Comments (4)
Hi @CourantNg for some reason the string (in sampler_resize.py)
is parsed from the config file as a user parameter, could you please post the relevant config file section?
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Thanks for your quick reply. Following is my config.
[image]
path_to_search =
filename_contains = volume
filename_not_contains = segmentation
spatial_window_size = (128, 128, 64)
interp_order = 1
axcodes=(A, R, S)
[label]
path_to_search =
filename_contains = segmentation
filename_not_contains = volume
spatial_window_size = (128, 128, 64)
interp_order = 0
axcodes=(A, R, S)
############################## system configuration sections
[SYSTEM]
cuda_devices = ""
num_threads = 2
num_gpus = 1
model_dir =
[NETWORK]
name = vnet
activation_function = prelu
batch_size = 2
# volume level preprocessing
volume_padding_size = 0
window_sampling = resize
normalisation = False
whitening = False
queue_length = 6
[TRAINING]
sample_per_volume = 4
lr = 0.00002
loss_type = Dice
starting_iter = 0
save_every_n = 400
max_iter = 10001
max_checkpoints = 20
tensorboard_every_n = 10
validation_every_n = 50
exclude_fraction_for_validation = 0.025
exclude_fraction_for_inference = 0.025
[INFERENCE]
border = (5, 5, 5)
save_seg_dir =
output_interp_order = 0
spatial_window_size = (0, 0, 3)
############################ custom configuration sections
[SEGMENTATION]
image = image
label = label
output_prob = False
num_classes = 2
label_normalisation = True
min_numb_labels = 2
min_sampling_ratio = 0.000001
from niftynet.
This bit is suspicious, , was it added for debugging?
E:\Yang\niftynet\engine\sampler_resize.py", line 60, in __init__
" [-1 for dynamic size]", self.window.shapes, "(in sampler_resize.py)")
removing , "(in sampler_resize.py)"
should work.
from niftynet.
Dear @wyli
You are right.
Thank you very much for your time and help.
from niftynet.
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