def load_xml(xml_path):
"""
Function that determines the full path to the XML file
:param xml_path: path to the XML file (could be a relative path)
:type xml_path: str
:return: XML_file -> full path to the XML file to be read if it exists in
the filesystem, None otherwise
:rtype: str
"""
# Read the XML file with the identifying DICOM fields
load_xml = PathMethods.resource_path(xml_path)
XML_filename = load_xml.return_path()
if os.path.isfile(XML_filename):
XML_file = XML_filename
else:
XML_filepath = os.path.dirname(os.path.abspath(__file__))
XML_file = XML_filepath + "/" + XML_filename
return XML_file if os.path.isfile(XML_file) else None
def load_xml(xml_path):
"""
Function that determines the full path to the XML file
:param xml_path: path to the XML file (could be a relative path)
:type xml_path: str
:return: XML_file -> full path to the XML file to be read if it exists in
the filesystem, None otherwise
:rtype: str
"""
# Read the XML file with the identifying DICOM fields
load_xml = PathMethods.resource_path(xml_path)
XML_filename = load_xml.return_path()
if os.path.isfile(XML_filename):
XML_file = XML_filename
else:
XML_filepath = os.path.dirname(os.path.abspath(__file__))
XML_file = XML_filepath + "/" + XML_filename
return XML_file if os.path.isfile(XML_file) else None
def initialize(self):
self.frame = Frame(self.parent)
self.frame.pack(expand=1, fill='both')
# Insert DICAT logo on the right side of the screen
load_img = PathMethods.resource_path("images/DICAT_logo.gif")
imgPath = load_img.return_path()
logo = PhotoImage(file=imgPath)
logo_image = Label(self.frame, image=logo, bg='white')
logo_image.image = logo
logo_image.pack(side='left', fill='both')
# Create the Welcome to DICAT text variable
text = Text(self.frame, padx=40, wrap='word')
scroll = Scrollbar(self.frame, command=text.yview)
text.configure(yscrollcommand=scroll.set)
text.tag_configure('title',
font=('Verdana', 20, 'bold', 'italic'),
justify='center')
text.tag_configure('bold', font=('Verdana', 12, 'bold'))
text.tag_configure('default', font=('Verdana', 12))
# Insert title into the text variable
title = "\nWelcome to DICAT!\n\n"
text.insert(END, title, 'title')
# Insert introduction of the tool into the text variable
intro = "DICAT (DICOM Anonymization Tool) is a simple tool for "
intro += "de-identification of DICOM datasets. In addition to "
intro += "de-identifying DICOM files, this tool contains a feature "
intro += "that allows mapping the candidate's information to its "
intro += "study identifier.\n"
text.insert(END, intro, 'default')
# Insert explanation of the DICOM anonymizer tab into the text variable
tab1 = "\n\nThe DICOM de-identifier tab allows to:\n"
text.insert(END, tab1, 'bold')
anonymizer = '''
1) select a DICOM directory
2) view the DICOM headers information
3) run the de-identifier tool on all DICOMs of the selected directory
'''
text.insert(END, anonymizer, 'default')
# Insert explanation of the ID key tab into the text variable
tab2 = "\n\nThe ID key tab allows to:\n"
text.insert(END, tab2, 'bold')
IDkey = '''
1) store ID information for a given candidate
2) look for ID information from a given candidate
'''
text.insert(END, IDkey, 'default')
# Display the text variable
text.pack(side='left', fill='both', expand=1)
scroll.pack(side="right", fill='y')
# Disable the edit functionality of the displayed text
text.config(state='disabled')
def deidentify(self):
# clear edit table if it exists
if hasattr(self, 'field_edit_win'):
self.field_edit_win.destroy()
# Read the XML file with the identifying DICOM fields
load_xml = PathMethods.resource_path("data/fields_to_zap.xml")
XML_filename = load_xml.return_path()
# Remove the message from the grid
self.messageView.grid_forget()
if os.path.isfile(XML_filename):
XML_file = XML_filename
else:
XML_filepath = os.path.dirname(os.path.abspath(__file__))
XML_file = XML_filepath + "/" + XML_filename
field_dict = methods.grep_dicom_fields(XML_file)
# Read DICOM header and grep identifying DICOM field values
field_dict = methods.grep_dicom_values(self.dirname, field_dict)
fields_keys = list(field_dict.keys())
keys_length = len(fields_keys) + 1
self.edited_entries = [Tkinter.StringVar() for i in range(keys_length)]
if len(field_dict) != 0:
self.field_edit_win = Frame(self.parent)
self.field_edit_win.pack(expand=1, fill='both')
self.field_edit_win.columnconfigure(0, weight=1)
self.field_edit_win.columnconfigure(1, weight=1)
self.field_edit_win.rowconfigure(0, weight=1)
self.field_edit_win.rowconfigure(1, weight=1)
# Set column names
self.field_edit_win.Name_field = Tkinter.Label(self.field_edit_win,
text="Dicom Field",
relief="ridge",
width=30,
anchor="w",
fg="white",
bg="#282828")
self.field_edit_win.Name_field.grid(column=0,
row=0,
padx=(5, 0),
pady=(5, 0),
sticky=N + S + W + E)
self.field_edit_win.Name_value = Tkinter.Label(
self.field_edit_win,
text="Value in Dicom",
relief="ridge",
width=55,
anchor="w",
fg="white",
bg="#282828")
self.field_edit_win.Name_value.grid(column=1,
row=0,
padx=(0, 5),
pady=(5, 0),
sticky=N + S + W + E)
# Display description of fields to zap in first column
self.key_index = 1
for keys in fields_keys:
self.field_edit_win.Field_label = Tkinter.Label(
self.field_edit_win,
text=str(field_dict[keys]['Description']) + ':',
relief="ridge",
width=30,
anchor="w",
fg="black",
bg="#B0B0B0")
self.field_edit_win.Field_label.grid(column=0,
row=self.key_index,
padx=(5, 0),
sticky=N + S + W + E)
# Enter value to modify
if not field_dict[keys]['Editable']: # kr#
var = Tkinter.StringVar()
self.field_edit_win.Field = Tkinter.Entry(
self.field_edit_win,
textvariable=var,
state="disable",
width=55)
if 'Value' in field_dict[keys]:
var.set(field_dict[keys]['Value'])
else:
self.field_edit_win.Field = Tkinter.Entry(
self.field_edit_win,
textvariable=self.edited_entries[self.key_index],
width=55)
if 'Value' in field_dict[keys]:
self.field_edit_win.Field.insert(
self.key_index, field_dict[keys]['Value'])
else:
self.field_edit_win.Field.insert(self.key_index, "")
self.field_edit_win.Field.grid(column=1,
row=self.key_index,
padx=(0, 5),
sticky=N + S + W + E)
self.field_edit_win.rowconfigure(self.key_index, weight=1)
self.key_index += 1
self.field_dict = field_dict
self.bottomPanel = Tkinter.Frame(self.field_edit_win)
self.bottomPanel.grid(row=self.key_index,
column=0,
columnspan=2,
pady=10)
self.field_edit_win.button_done = Tkinter.Button(
self.bottomPanel,
text=u"De-identify",
command=self.collect_edited_data)
self.field_edit_win.button_done.grid(column=0, row=0, padx=20)
self.field_edit_win.buttonClear = Tkinter.Button(
self.bottomPanel, text=u"Clear", command=self.clear, width=8)
self.field_edit_win.buttonClear.grid(column=1, row=0, padx=20)
def initialize(self):
self.frame = Frame(self.parent)
self.frame.pack(expand=1, fill='both')
# Insert DICAT logo on the right side of the screen
load_img = PathMethods.resource_path("images/DICAT_logo.gif")
imgPath = load_img.return_path()
logo = PhotoImage(file = imgPath)
logo_image = Label(self.frame,
image = logo,
bg='white'
)
logo_image.image = logo
logo_image.pack(side='left', fill='both')
# Create the Welcome to DICAT text variable
text = Text(self.frame, padx=40, wrap='word')
scroll = Scrollbar(self.frame, command=text.yview)
text.configure(yscrollcommand=scroll.set)
text.tag_configure('title',
font=('Verdana', 20, 'bold', 'italic'),
justify='center'
)
text.tag_configure('bold', font=('Verdana', 12, 'bold'))
text.tag_configure('default', font=('Verdana', 12))
# Insert title into the text variable
title = "\nWelcome to DICAT!\n\n"
text.insert(END, title, 'title')
# Insert introduction of the tool into the text variable
intro = "DICAT (DICOM Anonymization Tool) is a simple tool for "
intro += "de-identification of DICOM datasets. In addition to "
intro += "de-identifying DICOM files, this tool contains a feature "
intro += "that allows mapping the candidate's information to its "
intro += "study identifier.\n"
text.insert(END, intro, 'default')
# Insert explanation of the DICOM anonymizer tab into the text variable
tab1 = "\n\nThe DICOM de-identifier tab allows to:\n"
text.insert(END, tab1, 'bold')
anonymizer = '''
1) select a DICOM directory
2) view the DICOM headers information
3) run the de-identifier tool on all DICOMs of the selected directory
'''
text.insert(END, anonymizer, 'default')
# Insert explanation of the ID key tab into the text variable
tab2 = "\n\nThe ID key tab allows to:\n"
text.insert(END, tab2, 'bold')
IDkey = '''
1) store ID information for a given candidate
2) look for ID information from a given candidate
'''
text.insert(END, IDkey, 'default')
# Display the text variable
text.pack(side='left', fill='both', expand=1)
scroll.pack(side="right", fill='y')
# Disable the edit functionality of the displayed text
text.config(state='disabled')
def deidentify(self):
# Read the XML file with the identifying DICOM fields
load_xml = PathMethods.resource_path("data/fields_to_zap.xml")
XML_filename = load_xml.return_path()
# Remove the message from the grid
self.messageView.grid_forget()
if os.path.isfile(XML_filename):
XML_file = XML_filename
else:
XML_filepath = os.path.dirname(os.path.abspath(__file__))
XML_file = XML_filepath + "/" + XML_filename
field_dict = methods.grep_dicom_fields(XML_file)
# Read DICOM header and grep identifying DICOM field values
field_dict = methods.grep_dicom_values(self.dirname, field_dict)
fields_keys = list(field_dict.keys())
keys_length = len(fields_keys) + 1
self.edited_entries = [Tkinter.StringVar() for i in range(keys_length)]
if len(field_dict) != 0:
self.field_edit_win = Frame(self.parent)
self.field_edit_win.pack(expand=1, fill='both')
self.field_edit_win.columnconfigure(0, weight=1)
self.field_edit_win.columnconfigure(1, weight=1)
self.field_edit_win.rowconfigure(0, weight=1)
self.field_edit_win.rowconfigure(1, weight=1)
# Set column names
self.field_edit_win.Name_field = Tkinter.Label(self.field_edit_win,
text="Dicom Field",
relief="ridge",
width=30,
anchor="w",
fg="white",
bg="#282828")
self.field_edit_win.Name_field.grid(column=0,
row=0,
padx=(5, 0),
pady=(5, 0),
sticky=N + S + W + E)
self.field_edit_win.Name_value = Tkinter.Label(
self.field_edit_win,
text="Value in Dicom",
relief="ridge",
width=55,
anchor="w",
fg="white",
bg="#282828")
self.field_edit_win.Name_value.grid(column=1,
row=0,
padx=(0, 5),
pady=(5, 0),
sticky=N + S + W + E)
# Display description of fields to zap in first column
self.key_index = 1
for keys in fields_keys:
self.field_edit_win.Field_label = Tkinter.Label(
self.field_edit_win,
text=str(field_dict[keys]['Description']) + ':',
relief="ridge", width=30, anchor="w", fg="black",
bg="#B0B0B0")
self.field_edit_win.Field_label.grid(column=0,
row=self.key_index,
padx=(5, 0),
sticky=N + S + W + E)
# Enter value to modify
if not field_dict[keys]['Editable']: # kr#
var = Tkinter.StringVar()
self.field_edit_win.Field = Tkinter.Entry(
self.field_edit_win, textvariable=var, state="disable",
width=55)
if 'Value' in field_dict[keys]:
var.set(field_dict[keys]['Value'])
else:
self.field_edit_win.Field = Tkinter.Entry(
self.field_edit_win,
textvariable=self.edited_entries[self.key_index],
width=55)
if 'Value' in field_dict[keys]:
self.field_edit_win.Field.insert(self.key_index,
field_dict[keys][
'Value'])
else:
self.field_edit_win.Field.insert(self.key_index, "")
self.field_edit_win.Field.grid(column=1, row=self.key_index,
padx=(0, 5),
sticky=N + S + W + E)
self.field_edit_win.rowconfigure(self.key_index, weight=1)
self.key_index += 1
self.field_dict = field_dict
self.bottomPanel = Tkinter.Frame(self.field_edit_win)
self.bottomPanel.grid(row=self.key_index, column=0, columnspan=2,
pady=10)
self.field_edit_win.button_done = Tkinter.Button(
self.bottomPanel,
text=u"De-identify",
command=self.collect_edited_data)
self.field_edit_win.button_done.grid(column=0, row=0, padx=20)
self.field_edit_win.buttonClear = Tkinter.Button(self.bottomPanel,
text=u"Clear",
command=self.clear,
width=8)
self.field_edit_win.buttonClear.grid(column=1, row=0, padx=20)
