From 4669b3370bba0a033c5903c73c26a6b45c9ffce7 Mon Sep 17 00:00:00 2001
From: VasilyLebedev <2115578+LebedevV@users.noreply.github.com>
Date: Fri, 13 Mar 2026 12:01:16 +0000
Subject: [PATCH] std import added fro gaussian2D

Since in hyperspy-2.4.0 gaussian2D has std for variables, it would be nice to import them for atom object
---
 atomap/atom_finding_refining.py |  9 +++++++++
 atomap/atom_position.py         | 19 +++++++++++++------
 2 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/atomap/atom_finding_refining.py b/atomap/atom_finding_refining.py
index f7559be..5daf82c 100644
--- a/atomap/atom_finding_refining.py
+++ b/atomap/atom_finding_refining.py
@@ -786,6 +786,15 @@ def _copy_gaussian_parameters_to_atom(atom, g):
     atom.amplitude_gaussian = g.A.value
     atom._gaussian_fitted = True
 
+    #getattr instead of g.par.std to ensure compatibility with previous hs
+    atom.pixel_x_std = getattr(g.centre_x, "std", np.nan)
+    atom.pixel_y_std = getattr(g.centre_y, "std", np.nan)    
+    atom.rotation_std = getattr(g.rotation, "std", np.nan)
+    atom.sigma_x_std = getattr(g.sigma_x, "std", np.nan)
+    atom.sigma_y_std = getattr(g.sigma_y, "std", np.nan)
+    atom.amplitude_gaussian_std = getattr(g.A, "std", np.nan)
+    atom._gaussian_fitted = True
+
 
 def get_mask_slice(position_list, radius_list):
     """Get a NumPy slice for extracting atom positions and
diff --git a/atomap/atom_position.py b/atomap/atom_position.py
index 7da98fa..86b96fe 100644
--- a/atomap/atom_position.py
+++ b/atomap/atom_position.py
@@ -72,8 +72,14 @@ def __init__(self, x, y, sigma_x=1.0, sigma_y=1.0, rotation=0.01, amplitude=1.0)
 
         """
         self.pixel_x, self.pixel_y = x, y
+        self.pixel_x_std, self.pixel_y_std = np.nan, np.nan
+        
         self.sigma_x, self.sigma_y = sigma_x, sigma_y
+        self.sigma_x_std, self.sigma_y_std = np.nan, np.nan
+        
         self.rotation = rotation
+        self.rotation_std = np.nan
+        
         self.nearest_neighbor_list = None
         self.in_atomic_plane = []
         self._start_atom = []
@@ -83,6 +89,7 @@ def __init__(self, x, y, sigma_x=1.0, sigma_y=1.0, rotation=0.01, amplitude=1.0)
         self.old_pixel_x_list = []
         self.old_pixel_y_list = []
         self.amplitude_gaussian = amplitude
+        self.amplitude_gaussian_std = np.nan
         self._gaussian_fitted = False
         self.amplitude_max_intensity = 1.0
         self.amplitude_min_intensity = 0.0
@@ -93,12 +100,12 @@ def __repr__(self):
         return "<%s, %s (x:%s,y:%s,sx:%s,sy:%s,r:%s,e:%s)>" % (
             self.__class__.__name__,
             self._tag,
-            round(self.pixel_x, 1),
-            round(self.pixel_y, 1),
-            round(self.sigma_x, 1),
-            round(self.sigma_y, 1),
-            round(self.rotation, 1),
-            round(self.ellipticity, 1),
+            round(self.pixel_x, 3),
+            round(self.pixel_y, 3),
+            round(self.sigma_x, 3),
+            round(self.sigma_y, 3),
+            round(self.rotation, 3),
+            round(self.ellipticity, 3),
         )
 
     @property