DepthGuide/data/sophiar_config.json

{
  "variable_list": [
    {
      "name": "probe_ref_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "probe_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "femur_ref_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "femur_in_femur_ref",
      "type": "transform_obj",
      "value": [
        78.7201788489362,
        73.11713596096779,
        23.49171840405709,
        -0.21932850052780128,
        0.6801707950006277,
        -0.2076550105848499,
        -0.6679386910963054
      ]
    },
    {
      "name": "tibia_ref_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "tibia_in_tibia_ref",
      "type": "transform_obj"
    },
    {
      "name": "camera_ref_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "left_camera_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "right_camera_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "femur_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "tibia_in_tracker",
      "type": "transform_obj"
    },
    {
      "name": "probe_in_femur_ref",
      "type": "transform_obj"
    },
    {
      "name": "probe_in_tibia_ref",
      "type": "transform_obj"
    },
    {
      "name": "probe_in_femur",
      "type": "transform_obj"
    },
    {
      "name": "probe_in_tibia",
      "type": "transform_obj"
    },
    {
      "name": "probe_tip_in_femur_ref",
      "type": "scalarxyz_obj"
    },
    {
      "name": "probe_tip_in_tibia_ref",
      "type": "scalarxyz_obj"
    },
    {
      "name": "picked_point_in_femur_ref",
      "type": "scalarxyz_obj"
    },
    {
      "name": "picked_point_in_tibia_ref",
      "type": "scalarxyz_obj"
    },
    {
      "name": "femur_in_femur_ref_error",
      "type": "double_obj"
    },
    {
      "name": "tibia_in_tibia_ref_error",
      "type": "double_obj"
    },
    {
      "name": "probe_tip_in_femur",
      "type": "scalarxyz_obj"
    },
    {
      "name": "probe_tip_in_tibia",
      "type": "scalarxyz_obj"
    },
    {
      "name": "picked_point_in_femur",
      "type": "scalarxyz_obj"
    },
    {
      "name": "picked_point_in_tibia",
      "type": "scalarxyz_obj"
    },
    {
      "name": "left_camera_in_tracker_denoised",
      "type": "transform_obj"
    },
    {
      "name": "right_camera_in_tracker_denoised",
      "type": "transform_obj"
    },
    {
      "name": "femur_in_tracker_denoised",
      "type": "transform_obj"
    },
    {
      "name": "tibia_in_tracker_denoised",
      "type": "transform_obj"
    }
  ],
  "object_list": [
    {
      "type": "transform_tree",
      "name": "transform_tree",
      "init_config": {
        "node_list": [
          {
            "name": "tracker"
          },
          {
            "name": "probe_ref",
            "parent": "tracker",
            "transform_var_name": "probe_ref_in_tracker"
          },
          {
            "name": "probe",
            "parent": "probe_ref",
            // for polaris probe
//            "transform": [
//              -0.23,
//              -13.98,
//              -119.65,
//              1,
//              0,
//              0,
//              0
//            ],
            // for aurora probe
            "transform": [
              0,
              0,
              0,
              0,
              1,
              0,
              0
            ]
          },
          {
            "name": "femur_ref",
            "parent": "tracker",
            "transform_var_name": "femur_ref_in_tracker"
          },
          {
            "name": "femur",
            "parent": "femur_ref",
            "transform_var_name": "femur_in_femur_ref"
          },
          {
            "name": "tibia_ref",
            "parent": "tracker",
            "transform_var_name": "tibia_ref_in_tracker"
          },
          {
            "name": "tibia",
            "parent": "tibia_ref",
            "transform_var_name": "tibia_in_tibia_ref"
          },
          {
            "name": "camera_ref",
            "parent": "tracker",
            "transform_var_name": "camera_ref_in_tracker"
          },
          {
            "name": "left_camera",
            "parent": "camera_ref",
            "transform": [
              33.2854,
              -37.7917,
              -24.4682,
              0.6318,
              0.3547,
              0.4719,
              -0.5023
            ]
          },
          {
            "name": "right_camera",
            "parent": "camera_ref",
            "transform": [
              37.3992,
              -56.7108,
              -85.8847,
              0.6304,
              0.3605,
              0.4738,
              -0.4982
            ]
          }
        ]
      },
      "start_config": {
        "watch_list": [
          {
            "target": "left_camera",
            "observer": "tracker",
            "transform_var_name": "left_camera_in_tracker"
          },
          {
            "target": "right_camera",
            "observer": "tracker",
            "transform_var_name": "right_camera_in_tracker"
          },
          {
            "target": "femur",
            "observer": "tracker",
            "transform_var_name": "femur_in_tracker"
          },
          {
            "target": "tibia",
            "observer": "tracker",
            "transform_var_name": "tibia_in_tracker"
          },
          {
            "target": "probe",
            "observer": "tracker",
            "transform_var_name": "probe_in_tracker"
          },
          {
            "target": "probe",
            "observer": "femur_ref",
            "transform_var_name": "probe_in_femur_ref"
          },
          {
            "target": "probe",
            "observer": "tibia_ref",
            "transform_var_name": "probe_in_tibia_ref"
          },
          {
            "target": "probe",
            "observer": "femur",
            "transform_var_name": "probe_in_femur"
          },
          {
            "target": "probe",
            "observer": "tibia",
            "transform_var_name": "probe_in_tibia"
          }
        ]
      }
    },
    {
      "type": "ndi_interface",
      "name": "ndi",
      "init_config": {
        "address_type": "serial",
        "ip": "10.0.0.5",
        "tcp_port": 8765,
        "com_port": "/dev/ttyUSB0",
        "tool_list": [
          {
            "rom_path": "/home/tpx/data/roms/GlassProbe_4Ball_4.rom",
            "serial_number": "3DD50000",
            "outputs": {
              "transform": "probe_ref_in_tracker"
            }
          },
          {
            "rom_path": "/home/tpx/data/roms/Glass_4Ball_1_Camera_20240312.rom",
            "outputs": {
              "transform": "camera_ref_in_tracker"
            }
          },
          {
            "rom_path": "/home/tpx/data/roms/Glass_4Ball_2.rom",
            "serial_number": "39B33001",
            "outputs": {
              "transform": "femur_ref_in_tracker"
            }
          },
          {
            "rom_path": "/home/tpx/data/roms/Glass_3Ball_5_Combined.rom",
            "outputs": {
              "transform": "tibia_ref_in_tracker"
            }
          }
        ]
      },
      "start_config": {
        "allow_unreliable": true,
        "prefer_stream_tracking": false
      }
    },
    {
      "type": "variable_validity_watcher",
      "name": "probe_visibility_watcher",
      "start_config": {
        "variable_name": "probe_in_tracker"
      }
    },
    {
      "type": "transform_obj_validity_watcher",
      "name": "camera_visibility_watcher",
      "start_config": {
        "variable_name": "camera_ref_in_tracker"
      }
    },
    {
      "type": "transform_obj_validity_watcher",
      "name": "femur_visibility_watcher",
      "start_config": {
        "variable_name": "femur_ref_in_tracker"
      }
    },
    {
      "type": "transform_obj_validity_watcher",
      "name": "tibia_visibility_watcher",
      "start_config": {
        "variable_name": "tibia_ref_in_tracker"
      }
    },
    {
      "type": "scalarxyz_transformer",
      "name": "probe_tip_in_femur_ref_transformer",
      "start_config": {
        "transform_type": "point",
        "transform_var_name": "probe_in_femur_ref",
        "target_value": [
          0,
          0,
          0
        ],
        "output_var_name": "probe_tip_in_femur_ref"
      },
      "dependencies": [
        "ndi",
        "transform_tree"
      ]
    },
    {
      "type": "scalarxyz_transformer",
      "name": "probe_tip_in_tibia_ref_transformer",
      "start_config": {
        "transform_type": "point",
        "transform_var_name": "probe_in_tibia_ref",
        "target_value": [
          0,
          0,
          0
        ],
        "output_var_name": "probe_tip_in_tibia_ref"
      },
      "dependencies": [
        "ndi",
        "transform_tree"
      ]
    },
    {
      "type": "transform_stabilizer",
      "name": "point_picker_in_femur_ref",
      "start_config": {
        "stable_type": "point",
        "input_var_name": "probe_tip_in_femur_ref",
        "output_var_name": "picked_point_in_femur_ref",
        "linear_tolerance_mm": 0.05,
        "temporal_interval_s": 3
      },
      "dependencies": [
        "probe_tip_in_femur_ref_transformer"
      ]
    },
    {
      "type": "transform_stabilizer",
      "name": "point_picker_in_tibia_ref",
      "start_config": {
        "stable_type": "point",
        "input_var_name": "probe_tip_in_tibia_ref",
        "output_var_name": "picked_point_in_tibia_ref",
        "linear_tolerance_mm": 0.05,
        "temporal_interval_s": 3
      },
      "dependencies": [
        "probe_tip_in_tibia_ref_transformer"
      ]
    },
    {
      "type": "scalarxyz_obj_watcher",
      "name": "picked_point_watcher_for_femur_ref",
      "start_config": {
        "variable_name": "picked_point_in_femur_ref"
      }
    },
    {
      "type": "scalarxyz_obj_watcher",
      "name": "picked_point_watcher_for_tibia_ref",
      "start_config": {
        "variable_name": "picked_point_in_tibia_ref"
      }
    },
    {
      "type": "landmark_registration",
      "name": "femur_landmark",
      "start_config": {
        "fiducial_points": [
          [
            1.68412,
            22.5766,
            202.831
          ],
          [
            13.5083,
            -24.1831,
            200.386
          ],
          [
            26.621,
            2.0151,
            191.341
          ]
        ],
        "point_var_name": "picked_point_in_femur_ref",
        "transform_var_name": "femur_in_femur_ref",
        "error_var_name": "femur_in_femur_ref_error"
      },
      "dependencies": [
        "point_picker_in_femur_ref"
      ]
    },
    {
      "type": "landmark_registration",
      "name": "tibia_landmark",
      "start_config": {
        "fiducial_points": [
          [
            47.351,
            46.6799,
            -70.5804
          ],
          [
            -45.3668,
            23.3452,
            1.94304
          ],
          [
            -55.3382,
            -4.55638,
            54.7446
          ]
        ],
        "point_var_name": "picked_point_in_tibia_ref",
        "transform_var_name": "tibia_in_tibia_ref",
        "error_var_name": "tibia_in_tibia_ref_error"
      },
      "dependencies": [
        "point_picker_in_tibia_ref"
      ]
    },
    {
      "type": "transform_obj_watcher",
      "name": "femur_registration_result_watcher",
      "start_config": {
        "variable_name": "femur_in_femur_ref"
      }
    },
    {
      "type": "transform_obj_watcher",
      "name": "tibia_registration_result_watcher",
      "start_config": {
        "variable_name": "tibia_in_tibia_ref"
      }
    },
    {
      "type": "double_obj_watcher",
      "name": "femur_registration_error_watcher",
      "start_config": {
        "variable_name": "femur_in_femur_ref_error"
      }
    },
    {
      "type": "double_obj_watcher",
      "name": "tibia_registration_error_watcher",
      "start_config": {
        "variable_name": "tibia_in_tibia_ref_error"
      }
    },
    {
      "type": "scalarxyz_transformer",
      "name": "probe_tip_in_femur_transformer",
      "start_config": {
        "transform_type": "point",
        "transform_var_name": "probe_in_femur",
        "target_value": [
          0,
          0,
          0
        ],
        "output_var_name": "probe_tip_in_femur"
      },
      "dependencies": [
        "ndi",
        "transform_tree"
      ]
    },
    {
      "type": "scalarxyz_transformer",
      "name": "probe_tip_in_tibia_transformer",
      "start_config": {
        "transform_type": "point",
        "transform_var_name": "probe_in_tibia",
        "target_value": [
          0,
          0,
          0
        ],
        "output_var_name": "probe_tip_in_tibia"
      },
      "dependencies": [
        "ndi",
        "transform_tree"
      ]
    },
    {
      "type": "transform_stabilizer",
      "name": "point_picker_in_femur",
      "start_config": {
        "stable_type": "point",
        "input_var_name": "probe_tip_in_femur",
        "output_var_name": "picked_point_in_femur",
        "linear_tolerance_mm": 0.05,
        "temporal_interval_s": 3
      },
      "dependencies": [
        "probe_tip_in_femur_transformer"
      ]
    },
    {
      "type": "transform_stabilizer",
      "name": "point_picker_in_tibia",
      "start_config": {
        "stable_type": "point",
        "input_var_name": "probe_tip_in_tibia",
        "output_var_name": "picked_point_in_tibia",
        "linear_tolerance_mm": 0.05,
        "temporal_interval_s": 3
      },
      "dependencies": [
        "probe_tip_in_tibia_transformer"
      ]
    },
    {
      "type": "scalarxyz_obj_watcher",
      "name": "picked_point_watcher_for_femur",
      "start_config": {
        "variable_name": "picked_point_in_femur"
      }
    },
    {
      "type": "scalarxyz_obj_watcher",
      "name": "picked_point_watcher_for_tibia",
      "start_config": {
        "variable_name": "picked_point_in_tibia"
      }
    },
    {
      "type": "kalman_denoiser",
      "name": "left_camera_denoiser",
      "init_config": {
        "variable_in": "left_camera_in_tracker",
        "variable_out": "left_camera_in_tracker_denoised"
      }
    },
    {
      "type": "kalman_denoiser",
      "name": "right_camera_denoiser",
      "init_config": {
        "variable_in": "right_camera_in_tracker",
        "variable_out": "right_camera_in_tracker_denoised"
      }
    },
    {
      "type": "kalman_denoiser",
      "name": "femur_denoiser",
      "init_config": {
        "variable_in": "femur_in_tracker",
        "variable_out": "femur_in_tracker_denoised"
      }
    },
    {
      "type": "kalman_denoiser",
      "name": "tibia_denoiser",
      "init_config": {
        "variable_in": "tibia_in_tracker",
        "variable_out": "tibia_in_tracker_denoised"
      }
    },
    {
      "type": "empty_object",
      "name": "tracker_all",
      "dependencies": [
        "transform_tree",
        "ndi",
        "probe_visibility_watcher",
        "camera_visibility_watcher",
        "femur_visibility_watcher",
        "tibia_visibility_watcher",
        "left_camera_denoiser",
        "right_camera_denoiser",
        "femur_denoiser",
        "tibia_denoiser"
      ]
    },
    {
      "type": "empty_object",
      "name": "femur_landmark_all",
      "dependencies": [
        "tracker_all",
        "femur_landmark",
        "picked_point_watcher_for_femur_ref",
        "femur_registration_result_watcher",
        "femur_registration_error_watcher"
      ]
    },
    {
      "type": "empty_object",
      "name": "tibia_landmark_all",
      "dependencies": [
        "tracker_all",
        "tibia_landmark",
        "picked_point_watcher_for_tibia_ref",
        "tibia_registration_result_watcher",
        "tibia_registration_error_watcher"
      ]
    },
    {
      "type": "empty_object",
      "name": "femur_icp_all",
      "dependencies": [
        "tracker_all",
        "point_picker_in_femur",
        "picked_point_watcher_for_femur"
      ]
    },
    {
      "type": "empty_object",
      "name": "tibia_icp_all",
      "dependencies": [
        "tracker_all",
        "point_picker_in_tibia",
        "picked_point_watcher_for_tibia"
      ]
    }
  ]
}