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Scutoid_BC config #64

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41 changes: 41 additions & 0 deletions configs/Scutoid_Exp_1_BC.yaml
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# For binary mask & instance contour prediction.
# All other configurations are set by default. If you want to add new config options,
# please modify ../connectomics/config/config.py
# 30x8x8 nm in (z,y,x), 1000x4096x4096 voxel
SYSTEM:
NUM_GPUS: 4
NUM_CPUS: 4
MODEL:
ARCHITECTURE: 'unet_residual_3d'
INPUT_SIZE: [32, 256, 256]
OUTPUT_SIZE: [32, 256, 256]
IN_PLANES: 1
OUT_PLANES: 2
LOSS_OPTION: [['WeightedBCE'], ['WeightedBCE']]
LOSS_WEIGHT: [[1.0], [1.0]]
TARGET_OPT: ['0','4-2-1']
WEIGHT_OPT: [['1'],['1']]
DATASET:
IMAGE_NAME: 'Raw_LateralMembranes/vol00.tif'
LABEL_NAME: 'Labelled/vol00.tif'
INPUT_PATH: '/n/pfister_lab2/Lab/vcg_connectomics/LM/Cysts_Dec2020/'
OUTPUT_PATH: 'outputs/Scutoid_Exp_1/'
PAD_SIZE: [16, 128, 128]
SOLVER:
LR_SCHEDULER_NAME: "WarmupMultiStepLR"
BASE_LR: 1e-03
ITERATION_STEP: 1
ITERATION_SAVE: 200
ITERATION_TOTAL: 100000
SAMPLES_PER_BATCH: 4
INFERENCE:
INPUT_SIZE: [32, 256, 256]
OUTPUT_SIZE: [32, 256, 256]
IMAGE_NAME: 'Raw_LaterMembranes/vol01.tif@Raw_LateralMembranes/vol02.tif@Raw_LateralMembranes/vol03.tif@Raw_LateralMembranes/vol04.tif@Raw_LateralMembranes/vol05.tif@Raw_LateralMembranes/vol06.tif@Raw_LateralMembranes/vol07.tif@Raw_LateralMembranes/vol08.tif@Raw_LateralMembranes/vol09.tif@Raw_LateralMembranes/vol10.tif@Raw_LateralMembranes/vol11.tif@Raw_LateralMembranes/vol12.tif@Raw_LateralMembranes/vol13.tif@Raw_LateralMembranes/vol14.tif@Raw_LateralMembranes/vol15.tif@Raw_LateralMembranes/vol16.tif@Raw_LateralMembranes/vol17.tif@Raw_LateralMembranes/vol18.tif@Raw_LateralMembranes/vol19.tif'
OUTPUT_PATH: 'outputs/Scutoid_Exp_1/test'
OUTPUT_NAME: 'result.h5'
PAD_SIZE: [16, 128, 128]
AUG_MODE: 'mean'
AUG_NUM: 4
STRIDE: [16, 128, 128]
SAMPLES_PER_BATCH: 16