Update docstrings

matpam/extract_2Dplot.m

@@ -1,5 +1,5 @@
 % Extract 2D histogram drawn in PAM and exported to a Matlab figure
-
+%
 % Specify any additional dictionary elements to be included in the json
 % output file as name-value pairs. 
 % 
@@ -10,8 +10,8 @@
 % - gamma_factor (float)
 % - donor_lifetime (float)
 %
-% Example: extract_2Dplot('photons_per_window', 5, 'direct_excitation', 0.046, ... 
-%                         'crosstalk', 0.11, 'gamma_factor', 0.89)
+% Example: extract_2Dplot('photons_per_window', 5, 'direct_excitation', 0.02, ... 
+%                         'crosstalk', 0.1, 'gamma_factor', 0.7)
 %
 
 function extract_2Dplot(varargin)

matpam/write_FCS.m

@@ -1,5 +1,5 @@
 % FCS data from workspace to file
-
+%
 % FCS : struct
 %       columns are "time", "data", "error", "fit" and "residuals"
 % average_counts : column vector (n x 1 double) => manually copy from table into a column vector [c1;c2;...] on the Matlab command line

pypam/pamplot.py

@@ -524,6 +524,18 @@ def PR2FRET(self, proximity_ratio, verbose=False):
     def sigma_shotnoise(self, verbose=False):
         """
         Calculate shot noise limit from Burst Variance Analysis (BVA)
+
+        Notes
+        -----
+        Preprocessing done in PAM: Each burst is segmented into M samples of n consecutive photons 
+        (n is set in Dynamic Analysis Window in PAM). The transfer efficiency (or proximity ratio) is 
+        calculated for each n-photon sample and the standard deviation is calculated from these M FRET values,
+        giving one std per burst.
+        Here: the shot noise limit is calculated as sqrt(PR*(1-PR)/n)
+
+        References
+        ----------
+        Torella, Holden, Santosio, Hohlbein, Kapanidis, Biophysical J., 2011.
         """
         self.BVA = {}
         self.BVA['PR'] = np.linspace(0,1,1000)