def make_entry(self, frame, var, label, row, column, minval, maxval,
increment):
Label(frame, text=label).grid(row=row, column=column, sticky="EW")
e = Spinbox(frame,
width=10,
textvariable=var,
from_=minval,
to=maxval,
increment=increment)
e.grid(row=row, column=column + 1, sticky="EW", padx=5, pady=2.5)
def make_slider(self,
frame,
var,
label,
row,
minval,
maxval,
command=None):
Label(frame, text=label, width=20).grid(row=row, column=0, sticky="W")
e = Spinbox(frame,
width=10,
textvariable=var,
from_=minval,
to=maxval,
increment=0.1)
e.grid(row=row, column=1, sticky="EW", padx=5)
slider = Scale(frame,
variable=var,
from_=minval,
to=maxval,
command=command)
slider.grid(row=row, column=2, columnspan=2, sticky="EW")
class VideoStreamFrame(Frame):
"""docstring for VideoStreamFrame"""
def __init__(self, parent, stream, app=None):
super().__init__()
self.stream = stream
self.app = app
self.panel = None
self.frame_delay = 50
self.frametime = 0.05
self.brightness = 1.0
self.display_range = self.display_range_default = self.stream.cam.dynamic_range
# Maximum number from image readout
self.auto_contrast = True
self.resize_image = False
self.last = time.perf_counter()
self.nframes = 1
self.update_frequency = 0.25
self.last_interval = self.frametime
self._atexit_funcs = []
#######################
self.parent = parent
self.init_vars()
self.buttonbox(self.parent)
self.header(self.parent)
self.makepanel(self.parent)
self.parent.wm_title("Video stream")
self.parent.wm_protocol("WM_DELETE_WINDOW", self.close)
self.parent.bind('<Escape>', self.close)
self.start_stream()
def init_vars(self):
self.var_fps = DoubleVar()
self.var_interval = DoubleVar()
# self.var_overhead = DoubleVar()
self.var_frametime = DoubleVar()
self.var_frametime.set(self.frametime)
self.var_frametime.trace_add("write", self.update_frametime)
self.var_brightness = DoubleVar(value=self.brightness)
self.var_brightness.trace_add("write", self.update_brightness)
self.var_display_range = DoubleVar(value=self.display_range_default)
self.var_display_range.trace_add("write", self.update_display_range)
self.var_resize_image = BooleanVar(value=self.resize_image)
self.var_resize_image.trace_add("write", self.update_resize_image)
self.var_auto_contrast = BooleanVar(value=self.auto_contrast)
self.var_auto_contrast.trace_add("write", self.update_auto_contrast)
def buttonbox(self, master):
btn = Button(master, text="Save image", command=self.saveImage)
btn.pack(side="bottom", fill="both", padx=10, pady=10)
def header(self, master):
ewidth = 8
lwidth = 12
frame = Frame(master)
self.cb_resize = Checkbutton(frame,
text="Increase size",
variable=self.var_resize_image)
self.cb_resize.grid(row=1, column=4)
self.cb_contrast = Checkbutton(frame,
text="Auto contrast",
variable=self.var_auto_contrast)
self.cb_contrast.grid(row=1, column=5)
self.e_fps = Entry(frame,
width=lwidth,
textvariable=self.var_fps,
state=DISABLED)
self.e_interval = Entry(frame,
width=lwidth,
textvariable=self.var_interval,
state=DISABLED)
# self.e_overhead = Entry(frame, bd=0, width=ewidth, textvariable=self.var_overhead, state=DISABLED)
Label(frame, width=lwidth, text="fps:").grid(row=1, column=0)
self.e_fps.grid(row=1, column=1, sticky='we')
Label(frame, width=lwidth, text="interval (ms):").grid(row=1, column=2)
self.e_interval.grid(row=1, column=3, sticky='we')
# Label(frame, width=lwidth, text="overhead (ms):").grid(row=1, column=4)
# self.e_overhead.grid(row=1, column=5)
frame.pack()
frame = Frame(master)
self.e_frametime = Spinbox(frame,
width=ewidth,
textvariable=self.var_frametime,
from_=0.0,
to=1.0,
increment=0.01)
Label(frame, width=lwidth, text="exposure (s)").grid(row=1, column=0)
self.e_frametime.grid(row=1, column=1)
self.e_brightness = Spinbox(frame,
width=ewidth,
textvariable=self.var_brightness,
from_=0.0,
to=10.0,
increment=0.1)
Label(frame, width=lwidth, text="Brightness").grid(row=1, column=2)
self.e_brightness.grid(row=1, column=3)
Label(frame, width=lwidth, text="DisplayRange").grid(row=1, column=4)
self.e_display_range = Spinbox(frame,
width=ewidth,
textvariable=self.var_display_range,
from_=1,
to=self.display_range_default,
increment=1000)
self.e_display_range.grid(row=1, column=5)
frame.pack()
def makepanel(self, master, resolution=(512, 512)):
if self.panel is None:
image = Image.fromarray(np.zeros(resolution))
image = ImageTk.PhotoImage(image)
self.panel = Label(image=image)
self.panel.image = image
self.panel.pack(side="left", padx=10, pady=10)
def setup_stream(self):
pass
def update_resize_image(self, name, index, mode):
# print name, index, mode
try:
self.resize_image = self.var_resize_image.get()
except:
pass
def update_auto_contrast(self, name, index, mode):
# print name, index, mode
try:
self.auto_contrast = self.var_auto_contrast.get()
except:
pass
def update_frametime(self, name, index, mode):
# print name, index, mode
try:
self.frametime = self.var_frametime.get()
except:
pass
else:
self.stream.update_frametime(self.frametime)
def update_brightness(self, name, index, mode):
# print name, index, mode
try:
self.brightness = self.var_brightness.get()
except:
pass
def update_display_range(self, name, index, mode):
try:
val = self.var_display_range.get()
self.display_range = max(1, val)
except:
pass
def saveImage(self):
"""Dump the current frame to a file"""
outfile = datetime.datetime.now().strftime(
"%Y%m%d-%H%M%S.%f") + ".tiff"
if self.app:
module_io = self.app.get_module("io")
drc = module_io.get_experiment_directory()
drc.mkdir(exist_ok=True, parents=True)
outfile = drc / outfile
try:
flatfield, h = read_tiff(module_io.get_flatfield())
frame = apply_flatfield_correction(self.frame, flatfield)
except:
frame = self.frame
h = {}
else:
frame = self.frame
h = {}
write_tiff(outfile, frame, header=h)
print(" >> Wrote file:", outfile)
def close(self):
self.stream.close()
self.parent.quit()
# for func in self._atexit_funcs:
# func()
def start_stream(self):
self.stream.update_frametime(self.frametime)
self.parent.after(500, self.on_frame)
def on_frame(self, event=None):
self.stream.lock.acquire(True)
self.frame = frame = self.stream.frame
self.stream.lock.release()
# the display range in ImageTk is from 0 to 256
if self.auto_contrast:
frame = frame * (256.0 / (1 + np.percentile(frame[::4, ::4], 99.5))
) # use 128x128 array for faster calculation
image = Image.fromarray(frame)
elif self.display_range != self.display_range_default:
image = np.clip(frame, 0, self.display_range)
image = (256.0 / self.display_range) * image
image = Image.fromarray(image)
else:
image = Image.fromarray(frame)
if self.brightness != 1:
image = ImageEnhance.Brightness(image.convert("L")).enhance(
self.brightness)
# Can also use ImageEnhance.Sharpness or ImageEnhance.Contrast if needed
if self.resize_image:
image = image.resize((950, 950))
image = ImageTk.PhotoImage(image=image)
self.panel.configure(image=image)
# keep a reference to avoid premature garbage collection
self.panel.image = image
self.update_frametimes()
# self.parent.update_idletasks()
self.parent.after(self.frame_delay, self.on_frame)
def update_frametimes(self):
self.current = time.perf_counter()
delta = self.current - self.last
if delta > self.update_frequency:
interval = delta / self.nframes
interval = (interval * 0.5) + (self.last_interval * 0.5)
fps = 1.0 / interval
# overhead = interval - self.stream.frametime
self.var_fps.set(round(fps, 2))
self.var_interval.set(round(interval * 1000, 2))
# self.var_overhead.set(round(overhead*1000, 2))
self.last = self.current
self.nframes = 1
self.last_interval = interval
else:
self.nframes += 1
def __init__(self, parent):
LabelFrame.__init__(self, parent, text="Stage Control")
self.parent = parent
self.init_vars()
frame = Frame(self)
b_stage_stop = Button(frame,
text="Stop stage",
command=self.stage_stop)
b_stage_stop.grid(row=0, column=2, sticky="W")
cb_nowait = Checkbutton(frame,
text="Wait for stage",
variable=self.var_stage_wait)
cb_nowait.grid(row=0, column=3)
b_find_eucentric_height = Button(frame,
text="Find eucentric height",
command=self.find_eucentric_height)
b_find_eucentric_height.grid(row=0,
column=0,
sticky="EW",
columnspan=2)
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',
command=self.set_mode)
self.o_mode.grid(row=8, column=1, sticky="W", padx=10)
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
Label(frame, text="Angle (-)", width=20).grid(row=1,
column=0,
sticky="W")
Label(frame, text="Angle (0)", width=20).grid(row=2,
column=0,
sticky="W")
Label(frame, text="Angle (+)", width=20).grid(row=3,
column=0,
sticky="W")
Label(frame, text="Alpha wobbler (±)", width=20).grid(row=4,
column=0,
sticky="W")
Label(frame, text="Stage(XY)", width=20).grid(row=5,
column=0,
sticky="W")
e_negative_angle = Spinbox(frame,
width=10,
textvariable=self.var_negative_angle,
from_=-90,
to=90,
increment=5)
e_negative_angle.grid(row=1, column=1, sticky="EW")
e_neutral_angle = Spinbox(frame,
width=10,
textvariable=self.var_neutral_angle,
from_=-90,
to=90,
increment=5)
e_neutral_angle.grid(row=2, column=1, sticky="EW")
e_positive_angle = Spinbox(frame,
width=10,
textvariable=self.var_positive_angle,
from_=-90,
to=90,
increment=5)
e_positive_angle.grid(row=3, column=1, sticky="EW")
e_alpha_wobbler = Spinbox(frame,
width=10,
textvariable=self.var_alpha_wobbler,
from_=-90,
to=90,
increment=1)
e_alpha_wobbler.grid(row=4, column=1, sticky="EW")
self.b_start_wobble = Button(frame,
text="Start",
command=self.start_alpha_wobbler)
self.b_start_wobble.grid(row=4, column=2, sticky="W")
self.b_stop_wobble = Button(frame,
text="Stop",
command=self.stop_alpha_wobbler,
state=DISABLED)
self.b_stop_wobble.grid(row=4, column=3, sticky="W")
e_stage_x = Entry(frame, width=10, textvariable=self.var_stage_x)
e_stage_x.grid(row=5, column=1, sticky="EW")
e_stage_y = Entry(frame, width=10, textvariable=self.var_stage_y)
e_stage_y.grid(row=5, column=2, sticky="EW")
b_negative_angle = Button(frame,
text="Set",
command=self.set_negative_angle)
b_negative_angle.grid(row=1, column=2, sticky="W")
b_neutral_angle = Button(frame,
text="Set",
command=self.set_neutral_angle)
b_neutral_angle.grid(row=2, column=2, sticky="W")
b_positive_angle = Button(frame,
text="Set",
command=self.set_positive_angle)
b_positive_angle.grid(row=3, column=2, sticky="W")
b_stage = Button(frame, text="Set", command=self.set_stage)
b_stage.grid(row=5, column=3, sticky="W")
b_stage_get = Button(frame, text="Get", command=self.get_stage)
b_stage_get.grid(row=5, column=4, sticky="W")
# frame.grid_columnconfigure(1, weight=1)
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
Label(frame, text="Brightness", width=20).grid(row=11,
column=0,
sticky="W")
e_brightness = Entry(frame, width=10, textvariable=self.var_brightness)
e_brightness.grid(row=11, column=1, sticky="W")
b_brightness = Button(frame, text="Set", command=self.set_brightness)
b_brightness.grid(row=11, column=2, sticky="W")
b_brightness_get = Button(frame,
text="Get",
command=self.get_brightness)
b_brightness_get.grid(row=11, column=3, sticky="W")
slider = Scale(frame,
variable=self.var_brightness,
from_=0,
to=2**16 - 1,
orient=HORIZONTAL,
command=self.set_brightness)
slider.grid(row=12, column=0, columnspan=3, sticky="EW")
frame.pack(side="top", fill="x", padx=10, pady=10)
frame = Frame(self)
Label(frame, text="DiffFocus", width=20).grid(row=11,
column=0,
sticky="W")
e_difffocus = Entry(frame, width=10, textvariable=self.var_difffocus)
e_difffocus.grid(row=11, column=1, sticky="W")
b_difffocus = Button(frame, text="Set", command=self.set_difffocus)
b_difffocus.grid(row=11, column=2, sticky="W")
b_difffocus_get = Button(frame, text="Get", command=self.get_difffocus)
b_difffocus_get.grid(row=11, column=3, sticky="W")
slider = Scale(frame,
variable=self.var_difffocus,
from_=0,
to=2**16 - 1,
orient=HORIZONTAL,
command=self.set_difffocus)
slider.grid(row=12, column=0, columnspan=3, sticky="EW")
frame.pack(side="top", fill="x", padx=10, pady=10)
from instamatic import TEMController
self.ctrl = TEMController.get_instance()
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_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 IOFrame(LabelFrame):
"""Simple interface to set the working directory and experiment
name/numbering, and access the configs/work directory."""
def __init__(self, parent):
LabelFrame.__init__(self, parent, text='Input/Output')
self.parent = parent
self.workdrc = Path(config.settings.work_directory)
self.init_vars()
frame = Frame(self)
self.directory = Entry(frame,
width=50,
textvariable=self.var_directory)
self.directory.grid(row=2, column=1, sticky='EW')
self.BrowseButton = Button(frame,
text='Browse..',
command=self.browse_directory)
self.BrowseButton.grid(row=2, column=2, sticky='EW')
self.sample_name = Entry(frame,
width=50,
textvariable=self.var_sample_name)
self.sample_name.grid(row=3, column=1, sticky='EW')
self.flatfield = Entry(frame,
width=50,
textvariable=self.var_flatfield)
self.flatfield.grid(row=4, column=1, sticky='EW')
self.BrowseFFButton = Button(frame,
text='Browse..',
command=self.browse_flatfield)
self.BrowseFFButton.grid(row=4, column=2, sticky='EW')
Label(frame, text='Directory:').grid(row=2, column=0, sticky='W')
Label(frame, text='Sample name:').grid(row=3, column=0, sticky='W')
Label(frame, text='Flatfield:').grid(row=4, column=0, sticky='W')
self.incrementer = Spinbox(frame,
width=10,
from_=0,
to=999,
increment=1,
textvariable=self.var_experiment_number)
self.incrementer.grid(row=3, column=2)
frame.grid_columnconfigure(1, weight=1)
frame.pack(side='top', fill='x', padx=10)
frame = Frame(self)
self.OpenDatadirButton = Button(frame,
text='Open work directory',
command=self.open_data_directory)
self.OpenDatadirButton.grid(row=1, column=0, sticky='EW')
self.OpenConfigdirButton = Button(frame,
text='Open settings directory',
command=self.open_config_directory)
self.OpenConfigdirButton.grid(row=1, column=1, sticky='EW')
self.DeleteButton = Button(frame,
text='Delete last experiment',
command=self.delete_last)
self.DeleteButton.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='both', padx=10, pady=10)
self.update_experiment_number()
def init_vars(self):
workdrc = self.workdrc
ff = config.settings.flatfield
if not ff:
self.var_flatfield = StringVar(value='')
else:
self.var_flatfield = StringVar(value=Path(ff).absolute())
self.var_directory = StringVar(value=workdrc.absolute())
self.var_sample_name = StringVar(value='experiment')
self.var_experiment_number = IntVar(value=1)
def get_working_directory(self):
drc = self.var_directory.get()
return Path(drc)
def update_experiment_number(self):
drc = Path(self.var_directory.get())
name = self.var_sample_name.get()
number = self.var_experiment_number.get()
path = drc / f'{name}_{number}'
while path.exists():
number += 1
path = drc / f'{name}_{number}'
self.var_experiment_number.set(number)
return number
def get_new_experiment_directory(self):
self.update_experiment_number()
return self.get_experiment_directory()
def get_experiment_directory(self):
drc = Path(self.var_directory.get())
name = self.var_sample_name.get()
number = self.var_experiment_number.get()
path = drc / f'{name}_{number}'
return path
def browse_directory(self):
drc = tkinter.filedialog.askdirectory(parent=self.parent,
title='Select working directory')
if not drc:
return
drc = Path(drc).absolute()
self.var_directory.set(drc)
print(self.get_experiment_directory())
self.update_experiment_number() # TODO: set to 1 on experiment update
return drc
def browse_flatfield(self):
ff = tkinter.filedialog.askopenfilename(
parent=self.parent,
initialdir=self.var_directory.get(),
title='Select flatfield')
if not ff:
return
ff = Path(ff).absolute()
self.var_flatfield.set(ff)
return ff
def get_flatfield(self):
ff = self.var_flatfield.get()
if ff == '':
ff = None
return ff
def delete_last(self):
drc = self.get_experiment_directory()
date = datetime.datetime.now().strftime('%H%M%S')
newdrc = drc.parent / f'delete_me-{date}'
if drc.exists():
drc.rename(newdrc)
print(f'Marked {drc} for deletion')
else:
print(f'{drc} does not exist')
def open_data_directory(self):
drc = self.get_working_directory()
try:
os.startfile(drc)
except FileNotFoundError:
os.startfile(drc.parent)
def open_config_directory(self):
drc = config.locations['base']
os.startfile(drc)
class VideoStreamFrame(LabelFrame):
"""GUI panel to continuously display the last frame streamed from the
camera."""
def __init__(self, parent, stream, app=None):
LabelFrame.__init__(self, parent, text='Stream')
self.parent = parent
self.stream = stream
self.app = app
self.panel = None
self.frame_delay = 50
self.frametime = 0.05
self.brightness = 1.0
self.display_range = self.display_range_default = self.stream.cam.dynamic_range
# Maximum number from image readout
self.auto_contrast = True
self.resize_image = False
self.last = time.perf_counter()
self.nframes = 1
self.update_frequency = 0.25
self.last_interval = self.frametime
self._atexit_funcs = []
#######################
self.parent = parent
self.init_vars()
self.buttonbox(self)
self.header(self)
self.makepanel(self)
try:
self.parent.wm_title('Video stream')
self.parent.wm_protocol('WM_DELETE_WINDOW', self.close)
except AttributeError:
pass
self.parent.bind('<Escape>', self.close)
self.start_stream()
def init_vars(self):
self.var_fps = DoubleVar()
self.var_interval = DoubleVar()
# self.var_overhead = DoubleVar()
self.var_frametime = DoubleVar()
self.var_frametime.set(self.frametime)
self.var_frametime.trace_add('write', self.update_frametime)
self.var_brightness = DoubleVar(value=self.brightness)
self.var_brightness.trace_add('write', self.update_brightness)
self.var_display_range = DoubleVar(value=self.display_range_default)
self.var_display_range.trace_add('write', self.update_display_range)
self.var_resize_image = BooleanVar(value=self.resize_image)
self.var_resize_image.trace_add('write', self.update_resize_image)
self.var_auto_contrast = BooleanVar(value=self.auto_contrast)
self.var_auto_contrast.trace_add('write', self.update_auto_contrast)
def buttonbox(self, master):
btn = Button(master, text='Save image', command=self.saveImage)
btn.pack(side='bottom', fill='both', padx=10, pady=10)
def header(self, master):
ewidth = 8
lwidth = 12
frame = Frame(master)
self.cb_resize = Checkbutton(frame,
text='Increase size',
variable=self.var_resize_image)
self.cb_resize.grid(row=1, column=4)
self.cb_contrast = Checkbutton(frame,
text='Auto contrast',
variable=self.var_auto_contrast)
self.cb_contrast.grid(row=1, column=5)
self.e_fps = Entry(frame,
width=lwidth,
textvariable=self.var_fps,
state=DISABLED)
self.e_interval = Entry(frame,
width=lwidth,
textvariable=self.var_interval,
state=DISABLED)
# self.e_overhead = Entry(frame, bd=0, width=ewidth, textvariable=self.var_overhead, state=DISABLED)
Label(frame, width=lwidth, text='fps:').grid(row=1, column=0)
self.e_fps.grid(row=1, column=1, sticky='we')
Label(frame, width=lwidth, text='interval (ms):').grid(row=1, column=2)
self.e_interval.grid(row=1, column=3, sticky='we')
# Label(frame, width=lwidth, text="overhead (ms):").grid(row=1, column=4)
# self.e_overhead.grid(row=1, column=5)
frame.pack()
frame = Frame(master)
self.e_frametime = Spinbox(frame,
width=ewidth,
textvariable=self.var_frametime,
from_=0.0,
to=1.0,
increment=0.01)
Label(frame, width=lwidth, text='exposure (s)').grid(row=1, column=0)
self.e_frametime.grid(row=1, column=1)
self.e_brightness = Spinbox(frame,
width=ewidth,
textvariable=self.var_brightness,
from_=0.0,
to=10.0,
increment=0.1)
Label(frame, width=lwidth, text='Brightness').grid(row=1, column=2)
self.e_brightness.grid(row=1, column=3)
Label(frame, width=lwidth, text='DisplayRange').grid(row=1, column=4)
self.e_display_range = Spinbox(frame,
width=ewidth,
textvariable=self.var_display_range,
from_=1,
to=self.display_range_default,
increment=1000)
self.e_display_range.grid(row=1, column=5)
frame.pack()
def makepanel(self, master, resolution=(512, 512)):
if self.panel is None:
image = Image.fromarray(np.zeros(resolution))
image = ImageTk.PhotoImage(image)
self.panel = Label(master, image=image)
self.panel.image = image
self.panel.pack(side='left', padx=10, pady=10)
def setup_stream(self):
pass
def update_resize_image(self, name, index, mode):
# print name, index, mode
try:
self.resize_image = self.var_resize_image.get()
except BaseException:
pass
def update_auto_contrast(self, name, index, mode):
# print name, index, mode
try:
self.auto_contrast = self.var_auto_contrast.get()
except BaseException:
pass
def update_frametime(self, name, index, mode):
# print name, index, mode
try:
self.frametime = self.var_frametime.get()
except BaseException:
pass
else:
self.stream.update_frametime(self.frametime)
def update_brightness(self, name, index, mode):
# print name, index, mode
try:
self.brightness = self.var_brightness.get()
except BaseException:
pass
def update_display_range(self, name, index, mode):
try:
val = self.var_display_range.get()
self.display_range = max(1, val)
except BaseException:
pass
def saveImage(self):
"""Dump the current frame to a file."""
self.q.put(('save_image', {'frame': self.frame}))
self.triggerEvent.set()
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def close(self):
self.stream.close()
self.parent.quit()
# for func in self._atexit_funcs:
# func()
def start_stream(self):
self.stream.update_frametime(self.frametime)
self.after(500, self.on_frame)
def on_frame(self, event=None):
self.stream.lock.acquire(True)
self.frame = frame = self.stream.frame
self.stream.lock.release()
# the display range in ImageTk is from 0 to 256
if self.auto_contrast:
frame = frame * (256.0 / (1 + np.percentile(frame[::4, ::4], 99.5))
) # use 128x128 array for faster calculation
image = Image.fromarray(frame)
elif self.display_range != self.display_range_default:
image = np.clip(frame, 0, self.display_range)
image = (256.0 / self.display_range) * image
image = Image.fromarray(image)
else:
image = Image.fromarray(frame)
if self.brightness != 1:
image = ImageEnhance.Brightness(image.convert('L')).enhance(
self.brightness)
# Can also use ImageEnhance.Sharpness or ImageEnhance.Contrast if needed
if self.resize_image:
image = image.resize((950, 950))
image = ImageTk.PhotoImage(image=image)
self.panel.configure(image=image)
# keep a reference to avoid premature garbage collection
self.panel.image = image
self.update_frametimes()
# self.parent.update_idletasks()
self.after(self.frame_delay, self.on_frame)
def update_frametimes(self):
self.current = time.perf_counter()
delta = self.current - self.last
if delta > self.update_frequency:
interval = delta / self.nframes
interval = (interval * 0.5) + (self.last_interval * 0.5)
fps = 1.0 / interval
# overhead = interval - self.stream.frametime
self.var_fps.set(round(fps, 2))
self.var_interval.set(round(interval * 1000, 2))
# self.var_overhead.set(round(overhead*1000, 2))
self.last = self.current
self.nframes = 1
self.last_interval = interval
else:
self.nframes += 1
def __init__(self, parent):
LabelFrame.__init__(self, parent, text='Stage Control')
self.parent = parent
self.init_vars()
frame = Frame(self)
b_stage_stop = Button(frame,
text='Stop stage',
command=self.stage_stop)
b_stage_stop.grid(row=0, column=2, sticky='W')
cb_nowait = Checkbutton(frame,
text='Wait for stage',
variable=self.var_stage_wait)
cb_nowait.grid(row=0, column=3)
b_find_eucentric_height = Button(frame,
text='Find eucentric height',
command=self.find_eucentric_height)
b_find_eucentric_height.grid(row=0,
column=0,
sticky='EW',
columnspan=2)
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',
command=self.set_mode)
self.o_mode.grid(row=8, column=1, sticky='W', padx=10)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
Label(frame, text='Angle (-)', width=20).grid(row=1,
column=0,
sticky='W')
Label(frame, text='Angle (0)', width=20).grid(row=2,
column=0,
sticky='W')
Label(frame, text='Angle (+)', width=20).grid(row=3,
column=0,
sticky='W')
Label(frame, text='Alpha wobbler (±)', width=20).grid(row=4,
column=0,
sticky='W')
Label(frame, text='Stage(XY)', width=20).grid(row=6,
column=0,
sticky='W')
e_negative_angle = Spinbox(frame,
width=10,
textvariable=self.var_negative_angle,
from_=-90,
to=90,
increment=5)
e_negative_angle.grid(row=1, column=1, sticky='EW')
e_neutral_angle = Spinbox(frame,
width=10,
textvariable=self.var_neutral_angle,
from_=-90,
to=90,
increment=5)
e_neutral_angle.grid(row=2, column=1, sticky='EW')
e_positive_angle = Spinbox(frame,
width=10,
textvariable=self.var_positive_angle,
from_=-90,
to=90,
increment=5)
e_positive_angle.grid(row=3, column=1, sticky='EW')
e_alpha_wobbler = Spinbox(frame,
width=10,
textvariable=self.var_alpha_wobbler,
from_=-90,
to=90,
increment=1)
e_alpha_wobbler.grid(row=4, column=1, sticky='EW')
self.b_start_wobble = Button(frame,
text='Start',
command=self.start_alpha_wobbler)
self.b_start_wobble.grid(row=4, column=2, sticky='W')
self.b_stop_wobble = Button(frame,
text='Stop',
command=self.stop_alpha_wobbler,
state=DISABLED)
self.b_stop_wobble.grid(row=4, column=3, sticky='W')
e_stage_x = Entry(frame, width=10, textvariable=self.var_stage_x)
e_stage_x.grid(row=6, column=1, sticky='EW')
e_stage_y = Entry(frame, width=10, textvariable=self.var_stage_y)
e_stage_y.grid(row=6, column=2, sticky='EW')
if config.settings.use_goniotool:
Label(frame, text='Rot. Speed', width=20).grid(row=5,
column=0,
sticky='W')
e_goniotool_tx = Spinbox(frame,
width=10,
textvariable=self.var_goniotool_tx,
from_=1,
to=12,
increment=1)
e_goniotool_tx.grid(row=5, column=1, sticky='EW')
b_goniotool_set = Button(frame,
text='Set',
command=self.set_goniotool_tx)
b_goniotool_set.grid(row=5, column=2, sticky='W')
b_goniotool_default = Button(frame,
text='Default',
command=self.set_goniotool_tx_default)
b_goniotool_default.grid(row=5, column=3, sticky='W')
b_negative_angle = Button(frame,
text='Set',
command=self.set_negative_angle)
b_negative_angle.grid(row=1, column=2, sticky='W')
b_neutral_angle = Button(frame,
text='Set',
command=self.set_neutral_angle)
b_neutral_angle.grid(row=2, column=2, sticky='W')
b_positive_angle = Button(frame,
text='Set',
command=self.set_positive_angle)
b_positive_angle.grid(row=3, column=2, sticky='W')
b_stage = Button(frame, text='Set', command=self.set_stage)
b_stage.grid(row=6, column=3, sticky='W')
b_stage_get = Button(frame, text='Get', command=self.get_stage)
b_stage_get.grid(row=6, column=4, sticky='W')
# defocus button
Label(frame, text='Diff defocus:', width=20).grid(row=13,
column=0,
sticky='W')
self.e_diff_defocus = Spinbox(frame,
textvariable=self.var_diff_defocus,
width=10,
from_=-10000,
to=10000,
increment=100)
self.e_diff_defocus.grid(row=13, column=1, sticky='EW')
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=13, column=2, sticky='W', columnspan=2)
self.b_reset_defocus = Button(frame,
text='Reset',
command=self.reset_diff_defocus,
state=DISABLED)
self.b_reset_defocus.grid(row=13, column=4, sticky='EW')
# frame.grid_columnconfigure(1, weight=1)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
Label(frame, text='Brightness', width=20).grid(row=11,
column=0,
sticky='W')
e_brightness = Entry(frame, width=10, textvariable=self.var_brightness)
e_brightness.grid(row=11, column=1, sticky='W')
b_brightness = Button(frame, text='Set', command=self.set_brightness)
b_brightness.grid(row=11, column=2, sticky='W')
b_brightness_get = Button(frame,
text='Get',
command=self.get_brightness)
b_brightness_get.grid(row=11, column=3, sticky='W')
slider = Scale(frame,
variable=self.var_brightness,
from_=0,
to=2**16 - 1,
orient=HORIZONTAL,
command=self.set_brightness)
slider.grid(row=12, column=0, columnspan=3, sticky='EW')
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
Label(frame, text='DiffFocus', width=20).grid(row=11,
column=0,
sticky='W')
e_difffocus = Entry(frame, width=10, textvariable=self.var_difffocus)
e_difffocus.grid(row=11, column=1, sticky='W')
b_difffocus = Button(frame, text='Set', command=self.set_difffocus)
b_difffocus.grid(row=11, column=2, sticky='W')
b_difffocus_get = Button(frame, text='Get', command=self.get_difffocus)
b_difffocus_get.grid(row=11, column=3, sticky='W')
slider = Scale(frame,
variable=self.var_difffocus,
from_=0,
to=2**16 - 1,
orient=HORIZONTAL,
command=self.set_difffocus)
slider.grid(row=12, column=0, columnspan=3, sticky='EW')
frame.pack(side='top', fill='x', padx=10, pady=10)
from instamatic import TEMController
self.ctrl = TEMController.get_instance()
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()
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
class ExperimentalCtrl(LabelFrame):
"""This panel holds some frequently used functions to control the electron
microscope."""
def __init__(self, parent):
LabelFrame.__init__(self, parent, text='Stage Control')
self.parent = parent
self.init_vars()
frame = Frame(self)
b_stage_stop = Button(frame,
text='Stop stage',
command=self.stage_stop)
b_stage_stop.grid(row=0, column=2, sticky='W')
cb_nowait = Checkbutton(frame,
text='Wait for stage',
variable=self.var_stage_wait)
cb_nowait.grid(row=0, column=3)
b_find_eucentric_height = Button(frame,
text='Find eucentric height',
command=self.find_eucentric_height)
b_find_eucentric_height.grid(row=0,
column=0,
sticky='EW',
columnspan=2)
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',
command=self.set_mode)
self.o_mode.grid(row=8, column=1, sticky='W', padx=10)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
Label(frame, text='Angle (-)', width=20).grid(row=1,
column=0,
sticky='W')
Label(frame, text='Angle (0)', width=20).grid(row=2,
column=0,
sticky='W')
Label(frame, text='Angle (+)', width=20).grid(row=3,
column=0,
sticky='W')
Label(frame, text='Alpha wobbler (±)', width=20).grid(row=4,
column=0,
sticky='W')
Label(frame, text='Stage(XY)', width=20).grid(row=6,
column=0,
sticky='W')
e_negative_angle = Spinbox(frame,
width=10,
textvariable=self.var_negative_angle,
from_=-90,
to=90,
increment=5)
e_negative_angle.grid(row=1, column=1, sticky='EW')
e_neutral_angle = Spinbox(frame,
width=10,
textvariable=self.var_neutral_angle,
from_=-90,
to=90,
increment=5)
e_neutral_angle.grid(row=2, column=1, sticky='EW')
e_positive_angle = Spinbox(frame,
width=10,
textvariable=self.var_positive_angle,
from_=-90,
to=90,
increment=5)
e_positive_angle.grid(row=3, column=1, sticky='EW')
e_alpha_wobbler = Spinbox(frame,
width=10,
textvariable=self.var_alpha_wobbler,
from_=-90,
to=90,
increment=1)
e_alpha_wobbler.grid(row=4, column=1, sticky='EW')
self.b_start_wobble = Button(frame,
text='Start',
command=self.start_alpha_wobbler)
self.b_start_wobble.grid(row=4, column=2, sticky='W')
self.b_stop_wobble = Button(frame,
text='Stop',
command=self.stop_alpha_wobbler,
state=DISABLED)
self.b_stop_wobble.grid(row=4, column=3, sticky='W')
e_stage_x = Entry(frame, width=10, textvariable=self.var_stage_x)
e_stage_x.grid(row=6, column=1, sticky='EW')
e_stage_y = Entry(frame, width=10, textvariable=self.var_stage_y)
e_stage_y.grid(row=6, column=2, sticky='EW')
if config.settings.use_goniotool:
Label(frame, text='Rot. Speed', width=20).grid(row=5,
column=0,
sticky='W')
e_goniotool_tx = Spinbox(frame,
width=10,
textvariable=self.var_goniotool_tx,
from_=1,
to=12,
increment=1)
e_goniotool_tx.grid(row=5, column=1, sticky='EW')
b_goniotool_set = Button(frame,
text='Set',
command=self.set_goniotool_tx)
b_goniotool_set.grid(row=5, column=2, sticky='W')
b_goniotool_default = Button(frame,
text='Default',
command=self.set_goniotool_tx_default)
b_goniotool_default.grid(row=5, column=3, sticky='W')
b_negative_angle = Button(frame,
text='Set',
command=self.set_negative_angle)
b_negative_angle.grid(row=1, column=2, sticky='W')
b_neutral_angle = Button(frame,
text='Set',
command=self.set_neutral_angle)
b_neutral_angle.grid(row=2, column=2, sticky='W')
b_positive_angle = Button(frame,
text='Set',
command=self.set_positive_angle)
b_positive_angle.grid(row=3, column=2, sticky='W')
b_stage = Button(frame, text='Set', command=self.set_stage)
b_stage.grid(row=6, column=3, sticky='W')
b_stage_get = Button(frame, text='Get', command=self.get_stage)
b_stage_get.grid(row=6, column=4, sticky='W')
# defocus button
Label(frame, text='Diff defocus:', width=20).grid(row=13,
column=0,
sticky='W')
self.e_diff_defocus = Spinbox(frame,
textvariable=self.var_diff_defocus,
width=10,
from_=-10000,
to=10000,
increment=100)
self.e_diff_defocus.grid(row=13, column=1, sticky='EW')
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=13, column=2, sticky='W', columnspan=2)
self.b_reset_defocus = Button(frame,
text='Reset',
command=self.reset_diff_defocus,
state=DISABLED)
self.b_reset_defocus.grid(row=13, column=4, sticky='EW')
# frame.grid_columnconfigure(1, weight=1)
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
Label(frame, text='Brightness', width=20).grid(row=11,
column=0,
sticky='W')
e_brightness = Entry(frame, width=10, textvariable=self.var_brightness)
e_brightness.grid(row=11, column=1, sticky='W')
b_brightness = Button(frame, text='Set', command=self.set_brightness)
b_brightness.grid(row=11, column=2, sticky='W')
b_brightness_get = Button(frame,
text='Get',
command=self.get_brightness)
b_brightness_get.grid(row=11, column=3, sticky='W')
slider = Scale(frame,
variable=self.var_brightness,
from_=0,
to=2**16 - 1,
orient=HORIZONTAL,
command=self.set_brightness)
slider.grid(row=12, column=0, columnspan=3, sticky='EW')
frame.pack(side='top', fill='x', padx=10, pady=10)
frame = Frame(self)
Label(frame, text='DiffFocus', width=20).grid(row=11,
column=0,
sticky='W')
e_difffocus = Entry(frame, width=10, textvariable=self.var_difffocus)
e_difffocus.grid(row=11, column=1, sticky='W')
b_difffocus = Button(frame, text='Set', command=self.set_difffocus)
b_difffocus.grid(row=11, column=2, sticky='W')
b_difffocus_get = Button(frame, text='Get', command=self.get_difffocus)
b_difffocus_get.grid(row=11, column=3, sticky='W')
slider = Scale(frame,
variable=self.var_difffocus,
from_=0,
to=2**16 - 1,
orient=HORIZONTAL,
command=self.set_difffocus)
slider.grid(row=12, column=0, columnspan=3, sticky='EW')
frame.pack(side='top', fill='x', padx=10, pady=10)
from instamatic import TEMController
self.ctrl = TEMController.get_instance()
def init_vars(self):
self.var_negative_angle = DoubleVar(value=-40)
self.var_neutral_angle = DoubleVar(value=0)
self.var_positive_angle = DoubleVar(value=40)
self.var_mode = StringVar(value='diff')
self.var_alpha_wobbler = DoubleVar(value=5)
self.var_stage_x = IntVar(value=0)
self.var_stage_y = IntVar(value=0)
self.var_goniotool_tx = IntVar(value=1)
self.var_brightness = IntVar(value=65535)
self.var_difffocus = IntVar(value=65535)
self.var_diff_defocus = IntVar(value=1500)
self.var_toggle_diff_defocus = BooleanVar(value=False)
self.var_stage_wait = BooleanVar(value=True)
def set_trigger(self, trigger=None, q=None):
self.triggerEvent = trigger
self.q = q
def set_mode(self, event=None):
self.ctrl.mode.set(self.var_mode.get())
def set_brightness(self, event=None):
self.var_brightness.set(self.var_brightness.get())
self.q.put(('ctrl', {
'task': 'brightness.set',
'value': self.var_brightness.get()
}))
self.triggerEvent.set()
def get_brightness(self, event=None):
self.var_brightness.set(self.ctrl.brightness.get())
def set_difffocus(self, event=None):
self.var_difffocus.set(self.var_difffocus.get())
self.q.put(('ctrl', {
'task': 'difffocus.set',
'value': self.var_difffocus.get()
}))
self.triggerEvent.set()
def get_difffocus(self, event=None):
self.var_difffocus.set(self.ctrl.difffocus.get())
def set_negative_angle(self):
self.q.put(('ctrl', {
'task': 'stage.set',
'a': self.var_negative_angle.get(),
'wait': self.var_stage_wait.get()
}))
self.triggerEvent.set()
def set_neutral_angle(self):
self.q.put(('ctrl', {
'task': 'stage.set',
'a': self.var_neutral_angle.get(),
'wait': self.var_stage_wait.get()
}))
self.triggerEvent.set()
def set_positive_angle(self):
self.q.put(('ctrl', {
'task': 'stage.set',
'a': self.var_positive_angle.get(),
'wait': self.var_stage_wait.get()
}))
self.triggerEvent.set()
def set_goniotool_tx(self, event=None, value=None):
if not value:
value = self.var_goniotool_tx.get()
self.ctrl.stage.set_rotation_speed(value)
def set_goniotool_tx_default(self, event=None):
value = 12
self.set_goniotool_tx(value=value)
def set_stage(self):
self.q.put(('ctrl', {
'task': 'stage.set',
'x': self.var_stage_x.get(),
'y': self.var_stage_y.get(),
'wait': self.var_stage_wait.get()
}))
self.triggerEvent.set()
def get_stage(self, event=None):
x, y, _, _, _ = self.ctrl.stage.get()
self.var_stage_x.set(int(x))
self.var_stage_y.set(int(y))
def start_alpha_wobbler(self):
self.wobble_stop_event = threading.Event()
self.b_stop_wobble.config(state=NORMAL)
self.b_start_wobble.config(state=DISABLED)
self.q.put(('ctrl', {
'task': 'stage.alpha_wobbler',
'delta': self.var_alpha_wobbler.get(),
'event': self.wobble_stop_event
}))
self.triggerEvent.set()
def stop_alpha_wobbler(self):
self.wobble_stop_event.set()
self.b_stop_wobble.config(state=DISABLED)
self.b_start_wobble.config(state=NORMAL)
def stage_stop(self):
self.q.put(('ctrl', {'task': 'stage.stop'}))
self.triggerEvent.set()
def find_eucentric_height(self):
self.q.put(('ctrl', {'task': 'find_eucentric_height'}))
self.triggerEvent.set()
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)
self.get_difffocus()
def reset_diff_defocus(self):
self.ctrl.difffocus.refocus()
self.var_toggle_diff_defocus.set(False)
self.get_difffocus()
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 IOFrame(LabelFrame):
"""docstring for ExperimentalSED"""
def __init__(self, parent):
LabelFrame.__init__(self, parent, text="Input/Output")
self.parent = parent
self.workdrc = Path(config.cfg.work_directory)
self.init_vars()
frame = Frame(self)
self.directory = Entry(frame,
width=50,
textvariable=self.var_directory)
self.directory.grid(row=2, column=1, sticky="EW")
self.BrowseButton = Button(frame,
text="Browse..",
command=self.browse_directory)
self.BrowseButton.grid(row=2, column=2, sticky="EW")
self.sample_name = Entry(frame,
width=50,
textvariable=self.var_sample_name)
self.sample_name.grid(row=3, column=1, sticky="EW")
self.flatfield = Entry(frame,
width=50,
textvariable=self.var_flatfield)
self.flatfield.grid(row=4, column=1, sticky="EW")
self.BrowseFFButton = Button(frame,
text="Browse..",
command=self.browse_flatfield)
self.BrowseFFButton.grid(row=4, column=2, sticky="EW")
Label(frame, text="Directory:").grid(row=2, column=0, sticky="W")
Label(frame, text="Sample name:").grid(row=3, column=0, sticky="W")
Label(frame, text="Flatfield:").grid(row=4, column=0, sticky="W")
self.incrementer = Spinbox(frame,
width=10,
from_=0,
to=999,
increment=1,
textvariable=self.var_experiment_number)
self.incrementer.grid(row=3, column=2)
frame.grid_columnconfigure(1, weight=1)
frame.pack(side="top", fill="x", padx=10)
frame = Frame(self)
self.OpenDatadirButton = Button(frame,
text="Open work directory",
command=self.open_data_directory)
self.OpenDatadirButton.grid(row=1, column=0, sticky="EW")
self.OpenConfigdirButton = Button(frame,
text="Open settings directory",
command=self.open_config_directory)
self.OpenConfigdirButton.grid(row=1, column=1, sticky="EW")
self.DeleteButton = Button(frame,
text="Delete last experiment",
command=self.delete_last)
self.DeleteButton.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="both", padx=10, pady=10)
self.update_experiment_number()
def init_vars(self):
workdrc = self.workdrc
ff = config.cfg.flatfield
if not ff:
self.var_flatfield = StringVar(value="")
else:
self.var_flatfield = StringVar(value=Path(ff).absolute())
self.var_directory = StringVar(value=workdrc.absolute())
self.var_sample_name = StringVar(value="experiment")
self.var_experiment_number = IntVar(value=1)
def get_working_directory(self):
drc = self.var_directory.get()
return Path(drc)
def update_experiment_number(self):
drc = Path(self.var_directory.get())
name = self.var_sample_name.get()
number = self.var_experiment_number.get()
path = drc / f"{name}_{number}"
while path.exists():
number += 1
path = drc / f"{name}_{number}"
self.var_experiment_number.set(number)
return number
def get_new_experiment_directory(self):
number = self.update_experiment_number()
return self.get_experiment_directory()
def get_experiment_directory(self):
drc = Path(self.var_directory.get())
name = self.var_sample_name.get()
number = self.var_experiment_number.get()
path = drc / f"{name}_{number}"
return path
def browse_directory(self):
drc = tkinter.filedialog.askdirectory(parent=self.parent,
title="Select working directory")
if not drc:
return
drc = Path(drc).absolute()
self.var_directory.set(drc)
print(self.get_experiment_directory())
self.update_experiment_number() # TODO: set to 1 on experiment update
return drc
def browse_flatfield(self):
ff = tkinter.filedialog.askopenfilename(
parent=self.parent,
initialdir=self.var_directory.get(),
title="Select flatfield")
if not ff:
return
ff = Path(ff).absolute()
self.var_flatfield.set(ff)
return ff
def get_flatfield(self):
ff = self.var_flatfield.get()
if ff == "":
ff = None
return ff
def delete_last(self):
drc = self.get_experiment_directory()
date = datetime.datetime.now().strftime("%H%M%S")
newdrc = drc.parent / f"delete_me-{date}"
if drc.exists():
drc.rename(newdrc)
print(f"Marked {drc} for deletion")
else:
print(f"{drc} does not exist")
def open_data_directory(self):
drc = self.get_working_directory()
try:
os.startfile(drc)
except FileNotFoundError:
os.startfile(drc.parent)
def open_config_directory(self):
drc = config.base_drc
os.startfile(drc)