postprocessingscript.md

@@ -14,11 +14,37 @@ diagnostics
 ```
 By typing the function name you are calling the diagnostics script. This function does not contain any input values but directly starts accessing your loaded dataset. Figures will be generated and you can browse them as you would like. The figures contain some visual representations of the calculations that are being preformed, and on the quality of the data file. Follow along below for a more in depth view of some of the figures
 
-*Time Flags*
+**Data Quality**
+The first plot is a general overview of how much good data has been found in your data set. If the % of time and the % of channels of your data is very high you might want to reconsider your experiment modality. From the figure below:
+
+![diag4](/uploads/0264d39ab0337a36484d1867fd9bb4bf/diag4.png)
+
+Looking into this further you can see from the editor printout that their is:
+ * 41 bad channels out of 135
+ * ~21% of data time flagged as bad
+
+The designation of *Bad* is based off a few simple calculations which parameters are controlled by the configuration files. We will look at these calculations  in more detail below.
+
+![diag7](/uploads/dc996102b39d4da75a173af582a53db6/diag7.png)
+
+*As a side Note is is possible but not likely for a channel to be flagged for more than one of these classifications. This would mean diagnostics will find high numbers of bad channels but a lower number of removals.*
 
 *Channel Flags*
+Channel flags are the way that channels are identified and staged for removal. A few examples of cahnnel flag calculations are:
+ * Standard Deviation (Comicaly Bad)
+ * High correlation (Bridging)
+ * Low Correlation
+![diag1](/uploads/e847ad6b6edadcc445473fe0f31cfae1/diag1.png)
+
+The figures below are separated into 3 sub figures to show how the calculations are done.
+For example lets review the Standard deviation plot (Figure: 4) subplots from left to right.  
+ * Sub Figure 1 
+This figure are the raw standard deviation values for each channels for every epoch of time. The colour represents how much deviation there is at the point. In this particular case the red colour means there is a high deviation and the blue means lower. 
+ * Sub Figure 2
+This plot expands on thevalues from the first subfigure. In this plot only the bvery highest values are slected on ploted as a 0 or 1. In this particular case blue means that the designated epoch was not over the specified criteria for time removal.
+ * Sub Figure 3
 
-*Data Quality
+*Time Flags*
 
 *Component Classification*