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lightmycells_actin.yaml
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lightmycells_actin.yaml
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# BiaPy version: 3.4.3
SYSTEM:
NUM_CPUS: -1
NUM_WORKERS: 5
PROBLEM:
TYPE: IMAGE_TO_IMAGE
NDIM: 2D
IMAGE_TO_IMAGE:
MULTIPLE_RAW_ONE_TARGET_LOADER: True
DATA:
PATCH_SIZE: (1024, 1024, 1)
EXTRACT_RANDOM_PATCH: False
REFLECT_TO_COMPLETE_SHAPE: True
NORMALIZATION:
TYPE: 'custom'
APPLICATION_MODE: 'image'
TRAIN:
PATH: /path/actin/x
GT_PATH: /path/actin/y
IN_MEMORY: False
VAL:
DIST_EVAL: True
PATH: /path/actin/val_x
GT_PATH: /path/actin/val_y
IN_MEMORY: False
FROM_TRAIN: False
SPLIT_TRAIN: 0.1
TEST:
PATH: /path/actin/val_x
IN_MEMORY: False
LOAD_GT: False
PADDING: (200,200)
AUGMENTOR:
ENABLE: True
ROT90: True
VFLIP: True
HFLIP: True
BRIGHTNESS: True
CONTRAST: True
ELASTIC: True
RANDOM_ROT: True
AFFINE_MODE: 'mirror'
GRIDMASK: True
GRID_D_RANGE: (0.2, 0.6)
MODEL:
ARCHITECTURE: unetr
VIT_TOKEN_SIZE: 32
VIT_EMBED_DIM: 768
VIT_NUM_LAYERS: 12
VIT_NUM_HEADS: 12
VIT_MLP_RATIO: 4.
VIT_NORM_EPS: 1.E-6
UNETR_VIT_HIDD_MULT: 3
UNETR_VIT_NUM_FILTERS: 32
UNETR_DEC_ACTIVATION: 'relu'
UNETR_DEC_KERNEL_SIZE: 9
N_CLASSES: 2
LOAD_CHECKPOINT: True
TRAIN:
ENABLE: False
OPTIMIZER: ADAMW
LR: 1.E-4
BATCH_SIZE: 1
EPOCHS: 1300
PATIENCE: 500
LR_SCHEDULER:
NAME: 'warmupcosine'
MIN_LR: 5.E-6
WARMUP_COSINE_DECAY_EPOCHS: 80
TEST:
ENABLE: True
AUGMENTATION: False
PATHS:
CHECKPOINT_FILE: /path/checkpoints/lightmycells_actin.pth