plot_model throws AssertionError

[Devedse]

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Introduction

I'm currently following the Plural Sight course on setting up Keras and using it for Object Detection. However with the second script I'm running into an AssertionError:

Code used for the course:

#   deep_circles.py
#   Defines a network that can find separate circles of data
#

#   Imports
from sklearn.datasets import make_circles
import numpy as np
import matplotlib.pyplot as plt
import os
os.environ["TF_CPP_MIN_LOG_LEVEL"]="2"

#   Helper functions

#   plot the data on a figure
def plot_data(pl, X, y):
    # plot class where y==0
    pl.plot(X[y==0, 0], X[y==0,1], 'ob', alpha=0.5)
    # plot class where y==1
    pl.plot(X[y==1, 0], X[y==1,1], 'xr', alpha=0.5)
    pl.legend(['0', '1'])
    return pl

#   Common function that draws the decision boundaries
def plot_decision_boundary(model, X, y):

    amin, bmin = X.min(axis=0) - 0.1
    amax, bmax = X.max(axis=0) + 0.1
    hticks = np.linspace(amin, amax, 101)
    vticks = np.linspace(bmin, bmax, 101)
    
    aa, bb = np.meshgrid(hticks, vticks)
    ab = np.c_[aa.ravel(), bb.ravel()]
    
    # make prediction with the model and reshape the output so contourf can plot it
    c = model.predict(ab)
    Z = c.reshape(aa.shape)

    plt.figure(figsize=(12, 8))
    # plot the contour
    plt.contourf(aa, bb, Z, cmap='bwr', alpha=0.2)
    # plot the moons of data
    plot_data(plt, X, y)

    return plt


# Generate some data blobs.  Data will be either 0 or 1 when 2 is number of centers.
# X is a [number of samples, 2] sized array. X[sample] contains its x,y position of the sample in the space
# ex: X[1] = [1.342, -2.3], X[2] = [-4.342, 2.12]
# y is a [number of samples] sized array. y[sample] contains the class index (ie. 0 or 1 when there are 2 centers)
# ex: y[1] = 0 , y[1] = 1
X, y = make_circles(n_samples=1000, factor=.6, noise=0.1, random_state=42)
#pl = plot_data(plt, X, y)
#pl.show()

# Split the data into Training and Test sets
from sklearn.model_selection import train_test_split
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.3, random_state=42)

# Create the keras model
from keras.models import Sequential
from keras.layers import Dense
from keras.optimizers import Adam

#   Simple Sequential model
model = Sequential()
model.add(Dense(4, input_shape=(2,), activation="tanh", name="Hidden-1"))
model.add(Dense(4, activation="tanh", name="Hidden-2"))
#   Add a Dense Fully Connected Layer with 1 neuron.  Using input_shape = (2,) says the input will 
#       be arrays of the form (*,2).  The first dimension will be an unspecified 
#       number of batches (rows) of data.  The second dimension is 2 which are the X, Y positions of each data element.
#       The sigmoid activation function is used to return 0 or 1, signifying the data 
#       cluster the position is predicted to belong to.
model.add(Dense(1, activation="sigmoid", name="output_layer"))
model.summary()
#   Compile the model.  Minimize crossentopy for a binary.  Maximize for accuracy
model.compile(Adam(lr=0.05), 'binary_crossentropy', metrics=['accuracy'])
from keras.utils import plot_model
plot_model(model, to_file="model.png", show_shapes=True, show_layer_names=True)

# The line above here fails




#   Define early stopping callback
from keras.callbacks import EarlyStopping
my_callbacks = [EarlyStopping(monitor='val_acc', patience=5, mode='max')]
#   Fit the model with the data from make_blobs.  Make 100 cycles through the data.
#       Set verbose to 0 to supress progress messages 
model.fit(X_train, y_train, epochs=100, verbose=1, callbacks=my_callbacks, validation_data=(X_test, y_test))
#   Get loss and accuracy on test data
eval_result = model.evaluate(X_test, y_test)
#   Print test accuracy
print("\n\nTest loss:", eval_result[0], "Test accuracy:", eval_result[1])
#   Plot the decision boundary
plot_decision_boundary(model, X, y).show()

There's already a duplicate of this issue but it was closed without a fix: #12538

I mean honestly wtf, hacking code into the Keras library without actually commiting it != a fix 😄

@ymodak, you asked for a way to reproduce this error. All this information should be enough for this.

My environment

OS: Windows 10
Python install: MiniConda with 3.6
CUDA: Yes

Commands I ran:

conda create -n POMP2 python=3.6
activate POMP2

conda install tensorflow-gpu
conda install keras

conda install scikit-learn matplotlib pydot

Note: graphviz is automatically installed.

My investigation

I already tried to figure out what's going on and it seems that at some point a file named dot.bat is called which returned exit code 1.

Path of dot.bat: C:\Users\******\AppData\Local\conda\conda\pkgs\graphviz-2.38-hfd603c8_2\Library\bin\dot.bat

If I check out that file it calls dot.exe
Path of dot.exe: C:\Users\********\AppData\Local\conda\conda\pkgs\graphviz-2.38-hfd603c8_2\Library\bin\graphviz\dot.exe

When you check out the screenshot, you can see on the bottom the commands that are being used to call dot.bat:

['dot.bat', '-Tps', 'C:\\Users\\********\\AppData\\Local\\Temp\\tmpd7q3ltxy'] return code: 1

If I however check the Temp directory to see if there's a file named tmpd7q3ltxy. There is none.

Question

Does anyone have any idea what's going on here?

[Anurag Singh]

Just to add to this, I am also facing the same issue. Is any working solution/workaround available yet?

[Luca.Amerio]

Same issue here

[Raazzta]

my case, I modify layer's name and it works. I think it's because of layer's name

[Sandeep Menon]

+1
same issue

[Luca.Amerio]

Try this fix pydot/pydot#222