def begin_session(self):
set_state(self.root, 'disabled')
set_state(self.switch_button, 'enabled')
self.real_root.withdraw()
# Try to find SUMA. If we can't, look for a config
# file telling us where it is. If there is none,
# ask the user where it is and create a config file.
try:
self.suma_file = subprocess.check_output(
["which", "suma"]).strip()
except subprocess.CalledProcessError:
config_name = os.path.join(
os.path.dirname(inspect.stack()[-1][1]),
'suma.config')
try:
config_fi = open(config_name, 'r')
config = config_fi.read()
config_fi.close()
self.suma_file = json.loads(config)["suma"]
if not self.suma_file:
raise IOError()
except (IOError, KeyError):
try:
self.configure()
except ValueError:
# We can't continue without a path to SUMA.
sys.exit(1)
# If we're not connected, we need to choose a local dataset or server
init = None
if self.net_thread and self.net_thread.authenticated:
mode = 'server'
else:
init_dialog = tk.Toplevel()
init_dialog.title("COVI: Choose data source")
if self.net_thread:
self.net_thread.job_q.put(["die"])
# self.net_thread = NetworkThread()
init = InitWindow(init_dialog, NetworkThread())
center_window(init_dialog)
root.wait_window(init_dialog)
mode = init.mode
if mode == 'server':
if init:
self.net_thread = init.net_thread
dset_dialog = ServerDsetWindow(self.real_root,
net_thread=self.net_thread,
title="COVI: %s: Datasets"%init.user_var.get())
else:
dset_dialog = ServerDsetWindow(self.real_root,
net_thread=self.net_thread,
title="COVI: Server Datasets")
if hasattr(dset_dialog, 'dset'):
self.dset = dset_dialog.dset
if type(self.dset) == list:
dset_name = '/'.join(self.dset)
else:
dset_name = self.dset
if type(self.dset) == list:
self.proc_thread = ProcessingThread(dset=self.dset[1],
net_thread=self.net_thread, owner=self.dset[0],
suma_file = self.suma_file)
else:
self.proc_thread = ProcessingThread(dset=self.dset,
net_thread=self.net_thread,
suma_file = self.suma_file)
self.proc_thread.start()
elif mode == 'local':
self.dset = init.dset_var.get()
# TODO: Load dataset & surfaces
sv_window = LocalSpecAndVolWindow(self.real_root,
title="COVI: Select Spec "
+"and Volume Files",
dset_path=self.dset)
if sv_window.spec_file and sv_window.vol_file:
self.spec_file = sv_window.spec_file
self.vol_file = sv_window.vol_file
self.annot_file = sv_window.annot_file
self.proc_thread = ProcessingThread(
spec_file=self.spec_file,
surfvol_file=self.vol_file,
dset_path = self.dset,
annot_file = self.annot_file,
suma_file = self.suma_file)
self.proc_thread.start()
# Re-enable main window widgets
set_state(self.real_root, 'enabled')
self.real_root.deiconify()
class MainWindow:
def begin_session(self):
set_state(self.root, 'disabled')
set_state(self.switch_button, 'enabled')
self.real_root.withdraw()
# Try to find SUMA. If we can't, look for a config
# file telling us where it is. If there is none,
# ask the user where it is and create a config file.
try:
self.suma_file = subprocess.check_output(
["which", "suma"]).strip()
except subprocess.CalledProcessError:
config_name = os.path.join(
os.path.dirname(inspect.stack()[-1][1]),
'suma.config')
try:
config_fi = open(config_name, 'r')
config = config_fi.read()
config_fi.close()
self.suma_file = json.loads(config)["suma"]
if not self.suma_file:
raise IOError()
except (IOError, KeyError):
try:
self.configure()
except ValueError:
# We can't continue without a path to SUMA.
sys.exit(1)
# If we're not connected, we need to choose a local dataset or server
init = None
if self.net_thread and self.net_thread.authenticated:
mode = 'server'
else:
init_dialog = tk.Toplevel()
init_dialog.title("COVI: Choose data source")
if self.net_thread:
self.net_thread.job_q.put(["die"])
# self.net_thread = NetworkThread()
init = InitWindow(init_dialog, NetworkThread())
center_window(init_dialog)
root.wait_window(init_dialog)
mode = init.mode
if mode == 'server':
if init:
self.net_thread = init.net_thread
dset_dialog = ServerDsetWindow(self.real_root,
net_thread=self.net_thread,
title="COVI: %s: Datasets"%init.user_var.get())
else:
dset_dialog = ServerDsetWindow(self.real_root,
net_thread=self.net_thread,
title="COVI: Server Datasets")
if hasattr(dset_dialog, 'dset'):
self.dset = dset_dialog.dset
if type(self.dset) == list:
dset_name = '/'.join(self.dset)
else:
dset_name = self.dset
if type(self.dset) == list:
self.proc_thread = ProcessingThread(dset=self.dset[1],
net_thread=self.net_thread, owner=self.dset[0],
suma_file = self.suma_file)
else:
self.proc_thread = ProcessingThread(dset=self.dset,
net_thread=self.net_thread,
suma_file = self.suma_file)
self.proc_thread.start()
elif mode == 'local':
self.dset = init.dset_var.get()
# TODO: Load dataset & surfaces
sv_window = LocalSpecAndVolWindow(self.real_root,
title="COVI: Select Spec "
+"and Volume Files",
dset_path=self.dset)
if sv_window.spec_file and sv_window.vol_file:
self.spec_file = sv_window.spec_file
self.vol_file = sv_window.vol_file
self.annot_file = sv_window.annot_file
self.proc_thread = ProcessingThread(
spec_file=self.spec_file,
surfvol_file=self.vol_file,
dset_path = self.dset,
annot_file = self.annot_file,
suma_file = self.suma_file)
self.proc_thread.start()
# Re-enable main window widgets
set_state(self.real_root, 'enabled')
self.real_root.deiconify()
def configure(self):
config_name = os.path.join(
os.path.dirname(inspect.stack()[-1][1]),
'suma.config')
config_dialog = ConfigDialog(parent=self.root,
title='COVI Configuration')
self.suma_file = config_dialog.suma_file
if self.suma_file:
config = {"suma":self.suma_file}
config_fi = open(config_name, 'w')
json.dump(config, config_fi, indent=4, separators=(',',':'))
if self.proc_thread and self.proc_thread.ready():
self.proc_thread.job_q.put_nowait(["suma_path",
self.suma_file])
return True
else:
raise ValueError("The user did not specify the path to SUMA.")
def __init__(self, real_root):
self.proc_thread = False
self.net_thread = False
self.real_root = real_root
self.real_root.resizable(0,0)
self.real_root.title("COVI")
self.menu_vars = []
self.real_root.protocol("WM_DELETE_WINDOW", self.cleanup)
# Put all of our widgets inside a frame, not the Toplevel object
self.root = ttk.Frame(real_root)
root = self.root
root.pack(fill=tk.BOTH, expand=tk.YES)
self.body()
#rootlabel = ttk.Label(root,
# text="I'm the main window!\nWhen I grow up, I'll be full of widgets!")
#rootlabel.pack()
center_window(real_root)
set_state(self.root, 'disabled')
set_state(self.switch_button, 'enabled')
self.begin_session()
set_state(self.root, 'disabled')
set_state(self.switch_button, 'enabled')
self.poll()
def poll(self):
'''
Check for events from SUMA.
'''
if self.proc_thread:
if self.proc_thread not in threading.enumerate():
tkMessageBox.showwarning("Connection to SUMA lost",
"The connection to SUMA has been lost. "+
"Reload your dataset to continue using COVI.")
self.proc_not_ready()
self.proc_thread = False
if self.proc_thread and self.proc_thread.ready():
try:
res = self.proc_thread.res_q.get_nowait()
self.proc_thread.res_q.task_done()
if res:
if res[0] == 'node':
self.node_number_label['text'] = '%i'%res[1]
elif res[0] == 'cluster':
self.cluster_number_label['text'] = '%i'%res[1]
elif res[0] == 'area':
self.curr_area_label['text'] = res[1]
elif res[0] == 'ready':
# Re-enable main window widgets
set_state(self.real_root, 'enabled')
except Empty:
pass
if self.net_thread and self.net_thread not in threading.enumerate():
tkMessageBox.showwarning("Connection to server lost",
"The connection to the server has been lost. "+
"Reload your dataset to continue using COVI.")
self.proc_not_ready()
self.net_thread = False
self.root.after(100, self.poll)
def cleanup(self):
if self.net_thread:
self.net_thread.job_q.put_nowait(["close"])
self.net_thread.job_q.put_nowait(["die"])
if self.proc_thread:
self.proc_thread.job_q.put_nowait(["die"])
self.real_root.quit()
def proc_not_ready(self):
'''
What to do if no dataset is loaded into SUMA.
Disable interface widgets that won't work without SUMA
and display a message.
'''
set_state(self.root, 'disabled')
set_state(self.switch_button, 'enabled')
"""
tkMessageBox.showwarning("Warning",
"A dataset needs to be loaded into SUMA to do that.")"""
def scale_command(self, event=None):
threshold = self.threshold.get()
self.threshold_label['text'] = str(threshold)
def switch_command(self):
'''
Switch datasets
'''
answer = True
if self.proc_thread and self.proc_thread.ready():
answer = tkMessageBox.askyesno("Warning",
"This will end your current COVI session. Continue?")
if answer:
if self.proc_thread:
self.proc_thread.job_q.put_nowait(["die"])
self.proc_thread = False
self.proc_not_ready()
self.begin_session()
def open_command(self):
pass
def mode_command(self, mode):
if self.proc_thread and self.proc_thread.ready():
self.proc_thread.job_q.put_nowait(["shape", mode])
else:
self.proc_not_ready()
def color_command(self, color):
if self.proc_thread and self.proc_thread.ready():
if color == 'annot' and not self.proc_thread.annot:
tkMessageBox.showerror("Coloring Error",
"Can't use brain area-based coloring without an annot file.")
self.color_var.set(self.last_color)
return
elif color == 'brightness' and self.proc_thread.no_surface:
tkMessageBox.showerror("Coloring Error",
"Coordinate-based coloring can't be used, since "+
"COVI could not find a valid FreeSurfer ASCII surface "+
"file for the current surface. You can use the AFNI "+
"program ConvertSurface to create a FreeSurfer ASCII "+
"file for the current surface.")
self.color_var.set(self.last_color)
return
else:
self.proc_thread.job_q.put_nowait(["color", color])
self.last_color = color
else:
self.proc_not_ready()
def redraw_command(self):
if self.proc_thread and self.proc_thread.ready():
threshold = float(self.threshold.get())
# Avoid divide by zero error
threshold = max(threshold, 10**-9)
self.proc_thread.job_q.put_nowait(["threshold",
float(self.threshold.get())/100.])
self.proc_thread.job_q.put_nowait(["redraw"])
else:
self.proc_not_ready()
def relaunch_command(self):
if self.proc_thread and self.proc_thread.ready():
self.proc_thread.job_q.put_nowait(['suma'])
else:
self.proc_not_ready()
def disconnect_command(self):
'''
End a network session and disconnect from the server
'''
answer = tkMessageBox.askyesno("Warning",
"This will end your current COVI session. Continue?")
if not answer:
return
if self.net_thread:
if self.net_thread in threading.enumerate():
self.net_thread.job_q.put(["close"])
self.net_thread.job_q.put(["die"])
self.net_thread = False
if self.proc_thread and self.proc_thread.ready():
self.proc_thread.job_q.put(["die"])
else:
tkMessageBox.showinfo("Can't disconnect from server",
"COVI Client is not connected to a server.")
def make_mode_menu(self, root_menu):
'''
Make a menu to choose among graph modes.
'''
if not hasattr(self, "mode_var"):
self.mode_var = tk.StringVar()
self.mode_var.set("sized spheres")
mode_menu = tk.Menu(root_menu, tearoff=0)
mode_menu.add_radiobutton(label="Paths", variable=self.mode_var,
command=lambda: self.mode_command("paths"),
value="paths")
mode_menu.add_radiobutton(label="Spheres", variable=self.mode_var,
command=lambda: self.mode_command("spheres"),
value="spheres")
mode_menu.add_radiobutton(label="Sized Spheres", variable=self.mode_var,
command=lambda: self.mode_command("sized spheres"),
value="sized spheres")
return mode_menu
def make_color_menu(self, root_menu):
'''
Make a menu to choose among color modes.
'''
if not hasattr(self, "mode_var"):
self.mode_var = tk.StringVar()
if not hasattr(self, "color_var"):
self.color_var = tk.StringVar()
self.color_var.set("heat")
color_menu = tk.Menu(self.edit_menu,tearoff=0)
color_menu.add_radiobutton(label="Heatmap",
command=lambda: self.color_command("heat"),
variable=self.color_var, value="heat")
color_menu.add_radiobutton(label="Coordinate-based",
command=lambda: self.color_command("brightness"),
variable=self.color_var, value="brightness")
color_menu.add_radiobutton(label=" Brain Area-based",
command=lambda: self.color_command("annot"),
variable=self.color_var, value="annot")
return color_menu
def body(self):
self.threshold = tk.IntVar(0)
self.menu = tk.Menu()
self.file_menu = tk.Menu(self.menu, tearoff=0)
self.file_menu.add_command(label="Open dataset/Connect to server",
command=self.begin_session)
self.file_menu.add_command(label="Disconnect from server",
command=self.disconnect_command)
self.file_menu.add_separator()
self.file_menu.add_command(label="Quit", command=self.cleanup)
self.menu.add_cascade(label="File", menu=self.file_menu)
self.edit_menu = tk.Menu(self.menu, tearoff=0)
self.edit_menu.add_cascade(label="Graph mode",
menu=self.make_mode_menu(self.edit_menu))
self.last_color = 'heat'
self.edit_menu.add_cascade(label="Color mode",
menu=self.make_color_menu(self.edit_menu))
self.edit_menu.add_command(label="Relaunch SUMA",
command=self.relaunch_command)
self.edit_menu.add_command(label="Reconfigure",
command=self.configure)
self.menu.add_cascade(label="Edit", menu=self.edit_menu)
self.real_root.config(menu=self.menu)
self.scale = ttk.Scale(self.root, from_=100, to=0,
variable=self.threshold,
orient=tk.VERTICAL,
command=self.scale_command)
self.threshold.set(50)
self.scale.grid(column=0, row=0, rowspan=8, sticky=(tk.N+tk.S),
padx='3m', pady='1m')
self.threshold_label = ttk.Label(self.root, text="0", justify=tk.LEFT)
self.threshold_label.grid(column=0, row=8)
self.scale_command()
self.node_label = ttk.Label(self.root, text="Node")
self.node_label.grid(column=1, row=0, sticky=tk.W+tk.E, padx='1m')
self.node_number_label = ttk.Label(self.root, text='%i'%0, width='6',
relief=tk.SUNKEN, justify=tk.RIGHT)
self.node_number_label.grid(column=1, row=1, sticky=tk.W+tk.E, padx='1m')
self.cluster_label = ttk.Label(self.root, text="Cluster")
self.cluster_label.grid(column=1, row=2, sticky=tk.W+tk.E, padx='1m')
self.cluster_number_label = ttk.Label(self.root, text='%i'%0, width='6',
relief=tk.SUNKEN, justify=tk.RIGHT)
self.cluster_number_label.grid(column=1, row=3, sticky=tk.W+tk.E, padx='1m')
self.area_label = ttk.Label(self.root, text="Area")
self.area_label.grid(column=1, row=4, sticky=tk.W+tk.E, padx='1m')
self.curr_area_label = ttk.Label(self.root, text='',
relief=tk.SUNKEN, justify=tk.RIGHT)
self.curr_area_label.grid(column=1, row=5, sticky=tk.W+tk.E, padx='1m')
"""
self.open_button = ttk.Button(self.root, text= "Open\nDataset",
command=self.open_command)
self.open_button.grid(column=1, row=3, sticky=tk.W+tk.E, padx='1m')
"""
self.switch_button = ttk.Button(self.root, text= "Switch\nDataset",
command=self.switch_command)
self.switch_button.grid(column=1, row=6, sticky=tk.W+tk.E, padx='1m')
self.mode_button = ttk.Menubutton(self.root, text= "Graph\nMode")
self.mode_button['menu'] = self.make_mode_menu(self.mode_button)
self.mode_button.grid(column=1, row=7, sticky=tk.W+tk.E, padx='1m')
self.color_button = ttk.Menubutton(self.root, text= "Color\nMode")
self.color_button['menu'] = self.make_color_menu(self.color_button)
self.color_button.grid(column=1, row=8, sticky=tk.W+tk.E, padx='1m')
self.redraw_button = ttk.Button(self.root, text= "Redraw",
command=self.redraw_command)
self.redraw_button.grid(column=0, row=9, sticky=(tk.W+tk.E),
columnspan=2, padx='1m')
add_padding(self.root)