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ENH: adding ground truth creator. Closes #108.
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| /*========================================================================= | ||
| * | ||
| * Copyright Insight Software Consortium | ||
| * | ||
| * Licensed under the Apache License, Version 2.0 (the "License"); | ||
| * you may not use this file except in compliance with the License. | ||
| * You may obtain a copy of the License at | ||
| * | ||
| * http://www.apache.org/licenses/LICENSE-2.0.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. | ||
| * | ||
| *=========================================================================*/ | ||
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|
||
| #include "itkImageFileReader.h" | ||
| #include "itkImageFileWriter.h" | ||
| #include "itkMersenneTwisterRandomVariateGenerator.h" | ||
| #include "itkResampleImageFilter.h" | ||
| #include "itkRGBPixel.h" | ||
| #include "itkTileMontage.h" | ||
|
|
||
| template< unsigned Dimension > | ||
| struct Tile | ||
| { | ||
| using PointType = itk::ContinuousIndex< double, Dimension >; | ||
| PointType Position; // x, y... coordinates | ||
| std::string FileName; | ||
| }; | ||
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||
| // calculate nD-index given linear index and montage size | ||
| template< unsigned Dimension > | ||
| itk::Size< Dimension > | ||
| linearToNDindex( itk::SizeValueType linearIndex, const std::vector< unsigned >& montageSize ) | ||
| { | ||
| assert( montageSize.size() == Dimension ); | ||
| itk::Size< Dimension > ind; | ||
| itk::SizeValueType stride = 1u; | ||
| for ( unsigned d = 0; d < Dimension; d++ ) | ||
| { | ||
| stride *= montageSize[d]; | ||
| ind[d] = linearIndex % stride; | ||
| linearIndex /= stride; | ||
| } | ||
| return ind; | ||
| } | ||
|
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||
| template< typename PixelType, unsigned Dimension > | ||
| int | ||
| CreateGroundTruth( char* inFilename, const std::vector< unsigned >& montageSize, const std::vector< double >& overlap, | ||
| const std::string& outDir ) | ||
| { | ||
| using ImageType = itk::Image< PixelType, Dimension >; | ||
| using ReaderType = itk::ImageFileReader< ImageType >; | ||
| typename ReaderType::Pointer reader = ReaderType::New(); | ||
| reader->SetFileName( inFilename ); | ||
| reader->Update(); | ||
| typename ImageType::Pointer inImage = reader->GetOutput(); | ||
| typename ImageType::SizeType size = inImage->GetLargestPossibleRegion().GetSize(); | ||
| typename ImageType::SizeType tileSize; | ||
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||
| // calculate tile sizes in index space | ||
| std::vector< double > tileSizes( Dimension ); | ||
| constexpr double slopeFactor = 0.40; // varMax as fraction of overlap (MUST be < 0.50) | ||
| std::vector< double > varMax( Dimension ); | ||
| itk::SizeValueType totalTiles = 1; | ||
| for ( unsigned d = 0; d < Dimension; d++ ) | ||
| { | ||
| tileSizes[d] = size[d] / ( montageSize[d] + overlap[d] - montageSize[d] * overlap[d] ); | ||
| tileSize[d] = std::round( tileSizes[d] ); | ||
| varMax[d] = slopeFactor * tileSizes[d] * overlap[d]; | ||
| totalTiles *= montageSize[d]; | ||
| } | ||
|
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||
| using ScalarImage = itk::Image< typename itk::NumericTraits< PixelType >::ValueType, Dimension >; | ||
| using MontageType = itk::TileMontage< ScalarImage, double >; | ||
| std::ofstream f( outDir + "TileConfiguration.txt" ); | ||
| f << "# Tile coordinates are in index space, not physical space\n"; | ||
| f << "dim = " << Dimension << "\n\n"; | ||
| std::ofstream fr( outDir + "TileConfiguration.registered.txt" ); | ||
| fr << "# Tile coordinates are in index space, not physical space\n"; | ||
| fr << "dim = " << Dimension << "\n\n"; | ||
|
|
||
| using MersenneTwister = itk::Statistics::MersenneTwisterRandomVariateGenerator; | ||
| typename MersenneTwister::Pointer randomizer = MersenneTwister::New(); | ||
| randomizer->SetSeed( 1983 ); // make the pseudorandom seqence fully reproducible | ||
|
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||
| // calculate tile positions | ||
| std::vector< Tile< Dimension > > tiles( totalTiles ); | ||
| for ( itk::SizeValueType linearIndex = 0; linearIndex < totalTiles; linearIndex++ ) | ||
| { | ||
| typename MontageType::TileIndexType ind = linearToNDindex< Dimension >( linearIndex, montageSize ); | ||
| tiles[linearIndex].FileName = "tile_" + std::to_string( linearIndex ) + ".nrrd"; | ||
| f << tiles[linearIndex].FileName << ";;("; | ||
| fr << tiles[linearIndex].FileName << ";;("; | ||
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| for ( unsigned d = 0; d < Dimension; d++ ) | ||
| { | ||
| double regularPosition = ind[d] * ( 1 - overlap[d] ) * tileSizes[d]; | ||
| tiles[linearIndex].Position[d] = regularPosition; | ||
| if ( ind[d] > 0 && ind[d] < montageSize[d] - 1 ) // not at the outer perimeter of the montage | ||
| { | ||
| tiles[linearIndex].Position[d] += randomizer->GetUniformVariate( -varMax[d], varMax[d] ); | ||
| } | ||
|
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||
| if ( d > 0 ) | ||
| { | ||
| f << ", "; | ||
| fr << ", "; | ||
| } | ||
| f << regularPosition; | ||
| fr << tiles[linearIndex].Position[d]; | ||
| } | ||
| f << ')' << std::endl; | ||
| fr << ')' << std::endl; | ||
| } | ||
| f.close(); | ||
| fr.close(); | ||
|
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||
| // now resample the tiles | ||
| using ResampleFilterType = itk::ResampleImageFilter< ImageType, ImageType >; | ||
| typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New(); | ||
| resampleFilter->SetOutputDirection( inImage->GetDirection() ); | ||
| resampleFilter->SetOutputSpacing( inImage->GetSpacing() ); | ||
| resampleFilter->SetInput( inImage ); | ||
| resampleFilter->SetSize( tileSize ); | ||
| // resampleFilter->SetTransform( scaleTransform ); // identity | ||
| // resampleFilter->SetInterpolator( interpolator ); | ||
| using WriterType = itk::ImageFileWriter< ImageType >; | ||
| typename WriterType::Pointer writer = WriterType::New(); | ||
| writer->SetInput( resampleFilter->GetOutput() ); | ||
|
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| for ( itk::SizeValueType linearIndex = 0; linearIndex < totalTiles; linearIndex++ ) | ||
| { | ||
| typename ImageType::PointType p; | ||
| inImage->TransformContinuousIndexToPhysicalPoint( tiles[linearIndex].Position, p ); | ||
| resampleFilter->SetOutputOrigin( p ); | ||
| std::cout << "Resampling " << tiles[linearIndex].FileName << std::flush; | ||
| resampleFilter->Update(); | ||
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| std::cout << " Writing " << std::flush; | ||
| writer->SetFileName( outDir + tiles[linearIndex].FileName ); | ||
| writer->Update(); | ||
| std::cout << " Done" << std::endl; | ||
| } | ||
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|
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| return EXIT_SUCCESS; | ||
| } | ||
|
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||
| template< typename PixelType > | ||
| int CreateGroundTruth( int argc, char* argv[], unsigned dimension ) | ||
| { | ||
| std::string outputPath = argv[2]; | ||
| if ( outputPath.back() != '/' && outputPath.back() != '\\' ) | ||
| { | ||
| outputPath += '/'; | ||
| } | ||
|
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||
| std::vector< unsigned > montageSize( dimension, 10 ); | ||
| if ( argc >= 3 + int(dimension) ) | ||
| { | ||
| for ( unsigned i = 0; i < dimension; i++ ) | ||
| { | ||
| montageSize[i] = std::stoul( argv[3 + i] ); | ||
| } | ||
| } | ||
|
|
||
| std::vector< double > overlap( dimension, 0.1 ); | ||
| if ( argc >= 3 + 2 * int(dimension) ) | ||
| { | ||
| for ( unsigned i = 0; i < dimension; i++ ) | ||
| { | ||
| overlap[i] = std::stod( argv[3 + dimension + i] ) / 100.0; | ||
| } | ||
| } | ||
|
|
||
| if ( dimension == 2 ) | ||
| { | ||
| return CreateGroundTruth< PixelType, 2 >( argv[1], montageSize, overlap, outputPath ); | ||
| } | ||
| else if ( dimension == 3 ) | ||
| { | ||
| return CreateGroundTruth< PixelType, 3 >( argv[1], montageSize, overlap, outputPath ); | ||
| } | ||
| else | ||
| { | ||
| std::cerr << "Only dimensions 2 and 3 are supported!" << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| } | ||
|
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||
| template< typename ComponentType > | ||
| int | ||
| CreateGroundTruth( int argc, char* argv[], unsigned dimension, itk::ImageIOBase::IOPixelType pixelType ) | ||
| { | ||
| if ( pixelType == itk::ImageIOBase::IOPixelType::RGB ) // possibly add RGBA | ||
| { | ||
| return CreateGroundTruth< itk::RGBPixel< ComponentType > >( argc, argv, dimension ); | ||
| } | ||
| else | ||
| { | ||
| return CreateGroundTruth< ComponentType >( argc, argv, dimension ); | ||
| } | ||
| } | ||
|
|
||
| int itkMontageTruthCreator( int argc, char* argv[] ) | ||
| { | ||
| if ( argc < 3 ) | ||
| { | ||
| std::cerr << "Usage: " << argv[0] << " <inputImage> <outputDirectory> [montageSize] [overlap%]" << std::endl; | ||
| std::cerr << "Example:" << argv[0] << " slice2D.png ./outGT/ 8 6 15.0 10.0" << std::endl; | ||
| std::cerr << "Example:" << argv[0] << " volume3D.nrrd ./outGT/ 8 6 4 15.0 10.0 5.0" << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
|
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||
| itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO( argv[1], itk::ImageIOFactory::ReadMode ); | ||
| imageIO->SetFileName( argv[1] ); | ||
| imageIO->ReadImageInformation(); | ||
| unsigned dim = imageIO->GetNumberOfDimensions(); | ||
| const itk::ImageIOBase::IOComponentType cType = imageIO->GetComponentType(); | ||
|
|
||
| if ( cType == itk::ImageIOBase::IOComponentType::UCHAR ) | ||
| { | ||
| return CreateGroundTruth< unsigned char >( argc, argv, dim, imageIO->GetPixelType() ); | ||
| } | ||
| else if ( cType == itk::ImageIOBase::IOComponentType::USHORT ) | ||
| { | ||
| return CreateGroundTruth< unsigned short >( argc, argv, dim, imageIO->GetPixelType() ); | ||
| } | ||
| else if ( cType == itk::ImageIOBase::IOComponentType::SHORT ) | ||
| { | ||
| return CreateGroundTruth< short >( argc, argv, dim, imageIO->GetPixelType() ); | ||
| } | ||
| else | ||
| { | ||
| std::cerr << "Unsupported component type: " << itk::ImageIOBase::GetComponentTypeAsString( cType ) << std::endl; | ||
| return EXIT_FAILURE; | ||
| } | ||
| } |