class ExperimentalcRED_FEI(LabelFrame):
"""Simple panel to assist cRED data collection (mainly rotation control) on
a FEI microscope."""
def __init__(self, parent):
LabelFrame.__init__(self, parent, text='cRED_FEI')
self.parent = parent
sbwidth = 10
self.init_vars()
frame = Frame(self)
Label(frame, text='Exposure time (s):').grid(row=4,
column=0,
sticky='W')
self.e_exposure_time = Spinbox(frame,
textvariable=self.var_exposure_time,
width=sbwidth,
from_=0.1,
to=9999,
increment=0.1)
self.e_exposure_time.grid(row=4, column=1, sticky='W', padx=10)
Label(frame, text='Target angle (deg):').grid(row=5,
column=0,
sticky='W')
self.e_endangle = Spinbox(frame,
textvariable=self.var_endangle,
width=sbwidth,
from_=0.1,
to=9999,
increment=0.5)
self.e_endangle.grid(row=5, column=1, sticky='W', padx=10)
Label(frame, text='Rotation speed (0 - 1):').grid(row=6,
column=0,
sticky='W')
self.e_rotspeed = Spinbox(frame,
textvariable=self.var_rotspeed,
width=sbwidth,
from_=-10.0,
to=10.0,
increment=0.2)
self.e_rotspeed.grid(row=6, column=1, sticky='W', padx=10)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
Label(frame, text='Output formats:').grid(row=5,
columnspan=2,
sticky='EW')
Checkbutton(frame,
text='PETS (.tiff)',
variable=self.var_save_tiff,
state=DISABLED).grid(row=5, column=2, sticky='EW')
Checkbutton(frame,
text='REDp (.mrc)',
variable=self.var_save_red,
state=DISABLED).grid(row=5, column=3, sticky='EW')
frame.grid_columnconfigure(0, weight=1)
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
self.StartButton = Button(frame,
text='Start Rotation',
command=self.start_collection)
self.StartButton.grid(row=1, column=0, sticky='EW')
self.FinalizeButton = Button(frame,
text='Stop Rotation',
command=self.stop_collection,
state=DISABLED)
self.FinalizeButton.grid(row=1, column=2, sticky='EW')
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
frame.pack(side='bottom', fill='x', padx=10, pady=10)
def init_vars(self):
self.var_exposure_time = DoubleVar(value=0.5)
self.var_endangle = DoubleVar(value=60.0)
self.var_rotspeed = DoubleVar(value=1.0)
self.var_save_tiff = BooleanVar(value=True)
self.var_save_red = BooleanVar(value=True)
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def start_collection(self):
self.StartButton.config(state=DISABLED)
self.FinalizeButton.config(state=NORMAL)
self.e_exposure_time.config(state=DISABLED)
self.e_rotspeed.config(state=DISABLED)
self.q.put(('credfei', {
'task': 'stage.set_with_speed',
'a': self.var_endangle.get(),
'speed': self.var_rotspeed.get()
}))
self.triggerEvent.set()
def stop_collection(self):
self.StartButton.config(state=NORMAL)
self.FinalizeButton.config(state=DISABLED)
self.e_exposure_time.config(state=NORMAL)
self.e_rotspeed.config(state=NORMAL)
params = self.get_params(task='None')
self.q.put(('credfei', params))
self.triggerEvent.set()
def get_params(self, task=None):
params = {
'exposure_time': self.var_exposure_time.get(),
'endangle': self.var_endangle.get(),
'rotspeed': self.var_rotspeed.get(),
'task': task
}
return params
class ExperimentalcRED_FEI(LabelFrame):
"""docstring for ExperimentalcRED on FEI"""
def __init__(self, parent):
LabelFrame.__init__(self, parent, text="cRED_FEI")
self.parent = parent
sbwidth = 10
self.init_vars()
frame = Frame(self)
Label(frame, text="Exposure time (s):").grid(row=4,
column=0,
sticky="W")
self.e_exposure_time = Spinbox(frame,
textvariable=self.var_exposure_time,
width=sbwidth,
from_=0.1,
to=9999,
increment=0.1)
self.e_exposure_time.grid(row=4, column=1, sticky="W", padx=10)
Label(frame, text="Target angle (deg):").grid(row=5,
column=0,
sticky="W")
self.e_endangle = Spinbox(frame,
textvariable=self.var_endangle,
width=sbwidth,
from_=0.1,
to=9999,
increment=0.5)
self.e_endangle.grid(row=5, column=1, sticky="W", padx=10)
Label(frame, text="Rotation speed (0 - 1):").grid(row=6,
column=0,
sticky="W")
self.e_rotspeed = Spinbox(frame,
textvariable=self.var_rotspeed,
width=sbwidth,
from_=-10.0,
to=10.0,
increment=0.2)
self.e_rotspeed.grid(row=6, column=1, sticky="W", padx=10)
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
Label(frame, text="Output formats:").grid(row=5,
columnspan=2,
sticky="EW")
Checkbutton(frame,
text="PETS (.tiff)",
variable=self.var_save_tiff,
state=DISABLED).grid(row=5, column=2, sticky="EW")
Checkbutton(frame,
text="REDp (.mrc)",
variable=self.var_save_red,
state=DISABLED).grid(row=5, column=3, sticky="EW")
frame.grid_columnconfigure(0, weight=1)
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
self.StartButton = Button(frame,
text="Start Rotation",
command=self.start_collection)
self.StartButton.grid(row=1, column=0, sticky="EW")
self.FinalizeButton = Button(frame,
text="Stop Rotation",
command=self.stop_collection,
state=DISABLED)
self.FinalizeButton.grid(row=1, column=2, sticky="EW")
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
frame.pack(side="bottom", fill="x", padx=10, pady=10)
def init_vars(self):
self.var_exposure_time = DoubleVar(value=0.5)
self.var_endangle = DoubleVar(value=60.0)
self.var_rotspeed = DoubleVar(value=1.0)
self.var_save_tiff = BooleanVar(value=True)
self.var_save_red = BooleanVar(value=True)
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def start_collection(self):
self.StartButton.config(state=DISABLED)
self.FinalizeButton.config(state=NORMAL)
self.e_exposure_time.config(state=DISABLED)
self.e_rotspeed.config(state=DISABLED)
self.q.put(("credfei", {
"task": "stageposition.set_with_speed",
"a": self.var_endangle.get(),
"speed": self.var_rotspeed.get()
}))
self.triggerEvent.set()
def stop_collection(self):
self.StartButton.config(state=NORMAL)
self.FinalizeButton.config(state=DISABLED)
self.e_exposure_time.config(state=NORMAL)
self.e_rotspeed.config(state=NORMAL)
params = self.get_params(task="None")
self.q.put(("credfei", params))
self.triggerEvent.set()
def get_params(self, task=None):
params = {
"exposure_time": self.var_exposure_time.get(),
"endangle": self.var_endangle.get(),
"rotspeed": self.var_rotspeed.get(),
"task": task
}
return params
class ExperimentalcRED(LabelFrame):
"""docstring for ExperimentalSED"""
def __init__(self, parent):
LabelFrame.__init__(self,
parent,
text="Continuous rotation electron diffraction")
self.parent = parent
sbwidth = 10
self.init_vars()
frame = Frame(self)
Label(frame, text="Exposure time (s):").grid(row=1,
column=0,
sticky="W")
exposure_time = Spinbox(frame,
textvariable=self.var_exposure_time,
width=sbwidth,
from_=0.0,
to=100.0,
increment=0.01)
exposure_time.grid(row=1, column=1, sticky="W", padx=10)
Checkbutton(frame,
text="Beam unblanker",
variable=self.var_unblank_beam).grid(row=1,
column=2,
sticky="W")
Separator(frame, orient=HORIZONTAL).grid(row=4,
columnspan=3,
sticky="ew",
pady=10)
Checkbutton(frame,
text="Enable image interval",
variable=self.var_enable_image_interval,
command=self.toggle_interval_buttons).grid(row=5,
column=2,
sticky="W")
self.c_toggle_defocus = Checkbutton(
frame,
text="Toggle defocus",
variable=self.var_toggle_diff_defocus,
command=self.toggle_diff_defocus,
state=DISABLED)
self.c_toggle_defocus.grid(row=6, column=2, sticky="W")
Label(frame, text="Image interval:").grid(row=5, column=0, sticky="W")
self.e_image_interval = Spinbox(frame,
textvariable=self.var_image_interval,
width=sbwidth,
from_=1,
to=9999,
increment=1,
state=DISABLED)
self.e_image_interval.grid(row=5, column=1, sticky="W", padx=10)
Label(frame, text="Diff defocus:").grid(row=6, column=0, sticky="W")
self.e_diff_defocus = Spinbox(frame,
textvariable=self.var_diff_defocus,
width=sbwidth,
from_=-10000,
to=10000,
increment=100,
state=DISABLED)
self.e_diff_defocus.grid(row=6, column=1, sticky="W", padx=10)
Label(frame, text="Image exposure (s):").grid(row=7,
column=0,
sticky="W")
self.e_image_exposure = Spinbox(
frame,
textvariable=self.var_exposure_time_image,
width=sbwidth,
from_=0.0,
to=100.0,
increment=0.01,
state=DISABLED)
self.e_image_exposure.grid(row=7, column=1, sticky="W", padx=10)
self.RelaxButton = Button(frame,
text="Relax beam",
command=self.relax_beam,
state=DISABLED)
self.RelaxButton.grid(row=7, column=2, sticky="EW")
if ENABLE_FOOTFREE_OPTION:
Separator(frame, orient=HORIZONTAL).grid(row=8,
columnspan=3,
sticky="ew",
pady=10)
Label(frame, text="Rotate to:").grid(row=9, column=0, sticky="W")
self.e_max_rotation = Spinbox(
frame,
textvariable=self.var_footfree_rotate_to,
width=sbwidth,
from_=0.0,
to=70.0,
increment=1.0,
state=DISABLED)
self.e_max_rotation.grid(row=9, column=1, sticky="W", padx=10)
Checkbutton(frame,
text="Footfree mode",
variable=self.var_toggle_footfree,
command=self.toggle_footfree).grid(row=9,
column=2,
sticky="W")
self.lb_coll0 = Label(frame, text="")
self.lb_coll1 = Label(frame, text="")
self.lb_coll2 = Label(frame, text="")
self.lb_coll0.grid(row=10, column=0, columnspan=3, sticky="EW")
self.lb_coll1.grid(row=11, column=0, columnspan=3, sticky="EW")
self.lb_coll2.grid(row=12, column=0, columnspan=3, sticky="EW")
frame.grid_columnconfigure(1, weight=1)
frame.pack(side="top", fill="x", expand=False, padx=10, pady=10)
frame = Frame(self)
Label(frame, text="Select output formats:").grid(row=5,
columnspan=2,
sticky="EW")
Checkbutton(frame, text=".tiff",
variable=self.var_save_tiff).grid(row=5,
column=2,
sticky="EW")
Checkbutton(frame, text="XDS (.smv)",
variable=self.var_save_xds).grid(row=5,
column=3,
sticky="EW")
Checkbutton(frame, text="DIALS (.smv)",
variable=self.var_save_dials).grid(row=6,
column=2,
sticky="EW")
Checkbutton(frame, text="REDp (.mrc)",
variable=self.var_save_red).grid(row=6,
column=3,
sticky="EW")
frame.grid_columnconfigure(0, weight=1)
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
self.CollectionButton = Button(frame,
text="Start Collection",
command=self.start_collection)
self.CollectionButton.grid(row=1, column=0, sticky="EW")
self.CollectionStopButton = Button(frame,
text="Stop Collection",
command=self.stop_collection,
state=DISABLED)
self.CollectionStopButton.grid(row=1, column=1, sticky="EW")
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.pack(side="bottom", fill="x", padx=10, pady=10)
self.stopEvent = threading.Event()
def init_vars(self):
self.var_exposure_time = DoubleVar(value=0.5)
self.var_unblank_beam = BooleanVar(value=False)
self.var_image_interval = IntVar(value=10)
self.var_diff_defocus = IntVar(value=1500)
self.var_enable_image_interval = BooleanVar(value=False)
self.var_toggle_diff_defocus = BooleanVar(value=False)
self.var_exposure_time_image = DoubleVar(value=0.01)
self.var_footfree_rotate_to = DoubleVar(value=65.0)
self.var_toggle_footfree = BooleanVar(value=False)
self.mode = "regular"
self.var_save_tiff = BooleanVar(value=True)
self.var_save_xds = BooleanVar(value=True)
self.var_save_dials = BooleanVar(value=True)
self.var_save_red = BooleanVar(value=True)
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def start_collection(self):
# TODO: make a pop up window with the STOP button?
if self.var_toggle_diff_defocus.get():
self.var_toggle_diff_defocus.set(False)
self.toggle_diff_defocus()
self.CollectionStopButton.config(state=NORMAL)
self.CollectionButton.config(state=DISABLED)
if self.mode == "footfree":
self.lb_coll1.config(text="Data collection has started.")
self.lb_coll2.config(
text="Click STOP COLLECTION to end the experiment.")
else:
self.lb_coll1.config(
text="Now you can start to rotate the goniometer at any time.")
self.lb_coll2.config(
text=
"Click STOP COLLECTION BEFORE removing your foot from the pedal!"
)
self.parent.bind_all("<space>", self.stop_collection)
params = self.get_params()
self.q.put(("cred", params))
self.triggerEvent.set()
def stop_collection(self, event=None):
self.stopEvent.set()
self.parent.unbind_all("<space>")
self.CollectionStopButton.config(state=DISABLED)
self.CollectionButton.config(state=NORMAL)
self.lb_coll1.config(text="")
self.lb_coll2.config(text="")
def get_params(self):
params = {
"exposure_time": self.var_exposure_time.get(),
"exposure_time_image": self.var_exposure_time_image.get(),
"unblank_beam": self.var_unblank_beam.get(),
"enable_image_interval": self.var_enable_image_interval.get(),
"image_interval": self.var_image_interval.get(),
"diff_defocus": self.var_diff_defocus.get(),
"mode": self.mode,
"footfree_rotate_to": self.var_footfree_rotate_to.get(),
"write_tiff": self.var_save_tiff.get(),
"write_xds": self.var_save_xds.get(),
"write_dials": self.var_save_dials.get(),
"write_red": self.var_save_red.get(),
"stop_event": self.stopEvent
}
return params
def toggle_interval_buttons(self):
enable = self.var_enable_image_interval.get()
if enable:
self.e_image_interval.config(state=NORMAL)
self.e_image_exposure.config(state=NORMAL)
self.e_diff_defocus.config(state=NORMAL)
self.c_toggle_defocus.config(state=NORMAL)
self.RelaxButton.config(state=NORMAL)
else:
self.e_image_interval.config(state=DISABLED)
self.e_image_exposure.config(state=DISABLED)
self.e_diff_defocus.config(state=DISABLED)
self.c_toggle_defocus.config(state=DISABLED)
self.RelaxButton.config(state=DISABLED)
def relax_beam(self):
difffocus = self.var_diff_defocus.get()
self.q.put(("relax_beam", {"value": difffocus}))
self.triggerEvent.set()
def toggle_footfree(self):
enable = self.var_toggle_footfree.get()
if enable:
self.mode = "footfree"
self.e_max_rotation.config(state=NORMAL)
else:
self.mode == "regular"
self.e_max_rotation.config(state=DISABLED)
def toggle_diff_defocus(self):
toggle = self.var_toggle_diff_defocus.get()
difffocus = self.var_diff_defocus.get()
self.q.put(("toggle_difffocus", {
"value": difffocus,
"toggle": toggle
}))
self.triggerEvent.set()
class ExperimentalRED(LabelFrame):
"""GUI panel to perform a simple RED experiment using discrete rotation
steps."""
def __init__(self, parent):
LabelFrame.__init__(self, parent, text='Rotation electron diffraction')
self.parent = parent
sbwidth = 10
self.init_vars()
frame = Frame(self)
Label(frame, text='Exposure time (s):').grid(row=4,
column=0,
sticky='W')
self.e_exposure_time = Spinbox(frame,
textvariable=self.var_exposure_time,
width=sbwidth,
from_=0.1,
to=9999,
increment=0.1)
self.e_exposure_time.grid(row=4, column=1, sticky='W', padx=10)
Label(frame, text='Tilt range (deg):').grid(row=5,
column=0,
sticky='W')
self.e_tilt_range = Spinbox(frame,
textvariable=self.var_tilt_range,
width=sbwidth,
from_=0.1,
to=9999,
increment=0.5)
self.e_tilt_range.grid(row=5, column=1, sticky='W', padx=10)
Label(frame, text='Step size (deg):').grid(row=6, column=0, sticky='W')
self.e_stepsize = Spinbox(frame,
textvariable=self.var_stepsize,
width=sbwidth,
from_=-10.0,
to=10.0,
increment=0.2)
self.e_stepsize.grid(row=6, column=1, sticky='W', padx=10)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
Label(frame, text='Output formats:').grid(row=5,
columnspan=2,
sticky='EW')
Checkbutton(frame,
text='PETS (.tiff)',
variable=self.var_save_tiff,
state=DISABLED).grid(row=5, column=2, sticky='EW')
Checkbutton(frame,
text='REDp (.mrc)',
variable=self.var_save_red,
state=DISABLED).grid(row=5, column=3, sticky='EW')
frame.grid_columnconfigure(0, weight=1)
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
self.StartButton = Button(frame,
text='Start Collection',
command=self.start_collection)
self.StartButton.grid(row=1, column=0, sticky='EW')
self.ContinueButton = Button(frame,
text='Continue',
command=self.continue_collection,
state=DISABLED)
self.ContinueButton.grid(row=1, column=1, sticky='EW')
self.FinalizeButton = Button(frame,
text='Finalize',
command=self.stop_collection,
state=DISABLED)
self.FinalizeButton.grid(row=1, column=2, sticky='EW')
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
frame.pack(side='bottom', fill='x', padx=10, pady=10)
def init_vars(self):
self.var_exposure_time = DoubleVar(value=0.5)
self.var_tilt_range = DoubleVar(value=5.0)
self.var_stepsize = DoubleVar(value=1.0)
self.var_save_tiff = BooleanVar(value=True)
self.var_save_red = BooleanVar(value=True)
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def start_collection(self):
self.StartButton.config(state=DISABLED)
self.ContinueButton.config(state=NORMAL)
self.FinalizeButton.config(state=NORMAL)
self.e_exposure_time.config(state=DISABLED)
self.e_stepsize.config(state=DISABLED)
params = self.get_params(task='start')
self.q.put(('red', params))
self.triggerEvent.set()
def continue_collection(self):
params = self.get_params(task='continue')
self.q.put(('red', params))
self.triggerEvent.set()
def stop_collection(self):
self.StartButton.config(state=NORMAL)
self.ContinueButton.config(state=DISABLED)
self.FinalizeButton.config(state=DISABLED)
self.e_exposure_time.config(state=NORMAL)
self.e_stepsize.config(state=NORMAL)
params = self.get_params(task='stop')
self.q.put(('red', params))
self.triggerEvent.set()
def get_params(self, task=None):
params = {
'exposure_time': self.var_exposure_time.get(),
'tilt_range': self.var_tilt_range.get(),
'stepsize': self.var_stepsize.get(),
'task': task
}
return params
class ExperimentalTVIPS(LabelFrame):
"""docstring for ExperimentalRED"""
def __init__(self, parent):
LabelFrame.__init__(self, parent, text="Continuous rotation electron diffraction (TVIPS)")
self.parent = parent
sbwidth = 10
self.init_vars()
frame = Frame(self)
Label(frame, text="Target angle (degrees):").grid(row=4, column=0, sticky="W")
self.e_target_angle = Spinbox(frame, textvariable=self.var_target_angle, width=sbwidth, from_=-80.0, to=80.0, increment=5.0, state=NORMAL)
self.e_target_angle.grid(row=4, column=1, sticky="W", padx=10)
self.InvertAngleButton = Button(frame, text="Invert", command=self.invert_angle)
self.InvertAngleButton.grid(row=4, column=2, sticky="EW")
self.c_toggle_manual_control = Checkbutton(frame, text="Manual rotation control", variable=self.var_toggle_manual_control, command=self.toggle_manual_control)
self.c_toggle_manual_control.grid(row=4, column=3, sticky="W")
# defocus button
Label(frame, text="Diff defocus:").grid(row=6, column=0, sticky="W")
self.e_diff_defocus = Spinbox(frame, textvariable=self.var_diff_defocus, width=sbwidth, from_=-10000, to=10000, increment=100)
self.e_diff_defocus.grid(row=6, column=1, sticky="W", padx=10)
Label(frame, text="Exposure (ms):").grid(row=7, column=0, sticky="W")
self.e_exposure = Spinbox(frame, textvariable=self.var_exposure, width=sbwidth, from_=0, to=10000, increment=100)
self.e_exposure.grid(row=7, column=1, sticky="W", padx=10)
Label(frame, text="Mode:").grid(row=8, column=0, sticky="W")
self.o_mode = OptionMenu(frame, self.var_mode, 'diff', 'diff', 'mag1', 'mag2', 'lowmag', 'samag')
self.o_mode.grid(row=8, column=1, sticky="W", padx=10)
self.c_toggle_defocus = Checkbutton(frame, text="Toggle defocus", variable=self.var_toggle_diff_defocus, command=self.toggle_diff_defocus)
self.c_toggle_defocus.grid(row=6, column=3, sticky="W")
self.b_reset_defocus = Button(frame, text="Reset", command=self.reset_diff_defocus, state=DISABLED)
self.b_reset_defocus.grid(row=6, column=2, sticky="EW")
self.c_toggle_diffraction = Checkbutton(frame, text="Toggle DIFF", variable=self.var_toggle_diff_mode, command=self.toggle_diff_mode)
self.c_toggle_diffraction.grid(row=7, column=3, sticky="W")
self.c_toggle_screen = Checkbutton(frame, text="Toggle screen", variable=self.var_toggle_screen, command=self.toggle_screen)
self.c_toggle_screen.grid(row=8, column=3, sticky="W")
self.b_start_liveview = Button(frame, text="Start live view", command=self.start_liveview)
self.b_start_liveview.grid(row=7, column=2, sticky="EW")
self.b_stop_liveview = Button(frame, text="Stop live view", command=self.stop_liveview)
self.b_stop_liveview.grid(row=8, column=2, sticky="EW")
self.c_toggle_beamblank = Checkbutton(frame, text="Toggle beamblank", variable=self.var_toggle_beamblank, command=self.toggle_beamblank)
self.c_toggle_beamblank.grid(row=10, column=3, sticky="W")
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
self.e_instructions = Entry(frame, width=50, textvariable=self.var_instruction_file)
self.e_instructions.grid(row=4, column=1, sticky="EW")
self.BrowseTrackButton = Button(frame, text="Browse..", command=self.browse_instructions)
self.BrowseTrackButton.grid(row=4, column=2, sticky="EW")
Label(frame, text="Instruction file:").grid(row=4, column=0, sticky="W")
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
self.SearchButton = Button(frame, text="Search", command=self.search)
self.SearchButton.grid(row=1, column=0, sticky="EW")
self.FocusButton = Button(frame, text="Focus", command=self.focus)
self.FocusButton.grid(row=1, column=1, sticky="EW")
self.GetImageButton = Button(frame, text="Get image", command=self.get_image)
self.GetImageButton.grid(row=1, column=2, sticky="EW")
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
frame.pack(fill="x", padx=10, pady=10)
frame = Frame(self)
self.SerialButton = Button(frame, text="Start serial acquisition", width=25, command=self.serial_collection)
self.SerialButton.grid(row=1, column=0, sticky="EW")
frame.pack(fill="x", padx=10, pady=10)
frame = Frame(self)
self.GetReadyButton = Button(frame, text="Get Ready", command=self.prime_collection)
self.GetReadyButton.grid(row=1, column=0, sticky="EW")
self.AcquireButton = Button(frame, text="Acquire", command=self.start_collection, state=DISABLED)
self.AcquireButton.grid(row=1, column=1, sticky="EW")
self.FinalizeButton = Button(frame, text="Finalize", command=self.stop_collection, state=DISABLED)
self.FinalizeButton.grid(row=1, column=2, sticky="EW")
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
frame.pack(side="bottom", fill="x", padx=10, pady=10)
from instamatic import TEMController
self.ctrl = TEMController.get_instance()
def init_vars(self):
self.var_target_angle = DoubleVar(value=40.0)
self.var_exposure = IntVar(value=400)
self.var_save_tiff = BooleanVar(value=True)
self.var_save_red = BooleanVar(value=True)
self.var_diff_defocus = IntVar(value=1500)
self.var_toggle_diff_defocus = BooleanVar(value=False)
self.var_toggle_beamblank = BooleanVar(value=False)
self.var_toggle_diff_mode = BooleanVar(value=False)
self.var_toggle_screen = BooleanVar(value=False)
self.var_toggle_manual_control = BooleanVar(value=False)
self.var_instruction_file = StringVar(value="")
self.var_mode = StringVar(value="diff")
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def invert_angle(self):
angle = self.var_target_angle.get()
self.var_target_angle.set(-angle)
def disable_ui(self):
self.InvertAngleButton.config(state=DISABLED)
self.GetReadyButton.config(state=DISABLED)
self.AcquireButton.config(state=NORMAL)
self.FinalizeButton.config(state=NORMAL)
self.SerialButton.config(state=DISABLED)
self.e_target_angle.config(state=DISABLED)
self.SearchButton.config(state=DISABLED)
self.FocusButton.config(state=DISABLED)
self.GetImageButton.config(state=DISABLED)
self.b_start_liveview.config(state=DISABLED)
self.b_stop_liveview.config(state=DISABLED)
def enable_ui(self):
self.InvertAngleButton.config(state=NORMAL)
self.GetReadyButton.config(state=NORMAL)
self.AcquireButton.config(state=DISABLED)
self.FinalizeButton.config(state=DISABLED)
self.SerialButton.config(state=NORMAL)
if not self.var_toggle_manual_control.get():
self.e_target_angle.config(state=NORMAL)
self.SearchButton.config(state=NORMAL)
self.FocusButton.config(state=NORMAL)
self.GetImageButton.config(state=NORMAL)
self.b_start_liveview.config(state=NORMAL)
self.b_stop_liveview.config(state=NORMAL)
def prime_collection(self):
self.disable_ui()
# self.e_target_angle.config(state=DISABLED)
params = self.get_params(task="get_ready")
self.q.put(("cred_tvips", params))
self.triggerEvent.set()
def start_collection(self):
self.AcquireButton.config(state=DISABLED)
params = self.get_params(task="acquire")
self.q.put(("cred_tvips", params))
self.triggerEvent.set()
def stop_collection(self):
self.enable_ui()
params = self.get_params(task="stop")
self.q.put(("cred_tvips", params))
self.triggerEvent.set()
def serial_collection(self):
self.disable_ui()
params = self.get_params(task="serial")
self.q.put(("cred_tvips", params))
self.triggerEvent.set()
def browse_instructions(self):
fn = filedialog.askopenfilename(parent=self.parent, initialdir=None, title="Select instruction file")
if not fn:
return
fn = Path(fn).absolute()
self.var_instruction_file.set(fn)
return fn
def get_params(self, task=None):
params = { "target_angle": self.var_target_angle.get(),
"instruction_file": self.var_instruction_file.get(),
"exposure": self.var_exposure.get(),
"mode": self.var_mode.get(),
"manual_control": self.var_toggle_manual_control.get(),
"task": task }
return params
def toggle_manual_control(self):
toggle = self.var_toggle_manual_control.get()
if toggle:
self.e_target_angle.config(state=DISABLED)
else:
self.e_target_angle.config(state=NORMAL)
def toggle_diff_mode(self):
toggle = self.var_toggle_diff_mode.get()
if toggle:
self.ctrl.mode_diffraction()
else:
self.ctrl.mode_mag1()
def toggle_beamblank(self):
toggle = self.var_toggle_beamblank.get()
if toggle:
self.ctrl.beamblank_on()
else:
self.ctrl.beamblank_off()
def toggle_screen(self):
toggle = self.var_toggle_screen.get()
if toggle:
self.ctrl.screen_up()
else:
self.ctrl.screen_down()
def start_liveview(self):
self.ctrl.cam.start_liveview()
def stop_liveview(self):
self.ctrl.cam.stop_liveview()
def toggle_diff_defocus(self):
toggle = self.var_toggle_diff_defocus.get()
if toggle:
offset = self.var_diff_defocus.get()
self.ctrl.difffocus.defocus(offset=offset)
self.b_reset_defocus.config(state=NORMAL)
else:
self.ctrl.difffocus.refocus()
self.var_toggle_diff_defocus.set(False)
def reset_diff_defocus(self):
self.ctrl.difffocus.refocus()
self.var_toggle_diff_defocus.set(False)
def search(self):
self.ctrl.run_script("search_mode.py")
def focus(self):
self.ctrl.run_script("focus_mode.py")
def get_image(self):
self.ctrl.cam.acquireImage()
class ExperimentalcRED(LabelFrame):
"""GUI panel for doing cRED experiments on a Timepix camera."""
def __init__(self, parent):
LabelFrame.__init__(self,
parent,
text='Continuous rotation electron diffraction')
self.parent = parent
sbwidth = 10
self.init_vars()
frame = Frame(self)
Label(frame, text='Exposure time (s):').grid(row=1,
column=0,
sticky='W')
exposure_time = Spinbox(frame,
textvariable=self.var_exposure_time,
width=sbwidth,
from_=0.0,
to=100.0,
increment=0.01)
exposure_time.grid(row=1, column=1, sticky='W', padx=10)
Checkbutton(frame,
text='Beam unblanker',
variable=self.var_unblank_beam).grid(row=1,
column=2,
sticky='W')
Separator(frame, orient=HORIZONTAL).grid(row=4,
columnspan=3,
sticky='ew',
pady=10)
Checkbutton(frame,
text='Enable image interval',
variable=self.var_enable_image_interval,
command=self.toggle_interval_buttons).grid(row=5,
column=2,
sticky='W')
self.c_toggle_defocus = Checkbutton(
frame,
text='Toggle defocus',
variable=self.var_toggle_diff_defocus,
command=self.toggle_diff_defocus,
state=DISABLED)
self.c_toggle_defocus.grid(row=6, column=2, sticky='W')
Label(frame, text='Image interval:').grid(row=5, column=0, sticky='W')
self.e_image_interval = Spinbox(frame,
textvariable=self.var_image_interval,
width=sbwidth,
from_=1,
to=9999,
increment=1,
state=DISABLED)
self.e_image_interval.grid(row=5, column=1, sticky='W', padx=10)
Label(frame, text='Diff defocus:').grid(row=6, column=0, sticky='W')
self.e_diff_defocus = Spinbox(frame,
textvariable=self.var_diff_defocus,
width=sbwidth,
from_=-10000,
to=10000,
increment=100,
state=DISABLED)
self.e_diff_defocus.grid(row=6, column=1, sticky='W', padx=10)
Label(frame, text='Image exposure (s):').grid(row=7,
column=0,
sticky='W')
self.e_image_exposure = Spinbox(
frame,
textvariable=self.var_exposure_time_image,
width=sbwidth,
from_=0.0,
to=100.0,
increment=0.01,
state=DISABLED)
self.e_image_exposure.grid(row=7, column=1, sticky='W', padx=10)
self.RelaxButton = Button(frame,
text='Relax beam',
command=self.relax_beam,
state=DISABLED)
self.RelaxButton.grid(row=7, column=2, sticky='EW')
if ENABLE_FOOTFREE_OPTION:
Separator(frame, orient=HORIZONTAL).grid(row=8,
columnspan=3,
sticky='ew',
pady=10)
Label(frame, text='Rotate to:').grid(row=9, column=0, sticky='W')
self.e_max_rotation = Spinbox(
frame,
textvariable=self.var_footfree_rotate_to,
width=sbwidth,
from_=0.0,
to=70.0,
increment=1.0,
state=DISABLED)
self.e_max_rotation.grid(row=9, column=1, sticky='W', padx=10)
Checkbutton(frame,
text='Footfree mode',
variable=self.var_toggle_footfree,
command=self.toggle_footfree).grid(row=9,
column=2,
sticky='W')
self.lb_coll0 = Label(frame, text='')
self.lb_coll1 = Label(frame, text='')
self.lb_coll2 = Label(frame, text='')
self.lb_coll0.grid(row=10, column=0, columnspan=3, sticky='EW')
self.lb_coll1.grid(row=11, column=0, columnspan=3, sticky='EW')
self.lb_coll2.grid(row=12, column=0, columnspan=3, sticky='EW')
frame.grid_columnconfigure(1, weight=1)
frame.pack(side='top', fill='x', expand=False, padx=10, pady=10)
frame = Frame(self)
Label(frame, text='Select output formats:').grid(row=5,
columnspan=2,
sticky='EW')
Checkbutton(frame, text='.tiff',
variable=self.var_save_tiff).grid(row=5,
column=2,
sticky='EW')
Checkbutton(frame, text='XDS (.smv)',
variable=self.var_save_xds).grid(row=5,
column=3,
sticky='EW')
Checkbutton(frame, text='DIALS (.smv)',
variable=self.var_save_dials).grid(row=6,
column=2,
sticky='EW')
Checkbutton(frame, text='REDp (.mrc)',
variable=self.var_save_red).grid(row=6,
column=3,
sticky='EW')
frame.grid_columnconfigure(0, weight=1)
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
self.CollectionButton = Button(frame,
text='Start Collection',
command=self.start_collection)
self.CollectionButton.grid(row=1, column=0, sticky='EW')
self.CollectionStopButton = Button(frame,
text='Stop Collection',
command=self.stop_collection,
state=DISABLED)
self.CollectionStopButton.grid(row=1, column=1, sticky='EW')
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.pack(side='bottom', fill='x', padx=10, pady=10)
self.stopEvent = threading.Event()
def init_vars(self):
self.var_exposure_time = DoubleVar(value=0.5)
self.var_unblank_beam = BooleanVar(value=False)
self.var_image_interval = IntVar(value=10)
self.var_diff_defocus = IntVar(value=1500)
self.var_enable_image_interval = BooleanVar(value=False)
self.var_toggle_diff_defocus = BooleanVar(value=False)
self.var_exposure_time_image = DoubleVar(value=0.01)
self.var_footfree_rotate_to = DoubleVar(value=65.0)
self.var_toggle_footfree = BooleanVar(value=False)
self.mode = 'regular'
self.var_save_tiff = BooleanVar(value=True)
self.var_save_xds = BooleanVar(value=True)
self.var_save_dials = BooleanVar(value=True)
self.var_save_red = BooleanVar(value=True)
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def start_collection(self):
# TODO: make a pop up window with the STOP button?
if self.var_toggle_diff_defocus.get():
self.var_toggle_diff_defocus.set(False)
self.toggle_diff_defocus()
self.CollectionStopButton.config(state=NORMAL)
self.CollectionButton.config(state=DISABLED)
if self.mode == 'footfree':
self.lb_coll1.config(text='Data collection has started.')
self.lb_coll2.config(
text='Click STOP COLLECTION to end the experiment.')
else:
self.lb_coll1.config(
text='Now you can start to rotate the goniometer at any time.')
self.lb_coll2.config(
text=
'Click STOP COLLECTION BEFORE removing your foot from the pedal!'
)
self.parent.bind_all('<space>', self.stop_collection)
params = self.get_params()
self.q.put(('cred', params))
self.triggerEvent.set()
def stop_collection(self, event=None):
self.stopEvent.set()
self.parent.unbind_all('<space>')
self.CollectionStopButton.config(state=DISABLED)
self.CollectionButton.config(state=NORMAL)
self.lb_coll1.config(text='')
self.lb_coll2.config(text='')
def get_params(self):
params = {
'exposure_time': self.var_exposure_time.get(),
'exposure_time_image': self.var_exposure_time_image.get(),
'unblank_beam': self.var_unblank_beam.get(),
'enable_image_interval': self.var_enable_image_interval.get(),
'image_interval': self.var_image_interval.get(),
'diff_defocus': self.var_diff_defocus.get(),
'mode': self.mode,
'footfree_rotate_to': self.var_footfree_rotate_to.get(),
'write_tiff': self.var_save_tiff.get(),
'write_xds': self.var_save_xds.get(),
'write_dials': self.var_save_dials.get(),
'write_red': self.var_save_red.get(),
'stop_event': self.stopEvent
}
return params
def toggle_interval_buttons(self):
enable = self.var_enable_image_interval.get()
if enable:
self.e_image_interval.config(state=NORMAL)
self.e_image_exposure.config(state=NORMAL)
self.e_diff_defocus.config(state=NORMAL)
self.c_toggle_defocus.config(state=NORMAL)
self.RelaxButton.config(state=NORMAL)
else:
self.e_image_interval.config(state=DISABLED)
self.e_image_exposure.config(state=DISABLED)
self.e_diff_defocus.config(state=DISABLED)
self.c_toggle_defocus.config(state=DISABLED)
self.RelaxButton.config(state=DISABLED)
def relax_beam(self):
difffocus = self.var_diff_defocus.get()
self.q.put(('relax_beam', {'value': difffocus}))
self.triggerEvent.set()
def toggle_footfree(self):
enable = self.var_toggle_footfree.get()
if enable:
self.mode = 'footfree'
self.e_max_rotation.config(state=NORMAL)
else:
self.mode == 'regular'
self.e_max_rotation.config(state=DISABLED)
def toggle_diff_defocus(self):
toggle = self.var_toggle_diff_defocus.get()
difffocus = self.var_diff_defocus.get()
self.q.put(('toggle_difffocus', {
'value': difffocus,
'toggle': toggle
}))
self.triggerEvent.set()
class ExperimentalRED(LabelFrame):
"""docstring for ExperimentalRED"""
def __init__(self, parent):
LabelFrame.__init__(self, parent, text="Rotation electron diffraction")
self.parent = parent
sbwidth = 10
self.init_vars()
frame = Frame(self)
Label(frame, text="Exposure time (s):").grid(row=4,
column=0,
sticky="W")
self.e_exposure_time = Spinbox(frame,
textvariable=self.var_exposure_time,
width=sbwidth,
from_=0.1,
to=9999,
increment=0.1)
self.e_exposure_time.grid(row=4, column=1, sticky="W", padx=10)
Label(frame, text="Tilt range (deg):").grid(row=5,
column=0,
sticky="W")
self.e_tilt_range = Spinbox(frame,
textvariable=self.var_tilt_range,
width=sbwidth,
from_=0.1,
to=9999,
increment=0.5)
self.e_tilt_range.grid(row=5, column=1, sticky="W", padx=10)
Label(frame, text="Step size (deg):").grid(row=6, column=0, sticky="W")
self.e_stepsize = Spinbox(frame,
textvariable=self.var_stepsize,
width=sbwidth,
from_=-10.0,
to=10.0,
increment=0.2)
self.e_stepsize.grid(row=6, column=1, sticky="W", padx=10)
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
Label(frame, text="Output formats:").grid(row=5,
columnspan=2,
sticky="EW")
Checkbutton(frame,
text="PETS (.tiff)",
variable=self.var_save_tiff,
state=DISABLED).grid(row=5, column=2, sticky="EW")
Checkbutton(frame,
text="REDp (.mrc)",
variable=self.var_save_red,
state=DISABLED).grid(row=5, column=3, sticky="EW")
frame.grid_columnconfigure(0, weight=1)
frame.grid_columnconfigure(1, weight=1)
frame.grid_columnconfigure(2, weight=1)
frame.grid_columnconfigure(3, weight=1)
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
self.StartButton = Button(frame,
text="Start Collection",
command=self.start_collection)
self.StartButton.grid(row=1, column=0, sticky="EW")
self.ContinueButton = Button(frame,
text="Continue",
command=self.continue_collection,
state=DISABLED)
self.ContinueButton.grid(row=1, column=1, sticky="EW")
self.FinalizeButton = Button(frame,
text="Finalize",
command=self.stop_collection,
state=DISABLED)
self.FinalizeButton.grid(row=1, column=2, sticky="EW")
frame.columnconfigure(0, weight=1)
frame.columnconfigure(1, weight=1)
frame.columnconfigure(2, weight=1)
frame.pack(side="bottom", fill="x", padx=10, pady=10)
def init_vars(self):
self.var_exposure_time = DoubleVar(value=0.5)
self.var_tilt_range = DoubleVar(value=5.0)
self.var_stepsize = DoubleVar(value=1.0)
self.var_save_tiff = BooleanVar(value=True)
self.var_save_red = BooleanVar(value=True)
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def start_collection(self):
self.StartButton.config(state=DISABLED)
self.ContinueButton.config(state=NORMAL)
self.FinalizeButton.config(state=NORMAL)
self.e_exposure_time.config(state=DISABLED)
self.e_stepsize.config(state=DISABLED)
params = self.get_params(task="start")
self.q.put(("red", params))
self.triggerEvent.set()
def continue_collection(self):
params = self.get_params(task="continue")
self.q.put(("red", params))
self.triggerEvent.set()
def stop_collection(self):
self.StartButton.config(state=NORMAL)
self.ContinueButton.config(state=DISABLED)
self.FinalizeButton.config(state=DISABLED)
self.e_exposure_time.config(state=NORMAL)
self.e_stepsize.config(state=NORMAL)
params = self.get_params(task="stop")
self.q.put(("red", params))
self.triggerEvent.set()
def get_params(self, task=None):
params = {
"exposure_time": self.var_exposure_time.get(),
"tilt_range": self.var_tilt_range.get(),
"stepsize": self.var_stepsize.get(),
"task": task
}
return params
