The problem is that you do not do any type conversion of the numpy array. You calculate a float32 variable and put it as an entry into a float64 numpy array. numpy then converts it properly back to float64

Try someting like this:

a = np.zeros(4,dtype="float64") 
print a.dtype
print type(a[0])
a = np.float32(a)
print a.dtype
print type(a[0])

The output (tested with python 2.7)

float64
<type 'numpy.float64'>
float32
<type 'numpy.float32'>

a is in your case the array tree.tree_.threshold

Use val.item() to convert most NumPy values to a native Python type:

import numpy as np

# for example, numpy.float32 -> python float
val = np.float32(0)
pyval = val.item()
print(type(pyval))         # <class 'float'>

# and similar...
type(np.float64(0).item()) # <class 'float'>
type(np.uint32(0).item())  # <class 'int'>
type(np.int16(0).item())   # <class 'int'>
type(np.cfloat(0).item())  # <class 'complex'>
type(np.datetime64(0, 'D').item())  # <class 'datetime.date'>
type(np.datetime64('2001-01-01 00:00:00').item())  # <class 'datetime.datetime'>
type(np.timedelta64(0, 'D').item()) # <class 'datetime.timedelta'>
...

(A related method np.asscalar(val) was deprecated with 1.16, and removed with 1.23).

For the curious, to build a table of conversions of NumPy array scalars for your system:

for name in dir(np):
    obj = getattr(np, name)
    if hasattr(obj, 'dtype'):
        try:
            if 'time' in name:
                npn = obj(0, 'D')
            else:
                npn = obj(0)
            nat = npn.item()
            print('{0} ({1!r}) -> {2}'.format(name, npn.dtype.char, type(nat)))
        except:
            pass

There are a few NumPy types that have no native Python equivalent on some systems, including: clongdouble, clongfloat, complex192, complex256, float128, longcomplex, longdouble and longfloat. These need to be converted to their nearest NumPy equivalent before using .item().