├── .gitattributes ├── .github ├── ISSUE_TEMPLATE │ └── niftynet-issue-template.md └── PULL_REQUEST_TEMPLATE.md ├── .gitignore ├── .gitlab-ci.yml ├── .gitlab ├── issue_templates │ └── Bug.md └── merge_request_templates │ └── Pull_request.md ├── .readthedocs.yml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── ci ├── bundlewheel.sh ├── findwheel.sh └── utils.sh ├── config ├── GAN_demo_train_config.ini ├── README.md ├── deepmedic_config.ini ├── default_eval_config.ini ├── default_monomodal_regression.ini ├── default_monomodal_regression_eval.ini ├── default_multimodal_segmentation.ini ├── default_multimodal_segmentation_eval.ini ├── default_segmentation.ini ├── default_segmentation_bf.ini ├── densevnet_config.ini ├── highres3dnet_config.ini ├── holisticnet_config.ini ├── label_driven_registration.ini ├── scalenet_config.ini ├── unet_config.ini ├── vae_config.ini ├── vnet_config.ini └── weighted_sample_regression.ini ├── data ├── IXI_autoencoder │ └── .gitignore ├── PROMISE12 │ └── setup.py └── us_simulator_gan │ └── .gitignore ├── demos ├── BRATS17 │ ├── README.md │ ├── __init__.py │ ├── example_outputs │ │ ├── ave_prob.png │ │ ├── label.png │ │ └── original.png │ └── rename_crop_BRATS.py ├── GAN │ └── README.md ├── Learning_Rate_Decay │ ├── Demo_applications │ │ ├── decay_lr_comparison_application.py │ │ └── no_decay_lr_comparison_application.py │ ├── Demo_for_learning_rate_decay_application.ipynb │ ├── README.md │ ├── decay_lr_application.py │ └── learning_rate_demo_train_config.ini ├── PROMISE12 │ ├── PROMISE12_Demo_Notebook.ipynb │ ├── README.md │ ├── promise12_balanced_train_config.ini │ ├── promise12_demo_inference_config.ini │ └── promise12_demo_train_config.ini ├── PyTorchNiftyNet │ ├── README.md │ ├── libs │ │ ├── __init__.py │ │ ├── dataset_niftynet.py │ │ ├── loss.py │ │ └── model.py │ └── segmentation.py ├── README.md ├── brain_parcellation │ ├── README.md │ └── example_outputs │ │ └── screenshot.png ├── crf_as_rnn │ └── crf_as_rnn_inference_demo.ipynb ├── module_examples │ ├── FullCSVReaderDemo.ipynb │ ├── ImageReader.ipynb │ ├── ImageSampler.ipynb │ ├── ParallelCSVReaderDemo.ipynb │ ├── README.md │ ├── mapping.txt │ └── visualise_coordinates.py ├── unet │ ├── HeLa.ini │ ├── README.md │ ├── U-Net_Demo.ipynb │ ├── U373.ini │ ├── file_sorter.py │ ├── generate_run_commands.py │ ├── make_cell_weights.py │ └── unet_demo_utils.py ├── unet_histology │ ├── config.ini │ ├── data_in_itksnap_scaled.png │ ├── tensorboard_scaled.png │ └── unet_histology_training.md └── variational_autoencoder │ ├── README.md │ ├── example_outputs │ ├── 1037.png │ ├── 464.png │ └── interpolation.gif │ └── vae_config.ini ├── doc ├── Makefile ├── make.bat ├── requirements.txt └── source │ ├── _static │ ├── .gitkeep │ ├── 3d_sampling.jpg │ ├── custom.css │ ├── grid.png │ ├── grid_cropped_50_12.png │ ├── grid_overlay.png │ ├── grid_pad_50.png │ ├── grid_pad_50_12.png │ ├── image.png │ ├── image_pad_50.png │ ├── uniform.png │ ├── uniform_pad_50.png │ └── uniform_pad_50_12.png │ ├── _templates │ ├── badge.html │ ├── globaltoc.html │ └── layout.html │ ├── buffer_queue.md │ ├── conf.py │ ├── config_spec.md │ ├── contributing.md │ ├── extending_app.md │ ├── extending_event_handler.md │ ├── extending_net.md │ ├── filename_matching.md │ ├── index.rst │ ├── installation.rst │ ├── introductory.md │ ├── list_modules.rst │ ├── model_zoo.md │ ├── transfer_learning.md │ ├── versioneer.rst │ └── window_sizes.rst ├── net_autoencoder.py ├── net_classify.py ├── net_download.py ├── net_gan.py ├── net_regress.py ├── net_run.py ├── net_segment.py ├── niftynet-logo.png ├── niftynet ├── __init__.py ├── application │ ├── __init__.py │ ├── autoencoder_application.py │ ├── base_application.py │ ├── classification_application.py │ ├── gan_application.py │ ├── label_driven_registration.py │ ├── regression_application.py │ └── segmentation_application.py ├── contrib │ ├── __init__.py │ ├── checkpoint_tools │ │ ├── __init__.py │ │ └── rename_checkpoint_to_partial.py │ ├── csv_reader │ │ ├── __init__.py │ │ ├── applications_maybe │ │ │ ├── __init__.py │ │ │ ├── autoencoder_application.py │ │ │ ├── gan_application.py │ │ │ ├── label_driven_registration.py │ │ │ ├── regression_application.py │ │ │ └── segmentation_application.py │ │ ├── class_seg_finnet.py │ │ ├── classification_application.py │ │ ├── csv_reader.py │ │ ├── default_segmentation_csvsampler.ini │ │ ├── default_segmentation_multitask.ini │ │ ├── highres3dnet_features.py │ │ ├── multitask_classifseg_application.py │ │ ├── sampler_balanced_v2_csv.py │ │ ├── sampler_csv_rows.py │ │ ├── sampler_csvpatch.py │ │ ├── sampler_grid_v2_csv.py │ │ ├── sampler_linear_interpolate_v2_csv.py │ │ ├── sampler_random_vector_v2_csv.py │ │ ├── sampler_resize_v2_csv.py │ │ ├── sampler_uniform_v2_csv.py │ │ ├── sampler_weighted_v2_csv.py │ │ ├── segmentation_application_patchsampler.py │ │ └── toynet_features.py │ ├── deep_boosted_regression │ │ ├── README.md │ │ ├── __init__.py │ │ ├── net_DBR.ini │ │ └── regression_rec_application.py │ ├── evaluation │ │ ├── __init__.py │ │ ├── classification_evaluations.py │ │ ├── regression_evaluations.py │ │ └── segmentation_evaluations.py │ ├── layer │ │ ├── __init__.py │ │ └── resampler_optional_niftyreg.py │ ├── learning_rate_schedule │ │ ├── README.md │ │ ├── __init__.py │ │ └── decay_lr_application.py │ ├── multi_output │ │ ├── __init__.py │ │ └── multi_output_test.py │ ├── niftyreg_image_resampling │ │ ├── .gitignore │ │ ├── LICENSE │ │ ├── README.md │ │ ├── __init__.py │ │ ├── niftyreg_gpu_resampler │ │ │ ├── CMakeLists.txt │ │ │ ├── _reg_common_cuda.cu │ │ │ ├── _reg_common_cuda.h │ │ │ ├── _reg_maths.cpp │ │ │ ├── _reg_maths.h │ │ │ ├── _reg_maths_eigen.cpp │ │ │ ├── _reg_maths_eigen.h │ │ │ ├── _reg_resampling.cpp │ │ │ ├── _reg_resampling.h │ │ │ ├── _reg_resampling_gpu.cu │ │ │ ├── _reg_resampling_gpu.h │ │ │ ├── _reg_tools.cpp │ │ │ ├── _reg_tools.h │ │ │ ├── cmake │ │ │ │ └── modules │ │ │ │ │ ├── FindNumPy.cmake │ │ │ │ │ └── FindTensorflow.cmake │ │ │ ├── interpolations.h │ │ │ ├── interpolations.tpp │ │ │ ├── nifti │ │ │ │ ├── LICENSE │ │ │ │ ├── nifti1.h │ │ │ │ ├── nifti1_io.c │ │ │ │ ├── nifti1_io.h │ │ │ │ ├── znzlib.c │ │ │ │ └── znzlib.h │ │ │ ├── niftyreg_cpu_resample_gradient_op.cpp │ │ │ ├── niftyreg_cpu_resample_gradient_op.h │ │ │ ├── niftyreg_cpu_resample_image_gradient_op.cpp │ │ │ ├── niftyreg_cpu_resample_image_gradient_op.h │ │ │ ├── niftyreg_cpu_resample_op.cpp │ │ │ ├── niftyreg_cpu_resample_op.h │ │ │ ├── niftyreg_gpu_resample_gradient_op.cu │ │ │ ├── niftyreg_gpu_resample_gradient_op.h │ │ │ ├── niftyreg_gpu_resample_op.cu │ │ │ ├── niftyreg_gpu_resample_op.h │ │ │ ├── niftyreg_resample_op.h │ │ │ ├── niftyreg_resample_op.tpp │ │ │ ├── resampleKernel.cu │ │ │ ├── resampleKernel.h │ │ │ ├── resampler_boundary.h │ │ │ └── resampler_boundary.tpp │ │ ├── niftyreg_image_resampling.py │ │ ├── niftyreg_module_loader.py.in │ │ ├── setup.py │ │ └── tests │ │ │ ├── __init__.py │ │ │ ├── test_python_wrapper.py │ │ │ └── test_resampler.py │ ├── preprocessors │ │ ├── __init__.py │ │ └── preprocessing.py │ ├── regression_weighted_sampler │ │ ├── README.md │ │ ├── __init__.py │ │ └── isample_regression.py │ ├── sampler_pairwise │ │ ├── __init__.py │ │ ├── sampler_pairwise_resize.py │ │ ├── sampler_pairwise_resize_csv.py │ │ ├── sampler_pairwise_uniform.py │ │ └── sampler_pairwise_uniform_csv.py │ ├── segmentation_bf_aug │ │ ├── __init__.py │ │ └── segmentation_application_bfaug.py │ ├── segmentation_selective_sampler │ │ ├── README.md │ │ ├── __init__.py │ │ ├── sampler_selective.py │ │ ├── selective_seg.ini │ │ ├── ss_app.py │ │ └── test_sampler_selective.py │ └── ultrasound_simulator_gan │ │ ├── README.md │ │ ├── __init__.py │ │ └── ultrasound_simulator_gan.py ├── engine │ ├── README.md │ ├── __init__.py │ ├── application_driver.py │ ├── application_factory.py │ ├── application_initializer.py │ ├── application_iteration.py │ ├── application_optimiser.py │ ├── application_variables.py │ ├── handler_console.py │ ├── handler_early_stopping.py │ ├── handler_gradient.py │ ├── handler_model.py │ ├── handler_network_output.py │ ├── handler_performance.py │ ├── handler_sampler.py │ ├── handler_tensorboard.py │ ├── image_window.py │ ├── image_window_dataset.py │ ├── sampler_balanced_v2.py │ ├── sampler_grid_v2.py │ ├── sampler_linear_interpolate_v2.py │ ├── sampler_random_vector_v2.py │ ├── sampler_resize_v2.py │ ├── sampler_uniform_v2.py │ ├── sampler_weighted_v2.py │ ├── signal.py │ ├── windows_aggregator_base.py │ ├── windows_aggregator_grid.py │ ├── windows_aggregator_identity.py │ └── windows_aggregator_resize.py ├── evaluation │ ├── __init__.py │ ├── base_evaluations.py │ ├── base_evaluator.py │ ├── classification_evaluations.py │ ├── classification_evaluator.py │ ├── evaluation_application_driver.py │ ├── pairwise_measures.py │ ├── region_properties.py │ ├── regression_evaluations.py │ ├── regression_evaluator.py │ ├── segmentation_evaluations.py │ └── segmentation_evaluator.py ├── io │ ├── __init__.py │ ├── image_loader.py │ ├── image_reader.py │ ├── image_sets_partitioner.py │ ├── image_type.py │ └── misc_io.py ├── layer │ ├── README.md │ ├── __init__.py │ ├── activation.py │ ├── additive_upsample.py │ ├── affine_augmentation.py │ ├── approximated_smoothing.py │ ├── base_layer.py │ ├── binary_masking.py │ ├── bn.py │ ├── channel_sparse_convolution.py │ ├── convolution.py │ ├── crf.py │ ├── crop.py │ ├── deconvolution.py │ ├── dilatedcontext.py │ ├── discrete_label_normalisation.py │ ├── downsample.py │ ├── downsample_res_block.py │ ├── elementwise.py │ ├── figures │ │ ├── elu_eq.pdf │ │ ├── elu_img.png │ │ ├── prelu_eq.pdf │ │ ├── prelu_img.png │ │ ├── relu_eq.pdf │ │ ├── relu_img.png │ │ ├── sigmoid_eq.pdf │ │ ├── sigmoid_img.png │ │ ├── softplus_eq.pdf │ │ ├── softplus_img.png │ │ ├── softsign_eq.pdf │ │ ├── softsign_img.png │ │ ├── tanh_eq.pdf │ │ └── tanh_img.png │ ├── fully_connected.py │ ├── gan_blocks.py │ ├── gn.py │ ├── grid_warper.py │ ├── histogram_normalisation.py │ ├── layer_util.py │ ├── linear_resize.py │ ├── loss_autoencoder.py │ ├── loss_classification.py │ ├── loss_classification_multi.py │ ├── loss_gan.py │ ├── loss_regression.py │ ├── loss_segmentation.py │ ├── mean_variance_normalisation.py │ ├── pad.py │ ├── post_processing.py │ ├── rand_bias_field.py │ ├── rand_elastic_deform.py │ ├── rand_flip.py │ ├── rand_rotation.py │ ├── rand_spatial_scaling.py │ ├── resampler.py │ ├── residual_unit.py │ ├── rgb_histogram_equilisation.py │ ├── spatial_gradient.py │ ├── spatial_transformer.py │ ├── squeeze_excitation.py │ ├── subpixel.py │ ├── upsample.py │ └── upsample_res_block.py ├── network │ ├── README.md │ ├── __init__.py │ ├── base_net.py │ ├── deepmedic.py │ ├── dense_vnet.py │ ├── highres3dnet.py │ ├── highres3dnet_large.py │ ├── highres3dnet_small.py │ ├── holistic_net.py │ ├── interventional_affine_net.py │ ├── interventional_dense_net.py │ ├── interventional_hybrid_net.py │ ├── no_new_net.py │ ├── resnet.py │ ├── scalenet.py │ ├── se_resnet.py │ ├── simple_gan.py │ ├── simulator_gan.py │ ├── toynet.py │ ├── unet.py │ ├── unet_2d.py │ ├── vae.py │ └── vnet.py └── utilities │ ├── __init__.py │ ├── decorators.py │ ├── download.py │ ├── filename_matching.py │ ├── histogram_standardisation.py │ ├── niftynet_global_config.py │ ├── niftynet_launch_config.py │ ├── restore_initializer.py │ ├── user_parameters_custom.py │ ├── user_parameters_default.py │ ├── user_parameters_helper.py │ ├── user_parameters_parser.py │ ├── user_parameters_regex.py │ ├── util_common.py │ ├── util_csv.py │ ├── util_import.py │ ├── versioneer_version.py │ └── versioning.py ├── requirements.txt ├── run_test.sh ├── setup.cfg ├── setup.py ├── tests ├── README.md ├── __init__.py ├── activation_test.py ├── additive_upsample_test.py ├── affine_augmentation_test.py ├── application_driver_test.py ├── application_factory_test.py ├── approximated_smoothing_test.py ├── binary_masking_test.py ├── bn_test.py ├── channel_sparse_convolution_test.py ├── classification_evaluator_test.py ├── convolution_test.py ├── crf_test.py ├── crop_test.py ├── deconvolution_test.py ├── deepmedic_test.py ├── dense_vnet_test.py ├── dilatedcontext_test.py ├── download_test.py ├── downsample_res_block_test.py ├── downsample_test.py ├── driver_partitioner_test.py ├── elementwise_test.py ├── entry_point_test.py ├── evaluation_test.py ├── filename_matching_test.py ├── fully_connected_test.py ├── get_gpu_index.py ├── gn_test.py ├── gradient_collector_test.py ├── grid_warper_test.py ├── handler_console_test.py ├── handler_early_stopping_test.py ├── handler_network_output_test.py ├── handler_performance_test.py ├── highres3dnet_test.py ├── highresblock_test.py ├── histogram_normalisation_test.py ├── holistic_net_test.py ├── image_loader_test.py ├── image_reader_test.py ├── image_sets_partitioner_test.py ├── image_type_test.py ├── image_window_dataset_generator_test.py ├── image_window_dataset_test.py ├── image_window_test.py ├── interventional_affine_net_test.py ├── interventional_dense_net_test.py ├── interventional_hybrid_net_test.py ├── linear_resize_test.py ├── loss_classification_multi_test.py ├── loss_classification_test.py ├── loss_regression_test.py ├── loss_segmentation_test.py ├── mean_variance_normalisation_test.py ├── niftynet_global_config_test.py ├── niftynet_testcase.py ├── output_collector_test.py ├── pad_test.py ├── post_processing_test.py ├── pylintrc ├── rand_bias_field_test.py ├── rand_elastic_deformation_test.py ├── rand_flip_test.py ├── rand_rotation_test.py ├── rand_spatial_scaling_test.py ├── reader_modular_test.py ├── resampler_batch_test.py ├── resampler_grid_warper_test.py ├── resampler_optional_niftyreg_test.py ├── resampler_test.py ├── residual_unit_test.py ├── residual_upsample_test.py ├── resnet_test.py ├── restorer_test.py ├── rgb_histogram_equilisation_test.py ├── run_vars_test.py ├── sampler_balanced_v2_test.py ├── sampler_csvpatch_v2_test.py ├── sampler_grid_v2_test.py ├── sampler_linear_interpolate_v2_test.py ├── sampler_random_vector_v2_test.py ├── sampler_resize_v2_test.py ├── sampler_uniform_v2_test.py ├── sampler_weighted_v2_test.py ├── scaleblock_test.py ├── scalenet_test.py ├── se_resnet_test.py ├── segmentation_evaluator_test.py ├── simple_gan_test.py ├── spatial_gradient_test.py ├── spatial_transformer_test.py ├── squeeze_excitation_test.py ├── subpixel_test.py ├── test_model_zoo.py ├── toy_application.py ├── toynet_test.py ├── unet_2d_test.py ├── unet_test.py ├── unetblock_test.py ├── upsample_res_block_test.py ├── upsample_test.py ├── user_parameters_default_test.py ├── user_parameters_regex_test.py ├── util_import_test.py ├── versioning_test.py ├── vnet_test.py ├── vnetblock_test.py ├── windows_aggregator_grid_v2_test.py ├── windows_aggregator_identity_v2_test.py └── windows_aggregator_resize_v2_test.py ├── 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