Add alignment gui 1d v1

Description

This MR adds a first draft for the alignment GUI. It is a preliminary version of the GUI which is not yet fully functional and can produce popup errors. Those are mostly link to its usage with its components which we will tackle in refactoring of the individual components. For the moment, I suggest to merge it and tackle the refactoring in separate MRs. A list of toDos will be added below.

Related Issues

relates to #350, #349 (closed), #348 (closed), #322 (closed), #323 (closed), #329 (closed)

Type of Change

• added plot_indicator_items (BECArrowItem and BECTickItem). They can be used to visualise the position of for instance a motor. The TickItem is attached to the layout and plotted below the Axis of the WaveformWidget, while the ArrowItem is attached to the plot_item allowing to follow the 1D curve or in future point to a specific pixel in the 2D plot. They consider log scale (note: the arrowItem is a bit off when moved to negative x values. There is a manual fix with the ViewBox.)
• added a button to the LMFitDialog that emits a signal with the parameter value of the fit. This can be hooked up to move the motor to the center position of the fit
• improves the linear region selector to consider logarithmic axis

Screenshots / GIFs (if applicable)

Plot Indicators:

Screen_Recording_2024-09-11_at_20.09.01

The full app is best tested with this branch. The recording was too large. Be aware, there are 3 prompt errors upon starting due to the filters in the comboboxes, and one more error if you change the motor. This is to be tackled via separate MRs.

Additional Comments

ToDo list for future improvements of the GUI:

• refactoring of filters for BECDeviceBox. Changing the filter after stating the GUI is generating errors because the currentTextChanged signal is already hooked up to adding a plot to the BECWaveformWidget. This creates issues since we cycle through devices that cannot be plotted, i.e. have no hinted signals/ no signals of type kind.normal/hinted at all. relates to these two issues #323 (closed) #322 (closed) #329 (closed)
• Related to the above, the logic for accepting device plot (scan_segment) and dap plots may be improved. Even with properly set filters, I would currently face the issue that I could change the x axis while a DAP process is still added with a different axis. This creates a popup error and removes the DAP. An easier logic to add/remove curves is desired and discussed in more detail, related issue is created (#349 (closed))
• Refactor of positioner_box to facilitate a more flexible arrangement of its components (#348 (closed) )
• Review LMFitDialog. A button has been added to the ListWidget for each parameter that can be hooked up to an action. This logic should be reviewed and optimised. Maybe we can generalise this even. (#350)

Definition of Done

• Documentation is up-to-date.

bec_widgets/utils/plot_indicator_items.py

 """Module to create an arrow item for a pyqtgraph plot"""
 
+import numpy as np
 import pyqtgraph as pg
 from qtpy.QtCore import QObject, Qt, Signal, Slot
 
@@ -12,6 +13,9 @@ class BECIndicatorItem(QObject):
         super().__init__(parent=parent)
         self.accent_colors = get_accent_colors()
         self.plot_item = plot_item
+        self._pos = None
+        self.is_log_x = False
+        self.is_log_y = False
 
     def add_to_plot(self) -> None:
         """Add the item to the plot"""
@@ -25,6 +29,12 @@ class BECIndicatorItem(QObject):
         """Set the position of the item"""
         raise NotImplementedError("Method set_position not implemented")
 
+    def check_log(self):
+        """Checks if the x or y axis is in log scale and updates the internal state accordingly."""
+        self.is_log_x = self.plot_item.ctrl.logXCheck.isChecked()
+        self.is_log_y = self.plot_item.ctrl.logYCheck.isChecked()
+        self.set_position(self._pos)
+
     def cleanup(self) -> None:
         """Cleanup the item"""
         self.remove_from_plot()
@@ -43,7 +53,8 @@ class BECTickItem(BECIndicatorItem):
         super().__init__(plot_item=plot_item, parent=parent)
         self.tick_item = pg.TickSliderItem(allowAdd=False, allowRemove=False)
         self.tick = None
-        self._tick_pos = 0
+        # Set _pos to float
+        self._pos = 0
         self._range = [0, 1]
 
     @Slot(float)
@@ -53,8 +64,15 @@ class BECTickItem(BECIndicatorItem):
         Args:
             pos (float): The position of the tick item.
         """
-        self._tick_pos = pos
-        self.update_range(self.plot_item.vb, self._range)
+        if self.is_log_x is True:
+            pos = pos if pos > 0 else 1e-10
+            pos = np.log10(pos)
+        self._pos = pos
+        view_box = self.plot_item.getViewBox()  # Ensure you're accessing the correct view box
+        view_range = view_box.viewRange()[0]
+        self.update_range(self.plot_item.vb, view_range)
+        self.position_changed.emit(pos)
+        self.position_changed_str.emit(str(pos))
 
     def update_range(self, vb, viewRange) -> None:
         """Update the range of the tick item
@@ -69,12 +87,9 @@ class BECTickItem(BECIndicatorItem):
         lengthIncludingPadding = length + self.tick_item.tickSize + 2
 
         self._range = viewRange
-
-        tickValueIncludingPadding = (self._tick_pos - viewRange[0]) / (viewRange[1] - viewRange[0])
+        tickValueIncludingPadding = (self._pos - viewRange[0]) / (viewRange[1] - viewRange[0])
         tickValue = (tickValueIncludingPadding * lengthIncludingPadding - origin) / length
         self.tick_item.setTickValue(self.tick, tickValue)
-        self.position_changed.emit(self._tick_pos)
-        self.position_changed_str.emit(str(self._tick_pos))
 
     def add_to_plot(self):
         """Add the tick item to the view box or plot item."""
@@ -82,6 +97,8 @@ class BECTickItem(BECIndicatorItem):
             self.plot_item.layout.addItem(self.tick_item, 4, 1)
             self.tick = self.tick_item.addTick(0, movable=False, color=self.accent_colors.highlight)
             self.plot_item.vb.sigXRangeChanged.connect(self.update_range)
+            self.plot_item.ctrl.logXCheck.checkStateChanged.connect(self.check_log)
+            self.plot_item.ctrl.logYCheck.checkStateChanged.connect(self.check_log)
 
     def remove_from_plot(self):
         """Remove the tick item from the view box or plot item."""
@@ -110,6 +127,7 @@ class BECArrowItem(BECIndicatorItem):
     def __init__(self, plot_item: pg.PlotItem = None, parent=None):
         super().__init__(plot_item=plot_item, parent=parent)
         self.arrow_item = pg.ArrowItem()
+        self._pos = (0, 0)
 
     @Slot(dict)
     def set_style(self, style: dict) -> None:
@@ -128,11 +146,23 @@ class BECArrowItem(BECIndicatorItem):
         Args:
             pos (tuple): The position of the arrow item as a tuple (x, y).
         """
+        self._pos = pos
         pos_x = pos[0]
         pos_y = pos[1]
+        if self.is_log_x is True:
+            pos_x = np.log10(pos_x) if pos_x > 0 else 1e-10
+            view_box = self.plot_item.getViewBox()  # Ensure you're accessing the correct view box
+            view_range = view_box.viewRange()[0]
+            # Avoid values outside the view range in the negative direction. Otherwise, there is
+            # a buggy behaviour of the arrow item and it appears at the wrong position.
+            if pos_x < view_range[0]:
+                pos_x = view_range[0]
+        if self.is_log_y is True:
+            pos_y = np.log10(pos_y) if pos_y > 0 else 1e-10
+
         self.arrow_item.setPos(pos_x, pos_y)
-        self.position_changed.emit((pos_x, pos_y))
-        self.position_changed_str.emit((str(pos_x), str(pos_y)))
+        self.position_changed.emit(self._pos)
+        self.position_changed_str.emit((str(self._pos[0]), str(self._pos[1])))
 
     def add_to_plot(self):
         """Add the arrow item to the view box or plot item."""
@@ -144,8 +174,16 @@ class BECArrowItem(BECIndicatorItem):
         )
         if self.plot_item is not None:
             self.plot_item.addItem(self.arrow_item)
+            self.plot_item.ctrl.logXCheck.checkStateChanged.connect(self.check_log)
+            self.plot_item.ctrl.logYCheck.checkStateChanged.connect(self.check_log)
 
     def remove_from_plot(self):
         """Remove the arrow item from the view box or plot item."""
         if self.plot_item is not None:
             self.plot_item.removeItem(self.arrow_item)
+
+    def check_log(self):
+        """Checks if the x or y axis is in log scale and updates the internal state accordingly."""
+        self.is_log_x = self.plot_item.ctrl.logXCheck.isChecked()
+        self.is_log_y = self.plot_item.ctrl.logYCheck.isChecked()
+        self.set_position(self._pos)