core.py

#!/usr/bin/env python 
#-*- coding: utf-8 -*-
""" 
********** DICOnyM Core ***************

DICOnyM is a pythonfoo project based in
the pydicom lib:
	http://code.google.com/p/pydicom/

Project Home: 
	https://github.com/pythonfoo/diconym

Project Members:
	Mechtilde
	Mikeadvo
	bison
	dodo
	dr1ll
	Oerb
"""
__author__ = "pyhtonfoo"
__copyright__ = "GPL 2013"
__license__ = "GPL v3 Plus" 

import os
import dicom
import random

def isDicom(fullpath):
	"""
	Check if a file is a DICOM file

	Args:
		fullpath (str): the FULL path of the file to check
	"""
	isOk = True
	try:
		dcm = dicom.read_file(fullpath)
	except Exception as ex:
		isOk = False
		# print fullpath
		# print ex
	return isOk

def getFilesFromDir(dirPath):
	"""
	Get a dictionary of fullpath:filename from a given path
	that contains ONLY valid DICOM files

	Args:
		dirPath (str): the FULL path of the directory to scan
	Returns:
		dictionary of fullpath:filename
	Raises:
		None
	"""
	dirList = os.listdir(dirPath)
	dcmFiles = {}
	for fname in dirList:
		fPath = os.path.join(dirPath, fname)
		if isDicom(fPath):
			dcmFiles[fPath] = fname
			#dcmFiles.append(fPath)
	return dcmFiles

def get_valuesfromImage(filename):                                              
	"""
	Read data element tag, value, VR, VM, description from DICOM file.
	"""
	datalist = []
	def tagbased_callback(ds, data_element):
		datalist.append((data_element.tag, data_element.value, data_element.VR, data_element.VM, data_element.description))


	# Load the current dicom file to get tag- and valuelist
	dataset = dicom.read_file(filename)

	# write tag and value into datalist
	dataset.walk(tagbased_callback)

	return datalist


def anonymize_byWhitelist_bak(whitelist, filename, newfilename):
	"""
	"""
	def tagbased_callback(ds, data_element):
		"""
		Delete the value in non Whitelisted Tags
		TODO:
		"""
		cnt = 0
		for whitelisttag in whitelist:
			if str(data_element.tag) != str(whitelisttag):
				cnt+=1
				data_element.value = ""
			else:
				print 'keep:', data_element.tag
		print cnt
	# Load the current dicom file to get tag- and valuelist
	dataset = dicom.read_file(filename)

	# write delete nonwhitelist tag values into datalist
	dataset.walk(tagbased_callback)

	# save file to newfilename
	dataset.save_as(newfilename)

def anonymize_byWhitelist(whitelist, filename, newfilename):
	"""
	"""
	# fix whitelist string-desaster!
	nwhitelist = []
	for ar in whitelist:
		for subAr in ar:
			nwhitelist.append(str(subAr).replace("'", ''))
	#print nwhitelist

	# Load the current dicom file to get tag- and valuelist
	dataset = dicom.read_file(filename)

	# write delete nonwhitelist tag values into datalist
	#dataset.walk(tagbased_callback)

	for dt in dataset:
		#print type(dt)
		#print dt, dt.__dict__
		#print dt.tag
		if str(dt.tag) in nwhitelist:
			pass
			#print 'keep:', str(dt)
			#print dataset[dt]
			#insatnce number
			#series number
		else:
			if 'value' in dt.__dict__:
				print 'del:', dt
				print 'val:', dataset.value
				dataset.value = ''
			else:
				print 'hard reset:', dt
				tmpType = type(dt._value)
				if tmpType is str:
					dt._value = ''
				elif tmpType is int or tmpType is float:
					dt._value = 0
				elif tmpType is list:
					dt._value = []
				elif str(tmpType) == "<class 'dicom.UID.UID'>":
					dt._value = "0"
					#print 'UID cant be reset', tmpType
				else:
					print 'unknown type:', '#'+str(tmpType)+'#'
					dt._value = ""
	#for whitelisttag in whitelist:
	#    if str(data_element.tag) != str(whitelisttag):
	 #       cnt+=1
	  #      data_element.value = ""
	   # else:
		#    print 'keep:', data_element.tag
	# save file to newfilename
	dataset.save_as(newfilename)