def get_continuous_signal(channel_name, sample_time, sample_points):
"""Acquire a continuous signal.
Parameters
-----------
channel_name : str
The continuous channel to view, e.g. I_t, Z_t, Df_t, Aux1_t
sample_time : float
The time to acquire in seconds
sample_points : int
The number of points to acquire
Returns
-------
x_data : Numpy array
y_data : Numpy array
Examples
--------
Acquire 60 points of I(t) data over 0.1 seconds
>>> from nOmicron.microscope import IO
>>> from nOmicron.utils.plotting import plot_linear_signal
>>> IO.connect()
>>> t, I = get_continuous_signal("I(t)", 1e-1, 60)
>>> plot_linear_signal(v, I, "I(V)")
>>> IO.disconnect()
Acquire 100 points of Z(t) data over 5 seconds
>>> from nOmicron.microscope import IO
>>> from nOmicron.utils.plotting import plot_linear_signal
>>> IO.connect()
>>> t, I = get_continuous_signal("Z(t)", 5, 100)
>>> plot_linear_signal(v, I, "I(V)")
>>> IO.disconnect()
"""
global view_count, x_data, y_data
x_data = y_data = None
view_count = 0
def view_continuous_callback():
global view_count, x_data, y_data
view_count += 1
pbar.update(1)
data_size = mo.view.Data_Size()
period = mo.clock.Period()
x_data = np.linspace(0, (data_size - 1) * period, data_size)
y_data = np.array(mo.sample_data(data_size))
IO.enable_channel(channel_name)
IO.set_clock(sample_time, sample_points)
mo.view.Data(view_continuous_callback)
mo.allocate_sample_memory(sample_points)
pbar = tqdm(total=1)
while view_count < 1 and mo.mate.rc == mo.mate.rcs['RMT_SUCCESS']:
mo.wait_for_event()
mo.clock.Enable(False)
mo.view.Data()
IO.disable_channel()
return x_data, y_data
def get_xy_scan(channel_name,
x_direction,
y_direction,
num_lines='all',
mode='new',
return_filename=False):
"""
Perform and get an xy scan
Parameters
----------
channel_name : str
The channel to acquire from, e.g. Z, I, Aux1, Aux2
x_direction : str
Must be one of 'Forward', 'Backward', or 'Forward-Backward'
y_direction : str
Must be one of 'Up' or 'Up-Down'
num_lines : int or str
Number of lines to get. If an int, must be less than the number of lines in the scanner window.
Default is 'all'
mode : str, optional
Must be one of ['new', 'pause', 'continue']. Default is 'new'
return_filename : bool, optional
If the full file name of the scan should be returned along with the data. Default is False
Returns
-------
xydata : ndarray
Max 4 dimensions (y_up/y_down, x_up/x_down, x, y). First two dimensions will only appear if
y_direction is "Up-Down" and x_direction is "Forward-Backward" - will be missing as appropriate
Examples
--------
>>> from nOmicron.microscope import IO
>>> from nOmicron.utils.plotting import plot_xy
>>> IO.connect()
>>> xydata = get_xy_scan("Z", x_direction="Forward", y_direction="Up-Down")
>>> plot_xy(xydata, pixel_scale=mo.xy_scanner.Width() * 1e9 / mo.xy_scanner.Points())
>>> IO.disconnect()
Warnings
--------
Quite often (but unreliably!), running this function will get Matrix into a state in which it will return one/two
lines (unless play/pause is clicked manually) when operating manually. To restore this functionality, run
utils.utils.restore_z_functionality() and restart your scan.
"""
global scan_dir_x, scan_dir_y, line_count_y, view_count, tot_packets, xydata
# Setup and parsing parameters
allowed = ["new", "pause", "continue"]
if mode not in allowed:
raise ValueError(f"Mode must be one of {allowed}")
if num_lines == 'all':
num_lines = mo.xy_scanner.Lines()
x_dir_dict = {"Forward": "Fw", "Backward": "Bw"}
x_direction_strings = [
x_dir_dict[x_dir] for x_dir in x_direction.split("-")
]
y_direction_strings = y_direction.split("-")
# Set triggers
if x_direction == "Forward-Backward":
mo.xy_scanner.X_Retrace(True)
else:
mo.xy_scanner.X_Retrace(False)
if y_direction == "Up-Down":
if num_lines != 'all' and num_lines != mo.xy_scanner.Lines(
): # Force set lines instead?
raise ValueError(
"If scanning in both directions, num_lines cannot be set")
mo.xy_scanner.Y_Retrace(True)
else:
mo.xy_scanner.Y_Retrace(False)
# while not mo.xy_scanner.Enable_Scan(): # Enforce that we won't take data during relocation and confuse the CU
# print("waiting")
# sleep(0.1)
# Set counters and pre-allocate
view_count = [None, None]
scan_dir_y = 0
scan_dir_x = 1
line_count_y = 0
tot_packets = 0
xydata = np.zeros((2, 2, num_lines, mo.xy_scanner.Points()))
xydata[:] = np.nan
def view_xy_callback():
global scan_dir_x, scan_dir_y, line_count_y, view_count, tot_packets, xydata
tot_packets += 1
mo.tot_packets = tot_packets
line_count_y += 1
if x_direction == "Forward-Backward":
scan_dir_x = int(not (bool(scan_dir_x)))
line_count_y = line_count_y - scan_dir_x
scan_dir_y = (line_count_y - 1) // num_lines
data_size = mo.view.Data_Size()
data_pts = np.array(mo.sample_data(data_size))
xydata[scan_dir_y,
int(not (bool(scan_dir_x))),
(line_count_y - (num_lines * scan_dir_y)) - 1, :] = data_pts
view_count = [mo.view.Run_Count(), mo.view.Cycle_Count()]
pbar.update(1)
# pbar.set_postfix({"Scanline": mo.view.Packet_Count()})
# if tot_packets % 2 == 1:
# pbar.set_postfix({"Scanline": mo.view.Packet_Count()+1})
# Enable channels
for x_direction_string in x_direction_strings:
IO.enable_channel(f"{channel_name}_{x_direction_string}")
mo.view.Data(view_xy_callback)
mo.allocate_sample_memory(mo.xy_scanner.Points())
if mode == 'new':
mo.experiment.start()
elif mode == 'pause':
mo.experiment.resume()
else:
pass
# Get the data
pbar = tqdm(total=num_lines * len(x_direction_strings) *
len(y_direction_strings))
while tot_packets < num_lines * len(x_direction_strings) * len(y_direction_strings) \
and mo.mate.rc == mo.mate.rcs['RMT_SUCCESS']:
mo.wait_for_event()
if mode == 'new':
mo.experiment.stop()
elif mode == 'pause':
mo.experiment.pause()
else:
pass
# Pretty the output to make physical sense
xydata = np.flip(xydata, axis=2)
if len(x_direction_strings) != 2:
xydata = xydata[:, 0, :, :]
if len(y_direction_strings) != 2:
xydata = xydata[0, :, :, :]
np.squeeze(xydata)
# Return nicely
if return_filename:
filename = f"{mo.experiment.Result_File_Path()}\\{mo.experiment.Result_File_Name()}--{mo.view.Run_Count()}_{mo.view.Cycle_Count()}.Z_mtrx"
return xydata, filename
else:
return xydata
def get_point_spectra(channel_name,
target_position,
start_end,
sample_time,
sample_points,
repeats=1,
forward_back=True,
return_filename=False):
"""
Go to a position and perform fixed point spectroscopy.
Parameters
----------
channel_name : str
The channel to acquire from, e.g. I_V, Z_V, Aux2_V
target_position : list
[x, y] in the range -1,1. Can be converted from real nm units with utils.convert...
start_end : tuple
Start and end I/Z/Aux2
sample_time : float
The time to acquire in seconds
sample_points : int
The number of points to acquire
repeats : int
The number of repeat spectra to take for each point
forward_back : bool
Scan in both directions, or just one.
return_filename : bool, optional
If the full file name of the scan should be returned along with the data. Default is False
Returns
-------
x_data : Numpy array
y_data :
If performing repeat spectra and:
Scanning in both directions: list of list of Numpy arrays, where inner list is [0] forwards, [1] backwards
Scanning in one direction: list of Numpy arrays
If no repeat spectra and:
Scanning in both directions: list of Numpy arrays, where list is [0] forwards, [1] backwards
Scanning in one direction: single Numpy array
Examples
--------
Acquire 60 points of I(V) data over 10 milliseconds, with tip placed in middle of scan window.
>>> from nOmicron.microscope import IO
>>> from nOmicron.utils.plotting import plot_linear_signal
>>> IO.connect()
>>> v, I = get_point_spectra("I(V)", start_end=[0, 1], target_position=[0, 0], ...
>>> repeats=3, sample_points=50, sample_time=10e-3, forward_back=True)
>>> plot_linear_signal(v, I, "I(V)")
>>> IO.disconnect()
"""
global view_count, view_name, x_data, y_data
modes = {
"V": 0,
"Z": 1,
"Varied Z": 2
} # Varied Z not fully supported yet!
max_count = (repeats * (forward_back + 1))
view_count = 0
x_data = None
y_data = []
[y_data.append([None] * (bool(forward_back) + 1))
for i in range(repeats)] # Can't use [] ** repeats
def view_spectroscopy_callback():
global view_count, view_name, x_data, y_data
pbar.update(1)
view_count += 1
view_name = [mo.view.Run_Count(), mo.view.Cycle_Count()]
cycle_count = mo.view.Cycle_Count() - 1
packet_count = mo.view.Packet_Count() - 1
data_size = mo.view.Data_Size()
x_data = np.linspace(start_end[0], start_end[1], data_size)
y_data[cycle_count][packet_count] = np.array(
mo.sample_data(data_size)) * 1e-9
if packet_count == 1:
y_data[cycle_count][packet_count] = np.flip(
y_data[cycle_count][packet_count])
# Set all the parameters
IO.enable_channel(channel_name)
mo.spectroscopy.Spectroscopy_Mode(modes[channel_name[-2]])
getattr(mo.spectroscopy,
f"Device_{modes[channel_name[-2]] + 1}_Points")(sample_points)
getattr(mo.spectroscopy,
f"Raster_Time_{modes[channel_name[-2]] + 1}")(sample_time)
getattr(mo.spectroscopy,
f"Device_{modes[channel_name[-2]] + 1}_Start")(start_end[0])
getattr(mo.spectroscopy,
f"Device_{modes[channel_name[-2]] + 1}_End")(start_end[1])
getattr(mo.spectroscopy,
f"Device_{modes[channel_name[-2]] + 1}_Repetitions")(repeats)
getattr(mo.spectroscopy,
f"Enable_Device_{modes[channel_name[-2]] + 1}_Ramp_Reversal")(
forward_back)
# Set up spec
mo.xy_scanner.Store_Current_Position(True)
mo.xy_scanner.Target_Position(target_position)
mo.xy_scanner.Trigger_Execute_At_Target_Position(True)
# Do it
mo.xy_scanner.move()
mo.allocate_sample_memory(sample_points)
mo.view.Data(view_spectroscopy_callback)
pbar = tqdm(total=max_count)
while view_count < max_count and mo.mate.rc == mo.mate.rcs['RMT_SUCCESS']:
mo.wait_for_event()
mo.view.Data()
# Return to normal
mo.xy_scanner.Trigger_Execute_At_Target_Position(False)
mo.xy_scanner.Return_To_Stored_Position(True)
mo.xy_scanner.Store_Current_Position(False)
IO.disable_channel()
if not forward_back:
y_data = [item[0] for item in y_data]
if repeats == 1:
y_data = y_data[0]
if return_filename:
filename = f"{mo.experiment.Result_File_Path()}\\{mo.experiment.Result_File_Name()}--{view_count[0]}_{view_count[1]}.{channel_name}_mtrx"
return x_data, y_data, filename
else:
return x_data, y_data