From 11bda2ccfecfca643701cb7c7f0ecc98e2b39dc7 Mon Sep 17 00:00:00 2001
From: Raul G <51966905+rmgonzal@users.noreply.github.com>
Date: Wed, 24 Mar 2021 12:46:37 +0100
Subject: [PATCH 1/2] Update poimangui.py

https://github.com/Ulm-IQO/qudi/issues/512#issue-440787920
This bug is affected because POI on the confocal image only saves the x, y position into the roi_origin, and since, by default, the values are set to zero. Since the z position is not saved into the POI file (which should be a fixed value) and take it from ROI origin.
So simply adding new_pos[2] = self.poimanagerlogic().scanner_position[2] line 629 "gui/poimanger/poimangui.py" will fix this bug.
---
 gui/poimanager/poimangui.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/gui/poimanager/poimangui.py b/gui/poimanager/poimangui.py
index cdb27e06b3..aebaeb36d7 100644
--- a/gui/poimanager/poimangui.py
+++ b/gui/poimanager/poimangui.py
@@ -626,6 +626,8 @@ def create_poi_from_click(self, button, pos):
         new_pos = self.poimanagerlogic().roi_origin
         new_pos[0] = pos.x()
         new_pos[1] = pos.y()
+        new_pos[2] = self.poimanagerlogic().scanner_position[2]  #Added by rmgonzal
+        
         self.sigAddPoiByClick.emit(new_pos)
         return
 

From c5f3f9455d382488c2f069a65befd259faae65fb Mon Sep 17 00:00:00 2001
From: Raul G <51966905+rmgonzal@users.noreply.github.com>
Date: Mon, 29 Mar 2021 14:36:00 +0200
Subject: [PATCH 2/2] Update poimangui.py

---
 gui/poimanager/poimangui.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/gui/poimanager/poimangui.py b/gui/poimanager/poimangui.py
index aebaeb36d7..3ee8f352fa 100644
--- a/gui/poimanager/poimangui.py
+++ b/gui/poimanager/poimangui.py
@@ -622,12 +622,8 @@ def create_poi_from_click(self, button, pos):
         # In our case this is most likely the POI marker to select the active POI from.
         if button != QtCore.Qt.LeftButton:
             return
-        # Z position from ROI origin, X and Y positions from click event
-        new_pos = self.poimanagerlogic().roi_origin
-        new_pos[0] = pos.x()
-        new_pos[1] = pos.y()
-        new_pos[2] = self.poimanagerlogic().scanner_position[2]  #Added by rmgonzal
-        
+        # Z position from scanner, X and Y positions from click event
+        new_pos =  np.array([pos.x(), pos.y(), self.poimanagerlogic().scanner_position[2]])              
         self.sigAddPoiByClick.emit(new_pos)
         return