WLeaf Disease Classification - ResNet50.ipynb - Colaboratory

2/8/23, 2:13 AM WLeaf Disease Classification_ResNet50.
ipynb - Colaboratory
Objective
- To classify the Collected Wheat_leaf image as healthy, Strip_rust,Leaf_rust,Powdery,Septoria,or TanSpot
- Multiclass classification problem
-bla bla....
Data Sources
-The dataset is originally collected from Research_Field @ Kulumsa_Agricultural_Research_Institute.
- A few dataset also collected from Previously collected by Researchers/Experts @KARC
DataSet_Folder structure
DataSet
Leaf_rust
LR1.jpg
LR2.jpg
...
Strip_rust
SR1.jpg
SR2.jpg
Automatic saving failed. This file was updated remotely or in another tab. Show diff
...
Powdery
Powd1.jpg
Powd2.jpg
...
Septoria
Sept1.jpg
Sept2.jpg
...
TanSpot
Tan1.jpg
Tan2.jpg
...
Healthy
Hlthy1.jpg
Hlthy2.jpg
...
Dependencies
import os
import numpy as np
import seaborn as sns
import pathlib
import PIL
from glob import glob
import matplotlib.pyplot as plt
from collections import Counter
from sklearn.metrics import confusion_matrix, classification_report
from tensorflow.keras.models import Sequential,Model
from tensorflow.keras.layers import Dense,Flatten,Dropout,Conv2D, MaxPooling2D, GlobalAveragePooling2D,Input
from tensorflow.keras.applications import ResNet50, resnet50, Xception, xception
from tensorflow.keras.applications.xception import preprocess_input
from tensorflow.keras.preprocessing.image import ImageDataGenerator
from tensorflow.keras.callbacks import EarlyStopping, ModelCheckpoint
https://colab.research.google.com/drive/1zGDYxQMqj0aijE6TtdVQHbRVSvfn0AdS#scrollTo=NmQLaeywDyD-&printMode=true 1/12
2/8/23, 2:13 AM WLeaf Disease Classification_ResNet50.ipynb - Colaboratory
from tensorflow.keras.losses import CategoricalCrossentropy
import tensorflow as tf
from tensorflow.keras.preprocessing.image import load_img, img_to_array
print(tf.__version__)
############ settings ############
2.9.2
from google.colab import drive

drive.mount('/content/drive')
Mounted at /content/drive
data_dir = "/content/drive/MyDrive/My_Recent_Data/WheatLeaf_Label_Resiz_Augm"
batch_size = 32
img_height = 200
img_width = 200
train_path = pathlib.Path(data_dir)
image_count = len(list(train_path.glob('*/*')))
print(image_count)
4554
Data preprocessing
- Loading and splitting data

- Train:80% and Validation:20%
train_ds = tf.keras.preprocessing.image_dataset_from_directory(
data_dir,
validation_split=0.2,
subset="training",
seed=123,
image_size=(img_height, img_width),
batch_size=batch_size)
Found 4554 files belonging to 6 classes.

Using 3644 files for training.
val_ds = tf.keras.preprocessing.image_dataset_from_directory(
data_dir,
validation_split=0.2,
subset="validation",
seed=123,
image_size=(img_height, img_width),
batch_size=batch_size)
Found 4554 files belonging to 6 classes.

Using 910 files for validation.
EDA
def plot_distribution(y, title):

a = Counter(y)
y = ['Healthy', 'Leaf_rust', 'Powdery_Mildew', 'Septoria_tritic_blotch','Strip_rust','Tanspot' ]
x = [a[i] for i in range(6)]

plt.figure(figsize=(8, 3))
plt.barh(y, x, color='Green')
plt.title(title)
return plt.show()
# Target distribution
y_train = np.concatenate([y for x, y in train_ds], axis=0)

y_val = np.concatenate([y for x, y in val_ds], axis=0)
plot_distribution(y_train, title="Train images")

plot_distribution(y_val, title = "Validation images")
## Sample images
class_names = train_ds.class_names
import matplotlib.pyplot as plt
for images, labels in train_ds.take(1):
for i in range(6):
ax = plt.subplot(4, 6, i + 1)
plt.imshow(images[i].numpy().astype("uint8"))
plt.title(class_names[labels[i]])
plt.axis("off")
Model Training
# Configure the dataset for performance
AUTOTUNE = tf.data.AUTOTUNE
train_ds = train_ds.cache().prefetch(buffer_size=AUTOTUNE)
val_ds = val_ds.cache().prefetch(buffer_size=AUTOTUNE)
# Model architecture
num_classes = 6
model = tf.keras.Sequential([
tf.keras.layers.InputLayer(input_shape=(img_height, img_width, 3)),
tf.keras.layers.experimental.preprocessing.Rescaling(1./255),
tf.keras.layers.Conv2D(16, 3, activation='relu'),
tf.keras.layers.MaxPooling2D(),
tf.keras.layers.Flatten(),
tf.keras.layers.Dense(128, activation='relu'),
tf.keras.layers.Dropout(0.5),
tf.keras.layers.Dense(num_classes, activation='softmax')
])
model.summary()
from tensorflow.keras.models import Sequential, Model

from tensorflow.keras.layers import Dense, Flatten, Conv2D, MaxPool2D, GlobalAveragePooling2D, Dropout
from tensorflow.keras.applications.resnet import ResNet50
# Defining the pretrained base model

base_model = ResNet50(include_top=False, weights='imagenet', input_shape =(200,200,3))
base_model.trainable=False
input_img=Input(shape=(200,200,3),name='input_image')
resnet=base_model(input_img,training=False)
resnet=GlobalAveragePooling2D()(resnet)
resnet=Dense(6,activation='softmax',name='classif_layer')(resnet)
resnet=Dropout(rate=0.2,name='drop_out')(resnet)
resnet_model=Model(inputs=input_img,outputs=resnet,name='WLD_Prediction_Model')
resnet_model.summary()
Model: "WLD_Prediction_Model"
_________________________________________________________________
Layer (type) Output Shape Param #
=================================================================
input_image (InputLayer) [(None, 200, 200, 3)] 0
resnet50 (Functional) (None, 7, 7, 2048) 23587712
global_average_pooling2d_2 (None, 2048) 0

(GlobalAveragePooling2D)
classif_layer (Dense) (None, 6) 12294
=================================================================
Total params: 23,600,006
Trainable params: 12,294
Non-trainable params: 23,587,712
_________________________________________________________________
from tensorflow.keras.applications.vgg19 import VGG19

base_model = VGG19(include_top=False, weights='imagenet', input_shape =(200,200,3) , pooling='avg')
# Making sure the existing weights ar not trained

for layer in base_model.layers:
layer.trainable=False
x = Flatten()(base_model.output)
#x = base_model.output
#x = GlobalAveragePooling2D()(x)
# Defining the head of the model where the prediction is conducted
pred = Dense(6, activation='softmax')(x)
# Combining base and head
model = Model(inputs=base_model.input, outputs=pred,name='My_Vgg19')
model.summary()
Show hidden output
Transfer learning with Xception
from keras.engine.sequential import input_layer

#Model building
base_model= tf.keras.applications.Xception(include_top=False,
input_shape=(200, 200,3),
#pooling='avg',
weights='imagenet')
xception=base_model(input_img,training=False)
xception=GlobalAveragePooling2D()(xception)
#xception=Dense(512,activation='relu')(xception)
xception=Dropout(rate=0.2,name='drop_out')(xception)
xception=Dense(6,activation='softmax',name='classif_layer')(xception)
xception_model=Model(inputs=input_img,outputs=xception,name='WLD_Prediction_Model')
xception_model.summary()
Downloading data from https://storage.googleapis.com/tensorflow/keras-applications/xception/xception_weights_tf_dim_ordering_tf_kernels

83683744/83683744 [==============================] - 0s 0us/step
_________________________________________________________________
=================================================================
xception (Functional) (None, 7, 7, 2048) 20861480
global_average_pooling2d (G (None, 2048) 0

lobalAveragePooling2D)
drop_out (Dropout) (None, 2048) 0
=================================================================
_________________________________________________________________
base_learning_rate = 0.001
resnet_model.compile(optimizer=tf.keras.optimizers.Adam(learning_rate=base_learning_rate),
loss='sparse_categorical_crossentropy',
metrics=['accuracy'])
earlystop_callback = tf.keras.callbacks.EarlyStopping(monitor='val_accuracy',
min_delta=0.0001,
# patience=5
)
history = resnet_model.fit(train_ds,
validation_data=val_ds,
epochs=20,
# callbacks=[earlystop_callback]
)
Epoch 1/20
114/114 [==============================] - 1917s 16s/step - loss: 1.0149 - accuracy: 0.6358 - val_loss: 0.6820 - val_accuracy: 0.7758
Automatic
Epochsaving
2/20 failed. This file was updated remotely or in another tab. Show diff
114/114 [==============================] - 13s 116ms/step - loss: 0.5432 - accuracy: 0.8304 - val_loss: 0.5335 - val_accuracy: 0.8374
Epoch 3/20
Epoch 4/20
Epoch 5/20
Epoch 6/20
Epoch 7/20
Epoch 8/20
Epoch 9/20
Epoch 10/20
Epoch 11/20
Epoch 12/20
Epoch 13/20
Epoch 14/20
Epoch 15/20
Epoch 16/20
Epoch 17/20
Epoch 18/20
Epoch 19/20
Epoch 20/20
loss, acc = resnet_model.evaluate(val_ds, batch_size=batch_size)

print("validation accuracy :", round(acc, 2))
print("validation loss :", round(loss,2))
29/29 [==============================] - 3s 93ms/step - loss: 0.3015 - accuracy: 0.9099

validation accuracy : 0.91
validation loss : 0.3
loss, acc = resnet_model.evaluate(train_ds, batch_size=batch_size)
print("Train accuracy :", round(acc, 2))
print("Train loss :", round(loss,2))

Train accuracy : 0.99
Train loss : 0.07
Model Evaluation
Feature Extraction
train_loss = history.history['loss']
train_acc = history.history['accuracy']
valid_loss = history.history['val_loss']
valid_acc = history.history['val_accuracy']
# Accuracy plots
plt.plot(train_acc, color='green', linestyle='-', label='train accuracy')
plt.plot(valid_acc, color='blue', linestyle='-', label='val accuracy')
plt.xlabel('Epochs')
plt.ylabel('Accuracy')
plt.legend()
plt.show()
#Automatic
loss plots
saving failed. This file was updated remotely or in another tab. Show diff
plt.plot(train_loss, color='orange', linestyle='-', label='train loss')
plt.plot(valid_loss, color='red', linestyle='-', label='val loss')
plt.ylabel('Loss')
plt.legend()
plt.show()
y_pred = [] # store predicted labels

y_true = [] # store true labels
# iterate over the dataset

for image_batch, label_batch in val_ds: # use dataset.unbatch() with repeat
# append true labels
y_true.append(label_batch)
# compute predictions
preds = resnet_model.predict(image_batch)
# append predicted labels
y_pred.append(np.argmax(preds, axis = - 1))
# convert the true and predicted labels into tensors

correct_labels = tf.concat([item for item in y_true], axis = 0)
predicted_labels = tf.concat([item for item in y_pred], axis = 0)
1/1 [==============================] - 1s 1s/step

1/1 [==============================] - 0s 31ms/step
1/1 [==============================] - 0s 38ms/step
1/1 [==============================] - 0s 36ms/step
1/1 [==============================] - 0s 42ms/step
1/1 [==============================] - 0s 35ms/step
1/1 [==============================] - 0s 31ms/step
1/1 [==============================] - 0s 34ms/step
1/1 [==============================] - 0s 39ms/step
1/1 [==============================] - 0s 36ms/step
1/1 [==============================] - 0s 44ms/step
1/1 [==============================] - 0s 34ms/step
1/1 [==============================] - 0s 30ms/step
1/1 [==============================] - 0s 35ms/step
1/1 [==============================] - 0s 29ms/step
1/1 [==============================] - 0s 30ms/step
1/1 [==============================] - 0s 29ms/step
1/1 [==============================] - 0s 32ms/step
1/1 [==============================] - 0s 35ms/step
1/1 [==============================] - 0s 34ms/step
1/1 [==============================] - 0s 34ms/step
1/1 [==============================] - 0s 32ms/step
1/1 [==============================] - 0s 29ms/step
1/1 [==============================] - 0s 29ms/step
1/1 [==============================] - 0s 30ms/step
1/1 [==============================] - 0s 34ms/step
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1/1 [==============================] - 0sor32ms/step
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1/1 [==============================] - 0s 28ms/step
1/1 [==============================] - 1s 802ms/step
cm = confusion_matrix(correct_labels, predicted_labels, normalize='true')

sns.heatmap(cm, annot=True, cmap='viridis', cbar=None)
tick_marks = np.arange(len(class_names))
plt.xticks(tick_marks, class_names, rotation=60,fontsize=10,fontweight='bold')
plt.yticks(tick_marks, class_names,fontsize=10,rotation=0,fontweight='bold')
plt.title("Confusion Matrix",fontsize=20, fontweight='bold')
plt.ylabel("Actual Value", fontsize=16)
plt.xlabel("Predicted Value", fontsize=16)
plt.show()
print(classification_report(correct_labels, predicted_labels,target_names=class_names))
precision recall f1-score support
Healthy 0.93 0.99 0.96 141

Leaf_rust 0.89 0.86 0.87 163
Powdery_Mildew 0.91 0.99 0.95 151
Septoria_tritic_blotch 0.90 0.86 0.88 163
Strip_rust 0.87 0.86 0.86 153
Tanspot 0.96 0.91 0.94 139
accuracy 0.91 910

macro avg 0.91 0.91 0.91 910
weighted avg 0.91 0.91 0.91 910
Fine Tuning

base_model = ResNet50(include_top=False, weights='imagenet', input_shape =(200,200,3))
resnet=base_model(input_img,training=False)
resnet=GlobalAveragePooling2D()(resnet)
resnet=Dropout(rate=0.2,name='drop_out')(resnet)
resnet=Dense(6,activation='softmax',name='classif_layer')(resnet)
resnet_model=Model(inputs=input_img,outputs=resnet,name='WLD_Prediction_Model')
_________________________________________________________________
=================================================================

=================================================================
_________________________________________________________________
base_model.trainable = True
# Let's take a look to see how many layers are in the base model
print("Number of layers in the base model: ", len(base_model.layers))
# Fine-tune from this layer onwards

fine_tune_at = 150
# Freeze all the layers before the `fine_tune_at` layer

for layer in base_model.layers[:fine_tune_at]:
layer.trainable = False
#resnet_model=Dropout(rate=0.2,name='drop_out')(resnet_model)
Number of layers in the base model: 175
_________________________________________________________________
=================================================================

=================================================================
Trainable params: 10,002,438
_________________________________________________________________
base_learning_rate = 0.0001
resnet_model.compile(optimizer=tf.keras.optimizers.Adam(learning_rate=base_learning_rate),
loss='sparse_categorical_crossentropy',
metrics=['accuracy'])
earlystop_callback = tf.keras.callbacks.EarlyStopping(monitor='val_accuracy',
min_delta=0.0001,
#patience=5
)
history = resnet_model.fit(train_ds,
validation_data=val_ds,
epochs=20,
#callbacks=[earlystop_callback]
)
Epoch 1/20
Epoch 2/20
Epoch 3/20
Epoch 4/20
Automatic
Epochsaving
5/20 failed. This file was updated remotely or in another tab. Show diff
Epoch 6/20
Epoch 7/20
Epoch 8/20
Epoch 9/20
Epoch 10/20
Epoch 11/20
Epoch 12/20
Epoch 13/20
Epoch 14/20
Epoch 15/20
Epoch 16/20
Epoch 17/20
Epoch 18/20
Epoch 19/20
Epoch 20/20
score_val = resnet_model.evaluate(val_ds, verbose=1)

accuracy_val = 100*score_val[1]
print('Validate accuracy = %.4f%% ' % accuracy_val)

Validate accuracy = 94.0659%
score_train = resnet_model.evaluate(train_ds, verbose=1)

accuracy_train = 100*score_train[1]
print('Train accuracy = %.4f%% ' % accuracy_train)

Train accuracy = 99.5335%
resnet_model.save("ResNet_Model_9953_9407.h5")
Model Evaluation After Fine Tuning
Training and Validation Plots
train_loss = history.history['loss']
train_acc = history.history['accuracy']
valid_loss = history.history['val_loss']
valid_acc = history.history['val_accuracy']
# Accuracy plots
plt.plot(train_acc, color='green', linestyle='-', label='train accuracy')
plt.plot(valid_acc, color='blue', linestyle='-', label='val accuracy')
plt.ylabel('Accuracy')
plt.legend()
plt.show()
# loss plots
plt.plot(train_loss, color='orange', linestyle='-', label='train loss')
plt.plot(valid_loss, color='red', linestyle='-', label='val loss')
plt.ylabel('Loss')
plt.legend()
Automatic saving failed. This file was updated remotely or in another tab.
plt.show() Show diff
y_pred = [] # store predicted labels

y_true = [] # store true labels
# iterate over the dataset

for image_batch, label_batch in val_ds: # use dataset.unbatch() with repeat
# append true labels
y_true.append(label_batch)
# compute predictions
preds = resnet_model.predict(image_batch)
# append predicted labels
y_pred.append(np.argmax(preds, axis = - 1))
# convert the true and predicted labels into tensors

correct_labels = tf.concat([item for item in y_true], axis = 0)
predicted_labels = tf.concat([item for item in y_pred], axis = 0)
1/1 [==============================] - 1s 837ms/step

1/1 [==============================] - 0s 31ms/step
1/1 [==============================] - 0s 35ms/step
1/1 [==============================] - 0s 39ms/step
1/1 [==============================] - 0s 32ms/step
1/1 [==============================] - 0s 31ms/step
1/1 [==============================] - 0s 32ms/step
1/1 [==============================] - 0s 33ms/step
1/1 [==============================] - 0s 45ms/step
1/1 [==============================] - 0s 31ms/step
1/1 [==============================] - 0s 36ms/step
1/1 [==============================] - 0s 38ms/step
1/1 [==============================] - 0s 30ms/step
1/1 [==============================] - 0s 32ms/step
1/1 [==============================] - 0s 41ms/step
1/1 [==============================] - 0s 33ms/step
1/1 [==============================] - 0s 36ms/step
1/1 [==============================] - 0s 35ms/step
1/1 [==============================] - 0s 40ms/step
1/1 [==============================] - 0s 43ms/step
1/1 [==============================] - 0s 31ms/step
1/1 [==============================] - 0s 32ms/step
1/1 [==============================] - 0s 30ms/step
1/1 [==============================] - 0s 29ms/step
1/1 [==============================] - 0s 37ms/step
1/1 [==============================] - 0s 33ms/step
1/1 [==============================] - 0s 34ms/step
1/1 [==============================] - 0s 32ms/step
1/1 [==============================] - 1s 1s/step
cm = confusion_matrix(correct_labels, predicted_labels, normalize='true')

sns.heatmap(cm, annot=True, cmap='viridis', cbar=None)
tick_marks = np.arange(len(class_names))
plt.xticks(tick_marks, class_names, rotation=60,fontsize=10,fontweight='bold')
plt.yticks(tick_marks, class_names,fontsize=10,rotation=0,fontweight='bold')
plt.title("Confusion Matrix",fontsize=20, fontweight='bold')
plt.ylabel("Actual Value", fontsize=16)
plt.xlabel("Predicted Value", fontsize=16)
plt.show()
print(classification_report(correct_labels, predicted_labels,target_names=class_names))
precision recall f1-score support
Healthy 0.97 0.99 0.98 141

Leaf_rust 0.90 0.89 0.90 163
Powdery_Mildew 0.95 1.00 0.97 151
Septoria_tritic_blotch 0.95 0.91 0.93 163
Strip_rust 0.92 0.90 0.91 153
Tanspot 0.96 0.96 0.96 139
accuracy 0.94 910

macro avg 0.94 0.94 0.94 910
weighted avg 0.94 0.94 0.94 910
Testing Trained model
check 0s completed at 2:08 AM

WLeaf Disease Classification - ResNet50.ipynb - Colaboratory

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2/8/23, 2:13 AM WLeaf Disease Classification_ResNet50.

from google.colab import drive

- Loading and splitting data

Found 4554 files belonging to 6 classes.

Found 4554 files belonging to 6 classes.

def plot_distribution(y, title):

x = [a[i] for i in range(6)]

y_train = np.concatenate([y for x, y in train_ds], axis=0)

plot_distribution(y_train, title="Train images")

from tensorflow.keras.models import Sequential, Model

# Defining the pretrained base model

resnet50 (Functional) (None, 7, 7, 2048) 23587712

global_average_pooling2d_2 (None, 2048) 0

classif_layer (Dense) (None, 6) 12294

from tensorflow.keras.applications.vgg19 import VGG19

# Making sure the existing weights ar not trained

Show hidden output

Transfer learning with Xception

from keras.engine.sequential import input_layer

Downloading data from https://storage.googleapis.com/tensorflow/keras-applications/xception/xception_weights_tf_dim_ordering_tf_kernels

xception (Functional) (None, 7, 7, 2048) 20861480

global_average_pooling2d (G (None, 2048) 0

drop_out (Dropout) (None, 2048) 0

classif_layer (Dense) (None, 6) 12294

loss, acc = resnet_model.evaluate(val_ds, batch_size=batch_size)

29/29 [==============================] - 3s 93ms/step - loss: 0.3015 - accuracy: 0.9099

114/114 [==============================] - 10s 90ms/step - loss: 0.0669 - accuracy: 0.9901

y_pred = [] # store predicted labels

# iterate over the dataset

# convert the true and predicted labels into tensors

1/1 [==============================] - 1s 1s/step

cm = confusion_matrix(correct_labels, predicted_labels, normalize='true')

precision recall f1-score support

Healthy 0.93 0.99 0.96 141

accuracy 0.91 910

# Defining the pretrained base model

global_average_pooling2d_8 (None, 2048) 0

drop_out (Dropout) (None, 2048) 0

classif_layer (Dense) (None, 6) 12294

# Fine-tune from this layer onwards

# Freeze all the layers before the `fine_tune_at` layer

Number of layers in the base model: 175

resnet50 (Functional) (None, 7, 7, 2048) 23587712

global_average_pooling2d_8 (None, 2048) 0

drop_out (Dropout) (None, 2048) 0

classif_layer (Dense) (None, 6) 12294

score_val = resnet_model.evaluate(val_ds, verbose=1)

29/29 [==============================] - 3s 97ms/step - loss: 0.3196 - accuracy: 0.9407

score_train = resnet_model.evaluate(train_ds, verbose=1)

114/114 [==============================] - 11s 95ms/step - loss: 0.0078 - accuracy: 0.9953

Model Evaluation After Fine Tuning

Training and Validation Plots

y_pred = [] # store predicted labels

# iterate over the dataset

# convert the true and predicted labels into tensors

1/1 [==============================] - 1s 837ms/step

cm = confusion_matrix(correct_labels, predicted_labels, normalize='true')

precision recall f1-score support

Healthy 0.97 0.99 0.98 141

accuracy 0.94 910

Testing Trained model

check 0s completed at 2:08 AM

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