Morpho 1 Example Scripts¶
The following are example yaml scripts for important Preprocessing, Postprocessing, and Plot routines in Morpho 1. The format of the yaml script for other methods can be obtained from the documentation for that method.
Preprocessing¶
“do_preprocessing : true” must be in the morpho dictionary. The dictionaries below should be placed in a “which_pp” dictionary inside the “preprocessing” dictionary.
bootstrapping¶
Resamples the contents of a tree. Instead of regenerating a fake data set on every sampler, one can generate a larger data set, then extract subsets.
- method_name: "boot_strapping"
module_name: "resampling"
input_file_name: "input.root" # Name of file to access
# Must be a root file
input_tree: "tree_name" # Name of tree to access
output_file_name: "output.root" # Name of the output file
# The default is the same the input_file_name
output_tree: "tree_name" # Tree output name
# Default is same as input.
number_data: int # Number of sub-samples the user wishes to extract.
option: "RECREATE" # Option for saving root file (default = RECREATE)
Postprocessing¶
“do_postprocessing : true” must be in the morpho dictionary. The dictionaries below should be placed in a “which_pp” dictionary inside the “postprocessing” dictionary.
general_data_reducer¶
Tranform a function defining a spectrum into a histogram of binned data points.
- method_name: "general_data_reducer"
module_name: "general_data_reducer"
input_file_name: "input.root" # Path to the root file that contains the raw data
input_file_format: "root" # Format of the input file
# Currently only root is supported
input_tree: "spectrum" # Name of the root tree containing data of interest
data: ["KE"] # Optional list of names of branches of the data to be binned
minX:[18500.] # Optional list of minimum x axis values of the data to be binned
maxX:[18600.] # Optional list of maximum x axis values of the data to be binned
nBinHisto:[50] # List of desired number of bins in each histogram
output_file_name: "out.root", # Path to the file where the binned data will be saved
output_file_format: "root", # Format of the output file
output_file_option: RECREATE # RECREATE will erase and recreate the output file
# UPDATE will open a file (after creating it, if it does not exist) and update the file.
Plot¶
“do_plots : true” must be in the morpho dictionary. The dictionaries below should be placed in a “which_plot” dictionary inside the “plot” dictionary.
contours¶
contours creates a matrix of contour plots using a stanfit object
- method_name: "contours"
module_name: "contours"
read_cache_name: "cache_name_file.txt" # File containing path to stan model cache
input_fit_name: "analysis_fit.pkl"# pickle file containing stan fit object
output_path: "./results/" # Directory to save results in
result_names: ["param1", "param2", "param3"] # Names of parameters to plot
output_format: "pdf"
spectra¶
Plot a 1D histogram using 2 lists of data giving an x point and the corresponding bin contents
- method_name: "spectra"
module_name: "histo"
title: "histo"
input_file_name : "input.root"
input_tree: "tree_name"
output_path: "output.root"
data:
- param_name
histo2D¶
Plot a 2D histogram using 2 lists of data
- method_name: "histo2D"
module_name: "histo"
input_file_name : "input.root"
input_tree: "tree_name"
root_plot_option: "contz"
data:
- list_x_branch
- list_y_branch
histo2D_divergence¶
Plot a 2D histogram with divergence indicated by point color
- method_name: "histo2D_divergence"
module_name: "histo"
input_file_name : "input.root"
input_tree: "tree_name"
root_plot_option: "contz"
data:
- list_x_branch
- list_y_branch
aposteriori_distribution¶
Plot a grid of 2D histograms
- method_name: "aposteriori_distribution"
module_name: "histo"
input_file_name : "input.root"
input_tree: "tree_name"
root_plot_option: "cont"
output_path: output.root
title: "aposteriori_plots"
output_format: pdf
output_width: 12000
output_height: 1100
data:
- param1
- param2
- param3
correlation_factors¶
Plot a grid of correlation factors
- method_name: "correlation_factors"
module_name: "histo"
input_file_name : "input.root"
input_tree: "tree_name"
root_plot_option: "cont"
output_path: output.root
title: "aposteriori_plots"
output_format: pdf
output_width: 12000
output_height: 1100
data:
- param1
- param2
- param3