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Add dither support to remote focus waveforms #1205

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Add dither support to remote focus waveforms #1205

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8 changes: 6 additions & 2 deletions src/navigate/config/config.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -744,8 +744,10 @@ def verify_waveform_constants(manager, configuration):
waveform_dict[microscope_name][zoom],
laser,
{
"amplitude": 0,
"offset": 0,
"amplitude": "0",
"offset": "0",
"dither_amplitude": "0",
"dither_frequency": "0",
# "percent_smoothing": "0",
# "delay": config_dict["remote_focus"][
# "delay"
Expand All @@ -756,6 +758,8 @@ def verify_waveform_constants(manager, configuration):
for k in [
"amplitude",
"offset",
"dither_amplitude",
"dither_frequency",
# "percent_smoothing",
# "delay",
]:
Expand Down
48 changes: 48 additions & 0 deletions src/navigate/config/waveform_constants.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,18 +5,24 @@
"488nm": {
"amplitude": "0.11",
"offset": "0.10",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"562nm": {
"amplitude": "0.115",
"offset": "0.062",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"642nm": {
"amplitude": "0",
"offset": "0",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
}
Expand All @@ -27,18 +33,24 @@
"488nm": {
"amplitude": "2.5",
"offset": "2.336",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"562nm": {
"amplitude": "2.5",
"offset": "2.336",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"642nm": {
"amplitude": "2.5",
"offset": "2.336",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
}
Expand All @@ -47,18 +59,24 @@
"488nm": {
"amplitude": "1",
"offset": "2.60",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"562nm": {
"amplitude": "0.53",
"offset": "2.46",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"642nm": {
"amplitude": "0.23",
"offset": "2.50",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
}
Expand All @@ -67,18 +85,24 @@
"488nm": {
"amplitude": "0.20",
"offset": "2.52",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"562nm": {
"amplitude": "0.466",
"offset": "1.534",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"642nm": {
"amplitude": "0.20",
"offset": "2.53",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
}
Expand All @@ -87,18 +111,24 @@
"488nm": {
"amplitude": "1",
"offset": "2.60",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"562nm": {
"amplitude": "0.15",
"offset": "2.50",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"642nm": {
"amplitude": "0.16",
"offset": "2.50",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
}
Expand All @@ -107,18 +137,24 @@
"488nm": {
"amplitude": "0.141",
"offset": "2.392",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"562nm": {
"amplitude": "0.141",
"offset": "2.392",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"642nm": {
"amplitude": "0.141",
"offset": "2.392",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
}
Expand All @@ -127,18 +163,24 @@
"488nm": {
"amplitude": "0.141",
"offset": "2.392",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"562nm": {
"amplitude": "0.141",
"offset": "2.392",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"642nm": {
"amplitude": "0.141",
"offset": "2.392",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
}
Expand All @@ -147,18 +189,24 @@
"488nm": {
"amplitude": "0.15",
"offset": "2.52",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"562nm": {
"amplitude": "0.15",
"offset": "2.51",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
},
"642nm": {
"amplitude": "0.15",
"offset": "2.51",
"dither_amplitude": "0",
"dither_frequency": "0",
"percent_smoothing": "0",
"percent_delay": "0"
}
Expand Down
96 changes: 82 additions & 14 deletions src/navigate/controller/sub_controllers/waveform_popup.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -126,6 +126,9 @@ def __init__(
#: float: the maximum value of remote focus device
self.laser_max = 1.0

#: float: the maximum dither amplitude for the remote focus device.
self.dither_amplitude_max = 1.0

#: dict: Dictionary of galvo minimum values
self.galvo_min = {}

Expand Down Expand Up @@ -154,6 +157,18 @@ def __init__(
"write",
self.update_remote_focus_settings(laser + " Off", laser, "offset"),
)
self.variables[laser + " Dither Amp"].trace_add(
"write",
self.update_remote_focus_settings(
laser + " Dither Amp", laser, "dither_amplitude"
),
)
self.variables[laser + " Dither Freq"].trace_add(
"write",
self.update_remote_focus_settings(
laser + " Dither Freq", laser, "dither_frequency"
),
)

# Changes to the galvo constants (amplitude, offset, etc.)
for i in range(self.configuration_controller.galvo_num):
Expand Down Expand Up @@ -246,6 +261,13 @@ def configure_widget_range(self) -> None:
self.laser_max = self.configuration_controller.remote_focus_dict["hardware"][
"max"
]
self.dither_amplitude_max = max(abs(self.laser_min), abs(self.laser_max))
dither_frequency_max = (
self.parent_controller.configuration["configuration"]["microscopes"][
self.resolution
]["daq"]["sample_rate"]
/ 2
)

precision = int(
self.configuration_controller.remote_focus_dict["hardware"].get(
Expand Down Expand Up @@ -280,6 +302,26 @@ def configure_widget_range(self) -> None:
self.widgets[laser + " Off"].widget.set_precision(precision)
self.widgets[laser + " Off"].widget.trigger_focusout_validation()

self.widgets[laser + " Dither Amp"].widget.configure(from_=0)
self.widgets[laser + " Dither Amp"].widget.configure(
to=self.dither_amplitude_max
)
self.widgets[laser + " Dither Amp"].widget.configure(
increment=self.increment
)
self.widgets[laser + " Dither Amp"].widget.set_precision(precision)
self.widgets[laser + " Dither Amp"].widget.trigger_focusout_validation()

self.widgets[laser + " Dither Freq"].widget.configure(from_=0)
self.widgets[laser + " Dither Freq"].widget.configure(
to=dither_frequency_max
)
self.widgets[laser + " Dither Freq"].widget.configure(
increment=max(self.increment, 0.1)
)
self.widgets[laser + " Dither Freq"].widget.set_precision(precision)
self.widgets[laser + " Dither Freq"].widget.trigger_focusout_validation()

for galvo, d in zip(self.galvos, self.galvo_dict):
galvo_min = d["hardware"]["min"]
galvo_max = d["hardware"]["max"]
Expand Down Expand Up @@ -398,15 +440,20 @@ def show_laser_info(self, *args: tuple) -> None:
# get magnification setting
self.mag = self.widgets["Mag"].widget.get()
for laser in self.lasers:
remote_focus_settings = self.resolution_info["remote_focus_constants"][
self.resolution
][self.mag][laser]
self.variables[laser + " Amp"].set(
self.resolution_info["remote_focus_constants"][self.resolution][
self.mag
][laser]["amplitude"]
remote_focus_settings.get("amplitude", 0)
)
self.variables[laser + " Off"].set(
self.resolution_info["remote_focus_constants"][self.resolution][
self.mag
][laser]["offset"]
remote_focus_settings.get("offset", 0)
)
self.variables[laser + " Dither Amp"].set(
remote_focus_settings.get("dither_amplitude", 0)
)
self.variables[laser + " Dither Freq"].set(
remote_focus_settings.get("dither_frequency", 0)
)

# do not tell the model to update galvo
Expand Down Expand Up @@ -496,9 +543,12 @@ def update_remote_focus_settings(
# and when changing magnification it will run 0.63x
# before whatever mag is selected
def func_laser(*args):
value = self.resolution_info["remote_focus_constants"][self.resolution][
self.mag
][laser][remote_focus_name]
remote_focus_settings = self.resolution_info["remote_focus_constants"][
self.resolution
][self.mag][laser]
value = remote_focus_settings.get(remote_focus_name, "0")
if remote_focus_name not in remote_focus_settings:
remote_focus_settings[remote_focus_name] = value

# Will only run code if value in constants does not match whats in GUI
# for Amp or Off AND in Live mode
Expand All @@ -517,13 +567,20 @@ def func_laser(*args):
value = float(variable_value)
except ValueError:
return
if value < self.laser_min or value > self.laser_max:
min_value = self.laser_min
max_value = self.laser_max
if remote_focus_name == "dither_amplitude":
min_value = 0
max_value = self.dither_amplitude_max
elif remote_focus_name == "dither_frequency":
min_value = 0
max_value = None

if value < min_value or (max_value is not None and value > max_value):
return
self.resolution_info["remote_focus_constants"][self.resolution][
self.mag
][laser][remote_focus_name] = variable_value
remote_focus_settings[remote_focus_name] = variable_value
logger.debug(
f"Remote Focus Amplitude/Offset Changed:, {variable_value}"
f"Remote Focus {remote_focus_name} Changed:, {variable_value}"
)

# Delay feature.
Expand Down Expand Up @@ -749,8 +806,14 @@ def toggle_waveform_state(self):
self.amplitude_dict[laser] = self.resolution_info[
"remote_focus_constants"
][self.resolution][self.mag][laser]["amplitude"]
self.amplitude_dict[laser + " dither"] = self.resolution_info[
"remote_focus_constants"
][self.resolution][self.mag][laser].get("dither_amplitude", 0)
self.variables[laser + " Amp"].set(0)
self.variables[laser + " Dither Amp"].set(0)
self.widgets[laser + " Amp"].widget.config(state="disabled")
self.widgets[laser + " Dither Amp"].widget.config(state="disabled")
self.widgets[laser + " Dither Freq"].widget.config(state="disabled")

for galvo in self.galvos:
self.amplitude_dict[galvo] = self.resolution_info["galvo_constants"][
Expand Down Expand Up @@ -800,7 +863,12 @@ def restore_amplitude(self) -> None:
self.resolution_info["remote_focus_constants"][resolution][mag][laser][
"amplitude"
] = self.amplitude_dict[laser]
self.resolution_info["remote_focus_constants"][resolution][mag][laser][
"dither_amplitude"
] = self.amplitude_dict[laser + " dither"]
self.widgets[laser + " Amp"].widget.config(state="normal")
self.widgets[laser + " Dither Amp"].widget.config(state="normal")
self.widgets[laser + " Dither Freq"].widget.config(state="normal")
for galvo in self.galvos:
self.resolution_info["galvo_constants"][galvo][resolution][mag][
"amplitude"
Expand Down
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