milxDeformableModelApp.cxx

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/*=========================================================================
  The Software is copyright (c) Commonwealth Scientific and Industrial Research Organisation (CSIRO)
  ABN 41 687 119 230.
  All rights reserved.

  Licensed under the CSIRO BSD 3-Clause License
  You may not use this file except in compliance with the License.
  You may obtain a copy of the License in the file LICENSE.md or at

  https://stash.csiro.au/projects/SMILI/repos/smili/browse/license.txt

  Unless required by applicable law or agreed to in writing, software
  distributed under the License is distributed on an "AS IS" BASIS,
  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  See the License for the specific language governing permissions and
  limitations under the License.
=========================================================================*/
#include <vector>
#include <tclap/CmdLine.h> //Command line parser library

// vtk includes
#include <vtkSmartPointer.h>
#include <vtkPolyData.h>
#include <vtkMultiThreader.h>
#include <vtkPolyDataCollection.h>
#include <vtkTransformCollection.h>
// SMILI
#include <milxFile.h>
#include <milxDeformableModel.h>

using namespace TCLAP;

typedef std::vector< std::string >::iterator stringiterator;
//Image output related
typedef unsigned char charPixelType;
typedef itk::Image<charPixelType, milx::imgDimension> charImageType;

//Supported operations
enum operations {none = 0, convert, duplicate, cat, split, scale, decimate, smooth, laplacian, thresholdscalars, flip, diffscalars, copyscalars, diffscalarspairs, statscalars, removescalars, mse, procrustes, icp, clip,
                voxelise, orient, flat};

int main(int argc, char *argv[])
{
  //---------------------------
  milx::PrintInfo("--------------------------------------------------------");
  milx::PrintInfo("SMILI Deformable Model Tool for Models/Surfaces/Meshes.");
  milx::PrintInfo("(c) Copyright Chandra et al., 2015.");
  milx::PrintInfo("Version: " + milx::NumberToString(milx::Version));
  milx::PrintInfo("University of Queensland, Australia.");
  milx::PrintInfo("Australian e-Health Research Centre, CSIRO, Australia.");
  milx::PrintInfo("--------------------------------------------------------\n");

  //---------------------------
  CmdLine cmd("A diagnostic tool for deformable models/surface operations", ' ', milx::NumberToString(milx::Version));

  ValueArg<size_t> threadsArg("", "threads", "Set he number of global threads to use.", false, milx::NumberOfProcessors(), "Threads");
  ValueArg<std::string> outputArg("o", "output", "Output Surface", false, "result.vtk", "Output");
  ValueArg<std::string> prefixArg("p", "prefix", "Output prefix for multiple output", false, "surface_", "Output Prefix");
  ValueArg<std::string> outputFormatArg("", "outputformat", "Specify the default output format for multiple outputs (vtk, vtp, ply, stl, default: same as input)", false, "vtk", "Output format");
//  MultiArg<std::string> altmultinames("s", "altsurfaces", "Another set of surfaces to be used in operation", false, "AltSurfaces");
  ValueArg<float> decimateArg("d", "decimate", "Decimate all the meshes provided using the Quadric Decimate algorithm with decimation factor.", false, 0.5, "Decimate");
  ValueArg<float> smoothArg("", "smooth", "Smooth all the meshes provided using the Windowed Sinc Algorithm with iterations.", false, 18, "Smooth");
  ValueArg<float> laplacianArg("", "laplacian", "Smooth all the meshes provided using the Laplacian Algorithm with iterations.", false, 18, "Laplacian");
  ValueArg<float> scaleArg("s", "scale", "Scale the coordinates of the points by scale.", false, 0.9, "Scale");
  ValueArg<float> thresholdAboveArg("", "thresholdabove", "Thresold scalars above value.", false, 0.0, "Above");
  ValueArg<float> thresholdBelowArg("", "thresholdbelow", "Thresold scalars below value.", false, 0.0, "Below");
  ValueArg<float> clipArg("", "clip", "Clip model based on scalars value (keeping only parts with value).", false, 1.0, "Clip");
  MultiArg<std::string> componentsArg("", "component", "Surface is a component of the surfaces.", false, "Component");
  std::vector<size_t> axesAllowed;
  axesAllowed.push_back(0);
  axesAllowed.push_back(1);
  axesAllowed.push_back(2);
  ValuesConstraint<size_t> allowedAxesVals( axesAllowed );
  ValueArg<size_t> flipArg("f", "flip", "Flip the meshes in the axis provided (0: x-axis, 1: y-axis, 2: z-axis).", false, 0, &allowedAxesVals);
  SwitchArg partitionArg("", "partitionList", "Partition the list of surfaces provided into two for operating on one vs the other", false);
  SwitchArg duplicateArg("", "duplicate", "Simply open and save the input file(s). Supports single (-o) or multiple (-p) input.", false);
  SwitchArg convertArg("c", "convert", "Convert the model from the current format to the one given at output (from file extension). Supports single (-o) or multiple (-p) input.", false);
  SwitchArg concatenateArg("", "cat", "Concatenate N surfaces into single mesh with filename provided.", false);
  SwitchArg colourConcatenateArg("", "colourcat", "Concatenate N surfaces into single mesh with filename provided and colour them.", false);
  SwitchArg splitArg("", "split", "Split each surface given components.", false);
  SwitchArg diffScalarArg("", "scalardiff", "Compute the differences in Scalars.", false);
  SwitchArg statsScalarArg("", "scalarstats", "Compute statistics of scalars (mean, variance etc. per point) output mesh with stats as arrays.", false);
  SwitchArg removeScalarArg("", "scalarremove", "Remove the scalars.", false);
  SwitchArg copyScalarArg("", "scalarcopy", "Copy the Scalars from first mesh to all others while removing existing ones.", false);
  SwitchArg mseArg("", "mse", "Mean Squared Error of Points in models.", false);
  SwitchArg procrustesArg("", "procrustes", "Similarity alignment of surfaces assuming points have correspondence. Use --rigid if rigid alignment is required.", false);
  SwitchArg rigidArg("", "rigid", "Rigid alignment of surfaces assuming points have correspondence. Use with procrustes or other registration arguments.", false);
  SwitchArg icpArg("", "icp", "Iterative Closest Points alignment of surfaces assuming points don't have correspondence. Last surface in list is used as the reference 'fixed' surface.", false);
  SwitchArg saveTransformsArg("", "savetransforms", "Save the transformation matrix after surface alignment. For use with --icp", false);

  UnlabeledMultiArg<std::string> multinames("surfaces", "Surfaces to operate on", true, "Surfaces");

  ValueArg<float> voxeliseArg("", "voxelise", "Voxelise a model into image space with given spacing. Output will be in Nifty format (*.nii.gz).", false, 0.5, "Voxelise");
  ValueArg<std::string> orientArg("", "orient", "Apply direction/orientation to a model from the given image", false, "image.nii.gz", "Orient");
  ValueArg<size_t> flatArg("", "flatten", "Flatten a model to either a sphere (0) or plane (1). Needs to be a genus zero (no topological hole) mesh.", false, 0, "Flatten");

  cmd.add( threadsArg );
  cmd.add( multinames );
//  cmd.add( altmultinames );
  cmd.add( outputArg );
  cmd.add( prefixArg );
  cmd.add( outputFormatArg );
  cmd.add( componentsArg );
  cmd.add( rigidArg );
  cmd.add( partitionArg );
  cmd.add( saveTransformsArg );
//  cmd.add( thresholdAboveArg );
//  cmd.add( thresholdBelowArg );
  std::vector<Arg*> xorlist;
  xorlist.push_back(&duplicateArg);
  xorlist.push_back(&convertArg);
  xorlist.push_back(&concatenateArg);
  xorlist.push_back(&colourConcatenateArg);
  xorlist.push_back(&splitArg);
  xorlist.push_back(&scaleArg);
  xorlist.push_back(&decimateArg);
  xorlist.push_back(&smoothArg);
  xorlist.push_back(&laplacianArg);
  xorlist.push_back(&diffScalarArg);
  xorlist.push_back(&statsScalarArg);
  xorlist.push_back(&removeScalarArg);
  xorlist.push_back(&copyScalarArg);
  xorlist.push_back(&mseArg);
  xorlist.push_back(&procrustesArg);
  xorlist.push_back(&icpArg);
  xorlist.push_back(&thresholdAboveArg);
  xorlist.push_back(&thresholdBelowArg);
  xorlist.push_back(&clipArg);
  xorlist.push_back(&flipArg);
  xorlist.push_back(&voxeliseArg);
  xorlist.push_back(&orientArg);
#ifdef ITK_USE_REVIEW //Review only members
  xorlist.push_back(&flatArg);
#endif

  cmd.xorAdd(xorlist);
  cmd.parse( argc, argv );

  const size_t threads = threadsArg.getValue();
  //Filenames of surfaces
  std::vector<std::string> filenames = multinames.getValue();
//  std::vector<std::string> altfilenames = altmultinames.getValue();
  std::string outputName = outputArg.getValue();
  std::string outputFormatName = outputFormatArg.getValue();
  const std::string prefixName = prefixArg.getValue();
  const float decimateFactor = decimateArg.getValue();
  const float scaleFactor = scaleArg.getValue();
  const float smoothIterations = smoothArg.getValue();
  const float laplacianIterations = laplacianArg.getValue();
  float thresholdAbove = thresholdAboveArg.getValue();
  float thresholdBelow = thresholdBelowArg.getValue();
  float clipValue = clipArg.getValue();
  size_t flipAxis = flipArg.getValue();
  std::vector<std::string> componentNames = componentsArg.getValue();

  vtkMultiThreader::SetGlobalDefaultNumberOfThreads(threads);
  milx::PrintInfo("Threads to use: " + milx::NumberToString(threads));

  const float voxelSpacing = voxeliseArg.getValue();
  std::string orientName = orientArg.getValue();
  const size_t flatMode = flatArg.getValue();

  operations operation = none;
  bool componentsValid = false;
  if(duplicateArg.isSet())
  {
    //Duplicate files
    milx::PrintInfo("Duplicating surfaces: ");
    operation = duplicate;
  }
  if(convertArg.isSet())
  {
    //Info
    milx::PrintInfo("Converting surfaces: ");

    //Info
    operation = convert;
  }
  if(concatenateArg.isSet() || colourConcatenateArg.isSet())
  {
    //Cat
    milx::PrintInfo("Concatenating surfaces: ");
    operation = cat;
  }
  if(mseArg.isSet())
  {
    //Cat
    milx::PrintInfo("MSE of surfaces: ");
    operation = mse;
  }
  if(componentsArg.isSet())
  {
    if(!splitArg.isSet())
    {
      milx::PrintError("Components Argument Error: One or more of the operations");
      milx::PrintError("required to use components is not set (such as split)");
      milx::PrintError("Operations needing components are split.");
      exit(EXIT_FAILURE);
    }
    milx::PrintInfo("Using components: ");
    for(stringiterator name = componentNames.begin(); name != componentNames.end(); name ++)
      std::cout << *name << ", ";
    std::cout << std::endl;
  }
  if(splitArg.isSet())
  {
    //Split
    if(!componentsArg.isSet())
    {
      milx::PrintError("Split Argument Error: Components of the given surfaces must be set.");
      milx::PrintError("These surfaces provide info for the splitting process.");
      milx::PrintError("Set components via the component argument as many times as needed.");
      exit(EXIT_FAILURE);
    }
    milx::PrintInfo("For splitting surfaces: ");
    operation = split;
    componentsValid = true;
  }
  if(scaleArg.isSet())
  {
    //Scale
    milx::PrintInfo("Scaling coordinates of each point in the surfaces: ");
    operation = scale;
  }
  if(smoothArg.isSet())
  {
    //Smooth
    milx::PrintInfo("Smoothing points in the surfaces: ");
    operation = smooth;
  }
  if(laplacianArg.isSet())
  {
    //Smooth Laplacian
    milx::PrintInfo("Laplacian smoothing points in the surfaces: ");
    operation = laplacian;
  }
  if(decimateArg.isSet())
  {
    //Smooth
    milx::PrintInfo("Decimating number of points in the surfaces: ");
    operation = decimate;
  }
  if(thresholdAboveArg.isSet() || thresholdBelowArg.isSet())
  {
    if(!prefixArg.isSet())
    {
      milx::PrintError("Threshold Argument Error: Output Prefix (-p) must be provided.");
      milx::PrintError("Re-run with the prefix name set.");
      exit(EXIT_FAILURE);
    }
    if(thresholdAboveArg.isSet() && !thresholdBelowArg.isSet())
    {
      thresholdBelow = -std::numeric_limits<float>::max(); //min negative value
    }
    else if(!thresholdAboveArg.isSet() && thresholdBelowArg.isSet())
    {
      thresholdAbove = std::numeric_limits<float>::max();
    }
    std::cout << "Threshold Above Value: " << thresholdAbove << std::endl;
    std::cout << "Threshold Below Value: " << thresholdBelow << std::endl;
    //threshold
    milx::PrintInfo("Thresholding Scalars of surfaces: ");
    operation = thresholdscalars;
  }
  if(clipArg.isSet())
  {
    //Scale
    milx::PrintInfo("Clipping surfaces: ");
    operation = clip;
  }
  if(diffScalarArg.isSet())
  {
    //Scale
    milx::PrintInfo("Differencing Scalars of surfaces: ");
    operation = diffscalars;
  }
  if(flipArg.isSet())
  {
    //Scale
    milx::PrintInfo("Flipping surfaces: ");
    operation = flip;
  }
  if(statsScalarArg.isSet())
  {
    //Scale
    milx::PrintInfo("Statistics of Scalars in surfaces: ");
    operation = statscalars;
  }
  if(removeScalarArg.isSet())
  {
    //Remove scalars
    milx::PrintInfo("Removing Scalars of surfaces: ");
    operation = removescalars;
  }
  if(copyScalarArg.isSet())
  {
    if(filenames.size() == 1)
    {
      milx::PrintError("Argument Error: Need another filename to copy from mesh A to mesh B.");
      exit(EXIT_FAILURE);
    }
    else if(filenames.size() == 2 && !outputArg.isSet())
    {
      milx::PrintError("Argument Error: Use Output (-o) for copying from mesh A to mesh B.");
      milx::PrintError("Re-run with the output name set.");
      exit(EXIT_FAILURE);
    }
    else if(filenames.size() > 2 && !prefixArg.isSet())
    {
      milx::PrintError("Argument Error: Output Prefix (-p) must be provided for more than 2 meshes.");
      milx::PrintError("Re-run with the prefix name set.");
      exit(EXIT_FAILURE);
    }

    //Remove scalars
    milx::PrintInfo("Copying Scalars of surfaces: ");
    operation = copyscalars;
  }
  if(rigidArg.isSet() && (!procrustesArg.isSet() && !icpArg.isSet()))
  {
    //Scale
    milx::PrintError("Rigid option can only be used with the Procrustes/ICP option");
    exit(EXIT_FAILURE);
  }
  if(procrustesArg.isSet())
  {
    if(!prefixArg.isSet())
    {
      milx::PrintError("Procrustes Argument Error: Output Prefix (-p) must be provided.");
      milx::PrintError("Re-run with the prefix name set.");
      exit(EXIT_FAILURE);
    }
    //align
    milx::PrintInfo("Computing Procrustes Alignment of surfaces: ");
    operation = procrustes;
  }
  if(icpArg.isSet())
  {
    if(!prefixArg.isSet())
    {
      milx::PrintError("ICP Argument Error: Output Prefix (-p) must be provided.");
      milx::PrintError("Re-run with the prefix name set.");
      exit(EXIT_FAILURE);
    }
    //align
    milx::PrintInfo("Computing ICP Alignment of surfaces: ");
    operation = icp;
  }

  if(voxeliseArg.isSet())
  {
    if(!prefixArg.isSet())
    {
      milx::PrintError("Voxelise Argument Error: Output Prefix (-p) must be provided.");
      milx::PrintError("Re-run with the prefix name set.");
      exit(EXIT_FAILURE);
    }
    if(!outputFormatArg.isSet())
    {
      milx::PrintWarning("No output format set. Using Nifty format (nii.gz) by default.");
      outputFormatName = "nii.gz";
    }
    //voxel
    milx::PrintInfo("Voxelising surfaces: ");
    operation = voxelise;
  }
  if(orientArg.isSet())
  {
    if(!prefixArg.isSet())
    {
      milx::PrintError("Orient Argument Error: Output Prefix (-p) must be provided.");
      milx::PrintError("Re-run with the prefix name set.");
      exit(EXIT_FAILURE);
    }
    //orient
    milx::PrintInfo("Orienting surfaces: ");
    operation = orient;
  }
  if(flatArg.isSet())
    {
      if(!prefixArg.isSet())
        {
          milx::PrintError("Orient Argument Error: Output Prefix (-p) must be provided.");
          milx::PrintError("Re-run with the prefix name set.");
          exit(EXIT_FAILURE);
        }
      //flat
      milx::PrintInfo("Flattening surfaces: ");
      operation = flat;
    }

  std::vector<std::string> altfilenames;
  if(partitionArg.isSet())
  {
    for(size_t j = filenames.size()/2; j < filenames.size(); j ++)
      altfilenames.push_back( filenames[j] );

    for(size_t j = 0; j < altfilenames.size(); j ++)
      filenames.pop_back();
  }

  std::cout << "Total Surfaces: " << filenames.size() << std::endl;
  for(stringiterator name = filenames.begin(); name != filenames.end(); name ++)
    std::cout << *name << ", ";
  std::cout << std::endl;

  if(partitionArg.isSet())
  {
    if(!diffScalarArg.isSet())
    {
      milx::PrintError("Partitioning list of surfaces is only supported with the following operations:");
      milx::PrintError(diffScalarArg.getName());
      exit(EXIT_FAILURE);
    }
    if(!prefixArg.isSet())
    {
      milx::PrintError("Partition Surfaces List Argument Error: Output Prefix (-p) must be provided.");
      milx::PrintError("Re-run with the prefix name set.");
      exit(EXIT_FAILURE);
    }

    //alt
    milx::PrintInfo("Operation will be applied in conjuction with surfaces: ");
    std::cout << "Total Surfaces: " << altfilenames.size() << std::endl;
    for(stringiterator name = altfilenames.begin(); name != altfilenames.end(); name ++)
      std::cout << *name << ", ";
    std::cout << std::endl;

    if(diffScalarArg.isSet())
      operation = diffscalarspairs;
  }

  //---------------------------
  std::cerr << "Reading Surfaces... ";
  vtkSmartPointer<vtkPolyDataCollection> collection;
  if( !milx::File::OpenModelCollection(filenames, collection) ) //Error printed inside
    exit(EXIT_FAILURE);
  std::cerr << "Done" << std::endl;
  std::cout << "Read " << collection->GetNumberOfItems() << " models" << std::endl;

  vtkSmartPointer<vtkPolyDataCollection> altcollection;
  if(partitionArg.isSet())
  {
    std::cerr << "Reading Alterate Surfaces... ";
    if( !milx::File::OpenModelCollection(altfilenames, altcollection) ) //Error printed inside
      exit(EXIT_FAILURE);
    std::cerr << "Done" << std::endl;
  }

  vtkSmartPointer<vtkPolyDataCollection> components;
  if(componentsArg.isSet() && componentsValid)
  {
    std::cerr << "Reading Components... ";
    if( !milx::File::OpenModelCollection(componentNames, components) ) //Error printed inside
      exit(EXIT_FAILURE);
    std::cerr << "Done" << std::endl;
  }

  itk::SmartPointer<charImageType> refImage;
  if(orientArg.isSet())
  {
    std::cerr << "Reading Reference Image... "; //dont need to read data just header
    if( !milx::File::OpenImage<charImageType>(orientName, refImage) ) //Error printed inside
      exit(EXIT_FAILURE);
    std::cerr << "Done" << std::endl;
  }

  if(colourConcatenateArg.isSet())
  {
    size_t count = 0;
    collection->InitTraversal();
    for(int j = 0; j < collection->GetNumberOfItems(); j ++)
    {
      vtkSmartPointer<vtkPolyData> mesh = collection->GetNextItem();
      const size_t numPoints = mesh->GetNumberOfPoints();

      vtkSmartPointer<vtkFloatArray> weights = vtkSmartPointer<vtkFloatArray>::New();
        weights->SetNumberOfComponents(1);
        weights->SetNumberOfTuples(numPoints);
        weights->FillComponent(0, count);

      mesh->GetPointData()->SetScalars(weights);
      count ++;
    }
  }

  //---------------------------
  vtkSmartPointer<vtkTransformCollection> transformCollection = vtkSmartPointer<vtkTransformCollection>::New();

  //---------------------------
  milx::DeformableModel Model;
  bool outputRequired = true;
  bool multiOutputRequired = false;
  bool standardOperation = false;
  bool imageOutputRequired = false;
  vtkSmartPointer<vtkPolyDataCollection> resultCollections;
  std::vector< itk::SmartPointer<charImageType> > imgCollection;

  if (collection->GetNumberOfItems() == 1)
  {
    outputRequired = true;
    multiOutputRequired = false;
  }
  else
  {
    outputRequired = false;
    multiOutputRequired = true;
  }

  std::cerr << "Applying... ";
  switch(operation)
  {
    case duplicate: //Tested 04/2016
      standardOperation = true;
      break;

    case convert: //Tested 04/2016
      standardOperation = true; //requires user to set output format
      break;

    case cat: //Tested 04/2016
      Model.ConcatenateCollection(collection);
      outputRequired = true;
      multiOutputRequired = false;
      break;

    case mse: //--------------------------------
      milx::PrintInfo( "MSE: " + milx::NumberToString(Model.MeanSquaredErrorCollection(collection)) );
      outputRequired = false; //write mean
      break;

    case split: //--------------------------------
      {// scope for local variables
      std::vector< vtkSmartPointer<vtkPolyDataCollection> > splitCollections;

      //Split surfaces
      Model.SplitCollection(collection, components, splitCollections);

      //write
      typedef std::vector< vtkSmartPointer<vtkPolyDataCollection> >::iterator iterator;
      stringiterator name = filenames.begin();
      for(iterator surfaces = splitCollections.begin();
        surfaces != splitCollections.end();
        surfaces ++, name ++)
      {
        std::vector<std::string> splitNames;

        std::string splitName = prefixName + milx::File::GetBaseName(*name) + "_";
        std::string ext = milx::File::GetFileExtension(*name);
        for(stringiterator componentname = componentNames.begin(); componentname != componentNames.end(); componentname ++)
        {
          splitNames.push_back(splitName + milx::File::GetBaseName(*componentname) + "." + ext);
          milx::PrintInfo("Wrote " + splitName + milx::File::GetBaseName(*componentname) + "." + ext);
        }
        if( !milx::File::SaveModelCollection(splitNames, *surfaces) )
          exit(EXIT_FAILURE);
      }
      }// scope for local variables

      outputRequired = false;
      multiOutputRequired = false;
      break;

    case scale: //Tested 04/2016
      Model.ScaleCollection(collection, scaleFactor);

      standardOperation = true;
      break;

    case smooth: //Tested 04/2016
      Model.SmoothCollection(collection, smoothIterations);

      standardOperation = true;
      break;

    case laplacian: //Tested 04/2016
      Model.LaplacianCollection(collection, laplacianIterations);

      standardOperation = true;
      break;

    case decimate: //Tested 04/2016
      Model.DecimateCollection(collection, decimateFactor);

      standardOperation = true;
      break;

    case thresholdscalars:
      Model.ScalarThresholdCollection(collection, thresholdAbove, thresholdBelow);

      standardOperation = true;
      break;

    case clip:
      Model.ClipCollection(collection, clipValue, clipValue);

      standardOperation = true;
      break;

    case flip:
      {
        bool xAxis = false, yAxis = false, zAxis = false;
        if(flipAxis == 2)
          zAxis = true;
        else if(flipAxis == 1)
          yAxis = true;
        else
          xAxis = true;
        Model.FlipCollection(collection, xAxis, yAxis, zAxis);

        standardOperation = true;
        break;
      }

    case diffscalars:
      Model.ScalarDifferenceCollection(collection);
      break;

    case diffscalarspairs:
      resultCollections = vtkSmartPointer<vtkPolyDataCollection>::New();
      Model.ScalarDifferenceCollection(collection, altcollection, resultCollections);

      standardOperation = true;
      collection = resultCollections;
      break;

    case statscalars:
      Model.ScalarStatisticsCollection(collection);
      break;

    case removescalars:
      Model.ScalarRemoveCollection(collection);
    
      standardOperation = true;
      break;

    case copyscalars:
      Model.ScalarCopyCollection(collection);

      if(filenames.size() == 2)
      {
        outputRequired = true;
        multiOutputRequired = false;
        collection->InitTraversal();
        collection->GetNextItem();
        Model.SetInput(collection->GetNextItem());
      }
      else
        standardOperation = true;
      break;

    case procrustes:
    {
      collection = Model.ProcrustesAlignCollection(collection, rigidArg.isSet()); 

      std::string ext = milx::File::GetFileExtension(filenames[0]);
      outputName = prefixName + "_mean." + ext;
      outputRequired = true; //write mean
      multiOutputRequired = true; //write collection
      break;
    } //scope for ext

    case icp:
      collection = Model.IterativeClosestPointsAlignCollection(collection, rigidArg.isSet(), transformCollection);

      standardOperation = true; //write collection
      break;

    case voxelise:
      Model.VoxeliseCollection<charImageType>(collection, voxelSpacing, imgCollection);

      outputRequired = false;
      multiOutputRequired = true;
      imageOutputRequired = true;
      break;

    case orient:
      Model.ApplyOrientationCollection<charImageType>(collection, refImage);

      outputRequired = false;
      multiOutputRequired = true;
      break;
#ifdef ITK_USE_REVIEW //Review only members
    case flat:
      Model.FlattenCollection(collection, flatMode);

      outputRequired = false;
      multiOutputRequired = true;
      break;
#endif

    case none: //--------------------------------
      break;
  }
  std::cerr << "Done" << std::endl;

  if (collection->GetNumberOfItems() == 1 && standardOperation)
  {
    collection->InitTraversal();
    Model.Result() = collection->GetNextItem();
  }

  //---------------------------
  if(outputRequired)
  {
    milx::PrintInfo("Writing result to " + outputName);
    milx::File::SaveModel(outputName, Model.Result());
  }
  if(multiOutputRequired)
  {
    if(collection->GetNumberOfItems() > 0)
    {
      const int N = collection->GetNumberOfItems();

      milx::PrintInfo("Writing results with prefix " + prefixName);
      std::vector<std::string> names;

      int n = 0;
      for(stringiterator filename = filenames.begin(); filename != filenames.end() && n < N; filename ++, n ++)
      {
        std::string ext;
        if (outputFormatArg.isSet() || imageOutputRequired) {
          ext = outputFormatName;
        } else {
          ext = milx::File::GetFileExtension(*filename);
        }

        names.push_back(prefixName + milx::File::GetBaseName(*filename) + "." + ext);
        milx::PrintInfo("Will be writing " + prefixName + milx::File::GetBaseName(*filename) + "." + ext);
      }

      if(imageOutputRequired)
        milx::File::SaveImages<charImageType>(names, imgCollection);
      else
        milx::File::SaveModelCollection(names, collection);

      // Saving the vtkTransforms
      if (saveTransformsArg.isSet() && transformCollection->GetNumberOfItems() == collection->GetNumberOfItems())
      {
        const std::string ext = "trsf.gz";
        std::vector<std::string> tnames;
        n = 0;
        for(stringiterator name = names.begin(); name != names.end() && n < N; name ++, n++)
        {
          tnames.push_back(milx::File::StripFileExtension(*name) + "." + ext);
          milx::PrintInfo("Will be writing " + tnames.back());
        }
        milx::File::SaveTransformCollection(tnames, transformCollection, false);
      }
    }
    else
    {
      milx::PrintError("Result was empty. Skipping Output.");
    }
  }

  milx::PrintInfo("Operation Complete");
  return EXIT_SUCCESS;
}