ConvertXmlToFcsv.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*/

// Local includes
#include "PlusConfigure.h"
#include "PlusPatternLocResultFile.h"

// VTK includes
#include <vtkSmartPointer.h>
#include <vtkXMLDataElement.h>
#include <vtkXMLUtilities.h>
#include <vtksys/CommandLineArguments.hxx>

// STL includes
#include <fstream>
#include <iostream>
#include <limits>
#include <sstream>

static const int FIDUCIAL_COUNT_PER_SLICE = 7;
static const int MAX_FIDUCIAL_COUNT = 50;

struct FiducialInfo
{
  std::string label;
  double x;
  double y;
  double z;
  int sel;
  int vis;
};

int main(int argc, char** argv)
{
  std::string inputXmlFileName;
  std::string outputFcsvFileName;

  int verboseLevel = vtkPlusLogger::LOG_LEVEL_UNDEFINED;

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

  args.AddArgument("--xml-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &inputXmlFileName, "Input XML file name");
  args.AddArgument("--output-xml-file", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &outputFcsvFileName, "Output FCSV file name");
  args.AddArgument("--verbose", vtksys::CommandLineArguments::EQUAL_ARGUMENT, &verboseLevel, "Verbose level (1=error only, 2=warning, 3=info, 4=debug, 5=trace)");

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

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

  if (inputXmlFileName.empty() || outputFcsvFileName.empty())
  {
    std::cerr << "input and output file names are required" << std::endl;
    exit(EXIT_FAILURE);
  }


  std::ofstream of;
  of.open(outputFcsvFileName.c_str());

  vtkSmartPointer<vtkXMLDataElement> rootElem = vtkSmartPointer<vtkXMLDataElement>::Take(vtkXMLUtilities::ReadElementFromFile(inputXmlFileName.c_str()));

  // check to make sure we have the right element
  if (rootElem == NULL)
  {
    LOG_ERROR("Reading XML data file failed: " << inputXmlFileName);
    exit(EXIT_FAILURE);
  }
  if (strcmp(rootElem->GetName(), PlusUsFidSegResultFile::TEST_RESULTS_ELEMENT_NAME) != 0)
  {
    LOG_ERROR("XML data file is invalid");
    exit(EXIT_FAILURE);
  }

  // Write header
  of << "# Fiducial List file " << outputFcsvFileName << std::endl;
  of << "# version = 2" << std::endl;
  of << "# name = UsFid" << std::endl;
  of << "# numPoints = 0" << std::endl;
  of << "# symbolScale = 5" << std::endl;
  of << "# symbolType = 12" << std::endl;
  of << "# visibility = 1" << std::endl;
  of << "# textScale = 4.5" << std::endl;
  of << "# color = 0.4,1,1" << std::endl;
  of << "# selectedColor = 1,0.5,0.5" << std::endl;
  of << "# opacity = 1" << std::endl;
  of << "# ambient = 0" << std::endl;
  of << "# diffuse = 1" << std::endl;
  of << "# specular = 0" << std::endl;
  of << "# power = 1" << std::endl;
  of << "# locked = 0" << std::endl;
  of << "# numberingScheme = 0" << std::endl;
  of << "# columns = label,x,y,z,sel,vis" << std::endl;

  // Write fiducial lines
  for (int nestedElemInd = 0; nestedElemInd < rootElem->GetNumberOfNestedElements(); nestedElemInd++)
  {
    vtkXMLDataElement* currentElem = rootElem->GetNestedElement(nestedElemInd);
    if (currentElem == NULL)
    {
      LOG_ERROR("Invalid current data element");
      exit(EXIT_FAILURE);
    }
    if (strcmp(currentElem->GetName(), PlusUsFidSegResultFile::TEST_CASE_ELEMENT_NAME) != 0)
    {
      // ignore all non-test-case elements
      continue;
    }

    vtkXMLDataElement* inputElem = currentElem->FindNestedElementWithName("Input");
    int frameIndex = 0;
    inputElem->GetScalarAttribute("ImageSeqFrameIndex", frameIndex);

    vtkXMLDataElement* outputElem = currentElem->FindNestedElementWithName("Output");

    const int MAX_FIDUCIAL_COORDINATE_COUNT = MAX_FIDUCIAL_COUNT * 2;
    double fiducialPoints[MAX_FIDUCIAL_COORDINATE_COUNT]; // baseline fiducial Points
    memset(fiducialPoints, 0, sizeof(fiducialPoints[0] * MAX_FIDUCIAL_COORDINATE_COUNT));
    int fidPointsRead = outputElem->GetVectorAttribute("SegmentationPoints", MAX_FIDUCIAL_COORDINATE_COUNT, fiducialPoints);

    if (fidPointsRead % 2 != 0)
    {
      LOG_ERROR("Unpaired baseline fiducial coordinates");
      exit(EXIT_FAILURE);
    }

    if (fidPointsRead > MAX_FIDUCIAL_COORDINATE_COUNT)
    {
      LOG_WARNING("Too many baseline fiducials");
    }

    std::vector<FiducialInfo> fids(FIDUCIAL_COUNT_PER_SLICE);
    for (int i = 0; i < FIDUCIAL_COUNT_PER_SLICE; i++)
    {
      fids[i].label = "test";
      fids[i].x = 0;
      fids[i].y = 0;
      fids[i].z = frameIndex;
      fids[i].sel = 0;
      fids[i].vis = 0;
    }

    const int FID_COUNT_TAB2_5_POINT = 5;
    const int FID_COUNT_TAB2_6_POINT = 6;
    int fidIndices[FID_COUNT_TAB2_5_POINT] = {0,/* skip 1 */ 2, 3, 4, /* skip 5 */ 6};

    if (fidPointsRead == FID_COUNT_TAB2_5_POINT * 2) // 5 fiducials are found, we assume that the 2nd and the 6th are not found
    {
      for (int f = 0; f < FID_COUNT_TAB2_5_POINT; ++f)
      {
        // X and Y coordinates should be inverted, because FCSV (Slicer) assumes RAS coordinate system, while
        // itk images use LPS coordinate system
        double x = -fiducialPoints[f * 2 + 0];
        double y = -fiducialPoints[f * 2 + 1];
        fids[fidIndices[f]].x = x;
        fids[fidIndices[f]].y = y;
        fids[fidIndices[f]].sel = 1;
        fids[fidIndices[f]].vis = 1;
      }
    }
    else // found no fiducials
    {
      for (int f = 0; f < FID_COUNT_TAB2_5_POINT; ++f)
      {
        // X and Y coordinates should be inverted, because FCSV (Slicer) assumes RAS coordinate system, while
        // itk images use LPS coordinate system
        fids[fidIndices[f]].x = 0;
        fids[fidIndices[f]].y = 0;
        fids[fidIndices[f]].sel = 1;
        fids[fidIndices[f]].vis = 0;
      }
    }

    if (fidPointsRead == FID_COUNT_TAB2_6_POINT * 2)
    {
      for (int fidIndex = 0; fidIndex < FID_COUNT_TAB2_6_POINT; ++fidIndex)
      {
        int fidIndices[FID_COUNT_TAB2_6_POINT] = {0, 1 , 2, 3, 4, 5 };
        // X and Y coordinates should be inverted, because FCSV (Slicer) assumes RAS coordinate system, while
        // itk images use LPS coordinate system
        double x = -fiducialPoints[fidIndex * 2 + 0];
        double y = -fiducialPoints[fidIndex * 2 + 1];
        fids[fidIndices[fidIndex]].x = x;
        fids[fidIndices[fidIndex]].y = y;
        fids[fidIndices[fidIndex]].vis = 1;
      }
    }

    for (int i = 0; i < FIDUCIAL_COUNT_PER_SLICE; i++)
    {
      of << fids[i].label << "," << fids[i].x << "," << fids[i].y << "," << fids[i].z << "," << fids[i].sel << "," << fids[i].vis << std::endl;
    }
  }

  LOG_DEBUG("Done!");

  return EXIT_SUCCESS;
}