SynPred/param_template.json at master · Heinze-lab/SynPred · GitHub

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{
    "input_size":          [54, 268, 268],
    "downsample_factors":  [[1, 3, 3], [1, 3, 3], [3, 3, 3]],
    "kernel_size":         3,
    "fmap_num":            12,
    "fmap_inc_factor":     4,
    "norm_type":           "group",
    "batch_size":          1,
    "learning_rate":       2.5e-4,
    "loss_comb_type":      "sum",
    "m_loss_scale":        3.0,
    "d_loss_scale":        0.02,
    "reject_probability":  0.85,
    "blob_radius":         [1, 6, 6],
    "d_blob_radius":       [3, 20, 20],
    "vec_channel_weights": [1.0, 1.0, 1.0],
    "vec_normalize_by_magnitude": true,
    "focal_gamma":         0,
    "focal_gamma_schedule": { "step": 400000, "gamma": 1.0 },
    "mask_pos_weight":     200.0,
    "warmup_steps":        8000,
    "cosine_period":       400000,
    "voxel_size":          [1, 1, 1],
    "max_iteration":       500000,
    "use_amp":             true,
    "device_num":          0,
    "model_name":          "my_model",
    "tensorboard_dir":     "tensorboard_my_model",
    "snapshot_dir":        "snapshots_my_model",
    "snapshot_every":      1000,
    "save_every":          10000,
    "log_every":           100,
    "num_data_workers":    8,

    "augmentation": {
        "simple":       { "enabled": true,  "apply_prob": 0.8 },
        "elastic":      { "enabled": true,  "apply_prob": 0.2, "control_point_spacing": [50, 10, 10], "jitter_sigma": [0, 4.0, 4.0], "prob_slip": 0.25, "prob_shift": 0.25, "prob_elastic": 0.2, "correct_vectors": false },
        "intensity":    { "enabled": true,  "apply_prob": 0.6, "scale_range": [0.8, 1.2], "shift_range": [-0.15, 0.15], "z_section_wise": true },
        "noise":        { "enabled": true,  "apply_prob": 0.75, "var_range": [0.0, 0.1] },
        "defect":       { "enabled": true,  "prob_missing": 0.03, "prob_dark": 0.03, "prob_shift": 0.03, "max_shift_px": 16 },
        "blur":         { "enabled": true,  "prob": 0.1, "sigma_range": [0.0, 0.7] },
        "gamma":        { "enabled": true,  "apply_prob": 0.6, "gamma_range": [0.6, 1.0] },
        "invert":       { "enabled": false, "prob": 0.01 },
        "cutout":       { "enabled": true,  "prob": 0.3, "n_holes": 2, "hole_size_yx": [20, 20] },
        "salt_pepper":  { "enabled": true,  "prob": 0.003 }
    },

    "zarr_locs": [
        "/path/to/zarrs/species_region_1.zarr",
        "/path/to/zarrs/species_region_2.zarr"
    ],
    "csv_dir":  "/path/to/csvs",

    "predict": {
        "input_size":      [54, 268, 268],
        "output_size":     [12, 134, 134],
        "raw_file":        "/path/to/raw_volume.zarr",
        "raw_dataset":     "RAW",
        "read_offset":     [-1, -1, -1],
        "read_shape":      [-1, -1, -1],
        "out_directory":   ".",
        "out_filename":    "prediction.zarr",
        "overwrite":       true,
        "checkpoint_dir":  "snapshots_my_model",
        "checkpoint_num":  500000,
        "model_name":      "my_model",
        "device_num":      "0",
        "batch_size":      3,
        "prefetch_blocks": 16,
        "compile":         true,
        "compile_mode":    "default",
        "out_properties": {
            "pred_syn_indicators": {
                "dsname": "pred_syn_indicators",
                "dtype":  "uint8",
                "scale":  255
            },
            "pred_partner_vectors": {
                "dsname": "pred_partner_vectors",
                "dtype":  "int8",
                "scale":  [1, 1, 1]
            }
        }
    },

    "extract_configs": {
        "inference_dir":   "./",
        "inference_file":  "prediction.zarr",
        "raw_file":        "/path/to/raw_volume.zarr",
        "raw_dataset":     "RAW",
        "cc_threshold":    0.7,
        "loc_type":        "centroid",
        "score_thr":       0.7,
        "score_type":      "mean",
        "size_thr":        20,
        "nms_radius":      10,
        "flipprepost":     false,
        "post_offset_scale": 0,
        "vector_scale":    [50, 1, 1],
        "block_size_zyx":  [24, 268, 268],
        "context_zyx":     [12, 20, 20],
        "num_workers":     4
    },

    "to_json_config": {
        "output_name": "./prediction.json"
    },

    "match_to_roots": {
        "synapses_filepath":  "./prediction.csv",
        "fragments_filepath": "/path/to/segmentation.zarr",
        "raw_file":           "/path/to/raw_volume.zarr",
        "pcg_datastack":      "my_datastack",
        "chunk_shape_xyz":    [500, 500, 100],
        "num_workers":        8,
        "output_file":        "./prediction_with-roots.csv",
        "only_catmaid":       false,
        "catmaid_pid":        0,
        "voxel_size_zyx":     [50, 10, 10]
    }
}