class AddManually(Frame):
def __init__(self, parent, controller):
Frame.__init__(self, parent)
self.controller = controller
self.place(relx=0.0, rely=0.0, relheight=0.62, relwidth=0.72)
self.configure(relief=GROOVE)
self.configure(borderwidth="2")
self.configure(relief=GROOVE)
self.configure(width=125)
self.label_top = Label(self)
self.label_top.place(relx=0.4, rely=0.03, height=21, width=112)
self.label_top.configure(text="Add items manually")
self.name = Entry(self, fg='grey')
self.name.place(relx=0.05, rely=0.31, relheight=0.08, relwidth=0.29)
self.name.insert(0, "Input name here")
self.name.bind('<Button-1>', lambda event: greytext(self.name))
self.link = Entry(self, fg='grey')
self.link.place(relx=0.65, rely=0.31, relheight=0.08, relwidth=0.29)
self.link.insert(0, "Input link here")
self.link.bind('<Button-1>', lambda event: greytext(self.link))
self.add_btn = Button(self, command=self.send_data)
self.add_btn.place(relx=0.42, rely=0.44, height=34, width=100)
self.add_btn.configure(text="Add item")
self.back = Button(self, command=lambda: controller.show_frame('Main'))
self.back.place(relx=0.42, rely=0.64, height=34, width=100)
self.back.configure(text="Go back")
name_label = Label(self)
name_label.place(relx=0.05, rely=0.22, height=21, width=38)
name_label.configure(text="Name")
link_label = Label(self)
link_label.place(relx=0.65, rely=0.22, height=21, width=28)
link_label.configure(text="Link")
def send_data(self):
if self.link.cget('fg') == 'grey' or self.name.cget('fg') == 'grey':
return
link = self.link.get()
if link.strip() != '':
name = self.name.get()
self.controller.add_item(link, name)
print("Item added")
class Main(Frame):
def __init__(self, parent, controller):
Frame.__init__(self, parent)
self.controller = controller
self.db_set = False
self.configure(relief=GROOVE)
self.configure(borderwidth="2")
# Manual link adding
self.manual_btn = Button(self)
self.manual_btn.place(relx=0.07, rely=0.81, height=45, width=130)
self.manual_btn.configure(activebackground="#d9d9d9")
self.manual_btn.configure(highlightbackground="#d9d9d9")
self.manual_btn.configure(pady="0")
self.manual_btn.configure(text="Add manually")
self.manual_btn.configure(width=130)
self.file_btn = Button(self)
self.file_btn.place(relx=0.67, rely=0.81, height=45, width=150)
self.file_btn.configure(activebackground="#d9d9d9")
self.file_btn.configure(highlightbackground="#d9d9d9")
self.file_btn.configure(pady="0")
self.file_btn.configure(text="Add from file")
self.label = Label(self)
self.label.place(relx=0.08, rely=0.0, height=61, width=484)
self.label.configure(text="Create new playlists and add content to them")
self.label.configure(width=485)
self.listbox = Listbox(self)
self.listbox.place(relx=0.38, rely=0.22, relheight=0.31, relwidth=0.17)
self.listbox.configure(background="white")
self.listbox.configure(disabledforeground="#a3a3a3")
self.listbox.configure(foreground="#000000")
self.listbox.configure(selectmode=SINGLE)
self.listbox.configure(width=105)
for name, value in config.configparser.items('Playlists'):
if os.path.isdir(value):
self.listbox.insert('end', name)
else:
config.remove_value('Playlists', name)
self.listbox.bind('<<ListboxSelect>>', self.onselect)
self.label_name = Label(self)
self.label_name.place(relx=0.7, rely=0.22, height=31, width=84)
self.label_name.configure(foreground="#000000")
self.label_name.configure(text="Name")
self.label_name.configure(width=85)
self.entry = Entry(self)
self.entry.place(relx=0.63, rely=0.31, relheight=0.08, relwidth=0.29)
self.entry.configure(background="white")
self.entry.configure(foreground="#000000")
self.entry.configure(insertbackground="black")
self.entry.configure(takefocus="0")
self.entry.configure(width=175)
self.change_name = Button(self)
self.change_name.place(relx=0.7, rely=0.42, height=34, width=97)
self.change_name.configure(activebackground="#d9d9d9")
self.change_name.configure(highlightbackground="#d9d9d9")
self.change_name.configure(highlightcolor="black")
self.change_name.configure(pady="0")
self.change_name.configure(text="Rename")
self.change_name.configure(width=100)
self.new_playlist = Button(self, command=self.new_database)
self.new_playlist.place(relx=0.08, rely=0.28, height=54, width=107)
self.new_playlist.configure(activebackground="#d9d9d9")
self.new_playlist.configure(highlightbackground="#d9d9d9")
self.new_playlist.configure(highlightcolor="black")
self.new_playlist.configure(pady="0")
self.new_playlist.configure(text="Create new playlist")
self.new_playlist.configure(width=105)
self.db_name = Entry(self)
self.db_name.place(relx=0.07, rely=0.44, relheight=0.08, relwidth=0.22)
self.db_name.configure(fg='grey')
self.db_name.configure(width=135)
self.db_name.insert(0, "Input database name here")
self.db_name.bind('<Button-1>', lambda event: greytext(self.db_name))
def onselect(self, event):
w = event.widget
index = int(w.curselection()[0])
value = w.get(index)
set_database(config.configparser.get('Playlists', value))
if not database.check_integrity():
messagebox.showwarning('Integrity check failed', 'You might be missing some entries in your list')
if not self.db_set:
self.manual_btn.configure(command=lambda: self.controller.show_frame('AddManually'))
self.file_btn.configure(command=lambda: self.controller.show_frame('ReadFromFile'))
self.db_set = True
def new_database(self):
name = self.db_name.get()
names = config.configparser.options('Playlists')
print(name, names)
if name.strip() == '' or self.db_name.cget('fg') == 'grey':
messagebox.showerror('Invalid name', "Please input a valid name for the database")
return
if name in names:
messagebox.showerror('Name already in use', "Please select another name")
return
path = '../playlists/%s/' % name
if set_database(path, create=True) is False:
return
config.set_value('Playlists', name, path)
self.listbox.insert('end', name)
def get_text_field(field: tk.Entry) -> str:
if field.cget('fg') != 'grey':
return field.get()
return ""
class GUI(Tk):
def __init__(self):
Tk.__init__(self)
self.user_frame = Frame()
self.back_button = Button(self.user_frame,
text="Back",
command=self.back_to_home_gui)
self.segmentation_button = Button(self.user_frame,
text="Segmentation",
command=self.segmentation_gui,
height=2,
width=10)
self.analysis_button = Button(self.user_frame,
text="Analysis",
command=self.analysis_gui,
height=2,
width=10)
self.progress = Progressbar(self.user_frame,
orient=HORIZONTAL,
length=200,
mode='indeterminate')
self.progress_label = Label(self.user_frame)
# output folder
self.output_path = StringVar("")
self.output_label = Label(self.user_frame,
text="please select "
"output path")
self.output_input = Entry(self.user_frame,
textvariable=self.output_path,
width=40)
self.select_output = Button(self.user_frame,
text=" ",
command=self.select_output_folder)
# original image
self.file_path = StringVar("")
self.file_label = Label(self.user_frame,
text="please select the CT "
"scan")
self.file_input = Entry(self.user_frame,
textvariable=self.file_path,
width=40)
self.select_file = Button(
self.user_frame,
text=" ",
command=lambda: self.select_nifti_file(self.file_path))
# seeds
self.seeds_path = StringVar("")
self.seeds_label = Label(self.user_frame,
text="please select the "
"marking")
self.seeds_input = Entry(self.user_frame,
textvariable=self.seeds_path,
width=40)
self.select_seeds = Button(
self.user_frame,
text=" ",
command=lambda: self.select_nifti_file(self.seeds_path))
# run buttons
self.segmentation_run = Button(self.user_frame,
text="Run "
"Segmentation",
command=self.run_segmentation)
self.analysis_run = Button(self.user_frame,
text="Run Analysis",
command=self.run_analysis)
self.default_background = self.output_input.cget("background")
self.scaphoid = None
self.radius = None
self.initilize_gui()
def __del__(self):
del self.user_frame
del self.back_button
del self.segmentation_button
del self.analysis_button
del self.progress
del self.progress_label
del self.output_path
del self.output_label
del self.output_input
del self.select_output
del self.file_path
del self.file_label
del self.file_input
del self.select_file
del self.seeds_path
del self.seeds_label
del self.seeds_input
del self.select_seeds
del self.segmentation_run
del self.analysis_run
del self.default_background
del self.scaphoid
del self.radius
def select_output_folder(self):
"""Select an output folder"""
path = filedialog.askdirectory()
self.output_path.set(path)
self.output_input.config(background=self.default_background)
del path
def select_nifti_file(self, var):
"""Select a nifti file"""
input_path = filedialog.askopenfilename()
var.set(input_path)
self.user_frame.grid_slaves(
int(str(var)[-1]) + 1,
1)[0].config(background=self.default_background)
del input_path
def back_to_home_gui(self):
"""forgets the other gui and reload the home gui"""
self.forget_non_home_gui()
self.seeds_path.set("")
self.initilize_gui()
def initilize_gui(self):
"""Initial GUI"""
self.title("Scaphoid Fracture Segmentation and analysis")
self.user_frame.grid()
self.segmentation_button.grid(row=0,
column=0,
padx=(100, 50),
pady=(30, 30))
self.analysis_button.grid(row=0,
column=1,
padx=(50, 100),
pady=(30, 30))
def segmentation_gui(self):
"""Initial GUI of the segmentation"""
self.segmentation_button.grid_forget()
self.analysis_button.grid_forget()
self.back_button.grid(row=0, pady=(2, 2))
self.title("Scaphoid Fracture Segmentation")
self.seeds_label.config(text="please select the marking")
self.output_label.grid(row=1, column=0)
self.output_input.grid(row=1, column=1)
self.select_output.grid(row=1, column=2)
self.file_label.grid(row=2, column=0)
self.file_input.grid(row=2, column=1)
self.select_file.grid(row=2, column=2)
self.seeds_label.grid(row=3, column=0)
self.seeds_input.grid(row=3, column=1)
self.select_seeds.grid(row=3, column=2)
self.segmentation_run.grid(row=4, columnspan=3, sticky=N + S + E + W)
def analysis_gui(self):
"""Initial the analysis GUI"""
self.segmentation_button.grid_forget()
self.analysis_button.grid_forget()
self.back_button.grid(row=0, pady=(2, 2))
self.title("Scaphoid Fracture analysis")
self.seeds_label.config(text="please select the segmentation")
self.output_label.grid(row=1, column=0)
self.output_input.grid(row=1, column=1)
self.select_output.grid(row=1, column=2)
self.file_label.grid(row=2, column=0)
self.file_input.grid(row=2, column=1)
self.select_file.grid(row=2, column=2)
self.seeds_label.grid(row=3, column=0)
self.seeds_input.grid(row=3, column=1)
self.select_seeds.grid(row=3, column=2)
self.analysis_run.grid(row=4, columnspan=3, sticky=N + S + E + W)
def forget_non_home_gui(self):
"""Forgets the grid of segmentation GUI"""
collect()
self.back_button.grid_forget()
self.output_label.grid_forget()
self.output_input.grid_forget()
self.select_output.grid_forget()
self.file_label.grid_forget()
self.file_input.grid_forget()
self.select_file.grid_forget()
self.seeds_label.grid_forget()
self.seeds_input.grid_forget()
self.select_seeds.grid_forget()
self.segmentation_run.grid_forget()
self.analysis_run.grid_forget()
def validate_data(self):
"""This function make sure that the data the user selected is valid"""
valid = True
if not exists(self.output_path.get()):
valid = False
self.output_input.config(background="tomato")
file_path = self.file_path.get()
seeds_path = self.seeds_path.get()
if not (file_path.endswith(".nii.gz") and exists(file_path)):
valid = False
self.file_input.config(background="tomato")
if not (seeds_path.endswith(".nii.gz") and exists(seeds_path)):
valid = False
self.seeds_input.config(background="tomato")
return valid
def run_segmentation(self):
"""Run the segmentation algorithm while updating the progressbar"""
def threaded_prog():
self.progress_label.grid(row=5, column=0)
self.progress.grid(row=5, column=1, columnspan=2)
self.progress.start()
self.progress_label.config(text="Running Segmentation")
self.segmentation_process()
self.progress.stop()
self.progress_label.grid_forget()
self.progress.grid_forget()
self.back_to_home_gui()
if self.validate_data():
Thread(target=threaded_prog).start()
else:
messagebox.showinfo("Error with the input", "Error with the input")
def segmentation_process(self):
"""Creates the segmentation of the scaphoid and the fracture"""
self.progress_label.config(text="Getting seeds")
scaphoid_seeds, fracture_seeds = generate_scaphoid_seeds(
self.seeds_path.get())
self.progress_label.config(text="Isolating The Scaphoid")
self.scaphoid = Scaphoid(self.file_path.get(), scaphoid_seeds,
fracture_seeds, 6)
self.scaphoid.region_growing_from_input(SCAPHOID_COLOR)
self.progress_label.config(text="Isolating The Fracture")
self.scaphoid.segment_fracture_region_growing_mean(
FRACTURE_COLOR, SCAPHOID_COLOR)
self.progress_label.config(text="Saving Files")
save_scaphoid_segmentations(self.scaphoid, self.output_path.get())
self.progress_label.config(text="Finishing")
self.scaphoid = None
del scaphoid_seeds, fracture_seeds
messagebox.showinfo("Process Finished Successfully",
"Process Finished Successfully")
def run_analysis(self):
"""runs the analysis algorithm while updating the progress bar"""
def threaded_prog():
self.progress_label.grid(row=5, column=0)
self.progress.grid(row=5, column=1, columnspan=2)
self.progress.start()
self.progress_label.config(text="Running Analysis")
self.analysis_process()
self.progress.stop()
self.progress_label.grid_forget()
self.progress.grid_forget()
self.back_to_home_gui()
if self.validate_data():
Thread(target=threaded_prog).start()
else:
messagebox.showinfo("Error with the input", "Error with the input")
def analysis_process(self):
"""The main analysis process"""
self.progress_label.config(text="Getting the fracture")
self.scaphoid = Scaphoid(self.file_path.get(), [], [], 1)
self.scaphoid.load_bone_fracture(self.seeds_path.get())
self.scaphoid.load_fracture_from_bone_fracture()
self.progress_label.config(text="Getting seeds")
radius_seeds, capitate_seg = generate_analysis_seeds(
self.seeds_path.get())
self.progress_label.config(text="Isolating The Radius")
self.radius = Radius(self.file_path.get(), radius_seeds, 6)
self.radius.region_growing_from_input(RADIUS_COLOR)
self.progress_label.config(text="Getting PCA from radius")
pca = self.radius.extract_PCA_components()
self.progress_label.config(text="Dividing the bone")
self.scaphoid.divide_bone_into_quarters(pca)
self.progress_label.config(text="Dividing the fracture")
self.scaphoid.divide_fracture_into_quarters(pca)
self.progress_label.config(text="Getting geometric information")
geo_features = self.scaphoid.get_geometric_features()
geo_features["Angle between Radius and Capitate"] = \
str(create_direction_vector_for_2_points_cloud(
capitate_seg, pca[0]))
self.progress_label.config(text="Saving Files")
save_analysis_segmentation(self.scaphoid, self.output_path.get())
file_name = str(
abspath(self.scaphoid.get_original_path()).split("\\")[-1].split(
".")[0])
save_geometric_features(geo_features, self.output_path.get(),
file_name)
self.progress_label.config(text="Finishing")
self.scaphoid = None
self.radius = None
del pca, geo_features
messagebox.showinfo("Process Finished Successfully",
"Process Finished Successfully")
