You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
{{ message }}
This repository has been archived by the owner on Mar 17, 2021. It is now read-only.
It has always been hard for me to find the line containing information about the errors in NiftyNet output. Oftentimes I find the line that seems to give trouble, but it's not clear to me what I need to do to solve it.
I think this is a recurrent issue for other users as well:
CRITICAL:niftynet: Don't know how to generate sampling locations: Spatial dimensions of the grouped input sources are not consistent. {(477, 451, 187), (391, 369, 147)}
Exception in thread Thread-2:
Solution:
the corresponding image and labels have different voxel spacing values stored in header
I'm just posting just the main error line, but for example the traceback for that last error was very verbose:
Traceback (most recent call last):
File "/Users/fernando/anaconda/envs/nn/bin/net_segment", line 11, in <module>
sys.exit(main())
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/__init__.py", line 115, in main
app_driver.run_application()
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/engine/application_driver.py", line 241, in run_applicationself.graph =self._create_graph(self.graph)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/engine/application_driver.py", line 309, in _create_graphself.gradients_collector)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/application/segmentation_application.py", line 266, in connect_data_and_network
net_out =self.net(image, is_training=self.is_training)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 34, in __call__returnself._op(*args, **kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 455, in __call__
result =self._call_func(args, kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 406, in _call_func
result =self._func(*args, **kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/network/vnet.py", line 121, in layer_op
name='R1')(concat_r1, up_1)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 34, in __call__returnself._op(*args, **kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 455, in __call__
result =self._call_func(args, kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 406, in _call_func
result =self._func(*args, **kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/network/vnet.py", line 186, in layer_op
kernel_size=1, with_bias=True)(res_flow)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 34, in __call__returnself._op(*args, **kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 455, in __call__
result =self._call_func(args, kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 406, in _call_func
result =self._func(*args, **kwargs)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/convolution.py", line 83, in layer_op
regularizer=self.regularizers['w'])
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/variable_scope.py", line 1297, in get_variable
constraint=constraint)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/variable_scope.py", line 1093, in get_variable
constraint=constraint)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/variable_scope.py", line 439, in get_variable
constraint=constraint)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/variable_scope.py", line 408, in _true_getter
use_resource=use_resource, constraint=constraint)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/variable_scope.py", line 735, in _get_single_variable
shape = tensor_shape.as_shape(shape)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/framework/tensor_shape.py", line 860, in as_shapereturn TensorShape(shape)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/framework/tensor_shape.py", line 458, in __init__self._dims = [as_dimension(d) for d in dims_iter]
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/framework/tensor_shape.py", line 458, in <listcomp>self._dims = [as_dimension(d) for d in dims_iter]
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/framework/tensor_shape.py", line 399, in as_dimensionreturn Dimension(value)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/framework/tensor_shape.py", line 39, in __init__raiseValueError("Dimension %d must be >= 0"%self._value)
ValueError: Dimension -1 must be >= 0
originally defined at:
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/convolution.py", line 50, in __init__super(ConvLayer, self).__init__(name=name)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 58, in __init__super(TrainableLayer, self).__init__(name=name)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 26, in __init__self._op = tf.make_template(name, self.layer_op, create_scope_now_=True)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 153, in make_template**kwargs)
originally defined at:
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/network/vnet.py", line 141, in __init__super(VNetBlock, self).__init__(name=name)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 58, in __init__super(TrainableLayer, self).__init__(name=name)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 26, in __init__self._op = tf.make_template(name, self.layer_op, create_scope_now_=True)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 153, in make_template**kwargs)
originally defined at:
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/engine/application_driver.py", line 295, in _create_graphself.app.initialise_network()
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/application/segmentation_application.py", line 235, in initialise_network
acti_func=self.net_param.activation_function)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/network/vnet.py", line 39, in __init__
name=name)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/network/base_net.py", line 21, in __init__super(BaseNet, self).__init__(name=name)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 58, in __init__super(TrainableLayer, self).__init__(name=name)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/niftynet/layer/base_layer.py", line 26, in __init__self._op = tf.make_template(name, self.layer_op, create_scope_now_=True)
File "/Users/fernando/anaconda/envs/nn/lib/python3.6/site-packages/tensorflow/python/ops/template.py", line 153, in make_template**kwargs)
It has always been hard for me to find the line containing information about the errors in NiftyNet output. Oftentimes I find the line that seems to give trouble, but it's not clear to me what I need to do to solve it.
I think this is a recurrent issue for other users as well:
#273
Error:
Solution:
#260
Error:
Solution:
#170
Error:
Solution:
Error:
Solution:
I'm just posting just the main error line, but for example the traceback for that last error was very verbose:
I think Keras does a good job handling this: https://blog.keras.io/user-experience-design-for-apis.html
The text was updated successfully, but these errors were encountered: