Bug to be fixed: When creating a poi by mouse click in poi manager gui, would creat a poi with its z-axis value is zero.

[diamond2nv]

What is affected by this bug?

• Win10 64bit
• Win10 . 1809
• Qudi branch - scanimage_plotwidget_improvement (merged into master 2019-04-15)
• gui/poimanger/poimangui.py

When does this occur?

• When creating a poi by mouse click in poi manager gui, would creat a poi with its z-axis value is zero.

Where on the platform does it happen?

• gui/poimanger/poimangui.py -- def create_poi_from_click() .
• (Just find POI z=0. in saved ROI file)

How do we replicate the issue?

1. qudi/example/default.cfg, open confocal scan gui
2. move z-axis to 50.0 to begin scanning
3. open POI Manager GUI, and get confocal scan ROI
4. add some poi created by mouse clicked
   • If there is an error, should roll back, ref: Bugs to be fixed, need a little roll back of "confocalgui.py" and "poimangui.py"  #510
5. save ROI
6. open saved ROI file, would find POI position z is 0.0, which should be 50.0

Expected behavior (i.e. solution)

• Solution1: z-axis value of the poi created by mouse clicked, would be set as same as scanner z position, below code should be a quick fix:
  line 572 in "gui/poimanger/poimangui.py"

            #TODO: Z position from ROI origin is 0.
            new_pos = self.poimanagerlogic().roi_origin
            new_pos[2] = self.poimanagerlogic().scanner_position[2]

• Solution2: Not so sure, but would restore clicked poi z-value from shifted ROI:
  line 572 in "gui/poimanger/poimangui.py"

            #TODO: restore z-axis value from shift origin postition ?
            new_pos = self.poimanagerlogic().roi_origin
            new_pos[2] = self.poimanagerlogic().scanner_position[2] -  new_pos[2]

Other Comments

• Does "roi_origin" most likely mean as "default shift"? Since its default value is np.zeros(3)

[rmgonzal]

This bug is affected because, as you mentioned, when you Add POI's or click a new POI on the confocal image, it only saves the x, y position into the roi_origin, and since, by default, the values are set to zero.
The z position is not saved into the POI file, which in this case, should be a fixed value (focal plane e.g. Z_pos = 50.00) and take it from ROI origin.

So simply adding new_pos[2] = self.poimanagerlogic().scanner_position[2] line 629 "gui/poimanger/poimangui.py"

625        # Z position from ROI origin, X and Y positions from click event
626        new_pos = self.poimanagerlogic().roi_origin
627        new_pos[0] = pos.x()
628        new_pos[1] = pos.y()
629        new_pos[2] = self.poimanagerlogic().scanner_position[2]  #Add this line

To check if the value is stored in the POI file, check on the console typing.

In[1]: poimanagerlogic.poi_positions

and the last value should be different from zero.
(Example 3 point)

Out[1]: 
{'poi_20210322102945044728': array([3.67941896e-05, 5.56220471e-05, 5.00000000e-05]),
 'poi_20210322102946548945': array([3.15235204e-05, 3.33681106e-05, 5.00000000e-05]),
 'poi_20210322102947693560': array([7.01750944e-05, 5.21082677e-05, 5.00000000e-05])}