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Added an argument to disable Automatic output extent setting. #1238

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Added an argument to disable Automatic output extent setting. #1238

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29 changes: 26 additions & 3 deletions src/PlusVolumeReconstruction/Tools/VolumeReconstructor.cxx
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ int main(int argc, char* argv[])
int verboseLevel = vtkPlusLogger::LOG_LEVEL_UNDEFINED;

bool disableCompression = false;
bool disableAutoExtent = false;

std::vector<std::string> customHeaderFieldsToSave;
std::vector<std::string> customHeaderValuesToSave;
Expand All @@ -51,6 +52,7 @@ int main(int argc, char* argv[])
cmdargs.AddArgument("--output-frame-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &outputFrameFileName, "A filename that will be used for storing the tracked image frames. Each frame will be exported individually, with the proper position and orientation in the reference coordinate system");
cmdargs.AddArgument("--help", vtksys::CommandLineArguments::NO_ARGUMENT, &printHelp, "Print this help.");
cmdargs.AddArgument("--disable-compression", vtksys::CommandLineArguments::NO_ARGUMENT, &disableCompression, "Do not compress output image files.");
cmdargs.AddArgument("--disable-auto-extent", vtksys::CommandLineArguments::NO_ARGUMENT, &disableAutoExtent, "Do not compute extent from the input sequence file but use OutputOrigin and OutputExtent specified in the configuration file.");
cmdargs.AddArgument("--save-custom-headers", vtksys::CommandLineArguments::MULTI_ARGUMENT, &customHeaderFieldsToSave, "List of custom header fields to pass into the output file.");
cmdargs.AddArgument("--verbose", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &verboseLevel, "Verbose level (1=error only, 2=warning, 3=info, 4=debug, 5=trace)");
cmdargs.AddArgument("--importance-mask-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &importanceMaskFileName, "The file to use as the importance mask.");
Expand Down Expand Up @@ -176,10 +178,31 @@ int main(int argc, char* argv[])

LOG_INFO("Set volume output extent...");
std::string errorDetail;
if (reconstructor->SetOutputExtentFromFrameList(trackedFrameList, transformRepository, errorDetail) != PLUS_SUCCESS)
if (!disableAutoExtent)
{
LOG_ERROR("Failed to set output extent of volume!");
return EXIT_FAILURE;
if (reconstructor->SetOutputExtentFromFrameList(trackedFrameList, transformRepository, errorDetail) != PLUS_SUCCESS)
{
LOG_ERROR("Failed to set output extent of volume!");
return EXIT_FAILURE;
}
}
else
{
LOG_INFO("Automatic extent computation disabled. Using OutputOrigin and OutputExtent specified in the configuration file.");

// When automatic extent computation is disabled, the reconstructor does not examine the first frame, therefore
// the output scalar type remains the default (VTK_DOUBLE). That default
// may differ from the actual scalar type of the incoming images, which results in the runtime error:
// OptimizedInsertSlice: input ScalarType (10) must match out ScalarType (11)
// The following explicit update prevents the mismatch.
if (trackedFrameList->GetNumberOfTrackedFrames() > 0)
{
vtkImageData* firstImage = trackedFrameList->GetTrackedFrame(0)->GetImageData()->GetImage();
if (firstImage != nullptr)
{
reconstructor->SetOutputScalarType(firstImage->GetScalarType());
}
}
}

LOG_INFO("Reconstruct volume...");
Expand Down