Merge branch 'add_rotation' of https://git.physi.uni-heidelberg.de/gao/analyseScript into origin/add_rotation

Analyser/FitAnalyser.py

@@ -26,7 +26,7 @@ from scipy.special import gamma as gamfcn
 from scipy.special import wofz
 from scipy.optimize import curve_fit
 from scipy.interpolate import CubicSpline
-from scipy.ndimage import gaussian_filter
+from scipy.ndimage import gaussian_filter, rotate
 
 import xarray as xr
 
@@ -159,9 +159,23 @@ def polylog2_2d(x, y=0.0, centerx=0.0, centery=0.0, amplitude=1.0, sigmax=1.0, s
     ## Approximation of the polylog function with 2D gaussian as argument. -> discribes the thermal part of the cloud
     return amplitude/1.643  * polylog_int(np.exp( -((x-centerx)**2/(2 * sigmax**2))-((y-centery)**2/( 2 * sigmay**2)) ))
 
+def rotate_coord(x,y, rot_angle):
+    
+    rot_angle *= 2*np.pi/360
+    x_og = x
+    x = x_og * np.cos(rot_angle) + y * np.sin(rot_angle)
+    y = -x_og * np.sin(rot_angle) + y * np.cos(rot_angle)
+    return x, y
     
 def density_profile_BEC_2d(x, y=0.0, amp_bec=1.0, amp_th=1.0, x0_bec=0.0, y0_bec=0.0, x0_th=0.0, y0_th=0.0,
-                           sigmax_bec=1.0, sigmay_bec=1.0, sigma_th=1.0):
+                           sigmax_bec=1.0, sigmay_bec=1.0, sigma_th=1.0, rot_angle=None):
+    
+    if rot_angle is not None:
+        x, y = rotate_coord(x,y, rot_angle)
+        x0_bec, y0_bec = rotate_coord(x0_bec, y0_bec, rot_angle)
+        x0_th, y0_th = rotate_coord(x0_th, y0_th, rot_angle)
+
+    
     return ThomasFermi_2d(x=x, y=y, centerx=x0_bec, centery=y0_bec,
                           amplitude=amp_bec, sigmax=sigmax_bec, sigmay=sigmay_bec
                           ) + polylog2_2d(x=x, y=y, centerx=x0_th, centery=y0_th,
@@ -403,11 +417,13 @@ class DensityProfileBEC2dModel(lmfit.Model):
         self.set_param_hint('sigmay_bec', min=0)
         self.set_param_hint('sigma_th', min=0)
 
+        self.set_param_hint('rot_angle', min=0, max=360)
+        
         self.set_param_hint('atom_number_bec', expr=f'{self.prefix}amp_bec / 5 * 2 * 3.14159265359 * {self.prefix}sigmax_bec * {self.prefix}sigmay_bec')
         self.set_param_hint('atom_number_th', expr=f'{self.prefix}amp_th * 2 * 3.14159265359 * 1.20206 / 1.643 * {self.prefix}sigma_th * {self.prefix}sigma_th')
         self.set_param_hint('condensate_fraction', expr=f'{self.prefix}atom_number_bec / ({self.prefix}atom_number_bec + {self.prefix}atom_number_th)')
 
-    def guess(self, data, x, y, pre_check=False, post_check=False, **kwargs):
+    def guess(self, data, x, y, rot_angle=0, vary_rot=False, pre_check=False, post_check=False, **kwargs):
         """Estimate and create initial model parameters for 2d  bimodal fit, by doing a 1d bimodal fit along an integrated slice of the image 
     
         :param data: Flattened 2d array, in form [a_00, a_10, a_20, ..., a_01, a_02, .. ,a_XY] with a_xy, x_dim=X, y_dim=Y
@@ -437,6 +453,9 @@ class DensityProfileBEC2dModel(lmfit.Model):
         data = np.reshape(data, (y_width, x_width))
         data = data.T
 
+        if rot_angle != 0:
+            data = rotate(data, rot_angle, reshape=False)
+
         shape = np.shape(data)
         if self.is_debug:
             print(f'shape: {shape}')
@@ -582,6 +601,8 @@ class DensityProfileBEC2dModel(lmfit.Model):
             else:
                 print('Error in small width BEC recogintion, s_width_ind should be 0 or 1')
 
+        params[f'{self.prefix}rot_angle'].set(value=-rot_angle, min=-rot_angle-30, max=-rot_angle+30, vary=vary_rot)
+
         if self.is_debug:
             print('')
             print('Init Params')