I'm new to python. I'm trying to import dicom files. The following code is used in many tutorials for import dicom files using pydicom (for example https://www.kaggle.com/gzuidhof/full-preprocessing-tutorial):
INPUT_FOLDER = '../input/sample_images/'
patients = os.listdir(INPUT_FOLDER)
patients.sort()
Load the scans in given folder path
def load_scan(path):
slices = [dicom.read_file(path + '/' + s) for s in os.listdir(path)]
slices.sort(key = lambda x: float(x.ImagePositionPatient[2]))
try:
slice_thickness = np.abs(slices[0].ImagePositionPatient[2] - slices[1].ImagePositionPatient[2])
except:
slice_thickness = np.abs(slices[0].SliceLocation - slices[1].SliceLocation)
for s in slices:
s.SliceThickness = slice_thickness
return slices
first_patient = load_scan(INPUT_FOLDER + patients[0])
Every time I run this, I get the following error:
AttributeError Traceback (most recent call last)
<ipython-input-14-883826d71e95> in <module>()
----> 1 first_patient = load_scan(INPUT_FOLDER + patients[0])
2 frames
/usr/local/lib/python3.6/dist-packages/dicom/dataset.py in __getattr__(self, name)
255 if tag not in self:
256 raise AttributeError("Dataset does not have attribute "
--> 257 "'{0:s}'.".format(name))
258 else: # do have that dicom data_element
259 return self[tag].value
AttributeError: Dataset does not have attribute 'ImagePositionPatient'.
It's probably obvious to everyone but this code imports separate dicom files that together make up a CT scan and combines them into a single array "slices." When I define "slices" as a single dicom file rather than trying to combine all of them, I can write slices.ImagePositionPatient and it returns something like [x, y] so the original files definitely have this attribute. It seems like when I import them all into a single array, it somehow loses the attribute. As far as I can tell, I'm the only one who has had this issue. Can anyone provide any insight?