diff --git a/Applications/Diffusion/CMakeLists.txt b/Applications/Diffusion/CMakeLists.txt
index c9b7b0c..7d4acd2 100644
--- a/Applications/Diffusion/CMakeLists.txt
+++ b/Applications/Diffusion/CMakeLists.txt
@@ -1,101 +1,102 @@
project(MitkDiffusion)
set(DIFFUSIONAPP_NAME MitkDiffusion)
# Create a cache entry for the provisioning file which is used to export
# the file name in the MITKConfig.cmake file. This will keep external projects
# which rely on this file happy.
set(DIFFUSIONIMAGINGAPP_PROVISIONING_FILE "${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/${DIFFUSIONAPP_NAME}.provisioning" CACHE INTERNAL "${DIFFUSIONAPP_NAME} provisioning file" FORCE)
# should be identical to the list in /CMake/mitkBuildConfigurationmitkDiffusion.cmake
# remember to set plugins which should be automatically toggled in target_libraries.cmake
set(_plugins
org.commontk.configadmin
org.commontk.eventadmin
org.blueberry.core.runtime
org.blueberry.core.expressions
org.blueberry.core.commands
org.blueberry.ui.qt
org.blueberry.ui.qt.log
org.blueberry.ui.qt.help
org.mitk.core.services
org.mitk.gui.common
org.mitk.planarfigure
org.mitk.core.ext
org.mitk.gui.qt.application
org.mitk.gui.qt.ext
org.mitk.gui.qt.diffusionimagingapp
org.mitk.gui.qt.common
org.mitk.gui.qt.stdmultiwidgeteditor
org.mitk.gui.qt.datamanager
org.mitk.gui.qt.measurementtoolbox
org.mitk.gui.qt.segmentation
org.mitk.gui.qt.python
org.mitk.gui.qt.volumevisualization
org.mitk.gui.qt.diffusionimaging
org.mitk.gui.qt.diffusionimaging.connectomics
org.mitk.gui.qt.diffusionimaging.fiberfox
org.mitk.gui.qt.diffusionimaging.fiberprocessing
org.mitk.gui.qt.diffusionimaging.ivim
org.mitk.gui.qt.diffusionimaging.odfpeaks
org.mitk.gui.qt.diffusionimaging.preprocessing
org.mitk.gui.qt.diffusionimaging.reconstruction
org.mitk.gui.qt.diffusionimaging.tractography
org.mitk.gui.qt.diffusionimaging.registration
org.mitk.gui.qt.diffusionimaging.python
org.mitk.gui.qt.diffusionimaging.denoising
org.mitk.gui.qt.diffusionimaging.partialvolume
org.mitk.gui.qt.matchpoint.algorithm.browser
org.mitk.gui.qt.matchpoint.algorithm.control
org.mitk.gui.qt.matchpoint.mapper
org.mitk.gui.qt.imagenavigator
org.mitk.gui.qt.moviemaker
org.mitk.gui.qt.basicimageprocessing
org.mitk.gui.qt.properties
org.mitk.gui.qt.viewnavigator
org.mitk.gui.qt.renderwindowmanager
+ org.mitk.gui.qt.pixelvalue
)
if(NOT MITK_USE_Python3)
list(REMOVE_ITEM _plugins org.mitk.gui.qt.diffusionimaging.python)
list(REMOVE_ITEM _plugins org.mitk.gui.qt.python)
endif()
# Plug-ins listed below will not be
# - added as a build-time dependency to the executable
# - listed in the provisioning file for the executable
# - installed if they are external plug-ins
set(_exclude_plugins
org.blueberry.test
org.blueberry.uitest
org.mitk.gui.qt.coreapplication
org.mitk.gui.qt.extapplication
)
set(_src_files
MitkDiffusion.cpp
)
qt5_add_resources(_src_files splashscreen.qrc)
mitkFunctionCreateBlueBerryApplication(
NAME ${DIFFUSIONAPP_NAME}
DESCRIPTION "MITK Diffusion"
PLUGINS ${_plugins}
EXCLUDE_PLUGINS ${_exclude_plugins}
SOURCES ${_src_files}
)
# Add meta dependencies (e.g. on auto-load modules from depending modules)
if(TARGET ${CMAKE_PROJECT_NAME}-autoload)
add_dependencies(${DIFFUSIONAPP_NAME} ${CMAKE_PROJECT_NAME}-autoload)
endif()
# Add a build time dependency to legacy BlueBerry bundles.
if(MITK_MODULES_ENABLED_PLUGINS)
add_dependencies(${DIFFUSIONAPP_NAME} ${MITK_MODULES_ENABLED_PLUGINS})
endif()
diff --git a/Modules/DiffusionCmdApps/FiberProcessing/FiberColoring.cpp b/Modules/DiffusionCmdApps/FiberProcessing/FiberColoring.cpp
index 53ab3b0..7b85d1a 100644
--- a/Modules/DiffusionCmdApps/FiberProcessing/FiberColoring.cpp
+++ b/Modules/DiffusionCmdApps/FiberProcessing/FiberColoring.cpp
@@ -1,114 +1,127 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include <vector>
#include <iostream>
#include <fstream>
#include <algorithm>
#include <itkImageFileWriter.h>
#include <itkMetaDataObject.h>
#include <itkVectorImage.h>
#include <mitkBaseData.h>
#include <mitkFiberBundle.h>
#include "mitkDiffusionCommandLineParser.h"
#include <mitkLexicalCast.h>
#include <mitkCoreObjectFactory.h>
#include <mitkIOUtil.h>
#include <itkFiberCurvatureFilter.h>
#include <mitkDiffusionDataIOHelper.h>
#include <mitkImage.h>
mitk::FiberBundle::Pointer LoadFib(std::string filename)
{
std::vector<mitk::BaseData::Pointer> fibInfile = mitk::IOUtil::Load(filename);
if( fibInfile.empty() )
std::cout << "File " << filename << " could not be read!";
mitk::BaseData::Pointer baseData = fibInfile.at(0);
return dynamic_cast<mitk::FiberBundle*>(baseData.GetPointer());
}
/*!
\brief Modify input tractogram: fiber resampling, compression, pruning and transformation.
*/
int main(int argc, char* argv[])
{
mitkDiffusionCommandLineParser parser;
parser.setTitle("Fiber Coloring");
parser.setCategory("Fiber Tracking and Processing Methods");
parser.setDescription("Color tractogram.");
parser.setContributor("MIC");
parser.setArgumentPrefix("--", "-");
parser.beginGroup("1. Mandatory arguments:");
parser.addArgument("", "i", mitkDiffusionCommandLineParser::String, "Input:", "Input fiber bundle (.fib, .trk, .tck)", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Input);
parser.addArgument("", "o", mitkDiffusionCommandLineParser::String, "Output:", "Output fiber bundle (.fib)", us::Any(), false, false, false, mitkDiffusionCommandLineParser::Output);
parser.addArgument("resample", "", mitkDiffusionCommandLineParser::Float, "", "");
parser.endGroup();
parser.beginGroup("2. Color by scalar map:");
parser.addArgument("scalar_map", "", mitkDiffusionCommandLineParser::String, "", "", us::Any(), true, false, false, mitkDiffusionCommandLineParser::Input);
+ parser.addArgument("lookup", "", mitkDiffusionCommandLineParser::String, "", "JET, MULTILABEL", us::Any(), true, false, false);
+ parser.addArgument("interpolate", "", mitkDiffusionCommandLineParser::Bool, "", "");
parser.endGroup();
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
std::string inFileName = us::any_cast<std::string>(parsedArgs["i"]);
std::string outFileName = us::any_cast<std::string>(parsedArgs["o"]);
float resample = -1;
if (parsedArgs.count("resample"))
resample = us::any_cast<float>(parsedArgs["resample"]);
+ std::string lookup = "JET";
+ if (parsedArgs.count("lookup"))
+ lookup = us::any_cast<std::string>(parsedArgs["lookup"]);
+
+ bool interpolate = false;
+ if (parsedArgs.count("interpolate"))
+ interpolate = us::any_cast<bool>(parsedArgs["interpolate"]);
+
try
{
mitk::FiberBundle::Pointer fib = LoadFib(inFileName);
if (resample>0)
fib->ResampleSpline(resample);
if (parsedArgs.count("scalar_map"))
{
auto scalar_map = mitk::IOUtil::Load<mitk::Image>(us::any_cast<std::string>(parsedArgs["scalar_map"]));
- fib->ColorFibersByScalarMap(scalar_map, false, false, mitk::LookupTable::MULTILABEL, 1.0);
+ if (lookup == "JET")
+ fib->ColorFibersByScalarMap(scalar_map, false, false, mitk::LookupTable::JET, 1.0, interpolate);
+ else
+ fib->ColorFibersByScalarMap(scalar_map, false, false, mitk::LookupTable::MULTILABEL, 1.0, false);
}
mitk::IOUtil::Save(fib.GetPointer(), outFileName );
}
catch (const itk::ExceptionObject& e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (std::exception& e)
{
std::cout << e.what();
return EXIT_FAILURE;
}
catch (...)
{
std::cout << "ERROR!?!";
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
diff --git a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp
index 1b22f33..dfa927c 100644
--- a/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp
+++ b/Modules/DiffusionIO/ReaderWriter/mitkFiberBundleTrackVisReader.cpp
@@ -1,100 +1,100 @@
/*===================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center.
All rights reserved.
This software is distributed WITHOUT ANY WARRANTY; without
even the implied warranty of MERCHANTABILITY or FITNESS FOR
A PARTICULAR PURPOSE.
See LICENSE.txt or http://www.mitk.org for details.
===================================================================*/
#include "mitkFiberBundleTrackVisReader.h"
#include <itkMetaDataObject.h>
#include <vtkPolyData.h>
#include <vtkDataReader.h>
#include <vtkPolyDataReader.h>
#include <vtkMatrix4x4.h>
#include <vtkPolyLine.h>
#include <vtkCellArray.h>
#include <vtkDataArray.h>
#include <vtkFloatArray.h>
#include <vtkCellData.h>
#include <vtkPointData.h>
#include <itksys/SystemTools.hxx>
#include <vtkCleanPolyData.h>
#include <mitkTrackvis.h>
#include <mitkCustomMimeType.h>
#include "mitkDiffusionIOMimeTypes.h"
mitk::FiberBundleTrackVisReader::FiberBundleTrackVisReader()
: mitk::AbstractFileReader( mitk::DiffusionIOMimeTypes::FIBERBUNDLE_TRK_MIMETYPE_NAME(), "TrackVis Fiber Bundle Reader" )
{
Options defaultOptions;
defaultOptions["Apply index to world transform stored in the TRK header"] = true;
defaultOptions["Print header"] = true;
- defaultOptions["Flip x"] = false;
+ defaultOptions["Flip x"] = true;
defaultOptions["Flip y"] = false;
defaultOptions["Flip z"] = false;
this->SetDefaultOptions(defaultOptions);
m_ServiceReg = this->RegisterService();
}
mitk::FiberBundleTrackVisReader::FiberBundleTrackVisReader(const FiberBundleTrackVisReader &other)
:mitk::AbstractFileReader(other)
{
}
mitk::FiberBundleTrackVisReader * mitk::FiberBundleTrackVisReader::Clone() const
{
return new FiberBundleTrackVisReader(*this);
}
std::vector<itk::SmartPointer<mitk::BaseData> > mitk::FiberBundleTrackVisReader::DoRead()
{
std::vector<itk::SmartPointer<mitk::BaseData> > result;
try
{
const std::string& locale = "C";
const std::string& currLocale = setlocale( LC_ALL, nullptr );
setlocale(LC_ALL, locale.c_str());
std::string filename = this->GetInputLocation();
MITK_INFO << "Loading tractogram (TrackVis format): " << itksys::SystemTools::GetFilenameName(filename);
std::string ext = itksys::SystemTools::GetFilenameLastExtension(filename);
ext = itksys::SystemTools::LowerCase(ext);
if (ext==".trk")
{
Options options = this->GetOptions();
bool apply_matrix = us::any_cast<bool>(options["Apply index to world transform stored in the TRK header"]);
bool flip_x = us::any_cast<bool>(options["Flip x"]);
bool flip_y = us::any_cast<bool>(options["Flip y"]);
bool flip_z = us::any_cast<bool>(options["Flip z"]);
bool print_header = us::any_cast<bool>(options["Print header"]);
FiberBundle::Pointer mitk_fib = FiberBundle::New();
TrackVisFiberReader reader;
reader.open(this->GetInputLocation().c_str());
reader.read(mitk_fib.GetPointer(), apply_matrix, flip_x, flip_y, flip_z, print_header);
result.push_back(mitk_fib.GetPointer());
return result;
}
setlocale(LC_ALL, currLocale.c_str());
MITK_INFO << "Fiber bundle read";
}
catch(...)
{
throw;
}
return result;
}