gevi/new_pipeline/config.json

{
    "basic_path": "/data_1/hendrik",
    "recoding_data": "2021-06-17",
    "mouse_identifier": "M3859M",
    //"basic_path": "/data_1/robert",
    //"recoding_data": "2021-10-05",
    //"mouse_identifier": "M3879M",
    "raw_path": "raw",
    "export_path": "output",
    "ref_image_path": "ref_images",
    // Ratio Sequence
    "classical_ratio_mode": true, // true: a/d false: 1+a-d
    // Regression
    "target_camera_acceptor": "acceptor",
    "regressor_cameras_acceptor": [
        "oxygenation",
        "volume"
    ],
    "target_camera_donor": "donor",
    "regressor_cameras_donor": [
        "oxygenation",
        "volume"
    ],
    // binning
    "binning_enable": true,
    "binning_at_the_end": false,
    "binning_kernel_size": 4,
    "binning_stride": 4,
    "binning_divisor_override": 1,
    // alignment
    "alignment_batch_size": 200,
    "rotation_stabilization_threshold_factor": 3.0, // >= 1.0
    "rotation_stabilization_threshold_border": 0.9, // <= 1.0
    // Heart beat detection
    "lower_freqency_bandpass": 5.0, // Hz
    "upper_freqency_bandpass": 14.0, // Hz
    "heartbeat_filtfilt_chuck_size": 10,
    // Gauss smear 
    "gauss_smear_spatial_width": 8,
    "gauss_smear_temporal_width": 0.1,
    "gauss_smear_use_matlab_mask": false,
    // LED Ramp on
    "skip_frames_in_the_beginning": 100, // Frames
    // PyTorch
    "dtype": "float32",
    "force_to_cpu": false,
    // Save
    "save_as_python": true, // produces .npz files (compressed)
    "save_as_matlab": false, // produces .hd5 file (compressed)
    // Save extra information
    "save_alignment": false,
    "save_heartbeat": false,
    "save_factors": false,
    "save_regression_coefficients": false,
    // Not important parameter
    "required_order": [
        "acceptor",
        "donor",
        "oxygenation",
        "volume"
    ]
}