Modifying a large number of DICOM (.dcm) files.

Question

bit of a simple question perhaps but I am not making progress and would appreciate help.

I have a list of size 422. Within index 0 there are 135 file paths to .dcm images. For example ‘~/images/0001.dcm’,’~/images/0135.dcm’ Within index 1, there are 112 image paths, index 2 has 110, etc.

All images are of size 512 x 512. I am looking to re-size them to be 64 x 64.

This is my first time working with both image and .dcm data so I’m very unsure about how to resize. I am also unsure how to access and modify the files within the ‘inner’ list, if you will.

Is something like this way off the mark?

IMG_PX_SIZE = 64 
result = []
for i in test_list:
    result_inner_list = []        
    for image in i:
    # resize all images at index position i and store in list
        new_img = cv2.resize(np.array(image.pixel_array (IMG_PX_SIZE,IMG_PX_SIZE))
        result_inner_list.append(new_img)
    # Once all images at index point i are modified, append them these to a master list.
    result.append(result_inner_list)

Asked By: Ciaran De Ceol

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Answer 1

You seem to be struggling with two issues:

accessing the file paths
resize

For you to win, better separate these two tasks, sample code below

IMG_PX_SIZE = 64 

def resize(image):
    # your resize code here similar to:        
    # return v2.resize(np.array(image.pixel_array(IMG_PX_SIZE,IMG_PX_SIZE))
    pass

def read(path):
    # your file read operation here
    pass


big_list = [['~/images/0001.dcm','~/images/0135.dcm'],
            ['~/images/0002.dcm','~/images/0136.dcm']]

resized_images = [[resize(read(path)) for path in paths] for paths in big_list]

Answered By: Evgeny

Modifying a large number of DICOM (.dcm) files.

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