Merge 6db3a16 into 10d7d17

.gitattributes

@@ -1 +1,2 @@
 /root_numpy/src/_librootnumpy.cpp binary
+/root_numpy/tmva/src/_libtmvanumpy.cpp binary

.travis.yml

@@ -5,9 +5,12 @@ python:
     - "3.4"
 env:
     - ROOT=v5-34-18
+    - ROOT=v5-34-18 NOTMVA=1
     - ROOT=master
 install: source ci/install.sh
 script: bash ci/test.sh
 after_success:
     - time coveralls
 cache: apt
+notifications:
+    email: false

Makefile

@@ -4,10 +4,11 @@ PYTHON := $(shell which python)
 CYTHON := $(shell which cython)
 NOSETESTS := $(shell which nosetests)
 
-CYTHON_PYX := root_numpy/src/_librootnumpy.pyx
-CYTHON_CPP := root_numpy/src/_librootnumpy.cpp
-CYTHON_SRC := $(filter-out $(CYTHON_PYX),$(filter-out $(CYTHON_CPP),$(wildcard root_numpy/src/*)))
-CYTHON_PYX_SRC := $(filter-out $(CYTHON_PYX),$(wildcard root_numpy/src/*.pyx))
+CYTHON_CORE_PYX := root_numpy/src/_librootnumpy.pyx
+CYTHON_TMVA_PYX := root_numpy/tmva/src/_libtmvanumpy.pyx
+CYTHON_CORE_CPP := $(CYTHON_CORE_PYX:.pyx=.cpp)
+CYTHON_TMVA_CPP := $(CYTHON_TMVA_PYX:.pyx=.cpp)
+CYTHON_PYX_SRC := $(filter-out $(CYTHON_CORE_PYX),$(wildcard root_numpy/src/*.pyx))
 
 INTERACTIVE := $(shell ([ -t 0 ] && echo 1) || echo 0)
 
@@ -18,7 +19,7 @@ else
 	OPEN := xdg-open
 endif
 
-all: $(CYTHON_CPP) clean inplace test
+all: clean cython inplace test
 
 clean-pyc:
 	@find . -name "*.pyc" -exec rm {} \;
@@ -34,15 +35,12 @@ clean-html:
 
 clean: clean-build clean-pyc clean-so
 
-$(CYTHON_PYX): $(CYTHON_SRC)
-
-$(CYTHON_CPP): $(CYTHON_PYX)
+.SECONDEXPANSION:
+%.cpp: %.pyx $$(filter-out $$@,$$(wildcard $$(@D)/*))
 	@echo "compiling $< ..."
-	@$(CYTHON) --cplus --fast-fail --line-directives $<
+	$(CYTHON) --cplus --fast-fail --line-directives $<
 
-cython:
-	@echo "compiling $(CYTHON_PYX) ..."
-	$(CYTHON) --cplus --fast-fail --line-directives $(CYTHON_PYX)
+cython: $(CYTHON_CORE_CPP) $(CYTHON_TMVA_CPP)
 
 show-cython: clean-html
 	@tmp=`mktemp -d`; \

ci/install.sh

@@ -6,16 +6,23 @@
 
 set -e
 
+# Install gcc 4.8
 sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
 sudo apt-get -qq update
 sudo apt-get -qq install g++-4.8
 sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 90
 sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 90
+
 sudo apt-get -qq install python-nose python-pip
 pip install coverage coveralls
 
 # Install the ROOT binary
-time wget --no-check-certificate https://copy.com/rtIyUdxgjt7h/ci/root_builds/root${ROOT}_python${TRAVIS_PYTHON_VERSION}_gcc4.8_x86_64.tar.gz
-time tar zxf root${ROOT}_python${TRAVIS_PYTHON_VERSION}_gcc4.8_x86_64.tar.gz
-mv root${ROOT}_python${TRAVIS_PYTHON_VERSION}_gcc4.8_x86_64 root
+build=root${ROOT}_python${TRAVIS_PYTHON_VERSION}_gcc4.8_x86_64
+if [ ! -z ${NOTMVA+x} ]; then
+    # Use a build without TMVA
+    build+=_notmva
+fi
+time wget --no-check-certificate https://copy.com/rtIyUdxgjt7h/ci/root_builds/${build}.tar.gz
+time tar zxf ${build}.tar.gz
+mv ${build} root
 source root/bin/thisroot.sh

ci/test.sh

@@ -20,5 +20,9 @@ export PYTHONPATH=/home/travis/.local/lib/python${TRAVIS_PYTHON_VERSION}/site-pa
 # Install into the user site-packages directory and run tests on that
 time make install-user
 time make test-installed
+
 # Run tests in the local directory with coverage
-time make test-coverage </dev/null
+if [ -z ${NOTMVA+x} ]; then
+    # TMVA is included in this build, so run the coverage
+    time make test-coverage </dev/null
+fi

docs/examples/tmva.py

@@ -0,0 +1,47 @@
+from array import array
+import numpy as np
+from numpy.random import RandomState
+from root_numpy.tmva import factory_add_events, reader_evaluate
+from ROOT import TMVA, TFile, TCut
+
+RNG = RandomState(42)
+
+# construct an example dataset
+n_vars = 5
+n_events = 1000
+signal = RNG.multivariate_normal(
+    np.ones(n_vars), np.diag(np.ones(n_vars)), n_events)
+background = RNG.multivariate_normal(
+    np.ones(n_vars) * -1, np.diag(np.ones(n_vars)), n_events)
+X = np.concatenate([signal, background])
+y = np.ones(signal.shape[0] + background.shape[0])
+w = RNG.randint(1, 10, n_events * 2)
+y[signal.shape[0]:] *= -1
+permute = RNG.permutation(y.shape[0])
+X = X[permute]
+y = y[permute]
+
+# split into training and test datasets
+X_train, y_train, w_train = X[:n_events], y[:n_events], w[:n_events]
+X_test, y_test, w_test = X[n_events:], y[n_events:], w[n_events:]
+
+output = TFile('tmva_output.root', 'recreate')
+factory = TMVA.Factory('classifier', output, 'AnalysisType=Classification')
+for n in range(n_vars):
+    factory.AddVariable('f{0}'.format(n), 'F')
+
+# call root_numpy's utility functions to add events from the arrays
+factory_add_events(factory, X_train, y_train, weights=w_train)
+factory_add_events(factory, X_test, y_test, weights=w_test, test=True)
+
+# train a BDT
+factory.PrepareTrainingAndTestTree(TCut('1'), 'NormMode=EqualNumEvents')
+factory.BookMethod('BDT', 'BDT', 'nCuts=-1:NTrees=10:MaxDepth=3')
+factory.TrainAllMethods()
+
+# classify the test dataset with the BDT
+reader = TMVA.Reader()
+for n in range(n_vars):
+    reader.AddVariable('f{0}'.format(n), array('f', [0.]))
+reader.BookMVA('BDT', 'weights/classifier_BDT.weights.xml')
+scores = reader_evaluate(reader, 'BDT', X_test)

docs/reference/index.rst

@@ -7,11 +7,14 @@ root_numpy Reference
 :Release: |version|
 :Date: |today|
 
-.. module:: root_numpy
-
 This reference manual details the functions included in root_numpy, describing
 what they are and what they do.
 
+root_numpy
+----------
+
+.. module:: root_numpy
+
 .. autosummary::
    :toctree: generated
 
@@ -39,6 +42,17 @@ what they are and what they do.
    dup_idx
    blockwise_inner_join
 
+root_numpy.tmva
+---------------
+
+.. module:: root_numpy.tmva
+
+.. autosummary::
+   :toctree: generated
+
+   factory_add_events
+   reader_evaluate
+
 .. _conversion_table:
 
 Type Conversion Table
@@ -70,7 +84,3 @@ vector<vector<t> >  np.object
 Variable length arrays (such as ``particletype[nparticle]``) and vectors
 (such as ``vector<int>``) are converted to NumPy arrays of the corresponding
 types. Fixed length arrays are converted to fixed length NumPy array fields.
-
-.. note::
-    Tab completion for numpy.recarray column names (yourdata.<TAB>)
-    is also available with this `numpy extension <https://github.com/piti118/inumpy>`_.

root_numpy/_hist.py

@@ -154,6 +154,10 @@ def hist2array(hist, include_overflow=False, copy=True):
     TypeError
         If hist is not a ROOT histogram.
 
+    See Also
+    --------
+    array2hist
+
     """
     import ROOT
     if isinstance(hist, ROOT.TH3):
@@ -234,6 +238,65 @@ def array2hist(array, hist):
     array data type matches the histogram data type and that overflow bins are
     included.
 
+    See Also
+    --------
+    hist2array
+
+    Examples
+    --------
+
+    >>> from root_numpy import array2hist, hist2array
+    >>> import numpy as np
+    >>> from rootpy.plotting import Hist2D
+    >>> hist = Hist2D(5, 0, 1, 3, 0, 1, type='F')
+    >>> array = np.random.randint(0, 10, size=(7, 5))
+    >>> array
+    array([[6, 7, 8, 3, 4],
+           [8, 9, 7, 6, 2],
+           [2, 3, 4, 5, 2],
+           [7, 6, 5, 7, 3],
+           [2, 0, 5, 6, 8],
+           [0, 0, 6, 5, 2],
+           [2, 2, 1, 5, 4]])
+    >>> array2hist(array, hist)
+    >>> # dtype matches histogram type (D, F, I, S, C)
+    >>> hist2array(hist)
+    array([[ 9.,  7.,  6.],
+           [ 3.,  4.,  5.],
+           [ 6.,  5.,  7.],
+           [ 0.,  5.,  6.],
+           [ 0.,  6.,  5.]], dtype=float32)
+    >>> # overflow is excluded by default
+    >>> hist2array(hist, include_overflow=True)
+    array([[ 6.,  7.,  8.,  3.,  4.],
+           [ 8.,  9.,  7.,  6.,  2.],
+           [ 2.,  3.,  4.,  5.,  2.],
+           [ 7.,  6.,  5.,  7.,  3.],
+           [ 2.,  0.,  5.,  6.,  8.],
+           [ 0.,  0.,  6.,  5.,  2.],
+           [ 2.,  2.,  1.,  5.,  4.]], dtype=float32)
+    >>> array2 = hist2array(hist, include_overflow=True, copy=False)
+    >>> hist[2, 2] = -10
+    >>> # array2 views the same memory as hist because copy=False
+    >>> array2
+    array([[  6.,   7.,   8.,   3.,   4.],
+           [  8.,   9.,   7.,   6.,   2.],
+           [  2.,   3., -10.,   5.,   2.],
+           [  7.,   6.,   5.,   7.,   3.],
+           [  2.,   0.,   5.,   6.,   8.],
+           [  0.,   0.,   6.,   5.,   2.],
+           [  2.,   2.,   1.,   5.,   4.]], dtype=float32)
+    >>> # x, y, z axes correspond to axes 0, 1, 2 in numpy
+    >>> hist[2, 3] = -10
+    >>> array2
+    array([[  6.,   7.,   8.,   3.,   4.],
+           [  8.,   9.,   7.,   6.,   2.],
+           [  2.,   3., -10., -10.,   2.],
+           [  7.,   6.,   5.,   7.,   3.],
+           [  2.,   0.,   5.,   6.,   8.],
+           [  0.,   0.,   6.,   5.,   2.],
+           [  2.,   2.,   1.,   5.,   4.]], dtype=float32)
+
     """
     import ROOT
     if isinstance(hist, ROOT.TH3):

root_numpy/src/ROOT.pxi

@@ -1,5 +1,3 @@
-from libcpp cimport bool
-from libcpp.string cimport string, const_char
 
 cdef extern from "TObject.h":
     cdef cppclass TObject: