Merge pull request #900 from annie-xd-wang/fix-multiposition-table-error

docs/source/user_guide/setup_microscope.rst

@@ -6,5 +6,4 @@ Setting Up A Microscope
    :maxdepth: 2
 
    software_configuration
-   hardware/hardware_home
    multiple_cameras

src/navigate/controller/controller.py

@@ -1213,7 +1213,7 @@ def update_event(self):
             elif event == "multiposition":
                 # Update the multi-position tab without appending to the list
                 update_table(
-                    table=self.view.settings.multiposition_tab.multipoint_list.get_table(),
+                    table=self.multiposition_tab_controller.table,
                     pos=value,
                 )
                 self.channels_tab_controller.is_multiposition_val.set(True)

src/navigate/controller/sub_controllers/acquire_bar_controller.py

@@ -246,6 +246,9 @@ def set_mode(self, mode):
             mode = list(reverse_dict.keys())[0]
         self.mode = mode
         self.view.pull_down.set(reverse_dict[mode])
+        self.parent_controller.configuration["experiment"]["MicroscopeState"][
+            "image_mode"
+        ] = mode
         self.show_verbose_info("Image mode is set to", mode)
 
     def get_mode(self):

src/navigate/controller/sub_controllers/camera_view_controller.py

@@ -455,8 +455,8 @@ def mark_position(self):
             stage_flip_flags = (
                 self.parent_controller.configuration_controller.stage_flip_flags
             )
-            stage_position["x"] += offset_x * (-1 if stage_flip_flags["x"] else 1)
-            stage_position["y"] -= offset_y * (-1 if stage_flip_flags["y"] else 1)
+            stage_position["x"] = float(stage_position["x"]) + offset_x * (-1 if stage_flip_flags["x"] else 1)
+            stage_position["y"] = float(stage_position["y"]) - offset_y * (-1 if stage_flip_flags["y"] else 1)
 
             # Place the stage position in the multi-position table.
             self.parent_controller.execute("mark_position", stage_position)

src/navigate/controller/sub_controllers/multi_position_controller.py

@@ -134,7 +134,7 @@ def get_positions(self):
             temp = list(self.table.model.df.iloc[i])
             if (
                 len(
-                    list(filter(lambda v: type(v) == float and not math.isnan(v), temp))
+                    list(filter(lambda v: type(v) in (float, int) and not math.isnan(v), temp))
                 )
                 == 5
             ):
@@ -211,12 +211,10 @@ def load_positions(self):
             )
             logger.info("The csv file isn't right, it should contain [X, Y, Z, R, F]")
             return
-        model = TableModel(dataframe=df)
-        self.table.updateModel(model)
-        try:
-            self.table.redraw()
-        except KeyError:
-            pass
+        self.table.model.df = df
+        self.table.update_rowcolors()
+        self.table.redraw()
+        self.table.tableChanged()
         self.show_verbose_info("loaded csv file", filename)
 
     def export_positions(self):

src/navigate/controller/sub_controllers/stage_controller.py

@@ -359,7 +359,7 @@ def get_position(self):
         position = {}
         try:
             for axis in ["x", "y", "z", "theta", "f"]:
-                position[axis] = self.widget_vals[axis].get()
+                position[axis] = float(self.widget_vals[axis].get())
                 if self.stage_limits is True:
                     if (
                         position[axis] < self.position_min[axis]
@@ -554,6 +554,9 @@ def position_callback(self, axis, *args, **kwargs):
 
         def handler(*args):
             """Callback functions bind to position variables."""
+            # check if focus on another window
+            if not self.view.focus_get():
+                return
             if self.event_id[axis]:
                 self.view.after_cancel(self.event_id[axis])
             # if position is not a number, then do not move stage

src/navigate/model/devices/stages/stage_pi.py

@@ -249,7 +249,6 @@ def move_absolute(self, move_dictionary, wait_until_done=False):
 
         if wait_until_done is True:
             return self.wait_on_target(axes=list(pos_dict.keys()))
-
         return True
 
     def stop(self):
@@ -274,7 +273,7 @@ def wait_on_target(self, axes=None):
         """
         try:
             self.pi_tools.waitontarget(
-                self.pi_device, axes=axes, timeout=1.75, polldelay=0.01
+                self.pi_device, axes=axes, timeout=10.75, polldelay=0.01
             )
         except GCSError as e:
             print("Wait on target failed")

src/navigate/model/microscope.py

@@ -371,6 +371,8 @@ def move_stage_offset(self, former_microscope=None):
         # print(self.stages)
         pos_dict = self.get_stage_position()
         for stage, axes in self.stages_list:
+
+            # x_abs: current x_pos + current_x_offset - former_x_offset
             pos = {
                 axis
                 + "_abs": (

test/controller/sub_controllers/test_acquire_bar_controller.py

@@ -236,6 +236,9 @@ def test_get_set_mode(self, mode):
         self.acquire_bar_controller.set_mode(mode)
         test = self.acquire_bar_controller.get_mode()
         assert test == mode, "Mode not set correctly"
+        # assert imaging mode is updated in the experiment
+        assert self.acquire_bar_controller.parent_controller.configuration[
+                "experiment"]["MicroscopeState"]["image_mode"] == mode
 
     def test_set_save(self):
         """Tests the set_save method of the AcquireBarController class
@@ -298,7 +301,7 @@ def test_update_microscope_mode(self, user_mode, expected_mode):
             the AcquireBarController class is not correct
         """
         # Assuming mode starts on live
-        assert self.acquire_bar_controller.mode == "live"
+        self.acquire_bar_controller.mode = "live"
 
         # Setting to mode specified by user
         self.acquire_bar_controller.view.pull_down.set(user_mode)
@@ -310,6 +313,8 @@ def test_update_microscope_mode(self, user_mode, expected_mode):
 
         # Checking that new mode gets set by function
         assert self.acquire_bar_controller.mode == expected_mode
+        assert self.acquire_bar_controller.parent_controller.configuration[
+                "experiment"]["MicroscopeState"]["image_mode"] == expected_mode
 
         # Resetting to live
         self.acquire_bar_controller.view.pull_down.set("Continuous Scan")

test/controller/test_controller.py

@@ -51,7 +51,8 @@ def controller(tk_root):
     )
     # To make sure the testcases won't hang on because of the model.event_queue
     # The changes here won't affect other testcases,
-    # because the testcases from other files use DummyController and DummyModel instead of this controller fixture
+    # because the testcases from other files use DummyController
+    # and DummyModel instead of this controller fixture
     controller.model = MagicMock()
     controller.model.get_offset_variance_maps.return_value = (None, None)
 
@@ -69,18 +70,98 @@ def test_update_buffer(controller):
     assert controller.img_width == camera_parameters["img_x_pixels"]
     assert controller.img_height == camera_parameters["img_y_pixels"]
 
+    # Make sure that the get_data_buffer method is not called.
+    assert controller.model.get_data_buffer.called is False
+
+    # Change the buffer size
+    controller.configuration["experiment"]["CameraParameters"]["img_x_pixels"] = 100
+    controller.configuration["experiment"]["CameraParameters"]["img_y_pixels"] = 100
+    controller.update_buffer()
+
+    # Make sure that the get_data_buffer method is called.
+    assert controller.model.get_data_buffer.called is True
+
+    # Confirm that the buffer size has been updated.
+    assert controller.img_width == 100
+    assert controller.img_height == 100
+
 
 def test_change_microscope(controller):
+    # Get the microscopes from the configuration file
     microscopes = controller.configuration["configuration"]["microscopes"]
+
+    # Iterate through the microscopes and change the microscope
     for microscope_name in microscopes.keys():
+
+        # Patch the configuration_controller
+        controller.configuration_controller.change_microscope = MagicMock()
+
+        # Default zoom is '0.63x'
         zoom = microscopes[microscope_name]["zoom"]["position"].keys()[0]
         controller.configuration["experiment"]["MicroscopeState"]["zoom"] = zoom
+
+        # Change the microscope without passing the zoom
         controller.change_microscope(microscope_name)
         assert (
             controller.configuration["experiment"]["MicroscopeState"]["microscope_name"]
             == microscope_name
         )
 
+        # Confirm that the zoom has not changed.
+        assert controller.configuration["experiment"]["MicroscopeState"]["zoom"] == zoom
+
+        # Call it and pass the zoom
+        zoom = microscopes[microscope_name]["zoom"]["position"].keys()[-1]
+        controller.change_microscope(microscope_name, zoom)
+        assert controller.configuration["experiment"]["MicroscopeState"]["zoom"] == zoom
+
+        # Make sure that the configuration_controller has been called.
+        assert controller.configuration_controller.change_microscope.called is True
+
+        # Have configuration controller return False
+        controller.configuration_controller.change_microscope.return_value = False
+
+        # Patch the stage controller, channels_tab_controller...
+        controller.stage_controller.initialize = MagicMock()
+        controller.channels_tab_controller.initialize = MagicMock()
+        camera_setting_controller = controller.camera_setting_controller
+        camera_setting_controller.update_camera_device_related_setting = MagicMock()
+        camera_setting_controller.calculate_physical_dimensions = MagicMock()
+        controller.camera_view_controller.update_snr = MagicMock()
+
+        # Call change microscope, assert patched methods are not called
+        controller.change_microscope(microscope_name)
+        assert controller.stage_controller.initialize.called is False
+        assert controller.channels_tab_controller.initialize.called is False
+        assert (
+            camera_setting_controller.update_camera_device_related_setting.called
+            is False
+        )
+        assert camera_setting_controller.calculate_physical_dimensions.called is False
+        assert controller.camera_view_controller.update_snr.called is False
+
+        # Have configuration controller return True
+        controller.configuration_controller.change_microscope.return_value = True
+
+        # Call change microscope, assert patched methods are called
+        controller.change_microscope(microscope_name)
+        assert controller.stage_controller.initialize.called is True
+        assert controller.channels_tab_controller.initialize.called is True
+        assert (
+            camera_setting_controller.update_camera_device_related_setting.called
+            is True
+        )
+        assert camera_setting_controller.calculate_physical_dimensions.called is True
+        assert controller.camera_view_controller.update_snr.called is True
+
+        # Test waveform popup controller.
+        controller.waveform_popup_controller = MagicMock()
+        controller.change_microscope(microscope_name)
+        assert (
+            controller.waveform_popup_controller.populate_experiment_values.called
+            is True
+        )
+
 
 def test_populate_experiment_setting(controller):
     controller.populate_experiment_setting(in_initialize=False)
@@ -98,14 +179,21 @@ def test_execute(controller):
 
 
 @pytest.mark.parametrize(
-    "acquisition_mode, sensor_mode, readout_direction, template_name, expected_template_name",
+    "acquisition_mode, sensor_mode, readout_direction, template_name, "
+    "expected_template_name",
     [
         ("live", "Normal", "", "Bidirectional", "Default"),
         ("z-stack", "Normal", "", "Bidirectional", "Default"),
         ("customized", "Normal", "", "Bidirectional", "Bidirectional"),
         ("live", "Light-Sheet", "Top-To-Bottom", "Bidirectional", "Default"),
         ("live", "Light-Sheet", "Bidirectional", "Bidirectional", "Bidirectional"),
-        ("customized", "Light-Sheet", "Bidirectional", "Bidirectional", "Bidirectional",),
+        (
+            "customized",
+            "Light-Sheet",
+            "Bidirectional",
+            "Bidirectional",
+            "Bidirectional",
+        ),
         ("z-stack", "Light-Sheet", "Bidirectional", "Default", "Bidirectional"),
         ("z-stack", "Light-Sheet", "Top-To-Bottom", "Default", "Default"),
     ],