From 68a211db3e9322fd5d0b80f9200c5fbba59805f2 Mon Sep 17 00:00:00 2001
From: mateusz <mateuszmroz@gmail.com>
Date: Tue, 12 Dec 2023 09:12:25 +0100
Subject: [PATCH 01/13] example_16: added soft no negative blending flux
 constrains for both sources and color prior

---
 examples/example_16/ob03235_2_full.yaml |  11 +-
 examples/example_16/ulens_model_fit.py  | 147 ++++++++++++++++++++++--
 source/MulensModel/data                 |   1 -
 3 files changed, 148 insertions(+), 11 deletions(-)
 delete mode 120000 source/MulensModel/data

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index b660b92e4..8b1fac17e 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -33,9 +33,18 @@ starting_parameters:
     s: uniform 1.09 1.11
     alpha: gauss 224.0 1.0
 fit_constraints:
-    negative_blending_flux_sigma_mag: 20.
+    negative_blending_flux_sigma_mag: 20. 
+    #you can specific which source flux should be constrain : sigma source_number(s)
+    #negative_blending_flux_sigma_mag: 20. 2
     # Alternative sharp constraint:
     # no_negative_blending_flux: True
+    #color constrains: gauss mu sigma flux_in_numerator flux_in_denominator
+    color : gauss 25. 5. 1 2 
+    #Alternative 
+    #color source 1 :  gauss 25. 5. 1 2 
+    #and/or 
+    #color source 2 :  gauss 25. 5. 1 2 
+    
     prior:
         t_E: Mroz et al. 2017
         # Other possibility:
diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index 614f29c2a..8a0d3bc4a 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -1414,7 +1414,15 @@ def _parse_fit_constraints(self):
 
         allowed_keys_flux = {
             "no_negative_blending_flux", "negative_blending_flux_sigma_mag"}
-        allowed_keys = {*allowed_keys_flux, "prior"}
+        
+        allowed_keys_color={'color',
+                        'color source 1',
+                        'color source 2',}
+        
+        
+        allowed_keys = {*allowed_keys_flux,
+                        *allowed_keys_color,
+                        "prior"}
         used_keys = set(self._fit_constraints.keys())
         if len(used_keys - allowed_keys) > 0:
             raise ValueError('unrecognized constraint: {:}'.format(
@@ -1426,10 +1434,70 @@ def _parse_fit_constraints(self):
         if "no_negative_blending_flux" not in self._fit_constraints:
             self._fit_constraints["no_negative_blending_flux"] = False
 
-        key = "negative_blending_flux_sigma_mag"
-        if key in used_keys:
-            self._fit_constraints[key] = mm.Utils.get_flux_from_mag(
-                self._fit_constraints[key])
+        if len(used_keys.intersection(allowed_keys_color))>=2 and ('color' in used_keys):
+            raise ValueError(
+               'you cannot specify both color and '+ str(used_keys.intersection(allowed_keys_color)-{'color'}))
+
+        for key in self._fit_constraints.keys():  
+            value=self._fit_constraints[key]
+           
+            if key == "negative_blending_flux_sigma_mag" :
+                
+                if isinstance(value, float):
+                    words=[value]
+                else:    
+                    words=value.split()
+    
+                if len(words)==1:    
+                    sets=[]
+                    for (j,idset) in enumerate(self._datasets):
+                        sets.append(int(j)+1)
+             
+                elif 2<=len(words)<=(len(self._datasets)+1):
+                    sets=[]
+                    for (j,idset) in enumerate(words[1:]):
+                        if 0<int(idset)<=len(self._datasets):
+                            sets.append(int(idset))
+                            
+                        else :
+                            raise ValueError(
+                   'dataset number specified in negative_blending_flux_sigma_mag do not match with provided datasets')
+                            
+                
+                
+                self._fit_constraints[key] =[mm.Utils.get_flux_from_mag(float(words[0])),sets]
+                
+                
+                
+                
+                
+            elif key in ['color','color source 1','color source 2']:
+                  
+                  words = value.split()
+                  if len(words) != 5 or words[0] != 'gauss':
+                      msg = "Something went wrong in parsing prior for "
+                      msg += "{:}: {:}"
+                      if len(words) == 3 and words[0] == 'gauss' :
+                          msg+=' color priors require the specification of datasets that should be used for color calculation  '
+                      raise ValueError(msg.format(key, value))
+                  try:
+                      settings = [words[0], float(words[1]), float(words[2]), int(words[3]), int(words[4])]
+                  except Exception:
+                      raise ValueError('error in parsing: ' + words[1] + " " +
+                                       words[2]+ " " + words[3]+ " " +words[4])
+                  if settings[2] < 0.:
+                      raise ValueError('sigma cannot be negative: ' + words[2])
+                  if settings[3]==settings[4] :
+                      raise ValueError( "in " + key +  " fluxes have to be from different datasets")
+                      
+                  if  (0>=settings[3]>=len(self._datasets)+1) or  (0>=settings[4]>=len(self._datasets)+1):
+                      raise ValueError(
+             'dataset number specified in color prior do not match with provided datasets')
+                     
+                      
+                  self._fit_constraints[key]  = settings
+                  
+            
 
         if 'prior' in self._fit_constraints:
             self._parse_fit_constraints_prior()
@@ -1462,6 +1530,8 @@ def _parse_fit_constraints_prior(self):
                 if settings[2] < 0.:
                     raise ValueError('sigma cannot be negative: ' + words[2])
                 priors[key] = settings
+                
+                
             else:
                 raise KeyError(
                     "Unrecognized key in fit_constraints/prior: " + key)
@@ -1966,6 +2036,7 @@ def _ln_prior(self, theta):
                     value = self._model.parameters.parameters[parameter]
                     ln_prior += self._get_ln_prior_for_1_parameter(
                         value, prior_settings)
+                                     
                 else:
                     raise ValueError('prior not handled: ' + parameter)
 
@@ -2092,11 +2163,69 @@ def _run_flux_checks_ln_prior(self, fluxes):
                 return outside
 
         key = "negative_blending_flux_sigma_mag"
+                  
+        
         if key in self._fit_constraints:
-            blend_index = self._n_fluxes_per_dataset - 1
-            if fluxes[blend_index] < 0.:
-                sigma = self._fit_constraints[key]
-                inside += -0.5 * (fluxes[blend_index] / sigma)**2
+                   
+            for (i, dataset) in enumerate(self._datasets):
+                if i+1 in  self._fit_constraints[key][1]:
+                    blend_index = ((i+1)*self._n_fluxes_per_dataset )- 1
+                    if fluxes[blend_index] < 0.:
+                        sigma = self._fit_constraints[key][0]
+                        inside += -0.5 * (fluxes[blend_index] / sigma)**2
+        
+        key='color'
+
+        if key in self._fit_constraints:
+            settings=self._fit_constraints[key]
+            if  self._n_fluxes_per_dataset == 2 :
+                index1=(settings[3]-1)*self._n_fluxes_per_dataset
+                index2=(settings[4]-1)*self._n_fluxes_per_dataset
+                value=fluxes[index1]/fluxes[index2]
+                inside +=self._get_ln_prior_for_1_parameter(
+                    value, settings[:-2])
+
+            if  self._n_fluxes_per_dataset == 3 :
+                index1=(settings[3]-1)*self._n_fluxes_per_dataset
+                index2=(settings[4]-1)*self._n_fluxes_per_dataset
+                value=fluxes[index1]/fluxes[index2]
+                inside +=self._get_ln_prior_for_1_parameter(
+                    value, settings[:-2])
+                
+                
+                index1=((settings[3]-1)*self._n_fluxes_per_dataset)+1
+                index2=((settings[4]-1)*self._n_fluxes_per_dataset)+1
+                value=fluxes[index1]/fluxes[index2]
+                inside +=self._get_ln_prior_for_1_parameter(
+                    value, settings[:-2])
+
+                
+            
+        key= 'color source 1'
+        if key in self._fit_constraints:
+            settings=self._fit_constraints[key]
+            index1=(settings[3]-1)*self._n_fluxes_per_dataset
+            index2=(settings[4]-1)*self._n_fluxes_per_dataset
+            value=fluxes[index1]/fluxes[index2]
+            inside +=self._get_ln_prior_for_1_parameter(
+                value, settings[:-2])
+            
+            
+            
+              
+        key= 'color source 2'
+        if key in self._fit_constraints:
+            settings=self._fit_constraints[key]
+            index1=(settings[3]-1)*self._n_fluxes_per_dataset+1
+            index2=(settings[4]-1)*self._n_fluxes_per_dataset+1
+            value=fluxes[index1]/fluxes[index2]
+            inside +=self._get_ln_prior_for_1_parameter(
+                value, settings[:-2])
+            
+            
+             
+             
+                
 
         return inside
 
diff --git a/source/MulensModel/data b/source/MulensModel/data
deleted file mode 120000
index e67b45590..000000000
--- a/source/MulensModel/data
+++ /dev/null
@@ -1 +0,0 @@
-../../data
\ No newline at end of file

From af94ae7ce5b128bfe5566a844bb6794045183e6c Mon Sep 17 00:00:00 2001
From: Mateusz Mroz <mmroz@grus.astrouw.edu.pl>
Date: Thu, 9 May 2024 18:50:23 +0200
Subject: [PATCH 02/13] Raphaels corrections

---
 examples/example_16/ob03235_2_full.yaml |   8 +-
 examples/example_16/ulens_model_fit.py  | 218 ++++++++++--------------
 2 files changed, 92 insertions(+), 134 deletions(-)

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index 322b672c9..4cc4aadcf 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -34,13 +34,13 @@ starting_parameters:
     alpha: gauss 224.0 1.0
 fit_constraints:
     negative_blending_flux_sigma_mag: 20. 
-    #you can specific which source flux should be constrain : sigma source_number(s)
-    #negative_blending_flux_sigma_mag: 20. 2
+    #one can specify for which dateset soft prior on blending flux should be applied: sigma dataset_number(s)
+    #negative_blending_flux_sigma_mag: 20. 1 3  
     # Alternative sharp constraint:
     # no_negative_blending_flux: True
-    #color constrains: gauss mu sigma flux_in_numerator flux_in_denominator
+    #color constrains, where color=flux_S_dataset_no._k/flux_S_dataset_no._m: gauss mu sigma k m 
     color : gauss 25. 5. 1 2 
-    #Alternative 
+    #Alternative for binary source models: 
     #color source 1 :  gauss 25. 5. 1 2 
     #and/or 
     #color source 2 :  gauss 25. 5. 1 2 
diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index 50b50d89c..aa437c4c5 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -306,13 +306,14 @@ class UlensModelFit(object):
             These files will have three columns: time, residuals, and
             uncertainties.
     """
+
     def __init__(
             self, photometry_files,
             starting_parameters=None, prior_limits=None, model=None,
             fixed_parameters=None,
             min_values=None, max_values=None, fitting_parameters=None,
             fit_constraints=None, plots=None, other_output=None
-            ):
+    ):
         self._check_MM_version()
         self._photometry_files = photometry_files
         self._starting_parameters_input = starting_parameters
@@ -462,7 +463,7 @@ def _set_default_parameters(self):
             xi_argument_of_latitude_reference='\\xi_u',
             xi_eccentricity='\\xi_e',
             xi_omega_periapsis='\\xi_{\\omege}',
-            )
+        )
         self._latex_conversion_other = dict()
 
     def _guess_fitting_method(self):
@@ -1442,12 +1443,11 @@ def _parse_fit_constraints(self):
 
         allowed_keys_flux = {
             "no_negative_blending_flux", "negative_blending_flux_sigma_mag"}
-        
-        allowed_keys_color={'color',
-                        'color source 1',
-                        'color source 2',}
-        
-        
+
+        allowed_keys_color = {'color',
+                              'color source 1',
+                              'color source 2', }
+
         allowed_keys = {*allowed_keys_flux,
                         *allowed_keys_color,
                         "prior"}
@@ -1462,70 +1462,54 @@ def _parse_fit_constraints(self):
         if "no_negative_blending_flux" not in self._fit_constraints:
             self._fit_constraints["no_negative_blending_flux"] = False
 
-        if len(used_keys.intersection(allowed_keys_color))>=2 and ('color' in used_keys):
+        if len(used_keys.intersection(allowed_keys_color)) >= 2 and ('color' in used_keys):
             raise ValueError(
-               'you cannot specify both color and '+ str(used_keys.intersection(allowed_keys_color)-{'color'}))
-
-        for key in self._fit_constraints.keys():  
-            value=self._fit_constraints[key]
-           
-            if key == "negative_blending_flux_sigma_mag" :
-                
-                if isinstance(value, float):
-                    words=[value]
-                else:    
-                    words=value.split()
-    
-                if len(words)==1:    
-                    sets=[]
-                    for (j,idset) in enumerate(self._datasets):
-                        sets.append(int(j)+1)
-             
-                elif 2<=len(words)<=(len(self._datasets)+1):
-                    sets=[]
-                    for (j,idset) in enumerate(words[1:]):
-                        if 0<int(idset)<=len(self._datasets):
-                            sets.append(int(idset))
-                            
-                        else :
-                            raise ValueError(
-                   'dataset number specified in negative_blending_flux_sigma_mag do not match with provided datasets')
-                            
-                
-                
-                self._fit_constraints[key] =[mm.Utils.get_flux_from_mag(float(words[0])),sets]
-                
-                
-                
-                
-                
-            elif key in ['color','color source 1','color source 2']:
-                  
-                  words = value.split()
-                  if len(words) != 5 or words[0] != 'gauss':
-                      msg = "Something went wrong in parsing prior for "
-                      msg += "{:}: {:}"
-                      if len(words) == 3 and words[0] == 'gauss' :
-                          msg+=' color priors require the specification of datasets that should be used for color calculation  '
-                      raise ValueError(msg.format(key, value))
-                  try:
-                      settings = [words[0], float(words[1]), float(words[2]), int(words[3]), int(words[4])]
-                  except Exception:
-                      raise ValueError('error in parsing: ' + words[1] + " " +
-                                       words[2]+ " " + words[3]+ " " +words[4])
-                  if settings[2] < 0.:
-                      raise ValueError('sigma cannot be negative: ' + words[2])
-                  if settings[3]==settings[4] :
-                      raise ValueError( "in " + key +  " fluxes have to be from different datasets")
-                      
-                  if  (0>=settings[3]>=len(self._datasets)+1) or  (0>=settings[4]>=len(self._datasets)+1):
-                      raise ValueError(
-             'dataset number specified in color prior do not match with provided datasets')
-                     
-                      
-                  self._fit_constraints[key]  = settings
-                  
-            
+                'you cannot specify both color and ' + str(used_keys.intersection(allowed_keys_color)-{'color'}))
+
+        for key in self._fit_constraints.keys():
+            value = self._fit_constraints[key]
+
+            if key == "negative_blending_flux_sigma_mag":
+
+                if isinstance(value, (float, int)):
+                    sigma = float(value)
+                    sets = list(range(1, len(self._datasets) + 1))
+                else:
+                    sigma = float(value.split()[0])
+                    sets = list(map(int, value.split()[1:]))
+                    if len(sets) > len(self._datasets):
+                        raise ValueError(
+                            'dataset number specified in negative_blending_flux_sigma_mag do not match with provided datasets')
+
+                self._fit_constraints[key] = [
+                    mm.Utils.get_flux_from_mag(sigma), sets]
+
+            elif key in ['color', 'color source 1', 'color source 2']:
+
+                words = value.split()
+                if len(words) != 5 or words[0] != 'gauss':
+                    msg = "Something went wrong in parsing prior for "
+                    msg += "{:}: {:}"
+                    if len(words) == 3 and words[0] == 'gauss':
+                        msg += ' color priors require the specification of datasets that should be used for color calculation  '
+                    raise ValueError(msg.format(key, value))
+                try:
+                    settings = [words[0], float(words[1]), float(
+                        words[2]), int(words[3]), int(words[4])]
+                except Exception:
+                    raise ValueError('error in parsing: ' + words[1] + " " +
+                                     words[2] + " " + words[3] + " " + words[4])
+                if settings[2] < 0.:
+                    raise ValueError('sigma cannot be negative: ' + words[2])
+                if settings[3] == settings[4]:
+                    raise ValueError(
+                        "in " + key + " fluxes have to be from different datasets")
+
+                if (0 >= settings[3] >= len(self._datasets)+1) or (0 >= settings[4] >= len(self._datasets)+1):
+                    raise ValueError(
+                        'dataset number specified in color prior do not match with provided datasets')
+
+                self._fit_constraints[key] = settings
 
         if 'prior' in self._fit_constraints:
             self._parse_fit_constraints_prior()
@@ -1558,8 +1542,7 @@ def _parse_fit_constraints_prior(self):
                 if settings[2] < 0.:
                     raise ValueError('sigma cannot be negative: ' + words[2])
                 priors[key] = settings
-                
-                
+
             else:
                 raise KeyError(
                     "Unrecognized key in fit_constraints/prior: " + key)
@@ -2067,7 +2050,7 @@ def _ln_prior(self, theta):
                     value = self._model.parameters.parameters[parameter]
                     ln_prior += self._get_ln_prior_for_1_parameter(
                         value, prior_settings)
-                                     
+
                 else:
                     raise ValueError('prior not handled: ' + parameter)
 
@@ -2080,8 +2063,8 @@ def _check_valid_Cassan08_trajectory(self):
         """
         sampling = self._model.parameters.uniform_caustic_sampling
         valid = sampling.check_valid_trajectory(
-                self._model.parameters.x_caustic_in,
-                self._model.parameters.x_caustic_out)
+            self._model.parameters.x_caustic_in,
+            self._model.parameters.x_caustic_out)
         return valid
 
     def _get_ln_prior_for_1_parameter(self, value, settings):
@@ -2181,6 +2164,16 @@ def _get_fluxes(self):
 
         return fluxes
 
+    def _sumup_inside_prior(self, fluxes, key, inside, idx_plus):
+
+        settings = self._fit_constraints[key]
+        index1 = (settings[3]-1)*self._n_fluxes_per_dataset + idx_plus
+        index2 = (settings[4]-1)*self._n_fluxes_per_dataset + idx_plus
+        value = fluxes[index1]/fluxes[index2]
+        inside += self._get_ln_prior_for_1_parameter(value, settings[:-2])
+
+        return inside
+
     def _run_flux_checks_ln_prior(self, fluxes):
         """
         Run the checks on fluxes - are they in the prior?
@@ -2194,69 +2187,34 @@ def _run_flux_checks_ln_prior(self, fluxes):
                 return outside
 
         key = "negative_blending_flux_sigma_mag"
-                  
-        
+
         if key in self._fit_constraints:
-                   
+
             for (i, dataset) in enumerate(self._datasets):
-                if i+1 in  self._fit_constraints[key][1]:
-                    blend_index = ((i+1)*self._n_fluxes_per_dataset )- 1
+                if i+1 in self._fit_constraints[key][1]:
+                    blend_index = ((i+1)*self._n_fluxes_per_dataset) - 1
                     if fluxes[blend_index] < 0.:
                         sigma = self._fit_constraints[key][0]
                         inside += -0.5 * (fluxes[blend_index] / sigma)**2
-        
-        key='color'
+
+        key = 'color'
 
         if key in self._fit_constraints:
-            settings=self._fit_constraints[key]
-            if  self._n_fluxes_per_dataset == 2 :
-                index1=(settings[3]-1)*self._n_fluxes_per_dataset
-                index2=(settings[4]-1)*self._n_fluxes_per_dataset
-                value=fluxes[index1]/fluxes[index2]
-                inside +=self._get_ln_prior_for_1_parameter(
-                    value, settings[:-2])
-
-            if  self._n_fluxes_per_dataset == 3 :
-                index1=(settings[3]-1)*self._n_fluxes_per_dataset
-                index2=(settings[4]-1)*self._n_fluxes_per_dataset
-                value=fluxes[index1]/fluxes[index2]
-                inside +=self._get_ln_prior_for_1_parameter(
-                    value, settings[:-2])
-                
-                
-                index1=((settings[3]-1)*self._n_fluxes_per_dataset)+1
-                index2=((settings[4]-1)*self._n_fluxes_per_dataset)+1
-                value=fluxes[index1]/fluxes[index2]
-                inside +=self._get_ln_prior_for_1_parameter(
-                    value, settings[:-2])
-
-                
-            
-        key= 'color source 1'
+            settings = self._fit_constraints[key]
+            if self._n_fluxes_per_dataset == 2:
+                inside = self._sumup_inside_prior(fluxes, key, inside, 0)
+
+            if self._n_fluxes_per_dataset == 3:
+                inside = self._sumup_inside_prior(fluxes, key, inside, 0)
+                inside = self._sumup_inside_prior(fluxes, key, inside, 1)
+
+        key = 'color source 1'
         if key in self._fit_constraints:
-            settings=self._fit_constraints[key]
-            index1=(settings[3]-1)*self._n_fluxes_per_dataset
-            index2=(settings[4]-1)*self._n_fluxes_per_dataset
-            value=fluxes[index1]/fluxes[index2]
-            inside +=self._get_ln_prior_for_1_parameter(
-                value, settings[:-2])
-            
-            
-            
-              
-        key= 'color source 2'
+            inside = self._sumup_inside_prior(fluxes, key, inside, 0)
+
+        key = 'color source 2'
         if key in self._fit_constraints:
-            settings=self._fit_constraints[key]
-            index1=(settings[3]-1)*self._n_fluxes_per_dataset+1
-            index2=(settings[4]-1)*self._n_fluxes_per_dataset+1
-            value=fluxes[index1]/fluxes[index2]
-            inside +=self._get_ln_prior_for_1_parameter(
-                value, settings[:-2])
-            
-            
-             
-             
-                
+            inside = self._sumup_inside_prior(fluxes, key, inside, 1)
 
         return inside
 

From f66f1313cbbbcb85daa35c673d1de0cbd1ecf441 Mon Sep 17 00:00:00 2001
From: Mateusz Mroz <mmroz@grus.astrouw.edu.pl>
Date: Thu, 9 May 2024 19:00:00 +0200
Subject: [PATCH 03/13] s ch

---
 examples/example_16/ob03235_2_full.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index 4cc4aadcf..300241a03 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -34,7 +34,7 @@ starting_parameters:
     alpha: gauss 224.0 1.0
 fit_constraints:
     negative_blending_flux_sigma_mag: 20. 
-    #one can specify for which dateset soft prior on blending flux should be applied: sigma dataset_number(s)
+    #one can specify for which dateset soft constrain on blending flux should be applied: sigma dataset_number(s)
     #negative_blending_flux_sigma_mag: 20. 1 3  
     # Alternative sharp constraint:
     # no_negative_blending_flux: True

From e8796b615f0476265504af2778ba221c228e3094 Mon Sep 17 00:00:00 2001
From: Mateusz Mroz <mmroz@grus.astrouw.edu.pl>
Date: Thu, 9 May 2024 19:01:15 +0200
Subject: [PATCH 04/13] S ch

---
 examples/example_16/ob03235_2_full.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index 300241a03..ed82b83c7 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -34,7 +34,7 @@ starting_parameters:
     alpha: gauss 224.0 1.0
 fit_constraints:
     negative_blending_flux_sigma_mag: 20. 
-    #one can specify for which dateset soft constrain on blending flux should be applied: sigma dataset_number(s)
+    #one can specify for which dataset soft constrain on blending flux should be applied: sigma dataset_number(s)
     #negative_blending_flux_sigma_mag: 20. 1 3  
     # Alternative sharp constraint:
     # no_negative_blending_flux: True

From 6bab7ad5a4fed82287dd54ce74fb2547f384f1d5 Mon Sep 17 00:00:00 2001
From: Mateusz Mroz <mmroz@grus.astrouw.edu.pl>
Date: Mon, 13 May 2024 17:40:49 +0200
Subject: [PATCH 05/13] color constrains put outside _parse_fit_constraints()
 dataset for color and blending constrain can be define by index or lable

---
 examples/example_16/ob03235_2_full.yaml |  10 +-
 examples/example_16/ulens_model_fit.py  | 129 +++++++++++++++++-------
 2 files changed, 96 insertions(+), 43 deletions(-)

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index ed82b83c7..c5bb512cb 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -38,13 +38,13 @@ fit_constraints:
     #negative_blending_flux_sigma_mag: 20. 1 3  
     # Alternative sharp constraint:
     # no_negative_blending_flux: True
-    #color constrains, where color=flux_S_dataset_no._k/flux_S_dataset_no._m: gauss mu sigma k m 
-    color : gauss 25. 5. 1 2 
+    #color constrains, where color=flux_S_dataset_k/flux_S_dataset_m: gauss mu sigma k m 
+    color : gauss 25. 5. "OGLE I-band" "OB03235_MOA.txt" 
     #Alternative for binary source models: 
-    #color source 1 :  gauss 25. 5. 1 2 
+    #color source 1 :  gauss 25. 5. "OGLE I-band" "OB03235_MOA.txt" 
     #and/or 
-    #color source 2 :  gauss 25. 5. 1 2 
-    
+    #color source 2 :  gauss 25. 5. 0 1
+        
     prior:
         t_E: Mroz et al. 2017
         # Other possibility:
diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index aa437c4c5..66eed00bc 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -9,6 +9,7 @@
 import warnings
 import math
 import numpy as np
+import shlex
 from scipy.interpolate import interp1d
 from matplotlib import pyplot as plt
 from matplotlib import gridspec, rcParams, rcParamsDefault
@@ -1470,49 +1471,66 @@ def _parse_fit_constraints(self):
             value = self._fit_constraints[key]
 
             if key == "negative_blending_flux_sigma_mag":
+                self._parse_fit_constraints_soft_blending(key, value)
 
-                if isinstance(value, (float, int)):
-                    sigma = float(value)
-                    sets = list(range(1, len(self._datasets) + 1))
-                else:
-                    sigma = float(value.split()[0])
-                    sets = list(map(int, value.split()[1:]))
-                    if len(sets) > len(self._datasets):
-                        raise ValueError(
-                            'dataset number specified in negative_blending_flux_sigma_mag do not match with provided datasets')
+            elif key in ['color', 'color source 1', 'color source 2']:
+                self._parse_fit_constraints_color(key, value)
 
-                self._fit_constraints[key] = [
-                    mm.Utils.get_flux_from_mag(sigma), sets]
+        if 'prior' in self._fit_constraints:
+            self._parse_fit_constraints_prior()
 
-            elif key in ['color', 'color source 1', 'color source 2']:
+    def _parse_fit_constraints_soft_blending(self, key, value):
+        """
+        Check if soft fit constraint on blending flux are correctly defined.
+        """
+        if isinstance(value, (float, int)):
+            sigma = float(value)
+            sets = list(range(1, len(self._datasets) + 1))
+        else:
+            sigma = float(value.split()[0])
+            sets = list(map(int, value.split()[1:]))
+            if len(sets) > len(self._datasets):
+                raise ValueError(
+                    'dataset number specified in negative_blending_flux_sigma_mag do not match with provided datasets')
 
-                words = value.split()
-                if len(words) != 5 or words[0] != 'gauss':
-                    msg = "Something went wrong in parsing prior for "
-                    msg += "{:}: {:}"
-                    if len(words) == 3 and words[0] == 'gauss':
-                        msg += ' color priors require the specification of datasets that should be used for color calculation  '
-                    raise ValueError(msg.format(key, value))
-                try:
-                    settings = [words[0], float(words[1]), float(
-                        words[2]), int(words[3]), int(words[4])]
-                except Exception:
-                    raise ValueError('error in parsing: ' + words[1] + " " +
-                                     words[2] + " " + words[3] + " " + words[4])
-                if settings[2] < 0.:
-                    raise ValueError('sigma cannot be negative: ' + words[2])
-                if settings[3] == settings[4]:
-                    raise ValueError(
-                        "in " + key + " fluxes have to be from different datasets")
+        self._fit_constraints[key] = [
+            mm.Utils.get_flux_from_mag(sigma), sets]
 
-                if (0 >= settings[3] >= len(self._datasets)+1) or (0 >= settings[4] >= len(self._datasets)+1):
-                    raise ValueError(
-                        'dataset number specified in color prior do not match with provided datasets')
+    def _parse_fit_constraints_color(self, key, value):
+        """
+        Check if fit constraint on color are correctly defined.
+        """
+        words = shlex.split(value, posix=False)
+        if len(words) != 5 or words[0] != 'gauss':
+            msg = "Something went wrong in parsing prior for "
+            msg += "{:}: {:}"
+            if len(words) == 3 and words[0] == 'gauss':
+                msg += ' color priors require the specification of datasets that should be used for color calculation  '
+            raise ValueError(msg.format(key, value))
+        try:
+            settings = [words[0], float(words[1]), float(
+                words[2]), words[3], words[4]]
+        except Exception:
+            raise ValueError('error in parsing: ' + words[1] + " " +
+                             words[2] + " " + words[3] + " " + words[4])
+        if settings[2] < 0.:
+            raise ValueError('sigma cannot be negative: ' + words[2])
+        if settings[3] == settings[4]:
+            raise ValueError(
+                "in " + key + " fluxes have to be from different datasets")
 
-                self._fit_constraints[key] = settings
+        if isinstance(settings[3], str) and isinstance(settings[4], str):
+            settings[3] = settings[3].strip('"')
+            settings[4] = settings[4].strip('"')
+            settings[3] = self._get_no_of_dataset_by_lable(settings[3])
+            settings[4] = self._get_no_of_dataset_by_lable(settings[4])
 
-        if 'prior' in self._fit_constraints:
-            self._parse_fit_constraints_prior()
+        if isinstance(settings[3], int) and isinstance(settings[4], int):
+            if (0 >= settings[3] >= len(self._datasets)-1) or (0 >= settings[4] >= len(self._datasets)-1):
+                raise ValueError(
+                    'dataset specified in color prior do not match with provided datasets')
+
+        self._fit_constraints[key] = settings
 
     def _parse_fit_constraints_prior(self):
         """
@@ -1551,6 +1569,25 @@ def _parse_fit_constraints_prior(self):
         if len(priors) > 0:
             self._priors = priors
 
+    def _get_no_of_dataset_by_lable(self, label):
+        """
+        Returns the index of a dataset with a specific label.
+
+        Parameters
+        ----------
+        label : str
+            Label of the dataset defined by MulensData.plot_properties['label'].
+
+        Returns
+        -------
+        int
+            Sequential index of the dataset [1,2,...,n_datasets]
+        """
+        for (i, dataset) in enumerate(self._datasets):
+            if dataset.plot_properties['label'] == label:
+                return i
+        return -99
+
     def _read_prior_t_E_data(self):
         """
         read data that specify t_E prior and parse them appropriately
@@ -2165,10 +2202,26 @@ def _get_fluxes(self):
         return fluxes
 
     def _sumup_inside_prior(self, fluxes, key, inside, idx_plus):
+        """
+        Calculates the contribution to the ln_prior from specified color constraints
+        Parameters
+        ----------
+        fluxes : array 
+            Array with fluxes of the current model.
+        key : str
+        inside : float
+        idx_plus : int
+            For a single source, idx_plus=0; 
+            for a binary source, idx_plus=0 or 1. 
+
+        Returns
+        -------
+        inside : float
+        """
 
         settings = self._fit_constraints[key]
-        index1 = (settings[3]-1)*self._n_fluxes_per_dataset + idx_plus
-        index2 = (settings[4]-1)*self._n_fluxes_per_dataset + idx_plus
+        index1 = (settings[3])*self._n_fluxes_per_dataset + idx_plus
+        index2 = (settings[4])*self._n_fluxes_per_dataset + idx_plus
         value = fluxes[index1]/fluxes[index2]
         inside += self._get_ln_prior_for_1_parameter(value, settings[:-2])
 

From 71a02fbc975789bea4a7ddd104deaa054e9f6ba8 Mon Sep 17 00:00:00 2001
From: Mateusz Mroz <mmroz@grus.astrouw.edu.pl>
Date: Mon, 13 May 2024 18:53:49 +0200
Subject: [PATCH 06/13] like previous

---
 examples/example_16/ob03235_2_full.yaml |  6 +--
 examples/example_16/ulens_model_fit.py  | 54 +++++++++++++++----------
 2 files changed, 36 insertions(+), 24 deletions(-)

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index c5bb512cb..59b38c9a3 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -33,13 +33,13 @@ starting_parameters:
     s: uniform 1.09 1.11
     alpha: gauss 224.0 1.0
 fit_constraints:
-    negative_blending_flux_sigma_mag: 20. 
+    negative_blending_flux_sigma_mag: 20.  
     #one can specify for which dataset soft constrain on blending flux should be applied: sigma dataset_number(s)
-    #negative_blending_flux_sigma_mag: 20. 1 3  
+    #negative_blending_flux_sigma_mag: 20. "OGLE I-band" 1
     # Alternative sharp constraint:
     # no_negative_blending_flux: True
     #color constrains, where color=flux_S_dataset_k/flux_S_dataset_m: gauss mu sigma k m 
-    color : gauss 25. 5. "OGLE I-band" "OB03235_MOA.txt" 
+    color : gauss 25. 5.  "OGLE I-band"  1
     #Alternative for binary source models: 
     #color source 1 :  gauss 25. 5. "OGLE I-band" "OB03235_MOA.txt" 
     #and/or 
diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index 66eed00bc..6b9b1fb74 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -1483,12 +1483,15 @@ def _parse_fit_constraints_soft_blending(self, key, value):
         """
         Check if soft fit constraint on blending flux are correctly defined.
         """
-        if isinstance(value, (float, int)):
+        if isinstance(value,  float):
             sigma = float(value)
-            sets = list(range(1, len(self._datasets) + 1))
+            sets = list(range(len(self._datasets)))
+
         else:
+
             sigma = float(value.split()[0])
-            sets = list(map(int, value.split()[1:]))
+            sets = list(map(self._get_no_of_dataset,
+                        shlex.split(value, posix=False)[1:]))
             if len(sets) > len(self._datasets):
                 raise ValueError(
                     'dataset number specified in negative_blending_flux_sigma_mag do not match with provided datasets')
@@ -1515,20 +1518,17 @@ def _parse_fit_constraints_color(self, key, value):
                              words[2] + " " + words[3] + " " + words[4])
         if settings[2] < 0.:
             raise ValueError('sigma cannot be negative: ' + words[2])
+
+        settings[3] = self._get_no_of_dataset(settings[3])
+        settings[4] = self._get_no_of_dataset(settings[4])
+
         if settings[3] == settings[4]:
             raise ValueError(
                 "in " + key + " fluxes have to be from different datasets")
 
-        if isinstance(settings[3], str) and isinstance(settings[4], str):
-            settings[3] = settings[3].strip('"')
-            settings[4] = settings[4].strip('"')
-            settings[3] = self._get_no_of_dataset_by_lable(settings[3])
-            settings[4] = self._get_no_of_dataset_by_lable(settings[4])
-
-        if isinstance(settings[3], int) and isinstance(settings[4], int):
-            if (0 >= settings[3] >= len(self._datasets)-1) or (0 >= settings[4] >= len(self._datasets)-1):
-                raise ValueError(
-                    'dataset specified in color prior do not match with provided datasets')
+        if (0 >= settings[3] >= len(self._datasets)-1) or (0 >= settings[4] >= len(self._datasets)-1):
+            raise ValueError(
+                'dataset specified in color prior do not match with provided datasets')
 
         self._fit_constraints[key] = settings
 
@@ -1569,24 +1569,36 @@ def _parse_fit_constraints_prior(self):
         if len(priors) > 0:
             self._priors = priors
 
-    def _get_no_of_dataset_by_lable(self, label):
+    def _get_no_of_dataset(self, label):
         """
         Returns the index of a dataset with a specific label.
 
         Parameters
         ----------
         label : str
-            Label of the dataset defined by MulensData.plot_properties['label'].
+            Label of the dataset defined by MulensData.plot_properties['label']
+            or sequential index of the dataset
 
         Returns
         -------
         int
-            Sequential index of the dataset [1,2,...,n_datasets]
+            Sequential index of the dataset from [0,1,...,n_datasets-1]
+
         """
-        for (i, dataset) in enumerate(self._datasets):
-            if dataset.plot_properties['label'] == label:
-                return i
-        return -99
+        if '"' in label:
+            label = label.strip('"')
+
+        try:
+            ind = int(label)
+            if 0 <= ind <= len(self._datasets)-1:
+                return ind
+        except:
+            for (i, dataset) in enumerate(self._datasets):
+
+                if dataset.plot_properties['label'] == label:
+                    return i
+            raise KeyError(
+                "Unrecognized dataset lable in fit_constraints/prior: " + label)
 
     def _read_prior_t_E_data(self):
         """
@@ -2244,7 +2256,7 @@ def _run_flux_checks_ln_prior(self, fluxes):
         if key in self._fit_constraints:
 
             for (i, dataset) in enumerate(self._datasets):
-                if i+1 in self._fit_constraints[key][1]:
+                if i in self._fit_constraints[key][1]:
                     blend_index = ((i+1)*self._n_fluxes_per_dataset) - 1
                     if fluxes[blend_index] < 0.:
                         sigma = self._fit_constraints[key][0]

From c7c558b688b12abbf5be855e5a8a9372612edb69 Mon Sep 17 00:00:00 2001
From: mjmroz <mateuszmroz@gmail.com>
Date: Tue, 14 May 2024 01:16:53 +0200
Subject: [PATCH 07/13] docstring improved

---
 examples/example_16/ulens_model_fit.py | 46 ++++++++++----------------
 1 file changed, 18 insertions(+), 28 deletions(-)

diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index 6b9b1fb74..77737f450 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -1570,21 +1570,15 @@ def _parse_fit_constraints_prior(self):
             self._priors = priors
 
     def _get_no_of_dataset(self, label):
-        """
+        """        
         Returns the index of a dataset with a specific label.
-
-        Parameters
-        ----------
-        label : str
-            Label of the dataset defined by MulensData.plot_properties['label']
+        :param label: Label of the dataset defined by MulensData.plot_properties['label']
             or sequential index of the dataset
-
-        Returns
-        -------
-        int
-            Sequential index of the dataset from [0,1,...,n_datasets-1]
-
+        :type label: str
+        :return: Sequential index of the dataset from [0,1,...,n_datasets-1]
+        :rtype: int
         """
+
         if '"' in label:
             label = label.strip('"')
 
@@ -2214,23 +2208,19 @@ def _get_fluxes(self):
         return fluxes
 
     def _sumup_inside_prior(self, fluxes, key, inside, idx_plus):
+        """Calculates the contribution to the ln_prior from specified color constraints
+        
+        :param fluxes:  Array with fluxes of the current model.
+        :type fluxes: array 
+        :param key: constrain key
+        :type key: str
+        :param inside: ln_prior contribution
+        :type inside: float
+        :param idx_plus:  For a single source, idx_plus=0; for a binary source, idx_plus=0 or 1. 
+        :type idx_plus: int
+        :return: evaluated ln_prior contribution
+        :rtype: float
         """
-        Calculates the contribution to the ln_prior from specified color constraints
-        Parameters
-        ----------
-        fluxes : array 
-            Array with fluxes of the current model.
-        key : str
-        inside : float
-        idx_plus : int
-            For a single source, idx_plus=0; 
-            for a binary source, idx_plus=0 or 1. 
-
-        Returns
-        -------
-        inside : float
-        """
-
         settings = self._fit_constraints[key]
         index1 = (settings[3])*self._n_fluxes_per_dataset + idx_plus
         index2 = (settings[4])*self._n_fluxes_per_dataset + idx_plus

From 570e74c221ba139d625eb3c2b4a4ccde68713313 Mon Sep 17 00:00:00 2001
From: Mateusz Mroz <mmroz@grus.astrouw.edu.pl>
Date: Tue, 21 May 2024 17:26:27 +0200
Subject: [PATCH 08/13] docstrings updated, t_0_shift bug solved

---
 examples/example_16/ob03235_2_full.yaml |  6 ++--
 examples/example_16/ulens_model_fit.py  | 45 +++++++++++++++----------
 2 files changed, 30 insertions(+), 21 deletions(-)

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index 59b38c9a3..32cc06d00 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -35,11 +35,11 @@ starting_parameters:
 fit_constraints:
     negative_blending_flux_sigma_mag: 20.  
     #one can specify for which dataset soft constrain on blending flux should be applied: sigma dataset_number(s)
-    #negative_blending_flux_sigma_mag: 20. "OGLE I-band" 1
+    #negative_blending_flux_sigma_mag: [20., "OGLE I-band", "OB03235_MOA.txt"]
     # Alternative sharp constraint:
     # no_negative_blending_flux: True
-    #color constrains, where color=flux_S_dataset_k/flux_S_dataset_m: gauss mu sigma k m 
-    color : gauss 25. 5.  "OGLE I-band"  1
+    #color constrains, where color=flux_S_dataset_k/flux_S_dataset_m: [gauss, mu ,sigma, k, m ,]
+    color : ["gauss", 25., 5. , "OGLE I-band" ,"OB03235_MOA.txt" ]
     #Alternative for binary source models: 
     #color source 1 :  gauss 25. 5. "OGLE I-band" "OB03235_MOA.txt" 
     #and/or 
diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index 77737f450..ec19892f1 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -1570,13 +1570,16 @@ def _parse_fit_constraints_prior(self):
             self._priors = priors
 
     def _get_no_of_dataset(self, label):
-        """        
+        """       
         Returns the index of a dataset with a specific label.
-        :param label: Label of the dataset defined by MulensData.plot_properties['label']
-            or sequential index of the dataset
-        :type label: str
-        :return: Sequential index of the dataset from [0,1,...,n_datasets-1]
-        :rtype: int
+        Parameters :
+            label: *str* ,*int*
+              Label of the dataset defined by MulensData.plot_properties['label'], or name of the data file if label is not specified, 
+              or a sequential index of the dataset.
+      
+        Returns :
+          idx: *int* Sequential index of the dataset from [0,1,...,n_datasets-1]
+
         """
 
         if '"' in label:
@@ -2208,18 +2211,20 @@ def _get_fluxes(self):
         return fluxes
 
     def _sumup_inside_prior(self, fluxes, key, inside, idx_plus):
-        """Calculates the contribution to the ln_prior from specified color constraints
-        
-        :param fluxes:  Array with fluxes of the current model.
-        :type fluxes: array 
-        :param key: constrain key
-        :type key: str
-        :param inside: ln_prior contribution
-        :type inside: float
-        :param idx_plus:  For a single source, idx_plus=0; for a binary source, idx_plus=0 or 1. 
-        :type idx_plus: int
-        :return: evaluated ln_prior contribution
-        :rtype: float
+        """
+        Calculates the contribution to the ln_prior from specified color constraints
+        Parameters :
+            fluxes: *array*  
+                Array with fluxes of the current model.
+            key: *str*
+                constrain key.
+            inside: *float*
+                ln_prior contribution
+            idx_plus: *int*
+                For a single source, idx_plus=0; for a binary source, idx_plus=0 or 1.
+        Returns :
+            inside: *float*
+                Evaluated ln_prior contribution
         """
         settings = self._fit_constraints[key]
         index1 = (settings[3])*self._n_fluxes_per_dataset + idx_plus
@@ -2699,6 +2704,10 @@ def _shift_t_0_in_samples(self):
                     if 'trace' in self._plots:
                         self._samples[:, :, index] = (
                             self._samples[:, :, index] - self._shift_t_0_val)
+            
+            if name in self._fixed_parameters.keys() :
+                 self._shift_t_0_val = int(self._fixed_parameters[name])
+
 
     def _get_fluxes_to_print_EMCEE(self):
         """

From 8e69d2f842b516ede8d64f0736fa2459906e0665 Mon Sep 17 00:00:00 2001
From: mjmroz <mateuszmroz@gmail.com>
Date: Wed, 12 Jun 2024 11:45:18 +0200
Subject: [PATCH 09/13] from last comment

---
 examples/example_16/ob03235_2_full.yaml |  12 +-
 examples/example_16/ulens_model_fit.py  | 208 ++++++++++++++++--------
 2 files changed, 145 insertions(+), 75 deletions(-)

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index 693570755..d59854b41 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -38,16 +38,16 @@ starting_parameters:
     # See also ob08092-o4_starting_file.yaml
 fit_constraints:
     negative_blending_flux_sigma_mag: 20.  
-    #one can specify for which dataset soft constrain on blending flux should be applied: sigma dataset_number(s)
-    #negative_blending_flux_sigma_mag: [20., "OGLE I-band", "OB03235_MOA.txt"]
+    #one can specify for which dataset soft constrain on blending flux should be applied: sigma dataset_label(s)
+    negative_blending_flux_sigma_mag: 20.  "OGLE I-band"  "OB03235_MOA.txt"
     # Alternative sharp constraint:
     # no_negative_blending_flux: True
-    #color constrains, where color=flux_S_dataset_k/flux_S_dataset_m: [gauss, mu ,sigma, k, m ,]
-    color : ["gauss", 25., 5. , "OGLE I-band" ,"OB03235_MOA.txt" ]
+    #color constrains, where color=source_mag_from_dataset_k-source_mag_from_dataset_m: gauss, mu ,sigma, k, m 
+    color : gauss 0.3 0.01 "OGLE I-band" "OB03235_MOA.txt" 
     #Alternative for binary source models: 
-    #color source 1 :  gauss 25. 5. "OGLE I-band" "OB03235_MOA.txt" 
+    #color source 1 :  gauss  0.3 0.01 "OGLE I-band" "OB03235_MOA.txt" 
     #and/or 
-    #color source 2 :  gauss 25. 5. 0 1
+    #color source 2 :  gauss 0.3 0.01  "OGLE I-band" "OB03235_MOA.txt" 
         
     prior:
         t_E: Mroz et al. 2017
diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index a2b728a8b..b9137b19c 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -198,14 +198,14 @@ class UlensModelFit(object):
             saved to temporary files and deleted at the end.
 
             ``multimodal`` (*bool*) - do you want multiple modes in
-            the prosterior to be detected and reported separately?
+            the posterior to be detected and reported separately?
 
             ``n_live_points`` (*int*) - number of live points, default value
             is 400.
 
             ``sampling efficiency`` (*float*) - requested sampling efficiency.
             MultiNest documentation suggests 0.8 (default value) for parameter
-            estimatrion and 0.3 for evidence evalutation.
+            estimation and 0.3 for evidence evaluation.
 
             ``evidence tolerance`` (*float*) - requested tolerance of ln(Z)
             calculation; default is 0.5 and should work well in most cases.
@@ -219,10 +219,31 @@ class UlensModelFit(object):
             blending flux if *True*
 
             ``'negative_blending_flux_sigma_mag'`` - impose a prior that
-            disfavours models with negative blending flux using gaussian prior
+            disfavors models with negative blending flux using gaussian prior
             for negative values; the value provided should be on the order of
             *20.*
 
+            ``'color'`` - specify gaussian prior for colors of the sources.
+            Parameters:
+                *mean* and *sigma* are floats in magnitudes.
+
+            ``'color'`` - specify gaussian prior for colors of the sources.
+            Parameters:
+                *mean* and *sigma* are floats in magnitudes, *dataset_label*
+                are str defined in MulensData.plot_properties['label']
+
+            ``'color source 1'`` - specify gaussian prior for color of
+            the primary source in binary source model.
+            Parameters:
+                *mean* and *sigma* are floats in magnitudes, *dataset_label*
+                are str defined in MulensData.plot_properties['label']
+
+            ``'color source 2'`` - specify gaussian prior for color of
+            the secondary source in binary source model.
+            Parameters:
+                *mean* and *sigma* are floats in magnitudes, *dataset_label*
+                are str defined in MulensData.plot_properties['label']
+
             ``'prior'`` - specifies the priors for quantities. It's also
             a *dict*. Possible key-value pairs:
 
@@ -480,7 +501,7 @@ def _guess_fitting_method(self):
                     "Both starting_parameters and prior_limits were defined "
                     "which makes impossible to choose the fitting method. "
                     "These settings indicate EMCEE and pyMultiNest "
-                    "rescpectively, and cannot be both set.")
+                    "respectively, and cannot be both set.")
             method = "MultiNest"
         if method is None:
             raise ValueError(
@@ -699,7 +720,7 @@ def _check_plots_parameters_best_model(self):
         for key in ['legend', 'rcParams', 'second Y scale']:
             if key in self._plots['best model']:
                 if not isinstance(self._plots['best model'][key], dict):
-                    msg = ('The value of {:} (in best model setttings)'
+                    msg = ('The value of {:} (in best model settings)'
                            'must be a dictionary, but you provided {:}')
                     args = [key, type(self._plots['best model'][key])]
                     raise TypeError(msg.format(*args))
@@ -870,7 +891,7 @@ def _check_model_parameters(self):
 
     def _check_other_fit_parameters(self):
         """
-        Check if there aren't any other inconsistenties between settings
+        Check if there aren't any other inconsistencies between settings
         """
         if self._fit_method == "MultiNest":
             if self._min_values is not None or self._max_values is not None:
@@ -991,7 +1012,7 @@ def _check_residual_files(self):
         """
         Check if provided names of output files with residuals make sense.
         We do not check here if the number of files provided is the same
-        as the number of input datests.
+        as the number of input datasets.
         """
         existing = []
         names = []
@@ -1033,7 +1054,7 @@ def _get_datasets(self):
                 out = '{:} vs {:}'.format(
                     len(self._datasets), len(self._residuals_files))
                 raise ValueError('The number of datasets and files for '
-                                 'residuals ouptut do not match: ' + out)
+                                 'residuals output do not match: ' + out)
 
     def _get_1_dataset(self, file_, kwargs):
         """
@@ -1301,7 +1322,7 @@ def _set_dict_safetly(self, target, source, keys_mapping):
 
     def _check_output_files_MultiNest(self):
         """
-        Check if output files exist and warn about overwrtting them.
+        Check if output files exist and warn about overwriting them.
 
         If they directory doesn't exist then raise error.
         """
@@ -1436,7 +1457,7 @@ def _parse_fit_constraints(self):
         self._priors = None
 
         if self._fit_constraints is None:
-            self._fit_constraints = {"no_negative_blending_flux": False}
+            self._set_default_fit_constraints()
             return
 
         if isinstance(self._fit_constraints, list):
@@ -1446,6 +1467,16 @@ def _parse_fit_constraints(self):
                 "the code. Most probably what you need is:\n" +
                 "fit_constraints = {'no_negative_blending_flux': True}")
 
+        self._parse_fit_constraints_keys()
+        self._parse_fit_constraints_fluxes()
+
+        if 'prior' in self._fit_constraints:
+            self._parse_fit_constraints_prior()
+
+    def _parse_fit_constraints_keys(self):
+        """
+        Validate the keys in the provided fit_constraints.
+        """
         allowed_keys_flux = {
             "no_negative_blending_flux", "negative_blending_flux_sigma_mag"}
 
@@ -1467,22 +1498,37 @@ def _parse_fit_constraints(self):
         if "no_negative_blending_flux" not in self._fit_constraints:
             self._fit_constraints["no_negative_blending_flux"] = False
 
-        if len(used_keys.intersection(allowed_keys_color)) >= 2 and ('color' in used_keys):
-            raise ValueError(
-                'you cannot specify both color and ' + str(used_keys.intersection(allowed_keys_color)-{'color'}))
+        self._check_color_constraints_conflict(allowed_keys_color)
+
+    def _set_default_fit_constraints(self):
+        """
+        Set default fitting constraints if none are provided.
+
+        """
+        self._fit_constraints = {"no_negative_blending_flux": False}
+
+    def _check_color_constraints_conflict(self, allowed_keys_color):
+        """
+        Check for conflicts among color constraints.
+        """
+        used_keys = set(self._fit_constraints.keys())
 
-        for key in self._fit_constraints.keys():
-            value = self._fit_constraints[key]
+        if len(used_keys.intersection(allowed_keys_color)) >= 2:
+            if 'color' in used_keys:
+                raise ValueError(
+                    'You cannot specify both color and ' +
+                    str(used_keys.intersection(allowed_keys_color)-{'color'}))
 
+    def _parse_fit_constraints_fluxes(self):
+        """msg +=
+        Process each constraint fit_constraints.
+        """
+        for key, value in self._fit_constraints.items():
             if key == "negative_blending_flux_sigma_mag":
                 self._parse_fit_constraints_soft_blending(key, value)
-
             elif key in ['color', 'color source 1', 'color source 2']:
                 self._parse_fit_constraints_color(key, value)
 
-        if 'prior' in self._fit_constraints:
-            self._parse_fit_constraints_prior()
-
     def _parse_fit_constraints_soft_blending(self, key, value):
         """
         Check if soft fit constraint on blending flux are correctly defined.
@@ -1498,7 +1544,9 @@ def _parse_fit_constraints_soft_blending(self, key, value):
                         shlex.split(value, posix=False)[1:]))
             if len(sets) > len(self._datasets):
                 raise ValueError(
-                    'dataset number specified in negative_blending_flux_sigma_mag do not match with provided datasets')
+                    "dataset number specified in" +
+                    "negative_blending_flux_sigma_mag" +
+                    "do not match with provided datasets")
 
         self._fit_constraints[key] = [
             mm.Utils.get_flux_from_mag(sigma), sets]
@@ -1507,12 +1555,15 @@ def _parse_fit_constraints_color(self, key, value):
         """
         Check if fit constraint on color are correctly defined.
         """
+        self._check_unique_datasets_labels()
         words = shlex.split(value, posix=False)
+
         if len(words) != 5 or words[0] != 'gauss':
             msg = "Something went wrong in parsing prior for "
             msg += "{:}: {:}"
             if len(words) == 3 and words[0] == 'gauss':
-                msg += ' color priors require the specification of datasets that should be used for color calculation  '
+                msg += "color priors require the specification"
+                msg += "of datasets that should be used for color calculation"
             raise ValueError(msg.format(key, value))
         try:
             settings = [words[0], float(words[1]), float(
@@ -1528,14 +1579,26 @@ def _parse_fit_constraints_color(self, key, value):
 
         if settings[3] == settings[4]:
             raise ValueError(
-                "in " + key + " fluxes have to be from different datasets")
-
-        if (0 >= settings[3] >= len(self._datasets)-1) or (0 >= settings[4] >= len(self._datasets)-1):
+                "in " + key + " color have to be from different datasets")
+        n = len(self._datasets)-1
+        if (0 >= settings[3] >= n) or (0 >= settings[4] >= n):
             raise ValueError(
-                'dataset specified in color prior do not match with provided datasets')
+                "label specified in color prior" +
+                "do not match with provided datasets")
 
         self._fit_constraints[key] = settings
 
+    def _check_unique_datasets_labels(self):
+        """
+        Check if the labels of datasets are unique.
+        """
+        labels = [
+            dataset.plot_properties['label']
+            for dataset in self._datasets
+        ]
+        if len(labels) != len(set(labels)):
+            raise ValueError("Declared labels of datasets must be unique.")
+
     def _parse_fit_constraints_prior(self):
         """
         Check if priors in fit constraint are correctly defined.
@@ -1574,32 +1637,28 @@ def _parse_fit_constraints_prior(self):
             self._priors = priors
 
     def _get_no_of_dataset(self, label):
-        """       
+        """
         Returns the index of a dataset with a specific label.
         Parameters :
             label: *str* ,*int*
-              Label of the dataset defined by MulensData.plot_properties['label'], or name of the data file if label is not specified, 
+              Label of the dataset defined by
+              MulensData.plot_properties['label'],
+              or name of the data file if label is not specified,
               or a sequential index of the dataset.
-      
+
         Returns :
-          idx: *int* Sequential index of the dataset from [0,1,...,n_datasets-1]
+          index: *int*
+          Sequential index of the dataset from [0,1,...,n_datasets-1]
 
         """
 
         if '"' in label:
             label = label.strip('"')
-
-        try:
-            ind = int(label)
-            if 0 <= ind <= len(self._datasets)-1:
-                return ind
-        except:
-            for (i, dataset) in enumerate(self._datasets):
-
-                if dataset.plot_properties['label'] == label:
-                    return i
-            raise KeyError(
-                "Unrecognized dataset lable in fit_constraints/prior: " + label)
+        for (i, dataset) in enumerate(self._datasets):
+            if dataset.plot_properties['label'] == label:
+                return i
+        raise KeyError(
+            "Unrecognized dataset label in fit_constraints/prior: " + label)
 
     def _read_prior_t_E_data(self):
         """
@@ -2214,26 +2273,29 @@ def _get_fluxes(self):
 
         return fluxes
 
-    def _sumup_inside_prior(self, fluxes, key, inside, idx_plus):
+    def _sumup_inside_prior(self, fluxes, key, inside, index_plus):
         """
-        Calculates the contribution to the ln_prior from specified color constraints
+        Calculates the contribution to the ln_prior
+        from specified color constraints
         Parameters :
-            fluxes: *array*  
+            fluxes: *array*
                 Array with fluxes of the current model.
             key: *str*
                 constrain key.
             inside: *float*
                 ln_prior contribution
-            idx_plus: *int*
-                For a single source, idx_plus=0; for a binary source, idx_plus=0 or 1.
+            index_plus: *int*
+                For a single source, index_plus=0;
+                for a binary source, index_plus=0 or 1.
         Returns :
             inside: *float*
                 Evaluated ln_prior contribution
         """
         settings = self._fit_constraints[key]
-        index1 = (settings[3])*self._n_fluxes_per_dataset + idx_plus
-        index2 = (settings[4])*self._n_fluxes_per_dataset + idx_plus
-        value = fluxes[index1]/fluxes[index2]
+        index1 = (settings[3])*self._n_fluxes_per_dataset + index_plus
+        index2 = (settings[4])*self._n_fluxes_per_dataset + index_plus
+        value = mm.Utils.get_mag_from_flux(
+            fluxes[index1])-mm.Utils.get_mag_from_flux(fluxes[index2])
         inside += self._get_ln_prior_for_1_parameter(value, settings[:-2])
 
         return inside
@@ -2250,36 +2312,45 @@ def _run_flux_checks_ln_prior(self, fluxes):
             if fluxes[blend_index] < 0.:
                 return outside
 
+        inside += self._apply_negative_blending_flux_sigma_mag_prior(fluxes)
+        inside += self._apply_color_prior(fluxes)
+
+        return inside
+
+    def _apply_negative_blending_flux_sigma_mag_prior(self, fluxes):
+        """
+        Apply the negative blending flux sigma magnitude priotr.
+        """
+        inside = 0.0
         key = "negative_blending_flux_sigma_mag"
 
         if key in self._fit_constraints:
+            sigma, datasets = self._fit_constraints[key]
+            for i, dataset in enumerate(self._datasets):
+                if i in datasets:
+                    blend_index = ((i + 1) * self._n_fluxes_per_dataset) - 1
+                    if fluxes[blend_index] < 0.0:
+                        inside += -0.5 * (fluxes[blend_index] / sigma) ** 2
 
-            for (i, dataset) in enumerate(self._datasets):
-                if i in self._fit_constraints[key][1]:
-                    blend_index = ((i+1)*self._n_fluxes_per_dataset) - 1
-                    if fluxes[blend_index] < 0.:
-                        sigma = self._fit_constraints[key][0]
-                        inside += -0.5 * (fluxes[blend_index] / sigma)**2
+        return inside
 
+    def _apply_color_prior(self, fluxes):
+        """
+        Apply the color constraints.
+        """
+        inside = 0.0
         key = 'color'
-
         if key in self._fit_constraints:
-            settings = self._fit_constraints[key]
-            if self._n_fluxes_per_dataset == 2:
-                inside = self._sumup_inside_prior(fluxes, key, inside, 0)
-
-            if self._n_fluxes_per_dataset == 3:
-                inside = self._sumup_inside_prior(fluxes, key, inside, 0)
-                inside = self._sumup_inside_prior(fluxes, key, inside, 1)
+            for i in range(self._n_fluxes_per_dataset - 1):
+                inside += self._sumup_inside_prior(fluxes, key, inside, i)
 
         key = 'color source 1'
         if key in self._fit_constraints:
-            inside = self._sumup_inside_prior(fluxes, key, inside, 0)
+            inside += self._sumup_inside_prior(fluxes, key, inside, 0)
 
         key = 'color source 2'
         if key in self._fit_constraints:
-            inside = self._sumup_inside_prior(fluxes, key, inside, 1)
-
+            inside += self._sumup_inside_prior(fluxes, key, inside, 1)
         return inside
 
     def _update_best_model_EMCEE(self, ln_prob, theta, fluxes):
@@ -2708,10 +2779,9 @@ def _shift_t_0_in_samples(self):
                     if 'trace' in self._plots:
                         self._samples[:, :, index] = (
                             self._samples[:, :, index] - self._shift_t_0_val)
-            
-            if name in self._fixed_parameters.keys() :
-                 self._shift_t_0_val = int(self._fixed_parameters[name])
 
+            if name in self._fixed_parameters.keys():
+                self._shift_t_0_val = int(self._fixed_parameters[name])
 
     def _get_fluxes_to_print_EMCEE(self):
         """

From e2bce87cea1926d2d8d39deadff0b42351d81cec Mon Sep 17 00:00:00 2001
From: mjmroz <mateuszmroz@gmail.com>
Date: Wed, 12 Jun 2024 11:50:00 +0200
Subject: [PATCH 10/13] small change

---
 examples/example_16/ulens_model_fit.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index b9137b19c..8d15c4df8 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -222,11 +222,7 @@ class UlensModelFit(object):
             disfavors models with negative blending flux using gaussian prior
             for negative values; the value provided should be on the order of
             *20.*
-
-            ``'color'`` - specify gaussian prior for colors of the sources.
-            Parameters:
-                *mean* and *sigma* are floats in magnitudes.
-
+            
             ``'color'`` - specify gaussian prior for colors of the sources.
             Parameters:
                 *mean* and *sigma* are floats in magnitudes, *dataset_label*

From 78ec79df1f610ed6677a152421e568e1a1d33953 Mon Sep 17 00:00:00 2001
From: mjmroz <mateuszmroz@gmail.com>
Date: Wed, 12 Jun 2024 12:12:46 +0200
Subject: [PATCH 11/13] small correction

---
 source/MulensModel/data | 1 +
 1 file changed, 1 insertion(+)
 create mode 100644 source/MulensModel/data

diff --git a/source/MulensModel/data b/source/MulensModel/data
new file mode 100644
index 000000000..e67b45590
--- /dev/null
+++ b/source/MulensModel/data
@@ -0,0 +1 @@
+../../data
\ No newline at end of file

From 99d1f5bde0be3e62b2706ff612bf734624269dc2 Mon Sep 17 00:00:00 2001
From: mjmroz <mateuszmroz@gmail.com>
Date: Thu, 13 Jun 2024 03:15:39 +0200
Subject: [PATCH 12/13] final corrections

---
 examples/example_16/ob03235_2_full.yaml | 2 +-
 examples/example_16/ulens_model_fit.py  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/examples/example_16/ob03235_2_full.yaml b/examples/example_16/ob03235_2_full.yaml
index d59854b41..6ae84dba5 100644
--- a/examples/example_16/ob03235_2_full.yaml
+++ b/examples/example_16/ob03235_2_full.yaml
@@ -39,7 +39,7 @@ starting_parameters:
 fit_constraints:
     negative_blending_flux_sigma_mag: 20.  
     #one can specify for which dataset soft constrain on blending flux should be applied: sigma dataset_label(s)
-    negative_blending_flux_sigma_mag: 20.  "OGLE I-band"  "OB03235_MOA.txt"
+    #negative_blending_flux_sigma_mag: 20.  "OGLE I-band"  "OB03235_MOA.txt"
     # Alternative sharp constraint:
     # no_negative_blending_flux: True
     #color constrains, where color=source_mag_from_dataset_k-source_mag_from_dataset_m: gauss, mu ,sigma, k, m 
diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index 8d15c4df8..316dc6b99 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -39,7 +39,7 @@
 except Exception:
     raise ImportError('\nYou have to install MulensModel first!\n')
 
-__version__ = '0.36.3'
+__version__ = '0.37.0'
 
 
 class UlensModelFit(object):

From b7b18ab1bf0d28c067759006c6ae00400adee465 Mon Sep 17 00:00:00 2001
From: mjmroz <mateuszmroz@gmail.com>
Date: Thu, 13 Jun 2024 03:28:48 +0200
Subject: [PATCH 13/13]  whitespace removed

---
 examples/example_16/ulens_model_fit.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/examples/example_16/ulens_model_fit.py b/examples/example_16/ulens_model_fit.py
index 316dc6b99..571e59db5 100644
--- a/examples/example_16/ulens_model_fit.py
+++ b/examples/example_16/ulens_model_fit.py
@@ -222,7 +222,7 @@ class UlensModelFit(object):
             disfavors models with negative blending flux using gaussian prior
             for negative values; the value provided should be on the order of
             *20.*
-            
+
             ``'color'`` - specify gaussian prior for colors of the sources.
             Parameters:
                 *mean* and *sigma* are floats in magnitudes, *dataset_label*