data_logging_utils.py 8.64 KB
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"""Data Logging Functions

Description:

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    This folder contains several functions which, either on their own or included in larger pieces of software, perform data logging tasks.
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Usage:

    To use content from this folder, import the functions and instantiate them as you wish to use them:

        from utils.data_logging_utils import function_name
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"""

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import os
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import matplotlib
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import matplotlib.pyplot as plt
import shutil
import logging
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import numpy as np
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import re
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from textwrap import wrap
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import torch
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# The SummaryWriter class provides a high-level API to create an event file in a given directory and add summaries and events to it.
# More here: https://tensorboardx.readthedocs.io/en/latest/tensorboard.html
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from tensorboardX import SummaryWriter
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import utils.data_evaluation_utils as evaluation

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plt.axis('scaled')

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class LogWriter():

    """Log Writer class for the BrainMapper U-net.

    This class contains the pytorch implementation of the several logging functions required for the BrainMapper project.
    These functions are designed to keep track of progress during training, and also aid debugging.

    Args:
        number_of_classes (int): Number of classes
        logs_directory (str): Directory for outputing training logs
        experiment_name (str): Name of the experiment
        use_last_checkpoint (bool): Flag for loading the previous checkpoint
        labels (arr): Vector/Array of labels (if applicable)
        confusion_matrix_cmap (class): Colour Map to be used for the Conusion Matrix
    """

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    def __init__(self, number_of_classes, logs_directory, experiment_name, use_last_checkpoint=False, labels=None, confusion_matrix_cmap=plt.cm.Blues):

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        self.number_of_classes = number_of_classes
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        training_logs_directory = os.path.join(
            logs_directory, experiment_name, "train")
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        validation_logs_directory = os.path.join(
            logs_directory, experiment_name, "validation")
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        # If the logs directory exist, we clear their contents to allow new logs to be created
        if not use_last_checkpoint:
            if os.path.exists(training_logs_directory):
                shutil.rmtree(training_logs_directory)
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            if os.path.exists(validation_logs_directory):
                shutil.rmtree(validation_logs_directory)
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        self.log_writer = {
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            'train': SummaryWriter(logdir=training_logs_directory),
            'validation': SummaryWriter(logdir=validation_logs_directory)
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        }
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        self.confusion_matrix_color_map = confusion_matrix_cmap

        self.current_iteration = 1

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        if labels is not None:
            self.labels = self.labels_generator(labels)
        else:
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            self.labels = ['rsfMRI']
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        self.logger = logging.getLogger()
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        file_handler = logging.FileHandler(
            "{}/{}.log".format(os.path.join(logs_directory, experiment_name), "console_logs"))
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        self.logger.addHandler(file_handler)

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    def log(self, message):
        """Log function

        This function logs a message in the logger.

        Args:
            message (str): Message to be logged
        """

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        self.logger.info(msg=message)
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    def loss_per_iteration(self, loss_per_iteration, batch_index, iteration):
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        """Log of loss / iteration
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        This function records the loss for every iteration.

        Args:
            loss_per_iteration (torch.tensor): Value of loss for every iteration step
            batch_index (int): Index of current batch
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            iteration (int): Current iteration value
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        """

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        print("Loss for Iteration {} is: {}".format(
            batch_index, loss_per_iteration))
        self.log_writer['train'].add_scalar(
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            'loss/iteration', loss_per_iteration, iteration)
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    def loss_per_epoch(self, losses, phase, epoch):
        """Log function

        This function records the loss for every epoch.

        Args:
            losses (list): Values of all the losses recorded during the training epoch
            phase (str): Current run mode or phase
            epoch (int): Current epoch value
        """

        if phase == 'train':
            loss = losses[-1]
        else:
            loss = np.mean(losses)

        print("Loss for Epoch {} of {} is: {}".format(epoch, phase, loss))
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        self.log_writer[phase].add_scalar('loss/epoch', loss, epoch)
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    def close(self):
        """Close the log writer
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        This function closes the two log writers.
        """
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        self.log_writer['train'].close()
        self.log_writer['validation'].close()

    def add_graph(self, model):
        """Produces network graph

        This function produces the network graph

        NOTE: Currently, the function suffers from bugs and is not implemented.
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        Args:
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            model (torch.nn.Module): Model to draw.
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        """

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        self.log_writer['train'].add_graph(model)

    # DEPRECATED / UNDEBUGGED FUNCTIONS
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    def plot_dice_score(self, dice_score, phase, plot_name, title, epochs=None):
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        """Function plotting dice score for multiple epochs
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        This function plots the dice score for each epoch.
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        Args:
            dice_score (torch.tensor): Dice score value for each class
            phase (str): Current run mode or phase
            plot_name (str): Caption name for later refference
            title (str): Plot title
            epoch (int): Current epoch value
        """

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        figure = matplotlib.figure.Figure()  # Might add some arguments here later
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        ax = figure.add_subplot(1, 1, 1)
        ax.set_xlabel(title)
        ax.xaxis.set_label_position('top')
        ax.bar(np.arange(self.number_of_classes), dice_score)
        ax.set_xticks(np.arange(self.number_of_classes))
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        if self.labels is None:
            pass
        else:
            ax.set_xticklabels(self.labels)
            ax.xaxis.tick_bottom()
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        if epochs:
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            self.log_writer[phase].add_figure(
                plot_name + '/' + phase, figure, global_step=epochs)
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        else:
            self.log_writer[phase].add_figure(plot_name + '/' + phase, figure)
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    def dice_score_per_epoch(self, phase, outputs, correct_labels, epoch):
        """Function calculating dice score for each epoch

        This function computes the dice score for each epoch.

        Args:
            phase (str): Current run mode or phase
            outputs (torch.tensor): Tensor of all the network outputs (Y-hat)
            correct_labels (torch.tensor): Output ground-truth labelled data (Y)
            epoch (int): Current epoch value
        """

        print("Dice Score is being calculated...", end='', flush=True)
        dice_score = evaluation.dice_score_calculator(
            outputs, correct_labels, self.number_of_classes)
        mean_dice_score = torch.mean(dice_score)
        self.plot_dice_score(
            dice_score, phase, plot_name='dice_score_per_epoch', title='Dice Score', epochs=epoch)
        print("Dice Score calculated successfully")
        return mean_dice_score.item()
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    def sample_image_per_epoch(self, prediction, ground_truth, phase, epoch):
        """Function plotting mirrored images

        This function plots a predicted and a grond truth images side-by-side.

        Args:
            prediction (torch.tensor): Predicted image after passing throught the network
            ground_truth (torch.tensor): Labelled ground truth image
            phase (str): Current run mode or phase
            epoch (int): Current epoch value
        """

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        print("Sample Image is being loaded...", end='', flush=True)
        figure, ax = plt.subplots(nrows=len(prediction), ncols=2)
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        for i in range(len(prediction)):
            ax[i][0].imshow(prediction[i])
            ax[i][0].set_title("Predicted Image")
            ax[i][0].axis('off')

            ax[i][1].imshow(ground_truth[i])
            ax[i][1].set_title('Ground Truth Image')
            ax[i][1].axis('off')

        figure.set_tight_layout()
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        self.log_writer[phase].add_figure(
            'sample_prediction/'+phase, figure, epoch)
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        print("Sample Image successfully loaded!")
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    def labels_generator(self, labels):
        """ Label Generator Function
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        This function processess an input array of labels.

        Args:
            labels (arr): Vector/Array of labels (if applicable)

        Returns:
            label_classes (list): List of processed labels
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        """
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        label_classes = []

        for label in labels:

            label_class = re.sub(
                r'([a-z](?=[A-Z])|[A-Z](?=[A-Z][a-z]))', r'\1 ', label)
            label_class = ['\n'.join(wrap(element, 40))
                           for element in label_class]
            label_classes.append(label_class)

        return label_classes