[med-svn] [gadgetron] 03/09: Merge tag 'upstream/3.1.0'
Ghislain Vaillant
ghisvail-guest at moszumanska.debian.org
Fri Feb 20 20:30:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
ghisvail-guest pushed a commit to branch master
in repository gadgetron.
commit 12ce70fd09565413f69365799ba0d1ed4d976400
Merge: ce11919 ccc611d
Author: Ghislain Antony Vaillant <ghisvail at gmail.com>
Date: Fri Feb 20 20:15:03 2015 +0000
Merge tag 'upstream/3.1.0'
Upstream version 3.1.0
.gitignore | 3 +
CMakeLists.txt | 283 +-
README | 2 +-
apps/CMakeLists.txt | 9 +-
apps/clients/CMakeLists.txt | 14 +-
.../gadgetron_ismrmrd_client/CMakeLists.txt | 24 +
.../gadgetron_ismrmrd_client.cpp | 1279 +++
apps/clients/mriclient/BlobFileWriter.h | 91 -
apps/clients/mriclient/CMakeLists.txt | 52 -
apps/clients/mriclient/HDF5ImageWriter.h | 76 -
apps/clients/mriclient/ImageWriter.h | 113 -
apps/clients/mriclient/gt_alive.cpp | 61 -
apps/clients/mriclient/main.cpp | 230 -
apps/clients/utilities/CMakeLists.txt | 47 +
apps/clients/utilities/DependencyQueryReader.h | 100 +
apps/clients/utilities/gt_alive.cpp | 69 +
apps/clients/utilities/gt_query.cpp | 98 +
apps/clients/utilities/gtquery.xml | 33 +
apps/clients/{mriclient => utilities}/isalive.xml | 0
apps/clients/utilities/main.cpp | 275 +
apps/gadgetron/CMakeLists.txt | 101 +-
apps/gadgetron/Gadget.cpp | 38 +
apps/gadgetron/Gadget.h | 50 +-
apps/gadgetron/GadgetContainerMessage.h | 42 +-
apps/gadgetron/GadgetMessageInterface.h | 21 +-
apps/gadgetron/GadgetServerAcceptor.cpp | 5 +-
apps/gadgetron/GadgetServerAcceptor.h | 5 +
apps/gadgetron/GadgetStreamController.cpp | 307 +-
apps/gadgetron/GadgetStreamController.h | 19 +-
apps/gadgetron/GadgetronExport.h | 12 +-
apps/gadgetron/gadgetbase_export.h | 16 +
apps/gadgetron/gadgetron.xml.example | 7 +-
apps/gadgetron/gadgetron_config.in | 12 +
apps/gadgetron/gadgetron_info.cpp | 88 +
apps/gadgetron/gadgetron_paths.h | 76 +
apps/gadgetron/gadgetron_xml.cpp | 95 +
apps/gadgetron/gadgetron_xml.h | 122 +
apps/gadgetron/main.cpp | 246 +-
apps/gadgetron/pugiconfig.hpp | 72 +
apps/gadgetron/pugixml.cpp | 10639 +++++++++++++++++++
apps/gadgetron/pugixml.hpp | 1332 +++
apps/gadgetron/schema/gadgetron.xsd | 100 +-
.../templates/CMakeLists_GadgetLibraryExample.txt | 55 -
.../templates/gadgetronEXAMPLELIB_export.h | 21 -
apps/gadgetron/webapp/CMakeLists.txt | 20 +
apps/gadgetron/webapp/gadgetron_web.conf.in | 16 +
apps/gadgetron/webapp/gadgetron_web_app.cfg | 2 +-
apps/gadgetron/webapp/gadgetron_web_app.in | 8 +
apps/gadgetron/webapp/gadgetron_web_app.py | 8 +-
apps/gadgetron/webapp/gadgetron_web_ld.conf.in | 2 +
apps/gadgetron/webapp/main.cpp | 8 +
apps/standalone/CMakeLists.txt | 6 +
apps/standalone/cpu/CMakeLists.txt | 18 +-
apps/standalone/cpu/denoising/2d/CMakeLists.txt | 33 +-
apps/standalone/cpu/gtplus/CMakeLists.txt | 33 +-
.../cpu/gtplus/Matlab_gt_read_analyze.cpp | 261 +
.../cpu/gtplus/Matlab_gt_write_analyze.cpp | 247 +
apps/standalone/cpu/registration/2d/CMakeLists.txt | 28 +-
apps/standalone/cpu/registration/3d/CMakeLists.txt | 10 +-
apps/standalone/cpu/registration/CMakeLists.txt | 3 +
apps/standalone/gpu/CMakeLists.txt | 29 +-
apps/standalone/gpu/ct/CMakeLists.txt | 3 +
.../gpu/ct/xray/CBCT_forwards_projection.cpp | 252 +
.../standalone/gpu/ct/xray/CBCT_reconstruct_CG.cpp | 204 +
.../gpu/ct/xray/CBCT_reconstruct_FDK_3d.cpp | 143 +
.../gpu/ct/xray/CBCT_reconstruct_FDK_4d.cpp | 157 +
.../gpu/ct/xray/CBCT_reconstruct_NLCG.cpp | 194 +
.../standalone/gpu/ct/xray/CBCT_reconstruct_SB.cpp | 281 +
apps/standalone/gpu/ct/xray/CMakeLists.txt | 64 +
apps/standalone/gpu/deblurring/2d/CMakeLists.txt | 8 +-
apps/standalone/gpu/deblurring/3d/CMakeLists.txt | 8 +-
apps/standalone/gpu/denoising/2d/CMakeLists.txt | 4 +-
apps/standalone/gpu/mri/nfft/2d/CMakeLists.txt | 18 +-
apps/standalone/gpu/mri/nfft/2d/main_cg.cpp | 3 +
apps/standalone/gpu/mri/nfft/2d/main_nfft.cpp | 8 +-
apps/standalone/gpu/mri/nfft/2d/main_sb.cpp | 5 +
apps/standalone/gpu/mri/nfft/ms2d/CMakeLists.txt | 12 +-
apps/standalone/gpu/mri/nfft/ms2d/nfft_main.cpp | 2 +-
.../standalone/gpu/mri/nfft/ms2d/nffth_generic.cpp | 161 +
apps/standalone/gpu/mri/nfft/ms2d/nffth_main.cpp | 6 +-
.../gpu/mri/sense/noncartesian/CMakeLists.txt | 8 +-
.../gpu/mri/sense/noncartesian/generic_cg.cpp | 200 +
.../radial/2d_golden_ratio/CMakeLists.txt | 20 +-
.../radial/2d_golden_ratio/main_cg.cpp | 8 +-
.../radial/2d_golden_ratio/main_gpbb.cpp | 8 +-
.../radial/2d_golden_ratio/main_nlcg.cpp | 341 +
.../radial/2d_golden_ratio/main_sbc.cpp | 5 +-
.../radial/2d_golden_ratio_gui/CMakeLists.txt | 10 +-
.../radial/2d_golden_ratio_kt/CMakeLists.txt | 6 +-
.../mri/sense/noncartesian/radial/CMakeLists.txt | 2 +-
apps/standalone/gpu/registration/2d/CMakeLists.txt | 54 +-
apps/standalone/gpu/registration/3d/CMakeLists.txt | 12 +-
chroot/CMakeLists.txt | 76 +
chroot/README.rst | 35 +
chroot/chroot-manual.txt | 156 +
chroot/copy-cuda-lib.sh.in | 33 +
chroot/copy_file_and_dependencies | 25 +
chroot/create_chroot.sh | 147 +
chroot/enter-chroot-env.sh.in | 3 +
chroot/gadgetron-dependency-query.sh.in | 15 +
chroot/gadgetron_chroot.conf | 27 +
chroot/gadgetron_ismrmrd_client.sh.in | 16 +
chroot/generate_gadgetron_root | 45 +
chroot/get_dependencies_for_binary | 12 +
chroot/install_chroot_image.sh | 91 +
chroot/make_list_of_dependencies | 25 +
chroot/mount.sh | 35 +
chroot/run-gadgetron-dependency-query.sh | 31 +
chroot/run-gadgetron_ismrmrd_client.sh | 32 +
chroot/run-siemens_to_ismrmrd.sh | 31 +
chroot/run-webapp.sh.in | 11 +
chroot/siemens_to_ismrmrd.sh.in | 15 +
chroot/start-env.sh | 18 +
chroot/start-gadgetron-from-image.sh | 29 +
chroot/start-gadgetron.sh.in | 10 +
chroot/start-webapp.sh | 18 +
chroot/start.sh | 23 +
chroot/stop.sh | 26 +
chroot/umount_image.sh | 28 +
chroot/unique_lines_in_file | 14 +
chroot/upstart-instructions.txt | 10 +
cmake/CMakeLists.txt | 18 +-
cmake/FindACE.cmake | 4 +-
cmake/FindArmadillo.cmake | 100 +
cmake/FindCUDA/cuda_compute_capability.c | 42 +
cmake/FindCUDA_advanced.cmake | 38 +
cmake/FindCULA.cmake | 63 -
cmake/FindFFTW3.cmake | 41 +-
cmake/FindIsmrmrd.cmake | 29 +-
cmake/FindMKL.cmake | 35 +-
cmake/FindXSD.cmake | 68 -
cmake/FindXalanC.cmake | 35 -
cmake/FindXercesC.cmake | 37 -
cmake/InstallLinuxDependencies.cmake | 24 +
cmake/InstallWinDependencies.cmake | 137 +
cmake/InstallWinGadgetron.bat | 6 +
cmake/cpack_options.cmake.in | 41 +
cmake/cpack_options_dependency.cmake.in | 37 +
cmake/cpack_options_web.cmake.in | 38 +
cmake/debian/postinst | 18 +
cmake/debian/prerm | 13 +
cmake/debian_web/postinst | 7 +
cmake/debian_web/prerm | 7 +
cmake/gadgetron_cpack.cmake | 33 +
cmake/gadgetron_web_cpack.cmake | 32 +
doc/CMakeLists.txt | 24 -
doc/doxygen/Doxyfile.in | 2 +-
doc/manual/CMakeLists.txt | 36 -
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doc/manual/figs/simple2dft.png | Bin 56594 -> 0 bytes
doc/manual/figs/simple2dft.svg | 355 -
doc/manual/gadgetron_manual.xml | 6472 -----------
gadgets/CMakeLists.txt | 53 +-
gadgets/cartesian/CMakeLists.txt | 24 +-
gadgets/cartesian/CartesianToGenericGadget.cpp | 36 +-
gadgets/cartesian/CartesianToGenericGadget.h | 3 +-
gadgets/dicom/CMakeLists.txt | 105 +-
gadgets/dicom/DicomFinishAttribGadget.cpp | 897 ++
gadgets/dicom/DicomFinishAttribGadget.h | 76 +
gadgets/dicom/DicomFinishGadget.cpp | 457 +-
gadgets/dicom/DicomFinishGadget.h | 11 +-
gadgets/dicom/DicomImageWriter.cpp | 162 +-
gadgets/dicom/DicomImageWriter.h | 10 +-
gadgets/dicom/dicom.xml | 61 +-
gadgets/epi/CMakeLists.txt | 49 +
gadgets/epi/CutXGadget.cpp | 91 +
gadgets/epi/CutXGadget.h | 33 +
gadgets/epi/EPICorrGadget.cpp | 197 +
gadgets/epi/EPICorrGadget.h | 48 +
gadgets/epi/EPIReconXGadget.cpp | 133 +
gadgets/epi/EPIReconXGadget.h | 38 +
gadgets/epi/FFTXGadget.cpp | 27 +
gadgets/epi/FFTXGadget.h | 25 +
gadgets/epi/epi.xml | 138 +
gadgets/epi/epi_gtplus_grappa.xml | 525 +
gadgets/epi/gadgetron_epi_export.h | 14 +
gadgets/grappa/CMakeLists.txt | 54 +-
gadgets/grappa/GrappaCalibrationBuffer.cpp | 17 +-
gadgets/grappa/GrappaCalibrationBuffer.h | 5 +-
gadgets/grappa/GrappaGadget.cpp | 129 +-
gadgets/grappa/GrappaGadget.h | 8 +-
gadgets/grappa/GrappaUnmixingGadget.cpp | 3 +
gadgets/grappa/GrappaUnmixingGadget.h | 2 +-
gadgets/grappa/GrappaWeightsCalculator.cpp | 16 +-
gadgets/grappa/config/CMakeLists.txt | 5 +-
gadgets/gtPlus/CMakeLists.txt | 170 +-
gadgets/gtPlus/GadgetCloudJobMessageReadWrite.h | 4 +-
gadgets/gtPlus/GadgetMRIHeadersExt.h | 231 -
gadgets/gtPlus/GadgetronMrReconCommon.h | 90 -
gadgets/gtPlus/GtPlusAccumulatorGadget.cpp | 1168 --
gadgets/gtPlus/GtPlusAccumulatorGadget.h | 198 -
gadgets/gtPlus/GtPlusAccumulatorIRT2DGadget.cpp | 615 --
gadgets/gtPlus/GtPlusAccumulatorIRT2DGadget.h | 42 -
.../gtPlus/GtPlusAccumulatorImageTriggerGadget.cpp | 746 ++
.../gtPlus/GtPlusAccumulatorImageTriggerGadget.h | 150 +
gadgets/gtPlus/GtPlusAccumulatorPerfAIFGadget.cpp | 55 -
gadgets/gtPlus/GtPlusAccumulatorPerfAIFGadget.h | 32 -
gadgets/gtPlus/GtPlusAccumulatorSLCGadget.cpp | 403 -
gadgets/gtPlus/GtPlusAccumulatorSLCGadget.h | 40 -
.../GtPlusAccumulatorWorkOrderTriggerGadget.cpp | 786 +-
.../GtPlusAccumulatorWorkOrderTriggerGadget.h | 63 +-
gadgets/gtPlus/GtPlusGadgetImageArray.cpp | 237 +-
gadgets/gtPlus/GtPlusGadgetImageArray.h | 24 +-
gadgets/gtPlus/GtPlusGadgetOpenMP.cpp | 32 +-
gadgets/gtPlus/GtPlusGadgetOpenMP.h | 5 +-
gadgets/gtPlus/GtPlusImageReconGadget.cpp | 711 ++
gadgets/gtPlus/GtPlusImageReconGadget.h | 135 +
gadgets/gtPlus/GtPlusRecon2DTCloudPackage.h | 98 +-
gadgets/gtPlus/GtPlusRecon2DTGadget.cpp | 155 +-
gadgets/gtPlus/GtPlusRecon2DTGadgetCloud.cpp | 284 +-
gadgets/gtPlus/GtPlusRecon2DTGadgetCloud.h | 4 +-
gadgets/gtPlus/GtPlusRecon3DTGadget.cpp | 95 +-
gadgets/gtPlus/GtPlusReconGadget.cpp | 2772 +++--
gadgets/gtPlus/GtPlusReconGadget.h | 66 +-
gadgets/gtPlus/GtPlusReconGadgetUtil.cpp | 710 ++
gadgets/gtPlus/GtPlusReconGadgetUtil.h | 76 +
gadgets/gtPlus/GtPlusReconJob2DTGadget.cpp | 30 +-
gadgets/gtPlus/GtPlusReconJob2DTGadget.h | 17 +-
gadgets/gtPlus/GtPlusReconJob2DTGadgetCloud.cpp | 130 +-
gadgets/gtPlus/GtPlusReconJob2DTGadgetCloud.h | 17 +-
gadgets/gtPlus/GtPlusReconJob3DTGadget.cpp | 32 +-
gadgets/gtPlus/GtPlusReconJob3DTGadget.h | 17 +-
gadgets/gtPlus/config/GT_2DT_Cartesian.xml | 850 ++
.../gtPlus/config/GT_2DT_Cartesian_CloudNode.xml | 77 +
gadgets/gtPlus/config/GT_2DT_Cartesian_Dicom.xml | 857 ++
...GT_2DT_Cartesian_DualLayer_Gateway_L1SPIRIT.xml | 851 ++
.../GT_2DT_Cartesian_DualLayer_Gateway_SPIRIT.xml | 845 ++
.../GT_2DT_Cartesian_FirstLayer_CloudNode.xml | 279 +
gadgets/gtPlus/config/GT_2DT_Cartesian_GFactor.xml | 872 ++
.../config/GT_2DT_Cartesian_ImageTrigger_Dicom.xml | 879 ++
.../gtPlus/config/GT_2DT_Cartesian_L1SPIRIT.xml | 836 ++
...GT_2DT_Cartesian_PseudoReplica_SNRUnitRecon.xml | 810 ++
gadgets/gtPlus/config/GT_2DT_Cartesian_SPIRIT.xml | 836 ++
.../GT_2DT_Cartesian_SingleLayer_CloudNode.xml | 279 +
gadgets/gtPlus/config/GT_2DT_FatWater.xml | 696 ++
gadgets/gtPlus/config/GT_2DT_HASTE.xml | 815 ++
gadgets/gtPlus/config/GT_2DT_HASTE_MOCO_AVE.xml | 1085 ++
gadgets/gtPlus/config/GT_2DT_LGE.xml | 701 ++
gadgets/gtPlus/config/GT_2DT_MOLLI.xml | 696 ++
gadgets/gtPlus/config/GT_2DT_MOLLI_Offline.xml | 699 ++
gadgets/gtPlus/config/GT_2DT_Perfusion.xml | 702 ++
...T_2DT_PseudoReplica_SNRUnitRecon_DataExport.xml | 74 +
.../config/GT_2DT_RTCine_L1SPIRIT_PhysioInterp.xml | 866 ++
...ine_L1SPIRIT_PhysioInterp_DualLayer_Gateway.xml | 875 ++
gadgets/gtPlus/config/GT_2DT_RealTimeCine.xml | 783 ++
gadgets/gtPlus/config/GT_2DT_RealTimeFlow.xml | 765 ++
gadgets/gtPlus/config/GT_2DT_T2W.xml | 701 ++
gadgets/gtPlus/config/GT_3DT_Cartesian.xml | 849 ++
.../gtPlus/config/GT_3DT_Cartesian_CloudNode.xml | 82 +
gadgets/gtPlus/config/GT_3DT_Cartesian_GFactor.xml | 735 ++
.../gtPlus/config/GT_3DT_Cartesian_L1SPIRIT.xml | 853 ++
gadgets/gtPlus/config/GT_3DT_Cartesian_SPIRIT.xml | 844 ++
.../GT_3DT_Cartesian_SingleLayer_L1SPIRIT.xml | 853 ++
gadgets/gtPlus/config/gtCloud/myCloud_2DT.txt | 8 +
.../config/gtCloud/myCloud_2DT_DualLayer.txt | 8 +
.../gtCloud/myCloud_2DT_DualLayer_FirstLayer.txt | 8 +
gadgets/gtPlus/config/gtCloud/myCloud_3DT.txt | 12 +
gadgets/interventional_mri/CMakeLists.txt | 54 +
.../DeviceChannelSplitterGadget.cpp | 95 +
.../DeviceChannelSplitterGadget.h | 45 +
.../gadgetron_interventional_mri_export.h | 14 +
gadgets/interventional_mri/grappa_device.xml | 147 +
gadgets/matlab/BaseGadget.m | 4 +-
gadgets/matlab/CMakeLists.txt | 19 +-
gadgets/matlab/MatlabGadget.cpp | 20 +-
gadgets/matlab/MatlabGadget.h | 11 +-
gadgets/matlab/accumulate_and_recon.m | 18 +-
gadgets/matlab/scale.m | 1 -
gadgets/moco/CMakeLists.txt | 48 +-
gadgets/moco/RegistrationAveragingGadget.h | 2 +-
gadgets/moco/RegistrationScatteringGadget.h | 2 +-
gadgets/moco/config/CMakeLists.txt | 4 +-
gadgets/moco/config/cpureg_cartesian_averaging.xml | 4 +-
gadgets/moco/config/gpureg_cartesian_averaging.xml | 4 +-
gadgets/moco/cpuRegistrationAveragingGadget.h | 5 +-
gadgets/moco/gpuRegistrationAveragingGadget.h | 3 +-
gadgets/moco/gpuRegistrationScatteringGadget.h | 2 -
gadgets/mri_core/AccumulatorGadget.cpp | 67 +-
gadgets/mri_core/AccumulatorGadget.h | 2 +-
.../AcquisitionAccumulateTriggerGadget.cpp | 403 +
.../mri_core/AcquisitionAccumulateTriggerGadget.h | 47 +
gadgets/mri_core/AcquisitionFinishGadget.h | 2 +-
gadgets/mri_core/AcquisitionPassthroughGadget.h | 2 +-
gadgets/mri_core/AsymmetricEchoAdjustROGadget.cpp | 142 +
gadgets/mri_core/AsymmetricEchoAdjustROGadget.h | 32 +
gadgets/mri_core/AutoScaleGadget.cpp | 6 +-
gadgets/mri_core/AutoScaleGadget.h | 2 +-
gadgets/mri_core/BucketToBufferGadget.cpp | 628 ++
gadgets/mri_core/BucketToBufferGadget.h | 52 +
gadgets/mri_core/CMakeLists.txt | 212 +-
gadgets/mri_core/CoilReductionGadget.cpp | 92 +-
gadgets/mri_core/CoilReductionGadget.h | 2 +-
gadgets/mri_core/CombineGadget.cpp | 69 +
gadgets/mri_core/CombineGadget.h | 27 +
gadgets/mri_core/ComplexToFloatAttribGadget.cpp | 88 +
gadgets/mri_core/ComplexToFloatAttribGadget.h | 34 +
gadgets/mri_core/CplxDumpGadget.cpp | 2 +-
gadgets/mri_core/CplxDumpGadget.h | 3 +-
gadgets/mri_core/CropAndCombineGadget.cpp | 18 +-
gadgets/mri_core/CropAndCombineGadget.h | 2 +-
gadgets/mri_core/DependencyQueryGadget.cpp | 200 +
gadgets/mri_core/DependencyQueryGadget.h | 53 +
gadgets/mri_core/DependencyQueryWriter.cpp | 76 +
gadgets/mri_core/DependencyQueryWriter.h | 28 +
gadgets/mri_core/ExtractGadget.cpp | 10 +-
gadgets/mri_core/ExtractGadget.h | 2 +-
gadgets/mri_core/FFTGadget.cpp | 111 +-
gadgets/mri_core/FFTGadget.h | 14 +-
gadgets/mri_core/FloatToUShortAttribGadget.cpp | 130 +
gadgets/mri_core/FloatToUShortAttribGadget.h | 43 +
gadgets/mri_core/FloatToUShortGadget.cpp | 12 +-
gadgets/mri_core/FloatToUShortGadget.h | 2 +-
gadgets/mri_core/FlowPhaseSubtractionGadget.cpp | 56 +-
gadgets/mri_core/FlowPhaseSubtractionGadget.h | 2 +-
gadgets/mri_core/GadgetIsmrmrdReadWrite.h | 41 +-
gadgets/mri_core/GadgetMRIHeaders.h | 37 +-
gadgets/mri_core/ImageFinishAttribGadget.cpp | 53 +
gadgets/mri_core/ImageFinishAttribGadget.h | 49 +
gadgets/mri_core/ImageFinishGadget.cpp | 6 +-
gadgets/mri_core/ImageFinishGadget.h | 2 +-
gadgets/mri_core/ImageWriterGadget.h | 2 +-
gadgets/mri_core/IsmrmrdDumpGadget.cpp | 250 +-
gadgets/mri_core/IsmrmrdDumpGadget.h | 6 +-
gadgets/mri_core/MRIImageAttribWriter.cpp | 154 +
gadgets/mri_core/MRIImageAttribWriter.h | 43 +
gadgets/mri_core/MRIImageWriter.cpp | 114 +-
gadgets/mri_core/MRIImageWriter.h | 42 +-
gadgets/mri_core/MaxwellCorrectionGadget.cpp | 246 +-
gadgets/mri_core/MaxwellCorrectionGadget.h | 2 +-
gadgets/mri_core/NoiseAdjustGadget.cpp | 709 +-
gadgets/mri_core/NoiseAdjustGadget.h | 47 +-
gadgets/mri_core/NoiseAdjustGadget_unoptimized.cpp | 24 +-
gadgets/mri_core/NoiseAdjustGadget_unoptimized.h | 2 +-
gadgets/mri_core/PCACoilGadget.cpp | 133 +-
gadgets/mri_core/PCACoilGadget.h | 7 +-
gadgets/mri_core/PartialFourierAdjustROGadget.cpp | 37 +-
gadgets/mri_core/PartialFourierAdjustROGadget.h | 4 +-
gadgets/mri_core/PhysioInterpolationGadget.cpp | 607 +-
gadgets/mri_core/PhysioInterpolationGadget.h | 40 +-
gadgets/mri_core/RemoveROOversamplingGadget.cpp | 201 +-
gadgets/mri_core/RemoveROOversamplingGadget.h | 40 +-
gadgets/mri_core/WhiteNoiseInjectorGadget.cpp | 197 +
gadgets/mri_core/WhiteNoiseInjectorGadget.h | 62 +
gadgets/mri_core/default.xml | 52 +-
.../mri_core/default_measurement_dependencies.xml | 40 +
gadgets/mri_core/default_optimized.xml | 56 +-
gadgets/mri_core/default_short.xml | 48 +-
gadgets/octave/CMakeLists.txt | 43 -
.../octave/GadgetronReturnIsmrmrdAcquisition.cpp | 136 -
gadgets/octave/GadgetronReturnIsmrmrdImage.cpp | 108 -
gadgets/octave/OctaveCommunicator.cpp | 68 -
gadgets/octave/OctaveCommunicator.h | 40 -
gadgets/octave/OctaveGadget.cpp | 232 -
gadgets/octave/OctaveGadget.h | 95 -
gadgets/octave/XMLGetXPath.cpp | 35 -
gadgets/octave/gadgetron_octave_export.h | 23 -
.../octave/gadgetron_octavecommunicator_export.h | 23 -
gadgets/octave/octave.xml | 84 -
gadgets/octave/octave/accumulator.m | 29 -
gadgets/octave/octave/configure_accumulator.m | 18 -
gadgets/octave/octave/configure_downsample_2x.m | 3 -
gadgets/octave/octave/downsample_2x.m | 11 -
.../octave/octave/gadget_reference_accumulator.m | 7 -
.../octave/octave/gadget_reference_downsample_2x.m | 7 -
.../octave/ismrm_transform_image_to_kspace.m | 34 -
.../octave/ismrm_transform_kspace_to_image.m | 35 -
gadgets/octave/octave/my_config_function.m | 3 -
gadgets/octave/octave/my_gadget_reference.m | 7 -
gadgets/octave/octave/my_recon_function.m | 8 -
gadgets/octave/pugiconfig.hpp | 69 -
gadgets/octave/pugixml.cpp | 10250 ------------------
gadgets/octave/pugixml.hpp | 1265 ---
gadgets/pmri/CMakeLists.txt | 62 +
gadgets/pmri/GenericReconJob.h | 27 +
gadgets/pmri/config/CMakeLists.txt | 16 +
.../pmri/config/generic_gpu_ktsense_singleshot.xml | 115 +
gadgets/pmri/config/generic_gpusense_cg.xml | 113 +
.../pmri/config/generic_gpusense_cg_singleshot.xml | 115 +
.../config/generic_gpusense_nlcg_singleshot.xml | 116 +
.../pmri/config/generic_gpusense_sb_singleshot.xml | 119 +
gadgets/pmri/gadgetron_gpupmri_export.h | 14 +
gadgets/pmri/gpuCgKtSenseGadget.cpp | 375 +
gadgets/pmri/gpuCgKtSenseGadget.h | 71 +
gadgets/pmri/gpuCgSenseGadget.cpp | 347 +
gadgets/pmri/gpuCgSenseGadget.h | 71 +
gadgets/pmri/gpuCgSpiritGadget.cpp | 357 +
gadgets/pmri/gpuCgSpiritGadget.h | 75 +
gadgets/pmri/gpuGenericSensePrepGadget.cpp | 941 ++
gadgets/pmri/gpuGenericSensePrepGadget.h | 127 +
gadgets/pmri/gpuNlcgSenseGadget.cpp | 387 +
gadgets/pmri/gpuNlcgSenseGadget.h | 82 +
gadgets/pmri/gpuSbSenseGadget.cpp | 435 +
gadgets/pmri/gpuSbSenseGadget.h | 85 +
gadgets/python/CMakeLists.txt | 23 +-
gadgets/python/GadgetReference.cpp | 2 +-
gadgets/python/GadgetReference.h | 2 +-
gadgets/python/GadgetronPythonMRI.cpp | 22 +-
gadgets/python/PythonCommunicator.cpp | 13 +-
gadgets/python/PythonCommunicator.h | 3 +
gadgets/python/PythonGadget.h | 15 +-
gadgets/radial/CMakeLists.txt | 59 +-
gadgets/radial/RadialPhaseCorrectionGadget.cpp | 314 +
gadgets/radial/RadialPhaseCorrectionGadget.h | 44 +
gadgets/radial/config/CMakeLists.txt | 10 +-
.../config/fixed_radial_mode0_gpu_ktsense.xml | 6 +-
.../config/fixed_radial_mode0_gpusense_cg.xml | 6 +-
.../fixed_radial_mode0_gpusense_cg_unoptimized.xml | 6 +-
.../config/fixed_radial_mode0_gpusense_sb.xml | 6 +-
.../fixed_radial_mode0_gpusense_sb_unoptimized.xml | 6 +-
.../radial/config/fixed_radial_mode0_realtime.xml | 6 +-
.../config/fixed_radial_mode1_gpu_ktsense.xml | 6 +-
.../config/fixed_radial_mode1_gpusense_cg.xml | 6 +-
.../fixed_radial_mode1_gpusense_cg_unoptimized.xml | 6 +-
.../config/fixed_radial_mode1_gpusense_sb.xml | 6 +-
.../fixed_radial_mode1_gpusense_sb_unoptimized.xml | 6 +-
.../radial/config/fixed_radial_mode1_realtime.xml | 6 +-
.../config/golden_radial_mode2_gpu_ktsense.xml | 6 +-
.../config/golden_radial_mode2_gpusense_cg.xml | 6 +-
...golden_radial_mode2_gpusense_cg_unoptimized.xml | 6 +-
.../config/golden_radial_mode2_gpusense_nlcg.xml | 158 +
...lden_radial_mode2_gpusense_nlcg_unoptimized.xml | 146 +
.../config/golden_radial_mode2_gpusense_sb.xml | 6 +-
...golden_radial_mode2_gpusense_sb_unoptimized.xml | 6 +-
.../radial/config/golden_radial_mode2_realtime.xml | 6 +-
.../config/golden_radial_mode3_gpusense_cg.xml | 155 +
.../config/golden_radial_mode3_gpusense_sb.xml | 6 +-
gadgets/radial/config/spirit.xml | 106 +
gadgets/radial/gpuRadialPrepGadget.cpp | 952 ++
gadgets/radial/gpuRadialPrepGadget.h | 207 +
gadgets/radial/gpuRadialSensePrepGadget.cpp | 1017 +-
gadgets/radial/gpuRadialSensePrepGadget.h | 190 +-
gadgets/radial/gpuRadialSpiritPrepGadget.cpp | 98 +
gadgets/radial/gpuRadialSpiritPrepGadget.h | 33 +
gadgets/radial/gpuRetroGatedSensePrepGadget.cpp | 890 ++
gadgets/radial/gpuRetroGatedSensePrepGadget.h | 133 +
gadgets/sense/CMakeLists.txt | 43 -
gadgets/sense/SenseJob.h | 27 -
gadgets/sense/config/CMakeLists.txt | 15 -
.../config/generic_gpu_ktsense_singleshot.xml | 115 -
gadgets/sense/config/generic_gpusense_cg.xml | 113 -
.../config/generic_gpusense_cg_singleshot.xml | 115 -
.../config/generic_gpusense_sb_singleshot.xml | 119 -
gadgets/sense/gadgetron_gpusense_export.h | 14 -
gadgets/sense/gpuCgKtSenseGadget.cpp | 370 -
gadgets/sense/gpuCgKtSenseGadget.h | 71 -
gadgets/sense/gpuCgSenseGadget.cpp | 321 -
gadgets/sense/gpuCgSenseGadget.h | 71 -
gadgets/sense/gpuGenericSensePrepGadget.cpp | 948 --
gadgets/sense/gpuGenericSensePrepGadget.h | 127 -
gadgets/sense/gpuSbSenseGadget.cpp | 426 -
gadgets/sense/gpuSbSenseGadget.h | 85 -
gadgets/spiral/CMakeLists.txt | 27 +-
gadgets/spiral/SpiralToGenericGadget.cpp | 173 +-
gadgets/spiral/SpiralToGenericGadget.h | 2 +-
gadgets/spiral/config/CMakeLists.txt | 4 +-
.../config/spiral_flow_generic_gpusense_cg.xml | 6 +-
.../config/spiral_flow_generic_gpusense_sb.xml | 6 +-
gadgets/spiral/config/spiral_flow_gpusense_cg.xml | 4 +-
.../spiral/config/spiral_flow_gpusense_cg_ecg.xml | 4 +-
.../config/spiral_flow_gpusense_cg_unoptimized.xml | 4 +-
gadgets/spiral/config/spiral_flow_gpusense_sb.xml | 4 +-
.../config/spiral_flow_gpusense_sb_unoptimized.xml | 4 +-
gadgets/spiral/config/spiral_interactive.xml | 4 +-
gadgets/spiral/gpuSpiralSensePrepGadget.cpp | 123 +-
gadgets/spiral/gpuSpiralSensePrepGadget.h | 2 +-
gadgets/util/CMakeLists.txt | 27 +
gadgets/util/ParameterRelayGadget.cpp | 20 +
gadgets/util/ParameterRelayGadget.h | 18 +
gadgets/util/gadgetron_util_gadgets_export.h | 14 +
test/CMakeLists.txt | 31 +-
test/hoNDArray_blas_test.cpp | 2 +-
test/hoNDArray_elemwise_test.cpp | 239 +
test/hoNDArray_operators_test.cpp | 1 -
test/integration/.gitignore | 8 +
test/integration/CMakeLists.txt | 47 +
test/integration/cases/always/simple_gre.cfg | 24 +
test/integration/cases/always/simple_gre_3d.cfg | 26 +
.../cases/gpu/gpu_fixed_radial_mode1_cg.cfg | 24 +
.../cases/gpu/gpu_fixed_radial_mode1_ktsense.cfg | 24 +
.../cases/gpu/gpu_fixed_radial_mode1_realtime.cfg | 24 +
.../cases/gpu/gpu_golden_radial_mode2_cg.cfg | 24 +
.../cases/gpu/gpu_golden_radial_mode2_ktsense.cfg | 24 +
.../cases/gpu/gpu_golden_radial_mode2_realtime.cfg | 24 +
test/integration/cases/gpu/gpu_grappa_simple.cfg | 25 +
test/integration/cases/gpu/gpu_spiral.cfg | 24 +
test/integration/cases/gpu/gpu_spiral_sb.cfg | 24 +
.../linux_mac_only/gpu_golden_radial_mode2_sb.cfg | 24 +
test/integration/cases/mkl/gtplus_3D_head.cfg | 24 +
test/integration/cases/mkl/gtplus_FatWater.cfg | 25 +
test/integration/cases/mkl/gtplus_FetalHASTE.cfg | 24 +
test/integration/cases/mkl/gtplus_LGE.cfg | 24 +
test/integration/cases/mkl/gtplus_Perfusion.cfg | 24 +
test/integration/cases/mkl/gtplus_T2W.cfg | 24 +
test/integration/cases/mkl/gtplus_localizer.cfg | 24 +
test/integration/cases/mkl/gtplus_molli.cfg | 24 +
.../cases/mkl/gtplus_real_time_cine.cfg | 24 +
.../cases/mkl/gtplus_real_time_cine_9slices.cfg | 24 +
test/integration/cases/mkl/gtplus_sasha.cfg | 24 +
.../mkl/gtplus_snr_unit_recon_builtin_noise.cfg | 24 +
.../cases/mkl/gtplus_snr_unit_recon_ipat4.cfg | 24 +
.../mkl/gtplus_snr_unit_recon_prospective_cine.cfg | 24 +
.../mkl/gtplus_snr_unit_recon_spat2_asym_pf.cfg | 24 +
.../cases/mkl/gtplus_snr_unit_recon_spat3.cfg | 24 +
.../cases/mkl/gtplus_snr_unit_recon_tpat3.cfg | 24 +
.../integration/cases/python/simple_gre_python.cfg | 24 +
test/integration/data.txt | 62 +
test/integration/get_data.py | 68 +
test/integration/run_all_tests.py | 71 +
test/integration/run_gadgetron_test.py | 328 +
test/tests.cpp | 1 +
test/unit/run_unit_tests.py | 62 +
toolboxes/CMakeLists.txt | 44 +-
toolboxes/cloudbus/CMakeLists.txt | 31 +
toolboxes/cloudbus/CloudBus.cpp | 220 +
toolboxes/cloudbus/CloudBus.h | 117 +
toolboxes/cloudbus/cloudbus_export.h | 14 +
toolboxes/cloudbus/cloudbus_main.cpp | 35 +
toolboxes/core/CMakeLists.txt | 6 +-
toolboxes/core/GadgetronCommon.h | 39 +-
toolboxes/core/GadgetronTimer.h | 5 +-
toolboxes/core/Gadgetron_enable_types.h | 12 +
toolboxes/core/NDArray.h | 264 +-
toolboxes/core/SerializableObject.h | 27 -
toolboxes/core/complext.h | 10 +-
toolboxes/core/cpu/CMakeLists.txt | 143 +-
toolboxes/core/cpu/algorithm/hoNDBSpline.h | 191 +
toolboxes/core/cpu/algorithm/hoNDBSpline.hxx | 2133 ++++
toolboxes/core/cpu/arma_math/CMakeLists.txt | 48 -
toolboxes/core/cpu/arma_math/cpucore_math_export.h | 22 -
toolboxes/core/cpu/arma_math/hoArmadillo.h | 84 -
toolboxes/core/cpu/arma_math/hoNDArray_blas.cpp | 648 --
toolboxes/core/cpu/arma_math/hoNDArray_blas.h | 181 -
.../core/cpu/arma_math/hoNDArray_elemwise.cpp | 4810 ---------
toolboxes/core/cpu/arma_math/hoNDArray_elemwise.h | 400 -
toolboxes/core/cpu/arma_math/hoNDArray_math.h | 6 -
.../core/cpu/arma_math/hoNDArray_operators.cpp | 457 -
toolboxes/core/cpu/arma_math/hoNDArray_operators.h | 239 -
.../core/cpu/arma_math/hoNDArray_reductions.cpp | 41 -
.../core/cpu/arma_math/hoNDArray_reductions.h | 12 -
toolboxes/core/cpu/dummy.cpp | 18 +
toolboxes/core/cpu/gadgetronmath.h | 26 +
toolboxes/core/cpu/ho2DArray.h | 34 +-
toolboxes/core/cpu/ho3DArray.h | 2 +-
toolboxes/core/cpu/ho4DArray.h | 2 +-
toolboxes/core/cpu/ho5DArray.h | 2 +-
toolboxes/core/cpu/ho5DArray.hxx | 2 +-
toolboxes/core/cpu/ho6DArray.h | 2 +-
toolboxes/core/cpu/ho6DArray.hxx | 2 +-
toolboxes/core/cpu/ho7DArray.h | 2 +-
toolboxes/core/cpu/ho7DArray.hxx | 2 +-
toolboxes/core/cpu/hoMatrix.cpp | 1327 +--
toolboxes/core/cpu/hoMatrix.h | 61 +-
toolboxes/core/cpu/hoMatrix.hxx | 901 +-
toolboxes/core/cpu/hoNDArray.h | 34 +-
toolboxes/core/cpu/hoNDArray.hxx | 1915 ++--
toolboxes/core/cpu/hoNDArray_utils.h | 208 +-
toolboxes/core/cpu/hoNDBoundaryHandler.h | 276 +
toolboxes/core/cpu/hoNDBoundaryHandler.hxx | 470 +
toolboxes/core/cpu/hoNDFFT.cpp | 1713 ---
toolboxes/core/cpu/hoNDFFT.h | 222 -
toolboxes/core/cpu/hoNDInterpolator.h | 307 +
toolboxes/core/cpu/hoNDInterpolatorBSpline.hxx | 339 +
toolboxes/core/cpu/hoNDInterpolatorLinear.hxx | 874 ++
.../core/cpu/hoNDInterpolatorNearestNeighbor.hxx | 94 +
toolboxes/core/cpu/hoNDObjectArray.h | 200 +
toolboxes/core/cpu/hoNDPoint.h | 338 +
toolboxes/core/cpu/hostutils/CMakeLists.txt | 10 +-
toolboxes/core/cpu/image/hoNDImage.h | 517 +
toolboxes/core/cpu/image/hoNDImage.hxx | 2980 ++++++
toolboxes/core/cpu/image/hoNDImageAttrib.h | 329 +
toolboxes/core/cpu/image/hoNDImageContainer2D.h | 1223 +++
toolboxes/core/cpu/math/CMakeLists.txt | 76 +
toolboxes/core/cpu/math/cpucore_math_export.h | 22 +
toolboxes/core/cpu/math/hoArmadillo.h | 89 +
toolboxes/core/cpu/math/hoNDArray_elemwise.cpp | 3158 ++++++
toolboxes/core/cpu/math/hoNDArray_elemwise.h | 641 ++
toolboxes/core/cpu/math/hoNDArray_linalg.cpp | 1949 ++++
toolboxes/core/cpu/math/hoNDArray_linalg.h | 90 +
toolboxes/core/cpu/math/hoNDArray_math.h | 4 +
toolboxes/core/cpu/math/hoNDArray_math_util.cpp | 2178 ++++
toolboxes/core/cpu/math/hoNDArray_math_util.h | 27 +
toolboxes/core/cpu/math/hoNDArray_reductions.cpp | 933 ++
toolboxes/core/cpu/math/hoNDArray_reductions.h | 203 +
toolboxes/core/cpu/math/hoNDImage_util.cpp | 877 ++
toolboxes/core/cpu/math/hoNDImage_util.h | 76 +
toolboxes/core/cpu/math/hoNDImage_util.hxx | 1020 ++
.../core/cpu/math/hoNDImage_util_instantiate.hxx | 15 +
toolboxes/core/gpu/CMakeLists.txt | 23 +-
toolboxes/core/gpu/CUBLASContextProvider.cpp | 16 +-
toolboxes/core/gpu/GPUTimer.h | 88 +-
toolboxes/core/gpu/cuNDArray.h | 1114 +-
toolboxes/core/gpu/cuNDArray_blas.h | 1 +
toolboxes/core/gpu/cuNDArray_elemwise.cu | 46 +
toolboxes/core/gpu/cuNDArray_elemwise.h | 16 +-
toolboxes/core/gpu/cuNDArray_fileio.h | 9 +
toolboxes/core/gpu/cuNDArray_math.h | 1 +
toolboxes/core/gpu/cuNDArray_operators.cu | 34 +-
toolboxes/core/gpu/cuNDArray_operators.h | 33 +-
toolboxes/core/gpu/cuNDArray_utils.cu | 20 +-
toolboxes/core/gpu/cuNDArray_utils.h | 170 +-
toolboxes/core/gpu/cuNDFFT.cpp | 156 -
toolboxes/core/gpu/cuNDFFT.h | 49 -
toolboxes/core/gpu/hoCuNDArray_math.h | 1 -
toolboxes/core/gpu/hoCuNDArray_operators.h | 9 -
toolboxes/core/gpu/radial_utilities.cu | 8 +-
toolboxes/core/vector_td.h | 10 +-
toolboxes/core/vector_td_utilities.h | 5 +-
toolboxes/ct/CMakeLists.txt | 3 +
toolboxes/ct/xray/CMakeLists.txt | 3 +
toolboxes/ct/xray/gpu/CBCT_acquisition.h | 298 +
toolboxes/ct/xray/gpu/CBCT_binning.h | 166 +
toolboxes/ct/xray/gpu/CMakeLists.txt | 49 +
toolboxes/ct/xray/gpu/conebeam_projection.cu | 1151 ++
toolboxes/ct/xray/gpu/conebeam_projection.h | 76 +
toolboxes/ct/xray/gpu/float3x3.h | 66 +
toolboxes/ct/xray/gpu/gpuxray_export.h | 19 +
.../ct/xray/gpu/hoCuConebeamProjectionOperator.cpp | 261 +
.../ct/xray/gpu/hoCuConebeamProjectionOperator.h | 150 +
toolboxes/fft/CMakeLists.txt | 11 +
toolboxes/fft/cpu/CMakeLists.txt | 45 +
toolboxes/fft/cpu/cpufft_export.h | 22 +
toolboxes/fft/cpu/hoNDFFT.cpp | 1693 +++
toolboxes/fft/cpu/hoNDFFT.h | 245 +
toolboxes/fft/gpu/CMakeLists.txt | 33 +
toolboxes/fft/gpu/cuNDFFT.cpp | 157 +
toolboxes/fft/gpu/cuNDFFT.h | 44 +
toolboxes/fft/gpu/gpufft_export.h | 18 +
toolboxes/gadgettools/CMakeLists.txt | 93 +-
toolboxes/gadgettools/GadgetCloudController.h | 126 +-
toolboxes/gadgettools/GadgetImageMessageReader.h | 71 -
toolboxes/gadgettools/GadgetServerAcceptor.cpp | 58 -
toolboxes/gadgettools/GadgetServerAcceptor.h | 27 -
toolboxes/gadgettools/GadgetStreamController.cpp | 459 -
toolboxes/gadgettools/GadgetStreamController.h | 559 -
toolboxes/gadgettools/GadgetronCloudConnector.h | 22 +-
toolboxes/gadgettools/GadgetronConnector.cpp | 17 +-
toolboxes/gadgettools/GadgetronConnector.h | 23 +-
toolboxes/gadgettools/GadgetronOSUtil.cpp | 50 +
toolboxes/gadgettools/GadgetronOSUtil.h | 21 +
toolboxes/gadgettools/GadgetronSlotContainer.h | 7 -
toolboxes/gadgettools/gadgettools_export.h | 2 +-
toolboxes/gadgettools/ismrmrd/CMakeLists.txt | 4 +
.../gadgettools/ismrmrd/GadgetImageMessageReader.h | 196 +
.../{ => ismrmrd}/GadgetImageMessageWriter.h | 0
toolboxes/gadgettools/schema/gadgetron.xsd | 89 +-
toolboxes/gtplus/CMakeLists.txt | 318 +-
toolboxes/gtplus/GtPlusDefinition.h | 222 +
toolboxes/gtplus/GtPlusIOExport.h | 20 +
.../FreeFormDeformation/gtplusBSplineFFD.h | 820 ++
.../FreeFormDeformation/gtplusBSplineFFD2D.h | 597 ++
.../FreeFormDeformation/gtplusBSplineFFD3D.h | 740 ++
.../FreeFormDeformation/gtplusBSplineFFD4D.h | 905 ++
.../algorithm/FreeFormDeformation/gtplusFFDBase.h | 1976 ++++
.../algorithm/FreeFormDeformation/gtplusMLFFD.h | 436 +
toolboxes/gtplus/algorithm/gtPlusAlgorithmBase.h | 6 +-
.../gtplus/algorithm/gtPlusDataFidelityOperator.h | 18 +-
toolboxes/gtplus/algorithm/gtPlusGRAPPA.h | 501 +-
toolboxes/gtplus/algorithm/gtPlusOperator.h | 32 +-
toolboxes/gtplus/algorithm/gtPlusSPIRIT.h | 816 +-
.../gtplus/algorithm/gtPlusSPIRIT2DOperator.h | 38 +-
.../gtplus/algorithm/gtPlusSPIRIT2DTOperator.h | 48 +-
.../algorithm/gtPlusSPIRITNoNullSpace2DTOperator.h | 4 +-
.../algorithm/gtPlusSPIRITNoNullSpaceOperator.h | 4 +-
toolboxes/gtplus/algorithm/gtPlusSPIRITOperator.h | 22 +-
.../gtplus/algorithm/gtPlusWavelet2DOperator.h | 65 +-
.../gtplus/algorithm/gtPlusWavelet3DOperator.h | 504 +-
.../algorithm/gtPlusWaveletNoNullSpace2DOperator.h | 6 +-
.../algorithm/gtPlusWaveletNoNullSpace3DOperator.h | 7 +-
toolboxes/gtplus/algorithm/gtPlusWaveletOperator.h | 144 +-
.../GadgetronProgram_gtPlus_2DT_Cartesian.xml | 798 --
...etronProgram_gtPlus_2DT_Cartesian_CloudNode.xml | 67 -
...us_2DT_Cartesian_DualLayer_Gateway_L1SPIRIT.xml | 808 --
...Plus_2DT_Cartesian_DualLayer_Gateway_SPIRIT.xml | 808 --
...m_gtPlus_2DT_Cartesian_FirstLayer_CloudNode.xml | 269 -
...getronProgram_gtPlus_2DT_Cartesian_L1SPIRIT.xml | 799 --
...adgetronProgram_gtPlus_2DT_Cartesian_SPIRIT.xml | 799 --
.../GadgetronProgram_gtPlus_2DT_FatWater.xml | 654 --
.../config/GadgetronProgram_gtPlus_2DT_LGE.xml | 654 --
.../config/GadgetronProgram_gtPlus_2DT_MOLLI.xml | 654 --
.../GadgetronProgram_gtPlus_2DT_Perfusion.xml | 655 --
.../GadgetronProgram_gtPlus_2DT_RealTimeCine.xml | 741 --
.../GadgetronProgram_gtPlus_2DT_RealTimeFlow.xml | 689 --
.../config/GadgetronProgram_gtPlus_2DT_T2W.xml | 654 --
.../GadgetronProgram_gtPlus_3DT_Cartesian.xml | 787 --
...etronProgram_gtPlus_3DT_Cartesian_CloudNode.xml | 72 -
...getronProgram_gtPlus_3DT_Cartesian_L1SPIRIT.xml | 816 --
...adgetronProgram_gtPlus_3DT_Cartesian_SPIRIT.xml | 795 --
toolboxes/gtplus/config/gtCloud/myCloud_2DT.txt | 8 -
.../config/gtCloud/myCloud_2DT_DualLayer.txt | 8 -
.../gtCloud/myCloud_2DT_DualLayer_FirstLayer.txt | 8 -
toolboxes/gtplus/config/gtCloud/myCloud_3DT.txt | 12 -
toolboxes/gtplus/matlab/CMakeLists.txt | 10 -
toolboxes/gtplus/matlab/FtkMatlabConverterBase.h | 569 -
toolboxes/gtplus/matlab/gtMatlab.h | 51 +
toolboxes/gtplus/matlab/gtMatlabConverter.h | 65 +-
toolboxes/gtplus/matlab/gtMatlabConverterComplex.h | 49 +-
toolboxes/gtplus/matlab/gtMatlabImage.h | 255 +
toolboxes/gtplus/solver/gtPlusLSQRSolver.h | 44 +-
toolboxes/gtplus/solver/gtPlusLinearSolver.h | 3 +-
toolboxes/gtplus/solver/gtPlusNCGSolver.h | 57 +-
toolboxes/gtplus/solver/gtPlusNonLinearSolver.h | 1 +
toolboxes/gtplus/solver/gtPlusSolver.h | 2 +-
toolboxes/gtplus/ut/CMakeLists.txt | 56 +-
toolboxes/gtplus/ut/grappa_test.cpp | 59 +-
toolboxes/gtplus/ut/spirit_test.cpp | 425 -
toolboxes/gtplus/ut/util_test.cpp | 1195 ---
toolboxes/gtplus/util/gtPlusIOAnalyze.cpp | 176 +-
toolboxes/gtplus/util/gtPlusIOAnalyze.h | 837 +-
toolboxes/gtplus/util/gtPlusIOBase.cpp | 146 +-
toolboxes/gtplus/util/gtPlusIOBase.h | 798 +-
toolboxes/gtplus/util/gtPlusMemoryManager.cpp | 17 +-
toolboxes/gtplus/util/gtPlusMemoryManager.h | 2 -
toolboxes/gtplus/util/gtPlusUtil.h | 96 +
toolboxes/gtplus/util/gtPlusUtil.hxx | 149 +
toolboxes/gtplus/workflow/gtPlusCloudScheduler.cpp | 2 +-
.../workflow/gtPlusISMRMRDReconCoilMapEstimation.h | 137 +
.../gtplus/workflow/gtPlusISMRMRDReconUtil.cpp | 2550 ++++-
toolboxes/gtplus/workflow/gtPlusISMRMRDReconUtil.h | 383 +-
.../gtplus/workflow/gtPlusISMRMRDReconUtil.hxx | 2036 ++--
.../gtplus/workflow/gtPlusISMRMRDReconWorkFlow.h | 109 +-
.../workflow/gtPlusISMRMRDReconWorkFlowCartesian.h | 1155 +-
.../gtPlusISMRMRDReconWorkFlowCartesian2DT.h | 21 +-
.../gtPlusISMRMRDReconWorkFlowCartesian3DT.h | 19 +-
.../gtplus/workflow/gtPlusISMRMRDReconWorkOrder.h | 880 +-
.../workflow/gtPlusISMRMRDReconWorkOrder2DT.h | 27 +
.../workflow/gtPlusISMRMRDReconWorkOrder3DT.h | 25 +
.../gtplus/workflow/gtPlusISMRMRDReconWorker.h | 50 +-
.../gtplus/workflow/gtPlusISMRMRDReconWorker2DT.h | 500 +-
.../workflow/gtPlusISMRMRDReconWorker2DTGRAPPA.h | 149 +-
.../gtPlusISMRMRDReconWorker2DTL1SPIRITNCG.h | 56 +-
.../gtPlusISMRMRDReconWorker2DTNoAcceleration.h | 50 +-
.../workflow/gtPlusISMRMRDReconWorker2DTSPIRIT.h | 107 +-
.../gtplus/workflow/gtPlusISMRMRDReconWorker3DT.h | 431 +-
.../workflow/gtPlusISMRMRDReconWorker3DTGRAPPA.h | 52 +-
.../gtPlusISMRMRDReconWorker3DTL1SPIRITNCG.h | 89 +-
.../gtPlusISMRMRDReconWorker3DTNoAcceleration.h | 44 +-
.../workflow/gtPlusISMRMRDReconWorker3DTSPIRIT.h | 53 +-
toolboxes/linalg/CMakeLists.txt | 37 +
toolboxes/linalg/generate_test_data.m | 32 +
toolboxes/linalg/linalg_export.h | 25 +
.../linalg/linalg_ground_truth_comparison.cpp | 418 +
toolboxes/linalg/linalg_test.cpp | 580 +
toolboxes/linalg/matrix_decomposition.cpp | 364 +
toolboxes/linalg/matrix_decomposition.h | 42 +
toolboxes/linalg/matrix_vector_op.cpp | 313 +
toolboxes/linalg/matrix_vector_op.h | 52 +
toolboxes/linalg/write_mr_raw.m | 18 +
toolboxes/mri/CMakeLists.txt | 5 +
toolboxes/mri/epi/CMakeLists.txt | 63 +
toolboxes/mri/epi/EPIExport.h | 20 +
toolboxes/mri/epi/EPIReconXObject.h | 73 +
toolboxes/mri/epi/EPIReconXObjectFlat.h | 189 +
toolboxes/mri/epi/EPIReconXObjectTrapezoid.h | 236 +
toolboxes/mri/pmri/CMakeLists.txt | 4 +-
toolboxes/mri/pmri/gpu/CMakeLists.txt | 46 +-
toolboxes/mri/pmri/gpu/b1_map.cu | 64 +-
toolboxes/mri/pmri/gpu/b1_map_NIH_Souheil.cu | 14 +-
toolboxes/mri/pmri/gpu/cuBuffer.cpp | 197 +
toolboxes/mri/pmri/gpu/cuBuffer.h | 61 +
toolboxes/mri/pmri/gpu/cuCartesianSenseOperator.cu | 4 +-
.../mri/pmri/gpu/cuNonCartesianSenseOperator.cu | 20 -
toolboxes/mri/pmri/gpu/cuSenseBuffer.cpp | 204 +-
toolboxes/mri/pmri/gpu/cuSenseBuffer.h | 57 +-
toolboxes/mri/pmri/gpu/cuSenseBufferCg.h | 2 +-
toolboxes/mri/pmri/gpu/cuSpiritBuffer.cpp | 89 +
toolboxes/mri/pmri/gpu/cuSpiritBuffer.h | 43 +
toolboxes/mri/pmri/gpu/cuSpiritOperator.h | 130 +
toolboxes/mri/pmri/gpu/htgrappa.cpp | 48 +
toolboxes/mri/pmri/gpu/htgrappa.cu | 387 +-
toolboxes/mri/pmri/gpu/htgrappa.h | 35 +-
toolboxes/mri/pmri/gpu/sense_utilities.cu | 4 +-
toolboxes/mri/pmri/gpu/spirit_calibration.cu | 363 +
toolboxes/mri/pmri/gpu/spirit_calibration.h | 22 +
toolboxes/mri_core/CMakeLists.txt | 3 +
toolboxes/mri_core/mri_core_data.h | 262 +
toolboxes/nfft/gpu/CMakeLists.txt | 26 +-
toolboxes/nfft/gpu/NFFT_C2NC_conv_kernel.cu | 16 +-
toolboxes/nfft/gpu/NFFT_NC2C_atomic_conv_kernel.cu | 14 +-
toolboxes/nfft/gpu/NFFT_NC2C_conv_kernel.cu | 10 +-
toolboxes/nfft/gpu/NFFT_preprocess_kernel.cu | 12 +-
toolboxes/nfft/gpu/cuNFFT.cu | 47 +-
toolboxes/nfft/gpu/cuNFFT.h | 82 +-
toolboxes/operators/CMakeLists.txt | 3 +-
toolboxes/operators/FFTOperator.h | 116 +-
toolboxes/operators/cpu/CMakeLists.txt | 4 +-
toolboxes/operators/cpu/hoDiagonalOperator.h | 20 +
toolboxes/operators/cpu/hoDiagonalSumOperator.h | 20 +
toolboxes/operators/diagonalOperator.h | 52 +-
toolboxes/operators/diagonalSumOperator.h | 95 +
toolboxes/operators/encodedImageOperator.h | 2 +-
toolboxes/operators/generalOperator.h | 25 +-
toolboxes/operators/gpu/CMakeLists.txt | 30 +-
toolboxes/operators/gpu/cuConvolutionOperator.cu | 2 +-
toolboxes/operators/gpu/cuConvolutionOperator.h | 3 +-
toolboxes/operators/gpu/cuDiagonalOperator.h | 2 +-
toolboxes/operators/gpu/cuDiagonalSumOperator.h | 20 +
toolboxes/operators/gpu/cuLaplaceOperator.cu | 6 +-
toolboxes/operators/gpu/cuLaplaceOperator.h | 3 +-
.../operators/gpu/cuPartialDerivativeOperator.cu | 8 +-
.../operators/gpu/cuPartialDerivativeOperator.h | 3 +-
toolboxes/operators/gpu/cuTv1dOperator.cu | 4 +-
toolboxes/operators/gpu/cuTv1dOperator.h | 2 +-
toolboxes/operators/gpu/cuTvOperator.cu | 167 +-
toolboxes/operators/gpu/cuTvOperator.h | 4 +-
toolboxes/operators/gpu/gpuoperators_export.h | 2 +-
toolboxes/operators/gpu/hoCuDiagonalOperator.h | 20 +
toolboxes/operators/gpu/hoCuIdentityOperator.h | 28 +
.../operators/gpu/hoCuPartialDerivativeOperator.h | 94 +
toolboxes/operators/gpu/hoCuTvOperator.h | 2 +-
toolboxes/registration/optical_flow/CMakeLists.txt | 7 +-
.../registration/optical_flow/cpu/CMakeLists.txt | 166 +-
.../hoImageRegContainer2DRegistration.h | 1449 +++
.../cpu/dissimilarity/hoImageRegDissimilarity.h | 251 +
.../hoImageRegDissimilarityHistogramBased.h | 226 +
.../hoImageRegDissimilarityLocalCCR.h | 412 +
.../hoImageRegDissimilarityMutualInformation.h | 295 +
...geRegDissimilarityNormalizedMutualInformation.h | 173 +
.../cpu/dissimilarity/hoImageRegDissimilaritySSD.h | 108 +
.../optical_flow/cpu/hoOpticalFlowSolver.h | 4 +-
.../optical_flow/cpu/hoRegistration_utils.cpp | 233 -
.../optical_flow/cpu/hoRegistration_utils.h | 13 -
...ImageRegDeformationFieldBidirectionalRegister.h | 501 +
.../register/hoImageRegDeformationFieldRegister.h | 527 +
.../cpu/register/hoImageRegNonParametricRegister.h | 148 +
.../cpu/register/hoImageRegParametricRegister.h | 408 +
.../optical_flow/cpu/register/hoImageRegRegister.h | 651 ++
...hoImageRegDeformationFieldBidirectionalSolver.h | 602 ++
.../cpu/solver/hoImageRegDeformationFieldSolver.h | 673 ++
.../cpu/solver/hoImageRegNonParametricSolver.h | 162 +
.../solver/hoImageRegParametricDownHillSolver.h | 166 +
.../hoImageRegParametricGradientDescentSolver.h | 146 +
.../cpu/solver/hoImageRegParametricSolver.h | 326 +
.../optical_flow/cpu/solver/hoImageRegSolver.h | 210 +
.../transformation/hoImageRegDeformationField.h | 964 ++
.../hoImageRegHomogenousTransformation.h | 475 +
.../hoImageRegNonParametricTransformation.h | 82 +
.../hoImageRegParametricTransformation.h | 227 +
.../hoImageRegRigid2DTransformation.h | 380 +
.../hoImageRegRigid3DTransformation.h | 491 +
.../cpu/transformation/hoImageRegTransformation.h | 408 +
.../optical_flow/cpu/warper/hoImageRegWarper.h | 529 +
.../registration/optical_flow/gpu/CMakeLists.txt | 12 +-
.../optical_flow/gpu/cuCKOpticalFlowSolver.cu | 8 +-
.../optical_flow/gpu/cuHSOpticalFlowSolver.cu | 8 +-
.../optical_flow/gpu/cuLinearResampleOperator.cu | 6 +-
.../optical_flow/gpu/cuOpticalFlowSolver.cu | 8 +-
toolboxes/solvers/CMakeLists.txt | 5 +-
toolboxes/solvers/cgPreconditioner.h | 6 +-
toolboxes/solvers/cpu/CMakeLists.txt | 5 +-
toolboxes/solvers/cpu/hoCgPreconditioner.h | 2 +-
toolboxes/solvers/cpu/hoCgSolver.h | 4 +-
toolboxes/solvers/cpu/hoGpBbSolver.h | 21 +-
toolboxes/solvers/cpu/hoSolverUtils.h | 26 +
toolboxes/solvers/gpBbSolver.h | 1 -
toolboxes/solvers/gpSolver.h | 2 +-
toolboxes/solvers/gpu/CMakeLists.txt | 31 +-
toolboxes/solvers/gpu/cuGpBbSolver.cu | 40 -
toolboxes/solvers/gpu/cuGpBbSolver.h | 14 +-
toolboxes/solvers/gpu/cuLbfgsSolver.h | 36 +
toolboxes/solvers/gpu/cuNlcgSolver.h | 24 +
toolboxes/solvers/gpu/cuSolverUtils.cu | 38 +
toolboxes/solvers/gpu/cuSolverUtils.h | 11 +
toolboxes/solvers/gpu/hoCuCgSolver.h | 34 +
toolboxes/solvers/gpu/hoCuGpBbSolver.h | 19 +-
toolboxes/solvers/gpu/hoCuNlcgSolver.h | 35 +
toolboxes/solvers/gpu/hoCuSbcCgSolver.h | 16 +
toolboxes/solvers/lbfgsSolver.h | 825 ++
toolboxes/solvers/lsqrSolver.h | 173 +
toolboxes/solvers/nlcgSolver.h | 776 ++
toolboxes/solvers/sbSolver.h | 14 +-
toolboxes/solvers/solver.h | 4 -
906 files changed, 129453 insertions(+), 69810 deletions(-)
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