Skip to content

DOC: Explain ElastixRegistrationMethod use "-tp" for initial transforms #912

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
N-Dekker merged 1 commit into from
Jun 19, 2023
Merged

DOC: Explain ElastixRegistrationMethod use "-tp" for initial transforms #912

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions Core/ComponentBaseClasses/elxTransformBase.hxx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -438,8 +438,9 @@ TransformBase<TElastix>::ReadFromFile()
this->GetAsITKBaseType()->SetUseComposition(howToCombineTransforms == "Compose");

/** Task 4 - Remember the name of the TransformParametersFileName.
* This will be needed when another transform will use this transform
* as an initial transform (see the WriteToFile method)
* This will be needed when another transform will use this transform as an initial transform (see the WriteToFile
* method), which is relevant for transformix, as well as for elastix (specifically
* ElastixRegistrationMethod::GenerateData(), when InitialTransformParameterObject is specified).
*/
this->SetTransformParametersFileName(configuration.GetCommandLineArgument("-tp"));

Expand Down
9 changes: 7 additions & 2 deletions Core/Main/itkElastixRegistrationMethod.hxx
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -179,9 +179,10 @@ ElastixRegistrationMethod<TFixedImage, TMovingImage>::GenerateData()

if (m_InitialTransformParameterObject && !m_OutputDirectory.empty())
{
// Write InitialTransformParameters.0.txt, InitialTransformParameters.1.txt, InitialTransformParameters.2.txt, etc.
std::string initialTransformParameterFileName = "NoInitialTransform";
unsigned i{};

// Write InitialTransformParameters.0.txt, InitialTransformParameters.1.txt, InitialTransformParameters.2.txt, etc.
unsigned i{};

for (auto transformParameterMap : m_InitialTransformParameterObject->GetParameterMaps())
{
Expand All @@ -193,6 +194,10 @@ ElastixRegistrationMethod<TFixedImage, TMovingImage>::GenerateData()
++i;
}

// Pass the last initial transform parameter file name to the argument map, in order to have it stored by
// elx::TransformBase::ReadFromFile(), so that it can be retrieved later by
// elx::TransformBase::GetInitialTransformParametersFileName(). Use "-tp", instead of "-t0", to avoid actual file
// reading of the initial transforms, as they are already in memory.
argumentMap["-tp"] = initialTransformParameterFileName;
}

Expand Down