Index DICOM files with Python to csv

#!/usr/bin/env python

# This script will read DICOM Files and output headers to csv

import os

import sys

import os.path

import csv

import pydicom   # Load dicom tools.  Install with: pip install pydicom

import time

timestr = time.strftime("%Y%m%d-%H%M%S")

global success_count

global total_file_count

# files extensions not to index

file__ex_list = ['.xml','.gz','.zip','.txt','.doc','csv']

# set output file name

csvfilename = 'c:\\support\\DicomFileList-' + timestr + '.csv'

success_count = 0

total_file_count = 0

skipped_file_count = 0

# Set the path to scan for files

tpath = 'E:\\PACS-EXPORT' # \\20200130\\1.2.840.113619.2.226.6067236.1580392212.0.5\\1.2.840.113619.2.226.6067236.1580392212.0.6'

# create the header for the CSV file

csvheader = "SOPInstanceUID,StudyInstanceUID,AccessionNumber,PatientID,SeriesDescription,StudyDate,PatientName,Modality"

csvfile = open(csvfilename,'w', newline='')

#print(tpath)

# Recursively upload a directory

with csvfile:

    fnames = ['SOPInstanceUID','StudyInstanceUID','AccessionNumber','PatientID','SeriesDescription','StudyDate','PatientName','Modality','PatientBirthDate',"FileName"]

    csvwriter = csv.DictWriter(csvfile, fieldnames=fnames)

    csvwriter.writeheader()

    for root, dirs, files in os.walk(tpath):

        for f in files:

                total_file_count += 1

                #print(tpath)

                myfile = os.path.join(root,f)

                print("Looking at file -",myfile)

                #print(myfile.lower().endswith())

                if f.lower().endswith(tuple(file__ex_list)):

                    sys.stdout.write(" => skipping " + os.path.splitext(f)[1] + " file\n")

                    skipped_file_count += 1

                else:

                    success_count += 1

                    dicomdata = pydicom.dcmread(myfile)

                    csvwriter.writerow({

                                        'SOPInstanceUID' :  getattr(dicomdata,'SOPInstanceUID',''),

                                        'StudyInstanceUID' : getattr(dicomdata,'StudyInstanceUID',''),

                                        'AccessionNumber' : getattr(dicomdata,'AccessionNumber',''),

                                        'PatientID' : getattr(dicomdata,'PatientID',''),

                                        'SeriesDescription' : getattr(dicomdata,'SeriesDescription',''),

                                        'StudyDate' : getattr(dicomdata,'StudyDate',''),

                                        'PatientName' : getattr(dicomdata,'PatientName',''),

                                        'Modality' : getattr(dicomdata,'Modality',''),

                                        'PatientBirthDate' : getattr(dicomdata,'PatientBirthDate',''),

                                        "FileName" : myfile

                                        }) #patientName

if success_count == total_file_count:

    print("\nSummary: all %d DICOM file(s) have been processed successfully" % success_count)

else:

    print("\nSummary: %d out of %d files have been processed successfully as DICOM, with %d files skipped" % (success_count, total_file_count, skipped_file_count))