├── .gitignore ├── LICENSE ├── README.md ├── configs ├── config_sononet_8.json ├── config_sononet_grid_att_8.json ├── config_sononet_grid_att_8_deepsup.json ├── config_sononet_grid_att_8_ft.json ├── config_unet_ct_dsv.json └── config_unet_ct_multi_att_dsv.json ├── dataio ├── __init__.py ├── loader │ ├── __init__.py │ ├── cmr_3D_dataset.py │ ├── hms_dataset.py │ ├── test_dataset.py │ ├── ukbb_dataset.py │ ├── us_dataset.py │ └── utils.py └── transformation │ ├── __init__.py │ ├── myImageTransformations.py │ └── transforms.py ├── figures ├── figure1.png └── figure2.jpg ├── models ├── __init__.py ├── aggregated_classifier.py ├── base_model.py ├── feedforward_classifier.py ├── feedforward_seg_model.py ├── layers │ ├── __init__.py │ ├── grid_attention_layer.py │ ├── loss.py │ └── nonlocal_layer.py ├── networks │ ├── __init__.py │ ├── sononet.py │ ├── sononet_grid_attention.py │ ├── unet_2D.py │ ├── unet_3D.py │ ├── unet_CT_dsv_3D.py │ ├── unet_CT_multi_att_dsv_3D.py │ ├── unet_CT_single_att_dsv_3D.py │ ├── unet_grid_attention_3D.py │ ├── unet_nonlocal_2D.py │ ├── unet_nonlocal_3D.py │ └── utils.py ├── networks_other.py └── utils.py ├── setup.py ├── test_classification.py ├── train_classifaction.py ├── train_segmentation.py ├── utils ├── __init__.py ├── error_logger.py ├── html.py ├── metrics.py ├── post_process_crf.py ├── util.py └── visualiser.py ├── validation.py ├── visualise_att_maps_epoch.py ├── visualise_attention.py └── visualise_fmaps.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/README.md -------------------------------------------------------------------------------- /configs/config_sononet_8.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/configs/config_sononet_8.json -------------------------------------------------------------------------------- /configs/config_sononet_grid_att_8.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/configs/config_sononet_grid_att_8.json -------------------------------------------------------------------------------- /configs/config_sononet_grid_att_8_deepsup.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/configs/config_sononet_grid_att_8_deepsup.json -------------------------------------------------------------------------------- /configs/config_sononet_grid_att_8_ft.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/configs/config_sononet_grid_att_8_ft.json -------------------------------------------------------------------------------- /configs/config_unet_ct_dsv.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/configs/config_unet_ct_dsv.json -------------------------------------------------------------------------------- /configs/config_unet_ct_multi_att_dsv.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/configs/config_unet_ct_multi_att_dsv.json -------------------------------------------------------------------------------- /dataio/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /dataio/loader/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/loader/__init__.py -------------------------------------------------------------------------------- /dataio/loader/cmr_3D_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/loader/cmr_3D_dataset.py -------------------------------------------------------------------------------- /dataio/loader/hms_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/loader/hms_dataset.py -------------------------------------------------------------------------------- /dataio/loader/test_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/loader/test_dataset.py -------------------------------------------------------------------------------- /dataio/loader/ukbb_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/loader/ukbb_dataset.py -------------------------------------------------------------------------------- /dataio/loader/us_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/loader/us_dataset.py -------------------------------------------------------------------------------- /dataio/loader/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/loader/utils.py -------------------------------------------------------------------------------- /dataio/transformation/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/transformation/__init__.py -------------------------------------------------------------------------------- /dataio/transformation/myImageTransformations.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/transformation/myImageTransformations.py -------------------------------------------------------------------------------- /dataio/transformation/transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/dataio/transformation/transforms.py -------------------------------------------------------------------------------- /figures/figure1.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/figures/figure1.png -------------------------------------------------------------------------------- /figures/figure2.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/figures/figure2.jpg -------------------------------------------------------------------------------- /models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/__init__.py -------------------------------------------------------------------------------- /models/aggregated_classifier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/aggregated_classifier.py -------------------------------------------------------------------------------- /models/base_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/base_model.py -------------------------------------------------------------------------------- /models/feedforward_classifier.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/feedforward_classifier.py -------------------------------------------------------------------------------- /models/feedforward_seg_model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/feedforward_seg_model.py -------------------------------------------------------------------------------- /models/layers/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /models/layers/grid_attention_layer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/layers/grid_attention_layer.py -------------------------------------------------------------------------------- /models/layers/loss.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/layers/loss.py -------------------------------------------------------------------------------- /models/layers/nonlocal_layer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/layers/nonlocal_layer.py -------------------------------------------------------------------------------- /models/networks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/__init__.py -------------------------------------------------------------------------------- /models/networks/sononet.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/sononet.py -------------------------------------------------------------------------------- /models/networks/sononet_grid_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/sononet_grid_attention.py -------------------------------------------------------------------------------- /models/networks/unet_2D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/unet_2D.py -------------------------------------------------------------------------------- /models/networks/unet_3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/unet_3D.py -------------------------------------------------------------------------------- /models/networks/unet_CT_dsv_3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/unet_CT_dsv_3D.py -------------------------------------------------------------------------------- /models/networks/unet_CT_multi_att_dsv_3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/unet_CT_multi_att_dsv_3D.py -------------------------------------------------------------------------------- /models/networks/unet_CT_single_att_dsv_3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/unet_CT_single_att_dsv_3D.py -------------------------------------------------------------------------------- /models/networks/unet_grid_attention_3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/unet_grid_attention_3D.py -------------------------------------------------------------------------------- /models/networks/unet_nonlocal_2D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/unet_nonlocal_2D.py -------------------------------------------------------------------------------- /models/networks/unet_nonlocal_3D.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/unet_nonlocal_3D.py -------------------------------------------------------------------------------- /models/networks/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks/utils.py -------------------------------------------------------------------------------- /models/networks_other.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/networks_other.py -------------------------------------------------------------------------------- /models/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/models/utils.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/setup.py -------------------------------------------------------------------------------- /test_classification.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/test_classification.py -------------------------------------------------------------------------------- /train_classifaction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/train_classifaction.py -------------------------------------------------------------------------------- /train_segmentation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/train_segmentation.py -------------------------------------------------------------------------------- /utils/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /utils/error_logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/utils/error_logger.py -------------------------------------------------------------------------------- /utils/html.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/utils/html.py -------------------------------------------------------------------------------- /utils/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/utils/metrics.py -------------------------------------------------------------------------------- /utils/post_process_crf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/utils/post_process_crf.py -------------------------------------------------------------------------------- /utils/util.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/utils/util.py -------------------------------------------------------------------------------- /utils/visualiser.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/utils/visualiser.py -------------------------------------------------------------------------------- /validation.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/validation.py -------------------------------------------------------------------------------- /visualise_att_maps_epoch.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/visualise_att_maps_epoch.py -------------------------------------------------------------------------------- /visualise_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/visualise_attention.py -------------------------------------------------------------------------------- /visualise_fmaps.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ozan-oktay/Attention-Gated-Networks/HEAD/visualise_fmaps.py --------------------------------------------------------------------------------