Logo ROOT  
Reference Guide
rf409_NumPyPandasToRooFit.py File Reference

Namespaces

namespace  rf409_NumPyPandasToRooFit
 

Detailed Description

View in nbviewer Open in SWAN Convert between NumPy arrays or Pandas DataFrames and RooDataSets.

This totorial first how to export a RooDataSet to NumPy arrays or a Pandas DataFrame, and then it shows you how to create a RooDataSet from a Pandas DataFrame.

import ROOT
import numpy as np
# The number of events that we use for the datasets created in this tutorial.
n_events = 10000
# Creating a RooDataSet and exporting it to the Python ecosystem
# --------------------------------------------------------------
# Define the observable.
x = ROOT.RooRealVar("x", "x", -10, 10)
# Define a Gaussian model with its parameters.
mean = ROOT.RooRealVar("mean", "mean of gaussian", 1, -10, 10)
sigma = ROOT.RooRealVar("sigma", "width of gaussian", 1, 0.1, 10)
gauss = ROOT.RooGaussian("gauss", "gaussian PDF", x, mean, sigma)
# Create a RooDataSet.
data = gauss.generate(ROOT.RooArgSet(x), 10000)
# Use RooDataSet.to_numpy() to export dataset to a dictionary of NumPy arrays.
# Real values will be of type `double`, categorical values of type `int`.
arrays = data.to_numpy()
# We can verify that the mean and standard deviation matches our model specification.
print("Mean of numpy array:", np.mean(arrays["x"]))
print("Standard deviation of numpy array:", np.std(arrays["x"]))
# It is also possible to create a Pandas DataFrame directly from the numpy arrays:
df = data.to_pandas()
# Now you can use the DataFrame e.g. for plotting. You can even combine this
# with the RooAbsReal.bins PyROOT function, which returns the binning from
# RooFit as a numpy array!
try:
import matplotlib.pyplot as plt
df.hist(column="x", bins=x.bins())
except Exception:
print(
'Skipping `df.hist(column="x", bins=x.bins())` because matplotlib could not be imported or was not able to display the plot.'
)
del data
del arrays
del df
# Creating a dataset with NumPy and importing it to a RooDataSet
# --------------------------------------------------------------
# Now we create some Gaussian toy data with numpy, this time with a different
# mean.
x_arr = np.random.normal(-1.0, 1.0, (n_events,))
# Import the data to a RooDataSet, passing a dictionary of arrays and the
# corresponding RooRealVars just like you would pass to the RooDataSet
# constructor.
data = ROOT.RooDataSet.from_numpy({"x": x_arr}, [x])
# Let's fit the Gaussian to the data. The mean is updated accordingly.
fit_result = gauss.fitTo(data, PrintLevel=-1, Save=True)
fit_result.Print()
# We can now plot the model and the dataset with RooFit.
xframe = x.frame(Title="Gaussian pdf")
data.plotOn(xframe)
gauss.plotOn(xframe)
# Draw RooFit plot on a canvas.
c = ROOT.TCanvas("rf409_NumPyPandasToRooFit", "rf409_NumPyPandasToRooFit", 800, 400)
xframe.Draw()
c.SaveAs("rf409_NumPyPandasToRooFit.png")
# Exporting a RooDataHist to NumPy arrays for histogram counts and bin edges
# --------------------------------------------------------------------------
def print_histogram_output(histogram_output):
counts, bin_edges = histogram_output
print(np.array(counts, dtype=int))
print(bin_edges[0])
# Create a binned clone of the dataset to show RooDataHist to NumPy export.
datahist = data.binnedClone()
# You can also export a RooDataHist to numpy arrays with
# RooDataHist.to_numpy(). As output, you will get a multidimensional array with
# the histogram counts and a list of arrays with bin edges. This is comparable
# to the ouput of numpy.histogram (or numpy.histogramdd for the
# multidimensional case).
counts, bin_edges = datahist.to_numpy()
print("Counts and bin edges from RooDataHist.to_numpy:")
print_histogram_output((counts, bin_edges))
# Let's compare the ouput to the counts and bin edges we get with
# numpy.histogramdd when we pass it the original samples:
print("Counts and bin edges from np.histogram:")
print_histogram_output(np.histogramdd([x_arr], bins=[x.bins()]))
# The array values should be the same!
# Importing a RooDataHist from NumPy arrays with histogram counts and bin edges
# -----------------------------------------------------------------------------
# There is also a `RooDataHist.from_numpy` function, again with an interface
# inspired by `numpy.histogramdd`. You need to pass at least the histogram
# counts and the list of variables. The binning is optional: the default
# binning of the RooRealVars is used if not explicitly specified.
datahist_new_1 = ROOT.RooDataHist.from_numpy(counts, [x])
print("RooDataHist imported with default binning and exported back to numpy:")
print_histogram_output(datahist_new_1.to_numpy())
# It's also possible to pass custom bin edges to `RooDataHist.from_numpy`, just
# like you pass them to `numpy.histogramdd` when you get the counts to fill the
# RooDataHist with:
bins = [np.linspace(-10, 10, 21)]
counts, _ = np.histogramdd([x_arr], bins=bins)
datahist_new_2 = ROOT.RooDataHist.from_numpy(counts, [x], bins=bins)
print("RooDataHist imported with linspace binning and exported back to numpy:")
print_histogram_output(datahist_new_2.to_numpy())
# Alternatively, you can specify only the number of bins and the range if your
# binning is uniform. This is preferred over passing the full list of bin
# edges, because RooFit will know that the binning is uniform and do some
# optimizations.
bins = [20]
ranges = [(-10, 10)]
counts, _ = np.histogramdd([x_arr], bins=bins, range=ranges)
datahist_new_3 = ROOT.RooDataHist.from_numpy(counts, [x], bins=bins, ranges=ranges)
print("RooDataHist imported with uniform binning and exported back to numpy:")
print_histogram_output(datahist_new_3.to_numpy())
␛[1mRooFit v3.60 -- Developed by Wouter Verkerke and David Kirkby␛[0m
Copyright (C) 2000-2013 NIKHEF, University of California & Stanford University
All rights reserved, please read http://roofit.sourceforge.net/license.txt
('Mean of numpy array:', 1.0066466535473984)
('Standard deviation of numpy array:', 0.9973499677811349)
Skipping `df.hist(column="x", bins=x.bins())` because matplotlib could not be imported or was not able to display the plot.
[#1] INFO:Minimization -- RooAbsMinimizerFcn::setOptimizeConst: activating const optimization
[#1] INFO:Minimization -- RooAbsMinimizerFcn::setOptimizeConst: deactivating const optimization
RooFitResult: minimized FCN value: 14155.6, estimated distance to minimum: 8.53251e-10
covariance matrix quality: Full, accurate covariance matrix
Status : MINIMIZE=0 HESSE=0
Floating Parameter FinalValue +/- Error
-------------------- --------------------------
mean -1.0072e+00 +/- 9.97e-03
sigma 9.9663e-01 +/- 7.05e-03
[#0] WARNING:Plotting -- Cannot apply a bin width correction and use Poisson errors. Not correcting for bin width.
Counts and bin edges from RooDataHist.to_numpy:
[ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 1 0 5 3 7 11 19 39 65 77 141
175 258 329 456 534 613 702 788 871 773 712 708 619 526 420 369 248 191
116 85 59 36 18 12 10 1 0 2 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0]
[-10. -9.8 -9.6 -9.4 -9.2 -9. -8.8 -8.6 -8.4 -8.2 -8. -7.8
-7.6 -7.4 -7.2 -7. -6.8 -6.6 -6.4 -6.2 -6. -5.8 -5.6 -5.4
-5.2 -5. -4.8 -4.6 -4.4 -4.2 -4. -3.8 -3.6 -3.4 -3.2 -3.
-2.8 -2.6 -2.4 -2.2 -2. -1.8 -1.6 -1.4 -1.2 -1. -0.8 -0.6
-0.4 -0.2 0. 0.2 0.4 0.6 0.8 1. 1.2 1.4 1.6 1.8
2. 2.2 2.4 2.6 2.8 3. 3.2 3.4 3.6 3.8 4. 4.2
4.4 4.6 4.8 5. 5.2 5.4 5.6 5.8 6. 6.2 6.4 6.6
6.8 7. 7.2 7.4 7.6 7.8 8. 8.2 8.4 8.6 8.8 9.
9.2 9.4 9.6 9.8 10. ]
Counts and bin edges from np.histogram:
[ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 1 0 5 3 7 11 19 39 65 77 141
175 258 329 456 534 613 702 788 871 773 712 708 619 526 420 369 248 191
116 85 59 36 18 12 10 1 0 2 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0]
[-10. -9.8 -9.6 -9.4 -9.2 -9. -8.8 -8.6 -8.4 -8.2 -8. -7.8
-7.6 -7.4 -7.2 -7. -6.8 -6.6 -6.4 -6.2 -6. -5.8 -5.6 -5.4
-5.2 -5. -4.8 -4.6 -4.4 -4.2 -4. -3.8 -3.6 -3.4 -3.2 -3.
-2.8 -2.6 -2.4 -2.2 -2. -1.8 -1.6 -1.4 -1.2 -1. -0.8 -0.6
-0.4 -0.2 0. 0.2 0.4 0.6 0.8 1. 1.2 1.4 1.6 1.8
2. 2.2 2.4 2.6 2.8 3. 3.2 3.4 3.6 3.8 4. 4.2
4.4 4.6 4.8 5. 5.2 5.4 5.6 5.8 6. 6.2 6.4 6.6
6.8 7. 7.2 7.4 7.6 7.8 8. 8.2 8.4 8.6 8.8 9.
9.2 9.4 9.6 9.8 10. ]
RooDataHist imported with default binning and exported back to numpy:
[ 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 1 1 0 5 3 7 11 19 39 65 77 141
175 258 329 456 534 613 702 788 871 773 712 708 619 526 420 369 248 191
116 85 59 36 18 12 10 1 0 2 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0]
[-10. -9.8 -9.6 -9.4 -9.2 -9. -8.8 -8.6 -8.4 -8.2 -8. -7.8
-7.6 -7.4 -7.2 -7. -6.8 -6.6 -6.4 -6.2 -6. -5.8 -5.6 -5.4
-5.2 -5. -4.8 -4.6 -4.4 -4.2 -4. -3.8 -3.6 -3.4 -3.2 -3.
-2.8 -2.6 -2.4 -2.2 -2. -1.8 -1.6 -1.4 -1.2 -1. -0.8 -0.6
-0.4 -0.2 0. 0.2 0.4 0.6 0.8 1. 1.2 1.4 1.6 1.8
2. 2.2 2.4 2.6 2.8 3. 3.2 3.4 3.6 3.8 4. 4.2
4.4 4.6 4.8 5. 5.2 5.4 5.6 5.8 6. 6.2 6.4 6.6
6.8 7. 7.2 7.4 7.6 7.8 8. 8.2 8.4 8.6 8.8 9.
9.2 9.4 9.6 9.8 10. ]
RooDataHist imported with linspace binning and exported back to numpy:
[ 0 0 0 0 1 16 211 1359 3508 3338 1344 210 13 0
0 0 0 0 0 0]
[-10. -9. -8. -7. -6. -5. -4. -3. -2. -1. 0. 1. 2. 3.
4. 5. 6. 7. 8. 9. 10.]
RooDataHist imported with uniform binning and exported back to numpy:
[ 0 0 0 0 1 16 211 1359 3508 3338 1344 210 13 0
0 0 0 0 0 0]
[-10. -9. -8. -7. -6. -5. -4. -3. -2. -1. 0. 1. 2. 3.
4. 5. 6. 7. 8. 9. 10.]
Date
November 2021
Author
Jonas Rembser

Definition in file rf409_NumPyPandasToRooFit.py.