Merge pull request #196 from ndawe/master

Work around thread safety issue in TMVA::Reader

.travis.yml

@@ -4,8 +4,9 @@ python:
     - "2.7"
     - "3.4"
 env:
+    - ROOT=v5-34-18
     - ROOT=v5-34-18 NOTMVA=1
-    - ROOT=master
+    - ROOT=master COVERAGE=1
 install: source ci/install.sh
 script: bash ci/test.sh
 after_success:

ci/test.sh

@@ -23,7 +23,8 @@ time make install-user
 time make test-installed
 
 # Run tests in the local directory with coverage
-if [ -z ${NOTMVA+x} ]; then
-    # TMVA is included in this build, so run the coverage
+if [ ! -z ${COVERAGE+x} ] && [ -z ${NOTMVA+x} ]; then
+    # COVERAGE is set and TMVA is included in this build
+    # so run the coverage
     time make test-coverage </dev/null
 fi

root_numpy/info.py

@@ -6,5 +6,5 @@
 |_|  \___/ \___/ \__|___|_| |_|\__,_|_| |_| |_| .__/ \__, |  {0}
                    |_____|                    |_|    |___/
 """
-__version__ = '4.1.0.dev0'
+__version__ = '4.1.1.dev0'
 __doc__ = __doc__.format(__version__)  # pylint:disable=redefined-builtin

root_numpy/tmva/_evaluate.py

@@ -36,16 +36,26 @@ def evaluate_reader(reader, name, events):
     """
     if not isinstance(reader, TMVA.Reader):
         raise TypeError("reader must be a TMVA.Reader instance")
-    method = reader.FindMVA(name)
-    if not method:
+    events = np.ascontiguousarray(events, dtype=np.float64)
+    if events.ndim == 1:
+        # convert to 2D
+        events = events[:, np.newaxis]
+    elif events.ndim != 2:
         raise ValueError(
-            "method '{0}' is not booked in this reader".format(name))
-    return evaluate_method(method, events)
+            "events must be a two-dimensional array "
+            "with one event per row")
+    return _libtmvanumpy.evaluate_reader(ROOT.AsCObject(reader), name, events)
 
 
 def evaluate_method(method, events):
     """Evaluate a TMVA::MethodBase over a NumPy array.
 
+    .. warning:: TMVA::Reader has known problems with thread safety in versions
+       of ROOT earlier than 6.03. There will potentially be a crash if you call
+       ``method = reader.FindMVA(name)`` in Python and then pass this
+       ``method`` here. Consider using ``evaluate_reader`` instead if you are
+       affected by this crash.
+
     Parameters
     ----------
     method : TMVA::MethodBase
@@ -75,28 +85,4 @@ def evaluate_method(method, events):
         raise ValueError(
             "events must be a two-dimensional array "
             "with one event per row")
-    if events.shape[1] != method.GetNVariables():
-        raise ValueError(
-            "this method was trained with events containing "
-            "{0} variables, but these events contain {1} variables".format(
-                method.GetNVariables(), events.shape[1]))
-    analysistype = method.GetAnalysisType()
-    if analysistype == TMVA.Types.kClassification:
-        return _libtmvanumpy.evaluate_twoclass(
-            ROOT.AsCObject(method), events)
-    elif analysistype == TMVA.Types.kMulticlass:
-        n_classes = method.DataInfo().GetNClasses()
-        if n_classes < 2:
-            raise AssertionError("there must be at least two classes")
-        return _libtmvanumpy.evaluate_multiclass(
-            ROOT.AsCObject(method), events, n_classes)
-    elif analysistype == TMVA.Types.kRegression:
-        n_targets = method.DataInfo().GetNTargets()
-        if n_targets < 1:
-            raise AssertionError("there must be at least one regression target")
-        output = _libtmvanumpy.evaluate_regression(
-            ROOT.AsCObject(method), events, n_targets)
-        if n_targets == 1:
-            return np.ravel(output)
-        return output
-    raise AssertionError("the analysis type of this method is not supported")
+    return _libtmvanumpy.evaluate_method(ROOT.AsCObject(method), events)

root_numpy/tmva/src/TMVA.pxi

@@ -7,18 +7,42 @@ cdef extern from "TMVA/Types.h" namespace "TMVA":
         kTraining "TMVA::Types::kTraining"
         kTesting "TMVA::Types::kTesting"
 
+    ctypedef enum EAnalysisType "TMVA::Types::EAnalysisType":
+        kClassification "TMVA::Types::kClassification"
+        kRegression "TMVA::Types::kRegression"
+        kMulticlass "TMVA::Types::kMulticlass"
+
 cdef extern from "TMVA/Event.h" namespace "TMVA":
     cdef cppclass Event:
         Event(vector[float]& features, unsigned int theclass)
         void SetVal(unsigned int ivar, float value)
 
-cdef extern from "TMVA/Factory.h" namespace "TMVA":
-    cdef cppclass Factory:
-        void AddEvent(string& classname, ETreeType treetype, vector[double]& event, double weight)
+cdef extern from "TMVA/DataSetInfo.h" namespace "TMVA":
+    cdef cppclass DataSetInfo:
+        unsigned int GetNClasses()
+        unsigned int GetNVariables()
+        unsigned int GetNTargets()
+        vector[string] GetListOfVariables()
+
+cdef extern from "TMVA/IMethod.h" namespace "TMVA":
+    cdef cppclass IMethod:
+        pass
 
 cdef extern from "TMVA/MethodBase.h" namespace "TMVA":
     cdef cppclass MethodBase:
+        EAnalysisType GetAnalysisType()
+        DataSetInfo DataInfo()
+        unsigned int GetNVariables()
+        unsigned int GetNTargets()
         double GetMvaValue()
         vector[float] GetMulticlassValues()
         vector[float] GetRegressionValues()
         Event* fTmpEvent
+
+cdef extern from "TMVA/Factory.h" namespace "TMVA":
+    cdef cppclass Factory:
+        void AddEvent(string& classname, ETreeType treetype, vector[double]& event, double weight)
+
+cdef extern from "TMVA/Reader.h" namespace "TMVA":
+    cdef cppclass Reader:
+        IMethod* FindMVA(string name)