Adding data augmentation classes

Author: JordiCorbilla

odir.py

@@ -1,4 +1,4 @@
-# Copyright 2019 Jordi Corbilla. All Rights Reserved.
+# Copyright 2019-2020 Jordi Corbilla. All Rights Reserved.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -15,15 +15,15 @@
 import numpy as np
 
 
-def load_data(image_size):
+def load_data(image_size, index):
     """Loads the ODIR dataset.
 
     Returns:
       Tuple of Numpy arrays: `(x_train, y_train), (x_test, y_test)`.
 
     """
-    x_train = np.load('odir_training'+'_' + str(image_size)+'.npy')
-    y_train = np.load('odir_training_labels'+'_' + str(image_size)+'.npy')
+    x_train = np.load('odir_training'+'_' + str(image_size) + '_' + str(index)+'.npy')
+    y_train = np.load('odir_training_labels'+'_' + str(image_size) + '_' + str(index)+'.npy')
 
     x_test = np.load('odir_testing'+'_' + str(image_size)+'.npy')
     y_test = np.load('odir_testing_labels'+'_' + str(image_size)+'.npy')

odir_advance_plotting.py

@@ -0,0 +1,272 @@
+# Copyright 2019 Jordi Corbilla. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+from __future__ import absolute_import, division, print_function, unicode_literals
+
+import sys
+
+import matplotlib.pyplot as plt
+from sklearn.metrics import confusion_matrix
+import numpy as np
+import seaborn as sns
+import matplotlib as mpl
+
+
+class Plotter:
+    def __init__(self, class_names):
+        self.class_names = class_names
+
+    def plot_metrics(self, history, test_run, index):
+        metrics2 = ['loss', 'auc', 'precision', 'recall']
+        for n, metric in enumerate(metrics2):
+            name = metric.replace("_", " ").capitalize()
+            plt.subplot(2, 2, n + 1)
+            plt.plot(history.epoch, history.history[metric], color='green', label='Train')
+            plt.plot(history.epoch, history.history['val_' + metric], color='green', linestyle="--", label='Val')
+            plt.xlabel('Epoch')
+            plt.ylabel(name)
+            if metric == 'loss':
+                plt.ylim([0, plt.ylim()[1]])
+            elif metric == 'auc':
+                plt.ylim([0.8, 1])
+            else:
+                plt.ylim([0, 1])
+
+            plt.legend()
+
+        plt.savefig('image_run' + str(index) + test_run + '.png')
+        plt.show()
+        plt.close()
+
+    def plot_input_images(self, x_train, y_train):
+        plt.figure(figsize=(9, 9))
+        for i in range(100):
+            plt.subplot(10, 10, i + 1)
+            plt.xticks([])
+            plt.yticks([])
+            plt.grid(False)
+            plt.imshow(x_train[i])
+            classes = ""
+            for j in range(8):
+                if y_train[i][j] >= 0.5:
+                    classes = classes + self.class_names[j] + "\n"
+            plt.xlabel(classes, fontsize=7, color='black', labelpad=1)
+
+        plt.subplots_adjust(bottom=0.04, right=0.95, top=0.94, left=0.06, wspace=0.56, hspace=0.17)
+        plt.show()
+
+    def plot_image(self, i, predictions_array, true_label, img):
+        predictions_array, true_label, img = predictions_array[i], true_label[i], img[i]
+        plt.grid(False)
+        plt.xticks([])
+        plt.yticks([])
+
+        plt.imshow(img)
+
+        ground = ""
+        count_true = 0
+        predicted_true = 0
+
+        for index in range(8):
+            if true_label[index] >= 0.5:
+                count_true = count_true + 1
+                ground = ground + self.class_names[index] + "\n"
+            if predictions_array[index] >= 0.5:
+                predicted_true = predicted_true + 1
+
+        if count_true == predicted_true:
+            color = 'green'
+        else:
+            color = 'red'
+
+        first, second, third, i, j, k = self.calculate_3_largest(predictions_array, 8)
+        prediction = "{} {:2.0f}% \n".format(self.class_names[i], 100 * first)
+        if second > 0.1:
+            prediction = prediction + "{} {:2.0f}% \n".format(self.class_names[j], 100 * second)
+        if third > 0.1:
+            prediction = prediction + "{} {:2.0f}% \n".format(self.class_names[k], 100 * third)
+        plt.xlabel("Predicted: {} Ground Truth: {}".format(prediction, ground), color=color)
+
+    def calculate_3_largest(self, arr, arr_size):
+        if arr_size < 3:
+            print(" Invalid Input ")
+            return
+
+        third = first = second = -sys.maxsize
+        index_1 = 0
+        index_2 = 0
+        index_3 = 0
+
+        for i in range(0, arr_size):
+            if arr[i] > first:
+                third = second
+                second = first
+                first = arr[i]
+            elif arr[i] > second:
+                third = second
+                second = arr[i]
+            elif arr[i] > third:
+                third = arr[i]
+
+        for i in range(0, arr_size):
+            if arr[i] == first:
+                index_1 = i
+        for i in range(0, arr_size):
+            if arr[i] == second and i != index_1:
+                index_2 = i
+        for i in range(0, arr_size):
+            if arr[i] == third and i != index_1 and i!= index_2:
+                index_3 = i
+        return first, second, third, index_1, index_2, index_3
+
+    def plot_value_array(self, i, predictions_array, true_label):
+        predictions_array, true_label = predictions_array[i], true_label[i]
+        plt.grid(False)
+        plt.xticks([])
+        plt.yticks([])
+        bar_plot = plt.bar(range(8), predictions_array, color="#777777")
+        plt.xticks(range(8), ('N', 'D', 'G', 'C', 'A', 'H', 'M', 'O'))
+        plt.ylim([0, 1])
+
+        for j in range(8):
+            if true_label[j] >= 0.5:
+                bar_plot[j].set_color('green')
+
+        for j in range(8):
+            if predictions_array[j] >= 0.5 and true_label[j] < 0.5:
+                bar_plot[j].set_color('red')
+
+        def bar_label(rects):
+            for rect in rects:
+                height = rect.get_height()
+                value = height * 100
+                if value > 1:
+                    plt.annotate('{:2.0f}%'.format(value),
+                                 xy=(rect.get_x() + rect.get_width() / 2, height),
+                                 xytext=(0, 3),  # 3 points vertical offset
+                                 textcoords="offset points",
+                                 ha='center', va='bottom')
+
+        bar_label(bar_plot)
+
+    def ensure_test_prediction_exists(self, predictions):
+        exists = False
+        for j in range(8):
+            if predictions[j] >= 0.5:
+                exists = True
+        return exists
+
+    def plot_output(self, test_predictions_baseline, y_test, x_test_drawing):
+        mpl.rcParams["font.size"] = 7
+        num_rows = 5
+        num_cols = 3
+        num_images = num_rows * num_cols
+        plt.figure(figsize=(2 * 2 * num_cols, 2 * num_rows))
+        j = 0
+        i = 0
+        while j < num_images:
+            if self.ensure_test_prediction_exists(test_predictions_baseline[i]):
+                plt.subplot(num_rows, 2 * num_cols, 2 * j + 1)
+                self.plot_image(i, test_predictions_baseline, y_test, x_test_drawing)
+                plt.subplot(num_rows, 2 * num_cols, 2 * j + 2)
+                self.plot_value_array(i, test_predictions_baseline, y_test)
+                j = j + 1
+            i = i + 1
+            if i > 400:
+                break
+
+        plt.subplots_adjust(bottom=0.08, right=0.95, top=0.94, left=0.05, wspace=0.11, hspace=0.56)
+        plt.show()
+
+    def plot_output_single(self, i, test_predictions_baseline, y_test, x_test_drawing):
+        plt.figure(figsize=(6, 3))
+        plt.subplot(1, 2, 1)
+        self.plot_image(i, test_predictions_baseline, y_test, x_test_drawing)
+        plt.subplot(1, 2, 2)
+        self.plot_value_array(i, test_predictions_baseline, y_test)
+        plt.show()
+
+    def plot_confusion_matrix(self, y_true, y_pred, classes, normalize=False, title=None, cmap=plt.cm.Blues):
+        """
+        This function prints and plots the confusion matrix.
+        Normalization can be applied by setting `normalize=True`.
+        """
+        if not title:
+            if normalize:
+                title = 'Normalized confusion matrix'
+            else:
+                title = 'Confusion matrix, without normalization'
+
+        # Compute confusion matrix
+        cm = confusion_matrix(y_true.argmax(axis=1), y_pred.argmax(axis=1))
+        # Only use the labels that appear in the data
+        if normalize:
+            cm = cm.astype('float') / cm.sum(axis=1)[:, np.newaxis]
+            print("Normalized confusion matrix")
+        else:
+            print('Confusion matrix, without normalization')
+
+        print(cm)
+
+        fig, ax = plt.subplots()
+        im = ax.imshow(cm, interpolation='nearest', cmap=cmap)
+        ax.figure.colorbar(im, ax=ax)
+        # We want to show all ticks...
+        ax.set(xticks=np.arange(cm.shape[1]),
+               yticks=np.arange(cm.shape[0]),
+               # ... and label them with the respective list entries
+               # xticklabels=classes, yticklabels=classes,
+               title=title,
+               ylabel='True label',
+               xlabel='Predicted label')
+        ax.set_ylim(8.0, -1.0)
+        # Rotate the tick labels and set their alignment.
+        plt.setp(ax.get_xticklabels(), rotation=45, ha="right",
+                 rotation_mode="anchor")
+
+        # Loop over data dimensions and create text annotations.
+        fmt = '.2f' if normalize else 'd'
+        thresh = cm.max() / 2.
+        for i in range(cm.shape[0]):
+            for j in range(cm.shape[1]):
+                ax.text(j, i, format(cm[i, j], fmt),
+                        ha="center", va="center",
+                        color="white" if cm[i, j] > thresh else "black")
+        fig.tight_layout()
+        return ax
+
+    def print_normalized_confusion_matrix(self, y_test, test_predictions_baseline):
+        np.set_printoptions(precision=2)
+
+        # Plot non-normalized confusion matrix
+        self.plot_confusion_matrix(y_test, test_predictions_baseline, classes=self.class_names,
+                                   title='Confusion matrix, without normalization')
+
+        # Plot normalized confusion matrix
+        self.plot_confusion_matrix(y_test, test_predictions_baseline, classes=self.class_names, normalize=True,
+                                   title='Normalized confusion matrix')
+
+        plt.show()
+
+    def plot_confusion_matrix_generic(self, labels2, predictions, test_run, p=0.5):
+        cm = confusion_matrix(labels2.argmax(axis=1), predictions.argmax(axis=1))
+        plt.figure(figsize=(6, 6))
+        ax = sns.heatmap(cm, annot=True, fmt="d")
+        ax.set_ylim(8.0, -1.0)
+        plt.title('Confusion matrix')
+        plt.ylabel('Actual label')
+        plt.xlabel('Predicted label')
+        plt.savefig('image_run3' + test_run + '.png')
+        plt.show()
+        plt.close()