Commit bbc3c0fb authored by Wenqi Li's avatar Wenqi Li

Merge branch 'unet-demo' into 'dev'

Unet demo See merge request CMIC/NiftyNet!272
parents 0039a418 bd2229e7
Pipeline #12143 passed with stages
in 84 minutes 12 seconds
......@@ -17,6 +17,7 @@ testing_data*
*.csv
*.swp
data/brain_parcellation/OASIS
data/u-net
dist
build
*.egg-info
......@@ -27,3 +28,6 @@ doc/source/niftynet*
doc/source/modules.rst
.vscode/
.ipynb_checkpoints
demos/unet/run_U373.sh
demos/unet/run_hela.sh
[cells]
path_to_search = ./data/u-net/DIC-C2DH-HeLa/niftynet_data
filename_contains = img_
spatial_window_size = (572, 572, 1)
interp_order = 3
loader = skimage
[label]
path_to_search = ./data/u-net/DIC-C2DH-HeLa/niftynet_data
filename_contains = bin_seg_
spatial_window_size = (388, 388, 1)
interp_order = 0
loader = skimage
[xent_weights]
path_to_search = ./data/u-net/DIC-C2DH-HeLa/niftynet_data
filename_contains = weight_
spatial_window_size = (388, 388, 1)
interp_order = 3
loader = skimage
[SYSTEM]
cuda_devices = ""
num_threads = 6
num_gpus = 1
[NETWORK]
name = unet_2d
activation_function = relu
batch_size = 4
# volume level preprocessing
volume_padding_size = (92, 92, 0)
volume_padding_mode = symmetric
whitening = True
normalise_foreground_only=False
queue_length = 20
window_sampling = uniform
[TRAINING]
sample_per_volume = 2
random_flipping_axes=-1
lr = 0.0003
loss_type = CrossEntropy
starting_iter = 0
save_every_n = 200
max_iter = 2000
max_checkpoints = 10
do_elastic_deformation = False
deformation_sigma = 50
num_ctrl_points = 6
proportion_to_deform=0.9
validation_every_n = 10
validation_max_iter = 1
[INFERENCE]
border = (92, 92, 0)
inference_iter = -1
save_seg_dir = ./output
output_interp_order = 0
spatial_window_size = (572,572,1)
############################ custom configuration sections
[SEGMENTATION]
image = cells
label = label
output_prob = False
num_classes = 2
label_normalisation = False
weight = xent_weights
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