How to read multiple DICOM files from a folder?

Question

I have the following code in which I am loading a single DICOM file and checking if there are sagittal and coronal view present or not.

I want to modify this to read all DICOM files from the folder.
print there is no sagittal and coronal view if sag_aspect,cor_aspect value is zero

How do I do this?

import pydicom
import numpy as np
import matplotlib.pyplot as plt
import sys
import glob

# load the DICOM files
files = []
print('glob: {}'.format(sys.argv[1]))
for fname in glob.glob('dicom/3.dcm', recursive=False):
    print("loading: {}".format(fname))
    files.append(pydicom.dcmread(fname))

print("file count: {}".format(len(files)))

# skip files with no SliceLocation (eg scout views)
slices = []
skipcount = 0
for f in files:
    if hasattr(f, 'SliceLocation'):
        slices.append(f)
    else:
        skipcount = skipcount + 1

print("skipped, no SliceLocation: {}".format(skipcount))

# ensure they are in the correct order
slices = sorted(slices, key=lambda s: s.SliceLocation)

# pixel aspects, assuming all slices are the same
ps = slices[0].PixelSpacing
ss = slices[0].SliceThickness
ax_aspect = ps[1]/ps[0]
sag_aspect = ps[1]/ss
cor_aspect = ss/ps[0]

# create 3D array
img_shape = list(slices[0].pixel_array.shape)
img_shape.append(len(slices))
img3d = np.zeros(img_shape)

# fill 3D array with the images from the files
for i, s in enumerate(slices):
    img2d = s.pixel_array
    img3d[:, :, i] = img2d

# plot 3 orthogonal slices
print(img3d.shape)
print(img_shape)
a1 = plt.subplot(2, 2, 1)
plt.imshow(img3d[:, :, img_shape[2]//2])
a1.set_title("transverse view")
a1.set_aspect(ax_aspect)

a2 = plt.subplot(2, 2, 2)
#print(img3d[:, img_shape[1]//2, :].shape)
plt.imshow(img3d[:, img_shape[1]//2, :])
a2.set_title("sagital view")
a2.set_aspect(sag_aspect)

a3 = plt.subplot(2, 2, 3)
plt.imshow(img3d[img_shape[0]//2, :, :].T)
a3.set_title("coronal view")
a3.set_aspect(cor_aspect)

plt.show()

blunova · Answer 1 · 2022-10-25T13:24:08.327

For reading multiple dicom files from a folder you can use the code below.

import os
from pathlib import Path
import pydicom

dir_path = r"path\to\dicom\files"

dicom_set = []
for root, _, filenames in os.walk(dir_path):
    for filename in filenames:
        dcm_path = Path(root, filename)
        if dcm_path.suffix == ".dcm":
            try:
                dicom = pydicom.dcmread(dcm_path, force=True)
            except IOError as e:
                print(f"Can't import {dcm_path.stem}")
            else:
                dicom_set.append(dicom)

I have leveraged the pathlib library which I strongly suggest to use whenever dealing with folder/file paths. I have also added an exception, but you can modify it to meet your needs.

How to read multiple DICOM files from a folder?

1 Answers1