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Error while fine-tuning the XDXD_SpaceNet4 model for Spacenet 2 dataset
File "train.py", line 25, in <module>
train()
File "train.py", line 19, in train
xdxd_trainer.train()
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/solaris/nets/train.py", line 123, in train
for batch_idx, batch in enumerate(self.train_datagen):
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 435, in __next__
data = self._next_data()
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/torch/utils/data/dataloader.py", line 475, in _next_data
data = self._dataset_fetcher.fetch(index) # may raise StopIteration
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in fetch
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/torch/utils/data/_utils/fetch.py", line 44, in <listcomp>
data = [self.dataset[idx] for idx in possibly_batched_index]
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/solaris/nets/datagen.py", line 343, in __getitem__
mask = imread(self.df['label'].iloc[idx])
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/solaris/utils/io.py", line 52, in imread
im_arr = skimage.io.imread(path)
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/skimage/io/_io.py", line 48, in imread
img = call_plugin('imread', fname, plugin=plugin, **plugin_args)
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/skimage/io/manage_plugins.py", line 209, in call_plugin
return func(*args, **kwargs)
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/skimage/io/_plugins/imageio_plugin.py", line 10, in imread
return np.asarray(imageio_imread(*args, **kwargs))
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/imageio/core/functions.py", line 265, in imread
reader = read(uri, format, "i", **kwargs)
File "/root/anaconda3/envs/solaris/lib/python3.7/site-packages/imageio/core/functions.py", line 182, in get_reader
"Could not find a format to read the specified file in %s mode" % modename
ValueError: Could not find a format to read the specified file in single-image mode
The Yaml file used for training is given below:
model_path:
train: true
infer: true
pretrained: false
nn_framework: torch
batch_size: 6
data_specs:
width: 512
height: 512
image_type: zscore
dtype: uint16
rescale: false
rescale_minima: auto
rescale_maxima: auto
channels: 3
label_type: mask
is_categorical: false
mask_channels: 1
val_holdout_frac: 0.025
data_workers:
training_data_csv: 'train.csv'
validation_data_csv:
inference_data_csv: 'test.csv'
training_augmentation:
augmentations:
SwapChannels:
axis: 2
first_idx: 0
second_idx: 2
p: 1.0
HorizontalFlip:
p: 0.5
RandomRotate90:
p: 0.5
RandomCrop:
height: 512
width: 512
p: 1.0
Normalize:
mean:
- 0.008168729867753285
- 0.00925316105319106
- 0.006374030239981403
std:
- 0.0015652700379067738
- 0.0015060764772977708
- 0.0008859458739022634
max_pixel_value: 65535.0
p: 1.0
p: 1.0
shuffle: true
validation_augmentation:
augmentations:
SwapChannels:
axis: 2
first_idx: 0
second_idx: 2
p: 1.0
CenterCrop:
height: 512
width: 512
p: 1.0
Normalize:
mean:
- 0.008168729867753285
- 0.00925316105319106
- 0.006374030239981403
std:
- 0.0015652700379067738
- 0.0015060764772977708
- 0.0008859458739022634
max_pixel_value: 65535.0
p: 1.0
p: 1.0
inference_augmentation:
augmentations:
SwapChannels:
axis: 2
first_idx: 0
second_idx: 2
p: 1.0
Normalize:
mean:
- 0.008168729867753285
- 0.00925316105319106
- 0.006374030239981403
std:
- 0.0015652700379067738
- 0.0015060764772977708
- 0.0008859458739022634
max_pixel_value: 65535.0
p: 1.0
p: 1.0
training:
epochs: 300
steps_per_epoch:
optimizer: Adam
lr: 1e-5
opt_args:
loss:
bcewithlogits:
jaccard:
loss_weights:
bcewithlogits: 10
jaccard: 2.5
metrics:
training:
validation:
checkpoint_frequency: 10
callbacks:
model_checkpoint:
filepath: 'models/xdxd_best.pth'
monitor: val_loss
model_dest_path: 'models/xdxd_final.pth'
verbose: true
inference:
window_step_size_x:
window_step_size_y:
output_dir: 'inference_out/'