model: add start values and frozen values to the printed parameter ta…

…ble (#369)
JeschkeLab · Aug 10, 2022 · d2dd2eb · d2dd2eb
1 parent 2112615
commit d2dd2eb
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Showing 4 changed files with 114 additions and 113 deletions.
diff --git a/deerlab/model.py b/deerlab/model.py
@@ -620,17 +620,18 @@ def _parameter_table(self):
     """)
         string += '\n'
         table = []
-        table.append(['Name','Lower','Upper','Type','Frozen','Unit','Description'])  
-        alignment = ['<','^','^','^','^','^','<']
+        table.append(['Name','Lower','Start','Upper','Type','Frozen','Unit','Description'])  
+        alignment = ['<','^','^','^','^','^','^','<']
         for n,paramname in enumerate(self._parameter_list(order='vector')): 
             param_str = paramname
             lb_str = f'{np.atleast_1d(getattr(self,paramname).lb)[0]:5.3g}'
             ub_str = f'{np.atleast_1d(getattr(self,paramname).ub)[0]:5.3g}'
+            par0_str = f'{np.atleast_1d(getattr(self,paramname).par0)[0]:5.3g}' if np.atleast_1d(getattr(self,paramname).par0)[0] is not None else "-"
             linear_str = "linear" if np.all(getattr(self,paramname).linear) else "nonlin"
-            frozen_str = "Yes" if np.all(getattr(self,paramname).frozen) else "No"
+            frozen_str = f'{np.atleast_1d(getattr(self,paramname).value)[0]:5.3g}' if np.all(getattr(self,paramname).frozen) else "No"
             unit_str = str(getattr(self,paramname).unit)
             desc_str = str(getattr(self,paramname).description)
-            table.append([param_str,lb_str,ub_str,linear_str,frozen_str,unit_str,desc_str])
+            table.append([param_str,lb_str,par0_str,ub_str,linear_str,frozen_str,unit_str,desc_str])
         string += formatted_table(table,alignment)
         return string
     #---------------------------------------------------------------------------------------

diff --git a/docsrc/source/basics.rst b/docsrc/source/basics.rst
@@ -34,12 +34,12 @@ Parametric distance distributions
                 Signature: (r, mean, std)
                 Constants: [r]
                 Parameter Table: 
-                ======= ======= ======= ======== ======== ======= ==================== 
-                Name    Lower   Upper    Type    Frozen   Units   Description         
-                ======= ======= ======= ======== ======== ======= ==================== 
-                mean        1      20   nonlin     No      nm     Mean                
-                std      0.05     2.5   nonlin     No      nm     Standard deviation  
-                ======= ======= ======= ======== ======== ======= ==================== 
+                ====== ======= ======= ======= ======== ======== ====== ==================== 
+                Name   Lower   Start   Upper    Type    Frozen   Unit   Description         
+                ====== ======= ======= ======= ======== ======== ====== ==================== 
+                mean       1     3.5      20   nonlin     No      nm    Mean                
+                std     0.05     0.2     2.5   nonlin     No      nm    Standard deviation  
+                ====== ======= ======= ======= ======== ======== ====== ==================== 
 
                 
 In least-squares fitting, non-parametric distance distributions make fewer assumptions about the distribution than parametric distance distributions. They are more flexible and introduce less bias.
@@ -57,12 +57,12 @@ In DeerLab, all inter-molecular contributions to the dipolar modulation (i.e. th
         Signature: (t, conc, lam)
         Constants: [t]
         Parameter Table: 
-        ====== ======= ======= ======== ======== ======= ==================== 
-         Name   Lower   Upper    Type    Frozen   Units   Description         
-        ====== ======= ======= ======== ======== ======= ==================== 
-         conc    0.01   5e+03   nonlin     No      μM     Spin concentration  
-         lam        0       1   nonlin     No             Pathway amplitude   
-        ====== ======= ======= ======== ======== ======= ==================== 
+        ====== ======= ======= ======= ======== ======== ====== ==================== 
+        Name   Lower   Start   Upper    Type    Frozen   Unit   Description         
+        ====== ======= ======= ======= ======== ======== ====== ==================== 
+        conc    0.01      50   5e+03   nonlin     No      μM    Spin concentration  
+        lam        0       1       1   nonlin     No            Pathway amplitude   
+        ====== ======= ======= ======= ======== ======== ====== ==================== 
 
 
 DeerLab's :ref:`background models<modelsref_bg>` fall into two categories, physical and phenomenological: 

diff --git a/docsrc/source/dipolar_guide_modelling.rst b/docsrc/source/dipolar_guide_modelling.rst
@@ -89,14 +89,14 @@ A full summary of the constructed model(s) can be inspected by printing the mode
     Signature: (mod, reftime, conc, P)
     Constants: []
     Parameter Table: 
-    ========= ======= ======= ======== ======== ======= ====================================== 
-     Name      Lower   Upper    Type    Frozen   Units   Description                           
-    ========= ======= ======= ======== ======== ======= ====================================== 
-     mod           0       1   nonlin     No             Modulation depth                      
-     reftime     0.4     0.6   nonlin     No      μs     Refocusing time                       
-     conc       0.01   5e+03   nonlin     No      μM     Spin concentration                    
-     P             0     inf   linear     No     None    Non-parametric distance distribution  
-    ========= ======= ======= ======== ======== ======= ====================================== 
+    ========= ======= ======= ======= ======== ======== ====== ====================================== 
+    Name      Lower   Start   Upper    Type    Frozen   Unit   Description                           
+    ========= ======= ======= ======= ======== ======== ====== ====================================== 
+    mod           0    0.01       1   nonlin     No            Modulation depth                      
+    reftime    -inf       0     inf   nonlin     No      μs    Refocusing time                       
+    conc       0.01      50   5e+03   nonlin     No      μM    Spin concentration                    
+    P             0       0     inf   linear     No     nm⁻¹   Non-parametric distance distribution  
+    ========= ======= ======= ======= ======== ======== ====== ====================================== 
 
 
 From this point on, the model can be modified, manipulated and expanded freely as any other DeerLab model. Check out the :ref:`modelling guide <modelling_guide>` for more details and instructions on model manipulation.