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Add hyperdaq hook to scanner #99

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Add hyperdaq hook to scanner #99

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686df38
adds run_scan function and data access functions
gadamc Apr 1, 2023
5af0097
Adds hyper-data acquisition function to piezoscanner.
gadamc Apr 2, 2023
71324d8
Changes internal naming.
gadamc Apr 2, 2023
c43b13c
Adds example of using confocal scan.
gadamc Apr 2, 2023
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ various spin-control experiments on quantum systems, such as NV centers in diamo
* Spin Core PulseBlaster
* Excelitas SPCM for photon detection
* NI-DAQ card (PCIx 6363) for data acquisition and control
* Jena System's Piezo Actuator Stage Control Amplifier
* Jena System's Piezo Actuator Control Amplifier
* [Future] spectrometer

The code in this package facilitates usages of these devices to perform
Expand Down
577 changes: 577 additions & 0 deletions examples/confocal-scan-random-and-hyperdaq.ipynb
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -10,7 +10,7 @@ description = "A package for performing experiments in the QT3 lab at UW."
readme = "README.md"
requires-python = ">=3.8"
license = {file = "LICENSE"}
keywords = ["qt3", "confocal scan", "nidaqmx", "piezo", "stage", "control", "electron spin control"]
keywords = ["qt3", "confocal scan", "nidaqmx", "electron spin control", "quantum computing", "nitrogen-vacancy center"]

authors = [
{name = "G. Adam Cox", email = "gadamc@gmail.com" },
Expand Down
58 changes: 26 additions & 32 deletions src/applications/piezoscan.py
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Expand Up @@ -80,18 +80,18 @@ def __init__(self, mplcolormap = 'gray'):
self.ax.set_ylabel('y position (um)')
self.log_data = False

def update(self, model):
def update(self, scanner):

if self.log_data:
data = np.log10(model.scanned_count_rate)
data = np.log10(scanner.get_count_rate())
data[np.isinf(data)] = 0 #protect against +-inf
else:
data = model.scanned_count_rate
data = scanner.get_count_rate()

self.artist = self.ax.imshow(data, cmap=self.cmap, extent=[model.xmin,
model.xmax + model.step_size,
model.current_y + model.step_size,
model.ymin])
self.artist = self.ax.imshow(data, cmap=self.cmap, extent=[scanner.xmin,
scanner.xmax + scanner.step_size,
scanner.get_current_position('y') + scanner.step_size,
scanner.ymin])
if self.cbar is None:
self.cbar = self.fig.colorbar(self.artist, ax=self.ax)
else:
Expand Down Expand Up @@ -294,8 +294,8 @@ class MainTkApplication():
def __init__(self, counter_scanner):
self.root = tk.Tk()
self.counter_scanner = counter_scanner
scan_range = [counter_scanner.stage_controller.minimum_allowed_position,
counter_scanner.stage_controller.maximum_allowed_position]
scan_range = [counter_scanner.actuator_controller.minimum_allowed_position,
counter_scanner.actuator_controller.maximum_allowed_position]
self.view = MainApplicationView(self.root, scan_range)
self.view.sidepanel.startButton.bind("<Button>", self.start_scan)
self.view.sidepanel.stopButton.bind("<Button>", self.stop_scan)
Expand All @@ -316,31 +316,31 @@ def __init__(self, counter_scanner):
self.scan_thread = None

self.optimized_position = {'x':0, 'y':0, 'z':-1}
if self.counter_scanner.stage_controller:
self.optimized_position['z'] = self.counter_scanner.stage_controller.get_current_position()[2]
if self.counter_scanner.actuator_controller:
self.optimized_position['z'] = self.counter_scanner.actuator_controller.get_current_position()[2]
else:
self.optimized_position['z'] = 20
self.view.sidepanel.z_entry_text.set(np.round(self.optimized_position['z'],4))


def run(self):
self.root.title("QT3Scan: Piezo Controlled NIDAQ Digital Count Rate Scanner")
self.root.title("QT3Scan: Piezo Control and NIDAQ Digital Signal Counter")
self.root.deiconify()
self.root.mainloop()

def go_to_position(self, event = None):
if self.counter_scanner.stage_controller:
self.counter_scanner.stage_controller.go_to_position(x = self.view.sidepanel.go_to_x_position_text.get(), y = self.view.sidepanel.go_to_y_position_text.get())
if self.counter_scanner.actuator_controller:
self.counter_scanner.actuator_controller.go_to_position(x = self.view.sidepanel.go_to_x_position_text.get(), y = self.view.sidepanel.go_to_y_position_text.get())
else:
print(f'stage_controller would have moved to x,y = {self.view.sidepanel.go_to_x_position_text.get():.2f}, {self.view.sidepanel.go_to_y_position_text.get():.2f}')
print(f'actuator_controller would have moved to x,y = {self.view.sidepanel.go_to_x_position_text.get():.2f}, {self.view.sidepanel.go_to_y_position_text.get():.2f}')
self.optimized_position['x'] = self.view.sidepanel.go_to_x_position_text.get()
self.optimized_position['y'] = self.view.sidepanel.go_to_y_position_text.get()

def go_to_z(self, event = None):
if self.counter_scanner.stage_controller:
self.counter_scanner.stage_controller.go_to_position(z = self.view.sidepanel.z_entry_text.get())
if self.counter_scanner.actuator_controller:
self.counter_scanner.actuator_controller.go_to_position(z = self.view.sidepanel.z_entry_text.get())
else:
print(f'stage_controller would have moved to z = {self.view.sidepanel.z_entry_text.get():.2f}')
print(f'actuator_controller would have moved to z = {self.view.sidepanel.z_entry_text.get():.2f}')
self.optimized_position['z'] = self.view.sidepanel.z_entry_text.get()

def set_color_map(self, event = None):
Expand Down Expand Up @@ -395,17 +395,12 @@ def scan_thread_function(self, xmin, xmax, ymin, ymax, step_size, N):
self.counter_scanner.set_num_data_samples_per_batch(N)

try:
self.counter_scanner.reset() #clears the data
self.counter_scanner.start() #starts the DAQ
self.counter_scanner.set_to_starting_position() #moves the stage to starting position

while self.counter_scanner.still_scanning():
self.counter_scanner.scan_x()
self.view.scan_view.update(self.counter_scanner)
def update_scan_view(counter_scanner):
self.view.scan_view.update(counter_scanner)
self.view.canvas.draw()
self.counter_scanner.move_y()

self.counter_scanner.stop()
self.counter_scanner.run_scan(reset_starting_position=True,
line_scan_callback=update_scan_view)

except nidaqmx.errors.DaqError as e:
logger.info(e)
Expand Down Expand Up @@ -486,7 +481,7 @@ def optimize_thread_function(self, axis, central, range, step_size):
range,
step_size)
self.optimized_position[axis] = opt_pos
self.counter_scanner.stage_controller.go_to_position(**{axis:opt_pos})
self.counter_scanner.actuator_controller.go_to_position(**{axis:opt_pos})
self.view.show_optimization_plot(f'Optimize {axis}',
central,
self.optimized_position[axis],
Expand All @@ -499,7 +494,6 @@ def optimize_thread_function(self, axis, central, range, step_size):
logger.info(e)
logger.info('Check for other applications using resources. If not, you may need to restart the application.')


self.view.sidepanel.startButton['state'] = 'normal'
self.view.sidepanel.stopButton['state'] = 'normal'
self.view.sidepanel.go_to_z_button['state'] = 'normal'
Expand Down Expand Up @@ -545,11 +539,11 @@ def on_closing(self):

def build_data_scanner():
if args.randomtest:
stage_controller = nipiezojenapy.BaseControl()
actuator_controller = nipiezojenapy.BaseControl()
data_acq = datasources.RandomRateCounter(simulate_single_light_source=True,
num_data_samples_per_batch=args.num_data_samples_per_batch)
else:
stage_controller = nipiezojenapy.PiezoControl(device_name = args.daq_name,
actuator_controller = nipiezojenapy.PiezoControl(device_name = args.daq_name,
write_channels = args.piezo_write_channels.split(','),
read_channels = args.piezo_read_channels.split(','))

Expand All @@ -561,7 +555,7 @@ def build_data_scanner():
args.rwtimeout,
args.signal_counter)

scanner = datasources.CounterAndScanner(data_acq, stage_controller)
scanner = datasources.CounterAndScanner(data_acq, actuator_controller)

return scanner

Expand Down
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