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ENH: apply transform to single slice of time series #1800

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Oct 3, 2024
Merged

ENH: apply transform to single slice of time series #1800

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66 changes: 65 additions & 1 deletion Examples/antsApplyTransforms.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -210,6 +210,18 @@ antsApplyTransforms(itk::ants::CommandLineParser::Pointer & parser, unsigned int
typename itk::ants::CommandLineParser::OptionType::Pointer inputOption = parser->GetOption("input");
typename itk::ants::CommandLineParser::OptionType::Pointer outputOption = parser->GetOption("output");

// Time-index to extract from time-series image
unsigned long extractTimeIndex = 0;

bool extractTimeIndexSet = false;

typename itk::ants::CommandLineParser::OptionType::Pointer timeIndexOption = parser->GetOption("time-index");
if (timeIndexOption && timeIndexOption->GetNumberOfFunctions())
{
extractTimeIndexSet = true;
extractTimeIndex = parser->Convert<unsigned int>(timeIndexOption->GetFunction(0)->GetName());
}

if (inputImageType == 5 && inputOption && inputOption->GetNumberOfFunctions())
{
if (verbose)
Expand All @@ -235,8 +247,48 @@ antsApplyTransforms(itk::ants::CommandLineParser::Pointer & parser, unsigned int
if (verbose)
{
std::cout << "Input time-series image: " << inputOption->GetFunction(0)->GetName() << std::endl;
if (extractTimeIndexSet)
{
std::cout << "Extracting time index: " << extractTimeIndex << std::endl;
}
}
if (!extractTimeIndexSet)
{
ReadImage<TimeSeriesImageType>(timeSeriesImage, (inputOption->GetFunction(0)->GetName()).c_str());
}
else
{
// Modifying inputImageType, because we're going to extract a single time point
// if we don't do this, the code will try to read from timeSeriesImage below and output a time series
inputImageType = 0;

// Set up the image reader with streaming support
using ReaderType = itk::ImageFileReader<TimeSeriesImageType>;
typename ReaderType::Pointer reader = ReaderType::New();
reader->SetFileName((inputOption->GetFunction(0)->GetName()).c_str());

// Update the reader's output information without loading the entire image into memory
reader->UpdateOutputInformation();
typename TimeSeriesImageType::RegionType extractRegion = reader->GetOutput()->GetLargestPossibleRegion();
typename TimeSeriesImageType::SizeType size = extractRegion.GetSize();

// Check if the extractTimeIndex is within range
if (extractTimeIndex >= size[3])
{
std::cerr << "Error: time index to extract is out of range [0, " << (size[3] - 1) << "]" << std::endl;
return EXIT_FAILURE;
}

extractRegion.SetIndex(Dimension, extractTimeIndex);
extractRegion.SetSize(Dimension, 0);
using ExtracterType = itk::ExtractImageFilter<TimeSeriesImageType, ImageType>;
typename ExtracterType::Pointer extracter = ExtracterType::New();
extracter->SetInput(reader->GetOutput());
extracter->SetExtractionRegion(extractRegion);
extracter->SetDirectionCollapseToSubmatrix();
extracter->Update();
inputImages.push_back(extracter->GetOutput());
}
ReadImage<TimeSeriesImageType>(timeSeriesImage, (inputOption->GetFunction(0)->GetName()).c_str());
}
else if (inputImageType == 2 && inputOption && inputOption->GetNumberOfFunctions())
{
Expand Down Expand Up @@ -896,6 +948,18 @@ antsApplyTransformsInitializeCommandLineOptions(itk::ants::CommandLineParser * p
parser->AddOption(option);
}

{
std::string description = std::string("Time index to extract from time series input (-e 3). ") +
std::string("This selects a single slice from time series input without reading ") +
std::string("the entire dataset into memory.");

OptionType::Pointer option = OptionType::New();
option->SetLongName("time-index");
option->SetUsageOption(0, "<timeIndex>");
option->SetDescription(description);
parser->AddOption(option);
}

{
std::string description = std::string("Currently, the only input objects supported are image ") +
std::string("objects. However, the current framework allows for ") +
Expand Down