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ENH: Display warning when saving into TIFF format
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Adds warning for TIFF file format saving. Prevents potential data loss.
Made translatable all messages that may be relevant to users.

see #7588

Co-authored-by: Andras Lasso <lasso@queensu.ca>
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@aramSofthenge @lassoan
aramSofthenge and lassoan committed Mar 22, 2024
1 parent bf693e2 commit c33335c
Showing 1 changed file with 82 additions and 52 deletions.
134 changes: 82 additions & 52 deletions Libs/MRML/Core/vtkMRMLVolumeArchetypeStorageNode.cxx
View file
Expand Up @@ -14,6 +14,7 @@ Version: $Revision: 1.6 $

// MRML includes
#include "vtkDataFileFormatHelper.h"
#include "vtkMRMLI18N.h"
#include "vtkDataIOManager.h"
#include "vtkMRMLMessageCollection.h"
#include "vtkMRMLScene.h"
Expand Down Expand Up @@ -325,8 +326,7 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)

if (fullName.empty())
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"File name not specified");
vtkErrorMacro("vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: File name not specified");
return 0;
}

Expand All @@ -349,8 +349,7 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
vtkMRMLScalarVolumeNode * volNode = vtkMRMLScalarVolumeNode::SafeDownCast(refNode);
if (volNode == nullptr)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Reference node is expected to be a vtkMRMLScalarVolumeNode");
vtkErrorMacro("vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Reference node is expected to be a vtkMRMLScalarVolumeNode");
return 0;
}

Expand All @@ -375,8 +374,7 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)

if (reader.GetPointer() == nullptr)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Failed to instantiate a file reader");
vtkErrorMacro("vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Failed to instantiate a file reader");
return 0;
}

Expand Down Expand Up @@ -426,24 +424,23 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
}
if (!readingWorked)
{
std::string reader0thFileName;
if (reader->GetFileName(0) != nullptr)
{
reader0thFileName = std::string("reader 0th file name = ") + std::string(reader->GetFileName(0));
}
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Cannot read file as a volume of type " << (refNode ? refNode->GetNodeTagName() : "null")
<< " [" << "fullName = " << fullName << "]: " << errorMessage << "."
<< " Number of files listed in the node = " << this->GetNumberOfFileNames() << "."
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode",
"Cannot read '%1' file as a volume of type '%2'. Details: %3."),
fullName.c_str(), refNode ? refNode->GetNodeTagName() : "", errorMessage.c_str());
// Log some more details for debugging (not displayed to user)
vtkErrorMacro("vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal: Reading of file '" << fullName << "' failed: " << errorMessage
<< " Number of files listed in the node is " << this->GetNumberOfFileNames() << "."
<< " File reader says it was able to read " << reader->GetNumberOfFileNames() << " files."
<< " File reader used the archetype file name of " << reader->GetArchetype() << " [" << reader0thFileName.c_str() << "].");
<< " File reader used the archetype file name of '" << reader->GetArchetype() << "' (first filename: '"
<< (reader->GetFileName(0) ? reader->GetFileName(0) : "") << "')"))
return 0;
}

if (reader->GetOutput() == nullptr || reader->GetOutput()->GetPointData() == nullptr)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Unable to read data from file: " << fullName);
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Unable to read data from file: '%1'"), fullName.c_str()));
return 0;
}

Expand All @@ -453,7 +450,7 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
if (pointData->GetTensors() == nullptr || pointData->GetTensors()->GetNumberOfTuples() == 0)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Unable to read DiffusionTensorVolume data from file: " << fullName );
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Unable to read DiffusionTensorVolume data from file: '%1'"), fullName.c_str()));
return 0;
}
}
Expand All @@ -462,7 +459,7 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
if (pointData->GetScalars() == nullptr || pointData->GetScalars()->GetNumberOfTuples() == 0)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Unable to read ScalarVolume data from file: " << fullName );
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Unable to read ScalarVolume data from file: '%1'"), fullName.c_str()));
return 0;
}
}
Expand All @@ -472,7 +469,7 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
&& reader->GetNumberOfComponents() != 1)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Not a scalar volume file: " << fullName );
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Not a scalar volume file: '%1'"), fullName.c_str()));
return 0;
}

Expand Down Expand Up @@ -515,7 +512,7 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
if (ici->GetOutput() == nullptr)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Cannot read file: " << fullName);
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Cannot read file: '%1'"), fullName.c_str()));
return 0;
}

Expand Down Expand Up @@ -543,7 +540,7 @@ int vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal(vtkMRMLNode *refNode)
if (rasToIjkMatrix == nullptr)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ReadDataInternal",
"Reader returned nullptr RasToIjkMatrix");
vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Image reader provided invalid RAS to IJK matrix"));
}

// If volume is left-handed coordinates, modify it to right-handed coordinate
Expand Down Expand Up @@ -572,8 +569,7 @@ int vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal(vtkMRMLNode *refNode)
vtkMRMLVolumeNode *volNode = vtkMRMLVolumeNode::SafeDownCast(refNode);
if (!volNode)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
"File writing failed: refNode is invalid");
vtkErrorMacro("vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal: File writing failed: refNode is invalid");
return 0;
}

Expand All @@ -589,8 +585,7 @@ int vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal(vtkMRMLNode *refNode)
std::string fullName = this->GetFullNameFromFileName();
if (fullName.empty())
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
"File name not specified");
vtkErrorMacro("vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal: File name not specified");
return 0;
}

Expand All @@ -599,17 +594,19 @@ int vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal(vtkMRMLNode *refNode)
if (volNode->GetImageData()->GetNumberOfScalarComponents() != 3)
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
"Voxel vector type is spatial but number of scalar components is not 3. Saved vector type will be non-spatial.");
vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode",
"Voxel vector type is spatial but number of scalar components is not 3. Saved vector type will be non-spatial."));
}
else
{
std::string extension = vtkMRMLStorageNode::GetLowercaseExtensionFromFileName(fullName);
if (extension != ".nrrd" && extension != ".nhdr")
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
"Spatial vectors will be written to non-nrrd file format (" << extension << "). In this format, voxels are saved"
<< " as regular vectors. If the file is imported again then vector axis directions may be flipped."
<< "\nIt is recommended to save volumes that contain spatial vectors into NRRD file format.");
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode",
"Spatial vectors will be written to non-NRRD file format (%1). In this format, voxels are saved"
" as regular vectors. If the file is imported again then vector axis directions may be flipped."
" It is recommended to save volumes that contain spatial vectors in NRRD file format."), extension.c_str()));
}
}
}
Expand Down Expand Up @@ -649,7 +646,7 @@ int vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal(vtkMRMLNode *refNode)
if (!vtksys::SystemTools::RemoveFile(targetFile.c_str()))
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
"Unable to remove old version of file " << targetFile);
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Unable to remove old version of file: '%1'"), fullName.c_str()));
}
}
std::string sourceFile = vtksys::SystemTools::JoinPath(sourcePathComponents);
Expand All @@ -659,7 +656,8 @@ int vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal(vtkMRMLNode *refNode)
if (renameReturn != 0 )
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
"Error renaming file to " << targetFile << ", renameReturn = " << renameReturn);
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Error renaming file to '%1', rename returned code %2"),
targetFile.c_str(), std::to_string(renameReturn).c_str()));
// fall back to doing a second write
moveSucceeded = false;
break;
Expand Down Expand Up @@ -750,17 +748,50 @@ int vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal(vtkMRMLNode *refNode)
if (!vtkAddonMathUtilities::MatrixAreEqual(currentIjkToRasDirection, identityIjkToRasDirection))
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
"VTK file format can only store LPS axis oriented images. Orientation of the saved image may be incorrect.");
vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode",
"VTK file format can only store LPS axis oriented images. Orientation of the saved image may be incorrect."
" NRRD file format is recommended for storing this image."));
}
}

// Display warning if saving TIFF file as 3D image
if ((vtksys::SystemTools::StringEndsWith(lowerCaseFileName, ".tiff") ||
vtksys::SystemTools::StringEndsWith(lowerCaseFileName, ".tif")))
{
// Display warning if saving TIFF file with non-LPS axes or non-zero origin
// (TIFF cannot store axis directions and origin position in standard fields)

vtkNew<vtkMatrix4x4> currentIjkToRas;
volNode->GetRASToIJKMatrix(currentIjkToRas);
double unitScale[3] = { 1.0, 1.0, 1.0 };
vtkAddonMathUtilities::NormalizeOrientationMatrixColumns(currentIjkToRas, unitScale);

vtkNew<vtkMatrix4x4> identityIjkToRas;
identityIjkToRas->SetElement(0, 0, -1.0);
identityIjkToRas->SetElement(1, 1, -1.0);

// Display warning if saving TIFF file with non-unit K spacing (TIFF cannot store spacing along K axis)
bool unitZSpacing = (fabs(unitScale[2] - 1.0) < 1e-3);

if (!vtkAddonMathUtilities::MatrixAreEqual(currentIjkToRas, identityIjkToRas)
|| !unitZSpacing)
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode",
"Saving this image in TIFF format will result in loss of information (image position, orientation, or spacing along the third image axis)."
" NRRD file format is recommended for storing this image."));
}
}

// Display warnings for Analyze files
if (vtksys::SystemTools::StringEndsWith(lowerCaseFileName, ".hdr")
|| vtksys::SystemTools::StringEndsWith(lowerCaseFileName, ".img")
|| vtksys::SystemTools::StringEndsWith(lowerCaseFileName, ".img.gz"))
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::WriteDataInternal",
"Analyze file format is not recommended, as its image orientation specification is ambiguous.");
vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode",
"Analyze file format is not recommended, as its image orientation specification is ambiguous."
" NRRD file format is recommended for storing this image."));
}

return result;
Expand Down Expand Up @@ -789,8 +820,7 @@ std::string vtkMRMLVolumeArchetypeStorageNode::UpdateFileList(vtkMRMLNode *refNo
// test whether refNode is a valid node to hold a volume
if (!refNode->IsA("vtkMRMLScalarVolumeNode") )
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"Reference node is not a vtkMRMLVolumeNode");
vtkErrorMacro("vtkMRMLVolumeArchetypeStorageNode::UpdateFileList: Reference node is not a volume");
return "";
}

Expand All @@ -799,15 +829,14 @@ std::string vtkMRMLVolumeArchetypeStorageNode::UpdateFileList(vtkMRMLNode *refNo
if (volNode == nullptr || volNode->GetImageData() == nullptr)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"Cannot write ImageData, it's NULL");
vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Cannot write volume, image data is empty"));
return "";
}

std::string oldName(this->GetFileName() ? this->GetFileName() : "");
if (oldName.empty())
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"File name not specified");
vtkErrorMacro("vtkMRMLVolumeArchetypeStorageNode::UpdateFileList failed: File name not specified");
return "";
}

Expand All @@ -817,7 +846,7 @@ std::string vtkMRMLVolumeArchetypeStorageNode::UpdateFileList(vtkMRMLNode *refNo
this->ResetFileNameList();

// make a new dir to write temporary stuff out to
// std::vector<std::string> pathComponents;
// std::vector<std::string> pathComponents;
// get the base dir of the destination
/*
// get the cache dir and make a subdir in it.
Expand Down Expand Up @@ -848,14 +877,14 @@ std::string vtkMRMLVolumeArchetypeStorageNode::UpdateFileList(vtkMRMLNode *refNo
if (!vtksys::SystemTools::RemoveADirectory(tempDir.c_str()))
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"Failed to delete directory '" << tempDir << "'.");
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Failed to delete directory '%1'"), tempDir.c_str()));
return "";
}
}
if (!vtksys::SystemTools::MakeDirectory(tempDir.c_str()))
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"Failed to create directory " << tempDir);
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Failed to create directory '%1'"), tempDir.c_str()));
return "";
}
// make a new name,
Expand Down Expand Up @@ -915,7 +944,7 @@ std::string vtkMRMLVolumeArchetypeStorageNode::UpdateFileList(vtkMRMLNode *refNo
if (!success)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"Failed to write '" << tempName.c_str() << "'.");
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Failed to write '%1'"), tempName.c_str()));
return "";
}

Expand All @@ -930,7 +959,7 @@ std::string vtkMRMLVolumeArchetypeStorageNode::UpdateFileList(vtkMRMLNode *refNo
if (!success)
{
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"Failed to open directory '" << tempDir.c_str() << "'.");
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Failed to open directory '%1'"), tempDir.c_str()));
return "";
}

Expand Down Expand Up @@ -1043,13 +1072,13 @@ std::string vtkMRMLVolumeArchetypeStorageNode::UpdateFileList(vtkMRMLNode *refNo
std::copy(++this->FileNameList.begin(), this->FileNameList.end(),
std::ostream_iterator<std::string>(addedFiles,", "));
vtkErrorToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"The archetype file '"
<< newArchetype.c_str() << "' wasn't written out when writing '"
<< tempName.c_str() << "' in '" << tempDir.c_str() << "'. "
<< "Only those " << dir.GetNumberOfFiles() - 2
<< " file(s) have been written: " << addedFiles.str().c_str() <<". "
<< "Old name is '" << oldName.c_str() << "'."
);
vtkMRMLI18N::Format(
vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode",
"The archetype file '%1' wasn't written out when writing '%2' in '%3'."
" Only these %4 file(s) have been written: %5."
" Old name is '%6'."),
newArchetype.c_str(), tempName.c_str(), tempDir.c_str(),
std::to_string(dir.GetNumberOfFiles() - 2).c_str(), addedFiles.str().c_str(), oldName.c_str()));
return "";
}
// restore the old file name
Expand All @@ -1067,7 +1096,7 @@ std::string vtkMRMLVolumeArchetypeStorageNode::UpdateFileList(vtkMRMLNode *refNo
if (!vtksys::SystemTools::RemoveADirectory(tempDir.c_str()))
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::UpdateFileList",
"Failed to remove temp dir '" << tempDir.c_str() << "'." );
vtkMRMLI18N::Format(vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode", "Failed to remove temporary directory '%1'"), tempDir.c_str()));
}
return "";
}
Expand Down Expand Up @@ -1116,6 +1145,7 @@ void vtkMRMLVolumeArchetypeStorageNode::ConvertSpatialVectorVoxelsBetweenRasLps(
else
{
vtkWarningToMessageCollectionMacro(this->GetUserMessages(), "vtkMRMLVolumeArchetypeStorageNode::ConvertSpatialVectorVoxelsBetweenRasLps",
"Displacements are expected to be stored as double or float. Vector values will not be converted from LPS to RAS.");
vtkMRMLTr("vtkMRMLVolumeArchetypeStorageNode",
"Displacements are expected to be stored as double or float. Vector values will not be converted from LPS to RAS."));
}
}

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