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Stage limits popup #1116

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Merged
merged 10 commits into from
Jul 30, 2025
Merged

Stage limits popup #1116

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504fa1b
Adding stage limits popup
AdvancedImagingUTSW Jul 19, 2025
fb95e5b
Stage Limits Controller
AdvancedImagingUTSW Jul 20, 2025
7972029
Sync stage limits state between menu and popup
AdvancedImagingUTSW Jul 21, 2025
4558824
Refactor stage limits to advanced stage parameters
AdvancedImagingUTSW Jul 21, 2025
922c70f
Add NI galvo stage support and flip flags to stage config
AdvancedImagingUTSW Jul 21, 2025
73495cc
Refactor advanced stage parameters popup and controller
AdvancedImagingUTSW Jul 24, 2025
b06905a
Finally...
AdvancedImagingUTSW Jul 25, 2025
d9c0ed4
Add stage offsets to advanced stage parameters
AdvancedImagingUTSW Jul 25, 2025
b6699bc
feat: add function to write to standard YAML file
annie-xd-wang Jul 30, 2025
18616f3
save configuration in standard yaml format
annie-xd-wang Jul 30, 2025
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38 changes: 15 additions & 23 deletions src/navigate/config/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -208,8 +208,7 @@ def update_config_dict(
config_name : str
Name of dictionary to replace
new_config : dict or str
Dictionary values or
yaml file name
Dictionary values or yaml file name

Returns
-------
Expand Down Expand Up @@ -751,16 +750,16 @@ def verify_waveform_constants(manager, configuration):
# "delay",
]:
if k not in waveform_dict[microscope_name][zoom][laser].keys():
waveform_dict[microscope_name][zoom][laser][
k
] = config_dict["remote_focus"].get(k, "0")
waveform_dict[microscope_name][zoom][laser][k] = (
config_dict["remote_focus"].get(k, "0")
)
else:
try:
float(waveform_dict[microscope_name][zoom][laser][k])
except ValueError:
waveform_dict[microscope_name][zoom][laser][
k
] = config_dict["remote_focus"].get(k, "0")
waveform_dict[microscope_name][zoom][laser][k] = (
config_dict["remote_focus"].get(k, "0")
)

# delete non-exist lasers
for k in waveform_dict[microscope_name][zoom].keys():
Expand Down Expand Up @@ -1004,24 +1003,16 @@ def verify_configuration(manager, configuration):
laser_hardware_config = {"type": "Synthetic"}
laser_hardware_config["wavelength"] = laser_config["wavelength"]

update_config_dict(
manager,
laser_config,
"hardware",
laser_hardware_config
)
update_config_dict(manager, laser_config, "hardware", laser_hardware_config)

# zoom
zoom_config = device_config[microscope_name]["zoom"]
if "hardware" not in zoom_config:
update_config_dict(
manager,
zoom_config,
"hardware",
{"type": "Synthetic", "servo_id": 0}
manager, zoom_config, "hardware", {"type": "Synthetic", "servo_id": 0}
)
elif "type" not in zoom_config["hardware"]:
zoom_config["hardware"]["type"] = "Synthetic"
zoom_config["hardware"]["type"] = "Synthetic"

filter_wheel_config = device_config[microscope_name]["filter_wheel"]
if type(filter_wheel_config) == DictProxy:
Expand All @@ -1034,7 +1025,6 @@ def verify_configuration(manager, configuration):
[filter_wheel_config],
)


temp_config = device_config[microscope_name]["filter_wheel"]
for _, filter_wheel_config in enumerate(temp_config):
filter_wheel_idx = build_ref_name(
Expand Down Expand Up @@ -1091,7 +1081,7 @@ def verify_positions_config(positions):
return []

position_num = len(positions)
for i in range(position_num - 1, start_index-1, -1):
for i in range(position_num - 1, start_index - 1, -1):
position = positions[i]
try:
for j in range(len(position)):
Expand All @@ -1101,6 +1091,7 @@ def verify_positions_config(positions):

return positions


def support_deceased_configuration(configuration):
"""Support old version of configurations.

Expand All @@ -1120,7 +1111,9 @@ def support_deceased_configuration(configuration):
for microscope_name in device_config.keys():
microscope_config = device_config[microscope_name]
if "remote_focus_device" in microscope_config.keys():
microscope_config["remote_focus"] = microscope_config.pop("remote_focus_device")
microscope_config["remote_focus"] = microscope_config.pop(
"remote_focus_device"
)
is_updated = True
if "lasers" in microscope_config.keys():
microscope_config["laser"] = microscope_config.pop("lasers")
Expand All @@ -1136,4 +1129,3 @@ def support_deceased_configuration(configuration):
if stage["type"] in deceased_device_type_names:
stage["type"] = deceased_device_type_names[stage["type"]]
is_updated = True

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