Merge pull request #845 from TheDeanLab/844-automatic-galvo-frequency-estimation

844 automatic galvo frequency estimation

Author: AdvancedImagingUTSW

src/navigate/controller/sub_controllers/waveform_popup_controller.py

@@ -533,11 +533,18 @@ def update_waveform_parameters(self, *args, **wargs):
         )
 
     def estimate_galvo_setting(self, *args, **kwargs):
-        """Estimate galvo settings according to the acquisition parameters.
+        """Digitally scanned light-sheet frequency estimation.
 
-        Will only work if all channels have the same exposure duration.
-        Gets the line interval from the camera, number of pixels from the light-sheet
-        mode, and estimates the frequency as 1 / (line interval * number of pixels).
+        When imaging in a digitally scanned light-sheet mode, the galvo must
+        operate at a specific frequency, otherwise periodic lines will appear in
+        the image. This function estimates the frequency of the galvo based on the
+        line interval and the number of pixels in the light-sheet mode.
+
+        Note
+        ----
+            Will only work if all channels have the same exposure duration.
+            The framerate widget doesn't update unless you change the
+            exposure time in the channel settings. Default is 100ms.
 
         Parameters
         ----------
@@ -547,37 +554,36 @@ def estimate_galvo_setting(self, *args, **kwargs):
             The key is the name of the galvo and the value is the galvo setting.
         """
 
+        # Get the name of the galvo.
         galvo_name = args[0]
 
+        # Get the number of pixels in the light-sheet mode.
         number_of_pixels = (
             self.parent_controller.camera_setting_controller.mode_widgets[
                 "Pixels"
             ].get()
         )
+
+        # If not in the light-sheet mode, widget returns an empty string.
         if number_of_pixels == "":
-            # If we are not in the light-sheet mode, widget returns an empty string.
             return
 
-        # TODO: Worth noting that this doesn't matter because it cancels out in the
-        # frequency bit, but this is often not the right value. The framerate widget
-        # doesn't update unless you change the exposure time in the channel settings.
-        # It launches as a default of 100 ms every time.
+        # Get the exposure time. Convert to seconds.
         exposure_time = (
             self.parent_controller.camera_setting_controller.framerate_widgets[
                 "exposure_time"
             ].get()
         )
+        exposure_time = exposure_time / 1000
 
-        # The camera line interval won't be set until starting acquisition,
-        # we need to calculate it directly
-        # exposure_time and light_sheet_exposure_time are both ms
+        # Get the light sheet exposure time.
         (
-            light_sheet_exposure_time,
-            _,
+            light_sheet_exposure_time, _, _,
         ) = self.parent_controller.model.get_camera_line_interval_and_exposure_time(
             exposure_time, int(number_of_pixels) + 1
-        )  # TODO: Unclear why we need the +1. Figure out the reason.
+        )
 
+        # Calculate the frequency of the galvo.
         frequency = 2 / light_sheet_exposure_time * exposure_time
 
         # Update the GUI

test/controller/sub_controllers/test_waveform_popup_controller.py

@@ -1,5 +1,6 @@
 import pytest
 import random
+from unittest.mock import MagicMock
 
 
 @pytest.fixture(scope="module")
@@ -23,10 +24,14 @@ def waveform_popup_controller(dummy_view, dummy_controller):
 
 
 def test_populate_experiment_values(waveform_popup_controller):
-    exp_dict = waveform_popup_controller.parent_controller.configuration["experiment"]["MicroscopeState"]
+    exp_dict = waveform_popup_controller.parent_controller.configuration["experiment"][
+        "MicroscopeState"
+    ]
     resolution = exp_dict["microscope_name"]
     zoom = exp_dict["zoom"]
-    waveform_constants = waveform_popup_controller.parent_controller.configuration["waveform_constants"]
+    waveform_constants = waveform_popup_controller.parent_controller.configuration[
+        "waveform_constants"
+    ]
     widgets = waveform_popup_controller.view.get_widgets()
 
     def assert_widget_values():
@@ -36,7 +41,9 @@ def assert_widget_values():
         assert widgets["Mag"].get() == zoom
 
         # remote focus
-        remote_focus_dict = waveform_constants["remote_focus_constants"][resolution][zoom]
+        remote_focus_dict = waveform_constants["remote_focus_constants"][resolution][
+            zoom
+        ]
         for k in remote_focus_dict.keys():
             assert widgets[k + " Amp"].get() == remote_focus_dict[k]["amplitude"]
             assert widgets[k + " Off"].get() == remote_focus_dict[k]["offset"]
@@ -50,11 +57,19 @@ def assert_widget_values():
                 assert widgets[g + " Off"].get() == galvo_info["offset"]
 
         # delay, fly back time, settle duraation, smoothing
-        assert widgets["Delay"].get() == str(waveform_constants["other_constants"]["remote_focus_delay"])
-        assert widgets["Ramp_falling"].get() == str(waveform_constants["other_constants"]["remote_focus_ramp_falling"])
-        assert widgets["Duty"].get() == str(waveform_constants["other_constants"]["remote_focus_settle_duration"])
-        assert widgets["Smoothing"].get() == str(waveform_constants["other_constants"]["percent_smoothing"])
-    
+        assert widgets["Delay"].get() == str(
+            waveform_constants["other_constants"]["remote_focus_delay"]
+        )
+        assert widgets["Ramp_falling"].get() == str(
+            waveform_constants["other_constants"]["remote_focus_ramp_falling"]
+        )
+        assert widgets["Duty"].get() == str(
+            waveform_constants["other_constants"]["remote_focus_settle_duration"]
+        )
+        assert widgets["Smoothing"].get() == str(
+            waveform_constants["other_constants"]["percent_smoothing"]
+        )
+
     # default values
     waveform_popup_controller.populate_experiment_values()
     assert_widget_values()
@@ -71,7 +86,7 @@ def assert_widget_values():
     exp_dict["zoom"] = zoom
     waveform_popup_controller.populate_experiment_values()
     assert_widget_values()
-    
+
     # update waveform_constants
     for k in waveform_constants["remote_focus_constants"][resolution][zoom].keys():
         amplitude = round(random.random() * 5, 2)
@@ -88,7 +103,12 @@ def assert_widget_values():
         temp["amplitude"] = amplitude
         temp["offset"] = offset
 
-    for k in ["remote_focus_ramp_falling", "remote_focus_settle_duration", "percent_smoothing", "remote_focus_delay"]:
+    for k in [
+        "remote_focus_ramp_falling",
+        "remote_focus_settle_duration",
+        "percent_smoothing",
+        "remote_focus_delay",
+    ]:
         waveform_constants["other_constants"][k] = round(random.random() * 100, 2)
 
     waveform_popup_controller.populate_experiment_values(force_update=True)
@@ -103,3 +123,56 @@ def test_show_laser_info(waveform_popup_controller):
 def test_configure_widget_range(waveform_popup_controller):
     waveform_popup_controller.configure_widget_range()
     assert True
+
+
+def test_estimate_galvo_setting_empty_string(waveform_popup_controller):
+    """Test if the function returns without calling the camera setting controller."""
+    # Galvo name
+    galvo_name = "galvo_0"
+
+    # Mocked camera setting controller
+    waveform_popup_controller.parent_controller.camera_setting_controller = MagicMock()
+    waveform_popup_controller.parent_controller.camera_setting_controller.mode_widgets[
+        "Pixels"
+    ].get = MagicMock(return_value="")
+    waveform_popup_controller.parent_controller.camera_setting_controller.framerate_widgets[
+        "exposure_time"
+    ].get = MagicMock()
+
+    waveform_popup_controller.estimate_galvo_setting(galvo_name)
+    waveform_popup_controller.parent_controller.camera_setting_controller.framerate_widgets[
+        "exposure_time"
+    ].get.assert_not_called()
+
+
+def test_estimate_galvo_setting_with_string(waveform_popup_controller):
+    """Test if the function calls the camera setting controller."""
+    # Galvo name
+    galvo_name = "galvo_0"
+    number_of_pixels = 50
+
+    # Mocked camera setting controller
+    waveform_popup_controller.parent_controller.camera_setting_controller = MagicMock()
+    waveform_popup_controller.parent_controller.camera_setting_controller.mode_widgets[
+        "Pixels"
+    ].get = MagicMock(return_value=str(number_of_pixels))
+    waveform_popup_controller.parent_controller.camera_setting_controller.framerate_widgets[
+        "exposure_time"
+    ].get = MagicMock()
+
+    # Mocked model
+    waveform_popup_controller.parent_controller.model = MagicMock()
+    mock_model = waveform_popup_controller.parent_controller.model
+    mock_model.get_camera_line_interval_and_exposure_time = MagicMock(
+        return_value=(0.05, 50, 500)
+    )
+
+    # Mocked view
+    waveform_popup_controller.view = MagicMock()
+    waveform_popup_controller.view.inputs[galvo_name].widget.set = MagicMock()
+
+    # Call the function
+    waveform_popup_controller.estimate_galvo_setting(galvo_name)
+
+    # Check to see what the view was called with.
+    waveform_popup_controller.view.inputs[galvo_name].widget.set.assert_called_once()