Cropping and storing bounding box image regions for a collection of images?

Question

The current code aims to crop and store multiple bounding box image regions for a set of images in a folder. The cropped bounding box image regions are store to a different folder. There are a total of 100 images, each image has multiple bounding boxes. The CSV file contains multiple bounding box coordinates for every given image. The code is as shown:

import pandas as pd
import cv2
import numpy as np
import glob
import os

filenames = glob.glob("folder/abnormal/*.png")
filenames.sort()
images = [cv2.imread(img) for img in filenames]
print(images)
df = pd.read_csv('abnormal.csv')

for img in images:
    for i in range(len(df)):
        name = df.loc[i]['patientId']
        start_point = (df.loc[i]['x_dis'],df.loc[i]['y_dis'])  
        end_point = (df.loc[i]['x_dis']+df.loc[i]['width_dis'],df.loc[i]['y_dis']+df.loc[i]['height_dis'])  
        crop = img[df.loc[i]['y_dis']:df.loc[i]['y_dis']+df.loc[i]['height_dis'],
                     df.loc[i]['x_dis']:df.loc[i]['x_dis']+df.loc[i]['width_dis']]
        cv2.imwrite("abnormal/crop_{0}.png".format(i), crop)

On running the code above, the loop continues indefinitely. It happens so that all crops are with respect of the bounding box image regions for image1, and then all crops stored are converted with respect of the bounding box image regions for image2, and so on. What is needed is the multiple box regions for each image and cropped and stored once.The images start with name patient*.png (patient1.png) or patient*.*.png (patient1_1.png).

So what is the issue? Seems very similar to your previous question. How do you name your images in folder1? You need two "for" loops. One over each image in folder1 and one over every crop from the csv file. — fmw42
@fmw42 well. need help in running multiple for loops as i am a beginner in python. The images start with patient* (e.g. patient1) or patient*.* (e.g. patient1_1) and are .png files. Thanks. — shiva
You need to loop over each file name in the list of images you have to load the image. Search Google for "python opencv load folder of images" and you will find many examples. For example, see stackoverflow.com/questions/38675389/…. That will be your outer (first) loop. Then you indent for your second loop that you have already that crops all the sections you want. It is always a good idea to search Google and/or this forum to find examples to learn before asking questions in this forum. Test loading and viewing. — fmw42
@fmw42: thanks. i modified the code as shown above. Each image has only one bounding box and there are 200 images. When I run the code above, the loop goes indefinite. The images start with patient* (e.g. patient1) or patient*.* (e.g. patient1_1) and are .png files. Could you please help with corrections in the code? thanks. — shiva
What is the length of images, i.e. the number of images in the list? If reasonable, then put a counter in your images list and print the count value as the processing is being done. If you have lots of images and do lots of crops, then it will take a long time. — fmw42

Sudhir Sudhir · Accepted Answer · 2020-05-20T03:06:45

The following code snippet should do the job:

filenames = glob.glob("folder/abnormal/*.png")
filenames.sort()
df = pd.read_csv('abnormal.csv')
im_csv_np = df.loc[:,"patientId"].values

for f in filenames:
    img = cv2.imread(f)
    img_name = f.split(os.sep)[-1]
    idx = np.where(im_csv_np == img_name)
    if idx[0].shape[0]: # if there is a match shape[0] should 1, if not 0
        for i in idx:
            name = df.loc[i]['patientId']
            start_point = (df.loc[i]['x_dis'],df.loc[i]['y_dis'])  
            end_point = (df.loc[i]['x_dis']+df.loc[i]['width_dis'],df.loc[i]['y_dis']+df.loc[i]['height_dis'])  
            crop = img[df.loc[i]['y_dis']:df.loc[i]['y_dis']+df.loc[i]['height_dis'],
                        df.loc[i]['x_dis']:df.loc[i]['x_dis']+df.loc[i]['width_dis']]
            cv2.imwrite("abnormal/crop_{0}.png".format(i), crop)

Cropping and storing bounding box image regions for a collection of images?

1 Answers