mitkImageTest.cpp
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00001 /*========================================================================= 00002 00003 Program: Medical Imaging & Interaction Toolkit 00004 Language: C++ 00005 Date: $Date$ 00006 Version: $Revision$ 00007 00008 Copyright (c) German Cancer Research Center, Division of Medical and 00009 Biological Informatics. All rights reserved. 00010 See MITKCopyright.txt or https://www.mitk.org/copyright.html for details. 00011 00012 This software is distributed WITHOUT ANY WARRANTY; without even 00013 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 00014 PURPOSE. See the above copyright notices for more information. 00015 00016 =========================================================================*/ 00017 00018 00019 #include <mitkImage.h> 00020 #include <mitkImageDataItem.h> 00021 #include <mitkImageCast.h> 00022 00023 #include <itkImage.h> 00024 00025 #include <fstream> 00026 #include <itkSmartPointerForwardReference.txx> 00027 #include <mitkDataNodeFactory.h> 00028 #include <mitkStandardFileLocations.h> 00029 00030 #include <vtkImageData.h> 00031 00032 #include <mitkTestingMacros.h> 00033 00034 00035 int mitkImageTest(int /*argc*/, char* /*argv*/[]) 00036 { 00037 MITK_TEST_BEGIN(mitkImageTest); 00038 00039 //Create Image out of nowhere 00040 mitk::Image::Pointer imgMem; 00041 mitk::PixelType pt(typeid(int)); 00042 unsigned int dim[]={100,100,20}; 00043 00044 std::cout << "Testing creation of Image: "; 00045 imgMem=mitk::Image::New(); 00046 if(imgMem.IsNull()) 00047 { 00048 std::cout<<"[FAILED]"<<std::endl; 00049 return EXIT_FAILURE; 00050 } 00051 std::cout<<"[PASSED]"<<std::endl; 00052 00053 std::cout << "Testing Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions): "; 00054 imgMem->Initialize(mitk::PixelType(typeid(int)), 3, dim); 00055 std::cout<<"[PASSED]"<<std::endl; 00056 00057 std::cout << "Testing IsInitialized(): "; 00058 if(imgMem->IsInitialized()==false) 00059 { 00060 std::cout<<"[FAILED]"<<std::endl; 00061 return EXIT_FAILURE; 00062 } 00063 std::cout<<"[PASSED]"<<std::endl; 00064 00065 std::cout << "Testing GetData(): "; 00066 int *p = (int*)imgMem->GetData(); 00067 if(p==NULL) 00068 { 00069 std::cout<<"[FAILED]"<<std::endl; 00070 return EXIT_FAILURE; 00071 } 00072 std::cout<<"[PASSED]"<<std::endl; 00073 00074 std::cout << "Filling image: "; 00075 unsigned int i; 00076 unsigned int size = dim[0]*dim[1]*dim[2]; 00077 for(i=0; i<size; ++i, ++p) 00078 *p= (signed int)i; 00079 std::cout<<"[PASSED]"<<std::endl; 00080 00081 std::cout << "Getting it again and compare with filled values: "; 00082 int *p2 = (int*)imgMem->GetData(); 00083 if(p2==NULL) 00084 { 00085 std::cout<<"[FAILED]"<<std::endl; 00086 return EXIT_FAILURE; 00087 } 00088 for(i=0; i<size; ++i, ++p2) 00089 { 00090 if(*p2!= (signed int)i ) 00091 { 00092 std::cout<<"[FAILED]"<<std::endl; 00093 return EXIT_FAILURE; 00094 } 00095 } 00096 std::cout<<"[PASSED]"<<std::endl; 00097 00098 std::cout << "Testing IsInitialized(): "; 00099 if(imgMem->IsInitialized()==false) 00100 { 00101 std::cout<<"[FAILED]"<<std::endl; 00102 return EXIT_FAILURE; 00103 } 00104 std::cout<<"[PASSED]"<<std::endl; 00105 00106 std::cout << "Testing GetSliceData() and compare with filled values: "; 00107 p2 = (int*)imgMem->GetSliceData(dim[2]/2)->GetData(); 00108 unsigned int xy_size = dim[0]*dim[1]; 00109 unsigned int start_mid_slice = (dim[2]/2)*xy_size; 00110 for(i=0; i<xy_size; ++i, ++p2) 00111 { 00112 if(*p2!=(signed int)(i+start_mid_slice)) 00113 { 00114 std::cout<<"[FAILED]"<<std::endl; 00115 return EXIT_FAILURE; 00116 } 00117 } 00118 std::cout<<"[PASSED]"<<std::endl; 00119 00120 //---- 00121 mitkIpPicDescriptor *pic_slice=mitkIpPicClone(imgMem->GetSliceData(dim[2]/2)->GetPicDescriptor()); 00122 imgMem=mitk::Image::New(); 00123 00124 std::cout << "Testing reinitializing via Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions): "; 00125 imgMem->Initialize(mitk::PixelType(typeid(int)), 3, dim); 00126 std::cout<<"[PASSED]"<<std::endl; 00127 00128 std::cout << "Testing slice-wise filling via SetPicSlice(): "; 00129 for(i=0;i<dim[2];++i) 00130 { 00131 imgMem->SetPicSlice(pic_slice, i, 0, 0); 00132 } 00133 std::cout<<"[PASSED]"<<std::endl; 00134 00135 std::cout << "Getting it again and compare with filled values: "; 00136 p2 = (int*)imgMem->GetData(); 00137 if(p2==NULL) 00138 { 00139 std::cout<<"[FAILED]"<<std::endl; 00140 return EXIT_FAILURE; 00141 } 00142 for(i=0; i<size; ++i, ++p2) 00143 { 00144 if(*p2!= (signed int)((i%xy_size)+start_mid_slice)) 00145 { 00146 std::cout<<"[FAILED]"<<std::endl; 00147 return EXIT_FAILURE; 00148 } 00149 } 00150 std::cout<<"[PASSED]"<<std::endl; 00151 00152 std::cout << "Testing IsInitialized(): "; 00153 if(imgMem->IsInitialized()==false) 00154 { 00155 std::cout<<"[FAILED]"<<std::endl; 00156 return EXIT_FAILURE; 00157 } 00158 std::cout<<"[PASSED]"<<std::endl; 00159 00160 std::cout << "Setting a copy of the volume once again: "; 00161 imgMem->SetPicVolume(mitkIpPicClone(imgMem->GetVolumeData(0)->GetPicDescriptor()),0); 00162 std::cout<<"[PASSED]"<<std::endl; 00163 00164 std::cout << "Set a slice with different content via SetPicSlice(): "; 00165 memset(pic_slice->data,0,xy_size*sizeof(int)); 00166 imgMem->SetPicSlice(pic_slice, 1); 00167 00168 std::cout << "Getting the volume again and compare the check the changed slice: "; 00169 p2 = (int*)imgMem->GetData(); 00170 if(p2==NULL) 00171 { 00172 std::cout<<"[FAILED]"<<std::endl; 00173 return EXIT_FAILURE; 00174 } 00175 p2+=xy_size; 00176 for(i=0; i<xy_size; ++i, ++p2) 00177 { 00178 if(*p2!=0) 00179 { 00180 std::cout<<"[FAILED]"<<std::endl; 00181 return EXIT_FAILURE; 00182 } 00183 } 00184 std::cout<<"[PASSED]"<<std::endl; 00185 00186 00187 std::cout << "Setting volume again: "; 00188 imgMem->SetVolume(imgMem->GetData()); 00189 std::cout<<"[PASSED]"<<std::endl; 00190 00191 std::cout << "Set a slice with different content via SetSlice(): "; 00192 memset(pic_slice->data,0,xy_size*sizeof(int)); 00193 imgMem->SetSlice(pic_slice->data, 0); 00194 00195 std::cout << "Getting the volume again and compare the check the changed slice: "; 00196 p2 = (int*)imgMem->GetData(); 00197 if(p2==NULL) 00198 { 00199 std::cout<<"[FAILED]"<<std::endl; 00200 return EXIT_FAILURE; 00201 } 00202 for(i=0; i<xy_size; ++i, ++p2) 00203 { 00204 if(*p2!=0) 00205 { 00206 std::cout<<"[FAILED]"<<std::endl; 00207 return EXIT_FAILURE; 00208 } 00209 } 00210 std::cout<<"[PASSED]"<<std::endl; 00211 00212 00213 00214 //std::cout << "Testing SetVolume(): "; 00215 //imgMem->SetVolume(data); 00216 //std::cout<<"[PASSED]"<<std::endl; 00217 00218 mitkIpPicFree(pic_slice); 00219 00220 //----------------- 00221 // geometry information for image 00222 mitk::Point3D origin; 00223 mitk::Vector3D right, bottom; 00224 mitk::Vector3D spacing; 00225 mitk::FillVector3D(origin, 17.0, 19.92, 7.83); 00226 mitk::FillVector3D(right, 1.0, 2.0, 3.0); 00227 mitk::FillVector3D(bottom, 0.0, -3.0, 2.0); 00228 mitk::FillVector3D(spacing, 0.78, 0.91, 2.23); 00229 00230 std::cout << "Testing InitializeStandardPlane(rightVector, downVector, spacing): " << std::flush; 00231 mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New(); 00232 planegeometry->InitializeStandardPlane(100, 100, right, bottom, &spacing); 00233 planegeometry->SetOrigin(origin); 00234 std::cout << "done" << std::endl; 00235 00236 std::cout << "Testing Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int slices) with PlaneGeometry and GetData(): "; 00237 imgMem->Initialize(mitk::PixelType(typeid(int)), *planegeometry); 00238 p = (int*)imgMem->GetData(); 00239 if(p==NULL) 00240 { 00241 std::cout<<"[FAILED]"<<std::endl; 00242 return EXIT_FAILURE; 00243 } 00244 std::cout<<"[PASSED]"<<std::endl; 00245 00246 std::cout << "Testing Initialize(const mitk::PixelType& type, int sDim, const mitk::PlaneGeometry& geometry) and GetData(): "; 00247 imgMem->Initialize(mitk::PixelType(typeid(int)), 40, *planegeometry); 00248 p = (int*)imgMem->GetData(); 00249 if(p==NULL) 00250 { 00251 std::cout<<"[FAILED]"<<std::endl; 00252 return EXIT_FAILURE; 00253 } 00254 std::cout<<"[PASSED]"<<std::endl; 00255 00256 //----------------- 00257 // testing origin information and methods 00258 std::cout << "Testing correctness of origin via GetGeometry()->GetOrigin(): "; 00259 if( mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin) == false) 00260 { 00261 std::cout<<"[FAILED]"<<std::endl; 00262 return EXIT_FAILURE; 00263 } 00264 std::cout<<"[PASSED]"<<std::endl; 00265 00266 std::cout << "Testing correctness of origin via GetTimeSlicedGeometry()->GetOrigin(): "; 00267 if( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetOrigin(), origin) == false) 00268 { 00269 std::cout<<"[FAILED]"<<std::endl; 00270 return EXIT_FAILURE; 00271 } 00272 std::cout<<"[PASSED]"<<std::endl; 00273 00274 mitk::FillVector3D(origin, 37.0, 17.92, 27.83); 00275 std::cout << "Setting origin via SetOrigin(origin): "; 00276 imgMem->SetOrigin(origin); 00277 std::cout<<"[PASSED]"<<std::endl; 00278 00279 std::cout << "Testing correctness of changed origin via GetGeometry()->GetOrigin(): "; 00280 if( mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin) == false) 00281 { 00282 std::cout<<"[FAILED]"<<std::endl; 00283 return EXIT_FAILURE; 00284 } 00285 std::cout<<"[PASSED]"<<std::endl; 00286 00287 std::cout << "Testing correctness of changed origin via GetTimeSlicedGeometry()->GetOrigin(): "; 00288 if( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetOrigin(), origin) == false) 00289 { 00290 std::cout<<"[FAILED]"<<std::endl; 00291 return EXIT_FAILURE; 00292 } 00293 std::cout<<"[PASSED]"<<std::endl; 00294 00295 std::cout << "Testing correctness of changed origin via GetSlicedGeometry()->GetGeometry2D(0)->GetOrigin(): "; 00296 if( mitk::Equal(imgMem->GetSlicedGeometry()->GetGeometry2D(0)->GetOrigin(), origin) == false) 00297 { 00298 std::cout<<"[FAILED]"<<std::endl; 00299 return EXIT_FAILURE; 00300 } 00301 std::cout<<"[PASSED]"<<std::endl; 00302 00303 //----------------- 00304 // testing spacing information and methods 00305 std::cout << "Testing correctness of spacing via GetGeometry()->GetSpacing(): "; 00306 if( mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing) == false) 00307 { 00308 std::cout<<"[FAILED]"<<std::endl; 00309 return EXIT_FAILURE; 00310 } 00311 std::cout<<"[PASSED]"<<std::endl; 00312 00313 std::cout << "Testing correctness of spacing via GetTimeSlicedGeometry()->GetSpacing(): "; 00314 if( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetSpacing(), spacing) == false) 00315 { 00316 std::cout<<"[FAILED]"<<std::endl; 00317 return EXIT_FAILURE; 00318 } 00319 std::cout<<"[PASSED]"<<std::endl; 00320 00321 mitk::FillVector3D(spacing, 7.0, 0.92, 1.83); 00322 std::cout << "Setting spacing via SetSpacing(spacing): "; 00323 imgMem->SetSpacing(spacing); 00324 std::cout<<"[PASSED]"<<std::endl; 00325 00326 std::cout << "Testing correctness of changed spacing via GetGeometry()->GetSpacing(): "; 00327 if( mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing) == false) 00328 { 00329 std::cout<<"[FAILED]"<<std::endl; 00330 return EXIT_FAILURE; 00331 } 00332 std::cout<<"[PASSED]"<<std::endl; 00333 00334 std::cout << "Testing correctness of changed spacing via GetTimeSlicedGeometry()->GetSpacing(): "; 00335 if( mitk::Equal(imgMem->GetTimeSlicedGeometry()->GetSpacing(), spacing) == false) 00336 { 00337 std::cout<<"[FAILED]"<<std::endl; 00338 return EXIT_FAILURE; 00339 } 00340 std::cout<<"[PASSED]"<<std::endl; 00341 00342 std::cout << "Testing correctness of changed spacing via GetSlicedGeometry()->GetGeometry2D(0)->GetSpacing(): "; 00343 if( mitk::Equal(imgMem->GetSlicedGeometry()->GetGeometry2D(0)->GetSpacing(), spacing) == false) 00344 { 00345 std::cout<<"[FAILED]"<<std::endl; 00346 return EXIT_FAILURE; 00347 } 00348 std::cout<<"[PASSED]"<<std::endl; 00349 00350 //----------------- 00351 MITK_TEST_OUTPUT(<< "Testing SetImportChannel"); 00352 mitk::Image::Pointer vecImg = mitk::Image::New(); 00353 vecImg->Initialize(*imgMem->GetPixelType().GetTypeId(), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/ ); 00354 vecImg->SetImportChannel(imgMem->GetData(), 0, mitk::Image::CopyMemory ); 00355 vecImg->SetImportChannel(imgMem->GetData(), 1, mitk::Image::CopyMemory ); 00356 std::cout<<"[PASSED]"<<std::endl; 00357 00358 MITK_TEST_OUTPUT(<< " Testing whether IsValidSlice returns valid after SetImportChannel"); 00359 MITK_TEST_CONDITION_REQUIRED( vecImg->IsValidSlice(0,0,1) , ""); 00360 00361 MITK_TEST_OUTPUT(<< " Testing whether CopyMemory worked"); 00362 MITK_TEST_CONDITION_REQUIRED(imgMem->GetData() != vecImg->GetData(), ""); 00363 00364 MITK_TEST_OUTPUT(<< " Testing destruction after SetImportChannel"); 00365 vecImg = NULL; 00366 std::cout<<"[PASSED]"<<std::endl; 00367 00368 //----------------- 00369 MITK_TEST_OUTPUT(<< "Testing initialization via vtkImageData"); 00370 MITK_TEST_OUTPUT(<< " Setting up vtkImageData"); 00371 vtkImageData* vtkimage = vtkImageData::New(); 00372 vtkimage->Initialize(); 00373 vtkimage->SetDimensions( 2, 3, 4); 00374 double vtkorigin[] = {-350,-358.203, -1363.5}; 00375 vtkimage->SetOrigin(vtkorigin); 00376 mitk::Point3D vtkoriginAsMitkPoint; 00377 mitk::vtk2itk(vtkorigin, vtkoriginAsMitkPoint); 00378 double vtkspacing[] = {1.367, 1.367, 2}; 00379 vtkimage->SetSpacing(vtkspacing); 00380 vtkimage->SetScalarType( VTK_SHORT ); 00381 vtkimage->AllocateScalars(); 00382 std::cout<<"[PASSED]"<<std::endl; 00383 00384 MITK_TEST_OUTPUT(<< " Testing mitk::Image::Initialize(vtkImageData*, ...)"); 00385 mitk::Image::Pointer mitkByVtkImage = mitk::Image::New(); 00386 mitkByVtkImage ->Initialize(vtkimage); 00387 MITK_TEST_CONDITION_REQUIRED(mitkByVtkImage->IsInitialized(), ""); 00388 00389 MITK_TEST_OUTPUT(<< " vtkimage->Delete"); 00390 vtkimage->Delete(); 00391 std::cout<<"[PASSED]"<<std::endl; 00392 00393 MITK_TEST_OUTPUT(<< " Testing whether spacing has been correctly initialized from vtkImageData"); 00394 mitk::Vector3D spacing2 = mitkByVtkImage->GetGeometry()->GetSpacing(); 00395 mitk::Vector3D vtkspacingAsMitkVector; 00396 mitk::vtk2itk(vtkspacing, vtkspacingAsMitkVector); 00397 MITK_TEST_CONDITION_REQUIRED(mitk::Equal(spacing2,vtkspacingAsMitkVector), ""); 00398 00399 MITK_TEST_OUTPUT(<< " Testing whether GetSlicedGeometry(0)->GetOrigin() has been correctly initialized from vtkImageData"); 00400 mitk::Point3D origin2 = mitkByVtkImage->GetSlicedGeometry(0)->GetOrigin(); 00401 MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); 00402 00403 MITK_TEST_OUTPUT(<< " Testing whether GetGeometry()->GetOrigin() has been correctly initialized from vtkImageData"); 00404 origin2 = mitkByVtkImage->GetGeometry()->GetOrigin(); 00405 MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); 00406 00407 MITK_TEST_OUTPUT(<< " Testing whether GetTimeSlicedGeometry()->GetOrigin() has been correctly initialized from vtkImageData"); 00408 origin2 = mitkByVtkImage->GetTimeSlicedGeometry()->GetOrigin(); 00409 MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2,vtkoriginAsMitkPoint), ""); 00410 00411 // TODO test the following initializers on channel-incorporation 00412 // void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions, unsigned int channels) 00413 // void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::Geometry2D& geometry2d, bool flipped, unsigned int channels, int tDim ) 00414 // void mitk::Image::Initialize(const mitk::Image* image) 00415 // void mitk::Image::Initialize(const mitkIpPicDescriptor* pic, int channels, int tDim, int sDim) 00416 00417 //mitk::Image::Pointer vecImg = mitk::Image::New(); 00418 //vecImg->Initialize(PixelType(typeid(float), 6, itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ ); 00419 //vecImg->Initialize(PixelType(typeid(itk::Vector<float,6>)), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ ); 00420 00421 00422 // testing access by index coordinates and by world coordinates 00423 00424 mitk::DataNode::Pointer node; 00425 mitk::DataNodeFactory::Pointer nodeReader = mitk::DataNodeFactory::New(); 00426 mitk::StandardFileLocations::Pointer locator = mitk::StandardFileLocations::GetInstance(); 00427 MITK_TEST_CONDITION_REQUIRED(locator.IsNotNull(),"Instantiating StandardFileLocations") 00428 try 00429 { 00430 const std::string filename = locator->FindFile("brain.mhd", "Core/Code/Testing/Data"); 00431 nodeReader->SetFileName(filename); 00432 nodeReader->Update(); 00433 node = nodeReader->GetOutput(); 00434 } 00435 catch(...) { 00436 MITK_TEST_FAILED_MSG(<< "Could not read file for testing: " << "brain.mhd"); 00437 return NULL; 00438 } 00439 00440 mitk::Image::Pointer image = dynamic_cast<mitk::Image*>(node->GetData()); 00441 00442 // test by index coordinates 00443 mitk::Index3D index; 00444 mitk::FillVector3D(index, 55, 39, 50); 00445 MITK_TEST_OUTPUT(<< "Testing mitk::Image::GetPixelValueByIndex"); 00446 double val = image->GetPixelValueByIndex(index); 00447 MITK_TEST_CONDITION_REQUIRED( mitk::Equal(val,112.22475433349609), ""); 00448 00449 //test by world coordinates 00450 MITK_TEST_OUTPUT(<< "Testing mitk::Image::GetPixelValueByWorldCoordinate"); 00451 mitk::Point3D point; 00452 mitk::FillVector3D(point, -5.93752, 18.7199, 6.74218); 00453 val = image->GetPixelValueByWorldCoordinate(point); 00454 MITK_TEST_CONDITION_REQUIRED( mitk::Equal(val,94.456184387207031), ""); 00455 00456 MITK_TEST_OUTPUT(<< "Convert to index and access value by mitk::Image::GetPixelValueByIndex again"); 00457 mitk::Index3D index2; 00458 image->GetGeometry()->WorldToIndex(point, index2); 00459 float val2 = image->GetPixelValueByIndex(index2); 00460 MITK_TEST_CONDITION_REQUIRED( mitk::Equal(val2,94.456184387207031), ""); 00461 00462 //access via itk 00463 MITK_TEST_OUTPUT(<< "Test conversion to itk::Image"); 00464 typedef itk::Image<float,3> ItkFloatImage3D; 00465 ItkFloatImage3D::Pointer itkimage; 00466 mitk::CastToItkImage(image, itkimage); 00467 std::cout<<"[PASSED]"<<std::endl; 00468 00469 MITK_TEST_OUTPUT(<< "Testing world->itk-physical->world consistency"); 00470 mitk::Point3D itkPhysicalPoint; 00471 image->GetGeometry()->WorldToItkPhysicalPoint(point, itkPhysicalPoint); 00472 00473 mitk::Point3D backTransformedPoint; 00474 image->GetGeometry()->ItkPhysicalPointToWorld(itkPhysicalPoint, backTransformedPoint); 00475 MITK_TEST_CONDITION_REQUIRED( mitk::Equal(point,backTransformedPoint), ""); 00476 00477 MITK_TEST_OUTPUT(<< "Compare value of pixel returned by mitk in comparison to itk"); 00478 itk::Index<3> idx; 00479 itkimage->TransformPhysicalPointToIndex(itkPhysicalPoint, idx); 00480 float valByItk = itkimage->GetPixel(idx); 00481 00482 MITK_TEST_CONDITION_REQUIRED( mitk::Equal(valByItk,94.456184387207031), ""); 00483 00484 MITK_TEST_END(); 00485 00486 return EXIT_SUCCESS; 00487 } 00488
