Merge pull request #955 from annie-xd-wang/953-confocal-projection-cl…

…eanup 953 confocal projection cleanup
TheDeanLab · Aug 2, 2024 · 2ab9f22 · 2ab9f22
2 parents af1c88e + c84a735
commit 2ab9f22
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Showing 10 changed files with 5 additions and 44 deletions.
diff --git a/src/navigate/config/config.py b/src/navigate/config/config.py
@@ -519,11 +519,6 @@ def verify_experiment_config(manager, configuration):
         "end_focus": 0.0,
         "abs_z_start": 0.0,
         "abs_z_end": 100.0,
-        "scanrange": 500.0,
-        "n_plane": 1.0,
-        "offset_start": 0.0,
-        "offset_end": 9.8,
-        "conpro_cycling_mode": "per_stack",
         "waveform_template": "Default",
     }
     if (

diff --git a/src/navigate/config/experiment.yml b/src/navigate/config/experiment.yml
@@ -63,11 +63,6 @@ MicroscopeState:
   end_focus: 0.0
   abs_z_start: 0.0
   abs_z_end: 200.0
-  scanrange: 500.0
-  n_plane: 1
-  offset_start: 0.0
-  offset_end: 10.0
-  conpro_cycling_mode: Per Stack
   waveform_template: Default
 MultiPositions:
   [[15000.0,12000.0,15500.0,0.0,70000.0], [35000.0,42000.0,15500.0,0.0,70000.0]]
diff --git a/src/navigate/controller/controller.py b/src/navigate/controller/controller.py
@@ -482,8 +482,6 @@ def update_experiment_setting(self):
         channel_warning = self.channels_tab_controller.verify_experiment_values()
         if channel_warning:
             return channel_warning
-        if self.configuration["experiment"]["MicroscopeState"]["scanrange"] == 0:
-            return "Scan range shouldn't be 0!"
         return ""
 
     def resize(self, event):

diff --git a/src/navigate/controller/sub_controllers/channels_tab.py b/src/navigate/controller/sub_controllers/channels_tab.py
@@ -223,11 +223,6 @@ def populate_experiment_values(self):
             if self.microscope_state_dict["stack_cycling_mode"] == "per_z"
             else "Per Stack"
         )
-        if self.microscope_state_dict["conpro_cycling_mode"] not in [
-            "per_plane",
-            "per_stack",
-        ]:
-            self.microscope_state_dict["conpro_cycling_mode"] = "per_plane"
         self.channel_setting_controller.populate_experiment_values(
             self.microscope_state_dict["channels"]
         )

diff --git a/src/navigate/controller/sub_controllers/plugins.py b/src/navigate/controller/sub_controllers/plugins.py
@@ -156,6 +156,7 @@ def load_plugins(self):
                             f"Plugin {plugin_name} needs to be uninstalled from "
                             f"navigate or reinstalled!"
                         )
+                        continue
                     plugin_controller = getattr(
                         plugin_controller_module, f"{plugin_class_name}Controller"
                     )

diff --git a/src/navigate/model/metadata_sources/metadata.py b/src/navigate/model/metadata_sources/metadata.py
@@ -229,10 +229,7 @@ def set_stack_order_from_configuration_experiment(self) -> None:
         state = self.configuration["experiment"]["MicroscopeState"]
         self._per_stack = (
             state["stack_cycling_mode"] == "per_stack"
-            and state["image_mode"] == "z-stack"
-        ) or (
-            state["conpro_cycling_mode"] == "per_stack"
-            and state["image_mode"] == "confocal-projection"
+            and state["image_mode"] != "single"
         )
 
     @property

diff --git a/src/navigate/model/microscope.py b/src/navigate/model/microscope.py
@@ -445,14 +445,6 @@ def prepare_acquisition(self):
     def end_acquisition(self):
         """End the acquisition."""
         self.daq.stop_acquisition()
-        # set NI Galvo stage to normal stage mode
-        if (
-            self.configuration["experiment"]["MicroscopeState"]["image_mode"]
-            == "confocal-projection"
-        ):
-            for stage, _ in self.stages_list:
-                if type(stage).__name__ == "GalvoNIStage":
-                    stage.switch_mode("normal")
         self.stop_stage()
         if self.central_focus is not None:
             self.move_stage({"f_abs": self.central_focus})

diff --git a/test/config/test_config.py b/test/config/test_config.py
@@ -353,11 +353,6 @@ def setUp(self):
             "end_focus": 0.0,
             "abs_z_start": 0.0,
             "abs_z_end": 100.0,
-            "scanrange": 500.0,
-            "n_plane": 1.0,
-            "offset_start": 0.0,
-            "offset_end": 9.8,
-            "conpro_cycling_mode": "per_stack",
             "waveform_template": "Default",
         }
 
@@ -641,10 +636,6 @@ def test_load_experiment_file_with_wrong_parameter_values(self):
             "end_focus",
             "abs_z_start",
             "abs_z_end",
-            "scanrange",
-            "n_plane",
-            "offset_start",
-            "offset_end",
         ]:
             experiment["MicroscopeState"][k] = "nonsense_value"
             config.verify_experiment_config(self.manager, configuration)

diff --git a/test/config/test_experiment.py b/test/config/test_experiment.py
@@ -171,11 +171,6 @@ def test_microscope_state(self):
             "end_focus": float,
             "abs_z_start": float,
             "abs_z_end": float,
-            "scanrange": float,
-            "n_plane": int,
-            "offset_start": float,
-            "offset_end": float,
-            "conpro_cycling_mode": str,
             "waveform_template": str,
         }
 

diff --git a/test/model/metadata_sources/test_metadata.py b/test/model/metadata_sources/test_metadata.py
@@ -63,7 +63,7 @@ def test_metadata_shape(dummy_model):
     "image_mode",
     [
         "single",
-        "live",
+        "Confocal Projection",
         "z-stack",
     ],
 )
@@ -90,5 +90,7 @@ def test_metadata_set_stack_order_from_configuration_experiment(
 
     if image_mode == "z-stack" and stack_cycling_mode == "per_stack":
         assert md._per_stack is True
+    elif image_mode == "Confocal Projection" and stack_cycling_mode == "per_stack":
+        assert md._per_stack is True
     else:
         assert md._per_stack is False