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----------- ENTRY ------------
----------- PHASE 2 ------------
Configuring CIP...
-- vtkInfovisBoostGraphAlgorithms not found! CIP will NOT use Boost
----------- DONE ------------
-- Configuring SEM CLI module: ConvertDicom
-- Configuring SEM CLI module: MergeParticleDataSets
-- Configuring SEM CLI module: RemoveParticlesFromParticlesDataSet
-- Configuring SEM CLI module: ExtractParticlesFromChestRegionChestType
-- Configuring SEM CLI module: GenerateOtsuLungCast
-- Configuring SEM CLI module: GenerateAtlasConvexHull
-- Configuring SEM CLI module: RegisterLungAtlas
-- Configuring SEM CLI module: ResampleLabelMap
-- Configuring SEM CLI module: RescaleLabelMap
-- Configuring CIP
-- Configuring SEM CLI module: ResampleCT
-- Configuring SEM CLI module: QualityControl
-- Configuring SEM CLI module: RemoveChestTypeFromLabelMapUsingParticles
-- Configuring SEM CLI module: SegmentLungLobes
-- Configuring SEM CLI module: ReadDicomWriteTags
-- Configuring SEM CLI module: SplitLeftLungRightLung
-- Configuring SEM CLI module: ExtractChestLabelMap
-- Configuring SEM CLI module: LabelParticlesByChestRegionChestType
-- Configuring SEM CLI module: GenerateStenciledLabelMapFromParticles
-- Configuring SEM CLI module: GenerateDistanceMapFromLabelMap
-- Configuring SEM CLI module: FilterVesselParticleData
-- Configuring SEM CLI module: FilterAirwayParticleData
-- Configuring SEM CLI module: ReadNRRDsWriteVTK
-- Configuring SEM CLI module: ReadVTKWriteNRRDs
-- Configuring SEM CLI module: ComputeCrossSectionalArea
-- Configuring SEM CLI module: ComputeIntensityStatistics
-- Configuring SEM CLI module: FilterFissureParticleData
-- Configuring SEM CLI module: GenerateLobeSurfaceModels
-- Configuring SEM CLI module: ClassifyFissureParticles
-- Configuring SEM CLI module: CropLung
-- Configuring SEM CLI module: GenerateModel
-- Configuring SEM CLI module: GenerateImageSubVolumes
-- Configuring SEM CLI module: GenerateMedianFilteredImage
-- Configuring SEM CLI module: FindPatchMatch
-- Configuring SEM CLI module: TransferRegionAndTypeIndicesToFromPoints
-- Configuring SEM CLI module: EvaluateLungLobeSegmentationResults
-- Configuring SEM CLI module: ConvertLabelMapValueToChestRegionChestType
-- Configuring SEM CLI module: GenerateParenchymaPhenotypes
-- Configuring SEM CLI module: ComputeDistanceMap
-- Configuring SEM CLI module: PerturbParticles
-- Configuring SEM CLI module: ReadWriteRegionAndTypePoints
-- Configuring SEM CLI module: PerformMorphological
-- Configuring SEM CLI module: GenerateOverlayImages
-- Configuring SEM CLI module: GetTransformationSimilarityMetric
-- Configuring SEM CLI module: GetTransformationKappa2D
-- Configuring SEM CLI module: GetTransformationKappa
-- Configuring SEM CLI module: ReadWriteImageData
-- Configuring SEM CLI module: GetStructuresInLabelMap
-- Configuring SEM CLI module: GeneratePartialLungLabelMap
-- Configuring SEM CLI module: ReadVidaWriteCIP
-- Configuring SEM CLI module: RegisterLabelMaps
-- Configuring SEM CLI module: RegisterCT
-- Configuring SEM CLI module: MergeChestLabelMaps
-- Configuring SEM CLI module: MaskOutLabelMapStructures
-- Configuring SEM CLI module: ComputeFeatureStrength
-- Configuring SEM CLI module: LabelMapFromRegionAndTypePoints
-- Configuring SEM CLI module: GenerateSimpleLungMask
-- Configuring SEM CLI module: GenerateBinaryThinning3D
-- Configuring SEM CLI module: ConvertChestRegionChestTypeToLabelMapValue
-- Configuring SEM CLI module: FilterConnectedComponents
-- Configuring SEM CLI module: EnhanceFissuresInImage
-- Configuring SEM CLI module: ComputeFissureFeatureVectors
-- Configuring SEM CLI module: FitLobeSurfaceModelsToParticleData
-- Configuring SEM CLI module: GenerateLesionSegmentation
-- Configuring SEM CLI module: RemapLabelMap
-- Configuring SEM CLI module: GenerateNLMFilteredImage
-- Configuring SEM CLI module: ComputeAirwayWallFromParticles
-- Configuring SEM CLI module: RegionTypeLocationsToROIVolume
-- Configuring SEM CLI module: ExtractFissureBoundaryFromLobeMap
-- Configuring SEM CLI module: ExecuteSystemCommand
-- Configuring SEM CLI module: AVGraphCut
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common/chest_conventions.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common/chest_conventions_static.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common/cipChestConventionsXmlParser.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common/geometry_topology_data.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common/paths.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common/tests/test_geometry_topology_data.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/common/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/apply_reader_labels.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/classify_image_subtypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor_from_ROI.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/distance_feature_extractor_from_xmlpoints.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/emphysema_classification.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/get_ct_patch_from_center.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/hist_dist_knn.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/hist_dist_scikit_knn.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/kde_.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/kde_bandwidth.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor_from_ROI.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/kde_histogram_feature_extractor_from_xmlpoints.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/lattice_classifier.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/local_histogram.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_apply_reader_labels.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_classify_image_subtypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor_from_ROI.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_feature_extractor_from_xml_points.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_distance_histogram_extractors.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_get_ct_patch_from_center.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_hist_dist_knn.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_hist_dist_scikit_knn.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor_from_ROI.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/tests/test_kde_histogram_feature_extractor_from_xmlpoints.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/classification/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/input_output
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/input_output/image_reader_writer.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/input_output/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/input_output/tests/test_image_reader_writer.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/input_output/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/airway_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/chest_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/diaphragm_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/feature_strength_map.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/fissure_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/multires_airway_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/multires_vessel_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/particle_metrics.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/tests/test_airway_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/tests/test_fissure_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/tests/test_particle_metrics.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/tests/test_vessel_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/vessel_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/particles/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/airway_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/body_composition_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/bronchiectasis.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/diaphragm_thickness.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/emphysema_severity.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/gas_trapping.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/laa_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/nodule_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/parenchyma_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests/test_body_composition_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests/test_emphysema_severity.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests/test_laa_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/tests/test_parenchyma_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/vasculature.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/vasculature_phenotypes.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/phenotypes/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/qualitycontrol
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/qualitycontrol/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/qualitycontrol/vasculature_qc.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/qualitycontrol/xml_points_qc.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/qualitycontrol/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/registration
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/registration/cip_registration.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/registration/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/registration/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/chest_partition.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/chest_partition_manager.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/comput_image_similarity.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/construct_chest_atlas.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/construct_pec_atlas_from_filenames.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/gaussian_rician.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/grid_segmenter.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/nodule_segmenter.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/pectoralis_segmentor.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/register_tobase_get_closest.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/rind_vs_core_partition.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/segment_chest_with_atlas.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/slic_segmenter.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/tests/test_grid_segmenter.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/tests/test_rind_vs_core_partition.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/segmentation/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/anonymize_dicom.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/apply_label_from_classification.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/cluster_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/compute_dice_coefficient.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/feature_maps.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/generate_CLIs_description.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/generate_overlay_image.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/get_closest_cases.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/get_mi_similarity_vec.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/locate_cardiac_gating_artifacts.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/locate_CARDIA_gated_artifacts.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/polynomial_feature_map.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/query_dicom_directories.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/quick_airway_vessel_segmentation.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/read_geometrytopologypoint_write_dataframe.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/read_geometrytopologypoint_write_polydata.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/read_nrrds_write_vtk.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/region_type_parser.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/remap_lm.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_anonymize_dicom.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_compute_dice_coefficient.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_feature_maps.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_read_geometrytopologypoint_write_dataframe.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_read_geometrytopologypoint_write_polydata.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_region_type_parser.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_remap_lm.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/tests/test_weighted_feature_map_densities.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/WeightedFeatureMapDensity.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/weighted_feature_map_densities.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/utils/__init__.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/visualization
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/visualization/display_particles.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/visualization/display_particles_volume.py
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/visualization/tests
-- Up-to-date: D:/Projects/CIP-build/CIP-build/cip_python/visualization/__init__.py
-- Configuring done
-- Generating done
-- Build files have been written to: D:/Projects/CIP-build/CIP-build

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