PE-script-Tutorial.md

@@ -17,7 +17,8 @@ You can view the options of the PE script by running
 
 That will show: 
 ```
-usage: pe_pyGWB [-h] --path_to_file PATH_TO_FILE [--Model MODEL] [--Model_Parameters_Dictionary MODEL_PARAMETERS_DICTIONARY] [--output_dir OUTPUT_DIR] [--fref FREF]
+usage: pe_pyGWB [-h] --path_to_file PATH_TO_FILE [--ifos IFOS] [--Model MODEL] [--Model_Parameters_Dictionary_Priors MODEL_PARAMETERS_DICTIONARY_PRIORS] [--Non_Prior_Arguments NON_PRIOR_ARGUMENTS]
+                [--output_dir OUTPUT_DIR] [--injection_parameters INJECTION_PARAMETERS] [--quantiles QUANTILES] [--f0 F0] [--fhigh FHIGH] [--df DF]
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -37,11 +38,13 @@ optional arguments:
                         The injected parameters.
   --quantiles QUANTILES
                         The quantiles used for plotting in plot corner, default is [0.05, 0.95].
-
+  --f0 F0               If no frequencies are saved in the loaded npz file, you can give f0, fhigh and df to the script. This is f0.
+  --fhigh FHIGH         If no frequencies are saved in the loaded npz file, you can give f0, fhigh and df to the script. This is fhigh.
+  --df DF               If no frequencies are saved in the loaded npz file, you can give f0, fhigh and df to the script. This is df.
 
 ```
 
-For the moment, these are the six parameters of the script. Only the first one is required if one wants to run for a power-law model. In the next lines, we will go over them quickly:
+For the moment, these are all the parameters of the script. Only the first one is required if one wants to run for a power-law model. In the next lines, we will go over them quickly:
 - `path_to_file`: This parameter must give the path to an `npz` file with information about the pyGWB run you want to analyse. The file needs to contain the point estimate spectrum, sigma spectrum and corresponding frequencies of that run. 
 - `ifos`: This parameters is a list with the names of the interferometers you are considering when running the PE, default value is '["H1", "L1"]'.
 - `Model`: The model you want to run PE for, currently all models from the PE module are in here. Default and easiest model to work with is `Power-Law`.
@@ -66,4 +69,17 @@ It is important that you add the correct amount of '\', single and double quotes
 
 Now, in the output folder, you can find the results and plots of the PE script.
 
+## 2. What if the loaded npz file does not have frequencies?
+
+This scenario can happen when you for example use a npz file produced by the script `pygwb_combine`. In that case, frequencies are not saved in the npz file and they have to be manually added to the script. Therefore, you can use the following parameters:
+- `f0`: The beginning frequency of the frequency array.
+- `fhigh`: The end frequency of the frequency array.
+- `df`: The frequency spacing of the frequency array. Has to be given as a float, cannot be utilised with as a fraction.
+
+An example would be something like this code: 
+```
+ ./pe_pyGWB --path_to_file {path_to_file.npz} --f0 20 --fhigh 500 --df 0.03125
+
+```
+