pi = '314159265358979323846264338327\

950288419716939937510582097494\

459230781640628620899862803482\

534211706798214808651328230664\

709384460955058223172535940812\

848111745028410270193852110555\

964462294895493038196442881097\

566593344612847564823378678316\

527120190914564856692346034861\

045432664821339360726024914127'

seq = np.arange(32,128)

randomizer = np.empty(0)

while (seq.size != 0) & (len(pi) > 1):

if int(pi[:2]) < seq.size:

randomizer = np.append(randomizer,seq[int(pi[:2])])

seq = np.delete(seq,int(pi[:2]))

pi = pi[2:]

elif int(pi[:1]) < seq.size:

randomizer = np.append(randomizer,seq[int(pi[:1])])

seq = np.delete(seq,int(pi[:1]))

pi = pi[1:]

else:

# Skip number

pi = pi[1:]

# ( dicomname, (bool_encrypt, bool_digitcheck))

dcmname = dcm[0]

opts = dcm[1]

bool_encrypt = opts[0]

bool_digitcheck = opts[1]

bool_write = False

try:

dcminf = dicom.read_file(dcmname)

except:

# If not readable, simply exit

return

# If it is a dicom, scramble all information.

for field in fields_to_anon:

# Check to make sure dicom field exists.

if hasattr(dcminf,field):

name = getattr(dcminf,field)

# If it's not a string, skip any anonymization for the field

if not isinstance(name, basestring):

continue

else:

name = name.encode('ascii','ignore')

if bool_encrypt:

# encrypt the dicomfield

if bool_digitcheck:

bool_hasdigits = re.findall('\d+',name)

else:

bool_hasdigits = False

# Ignore if the name has the words "anonymous" or "volunteer" in it

if ( name.lower().find("anonymous") >= 0 ) | ( name.lower().find("volunteer") >= 0 ):

continue

# The additional "_JNO" ending is a safety to prevent items

# from being re-encrypted. It is assumed that if the name

# has any numbers, the patient field has already been anonymized.

if (name[-4:] != "_JNO") & (not bool_hasdigits):

anon_name = encrypt_string(name,KEY) + "_JNO"

setattr(dcminf,field,anon_name)

bool_write = True

else:

# If the name has "_JNO" as the ending, it has been encrypted

# and needs to be unencrypted.

if name[-4:] == "_JNO":

anon_name = unencrypt_string(name[:-4],KEY)

setattr(dcminf,field,anon_name)

bool_write = True

if bool_write:

encryptd_string = ''

for char in string:

encryptd_string += chr(int(randomizer[int(ord(char)-32)]))

unencrypt = np.argsort(KEY) + 32

unencryptd_string = ''

for char in string:

unencryptd_string += chr(int(unencrypt[int(ord(char)-32)]))

# Example (need to change directory to where create_mr_db.py is located):

# create_mr_db.py -f neostem_database.csv -d Z:\Users\Shared\Sleepystuff\images\EFFERVESCENT PATIENTS

parser = OptionParser(usage="usage: %prog [options] filename")

parser.add_option("-d", "--dir",

action="store", # optional because action defaults to "store"

type="string",

dest="directory",

default=os.getcwd(),

help="Directory file to search through")

parser.add_option("-f", "--filename",

action="store", # optional because action defaults to "store"

type="string",

dest="filename",

default="",

help="Directory file to search through")

parser.add_option("-v", "--verbose",

action="store_true", # optional because action defaults to "store"

dest="verbose", # Do you want the script to show ALL directories it's going through?

help="Show current folder")

parser.add_option("-u", "--anon",

action="store_false" , # optional because action defaults to "store"

dest="anon", # flag to encrypt names

default=True, # default option is to encrypt

help="Flag to decrypt dicom fields. Default is to encrypt fields")

parser.add_option("-n", "--numbers",

action="store_true" , # optional because action defaults to "store"

dest="numbers", # flag to encrypt names

default=False,

help="Check for numbers (0-9) in the field. If numbers exist in field, do not encrypt")

(options, args) = parser.parse_args()

# Allow a textfile to be read to automatically anonymize multiple folders

if options.filename:

with open(options.filename,'r') as f:

dirs = f.read()

dirs = dirs.split('\n')

directories_to_anonymize = filter(None, dirs)

else:

# If no text file is specified, anonymize current directory

directories_to_anonymize = [options.directory]

# Create a tuple to send over to the encrypt_dicom_name

opt_tuple = (options.anon,options.numbers)

p = Pool(20) # Use 15 processes to paralleze dicom anonymization

print directories_to_anonymize

# base is the base directory to search in and get ALL subfolders

for base in directories_to_anonymize:

print "Current main directory:", base

if options.verbose:

if options.anon:

print "Encrypting the following folders..."

else:

print "Decrypting the following folders..."

# os.walk goes through every subdirectory as a loop. The current directory

# in the loop is "dirname". All files in dirname are in a list, "filenames"

for dirname, dirnames, filenames in os.walk(base):

if options.verbose:

print dirname

#Append dicom options to each item

fullfilenames_options = [ [os.path.join(dirname,filename),opt_tuple] for filename in filenames]

# Sometimes this pulls an error. I'm not sure why, but there are five chances for it to retry.

for x in xrange(5):

try:

# Use the pool to parallelze encryption

p.map(encrypt_dicom_name,fullfilenames_options)

except:

# If it's the fourth try, print the failed directory.

if x == 4:

print "DIRECTORY FAILED TO ANONYMIZE: ", dirname

# Continue onto next "iteration" if it fails; skip the break

continue