CreateSliceModels.cxx

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/*=Plus=header=begin======================================================
  Program: Plus
  Copyright (c) Laboratory for Percutaneous Surgery. All rights reserved.
  See License.txt for details.
=========================================================Plus=header=end*/

#include "PlusConfigure.h"

// STL includes
#include <iostream>
#include <algorithm>
#include <cctype>
#include <string>

// VTK includes
#include <vtkAppendPolyData.h>
#include <vtkCubeSource.h>
#include <vtkMatrix4x4.h>
#include <vtkPolyData.h>
#include <vtkPolyDataWriter.h>
#include <vtkSTLWriter.h>
#include <vtkSmartPointer.h>
#include <vtkTransform.h>
#include <vtkTransformPolyDataFilter.h>
#include <vtkXMLUtilities.h>
#include <vtksys/CommandLineArguments.hxx>

// IGSIO includes
#include <igsioTrackedFrame.h>
#include <vtkIGSIOSequenceIO.h>
#include <vtkIGSIOTrackedFrameList.h>
#include <vtkIGSIOTransformRepository.h>

// Plus includes
#include <vtkPlusVolumeReconstructor.h>

int main( int argc, char** argv )
{
  bool printHelp( false );
  std::string inputMetaFilename;
  std::string inputConfigFileName;
  std::string outputModelFilename;
  std::string imageToReferenceTransformNameStr;

  int verboseLevel = vtkPlusLogger::LOG_LEVEL_UNDEFINED;

  vtksys::CommandLineArguments args;
  args.Initialize( argc, argv );

  args.AddArgument( "--image-to-reference-transform", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &imageToReferenceTransformNameStr, "Image to reference transform name used for creating slice models" );
  args.AddArgument( "--source-seq-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &inputMetaFilename, "Tracked ultrasound recorded by Plus (e.g., by the TrackedUltrasoundCapturing application) in a sequence file (.mha/.nrrd)" );
  args.AddArgument( "--config-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &inputConfigFileName, "Config file used for volume reconstruction. It contains the probe calibration matrix, the ImageToTool transform (.xml) " );
  args.AddArgument( "--output-model-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &outputModelFilename, "A 3D model file that contains rectangles corresponding to each US image slice (.vtk)" );
  args.AddArgument( "--verbose", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &verboseLevel, "Verbose level (1=error only, 2=warning, 3=info, 4=debug, 5=trace)" );
  args.AddArgument( "--help", vtksys::CommandLineArguments::NO_ARGUMENT, &printHelp, "Print this help." );

  if ( !args.Parse() )
  {
    std::cerr << "Problem parsing arguments" << std::endl;
    std::cout << "Help: " << args.GetHelp() << std::endl;
    exit( EXIT_FAILURE );
  }

  if ( printHelp )
  {
    std::cout << args.GetHelp() << std::endl;
    exit( EXIT_SUCCESS );
  }

  vtkPlusLogger::Instance()->SetLogLevel( verboseLevel );

  if ( inputMetaFilename.empty() )
  {
    std::cerr << "--source-seq-file argument required!" << std::endl;
    exit( EXIT_FAILURE );
  }
  if ( outputModelFilename.empty() )
  {
    std::cerr << "--output-model-file argument required!" << std::endl;
    std::cout << "Help: " << args.GetHelp() << std::endl;
    exit( EXIT_FAILURE );
  }

  // Read input tracked ultrasound data.
  LOG_DEBUG( "Reading input... " );
  vtkSmartPointer< vtkIGSIOTrackedFrameList > trackedFrameList = vtkSmartPointer< vtkIGSIOTrackedFrameList >::New();
  if( vtkIGSIOSequenceIO::Read( inputMetaFilename, trackedFrameList ) != PLUS_SUCCESS )
  {
    LOG_ERROR( "Unable to load input sequences file." );
    exit( EXIT_FAILURE );
  }
  LOG_DEBUG( "Reading input done." );
  LOG_DEBUG( "Number of frames: " << trackedFrameList->GetNumberOfTrackedFrames() );

  // Get the image size
  FrameSizeType clipRectangleOrigin = { 0, 0, 0 };
  FrameSizeType clipRectangleSize = trackedFrameList->GetTrackedFrame(0)->GetFrameSize(); 
  if (clipRectangleSize[0] <= 0 || clipRectangleSize[1] <= 0 )
  {
    LOG_ERROR( "Invalid frame size: " << clipRectangleSize[0] << "x" << clipRectangleSize[1] );
    clipRectangleSize[0] = 0;
    clipRectangleSize[1] = 0;
  }

  // Read calibration matrices from the config file
  vtkSmartPointer<vtkIGSIOTransformRepository> transformRepository = vtkSmartPointer<vtkIGSIOTransformRepository>::New();
  if ( !inputConfigFileName.empty() )
  {
    LOG_DEBUG( "Reading config file..." );
    vtkSmartPointer<vtkXMLDataElement> configRootElement = vtkSmartPointer<vtkXMLDataElement>::New();
    if ( PlusXmlUtils::ReadDeviceSetConfigurationFromFile( configRootElement, inputConfigFileName.c_str() ) == PLUS_FAIL )
    {
      LOG_ERROR( "Unable to read configuration from file " << inputConfigFileName.c_str() );
      return EXIT_FAILURE;
    }

    vtkSmartPointer<vtkPlusVolumeReconstructor> reconstructor = vtkSmartPointer<vtkPlusVolumeReconstructor>::New();
    reconstructor->ReadConfiguration( configRootElement );
    LOG_DEBUG( "Reading config file done." );
    if ( transformRepository->ReadConfiguration( configRootElement ) != PLUS_SUCCESS )
    {
      LOG_ERROR( "Failed to read transforms for transform repository!" );
      return EXIT_FAILURE;
    }
    int* clipRectangleOriginInConfig = reconstructor->GetClipRectangleOrigin();
    if ( clipRectangleOriginInConfig != NULL && clipRectangleOriginInConfig[0] >= 0 && clipRectangleOriginInConfig[1] >= 0 )
    {
      clipRectangleOrigin[0] = static_cast<unsigned int>(clipRectangleOriginInConfig[0]);
      clipRectangleOrigin[1] = static_cast<unsigned int>(clipRectangleOriginInConfig[1]);
    }
    int* clipRectangleSizeInConfig = reconstructor->GetClipRectangleSize();
    if ( clipRectangleSizeInConfig != NULL && clipRectangleSizeInConfig[0] > 0 && clipRectangleSizeInConfig[1] > 0 )
    {
      clipRectangleSize[0] = static_cast<unsigned int>(clipRectangleSizeInConfig[0]);
      clipRectangleSize[1] = static_cast<unsigned int>(clipRectangleSizeInConfig[1]);
    }
  }
  else
  {
    LOG_INFO( "Configuration file is not specified. Only those transforms are available that are defined in the sequence metafile" );
  }

  // Prepare the output polydata.
  vtkSmartPointer<vtkAppendPolyData> appender = vtkSmartPointer<vtkAppendPolyData>::New();

  igsioTransformName imageToReferenceTransformName;
  if ( imageToReferenceTransformName.SetTransformName( imageToReferenceTransformNameStr.c_str() ) != PLUS_SUCCESS )
  {
    LOG_ERROR( "Invalid image to reference transform name: " << imageToReferenceTransformNameStr );
    return EXIT_FAILURE;
  }

  // Loop over each tracked image slice.
  for ( unsigned int frameIndex = 0; frameIndex < trackedFrameList->GetNumberOfTrackedFrames(); ++ frameIndex )
  {
    igsioTrackedFrame* frame = trackedFrameList->GetTrackedFrame( frameIndex );

    // Update transform repository
    if ( transformRepository->SetTransforms( *frame ) != PLUS_SUCCESS )
    {
      LOG_ERROR( "Failed to set repository transforms from tracked frame!" );
      continue;
    }

    vtkSmartPointer<vtkMatrix4x4> imageToReferenceTransformMatrix = vtkSmartPointer<vtkMatrix4x4>::New();
    if ( transformRepository->GetTransform( imageToReferenceTransformName, imageToReferenceTransformMatrix ) != PLUS_SUCCESS )
    {
      std::string strTransformName;
      imageToReferenceTransformName.GetTransformName( strTransformName );
      LOG_ERROR( "Failed to get transform from repository: " << strTransformName );
      continue;
    }

    vtkSmartPointer<vtkTransform> imageToReferenceTransform = vtkSmartPointer<vtkTransform>::New();
    imageToReferenceTransform->SetMatrix( imageToReferenceTransformMatrix );

    vtkSmartPointer<vtkTransform> tCubeToImage = vtkSmartPointer<vtkTransform>::New();
    tCubeToImage->Translate( clipRectangleOrigin[0], clipRectangleOrigin[1], clipRectangleOrigin[2] );
    tCubeToImage->Scale( clipRectangleSize[0], clipRectangleSize[1], clipRectangleSize[2] );
    tCubeToImage->Translate( 0.5, 0.5, 0.5 );  // Moving the corner to the origin.

    vtkSmartPointer<vtkTransform> tCubeToTracker = vtkSmartPointer<vtkTransform>::New();
    tCubeToTracker->Identity();
    tCubeToTracker->Concatenate( imageToReferenceTransform );
    tCubeToTracker->Concatenate( tCubeToImage );

    vtkSmartPointer<vtkTransformPolyDataFilter> cubeToTracker = vtkSmartPointer<vtkTransformPolyDataFilter>::New();
    cubeToTracker->SetTransform( tCubeToTracker );
    vtkSmartPointer<vtkCubeSource> source = vtkSmartPointer<vtkCubeSource>::New();
    source->Update();
    cubeToTracker->SetInputConnection( source->GetOutputPort() );
    cubeToTracker->Update();

    appender->AddInputConnection( cubeToTracker->GetOutputPort() );
  }
  
  // Write model output.
  LOG_DEBUG( "Writing output model file (" << outputModelFilename << ")..." );
  std::string copy(outputModelFilename);
  std::transform(copy.begin(), copy.end(), copy.begin(),
    [](unsigned char c) { return std::tolower(c); });
  if (copy.find("stl") != std::string::npos)
  {
    vtkSmartPointer<vtkSTLWriter> writer = vtkSmartPointer<vtkSTLWriter>::New();
    writer->SetFileName(outputModelFilename.c_str());
    writer->SetInputConnection(appender->GetOutputPort());
    writer->Update();
  }
  else
  {
    vtkSmartPointer<vtkPolyDataWriter> writer = vtkSmartPointer<vtkPolyDataWriter>::New();
    writer->SetFileName(outputModelFilename.c_str());
    writer->SetInputConnection(appender->GetOutputPort());
    writer->Update();
  }
  LOG_DEBUG( "Writing model file done." );

  LOG_INFO( "Model file created: " << outputModelFilename );

  return EXIT_SUCCESS;
}