WriterType::Pointer writer = WriterType::New();
//Parameters
nameGenerator->SetDirectory(argv[1]);
char outFileName[50];
bool option = atoi(argv[3]);
bool closeMessage;
if (argc == 5)
closeMessage = true;
//Pipeline
reader->SetImageIO(dicomIO);
nameGenerator->SetUseSeriesDetails(true);
nameGenerator->AddSeriesRestriction("0008|0021");
writer->SetInput(reader->GetOutput());
typedef std::vector<std::string> SeriesIdContainer;
const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
if (!closeMessage) {
std::cout << std::endl << "The directory: ";
std::cout << std::endl << argv[1] << std::endl << std::endl;
std::cout << "Contains the following DICOM Series: ";
std::cout << std::endl;
}
while (seriesItr != seriesEnd) {
if (!closeMessage)
std::cout << seriesItr->c_str() << std::endl;
++seriesItr;
}
seriesItr = seriesUID.begin();
while (seriesItr != seriesEnd) {
std::strcpy(outFileName, argv[2]);
std::string seriesIdentifier;
seriesIdentifier = seriesItr->c_str();
if (!closeMessage) {
std::cout << std::endl;
std::cout << "Now reading series: " << std::endl;
std::cout << seriesIdentifier << std::endl;
}
typedef std::vector<std::string> FileNamesContainer;
FileNamesContainer fileNames;
fileNames = nameGenerator->GetFileNames(seriesIdentifier);
reader->SetFileNames(fileNames);
reader->Update();
typedef itk::MetaDataDictionary DictionaryType;
const DictionaryType & dictionary = dicomIO->GetMetaDataDictionary();
typedef itk::MetaDataObject<std::string> MetaDataStringType;
DictionaryType::ConstIterator itr = dictionary.Begin();
DictionaryType::ConstIterator end = dictionary.End();
std::string entryId = "0010|0020";
DictionaryType::ConstIterator tagItr = dictionary.Find(entryId);
MetaDataStringType::ConstPointer entryvalue = dynamic_cast<const MetaDataStringType *>(tagItr->second.GetPointer());
std::string tagvalue1 = entryvalue->GetMetaDataObjectValue();
if (!closeMessage) {
std::cout << "Patient's Name (" << entryId << ") ";
std::cout << " is: " << tagvalue1.c_str() << std::endl;
}
entryId = "0008|0020";
tagItr = dictionary.Find(entryId);
entryvalue = dynamic_cast<const MetaDataStringType *>(tagItr->second.GetPointer());
std::string tagvalue2 = entryvalue->GetMetaDataObjectValue();
if (!closeMessage) {
std::cout << "Study Date (" << entryId << ") ";
std::cout << " is: " << tagvalue2.c_str() << std::endl;
}
char temp[100];
strcpy(temp, tagvalue1.c_str());
trimTrailing(temp);
std::strcat(outFileName, temp);
std::strcat(outFileName, "_");
strcpy(temp, tagvalue2.c_str());
trimTrailing(temp);
std::strcat(outFileName, temp);
std::strcat(outFileName, ".nii");
if (option) {
if (!closeMessage) {
std::cout << "Writing the image as " << std::endl;
std::cout << outFileName << std::endl << std::endl;
}
writer->SetFileName(outFileName);
} else {
if (!closeMessage) {
std::cout << "Writing the image as " << std::endl;
std::cout << argv[2] << std::endl << std::endl;
}
writer->SetFileName(argv[2]);
}
writer->Update();
++seriesItr;
}
return EXIT_SUCCESS;
}
#pragma warning(pop)