helper_functions.py

## We create a bunch of helpful functions throughout the course.
## Storing them here so they're easily accessible.

import tensorflow as tf

def importTensorflow(memory=None, precision=False):
    print(tf.__version__)
    gpus = tf.config.list_physical_devices('GPU')
    if gpus:
      try:
        if memory!=None:
            tf.config.set_logical_device_configuration(gpus[0],
                                                       [tf.config.LogicalDeviceConfiguration(memory_limit=memory)])
            logical_gpus = tf.config.list_logical_devices('GPU')
            print(len(gpus), "Physical GPUs,", len(logical_gpus), "Logical GPUs")
        elif memory==None:
            logical_gpus = tf.config.list_logical_devices('GPU')
            tf.config.experimental.set_memory_growth(gpus[0], True)
            print(len(gpus), "Physical GPUs,", len(logical_gpus), "Logical GPUs")
      except RuntimeError as e:
          print(e)
          pass

def precision(set=True):
    from tensorflow.keras import mixed_precision
    if set==True:
        mixed_precision.set_global_policy('mixed_float16')
        print(mixed_precision.global_policy())
    elif set==False:
        tf.keras.mixed_precision.set_global_policy('float32')
        print(mixed_precision.global_policy())

# Create a function to import an image and resize it to be able to be used with our model
def load_and_prep_image(filename, img_shape=224, scale=True):
  """
  Reads in an image from filename, turns it into a tensor and reshapes into
  (224, 224, 3).

  Parameters
  ----------
  filename (str): string filename of target image
  img_shape (int): size to resize target image to, default 224
  scale (bool): whether to scale pixel values to range(0, 1), default True
  """
  # Read in the image
  img = tf.io.read_file(filename)
  # Decode it into a tensor
  img = tf.image.decode_jpeg(img)
  # Resize the image
  img = tf.image.resize(img, [img_shape, img_shape])
  if scale:
    # Rescale the image (get all values between 0 and 1)
    return img/255.
  else:
    return img

# Note: The following confusion matrix code is a remix of Scikit-Learn's 
# plot_confusion_matrix function - https://scikit-learn.org/stable/modules/generated/sklearn.metrics.plot_confusion_matrix.html
import itertools
import matplotlib.pyplot as plt
import numpy as np
from sklearn.metrics import confusion_matrix

# Our function needs a different name to sklearn's plot_confusion_matrix
def make_confusion_matrix(y_true, y_pred, classes=None, figsize=(10, 10), text_size=15, norm=False, savefig=False): 
  """Makes a labelled confusion matrix comparing predictions and ground truth labels.

  If classes is passed, confusion matrix will be labelled, if not, integer class values
  will be used.

  Args:
    y_true: Array of truth labels (must be same shape as y_pred).
    y_pred: Array of predicted labels (must be same shape as y_true).
    classes: Array of class labels (e.g. string form). If `None`, integer labels are used.
    figsize: Size of output figure (default=(10, 10)).
    text_size: Size of output figure text (default=15).
    norm: normalize values or not (default=False).
    savefig: save confusion matrix to file (default=False).
  
  Returns:
    A labelled confusion matrix plot comparing y_true and y_pred.

  Example usage:
    make_confusion_matrix(y_true=test_labels, # ground truth test labels
                          y_pred=y_preds, # predicted labels
                          classes=class_names, # array of class label names
                          figsize=(15, 15),
                          text_size=10)
  """  
  # Create the confustion matrix
  cm = confusion_matrix(y_true, y_pred)
  cm_norm = cm.astype("float") / cm.sum(axis=1)[:, np.newaxis] # normalize it
  n_classes = cm.shape[0] # find the number of classes we're dealing with

  # Plot the figure and make it pretty
  fig, ax = plt.subplots(figsize=figsize)
  cax = ax.matshow(cm, cmap=plt.cm.Blues) # colors will represent how 'correct' a class is, darker == better
  fig.colorbar(cax)

  # Are there a list of classes?
  if classes:
    labels = classes
  else:
    labels = np.arange(cm.shape[0])
  
  # Label the axes
  ax.set(title="Confusion Matrix",
         xlabel="Predicted label",
         ylabel="True label",
         xticks=np.arange(n_classes), # create enough axis slots for each class
         yticks=np.arange(n_classes), 
         xticklabels=labels, # axes will labeled with class names (if they exist) or ints
         yticklabels=labels)
  
  # Make x-axis labels appear on bottom
  ax.xaxis.set_label_position("bottom")
  ax.xaxis.tick_bottom()

  # Set the threshold for different colors
  threshold = (cm.max() + cm.min()) / 2.

  # Plot the text on each cell
  for i, j in itertools.product(range(cm.shape[0]), range(cm.shape[1])):
    if norm:
      plt.text(j, i, f"{cm[i, j]} ({cm_norm[i, j]*100:.1f}%)",
              horizontalalignment="center",
              color="white" if cm[i, j] > threshold else "black",
              size=text_size)
    else:
      plt.text(j, i, f"{cm[i, j]}",
              horizontalalignment="center",
              color="white" if cm[i, j] > threshold else "black",
              size=text_size)

  # Save the figure to the current working directory
  if savefig:
    fig.savefig("confusion_matrix.png")
  
# Make a function to predict on images and plot them (works with multi-class)
def pred_and_plot(model, filename, class_names):
  """
  Imports an image located at filename, makes a prediction on it with
  a trained model and plots the image with the predicted class as the title.
  """
  # Import the target image and preprocess it
  img = load_and_prep_image(filename)

  # Make a prediction
  pred = model.predict(tf.expand_dims(img, axis=0))

  # Get the predicted class
  if len(pred[0]) > 1: # check for multi-class
    pred_class = class_names[pred.argmax()] # if more than one output, take the max
  else:
    pred_class = class_names[int(tf.round(pred)[0][0])] # if only one output, round

  # Plot the image and predicted class
  plt.imshow(img)
  plt.title(f"Prediction: {pred_class}")
  plt.axis(False);
  
import datetime

def create_tensorboard_callback(dir_name, experiment_name):
  """
  Creates a TensorBoard callback instand to store log files.

  Stores log files with the filepath:
    "dir_name/experiment_name/current_datetime/"

  Args:
    dir_name: target directory to store TensorBoard log files
    experiment_name: name of experiment directory (e.g. efficientnet_model_1)
  """
  log_dir = dir_name + "/" + experiment_name + "/" + datetime.datetime.now().strftime("%Y%m%d-%H%M%S")
  tensorboard_callback = tf.keras.callbacks.TensorBoard(
      log_dir=log_dir
  )
  print(f"Saving TensorBoard log files to: {log_dir}")
  return tensorboard_callback

# Plot the validation and training data separately
import matplotlib.pyplot as plt

def plot_loss_curves(history):
  """
  Returns separate loss curves for training and validation metrics.

  Args:
    history: TensorFlow model History object (see: https://www.tensorflow.org/api_docs/python/tf/keras/callbacks/History)
  """ 
  loss = history.history['loss']
  val_loss = history.history['val_loss']

  accuracy = history.history['accuracy']
  val_accuracy = history.history['val_accuracy']

  epochs = range(len(history.history['loss']))

  # Plot loss
  plt.plot(epochs, loss, label='training_loss')
  plt.plot(epochs, val_loss, label='val_loss')
  plt.title('Loss')
  plt.xlabel('Epochs')
  plt.legend()

  # Plot accuracy
  plt.figure()
  plt.plot(epochs, accuracy, label='training_accuracy')
  plt.plot(epochs, val_accuracy, label='val_accuracy')
  plt.title('Accuracy')
  plt.xlabel('Epochs')
  plt.legend();

def compare_historys(original_history, new_history, initial_epochs=5):
    """
    Compares two TensorFlow model History objects.
    
    Args:
      original_history: History object from original model (before new_history)
      new_history: History object from continued model training (after original_history)
      initial_epochs: Number of epochs in original_history (new_history plot starts from here) 
    """
    
    # Get original history measurements
    acc = original_history.history["accuracy"]
    loss = original_history.history["loss"]

    val_acc = original_history.history["val_accuracy"]
    val_loss = original_history.history["val_loss"]

    # Combine original history with new history
    total_acc = acc + new_history.history["accuracy"]
    total_loss = loss + new_history.history["loss"]

    total_val_acc = val_acc + new_history.history["val_accuracy"]
    total_val_loss = val_loss + new_history.history["val_loss"]

    # Make plots
    plt.figure(figsize=(8, 8))
    plt.subplot(2, 1, 1)
    plt.plot(total_acc, label='Training Accuracy')
    plt.plot(total_val_acc, label='Validation Accuracy')
    plt.plot([initial_epochs-1, initial_epochs-1],
              plt.ylim(), label='Start Fine Tuning') # reshift plot around epochs
    plt.legend(loc='lower right')
    plt.title('Training and Validation Accuracy')

    plt.subplot(2, 1, 2)
    plt.plot(total_loss, label='Training Loss')
    plt.plot(total_val_loss, label='Validation Loss')
    plt.plot([initial_epochs-1, initial_epochs-1],
              plt.ylim(), label='Start Fine Tuning') # reshift plot around epochs
    plt.legend(loc='upper right')
    plt.title('Training and Validation Loss')
    plt.xlabel('epoch')
    plt.show()
  
# Create function to unzip a zipfile into current working directory 
# (since we're going to be downloading and unzipping a few files)
import zipfile

def unzip_data(filename):
  """
  Unzips filename into the current working directory.

  Args:
    filename (str): a filepath to a target zip folder to be unzipped.
  """
  zip_ref = zipfile.ZipFile(filename, "r")
  zip_ref.extractall()
  zip_ref.close()

# Walk through an image classification directory and find out how many files (images)
# are in each subdirectory.
import os

def walk_through_dir(dir_path):
  """
  Walks through dir_path returning its contents.

  Args:
    dir_path (str): target directory
  
  Returns:
    A print out of:
      number of subdiretories in dir_path
      number of images (files) in each subdirectory
      name of each subdirectory
  """
  for dirpath, dirnames, filenames in os.walk(dir_path):
    print(f"There are {len(dirnames)} directories and {len(filenames)} images in '{dirpath}'.")
    
# Function to evaluate: accuracy, precision, recall, f1-score
from sklearn.metrics import accuracy_score, precision_recall_fscore_support

def calculate_results(y_true, y_pred):
  """
  Calculates model accuracy, precision, recall and f1 score of a binary classification model.

  Args:
      y_true: true labels in the form of a 1D array
      y_pred: predicted labels in the form of a 1D array

  Returns a dictionary of accuracy, precision, recall, f1-score.
  """
  # Calculate model accuracy
  model_accuracy = accuracy_score(y_true, y_pred) * 100
  # Calculate model precision, recall and f1 score using "weighted average
  model_precision, model_recall, model_f1, _ = precision_recall_fscore_support(y_true, y_pred, average="weighted")
  model_results = {"accuracy": model_accuracy,
                  "precision": model_precision,
                  "recall": model_recall,
                  "f1": model_f1}
  return model_results


def preprocess_text_with_line_numbers(filename):
    def get_lines(filename1):
        with open(filename1, "r") as f:
            return f.readlines()

    input_lines = get_lines(
        filename)  # get all lines from filename
    abstract_lines = ""  # create an empty abstract
    abstract_samples = []  # create an empty list of abstracts

    # Loop through each line in target file
    for line in input_lines:
        if line.startswith(
                "###"):  # check to see if line is an ID line
            abstract_id = line
            abstract_lines = ""  # reset abstract string
        elif line.isspace():  # check to see if line is a new line
            abstract_line_split = abstract_lines.splitlines()  # split abstract into separate lines

            # Iterate through each line in abstract and count them at the same time
            for abstract_line_number, abstract_line in enumerate(
                    abstract_line_split):
                line_data = {}  # create empty dict to store data from line
                target_text_split = abstract_line.split(
                    "\t")  # split target label from text
                line_data["target"] = target_text_split[
                    0]  # get target label
                line_data["text"] = target_text_split[
                    1].lower()  # get target text and lower it
                line_data[
                    "line_number"] = abstract_line_number  # what number line does the line appear in the abstract?
                line_data["total_lines"] = len(
                    abstract_line_split) - 1  # how many total lines are in the abstract? (start from 0)
                abstract_samples.append(
                    line_data)  # add line data to abstract samples list

        else:  # if the above conditions aren't fulfilled, the line contains a labelled sentence
            abstract_lines += line

    return abstract_samples


def make_windows(dataframe, windows_size=7, horizon=1, split_size=0.8, copy=True):
    windows = []
    labels = []
    if copy:
        dataframe = dataframe.copy()
    for i in range(1,windows_size+horizon):
        dataframe[f"Price:t-{i}"] = dataframe.Price.shift(i)
    dataframe = dataframe.dropna()
    for row in dataframe.itertuples():
        windows.append(list(row[horizon+1:][::-1]))
        if horizon == 1:
            labels.append([row[horizon]])
        else:
            labels.append(row[1:horizon+1])
    split_size1 = int(split_size*len(dataframe))
    return np.asarray(windows[:split_size1]), np.asarray(windows[split_size1:]), np.asarray(labels[:split_size1]), np.asarray(labels[split_size1:])