kmeans/__init__.py

# This file was automatically generated by SWIG (http://www.swig.org).
# Version 3.0.10
#
# Do not make changes to this file unless you know what you are doing--modify
# the SWIG interface file instead.

# This wrapper is part of IMP,
# Copyright 2007-2020 IMP Inventors. All rights reserved.

from __future__ import print_function, division, absolute_import




from sys import version_info as _swig_python_version_info
if _swig_python_version_info >= (2, 7, 0):
    def swig_import_helper():
        import importlib
        pkg = __name__.rpartition('.')[0]
        mname = '.'.join((pkg, '_IMP_kmeans')).lstrip('.')
        try:
            return importlib.import_module(mname)
        except ImportError:
            return importlib.import_module('_IMP_kmeans')
    _IMP_kmeans = swig_import_helper()
    del swig_import_helper
elif _swig_python_version_info >= (2, 6, 0):
    def swig_import_helper():
        from os.path import dirname
        import imp
        fp = None
        try:
            fp, pathname, description = imp.find_module('_IMP_kmeans', [dirname(__file__)])
        except ImportError:
            import _IMP_kmeans
            return _IMP_kmeans
        if fp is not None:
            try:
                _mod = imp.load_module('_IMP_kmeans', fp, pathname, description)
            finally:
                fp.close()
            return _mod
    _IMP_kmeans = swig_import_helper()
    del swig_import_helper
else:
    import _IMP_kmeans
del _swig_python_version_info
try:
    _swig_property = property
except NameError:
    pass  # Python < 2.2 doesn't have 'property'.

try:
    import builtins as __builtin__
except ImportError:
    import __builtin__

def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
    if (name == "thisown"):
        return self.this.own(value)
    if (name == "this"):
        if type(value).__name__ == 'SwigPyObject':
            self.__dict__[name] = value
            return
    method = class_type.__swig_setmethods__.get(name, None)
    if method:
        return method(self, value)
    if (not static):
        object.__setattr__(self, name, value)
    else:
        raise AttributeError("You cannot add attributes to %s" % self)


def _swig_setattr(self, class_type, name, value):
    return _swig_setattr_nondynamic(self, class_type, name, value, 0)


def _swig_getattr(self, class_type, name):
    if (name == "thisown"):
        return self.this.own()
    method = class_type.__swig_getmethods__.get(name, None)
    if method:
        return method(self)
    raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))


def _swig_repr(self):
    try:
        strthis = "proxy of " + self.this.__repr__()
    except __builtin__.Exception:
        strthis = ""
    return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)


def _swig_setattr_nondynamic_method(set):
    def set_attr(self, name, value):
        if (name == "thisown"):
            return self.this.own(value)
        if hasattr(self, name) or (name == "this"):
            set(self, name, value)
        else:
            raise AttributeError("You cannot add attributes to %s" % self)
    return set_attr


try:
    import weakref
    weakref_proxy = weakref.proxy
except __builtin__.Exception:
    weakref_proxy = lambda x: x


class IMP_KMEANS_SwigPyIterator(object):
    """Proxy of C++ swig::IMP_KMEANS_SwigPyIterator class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, *args, **kwargs):
        raise AttributeError("No constructor defined - class is abstract")
    __repr__ = _swig_repr
    __swig_destroy__ = _IMP_kmeans.delete_IMP_KMEANS_SwigPyIterator
    __del__ = lambda self: None

    def value(self):
        """value(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_value(self)


    def incr(self, n=1):
        """
        incr(IMP_KMEANS_SwigPyIterator self, size_t n=1) -> IMP_KMEANS_SwigPyIterator
        incr(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator
        """
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_incr(self, n)


    def decr(self, n=1):
        """
        decr(IMP_KMEANS_SwigPyIterator self, size_t n=1) -> IMP_KMEANS_SwigPyIterator
        decr(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator
        """
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_decr(self, n)


    def distance(self, x):
        """distance(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> ptrdiff_t"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_distance(self, x)


    def equal(self, x):
        """equal(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_equal(self, x)


    def copy(self):
        """copy(IMP_KMEANS_SwigPyIterator self) -> IMP_KMEANS_SwigPyIterator"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_copy(self)


    def next(self):
        """next(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_next(self)


    def __next__(self):
        """__next__(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___next__(self)


    def previous(self):
        """previous(IMP_KMEANS_SwigPyIterator self) -> PyObject *"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_previous(self)


    def advance(self, n):
        """advance(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator_advance(self, n)


    def __eq__(self, x):
        """__eq__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___eq__(self, x)


    def __ne__(self, x):
        """__ne__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> bool"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___ne__(self, x)


    def __iadd__(self, n):
        """__iadd__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___iadd__(self, n)


    def __isub__(self, n):
        """__isub__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___isub__(self, n)


    def __add__(self, n):
        """__add__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator"""
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___add__(self, n)


    def __sub__(self, *args):
        """
        __sub__(IMP_KMEANS_SwigPyIterator self, ptrdiff_t n) -> IMP_KMEANS_SwigPyIterator
        __sub__(IMP_KMEANS_SwigPyIterator self, IMP_KMEANS_SwigPyIterator x) -> ptrdiff_t
        """
        return _IMP_kmeans.IMP_KMEANS_SwigPyIterator___sub__(self, *args)

    def __iter__(self):
        return self
IMP_KMEANS_SwigPyIterator_swigregister = _IMP_kmeans.IMP_KMEANS_SwigPyIterator_swigregister
IMP_KMEANS_SwigPyIterator_swigregister(IMP_KMEANS_SwigPyIterator)


_value_types=[]
_object_types=[]
_raii_types=[]
_plural_types=[]

IMP_DEBUG = _IMP_kmeans.IMP_DEBUG
IMP_RELEASE = _IMP_kmeans.IMP_RELEASE
IMP_SILENT = _IMP_kmeans.IMP_SILENT
IMP_PROGRESS = _IMP_kmeans.IMP_PROGRESS
IMP_TERSE = _IMP_kmeans.IMP_TERSE
IMP_VERBOSE = _IMP_kmeans.IMP_VERBOSE
IMP_MEMORY = _IMP_kmeans.IMP_MEMORY
IMP_NONE = _IMP_kmeans.IMP_NONE
IMP_USAGE = _IMP_kmeans.IMP_USAGE
IMP_INTERNAL = _IMP_kmeans.IMP_INTERNAL
IMP_KERNEL_HAS_LOG4CXX = _IMP_kmeans.IMP_KERNEL_HAS_LOG4CXX
IMP_COMPILER_HAS_AUTO = _IMP_kmeans.IMP_COMPILER_HAS_AUTO
IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kmeans.IMP_COMPILER_HAS_DEBUG_VECTOR
IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_kmeans.IMP_COMPILER_HAS_UNIQUE_PTR
IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_kmeans.IMP_KERNEL_HAS_BOOST_RANDOM
IMP_KERNEL_HAS_NUMPY = _IMP_kmeans.IMP_KERNEL_HAS_NUMPY
IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kmeans.IMP_KERNEL_HAS_GPERFTOOLS
IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kmeans.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
IMPKERNEL_SHOW_WARNINGS = _IMP_kmeans.IMPKERNEL_SHOW_WARNINGS

import sys
class _DirectorObjects(object):
    """@internal Simple class to keep references to director objects
       to prevent premature deletion."""
    def __init__(self):
        self._objects = []
    def register(self, obj):
        """Take a reference to a director object; will only work for
           refcounted C++ classes"""
        if hasattr(obj, 'get_ref_count'):
            self._objects.append(obj)
    def cleanup(self):
        """Only drop our reference and allow cleanup by Python if no other
           Python references exist (we hold 3 references: one in self._objects,
           one in x, and one in the argument list for getrefcount) *and* no
           other C++ references exist (the Python object always holds one)"""
        objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
                                         or x.get_ref_count() > 1]
# Do in two steps so the references are kept until the end of the
# function (deleting references may trigger a fresh call to this method)
        self._objects = objs
    def get_object_count(self):
        """Get number of director objects (useful for testing only)"""
        return len(self._objects)
_director_objects = _DirectorObjects()

class _ostream(object):
    """Proxy of C++ std::ostream class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, *args, **kwargs):
        raise AttributeError("No constructor defined")
    __repr__ = _swig_repr

    def write(self, osa_buf):
        """write(_ostream self, char const * osa_buf)"""
        return _IMP_kmeans._ostream_write(self, osa_buf)

_ostream_swigregister = _IMP_kmeans._ostream_swigregister
_ostream_swigregister(_ostream)

IMP_COMPILER_HAS_OVERRIDE = _IMP_kmeans.IMP_COMPILER_HAS_OVERRIDE
IMP_COMPILER_HAS_FINAL = _IMP_kmeans.IMP_COMPILER_HAS_FINAL
IMP_HAS_NOEXCEPT = _IMP_kmeans.IMP_HAS_NOEXCEPT
IMP_C_OPEN_BINARY = _IMP_kmeans.IMP_C_OPEN_BINARY
import IMP
IMP_KMEANS_HAS_BOOST_FILESYSTEM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_FILESYSTEM
IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_PROGRAMOPTIONS
IMP_KMEANS_HAS_BOOST_RANDOM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_RANDOM
IMP_KMEANS_HAS_BOOST_SYSTEM = _IMP_kmeans.IMP_KMEANS_HAS_BOOST_SYSTEM
IMP_KMEANS_HAS_NUMPY = _IMP_kmeans.IMP_KMEANS_HAS_NUMPY
IMPKMEANS_SHOW_WARNINGS = _IMP_kmeans.IMPKMEANS_SHOW_WARNINGS

_object_types.append("KMeans")


def _object_cast_to_KMeans(o):
    """_object_cast_to_KMeans(Object o) -> KMeans"""
    return _IMP_kmeans._object_cast_to_KMeans(o)
KM_LLOYDS = _IMP_kmeans.KM_LLOYDS
KM_LOCAL_SWAP = _IMP_kmeans.KM_LOCAL_SWAP
KM_LOCAL_EZ_HYBRID = _IMP_kmeans.KM_LOCAL_EZ_HYBRID
KM_HYBRID = _IMP_kmeans.KM_HYBRID
class KMeans(IMP.Object):
    """Proxy of C++ IMP::kmeans::KMeans class."""

    thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')

    def __init__(self, *args):
        """
        __init__(IMP::kmeans::KMeans self, std::string const & fname_data, int dim, unsigned int max_nPts) -> KMeans
        __init__(IMP::kmeans::KMeans self) -> KMeans
        """
        this = _IMP_kmeans.new_KMeans(*args)
        try:
            self.this.append(this)
        except __builtin__.Exception:
            self.this = this

    def get_version_info(self):
        """get_version_info(KMeans self) -> VersionInfo"""
        return _IMP_kmeans.KMeans_get_version_info(self)


    def execute(self, *args):
        """
        execute(KMeans self, unsigned int k, IMP::kmeans::KM_ALG_TYPE alg_type, int stages=100)
        execute(KMeans self, unsigned int k, IMP::kmeans::KM_ALG_TYPE alg_type)
        execute(KMeans self, unsigned int k)
        """
        return _IMP_kmeans.KMeans_execute(self, *args)


    def add_data_pt(self, p):
        """add_data_pt(KMeans self, IMP::Floats const & p)"""
        return _IMP_kmeans.KMeans_add_data_pt(self, p)


    def clear_data(self):
        """clear_data(KMeans self)"""
        return _IMP_kmeans.KMeans_clear_data(self)


    def get_data_point(self, i):
        """get_data_point(KMeans self, unsigned int i) -> IMP::Floats const &"""
        return _IMP_kmeans.KMeans_get_data_point(self, i)


    def get_number_of_data_points(self):
        """get_number_of_data_points(KMeans self) -> unsigned int"""
        return _IMP_kmeans.KMeans_get_number_of_data_points(self)


    def print_centers(self, *args):
        """
        print_centers(KMeans self, IMP::LogLevel ll)
        print_centers(KMeans self)
        """
        return _IMP_kmeans.KMeans_print_centers(self, *args)


    def get_center(self, i):
        """get_center(KMeans self, unsigned int i) -> IMP::Floats"""
        return _IMP_kmeans.KMeans_get_center(self, i)


    def get_assignments(self):
        """get_assignments(KMeans self) -> IMP::Ints"""
        return _IMP_kmeans.KMeans_get_assignments(self)


    def get_squared_distance_to_centers(self):
        """get_squared_distance_to_centers(KMeans self) -> IMP::Floats"""
        return _IMP_kmeans.KMeans_get_squared_distance_to_centers(self)


    def get_number_of_centers(self):
        """get_number_of_centers(KMeans self) -> unsigned int"""
        return _IMP_kmeans.KMeans_get_number_of_centers(self)


    def __str__(self):
        """__str__(KMeans self) -> std::string"""
        return _IMP_kmeans.KMeans___str__(self)


    def __repr__(self):
        """__repr__(KMeans self) -> std::string"""
        return _IMP_kmeans.KMeans___repr__(self)


    @staticmethod
    def get_from(o):
       return _object_cast_to_KMeans(o)

KMeans_swigregister = _IMP_kmeans.KMeans_swigregister
KMeans_swigregister(KMeans)


def get_module_version():
    """get_module_version() -> std::string const"""
    return _IMP_kmeans.get_module_version()

def get_example_path(fname):
    """get_example_path(std::string fname) -> std::string"""
    return _IMP_kmeans.get_example_path(fname)

def get_data_path(fname):
    """get_data_path(std::string fname) -> std::string"""
    return _IMP_kmeans.get_data_path(fname)

from . import _version_check
_version_check.check_version(get_module_version())
__version__ = get_module_version()