root2npy

Documentation

Overview

root2npy converts the content of a ROOT TTree to a NumPy data file.

Usage of root2npy:
 -f string
   	path to input ROOT file name
 -o string
   	path to output npz file name (default "output.npz")
 -t string
   	name of the tree to convert (default "tree")

The NumPy data file format is described here:

https://numpy.org/neps/nep-0001-npy-format.html

Example:

$> root2npy -f $GOPATH/src/go-hep.org/x/hep/groot/testdata/simple.root -t tree -o output.npz
$> python2 -c 'import sys, numpy as np; print(dict(np.load(sys.argv[1])))' ./output.npz
{'one':   array([1, 2, 3, 4], dtype=int32),
 'two':   array([ 1.10000002,  2.20000005,  3.29999995,  4.4000001 ], dtype=float32),
 'three': array([u'uno', u'dos', u'tres', u'quatro'], dtype='<U6')}

$> python3 -c 'import sys, numpy as np; print(dict(np.load(sys.argv[1])))' ./output.npz
{'one':   array([1, 2, 3, 4], dtype=int32),
 'two':   array([ 1.10000002,  2.20000005,  3.29999995,  4.4000001 ], dtype=float32),
 'three': array(['uno', 'dos', 'tres', 'quatro'], dtype='<U6')}

$> go get github.com/sbinet/npyio/cmd/npyio-ls
$> npyio-ls ./output.npz
================================================================================
file: ./output.npz
entry: one
npy-header: Header{Major:2, Minor:0, Descr:{Type:<i4, Fortran:false, Shape:[4]}}
data = [1 2 3 4]

entry: two
npy-header: Header{Major:2, Minor:0, Descr:{Type:<f4, Fortran:false, Shape:[4]}}
data = [1.1 2.2 3.3 4.4]

entry: three
npy-header: Header{Major:2, Minor:0, Descr:{Type:<U6, Fortran:false, Shape:[4]}}
data = [uno dos tres quatro]

$> root-ls -t $GOPATH/src/go-hep.org/x/hep/groot/testdata/simple.root
=== [$GOPATH/src/go-hep.org/x/hep/groot/testdata/simple.root] ===
version: 60600
TTree   tree      fake data (entries=4)
  one   "one/I"   TBranch
  two   "two/F"   TBranch
  three "three/C" TBranch

If you have a 10-events tree with a branch "doubles" containing an array of 3 float64, root2npy will convert it to a NumPy data file containing a NumPy array with a shape (10,3).

Example:

$> root-ls -t $GOPATH/src/go-hep.org/x/hep/groot/testdata/small-flat-tree.root
=== [$GOPATH/src/go-hep.org/x/hep/groot/testdata/small-flat-tree.root] ===
version: 60806
TTree          tree                 my tree title (entries=100)
  Int32        "Int32/I"            TBranch
  Int64        "Int64/L"            TBranch
  UInt32       "UInt32/i"           TBranch
  UInt64       "UInt64/l"           TBranch
  Float32      "Float32/F"          TBranch
  Float64      "Float64/D"          TBranch
  Str          "Str/C"              TBranch
  ArrayInt32   "ArrayInt32[10]/I"   TBranch
  ArrayInt64   "ArrayInt64[10]/L"   TBranch
  ArrayUInt32  "ArrayInt32[10]/i"   TBranch
  ArrayUInt64  "ArrayInt64[10]/l"   TBranch
  ArrayFloat32 "ArrayFloat32[10]/F" TBranch
  ArrayFloat64 "ArrayFloat64[10]/D" TBranch
  N            "N/I"                TBranch
  SliceInt32   "SliceInt32[N]/I"    TBranch
  SliceInt64   "SliceInt64[N]/L"    TBranch
  SliceUInt32  "SliceInt32[N]/i"    TBranch
  SliceUInt64  "SliceInt64[N]/l"    TBranch
  SliceFloat32 "SliceFloat32[N]/F"  TBranch
  SliceFloat64 "SliceFloat64[N]/D"  TBranch

$> root2npy $GOPATH/src/go-hep.org/x/hep/groot/testdata/small-flat-tree.root
root2npy: scanning leaves...
root2npy: >>> "SliceInt32" []int32 not supported
root2npy: >>> "SliceInt64" []int64 not supported
root2npy: >>> "SliceInt32" []int32 not supported
root2npy: >>> "SliceInt64" []int64 not supported
root2npy: >>> "SliceFloat32" []float32 not supported
root2npy: >>> "SliceFloat64" []float64 not supported
root2npy: scanning leaves... [done]

$> npyio-ls ./output.npz
================================================================================
file: ./output.npz
entry: Int32
npy-header: Header{Major:2, Minor:0, Descr:{Type:<i4, Fortran:false, Shape:[100]}}
data = [0 1 2 3 4 5 6 7 8 9 10 11 ... 90 91 92 93 94 95 96 97 98 99]

entry: Int64
npy-header: Header{Major:2, Minor:0, Descr:{Type:<i8, Fortran:false, Shape:[100]}}
data = [0 1 2 3 4 5 6 7 8 9 10 11 ... 90 91 92 93 94 95 96 97 98 99]

[...]

entry: Float64
npy-header: Header{Major:2, Minor:0, Descr:{Type:<f8, Fortran:false, Shape:[100]}}
data = [0 1 2 3 4 5 6 7 8 9 10 11 ... 90 91 92 93 94 95 96 97 98 99]

entry: Str
npy-header: Header{Major:2, Minor:0, Descr:{Type:<U7, Fortran:false, Shape:[100]}}
data = [evt-000 evt-001 evt-002 evt-003 evt-004 evt-005 evt-006 evt-007 ...
evt-092 evt-093 evt-094 evt-095 evt-096 evt-097 evt-098 evt-099]

entry: ArrayInt32
npy-header: Header{Major:2, Minor:0, Descr:{Type:<i4, Fortran:false, Shape:[100 10]}}
data = [0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 ...
... 97 98 98 98 98 98 98 98 98 98 98 99 99 99 99 99 99 99 99 99 99]

[...]