simplified keras
Common used actions in keras
Table of contents
General info
This package is a set of common used actions in keras. At this moment includes (may be outdated):
- Main package
- Plots
- Metrics
- Transformations
Libraries
- Matplotlib - version 3.3.3
- NumPy - version 1.19.4
- Tensorflow - version 2.4.1
- Pandas - version 1.1.5
- Seaborn - version 0.11.1
Setup
- Install from PyPi:
pip install simplified-keras
Documentation
Main package
Generators
default generators
from keras.preprocessing.image import ImageDataGenerator
from simplified_keras.generators import get_train_val_generators, get_val_test_generators
img_size = (48, 48)
img_datagen = ImageDataGenerator(rescale=1/255)
# same for get_val_test_generators
# default: data_dir='../data', color_mode='rgb', batch_size=128, class_mode='categorical'
train_generator, validation_generator = get_train_val_generators(img_datagen, data_dir='../data/normal',
color_mode='grayscale', target_size=img_size)
val_generator, test_generator = get_val_test_generators(img_datagen, batch_size=32)
numpy_memmap_generator
from simplified_keras.generators import numpy_memmap_generator
# default batch_size=128, shuffle_array=True
train_gen = numpy_memmap_generator('imgs.npy', 'labels.npy', batch_size=64, shuffle_array=False)
Default callbacks
from simplified_keras.callbacks import get_default_callbacks
callbacks = get_default_callbacks('models/vgg16_calssifier.h5', monitor='val_loss', verbose=0)
hist = model.fit(train_generator, steps_per_epoch=train_steps, validation_data=validation_generator,
validation_steps=valid_steps, epochs=100, callbacks=callbacks, verbose=2)
Signature:
def get_default_callbacks(model_path, monitor='val_acc', base_patience=3, lr_reduce_factor=0.5, min_lr=1e-7, verbose=1):
return [
ReduceLROnPlateau(monitor=monitor, factor=lr_reduce_factor, min_lr=min_lr, patience=base_patience, verbose=verbose),
EarlyStopping(monitor=monitor, patience=(2 * base_patience + 1), verbose=verbose),
ModelCheckpoint(monitor=monitor, filepath=model_path, save_best_only=True, verbose=verbose)
]
Restore callbacks
Used to restore callback after paused learning. Model should come from last checkpoint.
from simplified_keras.callbacks import restore_callbacks, get_default_callbacks
callbacks = get_default_callbacks('models/vgg16_calssifier.h5', monitor='val_loss', verbose=0)
acc, loss = model.evaluate(val_ds)
# acc or loss depending on the compiled model metrics
restore_callbacks(callbacks, acc)
Plots
Accuracy and Loss plot
from simplified_keras.plots.history_plots import plot_acc_and_loss
history = model.fit(train_gen, teps_per_epoch=train_steps, epochs=5, validation_data=val_gen,
validation_steps=val_steps, callbacks=callbacks)
fig = plot_acc_and_loss(history)
Result:
Predictions with image plot
from keras.models import load_model
from keras.preprocessing.image import ImageDataGenerator
from simplified_keras.generators import get_train_val_generators
from simplified_keras.plots import plot_predictions_with_img
img_size = (48, 48)
img_datagen = ImageDataGenerator(rescale=1 / 255)
_, validation_generator = get_train_val_generators(img_datagen, data_dir='../data/normal',
color_mode='grayscale', target_size=img_size)
model = load_model('../models/standard_model.h5')
batch, labels = validation_generator.next()
preds = model.predict(batch)
named_labels = ['a', 'b', 'c', 'd', 'e', 'f', 'g']
fig = plot_predictions_with_img(1, preds, labels, batch, named_labels, grayscale=True)
Result:
Histogram with CDF and image plot
import cv2
from simplified_keras.plots import plot_gray_img_with_histogram
img = cv2.imread(f'{src_train_path}/0/241.png', 0)
fig1 = plot_gray_img_with_histogram(img)
img2 = stretch_histogram(img)
fig2 = plot_gray_img_with_histogram(img2)
Result:
Confusion matrix plot
from simplified_keras.transformations import predictions_to_classes, one_hot_to_sparse
from simplified_keras.metrics import get_confusion_matrixes
from simplified_keras.plots import plot_confusion_matrix
predictions = model.predict(validation_images)
predicted_classes = predictions_to_classes(predictions)
sparse_labels = one_hot_to_sparse(validation_labels)
cm, cm_normalized = get_confusion_matrixes(predicted_classes, sparse_labels)
classes = ['a', 'b', 'c', 'd', 'e', 'f', 'g']
f1 = plot_confusion_matrix(cm, classes)
f2 = plot_confusion_matrix(cm_normalized, classes, figsize=(10, 8))
Results:
Metrics
Confusion matrix
from simplified_keras.transformations import predictions_to_classes, one_hot_to_sparse
from simplified_keras.metrics import get_confusion_matrixes
predictions = model.predict(validation_images)
predicted_classes = predictions_to_classes(predictions)
sparse_labels = one_hot_to_sparse(validation_labels)
# Returns two numpy arrays: standard and normalized
cm, cm_normalized = get_confusion_matrixes(predicted_classes, sparse_labels)
Model Statistics
Calculates:
- FP
- FN
- TP
- TN
- TPR # Sensitivity/true positive rate
- TNR # Specificity/true negative rate
- PPV # Precision/positive predictive value
- NPV # Negative predictive value
- FPR # Fall out or false positive rate
- FNR # False negative rate
- FDR # False discovery rate
- ACC # Overall accuracy for each class
- Much more and still increasing
from simplified_keras.transformations import predictions_to_classes, one_hot_to_sparse
from simplified_keras.metrics import get_confusion_matrixes
from simplified_keras.metrics import get_model_statistics
predictions = model.predict(validation_images)
predicted_classes = predictions_to_classes(predictions)
sparse_labels = one_hot_to_sparse(validation_labels)
cm, cm_normalized = get_confusion_matrixes(predicted_classes, sparse_labels)
stats = get_model_statistics(cm)
classes = ['a', 'b', 'c', 'd', 'e', 'f', 'g']
fig = stats.visualize(classes)
print(stats.TN) #[2890 3530 2874 2361 2591 3000 2661]
Folder statistics
from simplified_keras.metrics import get_folders_statistics
stat = get_folders_statistics('../data/normal/train')
print(stat.nr_of_elements, stat.info) # 28709 {'0': 3995, '1': 436, '2': 4097, '3': 7215, '4': 4830, '5': 3171, '6': 4965}
fig = stat.bar_plot()
Result:
Model memory usage
from simplified_keras.metrics import get_model_memory_usage
batch_size = 64
# outputs usage in GB
usage = get_model_memory_usage(batch_size, model)
print(usage, 'GB') # 8.34 GB
Transformations
Convert predictions to classes array
from simplified_keras.transformations import predictions_to_classes
predictions = model.predict(validation_images)
predicted_classes = predictions_to_classes(predictions)
print(pedicted_classes) #[6 3 3 ... 6 2 0]
Convert one hot encoding to sparse
from simplified_keras.transformations import one_hot_to_sparse
sparse_labels = one_hot_to_sparse(validation_labels)
print(sprase_labels) #[6 6 6 ... 6 2 0]
Stretch histogram
from simplified_keras.transformations import stretch_histogram
# default color_mode='rgb'
stretch_histogram(image, color_mode='grayscale')
Unfreeze model
from simplified_keras.transformations import unfreeze_model
from tensorflow.keras.optimizers import Adam
# default params: optimizer=Adam(learning_rate=1e-5), metrics="acc"
unfreeze_model(model, optimizer=Adam(learning_rate=1e-4), metrics="loss")
Normalize histogram clahe
from simplified_keras.transformations import normalize_histogram_clahe
# default clip_limit=2.0, tile_grid_size=(8, 8), color_mode='rgb'
normalize_histogram_clahe(image)
Replace activations
Replaces all activation functions in given model
from simplified_keras.transformations import replace_activations
from tensorflow.keras.layers import LeakyReLU
l_relu = LeakyReLU()
replace_activations(model, l_relu)
Layers
Augumentation layers build on tensorflow image operations
from simplified_keras.transformations import RandomSaturation, RandomHue, RandomBrightness
from tensorflow.keras import Sequential
# for more informations about parameters see tf.image docs
augument_layers = Sequential([
RandomSaturation(0.5, 1.5),
# must be [0 - 0,5]
RandomHue(0.2),
RandomBrightness(0.2)
])
PyPi
TODO
- Add tests and a lot of features :)
Development
Want to contribute? Great!
To fix a bug or enhance an existing module, follow these steps:
- Fork the repo
- Create a new branch (
git checkout -b improve-feature
) - Make the appropriate changes in the files
- Verify if they are correct
- Add changes to reflect the changes made
- Commit changes
- Push to the branch (
git push origin improve-feature
) - Create a Pull Request
Status
Library is: in progress
Contact
albert.lis.1996@gmail.com - feel free to contact me!