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How does one read multiple DICOM and PNG files at once using pydicom.read_file() and cv2.imread()?

Currently working on a Fully CNN for renal segmentation in MR images. Have 40 images and their ground truth labels, attempting to load all of the images for pre-processing purposes.

Using Google Colab, with the latest versions of pydicom and pip installed, for this project. Currently have the Google Drive mounted to the Colab program and the code below shows the correct pathways to the images and their masks in the pydicom.read_file() and cv2.imread() calls, respectively.

However, when I use the "/../IMG*.dcm" or "/../IMG*.png" file paths (which should be legal?), I receive a "FileNotFoundError" as listed below. But, when I specify a specific .dcm or .png image, the pydicom.read_file() and cv2.imread() calls function quite normally.

Any suggestions on how to resolve this issue? I am struggling a lot with loading the data and pre-processing but have the model architecture ready to go once these preliminary hurdles are overcome.

 #import data as data
    import pydicom
    import numpy as np
    images= pydicom.read_file("/content/drive/My Drive/CHOAS_Kidney_Labels/Training_Images/T1DUAL/IMG*.dcm");
    numpyArray = images.pixel_array
    masks= cv2.imread("/content/drive/My Drive/CHOAS_Kidney_Labels/Ground_Truth_Training/T1DUAL/IMG*.png");

-----> FileNotFoundError: [Errno 2] No such file or directory: '/content/drive/My Drive/CHOAS_Kidney_Labels/Training_Images/T1DUAL/IMG*.dcm'

Solution

  • pydicom.read_file does not support wildcards. You have to iterate over the files yourself, something like (untested):

    import glob
import pydicom

pixel_data = []
paths = glob.glob("/content/drive/My Drive/CHOAS_Kidney_Labels/Training_Images/T1DUAL/IMG*.dcm")
for path in paths:
    dataset = pydicom.dcmread(path)
    pixel_data.append(dataset.pixel_array)