images = [os.path.join(dir, name) for name in os.listdir(dir) if
			os.path.isfile(os.path.join(dir, name)) & name.endswith('.jpg')]

#argsparse
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('-x', '--xml', help='blast xml input', nargs='+')
parser.add_argument('-a', '--aminoacid', help='genome_aa_file_name', nargs='+')

args = parser.parse_args()
xml_files=args.xml
genome_aa_file_name = args.aminoacid

from PIL import ImageEnhance, Image
resize_factor = 0.1
image = Image.open(image_path)
width, height = image.size
print(image.size)
height = int(height*resize_factor)
width = int(width*resize_factor)
image = image.resize((width, height))

# rotate image
if width > height:
angle = 270
print("rotate")
image = image.rotate(angle, expand=True)
width, height = image.size
print(image.size)
# enhancement
image = ImageEnhance.Contrast(image).enhance(0.6)
image = ImageEnhance.Brightness(image).enhance(1.7)
# image.show()
# pixel manipulation
image_data = image.load()
for loop1 in range(width):
    for loop2 in range(height):
        r,g,b = image_data[loop1,loop2]
        # print(r)
        if b>g or b>r:
            image_data[loop1,loop2] = 0,0,0
        elif r-b>200:
            image_data[loop1,loop2] = 0,0,0
new_file_name = file_name.loc[image_name].genotype + '_' + image_name
new_file_name = new_file_name.replace(' ','_')
new_file_name = new_file_name.replace('JPG','jpg')
new_file_name = shelter_num + new_file_name
image.save(new_file_name)	

import cv2
img_array = []
ww = 640
hh = 480
color = (0,0,0)

for img_path in img_path_list:	
	img = cv2.imread(img_path)
	height, width, layers = img.shape
	x = int((ww-width)/2)
	y = int((hh-height)/2)
	result = np.full((hh,ww,layers), color, dtype=np.uint8)
	result[y:y+height, x:x+width] = img
	img_array.append(result)

# write a video composed of images
size = (ww,hh)
#fourcc mp4v or avc1 for mac, windows and linux need different fourcc
video = cv2.VideoWriter('dirt_image_sequence.avi',cv2.VideoWriter_fourcc('M','J','P','G'), 6, size)
 
for i in range(len(img_array)):
    video.write(img_array[i])
video.release()