alex-krull
commented
5 years ago 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.
guijacquemet
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:
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.