From bd2f2e939de848e4d769670383cb59f768b45212 Mon Sep 17 00:00:00 2001 From: Shray Mathur Date: Tue, 12 Jan 2021 13:13:03 -0500 Subject: [PATCH] Scutoid Exp 1 BC config --- configs/Scutoid_Exp_1_BC.yaml | 41 +++++++++++++++++++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 configs/Scutoid_Exp_1_BC.yaml diff --git a/configs/Scutoid_Exp_1_BC.yaml b/configs/Scutoid_Exp_1_BC.yaml new file mode 100644 index 00000000..98866809 --- /dev/null +++ b/configs/Scutoid_Exp_1_BC.yaml @@ -0,0 +1,41 @@ +# 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