diff --git a/Modules/DICOM/cmdapps/DICOMVolumeDiagnostics.cpp b/Modules/DICOM/cmdapps/DICOMVolumeDiagnostics.cpp
index 3a8c3b31e5..ae7d47f01d 100644
--- a/Modules/DICOM/cmdapps/DICOMVolumeDiagnostics.cpp
+++ b/Modules/DICOM/cmdapps/DICOMVolumeDiagnostics.cpp
@@ -1,195 +1,199 @@
/*============================================================================
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 <mitkCommandLineParser.h>
#include <mitkIOUtil.h>
#include <mitkDICOMEnums.h>
#include <mitkDICOMFilesHelper.h>
#include <mitkDICOMFileReaderSelector.h>
#include <filesystem>
#include <nlohmann/json.hpp>
void InitializeCommandLineParser(mitkCommandLineParser& parser)
{
parser.setTitle("DICOM Volume Diagnostics");
parser.setCategory("DICOM");
parser.setDescription("Gives insights how MITK readers would convert a set of DICOM files into image volumes (e.g. number of volumes and the sorting of the files)");
parser.setContributor("German Cancer Research Center (DKFZ)");
parser.setArgumentPrefix("--", "-");
parser.addArgument("help", "h", mitkCommandLineParser::Bool, "Help:", "Show this help text");
parser.addArgument("only-own-series", "s", mitkCommandLineParser::Bool, "Only own series", "Analyze only files in the same directory that have the same DICOM Series UID, if a file is provided as input.", us::Any());
- parser.addArgument("check-3D", "d", mitkCommandLineParser::Bool, "Check 3D configs", "Analyze the input by using all known 3D configurations. If flag is not set all configurations (3D and 3D+t) will be used.", us::Any());
- parser.addArgument("check-3D+t", "t", mitkCommandLineParser::Bool, "Check 3D+t configs", "Analyze the input by using all known 3D+t configurations (thus dynamic image configurations). If flag is not set all configurations (3D and 3D+t) will be used.", us::Any());
+ parser.addArgument("check-3d", "d", mitkCommandLineParser::Bool, "Check 3D configs", "Analyze the input by using all known 3D configurations. If flag is not set all configurations (3D and 3D+t) will be used.", us::Any());
+ parser.addArgument("check-3d+t", "t", mitkCommandLineParser::Bool, "Check 3D+t configs", "Analyze the input by using all known 3D+t configurations (thus dynamic image configurations). If flag is not set all configurations (3D and 3D+t) will be used.", us::Any());
parser.addArgument("input", "i", mitkCommandLineParser::File, "Input file or path", "Input contour(s)", us::Any(), false, false, false, mitkCommandLineParser::Input);
parser.addArgument("output", "o", mitkCommandLineParser::File, "Output file", "Output file where the diagnostics results are stored as json.", us::Any());
}
int main(int argc, char* argv[])
{
int returnValue = EXIT_SUCCESS;
mitkCommandLineParser parser;
InitializeCommandLineParser(parser);
auto args = parser.parseArguments(argc, argv);
if (args.empty())
+ {
+ std::cout << parser.helpText();
return EXIT_FAILURE;
+ }
nlohmann::json diagnosticsResult;
try
{
auto inputFilename = us::any_cast<std::string>(args["input"]);
auto outputFilename = args.count("output")==0 ? std::string() : us::any_cast<std::string>(args["output"]);
bool onlyOwnSeries = args.count("only-own-series");
- bool check3D = args.count("check-3D");
- bool check3DPlusT = args.count("check-3D+t");
+ bool check3D = args.count("check-3d");
+ bool check3DPlusT = args.count("check-3d+t");
if (!check3D && !check3DPlusT)
{ //if no check option is selected all are activated by default.
check3D = true;
check3DPlusT = true;
}
diagnosticsResult["input"] = inputFilename;
diagnosticsResult["only-own-series"] = onlyOwnSeries;
- diagnosticsResult["check-3D"] = check3D;
- diagnosticsResult["check-3D+t"] = check3DPlusT;
+ diagnosticsResult["check-3d"] = check3D;
+ diagnosticsResult["check-3d+t"] = check3DPlusT;
mitk::StringList relevantFiles = mitk::GetDICOMFilesInSameDirectory(inputFilename);
if (relevantFiles.empty())
{
mitkThrow() << "DICOM Volume Diagnostics found no relevant files in specified location. No data is loaded. Location: " << inputFilename;
}
else
{
- bool pathIsDirectory = std::filesystem::is_directory(std::filesystem::path(inputFilename));
+ bool pathIsDirectory = std::filesystem::is_directory(inputFilename);
if (!pathIsDirectory && onlyOwnSeries)
{
relevantFiles = mitk::FilterDICOMFilesForSameSeries(inputFilename, relevantFiles);
}
diagnosticsResult["analyzed_files"] = relevantFiles;
auto selector = mitk::DICOMFileReaderSelector::New();
if (check3D) selector->LoadBuiltIn3DConfigs();
if (check3DPlusT) selector->LoadBuiltIn3DnTConfigs();
nlohmann::json readerInfos;
for (const auto& reader : selector->GetAllConfiguredReaders())
- {
+ {
nlohmann::json readerInfo;
readerInfo["class_name"] = reader->GetNameOfClass();
readerInfo["configuration_label"] = reader->GetConfigurationLabel();
readerInfo["configuration_description"] = reader->GetConfigurationDescription();
- readerInfos.emplace_back(readerInfo);
+ readerInfos.push_back(readerInfo);
}
diagnosticsResult["checked_readers"] = readerInfos;
selector->SetInputFiles(relevantFiles);
auto reader = selector->GetFirstReaderWithMinimumNumberOfOutputImages();
if (reader.IsNull())
{
mitkThrow() << "DICOM Volume Diagnostics service found no suitable reader configuration for relevant files.";
}
else
{
nlohmann::json readerInfo;
readerInfo["class_name"] = reader->GetNameOfClass();
readerInfo["configuration_label"] = reader->GetConfigurationLabel();
readerInfo["configuration_description"] = reader->GetConfigurationDescription();
readerInfo["configuration_description"] = reader->GetConfigurationDescription();
std::stringstream config;
reader->PrintConfiguration(config);
readerInfo["config_details"] = config.str();
diagnosticsResult["selected_reader"] = readerInfo;
nlohmann::json outputInfos;
unsigned int relevantOutputCount = 0;
const auto nrOfOutputs = reader->GetNumberOfOutputs();
- for (unsigned int outputIndex = 0; outputIndex < nrOfOutputs; ++outputIndex)
+ for (std::remove_const_t<decltype(nrOfOutputs)> outputIndex = 0; outputIndex < nrOfOutputs; ++outputIndex)
{
bool isRelevantOutput = true;
if (!pathIsDirectory)
{
const auto frameList = reader->GetOutput(outputIndex).GetImageFrameList();
auto finding = std::find_if(frameList.begin(), frameList.end(), [&](const mitk::DICOMImageFrameInfo::Pointer& frame)
{
std::filesystem::path framePath(frame->Filename);
std::filesystem::path inputPath(inputFilename);
return framePath == inputPath;
});
isRelevantOutput = finding != frameList.end();
}
if (isRelevantOutput)
{
- relevantOutputCount++;
+ ++relevantOutputCount;
nlohmann::json outputInfo;
const auto output = reader->GetOutput(outputIndex);
const auto frameList = output.GetImageFrameList();
mitk::DICOMFilePathList outputFiles;
outputFiles.resize(frameList.size());
std::transform(frameList.begin(), frameList.end(), outputFiles.begin(), [](const mitk::DICOMImageFrameInfo::Pointer& frame) { return frame->Filename; });
outputInfo["files"] = outputFiles;
outputInfo["timesteps"] = output.GetNumberOfTimeSteps();
outputInfo["frames_per_timesteps"] = output.GetNumberOfFramesPerTimeStep();
- outputInfos.emplace_back(outputInfo);
+ outputInfos.push_back(outputInfo);
}
}
diagnosticsResult["volume_count"] = relevantOutputCount;
diagnosticsResult["volumes"] = outputInfos;
}
}
- std::cout << std::endl << "### DIAGNOSTICS REPORT ###" << std::endl << std::endl;
+ std::cout << "\n### DIAGNOSTICS REPORT ###\n" << std::endl;
std::cout << std::setw(2) << diagnosticsResult << std::endl;
if (!outputFilename.empty())
{
std::ofstream fileout(outputFilename);
fileout << diagnosticsResult;
fileout.close();
}
}
catch (const mitk::Exception& e)
{
MITK_ERROR << e.GetDescription();
return EXIT_FAILURE;
}
catch (const std::exception& e)
{
MITK_ERROR << e.what();
return EXIT_FAILURE;
}
catch (...)
{
+ MITK_ERROR << "An unknown error occurred!";
return EXIT_FAILURE;
}
return returnValue;
}