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Copy pathparameter.json
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155 lines (149 loc) · 6.84 KB
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{
"input_size": [54, 268, 268],
"downsample_factors": [[1, 3, 3], [2, 3, 3], [3, 3, 3]],
"kernel_size": 3,
"fmap_num": 12,
"fmap_inc_factor": 4,
"norm_type": "group",
"batch_size": 1,
"learning_rate": 4e-4,
"loss_comb_type": "sum",
"m_loss_scale": 3.0,
"d_loss_scale": 0.02,
"reject_probability": 0.85,
"blob_radius": [1, 3, 3],
"d_blob_radius": [3, 15, 15],
"vec_normalize_by_magnitude": true,
"vec_channel_weights": [1.0, 1.0, 1.0],
"focal_gamma": 0,
"focal_gamma_schedule": { "step": 450000, "gamma": 1.0 },
"balance_labels": true,
"balance_scale": 2.0,
"warmup_steps": 10000,
"cosine_period": 700000,
"voxel_size": [1, 1, 1],
"max_iteration": 1000000,
"use_amp": true,
"grad_checkpoint": false,
"gpu_elastic": true,
"device_num": 0,
"model_name": "my_model",
"tensorboard_dir": "tensorboard_my_model",
"snapshot_dir": "snapshots_my_model",
"snapshot_every": 10000,
"save_every": 50000,
"log_every": 100,
"num_data_workers": 8,
"augmentation": {
"simple": { "enabled": true, "apply_prob": 0.9 },
"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": 0.4, "correct_vectors": true },
"intensity": { "enabled": true, "apply_prob": 0.85, "scale_range": [0.7, 1.3], "shift_range": [-0.2, 0.2], "z_section_wise": true },
"noise": { "enabled": true, "apply_prob": 0.85, "var_range": [0.0, 0.15] },
"defect": { "enabled": true, "prob_missing": 0.05, "prob_dark": 0.05, "prob_shift": 0.05, "max_shift_px": 24 },
"blur": { "enabled": true, "prob": 0.5, "sigma_range": [0.0, 1.2] },
"gamma": { "enabled": true, "apply_prob": 0.75, "gamma_range": [0.5, 1.2] },
"invert": { "enabled": true, "prob": 0.02 },
"cutout": { "enabled": true, "prob": 0.5, "n_holes": 3, "hole_size_yx": [30, 30] },
"salt_pepper": { "enabled": true, "prob": 0.005 }
},
"zarr_locs": [
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_FB_1.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_FB_2.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_FB_3.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_FB_4.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_FB_5.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_PB_1.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_PB_2.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_PB_3.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_PB_4.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_PB_5.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_PB_6.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_NO_1.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_NO_2.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_NO_3.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_NO_4.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_NO_5.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/megalopta_NO_6.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_FB_1.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_FB_2.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_FB_3.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_FB_4.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_FB_5.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_NO_1.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_NO_2.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_NO_3.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_NO_4.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_NO_5.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_PB_1.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_PB_2.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_PB_3.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_PB_4.zarr",
"/mnt/hdd3/DATA/syn_train_raws_3/zarrs/eciton_PB_5.zarr"
],
"csv_dir": "/mnt/hdd3/DATA/syn_train_raws_3/csvs",
"json_dir": "/mnt/hdd3/DATA/syn_train_raws_3/jsons",
"predict": {
"input_size": [54, 268, 268],
"output_size": [12, 134, 134],
"raw_file": "/mnt/hdd3/DATA/megalopta/megalopta_PB2_rechunked.zarr",
"raw_dataset": "RAW",
"read_offset": [-1, -1, -1],
"read_shape": [-1, -1, -1],
"out_directory": ".",
"out_filename": "output.zarr",
"overwrite": false,
"checkpoint_dir": "snapshots_my_model",
"checkpoint_num": 1000000,
"model_name": "my_model",
"device_num": "0",
"batch_size": 4,
"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": "output.zarr",
"raw_file": "/mnt/raid/image_data/megalopta/megalopta_PB2.zarr",
"raw_dataset": "raw",
"cc_threshold": 0.6,
"loc_type": "centroid",
"score_thr": 0.6,
"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": 8
},
"to_json_config": {
"output_name": "./output.json"
},
"match_to_roots": {
"synapses_filepath": "./output.csv",
"fragments_filepath": "/mnt/raid/segmentation/megalopta/megalopta_PB2_03.zarr",
"raw_file": "/mnt/raid/image_data/megalopta/megalopta_PB2.zarr",
"pcg_datastack": "megalopta_pb2_datastack",
"chunk_shape_xyz": [500, 500, 100],
"num_workers": 8,
"output_file": "./output_with-roots.csv",
"only_catmaid": false,
"catmaid_pid": 8,
"voxel_size_zyx": [50, 10, 10]
}
}