Add files via upload

Author: mano3-1

creating_dataset/augmentation_for_dataset.py

@@ -0,0 +1,52 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Apr 14 13:26:53 2020
+
+@author: Lenovo
+"""
+
+
+import os
+import cv2
+import numpy as np
+#import math
+import argparse
+from keras.preprocessing.image import ImageDataGenerator
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--category' ,type = str ,default = 'covid')
+args = parser.parse_args()
+category = args.category
+
+def load_images_and_labels(images ,dir):
+
+    X_train=[]
+    i=0
+    for image in images:
+        k=image
+        i=i+1
+        image=cv2.imread(dir+'/'+image)
+        image=cv2.resize(image,(224,224))
+        print(i,k,'is loaded')
+        X_train.append(image)
+
+    X_train=np.asarray(X_train)
+    return X_train
+
+def augmentation_and_save(images ,dir ,factor ,rotation_range ,save_dir):
+    X_train=load_images_and_labels(images ,dir)
+    print(X_train.shape)
+    dgen=ImageDataGenerator(rotation_range=rotation_range)
+    aug=dgen.flow(X_train ,save_to_dir=save_dir ,batch_size=1 ,save_prefix='aug',save_format='jpg')
+    k=X_train.shape[0]
+    for j in range(factor):
+        i=0
+        for X_batch in aug:
+            if i==k:
+                break
+            else:
+                i=i+1
+if __name__ == '__main__':
+    path = os.path.join('..\covid_cropped\train' ,category)
+    images = os.listdir(path)
+    augmentation_and_save(images, path, factor = 1, rotation_range = 30, save_dir = path)

creating_dataset/cropping.py

@@ -0,0 +1,42 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Sat Apr 18 13:14:38 2020
+
+@author: Lenovo
+"""
+
+
+from PIL import Image
+import os
+
+
+def crop_and_save(img_dir ,per_w ,per_h ,save_dir = None):
+    img = Image.open(img_dir)
+    width, height = img.size   
+    new_width ,new_height = int(per_w*width) ,int(per_h*height)
+    left = (width - new_width)/2
+    top = (height - new_height)/2
+    right = (width + new_width)/2
+    bottom = (height + new_height)/2
+    cropped = img.crop((left ,top ,right ,bottom))
+    if save_dir is not None:
+        cropped.save(save_dir)
+        
+if __name__ == '__main__':
+    directory = r'D:\COMPUTERS\AI\spare_copies\covid_dataset'
+    folders = os.listdir(directory)
+    for folder in folders:
+        print(folder)
+        save_dir = r'D:\COMPUTERS\AI\dataset_and_embeddings\covid_cropped'
+        os.mkdir(os.path.join(save_dir ,folder))
+        save_dir = save_dir +'/'+ folder
+        load_dir = directory +'/'+ folder
+        for subfolder in os.listdir(load_dir):
+            print('***',subfolder)
+            os.mkdir(os.path.join(save_dir ,subfolder))
+            sub_save_dir = save_dir + '/' + subfolder
+            present_load_dir = os.path.join(load_dir ,subfolder)
+            for file in os.listdir(present_load_dir):
+                file_name = present_load_dir + '/' + file
+                present_save_dir = sub_save_dir + '/' + file
+                crop_and_save(file_name ,0.80 ,0.85 ,present_save_dir)

creating_dataset/get_files.py

@@ -0,0 +1,33 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Mon Apr 13 20:14:07 2020
+
+@author: Lenovo
+"""
+
+
+import os
+import shutil
+import pandas as pd
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--virus' ,type = str ,default = 'COVID-19')
+parser.add_argument('--x_ray_view' ,type = str ,default = 'PA')
+parser.add_argument('--outputDir' ,type = str ,default = r'D:\COMPUTERS\AI\dataset_and_embeddings\covid_dataset\covid')
+args = parser.parse_args()
+
+virus = args.virus
+x_ray_view = args.x_ray_view
+outputDir = args.outputDir
+path = r'D:\COMPUTERS\AI\DEEP_LEARNING\COVID\covid-chestxray-dataset'
+metadata = r'D:\COMPUTERS\AI\DEEP_LEARNING\COVID\covid-chestxray-dataset\metadata.csv'
+
+metadata_csv = pd.read_csv(metadata)
+
+for (i,row) in metadata_csv.iterrows():
+    if row['finding'] != virus or row['view'] != x_ray_view:
+        continue
+    file_dir = os.path.join(path , row['folder'] ,row['filename'])
+    out_dir = os.path.join(outputDir ,row['filename'])
+    shutil.copy(file_dir ,out_dir)