Error messages while using the 2D example SEM in google colab
guijacquemet opened this issue · comments
When running the 2D example SEM example of n2v in google colab I now receive several error messages. It was working fine yesterday.
The main error happens during the training. One Epoch is completed successfully but then it crashes:
W0620 10:18:39.233062 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/optimizers.py:790: The name tf.train.Optimizer is deprecated. Please use tf.compat.v1.train.Optimizer instead.
W0620 10:18:47.475789 140231502292864 lazy_loader.py:50]
The TensorFlow contrib module will not be included in TensorFlow 2.0.
For more information, please see:
- https://github.com/tensorflow/community/blob/master/rfcs/20180907-contrib-sunset.md
- https://github.com/tensorflow/addons
- https://github.com/tensorflow/io (for I/O related ops)
If you depend on functionality not listed there, please file an issue.
W0620 10:18:47.630948 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/csbdeep/utils/tf.py:240: The name tf.summary.image is deprecated. Please use tf.compat.v1.summary.image instead.
W0620 10:18:48.145319 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/csbdeep/utils/tf.py:268: The name tf.summary.merge is deprecated. Please use tf.compat.v1.summary.merge instead.
W0620 10:18:48.149436 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/csbdeep/utils/tf.py:275: The name tf.summary.FileWriter is deprecated. Please use tf.compat.v1.summary.FileWriter instead.
Epoch 1/10
20/20 [==============================] - 23s 1s/step - loss: 1.2110 - n2v_mse: 1.2110 - n2v_abs: 0.8920 - val_loss: 1.5108 - val_n2v_mse: 1.5108 - val_n2v_abs: 0.9683
InvalidArgumentError Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py in _do_call(self, fn, *args)
1355 try:
-> 1356 return fn(*args)
1357 except errors.OpError as e:
12 frames
InvalidArgumentError: You must feed a value for placeholder tensor 'Placeholder' with dtype float and shape [?,?,?,1]
[[{{node Placeholder}}]]
During handling of the above exception, another exception occurred:
InvalidArgumentError Traceback (most recent call last)
/usr/local/lib/python3.6/dist-packages/tensorflow/python/client/session.py in _do_call(self, fn, *args)
1368 pass
1369 message = error_interpolation.interpolate(message, self._graph)
-> 1370 raise type(e)(node_def, op, message)
1371
1372 def _extend_graph(self):
InvalidArgumentError: You must feed a value for placeholder tensor 'Placeholder' with dtype float and shape [?,?,?,1]
[[node Placeholder (defined at /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:517) ]]
Original stack trace for 'Placeholder':
File "/usr/lib/python3.6/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/usr/lib/python3.6/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/usr/local/lib/python3.6/dist-packages/ipykernel_launcher.py", line 16, in
app.launch_new_instance()
File "/usr/local/lib/python3.6/dist-packages/traitlets/config/application.py", line 658, in launch_instance
app.start()
File "/usr/local/lib/python3.6/dist-packages/ipykernel/kernelapp.py", line 477, in start
ioloop.IOLoop.instance().start()
File "/usr/local/lib/python3.6/dist-packages/tornado/ioloop.py", line 888, in start
handler_func(fd_obj, events)
File "/usr/local/lib/python3.6/dist-packages/tornado/stack_context.py", line 277, in null_wrapper
return fn(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/zmq/eventloop/zmqstream.py", line 450, in _handle_events
self._handle_recv()
File "/usr/local/lib/python3.6/dist-packages/zmq/eventloop/zmqstream.py", line 480, in _handle_recv
self._run_callback(callback, msg)
File "/usr/local/lib/python3.6/dist-packages/zmq/eventloop/zmqstream.py", line 432, in _run_callback
callback(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/tornado/stack_context.py", line 277, in null_wrapper
return fn(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/ipykernel/kernelbase.py", line 283, in dispatcher
return self.dispatch_shell(stream, msg)
File "/usr/local/lib/python3.6/dist-packages/ipykernel/kernelbase.py", line 235, in dispatch_shell
handler(stream, idents, msg)
File "/usr/local/lib/python3.6/dist-packages/ipykernel/kernelbase.py", line 399, in execute_request
user_expressions, allow_stdin)
File "/usr/local/lib/python3.6/dist-packages/ipykernel/ipkernel.py", line 196, in do_execute
res = shell.run_cell(code, store_history=store_history, silent=silent)
File "/usr/local/lib/python3.6/dist-packages/ipykernel/zmqshell.py", line 533, in run_cell
return super(ZMQInteractiveShell, self).run_cell(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/IPython/core/interactiveshell.py", line 2718, in run_cell
interactivity=interactivity, compiler=compiler, result=result)
File "/usr/local/lib/python3.6/dist-packages/IPython/core/interactiveshell.py", line 2822, in run_ast_nodes
if self.run_code(code, result):
File "/usr/local/lib/python3.6/dist-packages/IPython/core/interactiveshell.py", line 2882, in run_code
exec(code_obj, self.user_global_ns, self.user_ns)
File "", line 1, in
history = model.train(X, X_val)
File "/usr/local/lib/python3.6/dist-packages/n2v/models/n2v_standard.py", line 218, in train
callbacks=self.callbacks, verbose=1)
File "/usr/local/lib/python3.6/dist-packages/keras/legacy/interfaces.py", line 91, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/keras/engine/training.py", line 1418, in fit_generator
initial_epoch=initial_epoch)
File "/usr/local/lib/python3.6/dist-packages/keras/engine/training_generator.py", line 94, in fit_generator
callbacks.set_model(callback_model)
File "/usr/local/lib/python3.6/dist-packages/keras/callbacks.py", line 54, in set_model
callback.set_model(model)
File "/usr/local/lib/python3.6/dist-packages/csbdeep/utils/tf.py", line 213, in set_model
self.gt_outputs = [K.placeholder(shape=_gt_shape(K.int_shape(x))) for x in self.model.outputs]
File "/usr/local/lib/python3.6/dist-packages/csbdeep/utils/tf.py", line 213, in
self.gt_outputs = [K.placeholder(shape=_gt_shape(K.int_shape(x))) for x in self.model.outputs]
File "/usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py", line 517, in placeholder
x = tf.placeholder(dtype, shape=shape, name=name)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/ops/array_ops.py", line 2143, in placeholder
return gen_array_ops.placeholder(dtype=dtype, shape=shape, name=name)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/ops/gen_array_ops.py", line 6262, in placeholder
"Placeholder", dtype=dtype, shape=shape, name=name)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/op_def_library.py", line 788, in _apply_op_helper
op_def=op_def)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/util/deprecation.py", line 507, in new_func
return func(*args, **kwargs)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/ops.py", line 3616, in create_op
op_def=op_def)
File "/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/ops.py", line 2005, in init
self._traceback = tf_stack.extract_stack()
Another issue happened also earlier
a name used to identify the model
model_name = 'n2v_2D'
the base directory in which our model will live
basedir = 'models'
We are now creating our network model.
model = N2V(config, model_name, basedir=basedir)
Errors:
WARNING: Logging before flag parsing goes to stderr.
W0620 10:18:26.427209 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:517: The name tf.placeholder is deprecated. Please use tf.compat.v1.placeholder instead.
W0620 10:18:26.472275 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:4138: The name tf.random_uniform is deprecated. Please use tf.random.uniform instead.
W0620 10:18:26.503654 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:74: The name tf.get_default_graph is deprecated. Please use tf.compat.v1.get_default_graph instead.
W0620 10:18:26.519927 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:174: The name tf.get_default_session is deprecated. Please use tf.compat.v1.get_default_session instead.
W0620 10:18:26.521225 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:181: The name tf.ConfigProto is deprecated. Please use tf.compat.v1.ConfigProto instead.
W0620 10:18:29.414467 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:1834: The name tf.nn.fused_batch_norm is deprecated. Please use tf.compat.v1.nn.fused_batch_norm instead.
W0620 10:18:29.695360 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:3976: The name tf.nn.max_pool is deprecated. Please use tf.nn.max_pool2d instead.
W0620 10:18:30.005542 140231502292864 deprecation_wrapper.py:119] From /usr/local/lib/python3.6/dist-packages/keras/backend/tensorflow_backend.py:2018: The name tf.image.resize_nearest_neighbor is deprecated. Please use tf.compat.v1.image.resize_nearest_neighbor instead.
Hello guijacquemet,
thanks for pointing out the problem!
This issue was created because of an incompatibility with the new csbdeep version 0.4.0.
I changed the dependency back to 0.3.0. Things are now working again.
You might have to uninstall and then reinstall n2v using pip.
Thanks works like a charm now