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ENH: Improve error reporting in transform file storage
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Errors occurring during transform file reading/writing are now displayed to the user.
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@lassoan @jcfr
lassoan authored and jcfr committed Feb 1, 2023
1 parent e0c4eb1 commit 6680e0f
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Showing 4 changed files with 95 additions and 64 deletions.
99 changes: 62 additions & 37 deletions Libs/MRML/Core/vtkMRMLTransformStorageNode.cxx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -153,31 +153,36 @@ int vtkMRMLTransformStorageNode::ReadFromITKv3BSplineTransformFile(vtkMRMLNode *
}
catch (itk::ExceptionObject &exc)
{
vtkErrorMacro("ITK exception caught reading transform file: "<< fullName.c_str() << "\n" << exc);
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromITKv3BSplineTransformFile",
"Error while reading transform file '" << fullName << "'. ITK exception:\n" << exc);
return 0;
}
catch (...)
{
vtkErrorMacro("Unknown exception caught while reading transform file: "<< fullName.c_str());
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromITKv3BSplineTransformFile",
"Error while reading transform file '" << fullName << "'.");
return 0;
}

// For now, grab the first two transforms from the file.
TransformListType *transforms = reader->GetTransformList();
if (transforms->size() == 0)
{
vtkErrorMacro("Could not find a transform in file: " << fullName.c_str());
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromITKv3BSplineTransformFile",
"Could not find a transform in file: '" << fullName << "'");
return 0;
}
if (transforms->size() > 2)
{
vtkWarningMacro(<< "More than two transform in the file: "<< fullName.c_str()<< ". Using only the first two transforms.");
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromITKv3BSplineTransformFile",
"More than two transform in the file: '" << fullName << "'. Using only the first two transforms.");
}
TransformListType::iterator it = transforms->begin();
TransformType::Pointer transform = (*it);
if (!transform)
{
vtkErrorMacro(<< "Invalid transform in the file: "<< fullName.c_str()<< ", (" << transforms->size() << ")");
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromITKv3BSplineTransformFile",
"Invalid transform in the file: '" << fullName << "'. Transform list size: " << transforms->size() << ".");
return 0;
}
++it;
Expand All @@ -187,7 +192,8 @@ int vtkMRMLTransformStorageNode::ReadFromITKv3BSplineTransformFile(vtkMRMLNode *
transform2 = (*it);
if (!transform2)
{
vtkErrorMacro(<< "Invalid transform (2) in the file: "<< fullName.c_str()<< ", (" << transforms->size() << ")");
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromITKv3BSplineTransformFile",
"Invalid transform (2) in the file: '" << fullName << "'. Transform list size: " << transforms->size() << ".");
return 0;
}
}
Expand Down Expand Up @@ -249,27 +255,29 @@ int vtkMRMLTransformStorageNode::ReadFromImageFile(vtkMRMLNode *refNode)
}
catch (...)
{
vtkErrorMacro("Unknown exception caught while reading grid transform image file: " << fullName.c_str());
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromImageFile",
"Error while reading image file as grid transform '" << fullName << "'.");
return 0;
}

if (!gridImage_Lps)
{
vtkErrorMacro("Failed to read image as a grid transform from file: " << fullName.c_str());
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromImageFile",
"Error while reading image file as grid transform '" << fullName << "'.");
return 0;
}

const itk::MetaDataDictionary & metadata = gridImage_Lps->GetMetaDataDictionary();
std::string niftiIntentCode;
if (itk::ExposeMetaData<std::string>(metadata, "intent_code", niftiIntentCode))
{
// This is a NIFTI file.
// Verify if the intent code corresponds to displacement field (1006).
// This is a NIFTI file. Verify that it contains a displacement vector image
// by checking that the "intent code" metadata field equals 1006 (NIFTI_INTENT_DISPVECT).
if (niftiIntentCode != "1006")
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromImageFile",
"NIFTI file does not contain valid displacement field, the transform may be incorrect."
<< " Intent code is expected to be '1006' (displacement vector), but the file contained : '" << niftiIntentCode << "'."
"NIFTI file may not contain valid displacement field, the transform may be incorrect."
<< " Intent code is expected to be '1006' (displacement vector), but the file contained: '" << niftiIntentCode << "'."
<< " Filename: '" << fullName << "'.");
}
}
Expand All @@ -293,7 +301,8 @@ int vtkMRMLTransformStorageNode::ReadFromImageFile(vtkMRMLNode *refNode)

//----------------------------------------------------------------------------
template<typename T>
vtkAbstractTransform* ReadFromTransformFile(vtkObject* loggerObject, const std::string& fullName)
vtkAbstractTransform* ReadFromTransformFile(vtkObject* loggerObject, const std::string& fullName,
vtkMRMLMessageCollection* userMessages)
{
typedef itk::TransformFileReaderTemplate<T> TransformReaderType;
typedef typename TransformReaderType::TransformListType TransformListType;
Expand All @@ -307,19 +316,22 @@ vtkAbstractTransform* ReadFromTransformFile(vtkObject* loggerObject, const std::
}
catch (itk::ExceptionObject &exc)
{
vtkErrorWithObjectMacro(loggerObject, "ITK exception caught reading transform file: "<< fullName.c_str() << "\n" << exc);
vtkErrorToMessageCollectionWithObjectMacro(loggerObject, userMessages, "vtkMRMLTransformStorageNode::ReadFromTransformFile",
"Error while reading transform file '" << fullName << "'. ITK exception:\n" << exc);
return nullptr;
}
catch (...)
{
vtkErrorWithObjectMacro(loggerObject, "Unknown exception caught while reading transform file: "<< fullName.c_str());
vtkErrorToMessageCollectionWithObjectMacro(loggerObject, userMessages, "vtkMRMLTransformStorageNode::ReadFromTransformFile",
"Error while reading transform file '" << fullName << "'.");
return nullptr;
}

TransformListType *transforms = reader->GetTransformList();
if (transforms==nullptr || transforms->empty())
{
vtkErrorWithObjectMacro(loggerObject, "Transforms not found in transform file: "<< fullName.c_str());
vtkErrorToMessageCollectionWithObjectMacro(loggerObject, userMessages, "vtkMRMLTransformStorageNode::ReadFromTransformFile",
"Transforms not found in transform file: " << fullName);
return nullptr;
}
if (transforms->size()>1)
Expand All @@ -328,13 +340,17 @@ vtkAbstractTransform* ReadFromTransformFile(vtkObject* loggerObject, const std::
// It is not necessarily a compositing, for example: in ITKv3 the list was used to store additive
// bulk transform for BSpline deformable transform. Therefore, if the file contains a transform list
// then we do not interpret it as a composite/ transform.
vtkErrorWithObjectMacro(loggerObject, "Multiple transforms are defined in the transform file but only one is allowed (composite transforms has to be stored as a single CompositeTransform). In file: "<< fullName.c_str());
vtkErrorToMessageCollectionWithObjectMacro(loggerObject, userMessages, "vtkMRMLTransformStorageNode::ReadFromTransformFile",
"Multiple transforms are defined in the transform file but only one is allowed"
" (composite transforms has to be stored as a single CompositeTransform). In file: "
<< fullName);
return nullptr;
}
TransformType *firstTransform = transforms->front();
if (firstTransform==nullptr)
{
vtkErrorWithObjectMacro(loggerObject, "Transforms not found in transform file: "<< fullName.c_str());
vtkErrorToMessageCollectionWithObjectMacro(loggerObject, userMessages, "vtkMRMLTransformStorageNode::ReadFromTransformFile",
"Transforms not found in transform file: " << fullName);
return nullptr;
}

Expand Down Expand Up @@ -420,17 +436,18 @@ int vtkMRMLTransformStorageNode::ReadFromTransformFile(vtkMRMLNode *refNode)
vtkSmartPointer<vtkAbstractTransform> transformVtk;

transformVtk = vtkSmartPointer<vtkAbstractTransform>::Take(
::ReadFromTransformFile<double>(this, fullName));
::ReadFromTransformFile<double>(this, fullName, this->GetUserMessages()));

if (transformVtk.GetPointer()==nullptr)
{
transformVtk = vtkSmartPointer<vtkAbstractTransform>::Take(
::ReadFromTransformFile<float>(this, fullName));
::ReadFromTransformFile<float>(this, fullName, this->GetUserMessages()));
}

if (transformVtk.GetPointer()==nullptr)
{
vtkErrorMacro("Failed to read transform from file: "<< fullName.c_str());
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadFromTransformFile",
"Failed to read transform from file: '" << fullName << "'");
return 0;
}

Expand Down Expand Up @@ -469,7 +486,8 @@ int vtkMRMLTransformStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
// Check that the file exists
if (vtksys::SystemTools::FileExists(fullName.c_str()) == false)
{
vtkErrorMacro("ReadDataInternal: transform file '" << fullName.c_str() << "' not found.");
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::ReadDataInternal",
"Failed to read transform. Transform from file not found: '" << fullName << "'.");
return 0;
}

Expand Down Expand Up @@ -515,7 +533,7 @@ int vtkMRMLTransformStorageNode::WriteToTransformFile(vtkMRMLNode *refNode)
this, transformVtk, secondaryTransformItk, this->PreferITKv3CompatibleTransforms, false);
if (transformItk.IsNull())
{
vtkErrorMacro("WriteTransform failed: cannot to convert VTK transform to ITK transform");
vtkErrorMacro("WriteTransform failed: cannot convert VTK transform to ITK transform");
return 0;
}

Expand All @@ -536,14 +554,14 @@ int vtkMRMLTransformStorageNode::WriteToTransformFile(vtkMRMLNode *refNode)
}
catch (itk::ExceptionObject &exc)
{
vtkErrorMacro("ITK exception caught writing transform file: "
<< fullName.c_str() << "\n" << exc);
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::WriteToTransformFile",
"Error while reading transform file '" << fullName << "'. ITK exception:\n" << exc);
return 0;
}
catch (...)
{
vtkErrorMacro("Unknown exception caught while writing transform file: "
<< fullName.c_str());
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::WriteToTransformFile",
"Error while reading transform file '" << fullName << "'");
return 0;
}

Expand All @@ -563,15 +581,18 @@ int vtkMRMLTransformStorageNode::WriteToImageFile(vtkMRMLNode *refNode)
vtkOrientedGridTransform* gridTransform_Ras = vtkOrientedGridTransform::SafeDownCast(transformNode->GetTransformFromParentAs("vtkOrientedGridTransform"));
if (gridTransform_Ras==nullptr)
{
vtkErrorMacro("Cannot retrieve grid transform from node");
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::WriteToImageFile",
"Cannot retrieve grid transform from node " << (transformNode->GetID() ? transformNode->GetID() : "(unknown)"));
return 0;
}

// Update is needed because it refreshes the inverse flag (the flag may be out-of-date if the transform depends on its inverse)
gridTransform_Ras->Update();
if (gridTransform_Ras->GetInverseFlag())
{
vtkErrorMacro("Cannot write inverse grid transform to image file. Either save the transform in a transform file (.h5) or invert the transform before saving it into an image file.");
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::WriteToImageFile",
"Cannot write inverse grid transform " << (transformNode->GetID() ? transformNode->GetID() : "(unknown)") << " to file."
<< " Either save the transform in a transform file (.h5) or invert the transform before saving it into an image file.");
return 0;
}

Expand All @@ -583,24 +604,27 @@ int vtkMRMLTransformStorageNode::WriteToImageFile(vtkMRMLNode *refNode)
std::string fullName = this->GetFullNameFromFileName();
writer->SetFileName( fullName );

// If this image is saved as a NIFTI then setting intent code to 1006 (NIFTI_INTENT_DISPVECT)
// will save the image as a displacement vector image.
itk::MetaDataDictionary& dictionary = gridImage_Lps->GetMetaDataDictionary();
itk::EncapsulateMetaData<std::string>(dictionary, "intent_code", "1006"); // NIFTI_INTENT_DISPVECT = 1006
itk::EncapsulateMetaData<std::string>(dictionary, "intent_code", "1006");

try
{
writer->Update();
}
catch (itk::ExceptionObject &exc)
{
vtkErrorMacro("Failed to save grid transform to file: " << fullName.c_str()
<< ". Make sure a 'Displacement field' format is selected for saving."
<< "ITK exception caught writing transform file: \n" << exc);
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::WriteToImageFile",
"Failed to save grid transform to file: '" << fullName << "'."
<< " Make sure a 'Displacement field' format is selected for saving."
<< " ITK exception caught writing transform file:\n" << exc);
return 0;
}
catch (...)
{
vtkErrorMacro("Unknown exception caught while writing transform file: "
<< fullName.c_str());
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::WriteToImageFile",
"Failed to save grid transform to file: '" << fullName << "'");
return 0;
}

Expand Down Expand Up @@ -653,9 +677,10 @@ bool vtkMRMLTransformStorageNode::IsImageFile(const std::string &filename)
{
// determine file type
std::string extension = this->GetSupportedFileExtension(filename.c_str());
if( extension.empty() )
if (extension.empty())
{
vtkErrorMacro("ReadData: no file extension specified: " << filename.c_str());
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLTransformStorageNode::IsImageFile",
"Filename does not contain extension: '" << filename.c_str() << "'");
return false;
}
if ( !extension.compare(".nrrd")
Expand Down
46 changes: 27 additions & 19 deletions Modules/Loadable/Transforms/Logic/vtkSlicerTransformLogic.cxx
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ or http://www.slicer.org/copyright/copyright.txt for details.
#include "vtkMRMLMarkupsNode.h"
#include "vtkMRMLMarkupsPlaneNode.h"
#include "vtkMRMLMarkupsROINode.h"
#include "vtkMRMLMessageCollection.h"
#include "vtkMRMLScalarVolumeDisplayNode.h"
#include "vtkMRMLScalarVolumeNode.h"
#include "vtkMRMLScene.h"
Expand Down Expand Up @@ -98,47 +99,49 @@ bool vtkSlicerTransformLogic::hardenTransform(vtkMRMLTransformableNode* transfor
}

//----------------------------------------------------------------------------
vtkMRMLTransformNode* vtkSlicerTransformLogic::AddTransform(const char* filename, vtkMRMLScene *scene)
vtkMRMLTransformNode* vtkSlicerTransformLogic::AddTransform(const char* filename, vtkMRMLScene *scene,
vtkMRMLMessageCollection* userMessages/*=nullptr*/)
{
vtkNew<vtkMRMLTransformStorageNode> storageNode;

if (scene == nullptr)
{
{
vtkErrorMacro("scene == nullptr in vtkSlicerTransformLogic::AddTransform");
return nullptr;
}
}

// check for local or remote files
int useURI = 0; // false;
if (scene->GetCacheManager() != nullptr)
{
{
useURI = scene->GetCacheManager()->IsRemoteReference(filename);
}
}

const char *localFile;
if (useURI)
{
{
vtkDebugMacro("AddTransforn: file name is remote: " << filename);
storageNode->SetURI(filename);
// reset filename to the local file name
localFile = ((scene)->GetCacheManager())->GetFilenameFromURI(filename);
}
}
else
{
{
storageNode->SetFileName(filename);
localFile = filename;
}
}

const std::string fname(localFile);
// the model name is based on the file name (itksys call should work even if
// file is not on disk yet)
const std::string name = itksys::SystemTools::GetFilenameName(fname);

if (!storageNode->SupportedFileType(name.c_str()))
{
vtkErrorMacro("Unsupported transform file format: " << filename);
{
vtkErrorToMessageCollectionMacro(userMessages, "vtkSlicerTransformLogic::AddTransform",
"Unsupported transform file format: " << filename);
return nullptr;
}
}

// check to see which node can read this type of file
vtkSmartPointer<vtkMRMLTransformNode> tnode;
Expand All @@ -149,7 +152,12 @@ vtkMRMLTransformNode* vtkSlicerTransformLogic::AddTransform(const char* filename
generalTransform->SetScene(scene);
if (!storageNode->ReadData(generalTransform.GetPointer()))
{
vtkErrorMacro("Failed to read transform from file: " << filename);
if (userMessages)
{
userMessages->AddMessages(storageNode->GetUserMessages());
}
vtkErrorToMessageCollectionMacro(userMessages, "vtkSlicerTransformLogic::AddTransform",
"Failed to read transform from file: " << filename);
return nullptr;
}

Expand All @@ -160,6 +168,7 @@ vtkMRMLTransformNode* vtkSlicerTransformLogic::AddTransform(const char* filename
// term we should get rid of specialized transform node classes and just use
// vtkMRMLTransformNode (anyway, transform classes are not meaningful when transforms
// are composited by hardening and we have mixed transforms).
storageNode->GetUserMessages()->ClearMessages();
switch (GetTransformKind(generalTransform.GetPointer()))
{
case TRANSFORM_LINEAR:
Expand All @@ -179,6 +188,11 @@ vtkMRMLTransformNode* vtkSlicerTransformLogic::AddTransform(const char* filename
tnode = generalTransform.GetPointer();
}

if (userMessages)
{
userMessages->AddMessages(storageNode->GetUserMessages());
}

const std::string basename(storageNode->GetFileNameWithoutExtension(fname.c_str()));
const std::string uname(scene->GetUniqueNameByString(basename.c_str()));
tnode->SetName(uname.c_str());
Expand All @@ -190,12 +204,6 @@ vtkMRMLTransformNode* vtkSlicerTransformLogic::AddTransform(const char* filename
return tnode;
}

int vtkSlicerTransformLogic::SaveTransform(const char* vtkNotUsed(filename),
vtkMRMLTransformNode *vtkNotUsed(transformNode))
{
return 1;
}

//----------------------------------------------------------------------------
const char* vtkSlicerTransformLogic::GetVisualizationDisplacementMagnitudeScalarName()
{
Expand Down
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