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confocal projection cleanup
1 parent 2637689 commit e0ef8d9

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8 files changed

+2
-34
lines changed

8 files changed

+2
-34
lines changed

src/navigate/config/config.py

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -518,11 +518,6 @@ def verify_experiment_config(manager, configuration):
518518
"end_focus": 0.0,
519519
"abs_z_start": 0.0,
520520
"abs_z_end": 100.0,
521-
"scanrange": 500.0,
522-
"n_plane": 1.0,
523-
"offset_start": 0.0,
524-
"offset_end": 9.8,
525-
"conpro_cycling_mode": "per_stack",
526521
"waveform_template": "Default",
527522
}
528523
if (

src/navigate/config/experiment.yml

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -63,11 +63,6 @@ MicroscopeState:
6363
end_focus: 0.0
6464
abs_z_start: 0.0
6565
abs_z_end: 200.0
66-
scanrange: 500.0
67-
n_plane: 1
68-
offset_start: 0.0
69-
offset_end: 10.0
70-
conpro_cycling_mode: Per Stack
7166
waveform_template: Default
7267
MultiPositions:
7368
[[15000.0,12000.0,15500.0,0.0,70000.0], [35000.0,42000.0,15500.0,0.0,70000.0]]

src/navigate/controller/controller.py

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -482,8 +482,6 @@ def update_experiment_setting(self):
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channel_warning = self.channels_tab_controller.verify_experiment_values()
483483
if channel_warning:
484484
return channel_warning
485-
if self.configuration["experiment"]["MicroscopeState"]["scanrange"] == 0:
486-
return "Scan range shouldn't be 0!"
487485
return ""
488486

489487
def resize(self, event):

src/navigate/controller/sub_controllers/channels_tab.py

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -223,11 +223,6 @@ def populate_experiment_values(self):
223223
if self.microscope_state_dict["stack_cycling_mode"] == "per_z"
224224
else "Per Stack"
225225
)
226-
if self.microscope_state_dict["conpro_cycling_mode"] not in [
227-
"per_plane",
228-
"per_stack",
229-
]:
230-
self.microscope_state_dict["conpro_cycling_mode"] = "per_plane"
231226
self.channel_setting_controller.populate_experiment_values(
232227
self.microscope_state_dict["channels"]
233228
)

src/navigate/controller/sub_controllers/plugins.py

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -156,6 +156,7 @@ def load_plugins(self):
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f"Plugin {plugin_name} needs to be uninstalled from "
157157
f"navigate or reinstalled!"
158158
)
159+
continue
159160
plugin_controller = getattr(
160161
plugin_controller_module, f"{plugin_class_name}Controller"
161162
)

src/navigate/model/metadata_sources/metadata.py

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -229,10 +229,7 @@ def set_stack_order_from_configuration_experiment(self) -> None:
229229
state = self.configuration["experiment"]["MicroscopeState"]
230230
self._per_stack = (
231231
state["stack_cycling_mode"] == "per_stack"
232-
and state["image_mode"] == "z-stack"
233-
) or (
234-
state["conpro_cycling_mode"] == "per_stack"
235-
and state["image_mode"] == "confocal-projection"
232+
and state["image_mode"] != "single"
236233
)
237234

238235
@property

src/navigate/model/microscope.py

Lines changed: 0 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -445,14 +445,6 @@ def prepare_acquisition(self):
445445
def end_acquisition(self):
446446
"""End the acquisition."""
447447
self.daq.stop_acquisition()
448-
# set NI Galvo stage to normal stage mode
449-
if (
450-
self.configuration["experiment"]["MicroscopeState"]["image_mode"]
451-
== "confocal-projection"
452-
):
453-
for stage, _ in self.stages_list:
454-
if type(stage).__name__ == "GalvoNIStage":
455-
stage.switch_mode("normal")
456448
self.stop_stage()
457449
if self.central_focus is not None:
458450
self.move_stage({"f_abs": self.central_focus})

test/config/test_experiment.py

Lines changed: 0 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -171,11 +171,6 @@ def test_microscope_state(self):
171171
"end_focus": float,
172172
"abs_z_start": float,
173173
"abs_z_end": float,
174-
"scanrange": float,
175-
"n_plane": int,
176-
"offset_start": float,
177-
"offset_end": float,
178-
"conpro_cycling_mode": str,
179174
"waveform_template": str,
180175
}
181176

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