Add Ridme example and changes examples from deadtime to tmin (#446)

* Add basic RIDME example

* Change from deadtime to tmin

* Change RIDME stretch value

* Replaced all Acquisition Deadtime with Start time.

* Missed one example

* Bug fix with propagate and evaluate functions

The propagate and evaluate functions had a bug that stopped them working on functions.

deerlab/fit.py

@@ -358,6 +358,8 @@ def fit(model_, y, *constants, par0=None, penalties=None, bootstrap=0, noiselvl=
         Fitted parameter vector ordered according to the model parameter indices.
     paramUncert : :ref:`UQResult`
         Uncertainty quantification of the parameter vector ordered according to the model parameter indices.
+    paramlist : list
+        List of the fitted parameter names ordered according to the model parameter indices.
     model : ndarray
         Fitted model response.     
     regparam : scalar
@@ -505,6 +507,15 @@ def bootstrap_fcn(ysim):
     FitResult_dict = {key: getattr(fitresults,key) for key in ['y','mask','param','paramUncert','model','cost','plot','residuals','stats','regparam','regparam_stats','__plot_inputs']}
     _paramlist = model._parameter_list('vector')
 
+    param_idx = [[] for _ in _paramlist]
+    idxprev = 0
+    for islinear in [False,True]:
+        for n,param in enumerate(_paramlist):
+            if np.all(getattr(model,param).linear == islinear):
+                N = len(np.atleast_1d(getattr(model,param).idx))
+                param_idx[n] = np.arange(idxprev,idxprev + N)
+                idxprev += N  
+
     # Enforce normalization of the linear parameters (if needed) for the final output
     FitResult_param_,FitResult_paramuq_ = FitResult_param.copy(),FitResult_paramuq.copy()
     if normalization:
@@ -526,7 +537,7 @@ def _scale(x):
         noiselvl = noiselvl[0]
 
     # Generate FitResult object from all the dictionaries
-    fitresult = FitResult({**FitResult_param_,**FitResult_paramuq_, **FitResult_dict,'penweights':penweights,'noiselvl':noiselvl}) 
+    fitresult = FitResult({**FitResult_param_,**FitResult_paramuq_, **FitResult_dict,'penweights':penweights,'noiselvl':noiselvl,'paramlist':_paramlist, '_param_idx':param_idx}) 
 
     fitresult._summary = _print_fitresults(fitresult,model)
 

deerlab/fitresult.py

@@ -87,45 +87,76 @@ def _extarct_params_from_model(self, model):
         if callable(model):
             try:
                 modelparam = model._parameter_list('vector')
+                function_type=False
             except AttributeError:
+                function_type=True
                 modelparam = inspect.getfullargspec(model).args
 
         if not hasattr(self,'param'):
             raise ValueError('The fit object does not contain any fitted parameters.')
 
-        # Enforce model normalization
-        normfactor_keys = []
-        for key in model._parameter_list():
-            param = getattr(model,key)
-            if np.all(param.linear):
-                if param.normalization is not None:
-                    normfactor_key = f'{key}_scale'
-                    normfactor_keys.append(normfactor_key)
-                    try:
-                        model.addnonlinear(normfactor_key,lb=-np.inf,ub=np.inf,par0=1,description=f'Normalization factor of {key}')
-                        getattr(model,normfactor_key).freeze(1)
-                    except KeyError:
-                        pass
+        # # Enforce model normalization
+        # normfactor_keys = []
+        # for key in modelparam:
+        #     param = getattr(model,key)
+        #     if np.all(param.linear):
+        #         if param.normalization is not None:
+        #             normfactor_key = f'{key}_scale'
+        #             normfactor_keys.append(normfactor_key)
+        #             try:
+        #                 model.addnonlinear(normfactor_key,lb=-np.inf,ub=np.inf,par0=1,description=f'Normalization factor of {key}')
+        #                 getattr(model,normfactor_key).freeze(1)
+        #             except KeyError:
+        #                 pass
 
 
-        # Get some basic information on the parameter vector
-        modelparam = model._parameter_list(order='vector')
-        param_idx = [[] for _ in model._parameter_list('vector')]
-        idxprev = 0
-        for islinear in [False,True]:
-            for n,param in enumerate(model._parameter_list('vector')):
-                if np.all(getattr(model,param).linear == islinear):
-                    N = len(np.atleast_1d(getattr(model,param).idx))
-                    param_idx[n] = np.arange(idxprev,idxprev + N)
-                    idxprev += N  
-
-        params = {key : fitvalue if len(fitvalue)>1 else fitvalue[0] for key,fitvalue in zip(modelparam,[self.param[idx] for idx in param_idx])}
+        # # Get some basic information on the parameter vector
+        # modelparam = model._parameter_list(order='vector')
+        # param_idx = [[] for _ in model._parameter_list('vector')]
+        # idxprev = 0
+        # for islinear in [False,True]:
+        #     for n,param in enumerate(model._parameter_list('vector')):
+        #         if np.all(getattr(model,param).linear == islinear):
+        #             N = len(np.atleast_1d(getattr(model,param).idx))
+        #             param_idx[n] = np.arange(idxprev,idxprev + N)
+        #             idxprev += N  
+
+        fitparams = {key : fitvalue if len(fitvalue)>1 else fitvalue[0] for key, fitvalue in zip(self.paramlist,[self.param[idx] for idx in self._param_idx])}
         # Check that all parameters are in the fit object
         for param in modelparam:
-            if not param in params: 
+            if not param in fitparams: 
                 raise KeyError(f'The fit object does not contain the {param} parameter.')
+
+
+        params = {param : fitparams[param] for param in modelparam}
+        params_idx = [self._param_idx[self.paramlist.index(param)] for param in modelparam]
+
+        return modelparam, params, params_idx
+
+    def _extract_params_from_function(self,function):
+        """
+        Extracts the fitted parameters from a callable function. 
+
+        Assumes that all parameters are length 1.
+        
+        """
+        # Get the parameter names from the function definition
+        modelparam = inspect.getfullargspec(function).args
+
+        fitparam_idx = self._param_idx
+
+        # Get the parameter values from the fit object
+        fitparams = {param : self.param[i] for i,param in enumerate(self.paramlist)}
+        params = {param : fitparams[param] for param in modelparam}
+        params_idx = [fitparam_idx[self.paramlist.index(param)] for param in modelparam]
+        # fitparams = {key : fitvalue if len(fitvalue)>1 else fitvalue[0] for key, fitvalue in zip(modelparam,[self.param[idx] for idx in fitparam_idx])}
+
+
+
+
+        return modelparam, params, params_idx
+
 
-        return modelparam, params, param_idx
 
     def evaluate(self, model, *constants):
     # ----------------------------------------------------------------------------
@@ -154,9 +185,14 @@ def evaluate(self, model, *constants):
         response : array_like 
             Model response at the fitted parameter values. 
         """
-
-        modelparam, params, _ = self._extarct_params_from_model(model)
-        parameters = {param: params[param] for param in modelparam}
+        try:
+            modelparam = model._parameter_list('vector')
+            modelparam, fitparams, fitparam_idx = self._extarct_params_from_model(model)
+        except AttributeError:
+            modelparam, fitparams, fitparam_idx = self._extract_params_from_function(model)
+
+
+        parameters = {param: fitparams[param] for param in modelparam}
 
         # Evaluate the input model
         response = model(*constants,**parameters)
@@ -195,11 +231,16 @@ def propagate(self, model, *constants, lb=None, ub=None):
             Uncertainty quantification of the model's response.
         """
 
-        modelparam,_, param_idx = self._extarct_params_from_model(model)
-        # Determine the indices of the subset of parameters the model depends on
-        subset = [param_idx[np.where(np.asarray(modelparam)==param)[0][0]] for param in modelparam]
+        try:
+            modelparam = model._parameter_list('vector')
+            modelparam, fitparams, fitparam_idx = self._extarct_params_from_model(model)
+
+        except AttributeError:
+            modelparam, fitparams, fitparam_idx = self._extract_params_from_function(model)
+
+
         # Propagate the uncertainty from that subset to the model
-        modeluq = self.paramUncert.propagate(lambda param: model(*constants,*[param[s] for s in subset]),lb,ub)
+        modeluq = self.paramUncert.propagate(lambda param: model(*constants,*[param[s] for s in fitparam_idx]),lb,ub)
         return modeluq
 
 

examples/advanced/ex_comparing_uncertainties.py

@@ -27,15 +27,16 @@
 # Experimental parameters
 tau1 = 0.3      # First inter-pulse delay, μs
 tau2 = 4.0      # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1      # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 
 # Pre-processing
 Vexp = dl.correctphase(Vexp) # Phase correction
 Vexp = Vexp/np.max(Vexp)     # Rescaling (aesthetic)
-t = t + deadtime             # Account for deadtime
+t = t - t[0]                 # Account for zerotime
+t = t + tmin   
 
 # Distance vector
 r = np.arange(2,6,0.05) # nm

examples/advanced/ex_dipolarpathways_selection.py

@@ -25,16 +25,16 @@
 # Experimental parameters
 tau1 = 0.5      # First inter-pulse delay, μs
 tau2 = 3.5      # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1      # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 
 # Pre-processing
 Vexp = dl.correctphase(Vexp) # Phase correction
 Vexp = Vexp/np.max(Vexp)     # Rescaling (aesthetic)
-t = t + deadtime             # Account for deadtime
-
+t = t - t[0]                 # Account for zerotime
+t = t + tmin   
 # Construct the distance vector
 r = np.arange(2,5,0.05)
 

examples/advanced/ex_extracting_gauss_constraints.py

@@ -23,15 +23,16 @@
 # Experimental parameters
 tau1 = 0.3      # First inter-pulse delay, μs
 tau2 = 4.0      # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1      # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 
 # Pre-processing
 Vexp = dl.correctphase(Vexp) # Phase correction
 Vexp = Vexp/np.max(Vexp)     # Rescaling (aesthetic)
-t = t + deadtime             # Account for deadtime
+t = t - t[0]                 # Account for zerotime
+t = t + tmin   
 
 # Construct the dipolar signal model
 r = np.arange(2,6,0.02)

examples/advanced/ex_forcefield_fit.py

@@ -48,15 +48,16 @@ def forcefield_P(c0,c1,c2,c3):
 # Experimental parameters
 tau1 = 0.3      # First inter-pulse delay, μs
 tau2 = 5.0      # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1      # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 
 # Pre-processing
 Vexp = dl.correctphase(Vexp) # Phase correction
 Vexp = Vexp/np.max(Vexp)     # Rescaling (aesthetic)
-t = t + deadtime             # Account for deadtime
+t = t - t[0]                     # Account for zerotime
+t = t + tmin   
 
 # Construct the energy and distance distribution models
 forcefield_energymodel = dl.Model(forcefield_energy)

examples/advanced/ex_global_twostates_parametric.py

@@ -30,7 +30,7 @@
 # Experimental parameters
 tau1 = 0.4  # First inter-pulse delay, μs
 tau2 = 4.5  # Second inter-pulse delay, μs
-deadtime = 0.2  # Acquisition deadtime, μs
+tmin = 0.2  # Start time, μs
 
 Vmodels, ts, Vexps = [], [], []
 for file in files:
@@ -39,10 +39,11 @@
     t, Vexp = dl.deerload(path + file)
 
     # Pre-processing
-    Vexp = dl.correctphase(Vexp)  # Phase correction
-    Vexp = Vexp / np.max(Vexp)  # Rescaling (aesthetic)
-    t = t + deadtime  # Account for deadtime
-
+    Vexp = dl.correctphase(Vexp)    # Phase correction
+    Vexp = Vexp / np.max(Vexp)      # Rescaling (aesthetic)
+    t = t - t[0]                    # Account for zerotime
+    t = t + tmin  
+
     # Put the datasets into lists
     ts.append(t)
     Vexps.append(Vexp)

examples/advanced/ex_identifiability_analysis.py

@@ -23,15 +23,16 @@
 # Experimental parameters
 tau1 = 0.3      # First inter-pulse delay, μs
 tau2 = 4.0      # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1      # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 
 # Pre-processing
 Vexp = dl.correctphase(Vexp) # Phase correction
 Vexp = Vexp/np.max(Vexp)     # Rescaling (aesthetic)
-t = t + deadtime             # Account for deadtime
+t = t - t[0]                 # Account for zerotime
+t = t + tmin
 
 # Truncate the signal
 Vexp_truncated = Vexp[t<=2]

examples/advanced/ex_long_threespin_analysis.py

@@ -20,7 +20,7 @@
 files = [f'../data/triradical_protein_deer_{dB}dB.DTA' for dB in [0,6,9]]
 
 # Experiment information
-t0  = 0.280 # Acquisition deadtime, μs
+t0  = 0.280 # Start time, μs
 tau1 = 0.40 # First interpulse delay, μs
 tau2 = 9.00 # Second interpulse delay, μs
 
@@ -34,7 +34,7 @@
     t,Vexp, descriptor = dl.deerload(file,full_output=True)
     t = t[:-80]
     Vexp = Vexp[:-80]
-    # Adjust the start time
+    # Adjust the Start time
     t = t - t[0] + t0
 
     # Pre-processing

examples/advanced/ex_multigauss_fitting_4pdeer.py

@@ -24,15 +24,16 @@
 # Experimental parameters
 tau1 = 0.3  # First inter-pulse delay, μs
 tau2 = 4.0  # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1  # Start time, μs
 
 # Load the experimental data
 t, Vexp = dl.deerload(path + file)
 
 # Pre-processing
-Vexp = dl.correctphase(Vexp)  # Phase correction
-Vexp = Vexp / np.max(Vexp)  # Rescaling (aesthetic)
-t = t + deadtime  # Account for deadtime
+Vexp = dl.correctphase(Vexp)    # Phase correction
+Vexp = Vexp / np.max(Vexp)      # Rescaling (aesthetic)
+t = t - t[0]                    # Account for zerotime
+t = t + tmin
 
 # Maximal number of Gaussians in the models
 Nmax = 5

examples/advanced/ex_profileanalysis.py

@@ -19,15 +19,16 @@
 # Experimental parameters
 tau1 = 0.3      # First inter-pulse delay, μs
 tau2 = 4.0      # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1      # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 
 # Pre-processing
 Vexp = dl.correctphase(Vexp) # Phase correction
 Vexp = Vexp/np.max(Vexp)     # Rescaling (aesthetic)
-t = t + deadtime             # Account for deadtime
+t = t - t[0]                 # Account for zerotime
+t = t + tmin
 
 # Distance vector
 r = np.arange(2,5,0.05) # nm

examples/basic/ex_bootstrapping.py

@@ -30,15 +30,16 @@
 # Experimental parameters
 tau1 = 0.3      # First inter-pulse delay, μs
 tau2 = 4.0      # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1      # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 
 # Pre-processing
 Vexp = dl.correctphase(Vexp) # Phase correction
 Vexp = Vexp/np.max(Vexp)     # Rescaling (aesthetic)
-t = t + deadtime             # Account for deadtime
+t = t - t[0]                 # Account for zerotime
+t = t + tmin    
 
 # Distance vector
 r = np.linspace(2,5,100) # nm

examples/basic/ex_fitting_4pdeer.py

@@ -21,16 +21,16 @@
 # Experimental parameters
 tau1 = 0.3      # First inter-pulse delay, μs
 tau2 = 4.0      # Second inter-pulse delay, μs
-deadtime = 0.1  # Acquisition deadtime, μs
+tmin = 0.1      # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 
 # Pre-processing
 Vexp = dl.correctphase(Vexp) # Phase correction
 Vexp = Vexp/np.max(Vexp)     # Rescaling (aesthetic)
-t = t + deadtime             # Account for deadtime
-
+t = t - t[0]                  # Account for zerotime
+t = t + tmin    
 # Distance vector
 r = np.arange(2.5,5,0.01) # nm