renamealldicoms

#!/usr/bin/env python

import os
import sys
import pydicom
from string import maketrans   # Required to call maketrans function.

# read in the datafile
if len(sys.argv) != 2:
    print("usage: renamealldicoms directoryname")
    exit()
datadirectory = sys.argv[1]
print("renamealldicoms: processing ", datadirectory)

alldirfiles = os.listdir(datadirectory)
dicomstorename = [thefilename for thefilename in alldirfiles if (thefilename.startswith("MR"))]

# first rename files at the top level to get rid of spaces
for thename in dicomstorename:
    plan = pydicom.read_file(datadirectory + "/" + thename)
    seriesnostr = plan.SeriesNumber
    imagenostr = plan.AcquisitionNumber
    protocolname = plan.SeriesDescription
    tempstring = protocolname + "_" + str(seriesnostr)
    thelist = tempstring.split()
    dirname = datadirectory + "/" + ''.join(thelist)
    outfilename = "IM-" + str(seriesnostr).rjust(4, '0') + "-" + str(imagenostr).rjust(4, '0') + ".dcm"
    print(dirname, outfilename)
    if not os.path.isdir(dirname + "/"):
        os.mkdir(dirname + "/")
    namestring = dirname + "/" + outfilename
    os.rename(datadirectory + "/" + thename, namestring)