I want to use niftynet pretrained segmentation model for segmenting custom data. I downloaded the pre trained weights and and modified model_dir path to downloaded one.
However when I run
python3 net_segment.py train -c /home/Container_data/config/promise12_demo_train_config.ini
I am getting the error below.
Caused by op 'save/Assign_17', defined at:
File "net_segment.py", line 8, in <module>
sys.exit(main())
File "/home/NiftyNet/niftynet/__init__.py", line 142, in main
app_driver.run(app_driver.app)
File "/home/NiftyNet/niftynet/engine/application_driver.py", line 197, in run
SESS_STARTED.send(application, iter_msg=None)
File "/usr/local/lib/python3.5/dist-packages/blinker/base.py", line 267, in send
for receiver in self.receivers_for(sender)]
File "/usr/local/lib/python3.5/dist-packages/blinker/base.py", line 267, in <listcomp>
for receiver in self.receivers_for(sender)]
File "/home/NiftyNet/niftynet/engine/handler_model.py", line 109, in restore_model
var_list=to_restore, save_relative_paths=True)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/training/saver.py", line 1102, in __init__
self.build()
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/training/saver.py", line 1114, in build
self._build(self._filename, build_save=True, build_restore=True)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/training/saver.py", line 1151, in _build
build_save=build_save, build_restore=build_restore)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/training/saver.py", line 795, in _build_internal
restore_sequentially, reshape)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/training/saver.py", line 428, in _AddRestoreOps
assign_ops.append(saveable.restore(saveable_tensors, shapes))
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/training/saver.py", line 119, in restore
self.op.get_shape().is_fully_defined())
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/ops/state_ops.py", line 221, in assign
validate_shape=validate_shape)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/ops/gen_state_ops.py", line 61, in assign
use_locking=use_locking, name=name)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/framework/op_def_library.py", line 787, in _apply_op_helper
op_def=op_def)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/util/deprecation.py", line 488, in new_func
return func(*args, **kwargs)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/framework/ops.py", line 3274, in create_op
op_def=op_def)
File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/framework/ops.py", line 1770, in __init__
self._traceback = tf_stack.extract_stack()
InvalidArgumentError (see above for traceback): Restoring from checkpoint failed. This is most likely due to a mismatch between the current graph and the graph from the checkpoint. Please ensure that you have not altered the graph expected based on the checkpoint. Original error:
Assign requires shapes of both tensors to match. lhs shape= [3,3,61,256] rhs shape= [3,3,3,61,9]
[[node save/Assign_17 (defined at /home/NiftyNet/niftynet/engine/handler_model.py:109) = Assign[T=DT_FLOAT, _class=["loc:@DenseVNet/conv/conv_/w"], use_locking=true, validate_shape=true, _device="/job:localhost/replica:0/task:0/device:GPU:0"](DenseVNet/conv/conv_/w, save/RestoreV2/_35)
https://github.com/tensorflow/models/issues/5390 Above link says to add
--initialize_last_layer = False
--last_layers_contain_logits_only = False
Can some one help me how to get rid of this error.
