Add Ridme example and changes examples from deadtime to tmin

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
 

examples/basic/ex_fitting_4pdeer_compactness.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    
 
 # Distance vector
 r = np.arange(2,5,0.025) # nm

examples/basic/ex_fitting_4pdeer_gauss.py

@@ -21,15 +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(1.5,6,0.01) # nm

examples/basic/ex_fitting_5pdeer.py

@@ -29,16 +29,17 @@
 file = 'example_5pdeer_1.DTA'
 
 # Experimental parameters (reversed 5pDEER)
-tau1 = 3.9               # First inter-pulse delay, μs
-tau2 = 3.7               # Second inter-pulse delay, μs
-tau3 = 0.5               # Third inter-pulse delay, μs
-deadtime = 0.3           # Acquisition deadtime, μs
+tau1 = 3.9              # First inter-pulse delay, μs
+tau2 = 3.7              # Second inter-pulse delay, μs
+tau3 = 0.5              # Third inter-pulse delay, μs
+tmin = 0.3              # Start time, μs
 
 # Load the experimental data
 t,Vexp = dl.deerload(path + file)
 Vexp = dl.correctphase(Vexp)    # Phase correction
-Vexp = Vexp/np.max(Vexp)         # Rescaling (aesthetic)
-t = t + deadtime       # Account for deadtime
+Vexp = Vexp/np.max(Vexp)        # Rescaling (aesthetic)
+t = t - t[0]                    # Account for zerotime
+t = t + tmin      
 
 # Distance vector
 r = np.arange(3,5,0.025) # nm

examples/basic/ex_fitting_ridme.py

@@ -0,0 +1,86 @@
+# %% [markdown]
+""" 
+Basic analysis of a RIDME signal
+-------------------------------------------------------------------------
+
+Fit a simple RIDME signal with a model with a non-parametric
+distribution and a stretched exponetial background, using Tikhonov regularization.
+""" 
+
+import numpy as np
+import matplotlib.pyplot as plt
+import deerlab as dl
+
+
+# %%
+
+# File location
+path = '../data/'
+file = 'example_ridme_1.DTA'
+
+# Experimental parameters
+tau1 = 0.4      # First inter-pulse delay, μs
+tau2 = 4.2      # Second inter-pulse delay, μs
+tmin = 0.28  # 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 - t[0]             # Account for zerotime
+t = t + tmin             
+
+# Distance vector
+r = np.linspace(1.5,6,50) # nm
+
+# Construct the model
+experimentmodel = dl.ex_ridme(tau1,tau2, pathways=[1])
+Vmodel = dl.dipolarmodel(t,r,Bmodel=dl.bg_strexp, experiment =experimentmodel)
+
+# Fit the model to the data
+results = dl.fit(Vmodel,Vexp)
+
+# Print results summary
+print(results)
+
+#%%
+
+# Extract fitted dipolar signal
+Vfit = results.model
+
+# Extract fitted distance distribution
+Pfit = results.P
+Pci95 = results.PUncert.ci(95)
+Pci50 = results.PUncert.ci(50)
+
+# Extract the unmodulated contribution
+Bfcn = lambda mod,decay,stretch,reftime: results.P_scale*(1-mod)*dl.bg_strexp(t-reftime,decay,stretch)
+Bfit = results.evaluate(Bfcn)
+Bci = results.propagate(Bfcn).ci(95)
+
+plt.figure(figsize=[6,7])
+violet = '#4550e6'
+plt.subplot(211)
+# Plot experimental and fitted data
+plt.plot(t,Vexp,'.',color='grey',label='Data')
+plt.plot(t,Vfit,linewidth=3,color=violet,label='Fit')
+plt.plot(t,Bfit,'--',linewidth=3,color=violet,label='Unmodulated contribution')
+plt.fill_between(t,Bci[:,0],Bci[:,1],color=violet,alpha=0.3)
+plt.legend(frameon=False,loc='best')
+plt.xlabel('Time $t$ (μs)')
+plt.ylabel('$V(t)$ (arb.u.)')
+# Plot the distance distribution
+plt.subplot(212)
+plt.plot(r,Pfit,color=violet,linewidth=3,label='Fit')
+plt.fill_between(r,Pci95[:,0],Pci95[:,1],alpha=0.3,color=violet,label='95%-Conf. Inter.',linewidth=0)
+plt.fill_between(r,Pci50[:,0],Pci50[:,1],alpha=0.5,color=violet,label='50%-Conf. Inter.',linewidth=0)
+plt.legend(frameon=False,loc='best')
+plt.autoscale(enable=True, axis='both', tight=True)
+plt.xlabel('Distance $r$ (nm)')
+plt.ylabel('$P(r)$ (nm$^{-1}$)')
+plt.tight_layout()
+plt.show()
+
+# %%

examples/basic/ex_restraints_4pdeer.py

@@ -28,15 +28,15 @@
 # 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 + tmin                # Account for zerotime
 
 # Distance vector
 r = np.arange(2,6,0.05) # nm