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/*
//
// Copyright 2016 Google, Inc.
//
// Copyright 1997-2010 Torsten Rohlfing
//
// Copyright 2004-2014 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit is free software: you can
// redistribute it and/or modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation, either version 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit is distributed in the hope that it
// will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#include <cmtkconfig.h>
#include <System/cmtkCommandLine.h>
#include <System/cmtkExitException.h>
#include <System/cmtkConsole.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkVector3D.h>
#include <IO/cmtkVolumeIO.h>
#include <iostream>
typedef enum
{
COORDINATES_INDEXED,
COORDINATES_ABSOLUTE,
COORDINATES_RELATIVE,
COORDINATES_PHYSICAL
} CoordinateModeEnum;
int
doMain( const int argc, const char *argv[] )
{
std::string inputImagePath;
const char* readOrientation = "RAS";
CoordinateModeEnum inputMode = COORDINATES_ABSOLUTE;
CoordinateModeEnum outputMode = COORDINATES_ABSOLUTE;
const char* radiusStr = "1";
try
{
cmtk::CommandLine cl;
cl.SetProgramInfo( cmtk::CommandLine::PRG_TITLE, "Search image neighborhoods for pixels." );
cl.SetProgramInfo( cmtk::CommandLine::PRG_DESCR, "This tool reads an image file, as well as a list of pixel coordinates from standard input. For each pixel, a local neighbourhood in the image is searched for the maximum "
"value. The location of the maximum is then written to standard output." );
typedef cmtk::CommandLine::Key Key;
cmtk::CommandLine::EnumGroup<CoordinateModeEnum>::SmartPtr inputModeGroup = cl.AddEnum( "input-coordinates", &inputMode, "Coordinate specification mode for program input." );
inputModeGroup->AddSwitch( Key( "absolute" ), COORDINATES_ABSOLUTE, "Use absolute volume coordinates. For each dimension, the valid range is [0,FOV]." );
inputModeGroup->AddSwitch( Key( "indexed" ), COORDINATES_INDEXED, "Use grid indexes to specify coordinates. For each dimension, the valid value range is [0,Dims-1]." );
inputModeGroup->AddSwitch( Key( "relative" ), COORDINATES_RELATIVE, "Use relative volume coordinates. For each dimension, the valid range is [0,1]." );
inputModeGroup->AddSwitch( Key( "physical" ), COORDINATES_PHYSICAL, "Use physical volume coordinates. "
"Each given location is transformed into image coordinates via the inverse of the images's index-to-physical space matrix." );
cmtk::CommandLine::EnumGroup<CoordinateModeEnum>::SmartPtr outputModeGroup = cl.AddEnum( "output-coordinates", &outputMode, "Coordinate specification mode for program output." );
outputModeGroup->AddSwitch( Key( "absolute" ), COORDINATES_ABSOLUTE, "Use absolute volume coordinates. For each dimension, the valid range is [0,FOV]." );
outputModeGroup->AddSwitch( Key( "indexed" ), COORDINATES_INDEXED, "Use grid indexes to specify coordinates. For each dimension, the valid value range is [0,Dims-1]." );
outputModeGroup->AddSwitch( Key( "relative" ), COORDINATES_RELATIVE, "Use relative volume coordinates. For each dimension, the valid range is [0,1]." );
outputModeGroup->AddSwitch( Key( "physical" ), COORDINATES_PHYSICAL, "Use physical volume coordinates. "
"Each given location is transformed into image coordinates via the inverse of the images's index-to-physical space matrix." );
cl.AddOption( Key( "radius" ), &radiusStr, "Radius of the search region in pixels (specified either as triple \"rX,rY,rZ\", or a single value, \"rXYZ\"). "
"The region searched is [2*rX+1,2*rY+1,2*rZ+1] pixels large, centered at the input location (but cropped at the image boundary)." );
cl.AddSwitch( Key( "no-reorient" ), &readOrientation, static_cast<const char*>( NULL ), "Disable image reorientation into RAS alignment." );
cl.AddParameter( &inputImagePath, "InputImage", "Input image path" )->SetProperties( cmtk::CommandLine::PROPS_IMAGE );
cl.Parse( argc, argv );
}
catch ( const cmtk::CommandLine::Exception& e )
{
cmtk::StdErr << e << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::UniformVolume::SmartPtr volume;
if ( readOrientation )
volume = cmtk::VolumeIO::ReadOriented( inputImagePath, readOrientation );
else
volume = cmtk::VolumeIO::Read( inputImagePath );
if ( ! volume || ! volume->GetData() )
{
cmtk::StdErr << "ERROR: could not read image " << inputImagePath << "\n";
throw cmtk::ExitException( 1 );
}
cmtk::FixedVector<3,int> radius;
if ( 3 != sscanf( radiusStr, "%6d,%6d,%6d", &radius[0], &radius[1], &radius[2] ) )
{
radius[0] = radius[1] = radius[2] = atof( radiusStr );
}
cmtk::UniformVolume::SpaceVectorType v;
std::string restOfLine;
cmtk::AffineXform::MatrixType physicalToImageMatrix;
try
{
physicalToImageMatrix = volume->GetImageToPhysicalMatrix().GetInverse();
}
catch ( const cmtk::AffineXform::MatrixType::SingularMatrixException& )
{
cmtk::StdErr << "ERROR: singular image-to-physical matrix encountered\n";
throw cmtk::ExitException( 1 );
}
while ( ! std::cin.eof() )
{
std::cin >> v;
std::getline( std::cin, restOfLine );
if ( std::cin.eof() )
break;
switch ( inputMode )
{
case COORDINATES_INDEXED:
// nothing to do - lookup will be done by absolute coordinate
break;
case COORDINATES_ABSOLUTE:
// index is absolute image coordinate divided (component-wise) by pixel size
v /= volume->m_Delta;
break;
case COORDINATES_RELATIVE:
// absolute image coordinate is relative times volume size
(v *= volume->m_Size) /= volume->m_Delta;
break;
case COORDINATES_PHYSICAL:
// absolute image coordinate is physical transformed by inverse image-to-physical matrix
(v *= physicalToImageMatrix) /= volume->m_Delta;
break;
}
// convert to discrete index by rounding (not simple truncation)
const cmtk::UniformVolume::IndexType ijk = v.AddScalar( 0.5 );
cmtk::DataGrid::IndexType maxIndex = ijk;
cmtk::Types::DataItem maxValue = volume->GetDataAt( volume->GetOffsetFromIndex( ijk ) );
cmtk::DataGrid::IndexType probe = ijk;
for ( probe[2] = std::max<cmtk::Types::GridIndexType>( 0, ijk[2]-radius[2] ); probe[2] < std::min( volume->m_Dims[2], ijk[2]+radius[2]+1 ); ++probe[2] )
for ( probe[1] = std::max<cmtk::Types::GridIndexType>( 0, ijk[1]-radius[1] ); probe[1] < std::min( volume->m_Dims[1], ijk[1]+radius[1]+1 ); ++probe[1] )
for ( probe[0] = std::max<cmtk::Types::GridIndexType>( 0, ijk[0]-radius[0] ); probe[0] < std::min( volume->m_Dims[0], ijk[0]+radius[0]+1 ); ++probe[0] )
{
const cmtk::Types::DataItem value = volume->GetDataAt( volume->GetOffsetFromIndex( probe ) );
if ( value > maxValue )
{
maxValue = value;
maxIndex = probe;
}
}
v = maxIndex;
switch ( outputMode )
{
case COORDINATES_INDEXED:
// nothing to do - already indexed
break;
case COORDINATES_ABSOLUTE:
// absolute image coordinate is index times pixel size
v *= volume->m_Delta;
break;
case COORDINATES_RELATIVE:
// absolute image coordinate is relative times volume size
(v *= volume->m_Delta) /= volume->m_Size;
break;
case COORDINATES_PHYSICAL:
// absolute image coordinate is obtained using image-to-physical matrix
(v *= volume->m_Delta) *= volume->GetImageToPhysicalMatrix();
break;
}
std::cout << v << restOfLine << "\n";
}
return 0;
}
#include "cmtkSafeMain"
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