quick and dirty script to glob a directory of dicom files and extract the header information into a csv file

dump_dicom_headers.py

''' quick and dirty script to glob a directory of dicom files and extract the header information into a csv file '''

import pydicom
import glob
import pandas as pd
from tqdm import tqdm
import numpy as np

###########################
# Parameters
tolerance = 0.01 # tolerance for checking if SliceLocation is consistently spaced
###########################
dicomseries = glob.glob('*.dcm')
tbl = pd.DataFrame(columns=['Filename', 'PatientID', 'PatientName', 'StudyDate', 'StudyTime', 'StudyDescription', 'SeriesNumber', 'SeriesDescription', 'InstanceNumber', 'ImagePositionPatient', 'ImageOrientationPatient', 'SliceLocation', 'Rows', 'Columns', 'PixelSpacing', 'SliceThickness', 'SpacingBetweenSlices', 'NumberOfFrames', 'BodyPartExamined', 'ProtocolName', 'SeriesInstanceUID', 'StudyInstanceUID', 'StudyID',  'WindowCenter', 'WindowWidth', 'StudyID', 'AcquisitionNumber'])

print('\n\n >> Reading DICOM headers\n')
for didx, dicom in tqdm(list(enumerate(dicomseries))):
    ds = pydicom.dcmread(dicom, stop_before_pixels=True)
    # try to collect items
    for item in tbl.columns:
        try:
            tbl.loc[didx, item] = ds[item].value
        except:
            tbl.loc[didx, item] = pd.NA

    tbl.loc[didx, 'Filename'] = dicom

tbl.to_csv('dicom_headers.csv', index=False)

# do some checks
unique_series = np.sort(tbl['SeriesNumber'].unique())

print('\n\n >> Checking for consistent slice spacing\n')
for series in unique_series:
    # check that SliceLocation is consistently spaced
    tbl_series = tbl[tbl['SeriesNumber'] == series]
    tbl_series = tbl_series.sort_values(by='SliceLocation')
    tbl_series['SliceLocation_diff'] = tbl_series['SliceLocation'].diff()

    # get data ptp
    ptp = np.ptp(tbl_series['SliceLocation_diff'])
    if ptp < tolerance:
        print('OK Series {} {}'.format(series, tbl_series['SeriesDescription'].iloc[0]))
    else:
        s_desc = tbl_series['SeriesDescription'].iloc[0]
        if ('MPR' in s_desc) or ('localizer' in s_desc):
            alert = '  '
            note = '| note: localizer or resliced series. spacing irrelevant.'
        else:
            alert = '!!'
            note = ''

        print('{} Series {} {} (inter-slice spacing range: {:2.2g} mm) {}'.format(alert, series, s_desc, ptp, note))

print('\n\n')