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launcher.py
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launcher.py
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import shutil
import tkinter as tk
from tkinter import MULTIPLE, NE, NW, SINGLE, W, filedialog, messagebox
import ttkbootstrap as ttk
from ttkbootstrap.constants import *
import ttkbootstrap.themes.standard
import time
import os, re
import os.path
from functools import partial
import subprocess
import platform
from progress_bar import ProgressBar
from dicom_converter import Bruker2DicomConverter
from glob import glob
from tabulate import tabulate
import datetime
from datetime import date
import threading
from dotenv import load_dotenv
from xnat_uploader import Dicom2XnatUploader, FileUploader
from accessory_functions import *
from idlelib.tooltip import Hovertip
from multiprocessing import Pool, cpu_count
from credential_manager import CredentialManager
import pandas
from layout_style import MyStyle
from multiprocessing import freeze_support
from ScrollableNotebook import *
from create_objects import ProjectManager, SubjectManager, ExperimentManager
from content_reader import *
from access_manager import AccessManager
from new_project_manager import NewProjectManager, NewSubjectManager, NewExperimentManager
import itertools
from Treeview import Treeview
PATH_IMAGE = "images\\"
# PATH_IMAGE = "lib\\images\\"
PERCENTAGE_SCREEN = 1 # Defines the size of the canvas. If equal to 1 (100%) ,it takes the whole screen
WHITE = "#ffffff"
LIGHT_GREY = "#F1FFFE"
LIGHT_GREY_DISABLED = "#91A3B1"
AZURE = "#008ad7"
AZURE_DISABLED = "#99D0EF"
DARKER_AZURE = "#006EAC"
TEXT_BTN_COLOR = "black"
TEXT_BTN_COLOR_2 = "white"
TEXT_LBL_COLOR = "black"
BG_BTN_COLOR = "#E5EAF0"
BG_LBL_COLOR = "black"
DISABLE_LBL_COLOR = '#D3D3D3'
TITLE_FONT = ("Inkfree", 36, "italic")
LARGE_FONT = ("Calibri", 22, "bold")
SMALL_FONT = ("Calibri", 16, "bold")
SMALL_FONT_2 = ("Calibri", 10)
SMALL_FONT_3 = ("Calibri", 12)
SMALL_FONT_4 = ("Calibri", 16)
CURSOR_HAND = "hand2"
QUESTION_HAND = "question_arrow"
BORDERWIDTH = 3
def check_credentials(root):
dir = os.getcwd().replace('\\', '/')
head, tail = os.path.split(dir)
load_dotenv()
if os.path.isfile(head + '/.env') == False or os.environ.get('secretKey') == '':
credential_manager = CredentialManager(root)
root.wait_window(credential_manager.popup)
class xnat_pic_gui():
def __init__(self, root):
self.root = root
self.root.state('zoomed') # The root widget is adapted to the screen size
# Define the style of the root widget
self.style_label = tk.StringVar()
self.style_label.set('cerculean')
style = MyStyle(self.style_label.get())
style.configure()
self.style = style.get_style()
# Get the screen resolution
if (platform.system()=='Linux'):
cmd_show_screen_resolution = subprocess.Popen("xrandr --query | grep -oG 'primary [0-9]*x[0-9]*'",\
stdout=subprocess.PIPE, shell=True)
screen_output =str(cmd_show_screen_resolution.communicate()).split()[1]
self.root.screenwidth, self.root.screenheight = re.findall("[0-9]+",screen_output)
else :
self.root.screenwidth=self.root.winfo_screenwidth()
self.root.screenheight=self.root.winfo_screenheight()
# Adjust size based on screen resolution
self.width = self.root.screenwidth
self.height = self.root.screenheight
self.my_width = self.width
self.my_height = self.height
self.root.geometry("%dx%d+0+0" % (self.width, self.height))
self.root.title(" XNAT-PIC ~ Molecular Imaging Center ~ University of Torino ")
self.root.minsize(width=int(self.width/2), height=int(self.height/2)) # Set the minimum size of the working window
# Load the images
# Load Accept icon
self.logo_accept = open_image(PATH_IMAGE + "Done.png", 15, 15)
# Load Delete icon
self.logo_delete = open_image(PATH_IMAGE + "Reject.png", 15, 15)
# Load Edit icon
self.logo_edit = open_image(PATH_IMAGE + "Edit.png", 15, 15)
# Load Clear icon
self.logo_clear = open_image(PATH_IMAGE + "delete.png", 15, 15)
# Load Search icon
self.logo_search = open_image(PATH_IMAGE + "search_icon.png", 15, 15)
# Load open eye
self.open_eye = open_image(PATH_IMAGE + "open_eye.png", 15, 15)
# Load closed eye
self.closed_eye = open_image(PATH_IMAGE + "closed_eye.png", 15, 15)
# Load sun icon DARK
self.sun_icon_dark = open_image(PATH_IMAGE + "sun_icon_dark.png", 20, 20)
# Load sun icon LIGHT
self.sun_icon_light = open_image(PATH_IMAGE + "sun_icon_light.png", 20, 20)
# Load home icon
self.logo_home = open_image(PATH_IMAGE + "home.png", 15, 15)
# Load add icon
self.logo_add = open_image(PATH_IMAGE + "add_icon.png", 15, 15)
# Load folder icon
self.logo_folder = open_image(PATH_IMAGE + "folder.png", 15, 15)
# Load save icon
self.logo_save = open_image(PATH_IMAGE + "save.png", 15, 15)
# Load exit icon
self.logo_exit = open_image(PATH_IMAGE + "exit.png", 15, 15)
# Load help icon
self.logo_help = open_image(PATH_IMAGE + "help.png", 15, 15)
# Load login icon
self.logo_login = open_image(PATH_IMAGE + "login.png", 15, 15)
# Load subdirectory icon
self.logo_subdirectory = open_image(PATH_IMAGE + "subdirectory.png", 15, 15)
# Load user icon
self.user_icon = open_image(PATH_IMAGE + "user.png", 20, 20)
# Load user icon
self.details_icon = open_image(PATH_IMAGE + "details_icon.png", 15, 15)
# Toolbar Menu
def new_prj():
project_manager = NewProjectManager(self.root)
self.root.wait_window(project_manager.popup_prj)
def new_sub():
subject_manager = NewSubjectManager(self.root)
self.root.wait_window(subject_manager.popup_sub)
def new_exp():
experiment_manager = NewExperimentManager(self.root)
self.root.wait_window(experiment_manager.popup_exp)
self.toolbar_menu = ttk.Menu(self.root)
fileMenu = ttk.Menu(self.toolbar_menu, tearoff=0)
new_menu = ttk.Menu(fileMenu, tearoff=0)
new_menu.add_command(label="Project", image = self.logo_folder, compound = 'left', command=new_prj)
new_menu.add_command(label="Subject", image = self.logo_folder, compound = 'left',command=new_sub)
new_menu.add_command(label="Experiment", image = self.logo_folder, compound = 'left',command=new_exp)
fileMenu.add_cascade(label="New...", image = self.logo_subdirectory, compound = 'left', menu=new_menu)
fileMenu.add_command(label="Login", image = self.logo_login, compound = 'left')
fileMenu.add_separator()
fileMenu.add_command(label="Exit", image = self.logo_exit, compound = 'left', command=lambda: self.root.destroy())
self.toolbar_menu.add_cascade(label="File", menu=fileMenu)
self.toolbar_menu.add_cascade(label="Edit")
self.toolbar_menu.add_cascade(label="Options")
self.root.config(menu=self.toolbar_menu)
# Logo on the top
self.root.iconbitmap(PATH_IMAGE + "logo3.ico")
# Initialize the Frame widget which parent is the root widgeth
self.frame = ttk.Frame(self.root)
self.frame.pack(fill='both', expand=1)
self.frame_label = tk.StringVar()
self.frame_label.set('Enter')
def resize_window(*args):
# Get the current window size
self.width = self.root.winfo_width()
self.height = self.root.winfo_height()
# Load Side Logo Panel
self.panel_img = open_image(PATH_IMAGE + "logo-panel.png", self.width/5, self.height)
self.panel_img.label = ttk.Label(self.frame, image=self.panel_img)
self.panel_img.label.place(x=0, y=0, anchor=tk.NW, relheight=1, relwidth=0.2)
# Load XNAT-PIC Logo
self.xnat_pic_logo_dark = open_image(PATH_IMAGE + "XNAT-PIC_logo.png", 2*self.width/5, self.height/3)
self.xnat_pic_logo_light = open_image(PATH_IMAGE + "XNAT-PIC-logo-light.png", 2*self.width/5, self.height/3)
if self.frame_label.get() in ["Enter", "Main"]:
if self.style_label.get() == 'cerculean':
self.xnat_pic_logo_label = ttk.Label(self.frame, image=self.xnat_pic_logo_dark)
else:
self.xnat_pic_logo_label = ttk.Label(self.frame, image=self.xnat_pic_logo_light)
self.xnat_pic_logo_label.place(relx=0.6, rely=0.3, anchor=tk.CENTER)
# Load Sun icon to swith to dark/light mode
def switch_mode(*args):
if self.style_label.get() == 'cerculean':
self.style_label.set('cyborg')
style = MyStyle('cyborg')
style.configure()
self.style = style.get_style()
self.dark_mode_btn.config(image=self.sun_icon_light)
if self.xnat_pic_logo_label.winfo_exists():
self.xnat_pic_logo_label.config(image=self.xnat_pic_logo_light)
elif self.xnat_pic_logo_label.winfo_exists() and self.frame_label.get() in ["Enter", "Main"]:
self.xnat_pic_logo_label = ttk.Label(self.frame, image=self.xnat_pic_logo_light)
self.xnat_pic_logo_label.place(relx=0.3, rely=0.1, anchor=tk.NW, relheight=0.3, relwidth=0.7)
else:
pass
self.frame.update()
else:
self.style_label.set('cerculean')
style = MyStyle('cerculean')
style.configure()
self.style = style.get_style()
self.dark_mode_btn.config(image=self.sun_icon_dark)
if self.xnat_pic_logo_label.winfo_exists():
self.xnat_pic_logo_label.config(image=self.xnat_pic_logo_dark)
elif self.xnat_pic_logo_label.winfo_exists() and self.frame_label.get() in ["Enter", "Main"]:
self.xnat_pic_logo_label = ttk.Label(self.frame, image=self.xnat_pic_logo_dark)
self.xnat_pic_logo_label.place(relx=0.3, rely=0.1, anchor=tk.NW, relheight=0.3, relwidth=0.7)
else:
pass
self.frame.update()
# Change font according to window size
if self.width > int(2/3*self.my_width):
self.style.configure('TButton', font = LARGE_FONT)
self.style.configure('Title.TLabel', font = ("Inkfree", 36, "italic"))
elif self.width > int(self.my_width/3) and self.width < int(2/3*self.my_width):
self.style.configure('TButton', font = SMALL_FONT)
self.style.configure('Title.TLabel', font = ("Inkfree", 30, "italic"))
elif self.width < int(self.my_width/3):
self.style.configure('TButton', font = SMALL_FONT_2)
self.style.configure('Title.TLabel', font = ("Inkfree", 24, "italic"))
# Update the frame widget
self.frame.update()
# Enter button handler method
def enter_handler(*args):
self.enter_btn.destroy() # Destroy the enter button and keep the Frame alive
xnat_pic_gui.choose_your_action(self)
# Enter button widget
self.enter_btn = ttk.Button(self.frame, text="ENTER",
command=enter_handler,
cursor=CURSOR_HAND, bootstyle="primary")
self.enter_btn.place(relx=0.6, rely=0.6, anchor=tk.CENTER, relwidth=0.2)
# Call the resize_window method if the window size is changed by the user
self.frame.bind("<Configure>", resize_window)
def closed_window():
self.root.destroy()
self.root.quit()
self.root.protocol("WM_DELETE_WINDOW", closed_window)
# Choose to upload files, fill in the info, convert files, process images
def choose_your_action(self):
if self.toolbar_menu.winfo_exists() == 0:
# Toolbar Menu
def new_prj():
project_manager = NewProjectManager(self.root)
self.root.wait_window(project_manager.popup_prj)
def new_sub():
subject_manager = NewSubjectManager(self.root)
self.root.wait_window(subject_manager.popup_sub)
def new_exp():
experiment_manager = NewExperimentManager(self.root)
self.root.wait_window(experiment_manager.popup_exp)
self.toolbar_menu = ttk.Menu(self.root)
fileMenu = ttk.Menu(self.toolbar_menu, tearoff=0)
new_menu = ttk.Menu(fileMenu, tearoff=0)
new_menu.add_command(label="Project", image = self.logo_folder, compound = 'left', command=new_prj)
new_menu.add_command(label="Subject", image = self.logo_folder, compound = 'left',command=new_sub)
new_menu.add_command(label="Experiment", image = self.logo_folder, compound = 'left',command=new_exp)
fileMenu.add_cascade(label="New...", image = self.logo_subdirectory, compound = 'left', menu=new_menu)
fileMenu.add_command(label="Login", image = self.logo_login, compound = 'left')
fileMenu.add_separator()
fileMenu.add_command(label="Exit", image = self.logo_exit, compound = 'left', command=lambda: self.root.destroy())
self.toolbar_menu.add_cascade(label="File", menu=fileMenu)
self.toolbar_menu.add_cascade(label="Edit")
self.toolbar_menu.add_cascade(label="Options")
self.root.config(menu=self.toolbar_menu)
if self.xnat_pic_logo_label.winfo_exists() == 0:
if self.style_label.get() == 'cerculean':
self.xnat_pic_logo_label = ttk.Label(self.frame, image=self.xnat_pic_logo_dark)
else:
self.xnat_pic_logo_label = ttk.Label(self.frame, image=self.xnat_pic_logo_light)
self.xnat_pic_logo_label.place(relx=0.6, rely=0.3, anchor=tk.CENTER)
self.frame_label.set("Main")
# Action buttons
# Convert files Bruker2DICOM
self.convert_btn = ttk.Button(self.frame, text="DICOM Converter",
command=partial(self.bruker2dicom_conversion, self), cursor=CURSOR_HAND)
self.convert_btn.place(relx=0.6, rely=0.5, anchor=tk.CENTER, relwidth=0.2)
Hovertip(self.convert_btn,'Convert images from Bruker ParaVision format to DICOM standard')
# Fill in the info
self.info_btn = ttk.Button(self.frame, text="Project Data",
command=partial(self.metadata, self), cursor=CURSOR_HAND)
self.info_btn.place(relx=0.6, rely=0.6, anchor=tk.CENTER, relwidth=0.2)
Hovertip(self.info_btn,'Fill in the information about the acquisition')
# Upload files
def upload_callback(*args):
self.XNATUploader(self)
self.upload_btn = ttk.Button(self.frame, text="Uploader",
command=upload_callback, cursor=CURSOR_HAND)
self.upload_btn.place(relx=0.6, rely=0.7, anchor=tk.CENTER, relwidth=0.2)
Hovertip(self.upload_btn,'Upload DICOM images to XNAT')
# Close button
def close_window(*args):
result = messagebox.askyesno("XNAT-PIC", "XNAT-PIC will be closed. Are you sure?")
if result:
self.root.destroy()
self.close_btn = ttk.Button(self.frame, text="Quit", command=close_window,
cursor=CURSOR_HAND)
self.close_btn.place(relx=0.95, rely=0.9, anchor=tk.NE, relwidth=0.1)
class bruker2dicom_conversion():
def __init__(self, master):
self.params = {}
try:
destroy_widgets([master.toolbar_menu, master.convert_btn, master.info_btn, master.upload_btn, master.close_btn, master.xnat_pic_logo_label])
except:
pass
self.overall_converter(master)
def overall_converter(self, master):
# Create new frame
master.frame_label.set("Converter")
# Menu bar
self.menu = ttk.Menu(master.root)
file_menu = ttk.Menu(self.menu, tearoff=0)
home_menu = ttk.Menu(self.menu, tearoff=0)
#exit_menu = ttk.Menu(self.menu, tearoff=0)
help_menu = ttk.Menu(self.menu, tearoff=0)
home_menu.add_command(label="Home", image = master.logo_home, compound='left', command = lambda: exit_converter())
file_menu.add_command(label="Clear Tree", image = master.logo_clear, compound='left', command = lambda: clear_tree())
#exit_menu.add_command(label="Exit", image = master.logo_exit, compound='left', command = lambda: self.exit_metadata(master))
help_menu.add_command(label="Help", image = master.logo_help, compound='left', command = lambda: messagebox.showinfo("XNAT-PIC","Help"))
self.menu.add_cascade(label='Home', menu=home_menu)
self.menu.add_cascade(label="File", menu=file_menu)
self.menu.add_cascade(label="About", menu=help_menu)
#self.menu.add_cascade(label="Exit", menu=exit_menu)
master.root.config(menu=self.menu)
# Label Frame Main (for Title only)
self.frame_converter = ttk.Frame(master.frame, style="Hidden.TLabelframe")
self.frame_converter.place(relx = 0.2, rely= 0, relheight=1, relwidth=0.8, anchor=tk.NW)
# Frame Title
self.frame_title = ttk.Label(self.frame_converter, text="XNAT-PIC Converter", style="Title.TLabel", anchor=tk.CENTER)
self.frame_title.place(relx = 0.5, rely = 0.05, anchor = CENTER)
# Initialize variables
self.conv_flag = tk.IntVar()
self.folder_to_convert = tk.StringVar()
self.converted_folder = tk.StringVar()
self.convertion_state = tk.IntVar()
# Convert Project
def prj_conv_handler(*args):
self.conv_flag.set(0)
self.check_buttons(master, press_btn=0)
self.prj_conv_btn = ttk.Button(self.frame_converter, text="Convert Project",
command=prj_conv_handler, cursor=CURSOR_HAND)
self.prj_conv_btn.place(relx = 0.05, rely = 0.16, relwidth=0.22, anchor = NW)
Hovertip(self.prj_conv_btn, "Convert a project from Bruker format to DICOM standard")
# Convert Subject
def sbj_conv_handler(*args):
self.conv_flag.set(1)
self.check_buttons(master, press_btn=1)
self.sbj_conv_btn = ttk.Button(self.frame_converter, text="Convert Subject",
command=sbj_conv_handler, cursor=CURSOR_HAND)
self.sbj_conv_btn.place(relx = 0.5, rely = 0.16, relwidth=0.22, anchor = N)
Hovertip(self.sbj_conv_btn, "Convert a subject from Bruker format to DICOM standard")
# Convert Experiment
def exp_conv_handler(*args):
self.conv_flag.set(2)
self.check_buttons(master, press_btn=2)
self.exp_conv_btn = ttk.Button(self.frame_converter, text="Convert Experiment",
command=exp_conv_handler, cursor=CURSOR_HAND)
self.exp_conv_btn.place(relx = 0.95, rely = 0.16, relwidth=0.22, anchor = NE)
Hovertip(self.exp_conv_btn, "Convert an experiment from Bruker format to DICOM standard")
# Overwrite button
self.overwrite_flag = tk.IntVar()
self.btn_overwrite = ttk.Checkbutton(self.frame_converter, text="Overwrite existing folders",
onvalue=1, offvalue=0, variable=self.overwrite_flag, bootstyle="round-toggle")
self.btn_overwrite.place(relx = 0.05, rely = 0.25, anchor = NW)
Hovertip(self.btn_overwrite, "Overwrite already existent folders if they occur")
# Results button
def add_results_handler(*args):
self.params['results_flag'] = self.results_flag.get()
self.results_flag = tk.IntVar()
self.btn_results = ttk.Checkbutton(self.frame_converter, text='Copy additional files', variable=self.results_flag,
onvalue=1, offvalue=0, command=add_results_handler, bootstyle="round-toggle")
self.btn_results.place(relx = 0.05, rely = 0.30, anchor = NW)
Hovertip(self.btn_results, "Copy additional files (results, parametric maps, graphs, ...)\ninto converted folders")
self.separator = ttk.Separator(self.frame_converter, bootstyle="primary")
self.separator.place(relx = 0.05, rely = 0.35, relwidth = 0.9, anchor = NW)
# Treeview
def select_folder(*args):
# Disable the buttons
disable_buttons([self.prj_conv_btn, self.sbj_conv_btn, self.exp_conv_btn])
# Define the initial directory
init_dir = os.path.expanduser("~").replace('\\', '/') + '/Desktop/Dataset'
# Ask for project directory
self.folder_to_convert.set(filedialog.askdirectory(parent=master.root, initialdir=init_dir,
title="XNAT-PIC: Select directory in Bruker ParaVision format"))
# Check if folder has not been selected (Cancel button)
if self.folder_to_convert.get() == '':
messagebox.showerror("XNAT-PIC Converter", "Please select a folder.")
#enable_buttons([self.prj_conv_btn, self.sbj_conv_btn, self.exp_conv_btn])
return
# Check if the selected folder is related to the right convertion flag
if self.conv_flag.get() == 0:
if glob(self.folder_to_convert.get() + '/**/**/**/**/**/2dseq', recursive=False) == []:
messagebox.showerror("XNAT-PIC Converter", "The selected folder is not project related.\nPlease select an other directory.")
return
elif self.conv_flag.get() == 1:
if glob(self.folder_to_convert.get() + '/**/**/**/**/2dseq', recursive=False) == []:
messagebox.showerror("XNAT-PIC Converter", "The selected folder is not subject related.\nPlease select an other directory.")
return
elif self.conv_flag.get() == 2:
if glob(self.folder_to_convert.get() + '/**/**/**/2dseq', recursive=False) == []:
messagebox.showerror("XNAT-PIC Converter", "The selected folder is not experiment related.\nPlease select an other directory.")
return
# Reset convertion_state parameter
self.convertion_state.set(0)
def display_folder_tree(*args):
if self.folder_to_convert.get() != '' and self.convertion_state.get() == 0:
dict_items = {}
if self.tree_to_convert.tree.exists(0):
self.tree_to_convert.tree.delete(*self.tree_to_convert.tree.get_children())
j = 0
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = ""
dict_items[str(j)]['text'] = self.folder_to_convert.get().split('/')[-1]
subdir = os.listdir(self.folder_to_convert.get())
subdirectories = [x for x in subdir if x.endswith('.ini') == False]
total_weight = 0
last_edit_time = ''
j = 1
for sub in subdirectories:
if os.path.isfile(os.path.join(self.folder_to_convert.get(), sub)):
# Check for last edit time
edit_time = str(time.strftime("%d/%m/%Y,%H:%M:%S", time.localtime(os.path.getmtime(os.path.join(self.folder_to_convert.get(), sub)))))
if last_edit_time == '' or edit_time > last_edit_time:
# Update the last edit time
last_edit_time = edit_time
# Check for file dimension
file_weight = round(os.path.getsize(os.path.join(self.folder_to_convert.get(), sub))/1024, 2)
total_weight += round(file_weight/1024, 2)
# Add the item like a file
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = '0'
dict_items[str(j)]['text'] = sub
dict_items[str(j)]['values'] = (edit_time, str(file_weight) + "KB", "File")
# Update the j counter
j += 1
elif os.path.isdir(os.path.join(self.folder_to_convert.get(), sub)):
current_weight = 0
last_edit_time_lev2 = ''
branch_idx = j
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = '0'
dict_items[str(j)]['text'] = sub
j += 1
# Scan directories to get subfolders
sub_level2 = os.listdir(os.path.join(self.folder_to_convert.get(), sub))
subdirectories2 = [x for x in sub_level2 if x.endswith('.ini') == False]
for sub2 in subdirectories2:
if os.path.isfile(os.path.join(self.folder_to_convert.get(), sub, sub2)):
# Check for last edit time
edit_time = str(time.strftime("%d/%m/%Y,%H:%M:%S", time.localtime(os.path.getmtime(os.path.join(self.folder_to_convert.get(), sub, sub2)))))
if last_edit_time_lev2 == '' or edit_time > last_edit_time_lev2:
# Update the last edit time
last_edit_time_lev2 = edit_time
if last_edit_time_lev2 > last_edit_time:
last_edit_time = last_edit_time_lev2
# Check for file dimension
file_weight = round(os.path.getsize(os.path.join(self.folder_to_convert.get(), sub, sub2))/1024, 2)
current_weight += round(file_weight/1024, 2)
# Add the item like a file
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = '1'
dict_items[str(j)]['text'] = sub2
dict_items[str(j)]['values'] = (edit_time, str(file_weight) + "KB", "File")
# Update the j counter
j += 1
elif os.path.isdir(os.path.join(self.folder_to_convert.get(), sub, sub2)):
# Check for last edit time
edit_time = str(time.strftime("%d/%m/%Y,%H:%M:%S", time.localtime(os.path.getmtime(os.path.join(self.folder_to_convert.get(), sub, sub2)))))
if last_edit_time_lev2 == '' or edit_time > last_edit_time_lev2:
# Update the last edit time
last_edit_time_lev2 = edit_time
if last_edit_time_lev2 > last_edit_time:
last_edit_time = last_edit_time_lev2
folder_size = round(get_dir_size(os.path.join(self.folder_to_convert.get(), sub, sub2))/1024/1024, 2)
current_weight += folder_size
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = '1'
dict_items[str(j)]['text'] = sub2
dict_items[str(j)]['values'] = (edit_time, str(folder_size) + 'MB', "Folder")
j += 1
total_weight += current_weight
dict_items[str(branch_idx)]['values'] = (last_edit_time_lev2, str(round(current_weight, 2)) + "MB", "Folder")
# Update the fields of the parent object
dict_items['0']['values'] = (last_edit_time, str(round(total_weight/1024, 2)) + "GB", "Folder")
self.tree_to_convert.set(dict_items)
# Initialize the folder_to_upload path
self.select_folder_button = ttk.Button(self.frame_converter, text="Select folder", style="Secondary1.TButton",
state='disabled', cursor=CURSOR_HAND, command=select_folder)
self.select_folder_button.place(relx = 0.05, rely = 0.4, anchor = NW)
# Clear Tree buttons
def clear_tree(*args):
if self.tree_to_convert.tree.exists(0):
self.tree_to_convert.tree.delete(*self.tree_to_convert.tree.get_children())
if self.tree_converted.tree.exists(0):
self.tree_converted.tree.delete(*self.tree_converted.tree.get_children())
self.clear_tree_btn = ttk.Button(self.frame_converter, image=master.logo_clear,
cursor=CURSOR_HAND, state='disabled', command=clear_tree, style="WithoutBack.TButton")
self.clear_tree_btn.place(relx = 0.37, rely = 0.72, anchor = NE)
Hovertip(self.clear_tree_btn, "Delete tree")
# Search entry to find objects
def scankey(*args):
if self.search_var.get() != '':
self.tree_to_convert.find_items(self.search_var.get())
else:
self.tree_to_convert.remove_selection()
self.search_var = tk.StringVar()
self.search_entry = ttk.Entry(self.frame_converter, cursor=CURSOR_HAND, state='disabled', textvariable=self.search_var)
self.search_entry.place(relx = 0.07, rely = 0.72, anchor = NW)
self.search_pre_btn = ttk.Button(self.frame_converter, image=master.logo_search, state='disabled',
cursor=CURSOR_HAND, command = lambda: self.search_entry.focus_set(), style="WithoutBack.TButton")
self.search_pre_btn.place(relx = 0.05, rely = 0.72, anchor = NW)
self.search_var.trace('w', scankey)
# Details Button
def show_folder_details_pre(*args):
folder_reader = FolderDetails(self.object_folder.get())
if glob(os.path.join(self.object_folder.get()).replace("\\", "/") + '/**/**/**/2dseq', recursive=False):
folder_reader.read_folder_details_raw_images()
folder_reader.save_folder_details()
folder_reader.show_folder_details(master.root)
master.root.wait_window(folder_reader.popup)
def selected_object_handler(*args):
curItem = self.tree_to_convert.tree.focus()
parentItem = self.tree_to_convert.tree.parent(curItem)
self.object_folder.set(os.path.join(self.folder_to_convert.get(), self.tree_to_convert.tree.item(parentItem)['text'],
self.tree_to_convert.tree.item(curItem)['text']).replace("\\", "/"))
if glob(self.object_folder.get() + '/**/**/**/2dseq', recursive=False) != []:
self.details_btn.config(state='normal')
else:
self.details_btn.config(state='disabled')
self.object_folder = tk.StringVar()
self.details_btn = ttk.Button(self.frame_converter, cursor=CURSOR_HAND, image=master.details_icon, command=show_folder_details_pre,
style="WithoutBack.TButton", state='disabled')
self.details_btn.place(relx = 0.4, rely = 0.72, anchor = NE)
Hovertip(self.details_btn, "Show details")
# Treeview widget pre_convertion
columns = [("#0", "Selected folder"), ("#1", "Last Update"), ("#2", "Size"), ("#3", "Type")]
self.tree_to_convert = Treeview(self.frame_converter, columns, width=100)
self.tree_to_convert.tree.place(relx = 0.05, rely = 0.48, relheight=0.2, relwidth=0.35, anchor = NW)
self.tree_to_convert.scrollbar.place(relx = 0.42, rely = 0.48, relheight=0.2, anchor = NW)
def tree_thread(*args):
progressbar_tree = ProgressBar(master.root, "XNAT-PIC Converter")
progressbar_tree.start_indeterminate_bar()
if self.convertion_state.get() == 0:
t = threading.Thread(target=display_folder_tree, args=())
elif self.convertion_state.get() == 1:
t = threading.Thread(target=display_converted_folder_tree, args=())
t.start()
while t.is_alive():
progressbar_tree.update_bar()
progressbar_tree.stop_progress_bar()
def display_converted_folder_tree(*args):
if self.converted_folder.get() != '' and self.convertion_state.get() == 1:
dict_items = {}
progressbar_tree = ProgressBar(master.root, "XNAT-PIC Converter")
progressbar_tree.start_indeterminate_bar()
if self.tree_converted.tree.exists(0):
self.tree_converted.tree.delete(*self.tree_converted.tree.get_children())
head, tail = os.path.split(self.converted_folder.get())
j = 0
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = ""
dict_items[str(j)]['text'] = self.converted_folder.get().split('/')[-1]
subdir = os.listdir(self.converted_folder.get())
subdirectories = [x for x in subdir if x.endswith('.ini') == False]
total_weight = 0
last_edit_time = ''
j = 1
for sub in subdirectories:
if os.path.isfile(os.path.join(self.converted_folder.get(), sub)):
# Check for last edit time
edit_time = str(time.strftime("%d/%m/%Y,%H:%M:%S", time.localtime(os.path.getmtime(os.path.join(self.converted_folder.get(), sub)))))
if last_edit_time == '' or edit_time > last_edit_time:
# Update the last edit time
last_edit_time = edit_time
# Check for file dimension
file_weight = round(os.path.getsize(os.path.join(self.converted_folder.get(), sub))/1024, 2)
total_weight += round(file_weight/1024, 2)
# Add the item like a file
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = '0'
dict_items[str(j)]['text'] = sub
dict_items[str(j)]['values'] = (edit_time, str(file_weight) + "KB", "File")
# Update the j counter
j += 1
elif os.path.isdir(os.path.join(self.converted_folder.get(), sub)):
current_weight = 0
last_edit_time_lev2 = ''
branch_idx = j
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = '0'
dict_items[str(j)]['text'] = sub
j += 1
# Scansiona le directory interne per ottenere il tree CHIUSO
sub_level2 = os.listdir(os.path.join(self.converted_folder.get(), sub))
subdirectories2 = [x for x in sub_level2 if x.endswith('.ini') == False]
for sub2 in subdirectories2:
if os.path.isfile(os.path.join(self.converted_folder.get(), sub, sub2)):
# Check for last edit time
edit_time = str(time.strftime("%d/%m/%Y,%H:%M:%S", time.localtime(os.path.getmtime(os.path.join(self.converted_folder.get(), sub, sub2)))))
if last_edit_time_lev2 == '' or edit_time > last_edit_time_lev2:
# Update the last edit time
last_edit_time_lev2 = edit_time
if last_edit_time_lev2 > last_edit_time:
last_edit_time = last_edit_time_lev2
# Check for file dimension
file_weight = round(os.path.getsize(os.path.join(self.converted_folder.get(), sub, sub2))/1024, 2)
current_weight += round(file_weight/1024, 2)
# Add the item like a file
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = '1'
dict_items[str(j)]['text'] = sub2
dict_items[str(j)]['values'] = (edit_time, str(file_weight) + "KB", "File")
# Update the j counter
j += 1
elif os.path.isdir(os.path.join(self.converted_folder.get(), sub, sub2)):
# Check for last edit time
edit_time = str(time.strftime("%d/%m/%Y,%H:%M:%S", time.localtime(os.path.getmtime(os.path.join(self.converted_folder.get(), sub, sub2)))))
if last_edit_time_lev2 == '' or edit_time > last_edit_time_lev2:
# Update the last edit time
last_edit_time_lev2 = edit_time
if last_edit_time_lev2 > last_edit_time:
last_edit_time = last_edit_time_lev2
folder_size = round(get_dir_size(os.path.join(self.converted_folder.get(), sub, sub2))/1024/1024, 2)
current_weight += folder_size
dict_items[str(j)] = {}
dict_items[str(j)]['parent'] = '1'
dict_items[str(j)]['text'] = sub2
dict_items[str(j)]['values'] = (edit_time, str(folder_size) + 'MB', "Folder")
j += 1
total_weight += current_weight
dict_items[str(branch_idx)]['values'] = (last_edit_time_lev2, str(round(current_weight, 2)) + "MB", "Folder")
# Update the fields of the parent object
dict_items['0']['values'] = (last_edit_time, str(round(total_weight/1024, 2)) + "GB", "Folder")
self.tree_converted.set(dict_items)
progressbar_tree.stop_progress_bar()
enable_buttons([self.prj_conv_btn, self.sbj_conv_btn, self.exp_conv_btn])
self.tree_to_convert.tree.bind("<ButtonRelease-1>", selected_object_handler)
# Treeview post_convertion
# Search entry to find objects
def scankey(*args):
if self.search_var.get() != '':
self.tree_converted.find_items(self.search_var.get())
else:
self.tree_converted.remove_selection()
self.search_var = tk.StringVar()
self.search_post_entry = ttk.Entry(self.frame_converter, cursor=CURSOR_HAND, state='disabled', textvariable=self.search_var)
self.search_post_entry.place(relx = 0.62, rely = 0.72, anchor = NW)
self.search_post_btn = ttk.Button(self.frame_converter, image=master.logo_search, state='disabled',
cursor=CURSOR_HAND, command = lambda: self.search_post_entry.focus_set(), style="WithoutBack.TButton")
self.search_post_btn.place(relx = 0.6, rely = 0.72, anchor = NW)
self.search_var.trace('w', scankey)
self.clear_tree_btn_post = ttk.Button(self.frame_converter, image=master.logo_clear,
cursor=CURSOR_HAND, state='normal', command=clear_tree, style="WithoutBack.TButton")
self.clear_tree_btn_post.place(relx = 0.92, rely = 0.72, anchor = NE)
Hovertip(self.clear_tree_btn_post, "Delete Tree")
def show_folder_details_post(*args):
folder_reader = FolderDetails(self.object_folder_post.get())
if glob(os.path.join(self.object_folder_post.get()).replace("\\", "/") + '/**/**/*.dcm', recursive=False):
folder_reader.read_folder_details_dcm_images()
folder_reader.save_folder_details()
folder_reader.show_folder_details(master.root)
master.root.wait_window(folder_reader.popup)
# Show Details Button
self.object_folder_post = tk.StringVar()
self.details_btn_post = ttk.Button(self.frame_converter, cursor=CURSOR_HAND, image=master.details_icon, command=show_folder_details_post,
style="WithoutBack.TButton", state='disabled')
self.details_btn_post.place(relx = 0.95, rely = 0.72, anchor = NE)
Hovertip(self.details_btn, "Show details")
# Treeview widget post_convertion
self.tree_converted = Treeview(self.frame_converter, columns, width=100)
self.tree_converted.tree.place(relx = 0.95, rely = 0.48, relheight=0.2, relwidth=0.35, anchor = NE)
self.tree_converted.scrollbar.place(relx = 0.58, rely = 0.48, relheight=0.2, anchor = NE)
def selected_object_handler_post(*args):
curItem = self.tree_converted.tree.focus()
parentItem = self.tree_converted.tree.parent(curItem)
self.object_folder_post.set(os.path.join(self.converted_folder.get(), self.tree_converted.tree.item(parentItem)['text'],
self.tree_converted.tree.item(curItem)['text']).replace("\\", "/"))
if glob(self.object_folder_post.get().replace("\\", "/") + '/**/**/*.dcm', recursive=False) != []:
self.details_btn_post.config(state='normal')
else:
self.details_btn_post.config(state='disabled')
self.convertion_state.trace('w', tree_thread)
self.tree_converted.tree.bind("<ButtonRelease-1>", selected_object_handler_post)
# EXIT Button
def exit_converter():
result = messagebox.askquestion("XNAT-PIC Converter", "Do you want to exit?", icon='warning')
if result == 'yes':
# Destroy all the existent widgets (Button, Checkbutton, ...)
destroy_widgets([self.frame_converter, self.menu])
# Restore the main frame
xnat_pic_gui.choose_your_action(master)
self.exit_text = tk.StringVar()
self.exit_btn = ttk.Button(self.frame_converter, cursor=CURSOR_HAND,
textvariable=self.exit_text, style="Secondary1.TButton", command=exit_converter)
self.exit_text.set('Exit')
self.exit_btn.place(relx = 0.05, rely = 0.9, relwidth=0.15, anchor = NW)
# NEXT Button
def next_btn_handler(*args):
if self.conv_flag.get() == 0:
self.converted_folder.set(self.folder_to_convert.get() + '_dcm')
disable_buttons([self.exit_btn, self.next_btn])
self.prj_convertion(master)
elif self.conv_flag.get() == 1:
conv_folder = str(os.path.join('/'.join(self.folder_to_convert.get().split('/')[:-1]) + '_dcm',
self.folder_to_convert.get().split('/')[-1]))
self.converted_folder.set(conv_folder.replace("\\",'/'))
disable_buttons([self.exit_btn, self.next_btn])
self.sbj_convertion(master)
elif self.conv_flag.get() == 2:
self.converted_folder.set(os.path.join('/'.join(self.folder_to_convert.get().split('/')[:-2]) + '_dcm',
'/'.join(self.folder_to_convert.get().split('/')[-2:])))
disable_buttons([self.exit_btn, self.next_btn])
self.exp_convertion(master)
else:
self.converted_folder.set('')
self.next_btn = ttk.Button(self.frame_converter, text="Next", cursor=CURSOR_HAND, style="Secondary1.TButton", command=next_btn_handler,
state='disabled')
self.next_btn.place(relx = 0.95, rely = 0.9, relwidth=0.15, anchor = NE)
def check_buttons(self, master, press_btn=0):
def back():
destroy_widgets([self.frame_converter])
self.overall_converter(master)
# Initialize the press button value
self.press_btn = press_btn
# Change the EXIT button into BACK button and modify the command associated with it
self.exit_text.set("Back")
self.exit_btn.configure(command=back)
# if press_btn == 0:
# Disable main buttons
disable_buttons([self.prj_conv_btn, self.sbj_conv_btn, self.exp_conv_btn])
enable_buttons([self.select_folder_button, self.search_entry, self.search_pre_btn, self.clear_tree_btn, self.search_post_entry, self.search_post_btn])
# View what conversion you are doing (Project, Subject, Experiment)
if self.conv_flag.get() == 0:
working_text = 'Convert Project'
elif self.conv_flag.get() == 1:
working_text = 'Convert Subject'
elif self.conv_flag.get() == 2:
working_text = 'Convert Experiment'
self.working_label = ttk.Label(self.frame_converter, text = working_text, font = SMALL_FONT)
self.working_label.place(relx = 0.5, rely = 0.35, anchor = CENTER)
# Enable NEXT button only if all the requested fields are filled
def enable_next(*args):
if self.folder_to_convert.get() != '':
enable_buttons([self.next_btn])
else:
disable_buttons([self.next_btn])
self.folder_to_convert.trace('w', enable_next)
def prj_convertion(self, master):
# Check for the chosen directory
if not self.folder_to_convert.get():
messagebox.showerror("XNAT-PIC Converter", "The selected folder does not exists. Please select an other one.")
return
if glob(self.folder_to_convert.get() + '/**/**/**/**/**/2dseq', recursive=False) == []:
messagebox.showerror("XNAT-PIC Converter", "The selected folder is not project related")
return
master.root.deiconify()
master.root.update()
# Define the project destination folder
# self.prj_dst = self.folder_to_convert.get() + '_dcm'
self.prj_dst = self.converted_folder.get()
# Initialize converter class
self.converter = Bruker2DicomConverter(self.params)
def prj_converter():
# Get the list of the subject into the project
list_sub = os.listdir(self.folder_to_convert.get())
# Clear list_sub from configuration files (e.g. desktop.ini)
list_sub = [sub for sub in list_sub if sub.endswith('.ini')==False]
# Initialize the list of conversion errors
self.conversion_err = []
# Loop over subjects
for j, dir in enumerate(list_sub, 0):
# Show the current step on the progress bar
progressbar.show_step(j + 1, len(list_sub))
# Define the current subject path
current_folder = os.path.join(self.folder_to_convert.get(), dir).replace('\\', '/')
if os.path.isdir(current_folder):
current_dst = os.path.join(self.prj_dst, dir).replace('\\', '/')
# Check if the current subject folder already exists
if os.path.isdir(current_dst):
# Case 1 --> The directory already exists
if self.overwrite_flag.get() == 1:
# Existent folder with overwrite flag set to 1 --> remove folder and generate new one
shutil.rmtree(current_dst)
os.makedirs(current_dst)
else:
# Existent folder without overwriting flag set to 0 --> ignore folder
self.conversion_err.append(current_folder.split('/')[-1])
continue
else:
# Case 2 --> The directory does not exist
if current_dst.split('/')[-1].count('_dcm') >= 1:
# Check to avoid already converted folders
self.conversion_err.append(current_folder.split('/')[-1])
continue
else:
# Create the new destination folder
os.makedirs(current_dst)
# Set progress bar caption to the current scan folder
progressbar.set_caption('Converting ' + str(current_folder.split('/')[-1]) + ' ...')
# Get the list of the experiments into the subject
list_exp = os.listdir(current_folder)
# Clear list_exp from configuration files (e.g. desktop.ini)
list_exp = [exp for exp in list_exp if exp.endswith('.ini')==False]
for k, exp in enumerate(list_exp):
print('Converting ' + str(exp))
exp_folder = os.path.join(current_folder, exp).replace('\\', '/')
exp_dst = os.path.join(current_dst, exp).replace('\\','/')
list_scans = self.converter.get_list_of_folders(exp_folder, exp_dst)
# Start the multiprocessing conversion: one pool per each scan folder
with Pool(processes=int(cpu_count() - 1)) as pool:
pool.map(self.converter.convert, list_scans)
# Update the current step of the progress bar
progressbar.update_progressbar(j + 1, len(list_sub))
# Set progress bar caption 'done' to the current folder
progressbar.set_caption('Converting ' + str(current_folder.split('/')[-1]) + ' ...done!')
start_time = time.time()
# Start the progress bar
progressbar = ProgressBar(master.root, bar_title='XNAT-PIC Project Converter')
progressbar.start_determinate_bar()
# Perform DICOM convertion through separate thread (different from the main thread)
tp = threading.Thread(target=prj_converter, args=())
tp.start()
while tp.is_alive() == True:
progressbar.update_bar(0)
else:
progressbar.stop_progress_bar()
end_time = time.time()
print('Total elapsed time: ' + str(end_time - start_time) + ' s')
messagebox.showinfo("XNAT-PIC Converter","The conversion of the project is done!\n\n\n\n"
"Exceptions:\n\n" +
str([str(x) for x in self.conversion_err])[1:-1])
self.convertion_state.set(1)
enable_buttons([self.exit_btn])
def sbj_convertion(self, master):
# Check for chosen directory
if not self.folder_to_convert.get():
enable_buttons([master.convert_btn, master.info_btn, master.upload_btn])
messagebox.showerror("XNAT-PIC Converter", "You have not chosen a directory")
return
if glob(self.folder_to_convert.get() + '/**/**/**/**/2dseq', recursive=False) == []:
enable_buttons([master.convert_btn, master.info_btn, master.upload_btn])
messagebox.showerror("XNAT-PIC Converter", "The selected folder is not subject related")
return
master.root.deiconify()
master.root.update()
# head, tail = os.path.split(self.folder_to_convert.get())
# head = head + '_dcm'
# project_foldername = tail.split('.',1)[0]
# self.sub_dst = os.path.join(head, project_foldername).replace('\\', '/')
self.sub_dst = self.converted_folder.get()
# Start converter
self.converter = Bruker2DicomConverter(self.params)
# If the destination folder already exists throw exception, otherwise create the new folder
if os.path.isdir(self.sub_dst):