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moritzdannhauermoritzdannhauer
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merge with master - new nrrd support
2 parents b495dc7 + e621deb commit f6f51cd

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‎README.md‎

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![alt text](http://www.sci.utah.edu/images/banners/splash-scirun.png "")
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![SCIRun Banner](http://www.sci.utah.edu/images/software/SCIRun/scirun.png "")
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## SCIRun 5
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https://github.com/SCIInstitute/SCIRun

‎src/CMakeLists.txt‎

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@@ -563,12 +563,14 @@ SET_PROPERTY(TARGET Algorithms_Factory PROPERTY FOLDER "Core/Algorithms")
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SET_PROPERTY(TARGET Core_Algorithms_Legacy_Fields PROPERTY FOLDER "Core/Algorithms")
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SET_PROPERTY(TARGET Core_Algorithms_Legacy_FiniteElements PROPERTY FOLDER "Core/Algorithms")
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SET_PROPERTY(TARGET Core_Algorithms_Legacy_DataIO PROPERTY FOLDER "Core/Algorithms")
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SET_PROPERTY(TARGET Core_Algorithms_Legacy_Converter PROPERTY FOLDER "Core/Algorithms")
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SET_PROPERTY(TARGET Dataflow_Network PROPERTY FOLDER "Dataflow")
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SET_PROPERTY(TARGET Core_Datatypes PROPERTY FOLDER "Core")
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SET_PROPERTY(TARGET Core_Datatypes_Mesh PROPERTY FOLDER "Core")
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SET_PROPERTY(TARGET Core_Datatypes_Legacy_Base PROPERTY FOLDER "Core")
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SET_PROPERTY(TARGET Core_Datatypes_Legacy_Field PROPERTY FOLDER "Core")
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SET_PROPERTY(TARGET Core_Datatypes_Legacy_Nrrd PROPERTY FOLDER "Core")
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SET_PROPERTY(TARGET Core_Datatypes_Legacy_Bundle PROPERTY FOLDER "Core")
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SET_PROPERTY(TARGET Core_Basis PROPERTY FOLDER "Core")
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SET_PROPERTY(TARGET Core_Persistent PROPERTY FOLDER "Core")

‎src/Core/Algorithms/Base/AlgorithmData.h‎

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#include <map>
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#include <boost/filesystem/path.hpp>
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#include <boost/any.hpp>
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#include <Core/Datatypes/DatatypeFwd.h>
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#include <Core/Algorithms/Base/Name.h>
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#include <Core/Algorithms/Base/Variable.h>

‎src/Core/Algorithms/DataIO/Tests/CMakeLists.txt‎

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ReadMatrixTests.cc
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WriteMatrixTests.cc
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ReadTriSurfTests.cc
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ReadWriteNrrdTests.cc
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)
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SCIRUN_ADD_UNIT_TEST(Algorithms_DataIO_Tests
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Algorithms_DataIO
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Core_Datatypes
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Testing_Utils
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Core_IEPlugin
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gtest_main
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gtest
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gmock

‎src/Core/Algorithms/DataIO/Tests/ReadWriteNrrdTests.cc‎

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/*
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For more information, please see: http://software.sci.utah.edu
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The MIT License
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Copyright (c) 2012 Scientific Computing and Imaging Institute,
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University of Utah.
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License for the specific language governing rights and limitations under
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Permission is hereby granted, free of charge, to any person obtaining a
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copy of this software and associated documentation files (the "Software"),
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to deal in the Software without restriction, including without limitation
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the rights to use, copy, modify, merge, publish, distribute, sublicense,
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and/or sell copies of the Software, and to permit persons to whom the
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Software is furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included
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in all copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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DEALINGS IN THE SOFTWARE.
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*/
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#include <Testing/Utils/SCIRunUnitTests.h>
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#include <Core/IEPlugin/NrrdField_Plugin.h>
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#include <Core/Datatypes/Legacy/Field/Field.h>
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#include <Core/Datatypes/Legacy/Field/VMesh.h>
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using namespace SCIRun;
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using namespace SCIRun::Core;
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using namespace SCIRun::Core::Datatypes;
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using namespace SCIRun::TestUtils;
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namespace
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{
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boost::filesystem::path testNrrd = TestResources::rootDir() / "ToolKits" / "FwdInvToolbox" / "pot_based_FEM_forward" / "Segmentation.nrrd";
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boost::filesystem::path testNrrdHeader = TestResources::rootDir() / "Fields" / "nrrd" / "fieldOut.nhdr";
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}
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TEST(ReadNrrdTests, CanReadFullNrrdFile)
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{
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auto field = NrrdToField_reader(nullptr, testNrrd.string().c_str());
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ASSERT_TRUE(field != nullptr);
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EXPECT_EQ(18869130, field->vmesh()->num_nodes());
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EXPECT_EQ(18620000, field->vmesh()->num_elems());
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EXPECT_EQ(1, field->vmesh()->basis_order());
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}
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TEST(ReadNrrdTests, CanReadNrrdHeaderFile)
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{
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auto field = NrrdToField_reader(nullptr, testNrrdHeader.string().c_str());
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ASSERT_TRUE(field != nullptr);
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EXPECT_EQ(19120104, field->vmesh()->num_nodes());
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EXPECT_EQ(18869130, field->vmesh()->num_elems());
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EXPECT_EQ(1, field->vmesh()->basis_order());
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}
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TEST(ReadNrrdTests, CanReadNrrdFile_Nodal)
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{
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auto field = Nodal_NrrdToField_reader(nullptr, testNrrd.string().c_str());
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ASSERT_TRUE(field != nullptr);
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EXPECT_EQ(18869130, field->vmesh()->num_nodes());
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EXPECT_EQ(18620000, field->vmesh()->num_elems());
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EXPECT_EQ(1, field->vmesh()->basis_order());
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}
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TEST(ReadNrrdTests, CanReadNrrdFile_Modal)
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{
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auto field = Modal_NrrdToField_reader(nullptr, testNrrd.string().c_str());
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ASSERT_TRUE(field != nullptr);
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EXPECT_EQ(19120104, field->vmesh()->num_nodes());
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EXPECT_EQ(18869130, field->vmesh()->num_elems());
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EXPECT_EQ(1, field->vmesh()->basis_order());
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}
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TEST(ReadNrrdTests, CanReadNrrdFile_IPNodal)
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{
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auto field = IPNodal_NrrdToField_reader(nullptr, testNrrd.string().c_str());
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ASSERT_TRUE(field != nullptr);
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EXPECT_EQ(18869130, field->vmesh()->num_nodes());
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EXPECT_EQ(18620000, field->vmesh()->num_elems());
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EXPECT_EQ(1, field->vmesh()->basis_order());
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}
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TEST(ReadNrrdTests, CanReadNrrdFile_IPModal)
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{
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auto field = IPModal_NrrdToField_reader(nullptr, testNrrd.string().c_str());
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ASSERT_TRUE(field != nullptr);
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EXPECT_EQ(19120104, field->vmesh()->num_nodes());
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EXPECT_EQ(18869130, field->vmesh()->num_elems());
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EXPECT_EQ(1, field->vmesh()->basis_order());
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}
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TEST(WriteNrrdTests, CanWriteNrrdFile)
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{
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auto field = NrrdToField_reader(nullptr, testNrrd.string().c_str());
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ASSERT_TRUE(field != nullptr);
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EXPECT_EQ(18869130, field->vmesh()->num_nodes());
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EXPECT_EQ(18620000, field->vmesh()->num_elems());
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EXPECT_EQ(1, field->vmesh()->basis_order());
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boost::filesystem::path out(TestResources::rootDir() / "TransientOutput" / "fieldOutUnit.nrrd");
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ASSERT_TRUE(FieldToNrrd_writer(nullptr, field, out.string().c_str()));
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}
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TEST(WriteNrrdTests, CanWriteNrrdFileHeader)
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{
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auto field = NrrdToField_reader(nullptr, testNrrd.string().c_str());
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ASSERT_TRUE(field != nullptr);
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EXPECT_EQ(18869130, field->vmesh()->num_nodes());
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EXPECT_EQ(18620000, field->vmesh()->num_elems());
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EXPECT_EQ(1, field->vmesh()->basis_order());
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boost::filesystem::path out(TestResources::rootDir() / "TransientOutput" / "fieldOutUnitHeader.nhdr");
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ASSERT_TRUE(FieldToNrrd_writer(nullptr, field, out.string().c_str()));
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}

‎src/Core/Algorithms/Legacy/CMakeLists.txt‎

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#
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# For more information, please see: http://software.sci.utah.edu
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#
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#
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# The MIT License
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#
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#
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# Copyright (c) 2012 Scientific Computing and Imaging Institute,
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# University of Utah.
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#
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#
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#
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#
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# Permission is hereby granted, free of charge, to any person obtaining a
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# copy of this software and associated documentation files (the "Software"),
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# to deal in the Software without restriction, including without limitation
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# the rights to use, copy, modify, merge, publish, distribute, sublicense,
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# and/or sell copies of the Software, and to permit persons to whom the
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# Software is furnished to do so, subject to the following conditions:
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#
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#
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# The above copyright notice and this permission notice shall be included
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# in all copies or substantial portions of the Software.
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#
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# in all copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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ADD_SUBDIRECTORY(Fields)
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ADD_SUBDIRECTORY(DataIO)
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ADD_SUBDIRECTORY(Converter)
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#ADD_SUBDIRECTORY(Math)
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ADD_SUBDIRECTORY(FiniteElements)

‎src/Core/Algorithms/Legacy/Converter/CMakeLists.txt‎

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#
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# For more information, please see: http://software.sci.utah.edu
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#
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# The MIT License
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#
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# Copyright (c) 2009 Scientific Computing and Imaging Institute,
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# University of Utah.
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#
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#
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# Permission is hereby granted, free of charge, to any person obtaining a
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# copy of this software and associated documentation files (the "Software"),
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# to deal in the Software without restriction, including without limitation
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# the rights to use, copy, modify, merge, publish, distribute, sublicense,
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# and/or sell copies of the Software, and to permit persons to whom the
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# Software is furnished to do so, subject to the following conditions:
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#
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# The above copyright notice and this permission notice shall be included
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# in all copies or substantial portions of the Software.
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#
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# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
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# OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
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# THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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#
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# Sources of Core/Algorithms/Converter classes
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SET(Core_Algorithms_Legacy_Converter_SRCS
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ConverterAlgo.cc
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#MatrixToField.cc
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NrrdToField.cc
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FieldToNrrd.cc
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#ConvertToNrrd.cc
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#MatricesToDipoleField.cc
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#ConvertBundleToField.cc
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)
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SET(Core_Algorithms_Legacy_Converter_HEADERS
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ConverterAlgo.h
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NrrdToField.h
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FieldToNrrd.h
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)
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ADD_LIBRARY(Core_Algorithms_Legacy_Converter
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${Core_Algorithms_Legacy_Converter_SRCS}
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${Core_Algorithms_Legacy_Converter_HEADERS})
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TARGET_LINK_LIBRARIES(Core_Algorithms_Legacy_Converter
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Algorithms_Base
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Core_Datatypes
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Core_Datatypes_Legacy_Field
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Core_Datatypes_Legacy_Nrrd
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#Core_Util
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#Core_Exceptions
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#Core_Thread
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#Core_Geom
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#Core_Geometry
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#Core_Persistent
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#Core_Basis
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#${M_LIBRARY}
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#${SCI_TEEM_LIBRARY}
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)
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IF(BUILD_SHARED_LIBS)
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ADD_DEFINITIONS(-DBUILD_Core_Algorithms_Legacy_Converter)
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ENDIF(BUILD_SHARED_LIBS)

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