Merge pull request #1030 from annie-xd-wang/speed-up-loading-multi-po…

…sitions

Speed up loading multi-positions

docs/source/contributing/feature_container.rst

@@ -253,7 +253,7 @@ To create a customized feature list, follow these steps:
                 {"name": PrepareNextChannel},
                 {
                     "name": LoopByCount,
-                    "args": ("experiment.MicroscopeState.selected_channels",),
+                    "args": ("channels",),
                 },
             )
         ]

docs/source/user_guide/acquiring_guide.rst

@@ -42,7 +42,7 @@ a :doc:`feature list <features>`, shown in its
         {"name": PrepareNextChannel},
         {
             "name": LoopByCount,
-            "args": ("experiment.MicroscopeState.selected_channels",),
+            "args": ("channels",),
         },
       )
     ]

docs/source/user_guide/features/example_feature_lists.rst

@@ -30,7 +30,7 @@ prior to moving to the next position in the multi-position table.
             {"name": CalculateFocusRange,},
             {"name": ZStackAcquisition,"args": (True,True,"z-stack",),},
             {"name": WaitToContinue,},
-            {"name": LoopByCount,"args": ("experiment.MicroscopeState.multiposition_count",),},
+            {"name": LoopByCount,"args": ("positions",),},
         ),
     ]
 

src/navigate/config/config.py

@@ -108,6 +108,7 @@ def get_configuration_paths():
         "rest_api_config.yml",
         "waveform_templates.yml",
         "gui_configuration.yml",
+        "multi_positions.yml"
     ]
 
     base_directory = Path(__file__).resolve().parent
@@ -520,8 +521,6 @@ def verify_experiment_config(manager, configuration):
         "timepoint_interval": 0,
         "experiment_duration": 1.03,
         "is_multiposition": False,
-        "multiposition_count": 1,
-        "selected_channels": 0,
         "stack_z_origin": 0,
         "stack_focus_origin": 0,
         "start_focus": 0.0,
@@ -654,31 +653,6 @@ def verify_experiment_config(manager, configuration):
             if channel_value[k] < 0:
                 channel_value[k] = temp[k]
 
-    microscope_setting_dict["selected_channels"] = selected_channel_num
-
-    # MultiPositions
-    if (
-        "MultiPositions" not in configuration["experiment"]
-        or type(configuration["experiment"]["MultiPositions"]) is not ListProxy
-    ):
-        update_config_dict(manager, configuration["experiment"], "MultiPositions", [])
-    position_ids = []
-    multipositions = configuration["experiment"]["MultiPositions"]
-    for i, position in enumerate(multipositions):
-        try:
-            for j in range(5):
-                float(position[j])
-        except (ValueError, KeyError):
-            position_ids.append(i)
-
-    for idx in position_ids[::-1]:
-        del multipositions[idx]
-    if len(multipositions) < 1:
-        multipositions.append([10.0, 10.0, 10.0, 10.0, 10.0])
-
-    microscope_setting_dict["multiposition_count"] = len(multipositions)
-
-
 def verify_waveform_constants(manager, configuration):
     """Verifies and updates the waveform constants in the configuration dictionary.
 
@@ -1119,3 +1093,18 @@ def verify_configuration(manager, configuration):
         "gui",
         {"channels": {"count": channel_count}},
     )
+
+def verify_positions_config(positions):
+    if positions is None or type(positions) not in (list, ListProxy):
+        return []
+    # MultiPositions
+    position_num = len(positions)
+    for i in range(position_num-1, -1, -1):
+        position = positions[i]
+        try:
+            for j in range(5):
+                float(position[j])
+        except (ValueError, KeyError, IndexError):
+            del positions[i]
+
+    return positions

src/navigate/config/experiment.yml

@@ -54,8 +54,6 @@ MicroscopeState:
   timepoint_interval: 0
   experiment_duration: 600.0899999999995
   is_multiposition: False
-  multiposition_count: 2
-  selected_channels: 3
   channels: {'channel_1': {'is_selected': True, 'laser': '488nm', 'laser_index': 0, 'filter': 'GFP - FF01-515/30-32', 'filter_position': 1, 'camera_exposure_time': 200.0, 'laser_power': '20', 'interval_time': '1', 'defocus': 100.0}, 'channel_2': {'is_selected': True, 'laser': '562nm', 'laser_index': 1, 'filter': 'RFP - FF01-595/31-32', 'filter_position': 2, 'camera_exposure_time': 200.0, 'laser_power': '20', 'interval_time': '1', 'defocus': 200.0}, 'channel_3': {'is_selected': True, 'laser': '642nm', 'laser_index': 2, 'filter': 'Far-Red - BLP01-647R/31-32', 'filter_position': 3, 'camera_exposure_time': 200.0, 'laser_power': '20', 'interval_time': '1', 'defocus': 0.0}}
   stack_z_origin: 0.0
   stack_focus_origin: 0.0

src/navigate/config/multi_positions.yml

@@ -0,0 +1 @@
+[[0, 0, 0, 0, 0]]

src/navigate/controller/controller.py

@@ -80,10 +80,16 @@
     update_config_dict,
     verify_experiment_config,
     verify_waveform_constants,
+    verify_positions_config,
     verify_configuration,
     get_navigate_path,
 )
-from navigate.tools.file_functions import create_save_path, save_yaml_file, get_ram_info
+from navigate.tools.file_functions import (
+    create_save_path,
+    load_yaml_file,
+    save_yaml_file,
+    get_ram_info,
+)
 from navigate.tools.common_dict_tools import update_stage_dict
 from navigate.tools.multipos_table_tools import update_table
 from navigate.tools.common_functions import combine_funcs
@@ -108,6 +114,7 @@ def __init__(
         rest_api_path,
         waveform_templates_path,
         gui_configuration_path,
+        multi_positions_path,
         args,
     ):
         """Initialize the Navigate Controller.
@@ -198,6 +205,10 @@ def __init__(
         verify_experiment_config(self.manager, self.configuration)
         verify_waveform_constants(self.manager, self.configuration)
 
+        positions = load_yaml_file(multi_positions_path)
+        positions = verify_positions_config(positions)
+        self.configuration["multi_positions"] = positions
+
         total_ram, available_ram = get_ram_info()
         logger.info(
             f"Total RAM: {total_ram / 1024**3:.2f} GB. "
@@ -460,7 +471,7 @@ def populate_experiment_setting(self, file_name=None, in_initialize=False):
         self.acquire_bar_controller.populate_experiment_values()
         # self.stage_controller.populate_experiment_values()
         self.multiposition_tab_controller.set_positions(
-            self.configuration["experiment"]["MultiPositions"]
+            self.configuration["multi_positions"]
         )
         self.channels_tab_controller.populate_experiment_values()
         self.camera_setting_controller.populate_experiment_values()
@@ -510,10 +521,7 @@ def update_experiment_setting(self):
 
         # update multi-positions
         positions = self.multiposition_tab_controller.get_positions()
-        self.configuration["experiment"]["MultiPositions"] = positions
-        self.configuration["experiment"]["MicroscopeState"][
-            "multiposition_count"
-        ] = len(positions)
+        self.configuration["multi_positions"] = positions
 
         if (
             self.configuration["experiment"]["MicroscopeState"]["is_multiposition"]
@@ -848,6 +856,13 @@ def execute(self, command, *args):
                 filename="waveform_constants.yml",
             )
 
+            # Save multi_positions.yml file
+            save_yaml_file(
+                file_directory=file_directory,
+                content_dict=self.configuration["multi_positions"],
+                filename="multi_positions.yml",
+            )
+
             self.camera_setting_controller.solvent = self.configuration["experiment"][
                 "Saving"
             ]["solvent"]
@@ -952,6 +967,12 @@ def execute(self, command, *args):
                 content_dict=self.configuration["experiment"],
                 filename="experiment.yml",
             )
+            save_yaml_file(
+                file_directory=file_directory,
+                content_dict=self.configuration["multi_positions"],
+                filename="multi_positions.yml",
+            )
+
             if hasattr(self, "waveform_popup_controller"):
                 self.waveform_popup_controller.save_waveform_constants()
 

src/navigate/controller/sub_controllers/acquire_bar.py

@@ -147,7 +147,7 @@ def progress_bar(
             number_of_positions = 1
         else:
             number_of_positions = len(
-                self.parent_controller.configuration["experiment"]["MultiPositions"]
+                self.parent_controller.configuration["multi_positions"]
             )
 
         if mode == "single":

src/navigate/controller/sub_controllers/camera_view.py

@@ -526,8 +526,8 @@ def initialize_non_live_display(self, microscope_state, camera_parameters):
         self.slice_index = 0
         self.image_mode = microscope_state["image_mode"]
         self.stack_cycling_mode = microscope_state["stack_cycling_mode"]
-        self.number_of_channels = int(microscope_state["selected_channels"])
         self.get_selected_channels(microscope_state)
+        self.number_of_channels = len(self.selected_channels)
         self.number_of_slices = int(microscope_state["number_z_steps"])
         self.total_images_per_volume = self.number_of_channels * self.number_of_slices
         self.original_image_width = int(camera_parameters["img_x_pixels"])
@@ -1169,8 +1169,7 @@ def slider_update(self, *_):
 
         slider_index = self.view.slider.get()
         channel_index = self.view.live_frame.channel.get()
-        channel_index = channel_index[-1]
-        channel_index = int(channel_index) - 1
+        channel_index = self.selected_channels.index(channel_index)
         image = self.spooled_images.load_image(
             channel=channel_index, slice_index=slider_index
         )

src/navigate/controller/sub_controllers/channels_tab.py

@@ -32,7 +32,6 @@
 
 # Standard Library Imports
 import logging
-from functools import reduce
 import datetime
 
 # Third Party Imports
@@ -773,12 +772,6 @@ def execute(self, command, *args):
             Returns parent_controller.execute(command) if command = 'get_stage_position'
         """
         if command == "recalculate_timepoint":
-            # update selected channels num
-            self.microscope_state_dict["selected_channels"] = reduce(
-                lambda count, channel: count + (channel["is_selected"] is True),
-                self.microscope_state_dict["channels"].values(),
-                0,
-            )
             self.update_timepoint_setting()
             # update framerate info in camera setting tab
             exposure_time = max(

src/navigate/controller/sub_controllers/multiposition.py

@@ -100,7 +100,12 @@ def set_positions(self, positions):
         """
         axis_dict = {"x": "X", "y": "Y", "z": "Z", "theta": "R", "f": "F"}
         data = {}
-
+        if len(positions) == 0:
+            # add current stage position to the table
+            stage_position = self.parent_controller.configuration["experiment"][
+                "StageParameters"
+            ]
+            positions = [[stage_position[axis] for axis in axis_dict.keys()]]
         for i, name in enumerate(axis_dict.keys()):
             data[axis_dict[name]] = list(pos[i] for pos in positions)
         self.table.model.df = pd.DataFrame(data)

src/navigate/main.py

@@ -103,6 +103,7 @@ def main():
         logging_path,
         configurator,
         gui_configuration_path,
+        multi_positions_path,
     ) = evaluate_parser_input_arguments(args)
 
     log_setup("logging.yml", logging_path)
@@ -119,6 +120,7 @@ def main():
             rest_api_path,
             waveform_templates_path,
             gui_configuration_path,
+            multi_positions_path,
             args,
         )