df026_AsNumpyArrays

Read data from RDataFrame into Numpy arrays.

Author: Stefan Wunsch (KIT, CERN)
This notebook tutorial was automatically generated with ROOTBOOK-izer from the macro found in the ROOT repository on Thursday, August 18, 2022 at 09:40 AM.

In [1]:
import ROOT
from sys import exit
Welcome to JupyROOT 6.27/01

Let's create a simple dataframe with ten rows and two columns

In [2]:
df = ROOT.RDataFrame(10) \
         .Define("x", "(int)rdfentry_") \
         .Define("y", "1.f/(1.f+rdfentry_)")

Next, we want to access the data from Python as Numpy arrays. To do so, the content of the dataframe is converted using the AsNumpy method. The returned object is a dictionary with the column names as keys and 1D numpy arrays with the content as values.

In [3]:
npy = df.AsNumpy()
print("Read-out of the full RDataFrame:\n{}\n".format(npy))
Read-out of the full RDataFrame:
{'x': ndarray([0, 1, 2, 3, 4, 5, 6, 7, 8, 9], dtype=int32), 'y': ndarray([1.        , 0.5       , 0.33333334, 0.25      , 0.2       ,
         0.16666667, 0.14285715, 0.125     , 0.11111111, 0.1       ],
        dtype=float32)}

Since reading out data to memory is expensive, always try to read-out only what is needed for your analysis. You can use all RDataFrame features to reduce your dataset, e.g., the Filter transformation. Furthermore, you can can pass to the AsNumpy method a whitelist of column names with the option columns or a blacklist with column names with the option exclude.

In [4]:
df2 = df.Filter("x>5")
npy2 = df2.AsNumpy()
print("Read-out of the filtered RDataFrame:\n{}\n".format(npy2))

npy3 = df2.AsNumpy(columns=["x"])
print("Read-out of the filtered RDataFrame with the columns option:\n{}\n".format(npy3))

npy4 = df2.AsNumpy(exclude=["x"])
print("Read-out of the filtered RDataFrame with the exclude option:\n{}\n".format(npy4))
Read-out of the filtered RDataFrame:
{'x': ndarray([6, 7, 8, 9], dtype=int32), 'y': ndarray([0.14285715, 0.125     , 0.11111111, 0.1       ], dtype=float32)}

Read-out of the filtered RDataFrame with the columns option:
{'x': ndarray([6, 7, 8, 9], dtype=int32)}

Read-out of the filtered RDataFrame with the exclude option:
{'y': ndarray([0.14285715, 0.125     , 0.11111111, 0.1       ], dtype=float32)}

You can read-out all objects from ROOT files since these are wrapped by PyROOT in the Python world. However, be aware that objects other than fundamental types, such as complex C++ objects and not int or float, are costly to read-out.

In [5]:
ROOT.gInterpreter.Declare("""
// Inject the C++ class CustomObject in the C++ runtime.
class CustomObject {
public:
    int x = 42;
};
// Create a function that returns such an object. This is called to fill the dataframe.
CustomObject fill_object() { return CustomObject(); }
""")

df3 = df.Define("custom_object", "fill_object()")
npy5 = df3.AsNumpy()
print("Read-out of C++ objects:\n{}\n".format(npy5["custom_object"]))
print("Access to all methods and data members of the C++ object:\nObject: {}\nAccess data member: custom_object.x = {}\n".format(
    repr(npy5["custom_object"][0]), npy5["custom_object"][0].x))
Read-out of C++ objects:
[<cppyy.gbl.CustomObject object at 0xc4efe50>
 <cppyy.gbl.CustomObject object at 0xc4efe54>
 <cppyy.gbl.CustomObject object at 0xc4efe58>
 <cppyy.gbl.CustomObject object at 0xc4efe5c>
 <cppyy.gbl.CustomObject object at 0xc4efe60>
 <cppyy.gbl.CustomObject object at 0xc4efe64>
 <cppyy.gbl.CustomObject object at 0xc4efe68>
 <cppyy.gbl.CustomObject object at 0xc4efe6c>
 <cppyy.gbl.CustomObject object at 0xc4efe70>
 <cppyy.gbl.CustomObject object at 0xc4efe74>]

Access to all methods and data members of the C++ object:
Object: <cppyy.gbl.CustomObject object at 0xc4efe50>
Access data member: custom_object.x = 42

Note that you can pass the object returned by AsNumpy directly to pandas.DataFrame including any complex C++ object that may be read-out.

In [6]:
try:
    import pandas
except:
    print("Please install the pandas package to run this section of the tutorial.")
    exit(1)

df = pandas.DataFrame(npy5)
print("Content of the ROOT.RDataFrame as pandas.DataFrame:\n{}\n".format(df))
Content of the ROOT.RDataFrame as pandas.DataFrame:
                                  custom_object  x         y
0  <cppyy.gbl.CustomObject object at 0xc4efe50>  0  1.000000
1  <cppyy.gbl.CustomObject object at 0xc4efe54>  1  0.500000
2  <cppyy.gbl.CustomObject object at 0xc4efe58>  2  0.333333
3  <cppyy.gbl.CustomObject object at 0xc4efe5c>  3  0.250000
4  <cppyy.gbl.CustomObject object at 0xc4efe60>  4  0.200000
5  <cppyy.gbl.CustomObject object at 0xc4efe64>  5  0.166667
6  <cppyy.gbl.CustomObject object at 0xc4efe68>  6  0.142857
7  <cppyy.gbl.CustomObject object at 0xc4efe6c>  7  0.125000
8  <cppyy.gbl.CustomObject object at 0xc4efe70>  8  0.111111
9  <cppyy.gbl.CustomObject object at 0xc4efe74>  9  0.100000

Draw all canvases

In [7]:
from ROOT import gROOT 
gROOT.GetListOfCanvases().Draw()