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IMP Reference Guide  2.14.0
The Integrative Modeling Platform
em2d/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 # This wrapper is part of IMP,
8 # Copyright 2007-2020 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_em2d')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_em2d')
25  _IMP_em2d = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_em2d', [dirname(__file__)])
34  except ImportError:
35  import _IMP_em2d
36  return _IMP_em2d
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_em2d', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_em2d = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_em2d
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_EM2D_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_EM2D_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_em2d.delete_IMP_EM2D_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
126  return _IMP_em2d.IMP_EM2D_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
132  incr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
133  """
134  return _IMP_em2d.IMP_EM2D_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
140  decr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
141  """
142  return _IMP_em2d.IMP_EM2D_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_em2d.IMP_EM2D_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
152  return _IMP_em2d.IMP_EM2D_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator"""
157  return _IMP_em2d.IMP_EM2D_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
162  return _IMP_em2d.IMP_EM2D_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
167  return _IMP_em2d.IMP_EM2D_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
172  return _IMP_em2d.IMP_EM2D_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
177  return _IMP_em2d.IMP_EM2D_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
182  return _IMP_em2d.IMP_EM2D_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
187  return _IMP_em2d.IMP_EM2D_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
192  return _IMP_em2d.IMP_EM2D_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
197  return _IMP_em2d.IMP_EM2D_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
202  return _IMP_em2d.IMP_EM2D_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator
208  __sub__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_em2d.IMP_EM2D_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_EM2D_SwigPyIterator_swigregister = _IMP_em2d.IMP_EM2D_SwigPyIterator_swigregister
215 IMP_EM2D_SwigPyIterator_swigregister(IMP_EM2D_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_em2d.IMP_DEBUG
224 IMP_RELEASE = _IMP_em2d.IMP_RELEASE
225 IMP_SILENT = _IMP_em2d.IMP_SILENT
226 IMP_PROGRESS = _IMP_em2d.IMP_PROGRESS
227 IMP_TERSE = _IMP_em2d.IMP_TERSE
228 IMP_VERBOSE = _IMP_em2d.IMP_VERBOSE
229 IMP_MEMORY = _IMP_em2d.IMP_MEMORY
230 IMP_NONE = _IMP_em2d.IMP_NONE
231 IMP_USAGE = _IMP_em2d.IMP_USAGE
232 IMP_INTERNAL = _IMP_em2d.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_em2d.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_em2d.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em2d.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_em2d.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_em2d.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em2d.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_em2d.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_em2d._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_em2d._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_em2d.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_em2d.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_em2d.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_em2d.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_em2d.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_em2d.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_em2d.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_em2d.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_em2d.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_em2d.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_em2d.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_GSL_HAS_IMP_CGAL = _IMP_em2d.IMP_GSL_HAS_IMP_CGAL
318 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_FILESYSTEM
319 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
320 IMP_GSL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_GSL_HAS_BOOST_RANDOM
321 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_SYSTEM
322 IMP_GSL_HAS_CGAL = _IMP_em2d.IMP_GSL_HAS_CGAL
323 IMP_GSL_HAS_NUMPY = _IMP_em2d.IMP_GSL_HAS_NUMPY
324 IMPGSL_SHOW_WARNINGS = _IMP_em2d.IMPGSL_SHOW_WARNINGS
325 import IMP.gsl
326 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
327 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
328 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
329 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
330 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
331 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_CGAL
332 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_HDF5
333 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_NUMPY
334 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em2d.IMPSCOREFUNCTOR_SHOW_WARNINGS
335 import IMP.score_functor
336 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_IMP_CGAL
337 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
338 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
339 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_RANDOM
340 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_SYSTEM
341 IMP_STATISTICS_HAS_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_CGAL
342 IMP_STATISTICS_HAS_NUMPY = _IMP_em2d.IMP_STATISTICS_HAS_NUMPY
343 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em2d.IMPSTATISTICS_SHOW_WARNINGS
344 import IMP.statistics
345 IMP_CORE_HAS_IMP_CGAL = _IMP_em2d.IMP_CORE_HAS_IMP_CGAL
346 IMP_CORE_HAS_IMP_KERNEL = _IMP_em2d.IMP_CORE_HAS_IMP_KERNEL
347 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_FILESYSTEM
348 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
349 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CORE_HAS_BOOST_RANDOM
350 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_SYSTEM
351 IMP_CORE_HAS_CGAL = _IMP_em2d.IMP_CORE_HAS_CGAL
352 IMP_CORE_HAS_HDF5 = _IMP_em2d.IMP_CORE_HAS_HDF5
353 IMP_CORE_HAS_NUMPY = _IMP_em2d.IMP_CORE_HAS_NUMPY
354 IMPCORE_SHOW_WARNINGS = _IMP_em2d.IMPCORE_SHOW_WARNINGS
355 import IMP.core
356 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em2d.IMP_CONTAINER_HAS_IMP_ALGEBRA
357 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_CGAL
358 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em2d.IMP_CONTAINER_HAS_IMP_DISPLAY
359 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_KERNEL
360 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
361 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
362 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
363 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_RANDOM
364 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_SYSTEM
365 IMP_CONTAINER_HAS_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_CGAL
366 IMP_CONTAINER_HAS_HDF5 = _IMP_em2d.IMP_CONTAINER_HAS_HDF5
367 IMP_CONTAINER_HAS_NUMPY = _IMP_em2d.IMP_CONTAINER_HAS_NUMPY
368 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em2d.IMP_CONTAINER_HAS_PYTHON_IHM
369 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em2d.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
370 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em2d.IMP_CONTAINER_HAS_ROBIN_MAP
371 IMPCONTAINER_SHOW_WARNINGS = _IMP_em2d.IMPCONTAINER_SHOW_WARNINGS
372 import IMP.container
373 IMP_ATOM_HAS_IMP_CGAL = _IMP_em2d.IMP_ATOM_HAS_IMP_CGAL
374 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em2d.IMP_ATOM_HAS_IMP_KERNEL
375 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
376 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
377 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ATOM_HAS_BOOST_RANDOM
378 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em2d.IMP_ATOM_HAS_BOOST_REGEX
379 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ATOM_HAS_BOOST_SYSTEM
380 IMP_ATOM_HAS_CGAL = _IMP_em2d.IMP_ATOM_HAS_CGAL
381 IMP_ATOM_HAS_HDF5 = _IMP_em2d.IMP_ATOM_HAS_HDF5
382 IMP_ATOM_HAS_NUMPY = _IMP_em2d.IMP_ATOM_HAS_NUMPY
383 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em2d.IMP_ATOM_HAS_PYTHON_IHM
384 IMPATOM_SHOW_WARNINGS = _IMP_em2d.IMPATOM_SHOW_WARNINGS
385 IMP_ATOM_TYPE_INDEX = _IMP_em2d.IMP_ATOM_TYPE_INDEX
386 IMP_RESIDUE_TYPE_INDEX = _IMP_em2d.IMP_RESIDUE_TYPE_INDEX
387 IMP_HIERARCHY_TYPE_INDEX = _IMP_em2d.IMP_HIERARCHY_TYPE_INDEX
388 IMP_CHAIN_TYPE_INDEX = _IMP_em2d.IMP_CHAIN_TYPE_INDEX
389 import IMP.atom
390 IMP_EM_HAS_IMP_CGAL = _IMP_em2d.IMP_EM_HAS_IMP_CGAL
391 IMP_EM_HAS_IMP_CONTAINER = _IMP_em2d.IMP_EM_HAS_IMP_CONTAINER
392 IMP_EM_HAS_IMP_DISPLAY = _IMP_em2d.IMP_EM_HAS_IMP_DISPLAY
393 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM_HAS_IMP_SCORE_FUNCTOR
394 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_FILESYSTEM
395 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
396 IMP_EM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM_HAS_BOOST_RANDOM
397 IMP_EM_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM_HAS_BOOST_REGEX
398 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_SYSTEM
399 IMP_EM_HAS_CGAL = _IMP_em2d.IMP_EM_HAS_CGAL
400 IMP_EM_HAS_HDF5 = _IMP_em2d.IMP_EM_HAS_HDF5
401 IMP_EM_HAS_NUMPY = _IMP_em2d.IMP_EM_HAS_NUMPY
402 IMP_EM_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM_HAS_PYTHON_IHM
403 IMPEM_SHOW_WARNINGS = _IMP_em2d.IMPEM_SHOW_WARNINGS
404 import IMP.em
405 IMP_SAXS_HAS_IMP_CGAL = _IMP_em2d.IMP_SAXS_HAS_IMP_CGAL
406 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_em2d.IMP_SAXS_HAS_IMP_CONTAINER
407 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_em2d.IMP_SAXS_HAS_IMP_DISPLAY
408 IMP_SAXS_HAS_IMP_KERNEL = _IMP_em2d.IMP_SAXS_HAS_IMP_KERNEL
409 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
410 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SAXS_HAS_BOOST_FILESYSTEM
411 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
412 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SAXS_HAS_BOOST_RANDOM
413 IMP_SAXS_HAS_BOOST_REGEX = _IMP_em2d.IMP_SAXS_HAS_BOOST_REGEX
414 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SAXS_HAS_BOOST_SYSTEM
415 IMP_SAXS_HAS_CGAL = _IMP_em2d.IMP_SAXS_HAS_CGAL
416 IMP_SAXS_HAS_HDF5 = _IMP_em2d.IMP_SAXS_HAS_HDF5
417 IMP_SAXS_HAS_NUMPY = _IMP_em2d.IMP_SAXS_HAS_NUMPY
418 IMP_SAXS_HAS_PYTHON_IHM = _IMP_em2d.IMP_SAXS_HAS_PYTHON_IHM
419 IMPSAXS_SHOW_WARNINGS = _IMP_em2d.IMPSAXS_SHOW_WARNINGS
420 import IMP.saxs
421 IMP_ISD_HAS_IMP_CGAL = _IMP_em2d.IMP_ISD_HAS_IMP_CGAL
422 IMP_ISD_HAS_IMP_DISPLAY = _IMP_em2d.IMP_ISD_HAS_IMP_DISPLAY
423 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
424 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ISD_HAS_BOOST_FILESYSTEM
425 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
426 IMP_ISD_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ISD_HAS_BOOST_RANDOM
427 IMP_ISD_HAS_BOOST_REGEX = _IMP_em2d.IMP_ISD_HAS_BOOST_REGEX
428 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ISD_HAS_BOOST_SYSTEM
429 IMP_ISD_HAS_CGAL = _IMP_em2d.IMP_ISD_HAS_CGAL
430 IMP_ISD_HAS_HDF5 = _IMP_em2d.IMP_ISD_HAS_HDF5
431 IMP_ISD_HAS_NUMPY = _IMP_em2d.IMP_ISD_HAS_NUMPY
432 IMP_ISD_HAS_PYTHON_IHM = _IMP_em2d.IMP_ISD_HAS_PYTHON_IHM
433 IMPISD_SHOW_WARNINGS = _IMP_em2d.IMPISD_SHOW_WARNINGS
434 import IMP.isd
435 IMP_RMF_HAS_IMP_CGAL = _IMP_em2d.IMP_RMF_HAS_IMP_CGAL
436 IMP_RMF_HAS_IMP_EM = _IMP_em2d.IMP_RMF_HAS_IMP_EM
437 IMP_RMF_HAS_IMP_SAXS = _IMP_em2d.IMP_RMF_HAS_IMP_SAXS
438 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
439 IMP_RMF_HAS_IMP_STATISTICS = _IMP_em2d.IMP_RMF_HAS_IMP_STATISTICS
440 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_FILESYSTEM
441 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
442 IMP_RMF_HAS_BOOST_RANDOM = _IMP_em2d.IMP_RMF_HAS_BOOST_RANDOM
443 IMP_RMF_HAS_BOOST_REGEX = _IMP_em2d.IMP_RMF_HAS_BOOST_REGEX
444 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_SYSTEM
445 IMP_RMF_HAS_CGAL = _IMP_em2d.IMP_RMF_HAS_CGAL
446 IMP_RMF_HAS_HDF5 = _IMP_em2d.IMP_RMF_HAS_HDF5
447 IMP_RMF_HAS_NUMPY = _IMP_em2d.IMP_RMF_HAS_NUMPY
448 IMP_RMF_HAS_PYTHON_IHM = _IMP_em2d.IMP_RMF_HAS_PYTHON_IHM
449 IMPRMF_SHOW_WARNINGS = _IMP_em2d.IMPRMF_SHOW_WARNINGS
450 import IMP.rmf
451 import RMF
452 IMP_DOMINO_HAS_IMP_ATOM = _IMP_em2d.IMP_DOMINO_HAS_IMP_ATOM
453 IMP_DOMINO_HAS_IMP_CGAL = _IMP_em2d.IMP_DOMINO_HAS_IMP_CGAL
454 IMP_DOMINO_HAS_IMP_EM = _IMP_em2d.IMP_DOMINO_HAS_IMP_EM
455 IMP_DOMINO_HAS_IMP_ISD = _IMP_em2d.IMP_DOMINO_HAS_IMP_ISD
456 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_em2d.IMP_DOMINO_HAS_IMP_KERNEL
457 IMP_DOMINO_HAS_IMP_RMF = _IMP_em2d.IMP_DOMINO_HAS_IMP_RMF
458 IMP_DOMINO_HAS_IMP_SAXS = _IMP_em2d.IMP_DOMINO_HAS_IMP_SAXS
459 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
460 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_FILESYSTEM
461 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
462 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_RANDOM
463 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_em2d.IMP_DOMINO_HAS_BOOST_REGEX
464 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_SYSTEM
465 IMP_DOMINO_HAS_CGAL = _IMP_em2d.IMP_DOMINO_HAS_CGAL
466 IMP_DOMINO_HAS_HDF5 = _IMP_em2d.IMP_DOMINO_HAS_HDF5
467 IMP_DOMINO_HAS_NUMPY = _IMP_em2d.IMP_DOMINO_HAS_NUMPY
468 IMP_DOMINO_HAS_RMF = _IMP_em2d.IMP_DOMINO_HAS_RMF
469 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_em2d.IMP_DOMINO_HAS_PYTHON_IHM
470 IMPDOMINO_SHOW_WARNINGS = _IMP_em2d.IMPDOMINO_SHOW_WARNINGS
471 import RMF_HDF5
472 import IMP.domino
473 IMP_EM2D_HAS_IMP_CGAL = _IMP_em2d.IMP_EM2D_HAS_IMP_CGAL
474 IMP_EM2D_HAS_IMP_ISD = _IMP_em2d.IMP_EM2D_HAS_IMP_ISD
475 IMP_EM2D_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM2D_HAS_IMP_KERNEL
476 IMP_EM2D_HAS_IMP_RMF = _IMP_em2d.IMP_EM2D_HAS_IMP_RMF
477 IMP_EM2D_HAS_IMP_SAXS = _IMP_em2d.IMP_EM2D_HAS_IMP_SAXS
478 IMP_EM2D_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM2D_HAS_IMP_SCORE_FUNCTOR
479 IMP_EM2D_HAS_IMP_STATISTICS = _IMP_em2d.IMP_EM2D_HAS_IMP_STATISTICS
480 IMP_EM2D_HAS_BOOST_GRAPH = _IMP_em2d.IMP_EM2D_HAS_BOOST_GRAPH
481 IMP_EM2D_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM2D_HAS_BOOST_RANDOM
482 IMP_EM2D_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM2D_HAS_BOOST_REGEX
483 IMP_EM2D_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM2D_HAS_BOOST_SYSTEM
484 IMP_EM2D_HAS_CGAL = _IMP_em2d.IMP_EM2D_HAS_CGAL
485 IMP_EM2D_HAS_GSL = _IMP_em2d.IMP_EM2D_HAS_GSL
486 IMP_EM2D_HAS_HDF5 = _IMP_em2d.IMP_EM2D_HAS_HDF5
487 IMP_EM2D_HAS_NUMPY = _IMP_em2d.IMP_EM2D_HAS_NUMPY
488 IMP_EM2D_HAS_OPENCV22 = _IMP_em2d.IMP_EM2D_HAS_OPENCV22
489 IMP_EM2D_HAS_RMF = _IMP_em2d.IMP_EM2D_HAS_RMF
490 IMP_EM2D_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM2D_HAS_PYTHON_IHM
491 IMP_EM2D_HAS_OPENCV21 = _IMP_em2d.IMP_EM2D_HAS_OPENCV21
492 IMP_EM2D_HAS_OPENCV3 = _IMP_em2d.IMP_EM2D_HAS_OPENCV3
493 IMPEM2D_SHOW_WARNINGS = _IMP_em2d.IMPEM2D_SHOW_WARNINGS
494 
495 PolarResamplingParametersList=list
496 _plural_types.append("PolarResamplingParametersList")
497 _value_types.append("PolarResamplingParameters")
498 
499 
500 ProjectionMasks=list
501 _plural_types.append("ProjectionMasks")
502 _value_types.append("ProjectionMask")
503 
504 
505 MasksManagers=list
506 _plural_types.append("MasksManagers")
507 _value_types.append("MasksManager")
508 
509 
510 RegistrationResults=list
511 _plural_types.append("RegistrationResults")
512 _value_types.append("RegistrationResult")
513 
514 
515 ClusterSets=list
516 _plural_types.append("ClusterSets")
517 _value_types.append("ClusterSet")
518 
519 
520 SingleLinkages=list
521 _plural_types.append("SingleLinkages")
522 _value_types.append("SingleLinkage")
523 
524 
525 CompleteLinkages=list
526 _plural_types.append("CompleteLinkages")
527 _value_types.append("CompleteLinkage")
528 
529 
530 AverageDistanceLinkages=list
531 _plural_types.append("AverageDistanceLinkages")
532 _value_types.append("AverageDistanceLinkage")
533 
534 
535 SegmentationParametersList=list
536 _plural_types.append("SegmentationParametersList")
537 _value_types.append("SegmentationParameters")
538 
539 
540 MatchTemplateResults=list
541 _plural_types.append("MatchTemplateResults")
542 _value_types.append("MatchTemplateResult")
543 
544 
545 ProjectingParametersList=list
546 _plural_types.append("ProjectingParametersList")
547 _value_types.append("ProjectingParameters")
548 
549 
550 ProjectingOptionsList=list
551 _plural_types.append("ProjectingOptionsList")
552 _value_types.append("ProjectingOptions")
553 
554 
555 Em2DRestraintParametersList=list
556 _plural_types.append("Em2DRestraintParametersList")
557 _value_types.append("Em2DRestraintParameters")
558 
559 
560 _object_types.append("ProjectionFinder")
561 
562 
563 def _object_cast_to_ProjectionFinder(o):
564  """_object_cast_to_ProjectionFinder(Object o) -> ProjectionFinder"""
565  return _IMP_em2d._object_cast_to_ProjectionFinder(o)
566 
567 _object_types.append("ScoreFunction")
568 
569 
570 def _object_cast_to_ScoreFunction(o):
571  """_object_cast_to_ScoreFunction(Object o) -> ScoreFunction"""
572  return _IMP_em2d._object_cast_to_ScoreFunction(o)
573 
574 _object_types.append("ChiSquaredScore")
575 
576 
577 def _object_cast_to_ChiSquaredScore(o):
578  """_object_cast_to_ChiSquaredScore(Object o) -> ChiSquaredScore"""
579  return _IMP_em2d._object_cast_to_ChiSquaredScore(o)
580 
581 _object_types.append("EM2DScore")
582 
583 
584 def _object_cast_to_EM2DScore(o):
585  """_object_cast_to_EM2DScore(Object o) -> EM2DScore"""
586  return _IMP_em2d._object_cast_to_EM2DScore(o)
587 
588 _object_types.append("MeanAbsoluteDifference")
589 
590 
591 def _object_cast_to_MeanAbsoluteDifference(o):
592  """_object_cast_to_MeanAbsoluteDifference(Object o) -> MeanAbsoluteDifference"""
593  return _IMP_em2d._object_cast_to_MeanAbsoluteDifference(o)
594 
595 _object_types.append("ProjectionParametersScoreState")
596 
597 
598 def _object_cast_to_ProjectionParametersScoreState(o):
599  """_object_cast_to_ProjectionParametersScoreState(Object o) -> ProjectionParametersScoreState"""
600  return _IMP_em2d._object_cast_to_ProjectionParametersScoreState(o)
601 
602 _object_types.append("Em2DRestraint")
603 
604 
605 def _object_cast_to_Em2DRestraint(o):
606  """_object_cast_to_Em2DRestraint(Object o) -> Em2DRestraint"""
607  return _IMP_em2d._object_cast_to_Em2DRestraint(o)
608 
609 _object_types.append("Image")
610 
611 
612 def _object_cast_to_Image(o):
613  """_object_cast_to_Image(Object o) -> Image"""
614  return _IMP_em2d._object_cast_to_Image(o)
615 
616 _object_types.append("ImageReaderWriter")
617 
618 
619 def _object_cast_to_ImageReaderWriter(o):
620  """_object_cast_to_ImageReaderWriter(Object o) -> ImageReaderWriter"""
621  return _IMP_em2d._object_cast_to_ImageReaderWriter(o)
622 
623 _object_types.append("JPGImageReaderWriter")
624 
625 
626 def _object_cast_to_JPGImageReaderWriter(o):
627  """_object_cast_to_JPGImageReaderWriter(Object o) -> JPGImageReaderWriter"""
628  return _IMP_em2d._object_cast_to_JPGImageReaderWriter(o)
629 
630 _object_types.append("TIFFImageReaderWriter")
631 
632 
633 def _object_cast_to_TIFFImageReaderWriter(o):
634  """_object_cast_to_TIFFImageReaderWriter(Object o) -> TIFFImageReaderWriter"""
635  return _IMP_em2d._object_cast_to_TIFFImageReaderWriter(o)
636 
637 _object_types.append("SpiderImageReaderWriter")
638 
639 
640 def _object_cast_to_SpiderImageReaderWriter(o):
641  """_object_cast_to_SpiderImageReaderWriter(Object o) -> SpiderImageReaderWriter"""
642  return _IMP_em2d._object_cast_to_SpiderImageReaderWriter(o)
643 
644 _object_types.append("CollisionCrossSection")
645 
646 
647 def _object_cast_to_CollisionCrossSection(o):
648  """_object_cast_to_CollisionCrossSection(Object o) -> CollisionCrossSection"""
649  return _IMP_em2d._object_cast_to_CollisionCrossSection(o)
650 
651 _object_types.append("GridStates")
652 
653 
654 def _object_cast_to_GridStates(o):
655  """_object_cast_to_GridStates(Object o) -> GridStates"""
656  return _IMP_em2d._object_cast_to_GridStates(o)
657 
658 _object_types.append("ProjectionStates")
659 
660 
661 def _object_cast_to_ProjectionStates(o):
662  """_object_cast_to_ProjectionStates(Object o) -> ProjectionStates"""
663  return _IMP_em2d._object_cast_to_ProjectionStates(o)
664 
665 _object_types.append("DistanceFilter")
666 
667 
668 def _object_cast_to_DistanceFilter(o):
669  """_object_cast_to_DistanceFilter(Object o) -> DistanceFilter"""
670  return _IMP_em2d._object_cast_to_DistanceFilter(o)
671 
672 _object_types.append("DistanceFilterTable")
673 
674 
675 def _object_cast_to_DistanceFilterTable(o):
676  """_object_cast_to_DistanceFilterTable(Object o) -> DistanceFilterTable"""
677  return _IMP_em2d._object_cast_to_DistanceFilterTable(o)
678 
679 _object_types.append("RigidBodiesImageFitRestraint")
680 
681 
682 def _object_cast_to_RigidBodiesImageFitRestraint(o):
683  """_object_cast_to_RigidBodiesImageFitRestraint(Object o) -> RigidBodiesImageFitRestraint"""
684  return _IMP_em2d._object_cast_to_RigidBodiesImageFitRestraint(o)
685 
686 _object_types.append("DummyRestraint")
687 
688 
689 def _object_cast_to_DummyRestraint(o):
690  """_object_cast_to_DummyRestraint(Object o) -> DummyRestraint"""
691  return _IMP_em2d._object_cast_to_DummyRestraint(o)
692 
693 _object_types.append("ParticlesDummyRestraint")
694 
695 
696 def _object_cast_to_ParticlesDummyRestraint(o):
697  """_object_cast_to_ParticlesDummyRestraint(Object o) -> ParticlesDummyRestraint"""
698  return _IMP_em2d._object_cast_to_ParticlesDummyRestraint(o)
699 
700 _object_types.append("RelativePositionMover")
701 
702 
703 def _object_cast_to_RelativePositionMover(o):
704  """_object_cast_to_RelativePositionMover(Object o) -> RelativePositionMover"""
705  return _IMP_em2d._object_cast_to_RelativePositionMover(o)
706 
707 _object_types.append("PCAFitRestraint")
708 
709 
710 def _object_cast_to_em2dPCAFitRestraint(o):
711  """_object_cast_to_em2dPCAFitRestraint(Object o) -> PCAFitRestraint"""
712  return _IMP_em2d._object_cast_to_em2dPCAFitRestraint(o)
713 
714 def ProjectionParametersList(l=[]):
715  return [ProjectionParameters(x) for x in l]
716 _plural_types.append("ProjectionParametersList")
717 
718 
719 _value_types.append("ProjectionParameters")
720 
721 
722 def show(*args):
723  """
724  show(cv::Mat const & m, _ostream out)
725  show(cv::Mat const & m)
726  """
727  return _IMP_em2d.show(*args)
728 
729 def write_matrix(m, name):
730  """write_matrix(cv::Mat & m, std::string name)"""
731  return _IMP_em2d.write_matrix(m, name)
732 class ImageReaderWriter(IMP.Object):
733  """Proxy of C++ IMP::em2d::ImageReaderWriter class."""
734 
735  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
736 
737  def __init__(self, *args, **kwargs):
738  raise AttributeError("No constructor defined - class is abstract")
739 
740  def read(self, filename, header, data):
741  """read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
742  return _IMP_em2d.ImageReaderWriter_read(self, filename, header, data)
743 
744 
745  def read_from_floats(self, filename, header, data):
746  """read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
747  return _IMP_em2d.ImageReaderWriter_read_from_floats(self, filename, header, data)
748 
749 
750  def read_from_ints(self, filename, header, data):
751  """read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
752  return _IMP_em2d.ImageReaderWriter_read_from_ints(self, filename, header, data)
753 
754 
755  def write(self, filename, header, data):
756  """write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
757  return _IMP_em2d.ImageReaderWriter_write(self, filename, header, data)
758 
759 
760  def write_to_floats(self, filename, header, data):
761  """write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
762  return _IMP_em2d.ImageReaderWriter_write_to_floats(self, filename, header, data)
763 
764 
765  def write_to_ints(self, filename, header, data):
766  """write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
767  return _IMP_em2d.ImageReaderWriter_write_to_ints(self, filename, header, data)
768 
769 
770  def get_version_info(self):
771  """get_version_info(ImageReaderWriter self) -> VersionInfo"""
772  return _IMP_em2d.ImageReaderWriter_get_version_info(self)
773 
774 
775  def __str__(self):
776  """__str__(ImageReaderWriter self) -> std::string"""
777  return _IMP_em2d.ImageReaderWriter___str__(self)
778 
779 
780  def __repr__(self):
781  """__repr__(ImageReaderWriter self) -> std::string"""
782  return _IMP_em2d.ImageReaderWriter___repr__(self)
783 
784 
785  @staticmethod
786  def get_from(o):
787  return _object_cast_to_ImageReaderWriter(o)
788 
789 ImageReaderWriter_swigregister = _IMP_em2d.ImageReaderWriter_swigregister
790 ImageReaderWriter_swigregister(ImageReaderWriter)
791 
792 class PolarResamplingParameters(object):
793  """Proxy of C++ IMP::em2d::PolarResamplingParameters class."""
794 
795  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
796 
797  def __init__(self, *args):
798  """
799  __init__(IMP::em2d::PolarResamplingParameters self) -> PolarResamplingParameters
800  __init__(IMP::em2d::PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
801  __init__(IMP::em2d::PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
802  """
803  this = _IMP_em2d.new_PolarResamplingParameters(*args)
804  try:
805  self.this.append(this)
806  except __builtin__.Exception:
807  self.this = this
808  __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
809  __del__ = lambda self: None
810 
811  def setup(self, rows, cols):
812  """setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
813  return _IMP_em2d.PolarResamplingParameters_setup(self, rows, cols)
814 
815 
816  def get_starting_radius(self):
817  """get_starting_radius(PolarResamplingParameters self) -> double"""
818  return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
819 
820 
821  def get_ending_radius(self):
822  """get_ending_radius(PolarResamplingParameters self) -> double"""
823  return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
824 
825 
826  def get_radius(self, n_ring):
827  """get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
828  return _IMP_em2d.PolarResamplingParameters_get_radius(self, n_ring)
829 
830 
831  def get_number_of_rings(self):
832  """get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
833  return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
834 
835 
836  def set_estimated_number_of_angles(self, aprox_value):
837  """set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
838  return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, aprox_value)
839 
840 
841  def get_number_of_angles(self):
842  """get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
843  return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
844 
845 
846  def get_angle_step(self):
847  """get_angle_step(PolarResamplingParameters self) -> double"""
848  return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
849 
850 
851  def get_radius_step(self):
852  """get_radius_step(PolarResamplingParameters self) -> double"""
853  return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
854 
855 
856  def create_maps_for_resampling(self):
857  """create_maps_for_resampling(PolarResamplingParameters self)"""
858  return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
859 
860 
861  def get_resampling_maps(self, m1, m2):
862  """get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
863  return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, m1, m2)
864 
865 
866  def get_resampling_map(self, m1):
867  """get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
868  return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, m1)
869 
870 
871  def show(self, out):
872  """show(PolarResamplingParameters self, _ostream out)"""
873  return _IMP_em2d.PolarResamplingParameters_show(self, out)
874 
875 
876  def get_is_setup(self):
877  """get_is_setup(PolarResamplingParameters self) -> bool"""
878  return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
879 
880 
881  def __str__(self):
882  """__str__(PolarResamplingParameters self) -> std::string"""
883  return _IMP_em2d.PolarResamplingParameters___str__(self)
884 
885 
886  def __repr__(self):
887  """__repr__(PolarResamplingParameters self) -> std::string"""
888  return _IMP_em2d.PolarResamplingParameters___repr__(self)
889 
890 PolarResamplingParameters_swigregister = _IMP_em2d.PolarResamplingParameters_swigregister
891 PolarResamplingParameters_swigregister(PolarResamplingParameters)
892 
893 class SegmentationParameters(object):
894  """Proxy of C++ IMP::em2d::SegmentationParameters class."""
895 
896  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
897  image_pixel_size = _swig_property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set)
898  diffusion_beta = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set)
899  diffusion_timesteps = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set)
900  fill_holes_stddevs = _swig_property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set)
901  opening_kernel = _swig_property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set)
902  remove_sizing_percentage = _swig_property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set)
903  binary_background = _swig_property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set)
904  binary_foreground = _swig_property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set)
905  threshold = _swig_property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set)
906 
907  def __init__(self, *args):
908  """
909  __init__(IMP::em2d::SegmentationParameters self) -> SegmentationParameters
910  __init__(IMP::em2d::SegmentationParameters self, double apix, double diff_beta, unsigned int diff_timesteps, double fh_stddevs, cv::Mat const & kr, int background, int foreground) -> SegmentationParameters
911  """
912  this = _IMP_em2d.new_SegmentationParameters(*args)
913  try:
914  self.this.append(this)
915  except __builtin__.Exception:
916  self.this = this
917 
918  def show(self, *args):
919  """
920  show(SegmentationParameters self, _ostream out)
921  show(SegmentationParameters self)
922  """
923  return _IMP_em2d.SegmentationParameters_show(self, *args)
924 
925 
926  def __str__(self):
927  """__str__(SegmentationParameters self) -> std::string"""
928  return _IMP_em2d.SegmentationParameters___str__(self)
929 
930 
931  def __repr__(self):
932  """__repr__(SegmentationParameters self) -> std::string"""
933  return _IMP_em2d.SegmentationParameters___repr__(self)
934 
935  __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
936  __del__ = lambda self: None
937 SegmentationParameters_swigregister = _IMP_em2d.SegmentationParameters_swigregister
938 SegmentationParameters_swigregister(SegmentationParameters)
939 
940 class MatchTemplateResult(object):
941  """Proxy of C++ IMP::em2d::MatchTemplateResult class."""
942 
943  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
944  pair = _swig_property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set)
945  cross_correlation = _swig_property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set)
946 
947  def __init__(self, p, cc):
948  """__init__(IMP::em2d::MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
949  this = _IMP_em2d.new_MatchTemplateResult(p, cc)
950  try:
951  self.this.append(this)
952  except __builtin__.Exception:
953  self.this = this
954 
955  def show(self, *args):
956  """
957  show(MatchTemplateResult self, _ostream out)
958  show(MatchTemplateResult self)
959  """
960  return _IMP_em2d.MatchTemplateResult_show(self, *args)
961 
962 
963  def __str__(self):
964  """__str__(MatchTemplateResult self) -> std::string"""
965  return _IMP_em2d.MatchTemplateResult___str__(self)
966 
967 
968  def __repr__(self):
969  """__repr__(MatchTemplateResult self) -> std::string"""
970  return _IMP_em2d.MatchTemplateResult___repr__(self)
971 
972  __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
973  __del__ = lambda self: None
974 MatchTemplateResult_swigregister = _IMP_em2d.MatchTemplateResult_swigregister
975 MatchTemplateResult_swigregister(MatchTemplateResult)
976 
977 
978 def apply_mask(m, result, mask, val):
979  """apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
980  return _IMP_em2d.apply_mask(m, result, mask, val)
981 
982 def apply_circular_mask(mat, result, radius, value=0.0):
983  """
984  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)
985  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius)
986  """
987  return _IMP_em2d.apply_circular_mask(mat, result, radius, value)
988 
989 def get_mean(mat, mask):
990  """get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
991  return _IMP_em2d.get_mean(mat, mask)
992 
993 def create_circular_mask(rows, cols, radius):
994  """create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
995  return _IMP_em2d.create_circular_mask(rows, cols, radius)
996 
997 def do_histogram_stretching(m, boxes, offset):
998  """do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
999  return _IMP_em2d.do_histogram_stretching(m, boxes, offset)
1000 
1001 def do_dilate_and_shrink_warp(m, grayscale, kernel):
1002  """do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
1003  return _IMP_em2d.do_dilate_and_shrink_warp(m, grayscale, kernel)
1004 
1005 def do_morphologic_reconstruction(mask, marker, neighbors_mode=4):
1006  """
1007  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)
1008  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker)
1009  """
1010  return _IMP_em2d.do_morphologic_reconstruction(mask, marker, neighbors_mode)
1011 
1012 def do_labeling(m, mat_to_label):
1013  """do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
1014  return _IMP_em2d.do_labeling(m, mat_to_label)
1015 
1016 def get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang):
1017  """get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
1018  return _IMP_em2d.get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang)
1019 
1020 def get_domes(m, result, h):
1021  """get_domes(cv::Mat & m, cv::Mat & result, double h)"""
1022  return _IMP_em2d.get_domes(m, result, h)
1023 
1024 def get_transformed(input, transformed, T):
1025  """get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
1026  return _IMP_em2d.get_transformed(input, transformed, T)
1027 
1028 def apply_threshold(m, result, threshold=0.0):
1029  """
1030  apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)
1031  apply_threshold(cv::Mat & m, cv::Mat & result)
1032  """
1033  return _IMP_em2d.apply_threshold(m, result, threshold)
1034 
1035 def do_morphologic_contrast_enhancement(m, result, kernel, iterations):
1036  """do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
1037  return _IMP_em2d.do_morphologic_contrast_enhancement(m, result, kernel, iterations)
1038 
1039 def get_morphologic_gradient(m, result, kernel):
1040  """get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
1041  return _IMP_em2d.get_morphologic_gradient(m, result, kernel)
1042 
1043 def get_overlap_percentage(m1, m2, center):
1044  """get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
1045  return _IMP_em2d.get_overlap_percentage(m1, m2, center)
1046 
1047 def get_best_template_matches(m, templ, n):
1048  """get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
1049  return _IMP_em2d.get_best_template_matches(m, templ, n)
1050 class Image(IMP.Object):
1051  """Proxy of C++ IMP::em2d::Image class."""
1052 
1053  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1054 
1055  def __init__(self, *args):
1056  """
1057  __init__(IMP::em2d::Image self) -> Image
1058  __init__(IMP::em2d::Image self, int rows, int cols) -> Image
1059  __init__(IMP::em2d::Image self, IMP::String filename, ImageReaderWriter reader) -> Image
1060  """
1061  this = _IMP_em2d.new_Image(*args)
1062  try:
1063  self.this.append(this)
1064  except __builtin__.Exception:
1065  self.this = this
1066 
1067  def get_data(self):
1068  """get_data(Image self) -> cv::Mat &"""
1069  return _IMP_em2d.Image_get_data(self)
1070 
1071 
1072  def set_data(self, mat):
1073  """set_data(Image self, cv::Mat const & mat)"""
1074  return _IMP_em2d.Image_set_data(self, mat)
1075 
1076 
1077  def set_zeros(self):
1078  """set_zeros(Image self)"""
1079  return _IMP_em2d.Image_set_zeros(self)
1080 
1081 
1082  def set_value(self, *args):
1083  """
1084  set_value(Image self, double val)
1085  set_value(Image self, int i, int j, double val)
1086  """
1087  return _IMP_em2d.Image_set_value(self, *args)
1088 
1089 
1090  def __call__(self, i, j):
1091  """__call__(Image self, int i, int j) -> double"""
1092  return _IMP_em2d.Image___call__(self, i, j)
1093 
1094 
1095  def get_header(self):
1096  """get_header(Image self) -> ImageHeader"""
1097  return _IMP_em2d.Image_get_header(self)
1098 
1099 
1100  def set_size(self, *args):
1101  """
1102  set_size(Image self, int rows, int cols)
1103  set_size(Image self, Image img)
1104  """
1105  return _IMP_em2d.Image_set_size(self, *args)
1106 
1107 
1108  def update_header(self):
1109  """update_header(Image self)"""
1110  return _IMP_em2d.Image_update_header(self)
1111 
1112 
1113  def read(self, filename, reader):
1114  """read(Image self, IMP::String filename, ImageReaderWriter reader)"""
1115  return _IMP_em2d.Image_read(self, filename, reader)
1116 
1117 
1118  def write(self, filename, writer):
1119  """write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
1120  return _IMP_em2d.Image_write(self, filename, writer)
1121 
1122 
1123  def show(self, out):
1124  """show(Image self, _ostream out)"""
1125  return _IMP_em2d.Image_show(self, out)
1126 
1127 
1128  def get_version_info(self):
1129  """get_version_info(Image self) -> VersionInfo"""
1130  return _IMP_em2d.Image_get_version_info(self)
1131 
1132 
1133  def set_name(self, name):
1134  """set_name(Image self, IMP::String const & name)"""
1135  return _IMP_em2d.Image_set_name(self, name)
1136 
1137 
1138  def get_name(self):
1139  """get_name(Image self) -> IMP::String"""
1140  return _IMP_em2d.Image_get_name(self)
1141 
1142 
1143  def get_min_and_max_values(self):
1144  """get_min_and_max_values(Image self) -> IMP::FloatRange"""
1145  return _IMP_em2d.Image_get_min_and_max_values(self)
1146 
1147 
1148  def __str__(self):
1149  """__str__(Image self) -> std::string"""
1150  return _IMP_em2d.Image___str__(self)
1151 
1152 
1153  def __repr__(self):
1154  """__repr__(Image self) -> std::string"""
1155  return _IMP_em2d.Image___repr__(self)
1156 
1157 
1158  @staticmethod
1159  def get_from(o):
1160  return _object_cast_to_Image(o)
1161 
1162 Image_swigregister = _IMP_em2d.Image_swigregister
1163 Image_swigregister(Image)
1164 
1165 
1166 def read_images(names, rw):
1167  """read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1168  return _IMP_em2d.read_images(names, rw)
1169 
1170 def save_images(images, names, rw):
1171  """save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1172  return _IMP_em2d.save_images(images, names, rw)
1173 
1174 def do_normalize(*args):
1175  """
1176  do_normalize(cv::Mat & m)
1177  do_normalize(Image im, bool force=False)
1178  do_normalize(Image im)
1179  """
1180  return _IMP_em2d.do_normalize(*args)
1181 
1182 def get_histogram(*args):
1183  """
1184  get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1185  get_histogram(Image img, int bins) -> IMP::Floats
1186  """
1187  return _IMP_em2d.get_histogram(*args)
1188 
1189 def apply_variance_filter(*args):
1190  """
1191  apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1192  apply_variance_filter(Image input, Image filtered, int kernelsize)
1193  """
1194  return _IMP_em2d.apply_variance_filter(*args)
1195 
1196 def apply_diffusion_filter(*args):
1197  """
1198  apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1199  apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1200  """
1201  return _IMP_em2d.apply_diffusion_filter(*args)
1202 
1203 def do_fill_holes(*args):
1204  """
1205  do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1206  do_fill_holes(Image input, Image result, double n_stddevs)
1207  """
1208  return _IMP_em2d.do_fill_holes(*args)
1209 
1210 def do_combined_fill_holes_and_threshold(*args):
1211  """
1212  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1213  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs)
1214  do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1215  """
1216  return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1217 
1218 def do_extend_borders(*args):
1219  """
1220  do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1221  do_extend_borders(Image im1, Image im2, unsigned int pix)
1222  """
1223  return _IMP_em2d.do_extend_borders(*args)
1224 
1225 def do_segmentation(*args):
1226  """
1227  do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1228  do_segmentation(Image input, Image result, SegmentationParameters params)
1229  """
1230  return _IMP_em2d.do_segmentation(*args)
1231 
1232 def do_remove_small_objects(*args):
1233  """
1234  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1235  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0)
1236  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage)
1237  do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1238  do_remove_small_objects(Image input, double percentage, int background=0)
1239  do_remove_small_objects(Image input, double percentage)
1240  """
1241  return _IMP_em2d.do_remove_small_objects(*args)
1242 
1243 def do_subtract_images(first, second, result):
1244  """do_subtract_images(Image first, Image second, Image result)"""
1245  return _IMP_em2d.do_subtract_images(first, second, result)
1246 
1247 def add_noise(*args):
1248  """
1249  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode, double df=3)
1250  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode)
1251  add_noise(cv::Mat & v, double op1, double op2)
1252  add_noise(Image im1, double op1, double op2, IMP::String const & mode, double df=3)
1253  add_noise(Image im1, double op1, double op2, IMP::String const & mode)
1254  add_noise(Image im1, double op1, double op2)
1255  """
1256  return _IMP_em2d.add_noise(*args)
1257 
1258 def do_resample_polar(*args):
1259  """
1260  do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1261  do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1262  """
1263  return _IMP_em2d.do_resample_polar(*args)
1264 
1265 def crop(*args):
1266  """
1267  crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1268  crop(Image img, IMP::IntPair const & center, int size)
1269  """
1270  return _IMP_em2d.crop(*args)
1271 
1272 def apply_mean_outside_mask(img, radius):
1273  """apply_mean_outside_mask(Image img, double radius)"""
1274  return _IMP_em2d.apply_mean_outside_mask(img, radius)
1275 class RegistrationResult(object):
1276  """Proxy of C++ IMP::em2d::RegistrationResult class."""
1277 
1278  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1279 
1280  def __init__(self, *args):
1281  """
1282  __init__(IMP::em2d::RegistrationResult self) -> RegistrationResult
1283  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1284  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1285  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0) -> RegistrationResult
1286  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift) -> RegistrationResult
1287  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1288  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1289  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0) -> RegistrationResult
1290  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift) -> RegistrationResult
1291  __init__(IMP::em2d::RegistrationResult self, Rotation3D R) -> RegistrationResult
1292  """
1293  this = _IMP_em2d.new_RegistrationResult(*args)
1294  try:
1295  self.this.append(this)
1296  except __builtin__.Exception:
1297  self.this = this
1298 
1299  def get_phi(self):
1300  """get_phi(RegistrationResult self) -> double"""
1301  return _IMP_em2d.RegistrationResult_get_phi(self)
1302 
1303 
1304  def get_theta(self):
1305  """get_theta(RegistrationResult self) -> double"""
1306  return _IMP_em2d.RegistrationResult_get_theta(self)
1307 
1308 
1309  def get_psi(self):
1310  """get_psi(RegistrationResult self) -> double"""
1311  return _IMP_em2d.RegistrationResult_get_psi(self)
1312 
1313 
1314  def get_shift(self):
1315  """get_shift(RegistrationResult self) -> Vector2D"""
1316  return _IMP_em2d.RegistrationResult_get_shift(self)
1317 
1318 
1319  def get_shift_3d(self):
1320  """get_shift_3d(RegistrationResult self) -> Vector3D"""
1321  return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1322 
1323 
1324  def get_projection_index(self):
1325  """get_projection_index(RegistrationResult self) -> int"""
1326  return _IMP_em2d.RegistrationResult_get_projection_index(self)
1327 
1328 
1329  def set_projection_index(self, index):
1330  """set_projection_index(RegistrationResult self, int index)"""
1331  return _IMP_em2d.RegistrationResult_set_projection_index(self, index)
1332 
1333 
1334  def get_image_index(self):
1335  """get_image_index(RegistrationResult self) -> int"""
1336  return _IMP_em2d.RegistrationResult_get_image_index(self)
1337 
1338 
1339  def set_image_index(self, index):
1340  """set_image_index(RegistrationResult self, int index)"""
1341  return _IMP_em2d.RegistrationResult_set_image_index(self, index)
1342 
1343 
1344  def get_name(self):
1345  """get_name(RegistrationResult self) -> IMP::String"""
1346  return _IMP_em2d.RegistrationResult_get_name(self)
1347 
1348 
1349  def get_ccc(self):
1350  """get_ccc(RegistrationResult self) -> double"""
1351  return _IMP_em2d.RegistrationResult_get_ccc(self)
1352 
1353 
1354  def set_ccc(self, ccc):
1355  """set_ccc(RegistrationResult self, double ccc)"""
1356  return _IMP_em2d.RegistrationResult_set_ccc(self, ccc)
1357 
1358 
1359  def get_score(self):
1360  """get_score(RegistrationResult self) -> double"""
1361  return _IMP_em2d.RegistrationResult_get_score(self)
1362 
1363 
1364  def set_score(self, Score):
1365  """set_score(RegistrationResult self, double Score)"""
1366  return _IMP_em2d.RegistrationResult_set_score(self, Score)
1367 
1368 
1369  def set_rotation(self, *args):
1370  """
1371  set_rotation(RegistrationResult self, double phi, double theta, double psi)
1372  set_rotation(RegistrationResult self, Rotation3D R)
1373  """
1374  return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1375 
1376 
1377  def set_shift(self, shift):
1378  """set_shift(RegistrationResult self, Vector2D shift)"""
1379  return _IMP_em2d.RegistrationResult_set_shift(self, shift)
1380 
1381 
1382  def set_name(self, name):
1383  """set_name(RegistrationResult self, IMP::String name)"""
1384  return _IMP_em2d.RegistrationResult_set_name(self, name)
1385 
1386 
1387  def add_in_plane_transformation(self, t):
1388  """add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1389  return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, t)
1390 
1391 
1392  def show(self, *args):
1393  """
1394  show(RegistrationResult self, _ostream out)
1395  show(RegistrationResult self)
1396  """
1397  return _IMP_em2d.RegistrationResult_show(self, *args)
1398 
1399 
1400  def write(self, *args):
1401  """
1402  write(RegistrationResult self, _ostream out)
1403  write(RegistrationResult self)
1404  """
1405  return _IMP_em2d.RegistrationResult_write(self, *args)
1406 
1407 
1408  def write_comment_line(self, *args):
1409  """
1410  write_comment_line(RegistrationResult self, _ostream out)
1411  write_comment_line(RegistrationResult self)
1412  """
1413  return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1414 
1415 
1416  def read(self, s):
1417  """read(RegistrationResult self, IMP::String const & s)"""
1418  return _IMP_em2d.RegistrationResult_read(self, s)
1419 
1420 
1421  def set_random_registration(self, index, maximum_shift):
1422  """set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1423  return _IMP_em2d.RegistrationResult_set_random_registration(self, index, maximum_shift)
1424 
1425 
1426  def get_rotation(self):
1427  """get_rotation(RegistrationResult self) -> Rotation3D"""
1428  return _IMP_em2d.RegistrationResult_get_rotation(self)
1429 
1430 
1431  def set_in_image(self, header):
1432  """set_in_image(RegistrationResult self, ImageHeader header)"""
1433  return _IMP_em2d.RegistrationResult_set_in_image(self, header)
1434 
1435 
1436  def read_from_image(self, header):
1437  """read_from_image(RegistrationResult self, ImageHeader header)"""
1438  return _IMP_em2d.RegistrationResult_read_from_image(self, header)
1439 
1440 
1441  def get_is_optimized_result(self):
1442  """get_is_optimized_result(RegistrationResult self) -> bool"""
1443  return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1444 
1445  __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1446  __del__ = lambda self: None
1447 
1448  def __str__(self):
1449  """__str__(RegistrationResult self) -> std::string"""
1450  return _IMP_em2d.RegistrationResult___str__(self)
1451 
1452 
1453  def __repr__(self):
1454  """__repr__(RegistrationResult self) -> std::string"""
1455  return _IMP_em2d.RegistrationResult___repr__(self)
1456 
1457 RegistrationResult_swigregister = _IMP_em2d.RegistrationResult_swigregister
1458 RegistrationResult_swigregister(RegistrationResult)
1459 
1460 
1461 def read_registration_results(filename):
1462  """read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1463  return _IMP_em2d.read_registration_results(filename)
1464 
1465 def write_registration_results(filename, results):
1466  """write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1467  return _IMP_em2d.write_registration_results(filename, results)
1468 
1469 def get_random_registration_results(n, maximum_shift=5.0):
1470  """
1471  get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults
1472  get_random_registration_results(unsigned int n) -> IMP::em2d::RegistrationResults
1473  """
1474  return _IMP_em2d.get_random_registration_results(n, maximum_shift)
1475 
1477  """get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1478  return _IMP_em2d.get_evenly_distributed_registration_results(n_projections)
1479 class SpiderImageReaderWriter(ImageReaderWriter):
1480  """Proxy of C++ IMP::em2d::SpiderImageReaderWriter class."""
1481 
1482  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1483  filename_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set)
1484  skip_type_check_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set)
1485  force_reversed_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set)
1486  skip_extra_checkings_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set)
1487 
1488  def __init__(self, *args):
1489  """
1490  __init__(IMP::em2d::SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1491  __init__(IMP::em2d::SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1492  """
1493  this = _IMP_em2d.new_SpiderImageReaderWriter(*args)
1494  try:
1495  self.this.append(this)
1496  except __builtin__.Exception:
1497  self.this = this
1498 
1499  def __str__(self):
1500  """__str__(SpiderImageReaderWriter self) -> std::string"""
1501  return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1502 
1503 
1504  def __repr__(self):
1505  """__repr__(SpiderImageReaderWriter self) -> std::string"""
1506  return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1507 
1508 
1509  @staticmethod
1510  def get_from(o):
1511  return _object_cast_to_SpiderImageReaderWriter(o)
1512 
1513 SpiderImageReaderWriter_swigregister = _IMP_em2d.SpiderImageReaderWriter_swigregister
1514 SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1515 
1516 class JPGImageReaderWriter(ImageReaderWriter):
1517  """Proxy of C++ IMP::em2d::JPGImageReaderWriter class."""
1518 
1519  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1520 
1521  def __init__(self):
1522  """__init__(IMP::em2d::JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1523  this = _IMP_em2d.new_JPGImageReaderWriter()
1524  try:
1525  self.this.append(this)
1526  except __builtin__.Exception:
1527  self.this = this
1528 
1529  def __str__(self):
1530  """__str__(JPGImageReaderWriter self) -> std::string"""
1531  return _IMP_em2d.JPGImageReaderWriter___str__(self)
1532 
1533 
1534  def __repr__(self):
1535  """__repr__(JPGImageReaderWriter self) -> std::string"""
1536  return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1537 
1538 
1539  @staticmethod
1540  def get_from(o):
1541  return _object_cast_to_JPGImageReaderWriter(o)
1542 
1543 JPGImageReaderWriter_swigregister = _IMP_em2d.JPGImageReaderWriter_swigregister
1544 JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1545 
1546 class TIFFImageReaderWriter(ImageReaderWriter):
1547  """Proxy of C++ IMP::em2d::TIFFImageReaderWriter class."""
1548 
1549  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1550 
1551  def __init__(self):
1552  """__init__(IMP::em2d::TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1553  this = _IMP_em2d.new_TIFFImageReaderWriter()
1554  try:
1555  self.this.append(this)
1556  except __builtin__.Exception:
1557  self.this = this
1558 
1559  def __str__(self):
1560  """__str__(TIFFImageReaderWriter self) -> std::string"""
1561  return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1562 
1563 
1564  def __repr__(self):
1565  """__repr__(TIFFImageReaderWriter self) -> std::string"""
1566  return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1567 
1568 
1569  @staticmethod
1570  def get_from(o):
1571  return _object_cast_to_TIFFImageReaderWriter(o)
1572 
1573 TIFFImageReaderWriter_swigregister = _IMP_em2d.TIFFImageReaderWriter_swigregister
1574 TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1575 
1576 
1578  """do_matrix_to_image_flip(cv::Mat & m)"""
1579  return _IMP_em2d.do_matrix_to_image_flip(m)
1580 
1582  """get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1583  return _IMP_em2d.get_autocorrelation2d_no_preprocessing(M, corr)
1584 
1585 def get_autocorrelation2d(*args):
1586  """
1587  get_autocorrelation2d(Image im1, Image im2)
1588  get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1589  """
1590  return _IMP_em2d.get_autocorrelation2d(*args)
1591 
1592 def get_correlation2d(*args):
1593  """
1594  get_correlation2d(Image im1, Image im2, Image corr)
1595  get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1596  """
1597  return _IMP_em2d.get_correlation2d(*args)
1598 
1599 def get_correlation2d_no_preprocessing(M1, M2, corr):
1600  """get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1601  return _IMP_em2d.get_correlation2d_no_preprocessing(M1, M2, corr)
1602 
1603 def get_fft_using_optimal_size(m, M):
1604  """get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1605  return _IMP_em2d.get_fft_using_optimal_size(m, M)
1606 
1607 def get_spectrum(m, real, imag):
1608  """get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1609  return _IMP_em2d.get_spectrum(m, real, imag)
1610 
1611 def get_rotation_error(rr1, rr2):
1612  """get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1613  return _IMP_em2d.get_rotation_error(rr1, rr2)
1614 
1615 def get_shift_error(rr1, rr2):
1616  """get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1617  return _IMP_em2d.get_shift_error(rr1, rr2)
1618 
1619 def get_average_rotation_error(correct_RRs, computed_RRs):
1620  """get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1621  return _IMP_em2d.get_average_rotation_error(correct_RRs, computed_RRs)
1622 
1623 def get_average_shift_error(correct_RRs, computed_RRs):
1624  """get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1625  return _IMP_em2d.get_average_shift_error(correct_RRs, computed_RRs)
1626 
1628  """
1629  get_cross_correlation_coefficient(Image im1, Image im2) -> double
1630  get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1631  """
1632  return _IMP_em2d.get_cross_correlation_coefficient(*args)
1633 
1634 def get_global_score(RRs):
1635  """get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1636  return _IMP_em2d.get_global_score(RRs)
1637 class ScoreFunction(IMP.Object):
1638  """Proxy of C++ IMP::em2d::ScoreFunction class."""
1639 
1640  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1641 
1642  def __init__(self, *args, **kwargs):
1643  raise AttributeError("No constructor defined - class is abstract")
1644 
1645  def get_score(self, image, projection):
1646  """get_score(ScoreFunction self, Image image, Image projection) -> double"""
1647  return _IMP_em2d.ScoreFunction_get_score(self, image, projection)
1648 
1649 
1650  def set_variance_image(self, var):
1651  """set_variance_image(ScoreFunction self, Image var)"""
1652  return _IMP_em2d.ScoreFunction_set_variance_image(self, var)
1653 
1654 
1655  def get_version_info(self):
1656  """get_version_info(ScoreFunction self) -> VersionInfo"""
1657  return _IMP_em2d.ScoreFunction_get_version_info(self)
1658 
1659 
1660  def __str__(self):
1661  """__str__(ScoreFunction self) -> std::string"""
1662  return _IMP_em2d.ScoreFunction___str__(self)
1663 
1664 
1665  def __repr__(self):
1666  """__repr__(ScoreFunction self) -> std::string"""
1667  return _IMP_em2d.ScoreFunction___repr__(self)
1668 
1669 
1670  @staticmethod
1671  def get_from(o):
1672  return _object_cast_to_ScoreFunction(o)
1673 
1674 ScoreFunction_swigregister = _IMP_em2d.ScoreFunction_swigregister
1675 ScoreFunction_swigregister(ScoreFunction)
1676 
1677 class ChiSquaredScore(ScoreFunction):
1678  """Proxy of C++ IMP::em2d::ChiSquaredScore class."""
1679 
1680  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1681 
1682  def __init__(self):
1683  """__init__(IMP::em2d::ChiSquaredScore self) -> ChiSquaredScore"""
1684  this = _IMP_em2d.new_ChiSquaredScore()
1685  try:
1686  self.this.append(this)
1687  except __builtin__.Exception:
1688  self.this = this
1689 
1690  def __str__(self):
1691  """__str__(ChiSquaredScore self) -> std::string"""
1692  return _IMP_em2d.ChiSquaredScore___str__(self)
1693 
1694 
1695  def __repr__(self):
1696  """__repr__(ChiSquaredScore self) -> std::string"""
1697  return _IMP_em2d.ChiSquaredScore___repr__(self)
1698 
1699 
1700  @staticmethod
1701  def get_from(o):
1702  return _object_cast_to_ChiSquaredScore(o)
1703 
1704  __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1705  __del__ = lambda self: None
1706 ChiSquaredScore_swigregister = _IMP_em2d.ChiSquaredScore_swigregister
1707 ChiSquaredScore_swigregister(ChiSquaredScore)
1708 
1709 class EM2DScore(ScoreFunction):
1710  """Proxy of C++ IMP::em2d::EM2DScore class."""
1711 
1712  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1713 
1714  def __init__(self):
1715  """__init__(IMP::em2d::EM2DScore self) -> EM2DScore"""
1716  this = _IMP_em2d.new_EM2DScore()
1717  try:
1718  self.this.append(this)
1719  except __builtin__.Exception:
1720  self.this = this
1721 
1722  def __str__(self):
1723  """__str__(EM2DScore self) -> std::string"""
1724  return _IMP_em2d.EM2DScore___str__(self)
1725 
1726 
1727  def __repr__(self):
1728  """__repr__(EM2DScore self) -> std::string"""
1729  return _IMP_em2d.EM2DScore___repr__(self)
1730 
1731 
1732  @staticmethod
1733  def get_from(o):
1734  return _object_cast_to_EM2DScore(o)
1735 
1736  __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1737  __del__ = lambda self: None
1738 EM2DScore_swigregister = _IMP_em2d.EM2DScore_swigregister
1739 EM2DScore_swigregister(EM2DScore)
1740 
1741 class MeanAbsoluteDifference(ScoreFunction):
1742  """Proxy of C++ IMP::em2d::MeanAbsoluteDifference class."""
1743 
1744  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1745 
1746  def __init__(self):
1747  """__init__(IMP::em2d::MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1748  this = _IMP_em2d.new_MeanAbsoluteDifference()
1749  try:
1750  self.this.append(this)
1751  except __builtin__.Exception:
1752  self.this = this
1753 
1754  def __str__(self):
1755  """__str__(MeanAbsoluteDifference self) -> std::string"""
1756  return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1757 
1758 
1759  def __repr__(self):
1760  """__repr__(MeanAbsoluteDifference self) -> std::string"""
1761  return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1762 
1763 
1764  @staticmethod
1765  def get_from(o):
1766  return _object_cast_to_MeanAbsoluteDifference(o)
1767 
1768  __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1769  __del__ = lambda self: None
1770 MeanAbsoluteDifference_swigregister = _IMP_em2d.MeanAbsoluteDifference_swigregister
1771 MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1772 
1773 
1774 def read_selection_file(fn):
1775  """read_selection_file(IMP::String fn) -> IMP::Strings"""
1776  return _IMP_em2d.read_selection_file(fn)
1777 
1778 def create_filenames(number, basic_name, extension):
1779  """create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1780  return _IMP_em2d.create_filenames(number, basic_name, extension)
1781 class ProjectionParameters(IMP.Decorator):
1782  """Proxy of C++ IMP::em2d::ProjectionParameters class."""
1783 
1784  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1785 
1786  def __init__(self, *args):
1787  """
1788  __init__(IMP::em2d::ProjectionParameters self) -> ProjectionParameters
1789  __init__(IMP::em2d::ProjectionParameters self, Model m, ParticleIndex id) -> ProjectionParameters
1790  __init__(IMP::em2d::ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1791  """
1792  this = _IMP_em2d.new_ProjectionParameters(*args)
1793  try:
1794  self.this.append(this)
1795  except __builtin__.Exception:
1796  self.this = this
1797 
1798  def show(self, *args):
1799  """
1800  show(ProjectionParameters self, _ostream out)
1801  show(ProjectionParameters self)
1802  """
1803  return _IMP_em2d.ProjectionParameters_show(self, *args)
1804 
1805 
1806  def setup_particle(*args):
1807  """
1808  setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
1809  setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1810  """
1811  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1812 
1813  setup_particle = staticmethod(setup_particle)
1814  __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1815  __del__ = lambda self: None
1816 
1817  def get_keys():
1818  """get_keys() -> IMP::FloatKeys const &"""
1819  return _IMP_em2d.ProjectionParameters_get_keys()
1820 
1821  get_keys = staticmethod(get_keys)
1822 
1823  def set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values):
1824  """set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1825  return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values)
1826 
1827 
1828  def get_is_setup(*args):
1829  """
1830  get_is_setup(_ParticleAdaptor p) -> bool
1831  get_is_setup(Model m, ParticleIndex pi) -> bool
1832  """
1833  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1834 
1835  get_is_setup = staticmethod(get_is_setup)
1836 
1837  def get_parameters_optimized(self):
1838  """get_parameters_optimized(ProjectionParameters self) -> bool"""
1839  return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1840 
1841 
1842  def get_translation(self):
1843  """get_translation(ProjectionParameters self) -> Vector3D"""
1844  return _IMP_em2d.ProjectionParameters_get_translation(self)
1845 
1846 
1847  def set_translation(self, v):
1848  """set_translation(ProjectionParameters self, Vector3D v)"""
1849  return _IMP_em2d.ProjectionParameters_set_translation(self, v)
1850 
1851 
1852  def get_rotation(self):
1853  """get_rotation(ProjectionParameters self) -> Rotation3D"""
1854  return _IMP_em2d.ProjectionParameters_get_rotation(self)
1855 
1856 
1857  def set_rotation(self, R):
1858  """set_rotation(ProjectionParameters self, Rotation3D R)"""
1859  return _IMP_em2d.ProjectionParameters_set_rotation(self, R)
1860 
1861 
1862  def set_parameters_optimized(self, tf):
1863  """set_parameters_optimized(ProjectionParameters self, bool tf)"""
1864  return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, tf)
1865 
1866 
1867  def get_quaternion_1(self):
1868  """get_quaternion_1(ProjectionParameters self) -> double"""
1869  return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1870 
1871 
1872  def set_quaternion_1(self, t):
1873  """set_quaternion_1(ProjectionParameters self, double t)"""
1874  return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, t)
1875 
1876 
1877  def get_quaternion_2(self):
1878  """get_quaternion_2(ProjectionParameters self) -> double"""
1879  return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1880 
1881 
1882  def set_quaternion_2(self, t):
1883  """set_quaternion_2(ProjectionParameters self, double t)"""
1884  return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, t)
1885 
1886 
1887  def get_quaternion_3(self):
1888  """get_quaternion_3(ProjectionParameters self) -> double"""
1889  return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1890 
1891 
1892  def set_quaternion_3(self, t):
1893  """set_quaternion_3(ProjectionParameters self, double t)"""
1894  return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, t)
1895 
1896 
1897  def get_quaternion_4(self):
1898  """get_quaternion_4(ProjectionParameters self) -> double"""
1899  return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1900 
1901 
1902  def set_quaternion_4(self, t):
1903  """set_quaternion_4(ProjectionParameters self, double t)"""
1904  return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, t)
1905 
1906 
1907  def get_translation_x(self):
1908  """get_translation_x(ProjectionParameters self) -> double"""
1909  return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1910 
1911 
1912  def set_translation_x(self, t):
1913  """set_translation_x(ProjectionParameters self, double t)"""
1914  return _IMP_em2d.ProjectionParameters_set_translation_x(self, t)
1915 
1916 
1917  def get_translation_y(self):
1918  """get_translation_y(ProjectionParameters self) -> double"""
1919  return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1920 
1921 
1922  def set_translation_y(self, t):
1923  """set_translation_y(ProjectionParameters self, double t)"""
1924  return _IMP_em2d.ProjectionParameters_set_translation_y(self, t)
1925 
1926 
1927  def add_attribute(self, *args):
1928  """
1929  add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1930  add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1931  add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1932  add_attribute(ProjectionParameters self, FloatsKey a0, IMP::Floats a1)
1933  add_attribute(ProjectionParameters self, IntsKey a0, IMP::Ints a1)
1934  add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1935  add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1936  add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1937  """
1938  return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1939 
1940 
1941  def get_value(self, *args):
1942  """
1943  get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1944  get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1945  get_value(ProjectionParameters self, FloatsKey a0) -> IMP::Floats
1946  get_value(ProjectionParameters self, IntsKey a0) -> IMP::Ints
1947  get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1948  get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1949  get_value(ProjectionParameters self, ObjectKey a0) -> Object
1950  """
1951  return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1952 
1953 
1954  def set_value(self, *args):
1955  """
1956  set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1957  set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1958  set_value(ProjectionParameters self, FloatsKey a0, IMP::Floats a1)
1959  set_value(ProjectionParameters self, IntsKey a0, IMP::Ints a1)
1960  set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1961  set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1962  set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1963  """
1964  return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1965 
1966 
1967  def remove_attribute(self, *args):
1968  """
1969  remove_attribute(ProjectionParameters self, FloatKey a0)
1970  remove_attribute(ProjectionParameters self, IntKey a0)
1971  remove_attribute(ProjectionParameters self, FloatsKey a0)
1972  remove_attribute(ProjectionParameters self, IntsKey a0)
1973  remove_attribute(ProjectionParameters self, StringKey a0)
1974  remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1975  remove_attribute(ProjectionParameters self, ObjectKey a0)
1976  """
1977  return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1978 
1979 
1980  def has_attribute(self, *args):
1981  """
1982  has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1983  has_attribute(ProjectionParameters self, IntKey a0) -> bool
1984  has_attribute(ProjectionParameters self, FloatsKey a0) -> bool
1985  has_attribute(ProjectionParameters self, IntsKey a0) -> bool
1986  has_attribute(ProjectionParameters self, StringKey a0) -> bool
1987  has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
1988  has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
1989  """
1990  return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
1991 
1992 
1993  def get_derivative(self, a0):
1994  """get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
1995  return _IMP_em2d.ProjectionParameters_get_derivative(self, a0)
1996 
1997 
1998  def get_name(self):
1999  """get_name(ProjectionParameters self) -> std::string"""
2000  return _IMP_em2d.ProjectionParameters_get_name(self)
2001 
2002 
2003  def clear_caches(self):
2004  """clear_caches(ProjectionParameters self)"""
2005  return _IMP_em2d.ProjectionParameters_clear_caches(self)
2006 
2007 
2008  def set_name(self, a0):
2009  """set_name(ProjectionParameters self, std::string a0)"""
2010  return _IMP_em2d.ProjectionParameters_set_name(self, a0)
2011 
2012 
2013  def set_check_level(self, a0):
2014  """set_check_level(ProjectionParameters self, IMP::CheckLevel a0)"""
2015  return _IMP_em2d.ProjectionParameters_set_check_level(self, a0)
2016 
2017 
2018  def add_to_derivative(self, a0, a1, a2):
2019  """add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2020  return _IMP_em2d.ProjectionParameters_add_to_derivative(self, a0, a1, a2)
2021 
2022 
2023  def set_is_optimized(self, a0, a1):
2024  """set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
2025  return _IMP_em2d.ProjectionParameters_set_is_optimized(self, a0, a1)
2026 
2027 
2028  def get_is_optimized(self, a0):
2029  """get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
2030  return _IMP_em2d.ProjectionParameters_get_is_optimized(self, a0)
2031 
2032 
2033  def get_check_level(self):
2034  """get_check_level(ProjectionParameters self) -> IMP::CheckLevel"""
2035  return _IMP_em2d.ProjectionParameters_get_check_level(self)
2036 
2037 
2038  def __eq__(self, *args):
2039  """
2040  __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
2041  __eq__(ProjectionParameters self, Particle d) -> bool
2042  """
2043  return _IMP_em2d.ProjectionParameters___eq__(self, *args)
2044 
2045 
2046  def __ne__(self, *args):
2047  """
2048  __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
2049  __ne__(ProjectionParameters self, Particle d) -> bool
2050  """
2051  return _IMP_em2d.ProjectionParameters___ne__(self, *args)
2052 
2053 
2054  def __le__(self, *args):
2055  """
2056  __le__(ProjectionParameters self, ProjectionParameters o) -> bool
2057  __le__(ProjectionParameters self, Particle d) -> bool
2058  """
2059  return _IMP_em2d.ProjectionParameters___le__(self, *args)
2060 
2061 
2062  def __lt__(self, *args):
2063  """
2064  __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
2065  __lt__(ProjectionParameters self, Particle d) -> bool
2066  """
2067  return _IMP_em2d.ProjectionParameters___lt__(self, *args)
2068 
2069 
2070  def __ge__(self, *args):
2071  """
2072  __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
2073  __ge__(ProjectionParameters self, Particle d) -> bool
2074  """
2075  return _IMP_em2d.ProjectionParameters___ge__(self, *args)
2076 
2077 
2078  def __gt__(self, *args):
2079  """
2080  __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
2081  __gt__(ProjectionParameters self, Particle d) -> bool
2082  """
2083  return _IMP_em2d.ProjectionParameters___gt__(self, *args)
2084 
2085 
2086  def __hash__(self):
2087  """__hash__(ProjectionParameters self) -> std::size_t"""
2088  return _IMP_em2d.ProjectionParameters___hash__(self)
2089 
2090 
2091  def __str__(self):
2092  """__str__(ProjectionParameters self) -> std::string"""
2093  return _IMP_em2d.ProjectionParameters___str__(self)
2094 
2095 
2096  def __repr__(self):
2097  """__repr__(ProjectionParameters self) -> std::string"""
2098  return _IMP_em2d.ProjectionParameters___repr__(self)
2099 
2100 ProjectionParameters_swigregister = _IMP_em2d.ProjectionParameters_swigregister
2101 ProjectionParameters_swigregister(ProjectionParameters)
2102 
2103 def ProjectionParameters_setup_particle(*args):
2104  """
2105  setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
2106  ProjectionParameters_setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
2107  """
2108  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
2109 
2110 def ProjectionParameters_get_keys():
2111  """ProjectionParameters_get_keys() -> IMP::FloatKeys const &"""
2112  return _IMP_em2d.ProjectionParameters_get_keys()
2113 
2114 def ProjectionParameters_get_is_setup(*args):
2115  """
2116  get_is_setup(_ParticleAdaptor p) -> bool
2117  ProjectionParameters_get_is_setup(Model m, ParticleIndex pi) -> bool
2118  """
2119  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
2120 
2121 
2122 def __lshift__(out, n):
2123  """__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
2124  return _IMP_em2d.__lshift__(out, n)
2125 class ProjectionParametersScoreState(IMP.ScoreState):
2126  """Proxy of C++ IMP::em2d::ProjectionParametersScoreState class."""
2127 
2128  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2129 
2130  def __init__(self, p):
2131  """__init__(IMP::em2d::ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
2132  this = _IMP_em2d.new_ProjectionParametersScoreState(p)
2133  try:
2134  self.this.append(this)
2135  except __builtin__.Exception:
2136  self.this = this
2137 
2138  def do_before_evaluate(self):
2139  """do_before_evaluate(ProjectionParametersScoreState self)"""
2140  return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
2141 
2142 
2143  def do_after_evaluate(self, da):
2144  """do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
2145  return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, da)
2146 
2147 
2148  def do_get_inputs(self):
2149  """do_get_inputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2150  return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
2151 
2152 
2153  def do_get_outputs(self):
2154  """do_get_outputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2155  return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
2156 
2157 
2158  def get_version_info(self):
2159  """get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
2160  return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
2161 
2162 
2163  def __str__(self):
2164  """__str__(ProjectionParametersScoreState self) -> std::string"""
2165  return _IMP_em2d.ProjectionParametersScoreState___str__(self)
2166 
2167 
2168  def __repr__(self):
2169  """__repr__(ProjectionParametersScoreState self) -> std::string"""
2170  return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
2171 
2172 
2173  @staticmethod
2174  def get_from(o):
2175  return _object_cast_to_ProjectionParametersScoreState(o)
2176 
2177 ProjectionParametersScoreState_swigregister = _IMP_em2d.ProjectionParametersScoreState_swigregister
2178 ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
2179 
2180 class ProjectionMask(object):
2181  """Proxy of C++ IMP::em2d::ProjectionMask class."""
2182 
2183  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2184 
2185  def __init__(self, *args, **kwargs):
2186  raise AttributeError("No constructor defined")
2187 
2188  def apply(self, m, v):
2189  """apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
2190  return _IMP_em2d.ProjectionMask_apply(self, m, v)
2191 
2192 
2193  def show(self, *args):
2194  """
2195  show(ProjectionMask self, _ostream out)
2196  show(ProjectionMask self)
2197  """
2198  return _IMP_em2d.ProjectionMask_show(self, *args)
2199 
2200  __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
2201  __del__ = lambda self: None
2202 
2203  def __str__(self):
2204  """__str__(ProjectionMask self) -> std::string"""
2205  return _IMP_em2d.ProjectionMask___str__(self)
2206 
2207 
2208  def __repr__(self):
2209  """__repr__(ProjectionMask self) -> std::string"""
2210  return _IMP_em2d.ProjectionMask___repr__(self)
2211 
2212 ProjectionMask_swigregister = _IMP_em2d.ProjectionMask_swigregister
2213 ProjectionMask_swigregister(ProjectionMask)
2214 
2215 
2216 def do_place(mask, m, v):
2217  """do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
2218  return _IMP_em2d.do_place(mask, m, v)
2219 class MasksManager(object):
2220  """Proxy of C++ IMP::em2d::MasksManager class."""
2221 
2222  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2223 
2224  def __init__(self, *args):
2225  """
2226  __init__(IMP::em2d::MasksManager self) -> MasksManager
2227  __init__(IMP::em2d::MasksManager self, double resolution, double pixelsize) -> MasksManager
2228  """
2229  this = _IMP_em2d.new_MasksManager(*args)
2230  try:
2231  self.this.append(this)
2232  except __builtin__.Exception:
2233  self.this = this
2234 
2235  def setup_kernel(self, resolution, pixelsize):
2236  """setup_kernel(MasksManager self, double resolution, double pixelsize)"""
2237  return _IMP_em2d.MasksManager_setup_kernel(self, resolution, pixelsize)
2238 
2239 
2240  def create_masks(self, ps):
2241  """create_masks(MasksManager self, IMP::ParticlesTemp const & ps)"""
2242  return _IMP_em2d.MasksManager_create_masks(self, ps)
2243 
2244 
2245  def create_mask(self, mass):
2246  """create_mask(MasksManager self, double mass)"""
2247  return _IMP_em2d.MasksManager_create_mask(self, mass)
2248 
2249 
2250  def find_mask(self, mass):
2251  """find_mask(MasksManager self, double mass) -> IMP::em2d::ProjectionMaskPtr"""
2252  return _IMP_em2d.MasksManager_find_mask(self, mass)
2253 
2254 
2255  def show(self, *args):
2256  """
2257  show(MasksManager self, _ostream out)
2258  show(MasksManager self)
2259  """
2260  return _IMP_em2d.MasksManager_show(self, *args)
2261 
2262 
2263  def get_number_of_masks(self):
2264  """get_number_of_masks(MasksManager self) -> unsigned int"""
2265  return _IMP_em2d.MasksManager_get_number_of_masks(self)
2266 
2267  __swig_destroy__ = _IMP_em2d.delete_MasksManager
2268  __del__ = lambda self: None
2269 
2270  def __str__(self):
2271  """__str__(MasksManager self) -> std::string"""
2272  return _IMP_em2d.MasksManager___str__(self)
2273 
2274 
2275  def __repr__(self):
2276  """__repr__(MasksManager self) -> std::string"""
2277  return _IMP_em2d.MasksManager___repr__(self)
2278 
2279 MasksManager_swigregister = _IMP_em2d.MasksManager_swigregister
2280 MasksManager_swigregister(MasksManager)
2281 
2282 class ProjectingParameters(object):
2283  """Proxy of C++ IMP::em2d::ProjectingParameters class."""
2284 
2285  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2286  pixel_size = _swig_property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set)
2287  resolution = _swig_property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set)
2288 
2289  def __init__(self, *args):
2290  """
2291  __init__(IMP::em2d::ProjectingParameters self) -> ProjectingParameters
2292  __init__(IMP::em2d::ProjectingParameters self, double ps, double res) -> ProjectingParameters
2293  """
2294  this = _IMP_em2d.new_ProjectingParameters(*args)
2295  try:
2296  self.this.append(this)
2297  except __builtin__.Exception:
2298  self.this = this
2299 
2300  def show(self, *args):
2301  """
2302  show(ProjectingParameters self, _ostream out)
2303  show(ProjectingParameters self)
2304  """
2305  return _IMP_em2d.ProjectingParameters_show(self, *args)
2306 
2307 
2308  def __str__(self):
2309  """__str__(ProjectingParameters self) -> std::string"""
2310  return _IMP_em2d.ProjectingParameters___str__(self)
2311 
2312 
2313  def __repr__(self):
2314  """__repr__(ProjectingParameters self) -> std::string"""
2315  return _IMP_em2d.ProjectingParameters___repr__(self)
2316 
2317  __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2318  __del__ = lambda self: None
2319 ProjectingParameters_swigregister = _IMP_em2d.ProjectingParameters_swigregister
2320 ProjectingParameters_swigregister(ProjectingParameters)
2321 
2322 class ProjectingOptions(ProjectingParameters):
2323  """Proxy of C++ IMP::em2d::ProjectingOptions class."""
2324 
2325  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2326  save_images = _swig_property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set)
2327  normalize = _swig_property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set)
2328  clear_matrix_before_projecting = _swig_property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set)
2329 
2330  def __init__(self, *args):
2331  """
2332  __init__(IMP::em2d::ProjectingOptions self) -> ProjectingOptions
2333  __init__(IMP::em2d::ProjectingOptions self, double ps, double res) -> ProjectingOptions
2334  __init__(IMP::em2d::ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2335  """
2336  this = _IMP_em2d.new_ProjectingOptions(*args)
2337  try:
2338  self.this.append(this)
2339  except __builtin__.Exception:
2340  self.this = this
2341 
2342  def show(self, *args):
2343  """
2344  show(ProjectingOptions self, _ostream out)
2345  show(ProjectingOptions self)
2346  """
2347  return _IMP_em2d.ProjectingOptions_show(self, *args)
2348 
2349 
2350  def __str__(self):
2351  """__str__(ProjectingOptions self) -> std::string"""
2352  return _IMP_em2d.ProjectingOptions___str__(self)
2353 
2354 
2355  def __repr__(self):
2356  """__repr__(ProjectingOptions self) -> std::string"""
2357  return _IMP_em2d.ProjectingOptions___repr__(self)
2358 
2359  __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2360  __del__ = lambda self: None
2361 ProjectingOptions_swigregister = _IMP_em2d.ProjectingOptions_swigregister
2362 ProjectingOptions_swigregister(ProjectingOptions)
2363 
2364 
2365 def get_projections(*args):
2366  """
2367  get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2368  get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2369  get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2370  get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2371  """
2372  return _IMP_em2d.get_projections(*args)
2373 
2374 def get_projection(*args):
2375  """
2376  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks, IMP::String name)
2377  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)
2378  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options)
2379  """
2380  return _IMP_em2d.get_projection(*args)
2381 
2382 def do_project_particles(ps, m2, R, translation, options, masks):
2383  """do_project_particles(IMP::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)"""
2384  return _IMP_em2d.do_project_particles(ps, m2, R, translation, options, masks)
2385 
2386 def create_evenly_distributed_projections(ps, n, options):
2387  """create_evenly_distributed_projections(IMP::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2388  return _IMP_em2d.create_evenly_distributed_projections(ps, n, options)
2389 
2390 def do_project_vectors(*args):
2391  """
2392  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2393  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2394  """
2395  return _IMP_em2d.do_project_vectors(*args)
2396 
2397 def get_enclosing_image_size(ps, pixel_size, slack):
2398  """get_enclosing_image_size(IMP::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2399  return _IMP_em2d.get_enclosing_image_size(ps, pixel_size, slack)
2400 
2401 def get_complete_alignment(input, m_to_align, apply=False):
2402  """
2403  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2404  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2405  """
2406  return _IMP_em2d.get_complete_alignment(input, m_to_align, apply)
2407 
2408 def get_rotational_alignment(input, m_to_align, apply=False):
2409  """
2410  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2411  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2412  """
2413  return _IMP_em2d.get_rotational_alignment(input, m_to_align, apply)
2414 
2415 def get_translational_alignment(input, m_to_align, apply=False):
2416  """
2417  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2418  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2419  """
2420  return _IMP_em2d.get_translational_alignment(input, m_to_align, apply)
2421 
2422 def get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply=False):
2423  """
2424  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align, cv::Mat const & POLAR2, bool apply=False) -> ResultAlign2D
2425  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align, cv::Mat const & POLAR2) -> ResultAlign2D
2426  """
2427  return _IMP_em2d.get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply)
2428 
2429 def get_rotational_alignment_no_preprocessing(POLAR1, POLAR2):
2430  """get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2431  return _IMP_em2d.get_rotational_alignment_no_preprocessing(POLAR1, POLAR2)
2432 
2434  """get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2435  return _IMP_em2d.get_translational_alignment_no_preprocessing(M1, M2)
2436 
2437 def get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2):
2438  """get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2439  return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2)
2440 
2441 def write_vectors_as_pdb(*args):
2442  """
2443  write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2444  write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2445  """
2446  return _IMP_em2d.write_vectors_as_pdb(*args)
2447 class Em2DRestraintParameters(ProjectingParameters):
2448  """Proxy of C++ IMP::em2d::Em2DRestraintParameters class."""
2449 
2450  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2451  n_projections = _swig_property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set)
2452  coarse_registration_method = _swig_property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set)
2453  save_match_images = _swig_property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set)
2454  optimization_steps = _swig_property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set)
2455  simplex_initial_length = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set)
2456  simplex_minimum_size = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set)
2457 
2458  def __init__(self, *args):
2459  """
2460  __init__(IMP::em2d::Em2DRestraintParameters self) -> Em2DRestraintParameters
2461  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2462  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res) -> Em2DRestraintParameters
2463  """
2464  this = _IMP_em2d.new_Em2DRestraintParameters(*args)
2465  try:
2466  self.this.append(this)
2467  except __builtin__.Exception:
2468  self.this = this
2469 
2470  def show(self, *args):
2471  """
2472  show(Em2DRestraintParameters self, _ostream out)
2473  show(Em2DRestraintParameters self)
2474  """
2475  return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2476 
2477 
2478  def __str__(self):
2479  """__str__(Em2DRestraintParameters self) -> std::string"""
2480  return _IMP_em2d.Em2DRestraintParameters___str__(self)
2481 
2482 
2483  def __repr__(self):
2484  """__repr__(Em2DRestraintParameters self) -> std::string"""
2485  return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2486 
2487  __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2488  __del__ = lambda self: None
2489 Em2DRestraintParameters_swigregister = _IMP_em2d.Em2DRestraintParameters_swigregister
2490 Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2491 cvar = _IMP_em2d.cvar
2492 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2493 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2494 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2495 
2496 class ProjectionFinder(IMP.Object):
2497  """Proxy of C++ IMP::em2d::ProjectionFinder class."""
2498 
2499  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2500 
2501  def __init__(self):
2502  """__init__(IMP::em2d::ProjectionFinder self) -> ProjectionFinder"""
2503  this = _IMP_em2d.new_ProjectionFinder()
2504  try:
2505  self.this.append(this)
2506  except __builtin__.Exception:
2507  self.this = this
2508 
2509  def setup(self, score_function, params):
2510  """setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2511  return _IMP_em2d.ProjectionFinder_setup(self, score_function, params)
2512 
2513 
2514  def set_subjects(self, subjects):
2515  """set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2516  return _IMP_em2d.ProjectionFinder_set_subjects(self, subjects)
2517 
2518 
2519  def set_projections(self, projections):
2520  """set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2521  return _IMP_em2d.ProjectionFinder_set_projections(self, projections)
2522 
2523 
2524  def set_variance_images(self, variances):
2525  """set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2526  return _IMP_em2d.ProjectionFinder_set_variance_images(self, variances)
2527 
2528 
2529  def set_model_particles(self, ps):
2530  """set_model_particles(ProjectionFinder self, IMP::ParticlesTemp const & ps)"""
2531  return _IMP_em2d.ProjectionFinder_set_model_particles(self, ps)
2532 
2533 
2534  def set_save_match_images(self, x):
2535  """set_save_match_images(ProjectionFinder self, bool x)"""
2536  return _IMP_em2d.ProjectionFinder_set_save_match_images(self, x)
2537 
2538 
2539  def get_save_match_images(self):
2540  """get_save_match_images(ProjectionFinder self) -> bool"""
2541  return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2542 
2543 
2544  def set_fast_mode(self, n):
2545  """set_fast_mode(ProjectionFinder self, unsigned int n)"""
2546  return _IMP_em2d.ProjectionFinder_set_fast_mode(self, n)
2547 
2548 
2549  def get_registration_results(self):
2550  """get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2551  return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2552 
2553 
2554  def get_coarse_registration(self):
2555  """get_coarse_registration(ProjectionFinder self)"""
2556  return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2557 
2558 
2559  def get_complete_registration(self):
2560  """get_complete_registration(ProjectionFinder self)"""
2561  return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2562 
2563 
2564  def get_global_score(self):
2565  """get_global_score(ProjectionFinder self) -> double"""
2566  return _IMP_em2d.ProjectionFinder_get_global_score(self)
2567 
2568 
2569  def show(self, out):
2570  """show(ProjectionFinder self, _ostream out)"""
2571  return _IMP_em2d.ProjectionFinder_show(self, out)
2572 
2573 
2574  def get_preprocessing_time(self):
2575  """get_preprocessing_time(ProjectionFinder self) -> double"""
2576  return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2577 
2578 
2579  def get_coarse_registration_time(self):
2580  """get_coarse_registration_time(ProjectionFinder self) -> double"""
2581  return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2582 
2583 
2584  def get_fine_registration_time(self):
2585  """get_fine_registration_time(ProjectionFinder self) -> double"""
2586  return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2587 
2588 
2589  def get_number_of_subjects(self):
2590  """get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2591  return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2592 
2593 
2594  def set_number_of_class_averages_members(self, n_members):
2595  """set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2596  return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, n_members)
2597 
2598 
2599  def get_number_of_projections(self):
2600  """get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2601  return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2602 
2603 
2604  def get_version_info(self):
2605  """get_version_info(ProjectionFinder self) -> VersionInfo"""
2606  return _IMP_em2d.ProjectionFinder_get_version_info(self)
2607 
2608 
2609  def __str__(self):
2610  """__str__(ProjectionFinder self) -> std::string"""
2611  return _IMP_em2d.ProjectionFinder___str__(self)
2612 
2613 
2614  def __repr__(self):
2615  """__repr__(ProjectionFinder self) -> std::string"""
2616  return _IMP_em2d.ProjectionFinder___repr__(self)
2617 
2618 
2619  @staticmethod
2620  def get_from(o):
2621  return _object_cast_to_ProjectionFinder(o)
2622 
2623 ProjectionFinder_swigregister = _IMP_em2d.ProjectionFinder_swigregister
2624 ProjectionFinder_swigregister(ProjectionFinder)
2625 
2626 class Em2DRestraint(IMP.Restraint):
2627  """Proxy of C++ IMP::em2d::Em2DRestraint class."""
2628 
2629  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2630 
2631  def __init__(self, m):
2632  """__init__(IMP::em2d::Em2DRestraint self, Model m) -> Em2DRestraint"""
2633  this = _IMP_em2d.new_Em2DRestraint(m)
2634  try:
2635  self.this.append(this)
2636  except __builtin__.Exception:
2637  self.this = this
2638 
2639  def setup(self, score_function, params):
2640  """setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2641  return _IMP_em2d.Em2DRestraint_setup(self, score_function, params)
2642 
2643 
2644  def set_particles(self, particles_container):
2645  """set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2646  return _IMP_em2d.Em2DRestraint_set_particles(self, particles_container)
2647 
2648 
2649  def set_images(self, em_images):
2650  """set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2651  return _IMP_em2d.Em2DRestraint_set_images(self, em_images)
2652 
2653 
2654  def set_variance_images(self, variance_images):
2655  """set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2656  return _IMP_em2d.Em2DRestraint_set_variance_images(self, variance_images)
2657 
2658 
2659  def set_fast_mode(self, n):
2660  """set_fast_mode(Em2DRestraint self, unsigned int n)"""
2661  return _IMP_em2d.Em2DRestraint_set_fast_mode(self, n)
2662 
2663 
2664  def set_coarse_registration_mode(self, opt):
2665  """set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2666  return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, opt)
2667 
2668 
2669  def get_registration_results(self):
2670  """get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2671  return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2672 
2673 
2674  def do_get_inputs(self):
2675  """do_get_inputs(Em2DRestraint self) -> IMP::ModelObjectsTemp"""
2676  return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2677 
2678 
2679  def get_version_info(self):
2680  """get_version_info(Em2DRestraint self) -> VersionInfo"""
2681  return _IMP_em2d.Em2DRestraint_get_version_info(self)
2682 
2683 
2684  def __str__(self):
2685  """__str__(Em2DRestraint self) -> std::string"""
2686  return _IMP_em2d.Em2DRestraint___str__(self)
2687 
2688 
2689  def __repr__(self):
2690  """__repr__(Em2DRestraint self) -> std::string"""
2691  return _IMP_em2d.Em2DRestraint___repr__(self)
2692 
2693 
2694  @staticmethod
2695  def get_from(o):
2696  return _object_cast_to_Em2DRestraint(o)
2697 
2698 Em2DRestraint_swigregister = _IMP_em2d.Em2DRestraint_swigregister
2699 Em2DRestraint_swigregister(Em2DRestraint)
2700 
2701 class ClusterSet(object):
2702  """Proxy of C++ IMP::em2d::ClusterSet class."""
2703 
2704  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2705 
2706  def __init__(self, N):
2707  """__init__(IMP::em2d::ClusterSet self, unsigned int N) -> ClusterSet"""
2708  this = _IMP_em2d.new_ClusterSet(N)
2709  try:
2710  self.this.append(this)
2711  except __builtin__.Exception:
2712  self.this = this
2713 
2714  def do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters):
2715  """do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2716  return _IMP_em2d.ClusterSet_do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters)
2717 
2718 
2719  def get_cluster_elements(self, id):
2720  """get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2721  return _IMP_em2d.ClusterSet_get_cluster_elements(self, id)
2722 
2723 
2724  def get_clusters_below_cutoff(self, cutoff):
2725  """get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2726  return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, cutoff)
2727 
2728 
2729  def get_cluster_formed_at_step(self, step):
2730  """get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2731  return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, step)
2732 
2733 
2734  def get_distance_at_step(self, step):
2735  """get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2736  return _IMP_em2d.ClusterSet_get_distance_at_step(self, step)
2737 
2738 
2739  def get_id_for_cluster_at_step(self, step):
2740  """get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2741  return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, step)
2742 
2743 
2744  def get_linkage_matrix(self):
2745  """get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2746  return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2747 
2748 
2749  def get_linkage_matrix_in_matlab_format(self):
2750  """get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2751  return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2752 
2753 
2754  def get_number_of_steps(self):
2755  """get_number_of_steps(ClusterSet self) -> unsigned int"""
2756  return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2757 
2758 
2759  def show(self, out):
2760  """show(ClusterSet self, _ostream out)"""
2761  return _IMP_em2d.ClusterSet_show(self, out)
2762 
2763 
2764  def __str__(self):
2765  """__str__(ClusterSet self) -> std::string"""
2766  return _IMP_em2d.ClusterSet___str__(self)
2767 
2768 
2769  def __repr__(self):
2770  """__repr__(ClusterSet self) -> std::string"""
2771  return _IMP_em2d.ClusterSet___repr__(self)
2772 
2773  __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2774  __del__ = lambda self: None
2775 ClusterSet_swigregister = _IMP_em2d.ClusterSet_swigregister
2776 ClusterSet_swigregister(ClusterSet)
2777 
2778 class SingleLinkage(object):
2779  """Proxy of C++ IMP::em2d::SingleLinkage class."""
2780 
2781  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2782 
2783  def __init__(self):
2784  """__init__(IMP::em2d::SingleLinkage self) -> SingleLinkage"""
2785  this = _IMP_em2d.new_SingleLinkage()
2786  try:
2787  self.this.append(this)
2788  except __builtin__.Exception:
2789  self.this = this
2790 
2791  def __call__(self, id1, id2, cluster_set, distances):
2792  """__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2793  return _IMP_em2d.SingleLinkage___call__(self, id1, id2, cluster_set, distances)
2794 
2795 
2796  def show(self, out):
2797  """show(SingleLinkage self, _ostream out)"""
2798  return _IMP_em2d.SingleLinkage_show(self, out)
2799 
2800 
2801  def __str__(self):
2802  """__str__(SingleLinkage self) -> std::string"""
2803  return _IMP_em2d.SingleLinkage___str__(self)
2804 
2805 
2806  def __repr__(self):
2807  """__repr__(SingleLinkage self) -> std::string"""
2808  return _IMP_em2d.SingleLinkage___repr__(self)
2809 
2810  __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2811  __del__ = lambda self: None
2812 SingleLinkage_swigregister = _IMP_em2d.SingleLinkage_swigregister
2813 SingleLinkage_swigregister(SingleLinkage)
2814 
2815 class CompleteLinkage(object):
2816  """Proxy of C++ IMP::em2d::CompleteLinkage class."""
2817 
2818  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2819 
2820  def __init__(self):
2821  """__init__(IMP::em2d::CompleteLinkage self) -> CompleteLinkage"""
2822  this = _IMP_em2d.new_CompleteLinkage()
2823  try:
2824  self.this.append(this)
2825  except __builtin__.Exception:
2826  self.this = this
2827 
2828  def __call__(self, id1, id2, cluster_set, distances):
2829  """__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2830  return _IMP_em2d.CompleteLinkage___call__(self, id1, id2, cluster_set, distances)
2831 
2832 
2833  def show(self, out):
2834  """show(CompleteLinkage self, _ostream out)"""
2835  return _IMP_em2d.CompleteLinkage_show(self, out)
2836 
2837 
2838  def __str__(self):
2839  """__str__(CompleteLinkage self) -> std::string"""
2840  return _IMP_em2d.CompleteLinkage___str__(self)
2841 
2842 
2843  def __repr__(self):
2844  """__repr__(CompleteLinkage self) -> std::string"""
2845  return _IMP_em2d.CompleteLinkage___repr__(self)
2846 
2847  __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2848  __del__ = lambda self: None
2849 CompleteLinkage_swigregister = _IMP_em2d.CompleteLinkage_swigregister
2850 CompleteLinkage_swigregister(CompleteLinkage)
2851 
2852 class AverageDistanceLinkage(object):
2853  """Proxy of C++ IMP::em2d::AverageDistanceLinkage class."""
2854 
2855  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2856 
2857  def __init__(self):
2858  """__init__(IMP::em2d::AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2859  this = _IMP_em2d.new_AverageDistanceLinkage()
2860  try:
2861  self.this.append(this)
2862  except __builtin__.Exception:
2863  self.this = this
2864 
2865  def __call__(self, id1, id2, cluster_set, distances):
2866  """__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2867  return _IMP_em2d.AverageDistanceLinkage___call__(self, id1, id2, cluster_set, distances)
2868 
2869 
2870  def show(self, out):
2871  """show(AverageDistanceLinkage self, _ostream out)"""
2872  return _IMP_em2d.AverageDistanceLinkage_show(self, out)
2873 
2874 
2875  def __str__(self):
2876  """__str__(AverageDistanceLinkage self) -> std::string"""
2877  return _IMP_em2d.AverageDistanceLinkage___str__(self)
2878 
2879 
2880  def __repr__(self):
2881  """__repr__(AverageDistanceLinkage self) -> std::string"""
2882  return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2883 
2884  __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2885  __del__ = lambda self: None
2886 AverageDistanceLinkage_swigregister = _IMP_em2d.AverageDistanceLinkage_swigregister
2887 AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2888 
2889 class CollisionCrossSection(IMP.Object):
2890  """Proxy of C++ IMP::em2d::CollisionCrossSection class."""
2891 
2892  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2893 
2894  def __init__(self, n_projections, resolution, pixel_size, projection_image_size):
2895  """__init__(IMP::em2d::CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2896  this = _IMP_em2d.new_CollisionCrossSection(n_projections, resolution, pixel_size, projection_image_size)
2897  try:
2898  self.this.append(this)
2899  except __builtin__.Exception:
2900  self.this = this
2901 
2902  def set_model_particles(self, ps):
2903  """set_model_particles(CollisionCrossSection self, IMP::ParticlesTemp const & ps)"""
2904  return _IMP_em2d.CollisionCrossSection_set_model_particles(self, ps)
2905 
2906 
2907  def get_ccs(self):
2908  """get_ccs(CollisionCrossSection self) -> double"""
2909  return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2910 
2911 
2912  def show(self, out):
2913  """show(CollisionCrossSection self, _ostream out)"""
2914  return _IMP_em2d.CollisionCrossSection_show(self, out)
2915 
2916 
2917  def get_version_info(self):
2918  """get_version_info(CollisionCrossSection self) -> VersionInfo"""
2919  return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2920 
2921 
2922  def __str__(self):
2923  """__str__(CollisionCrossSection self) -> std::string"""
2924  return _IMP_em2d.CollisionCrossSection___str__(self)
2925 
2926 
2927  def __repr__(self):
2928  """__repr__(CollisionCrossSection self) -> std::string"""
2929  return _IMP_em2d.CollisionCrossSection___repr__(self)
2930 
2931 
2932  @staticmethod
2933  def get_from(o):
2934  return _object_cast_to_CollisionCrossSection(o)
2935 
2936 CollisionCrossSection_swigregister = _IMP_em2d.CollisionCrossSection_swigregister
2937 CollisionCrossSection_swigregister(CollisionCrossSection)
2938 
2939 class GridStates(IMP.domino.ParticleStates):
2940  """Proxy of C++ IMP::em2d::GridStates class."""
2941 
2942  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2943 
2944  def __init__(self, *args):
2945  """
2946  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::String const & name) -> GridStates
2947  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations) -> GridStates
2948  """
2949  this = _IMP_em2d.new_GridStates(*args)
2950  try:
2951  self.this.append(this)
2952  except __builtin__.Exception:
2953  self.this = this
2954 
2955  def get_position(self, i):
2956  """get_position(GridStates self, unsigned int i) -> Vector3D"""
2957  return _IMP_em2d.GridStates_get_position(self, i)
2958 
2959 
2960  def get_orientation(self, i):
2961  """get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2962  return _IMP_em2d.GridStates_get_orientation(self, i)
2963 
2964 
2965  def get_version_info(self):
2966  """get_version_info(GridStates self) -> VersionInfo"""
2967  return _IMP_em2d.GridStates_get_version_info(self)
2968 
2969 
2970  def __str__(self):
2971  """__str__(GridStates self) -> std::string"""
2972  return _IMP_em2d.GridStates___str__(self)
2973 
2974 
2975  def __repr__(self):
2976  """__repr__(GridStates self) -> std::string"""
2977  return _IMP_em2d.GridStates___repr__(self)
2978 
2979 
2980  @staticmethod
2981  def get_from(o):
2982  return _object_cast_to_GridStates(o)
2983 
2984 GridStates_swigregister = _IMP_em2d.GridStates_swigregister
2985 GridStates_swigregister(GridStates)
2986 
2987 class ProjectionStates(GridStates):
2988  """Proxy of C++ IMP::em2d::ProjectionStates class."""
2989 
2990  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2991 
2992  def __init__(self, *args):
2993  """
2994  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections, IMP::String const & name) -> ProjectionStates
2995  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections) -> ProjectionStates
2996  """
2997  this = _IMP_em2d.new_ProjectionStates(*args)
2998  try:
2999  self.this.append(this)
3000  except __builtin__.Exception:
3001  self.this = this
3002 
3003  def get_projection(self, i):
3004  """get_projection(ProjectionStates self, unsigned int i) -> Image"""
3005  return _IMP_em2d.ProjectionStates_get_projection(self, i)
3006 
3007 
3008  def __str__(self):
3009  """__str__(ProjectionStates self) -> std::string"""
3010  return _IMP_em2d.ProjectionStates___str__(self)
3011 
3012 
3013  def __repr__(self):
3014  """__repr__(ProjectionStates self) -> std::string"""
3015  return _IMP_em2d.ProjectionStates___repr__(self)
3016 
3017 
3018  @staticmethod
3019  def get_from(o):
3020  return _object_cast_to_ProjectionStates(o)
3021 
3022 ProjectionStates_swigregister = _IMP_em2d.ProjectionStates_swigregister
3023 ProjectionStates_swigregister(ProjectionStates)
3024 
3025 class DistanceFilter(IMP.domino.SubsetFilter):
3026  """Proxy of C++ IMP::em2d::DistanceFilter class."""
3027 
3028  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3029 
3030  def __init__(self, subset_to_act_on, subset_to_restrain, ps_table, max_distance):
3031  """__init__(IMP::em2d::DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table, double max_distance) -> DistanceFilter"""
3032  this = _IMP_em2d.new_DistanceFilter(subset_to_act_on, subset_to_restrain, ps_table, max_distance)
3033  try:
3034  self.this.append(this)
3035  except __builtin__.Exception:
3036  self.this = this
3037 
3038  def show(self, *args):
3039  """
3040  show(DistanceFilter self, _ostream out)
3041  show(DistanceFilter self)
3042  """
3043  return _IMP_em2d.DistanceFilter_show(self, *args)
3044 
3045 
3046  def get_version_info(self):
3047  """get_version_info(DistanceFilter self) -> VersionInfo"""
3048  return _IMP_em2d.DistanceFilter_get_version_info(self)
3049 
3050 
3051  def __str__(self):
3052  """__str__(DistanceFilter self) -> std::string"""
3053  return _IMP_em2d.DistanceFilter___str__(self)
3054 
3055 
3056  def __repr__(self):
3057  """__repr__(DistanceFilter self) -> std::string"""
3058  return _IMP_em2d.DistanceFilter___repr__(self)
3059 
3060 
3061  @staticmethod
3062  def get_from(o):
3063  return _object_cast_to_DistanceFilter(o)
3064 
3065 DistanceFilter_swigregister = _IMP_em2d.DistanceFilter_swigregister
3066 DistanceFilter_swigregister(DistanceFilter)
3067 
3068 class DistanceFilterTable(IMP.domino.SubsetFilterTable):
3069  """Proxy of C++ IMP::em2d::DistanceFilterTable class."""
3070 
3071  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3072 
3073  def __init__(self, subset_to_act_on, ps_table, max_distance):
3074  """__init__(IMP::em2d::DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
3075  this = _IMP_em2d.new_DistanceFilterTable(subset_to_act_on, ps_table, max_distance)
3076  try:
3077  self.this.append(this)
3078  except __builtin__.Exception:
3079  self.this = this
3080 
3081  def show(self, *args):
3082  """
3083  show(DistanceFilterTable self, _ostream out)
3084  show(DistanceFilterTable self)
3085  """
3086  return _IMP_em2d.DistanceFilterTable_show(self, *args)
3087 
3088 
3089  def get_version_info(self):
3090  """get_version_info(DistanceFilterTable self) -> VersionInfo"""
3091  return _IMP_em2d.DistanceFilterTable_get_version_info(self)
3092 
3093 
3094  def __str__(self):
3095  """__str__(DistanceFilterTable self) -> std::string"""
3096  return _IMP_em2d.DistanceFilterTable___str__(self)
3097 
3098 
3099  def __repr__(self):
3100  """__repr__(DistanceFilterTable self) -> std::string"""
3101  return _IMP_em2d.DistanceFilterTable___repr__(self)
3102 
3103 
3104  @staticmethod
3105  def get_from(o):
3106  return _object_cast_to_DistanceFilterTable(o)
3107 
3108 DistanceFilterTable_swigregister = _IMP_em2d.DistanceFilterTable_swigregister
3109 DistanceFilterTable_swigregister(DistanceFilterTable)
3110 
3111 class IntsOrder(object):
3112  """Proxy of C++ IMP::em2d::IntsOrder class."""
3113 
3114  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3115  __repr__ = _swig_repr
3116 
3117  def __call__(self, a, b):
3118  """__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
3119  return _IMP_em2d.IntsOrder___call__(self, a, b)
3120 
3121 
3122  def __init__(self):
3123  """__init__(IMP::em2d::IntsOrder self) -> IntsOrder"""
3124  this = _IMP_em2d.new_IntsOrder()
3125  try:
3126  self.this.append(this)
3127  except __builtin__.Exception:
3128  self.this = this
3129  __swig_destroy__ = _IMP_em2d.delete_IntsOrder
3130  __del__ = lambda self: None
3131 IntsOrder_swigregister = _IMP_em2d.IntsOrder_swigregister
3132 IntsOrder_swigregister(IntsOrder)
3133 
3134 class RigidBodiesImageFitRestraint(IMP.Restraint):
3135  """Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class."""
3136 
3137  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3138 
3139  def get_version_info(self):
3140  """get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
3141  return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
3142 
3143 
3144  def __init__(self, scf, rbs, img):
3145  """__init__(IMP::em2d::RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
3146  this = _IMP_em2d.new_RigidBodiesImageFitRestraint(scf, rbs, img)
3147  try:
3148  self.this.append(this)
3149  except __builtin__.Exception:
3150  self.this = this
3151 
3152  def set_projecting_parameters(self, p):
3153  """set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
3154  return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, p)
3155 
3156 
3157  def set_orientations(self, rb, rots):
3158  """set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
3159  return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, rb, rots)
3160 
3161 
3162  def get_number_of_masks(self, rb):
3163  """get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
3164  return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, rb)
3165 
3166 
3167  def __str__(self):
3168  """__str__(RigidBodiesImageFitRestraint self) -> std::string"""
3169  return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
3170 
3171 
3172  def __repr__(self):
3173  """__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
3174  return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
3175 
3176 
3177  @staticmethod
3178  def get_from(o):
3179  return _object_cast_to_RigidBodiesImageFitRestraint(o)
3180 
3181 RigidBodiesImageFitRestraint_swigregister = _IMP_em2d.RigidBodiesImageFitRestraint_swigregister
3182 RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
3183 
3184 
3185 def get_unique_index(rot):
3186  """get_unique_index(Rotation3D rot) -> IMP::Ints"""
3187  return _IMP_em2d.get_unique_index(rot)
3188 class RelativePositionMover(IMP.core.RigidBodyMover):
3189  """Proxy of C++ IMP::em2d::RelativePositionMover class."""
3190 
3191  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3192 
3193  def __init__(self, d, max_translation, max_rotation):
3194  """__init__(IMP::em2d::RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
3195  this = _IMP_em2d.new_RelativePositionMover(d, max_translation, max_rotation)
3196  try:
3197  self.this.append(this)
3198  except __builtin__.Exception:
3199  self.this = this
3200 
3201  def add_internal_transformations(self, d, transforms):
3202  """add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
3203  return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, d, transforms)
3204 
3205 
3206  def set_random_move_probability(self, p):
3207  """set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
3208  return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, p)
3209 
3210 
3211  def __str__(self):
3212  """__str__(RelativePositionMover self) -> std::string"""
3213  return _IMP_em2d.RelativePositionMover___str__(self)
3214 
3215 
3216  def __repr__(self):
3217  """__repr__(RelativePositionMover self) -> std::string"""
3218  return _IMP_em2d.RelativePositionMover___repr__(self)
3219 
3220 
3221  @staticmethod
3222  def get_from(o):
3223  return _object_cast_to_RelativePositionMover(o)
3224 
3225 RelativePositionMover_swigregister = _IMP_em2d.RelativePositionMover_swigregister
3226 RelativePositionMover_swigregister(RelativePositionMover)
3227 
3228 class DummyRestraint(IMP.Restraint):
3229  """Proxy of C++ IMP::em2d::DummyRestraint class."""
3230 
3231  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3232 
3233  def __init__(self, p, q):
3234  """__init__(IMP::em2d::DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
3235  this = _IMP_em2d.new_DummyRestraint(p, q)
3236  try:
3237  self.this.append(this)
3238  except __builtin__.Exception:
3239  self.this = this
3240 
3241  def show(self, *args):
3242  """
3243  show(DummyRestraint self, _ostream out)
3244  show(DummyRestraint self)
3245  """
3246  return _IMP_em2d.DummyRestraint_show(self, *args)
3247 
3248 
3249  def do_get_inputs(self):
3250  """do_get_inputs(DummyRestraint self) -> IMP::ModelObjectsTemp"""
3251  return _IMP_em2d.DummyRestraint_do_get_inputs(self)
3252 
3253 
3254  def get_version_info(self):
3255  """get_version_info(DummyRestraint self) -> VersionInfo"""
3256  return _IMP_em2d.DummyRestraint_get_version_info(self)
3257 
3258 
3259  def __str__(self):
3260  """__str__(DummyRestraint self) -> std::string"""
3261  return _IMP_em2d.DummyRestraint___str__(self)
3262 
3263 
3264  def __repr__(self):
3265  """__repr__(DummyRestraint self) -> std::string"""
3266  return _IMP_em2d.DummyRestraint___repr__(self)
3267 
3268 
3269  @staticmethod
3270  def get_from(o):
3271  return _object_cast_to_DummyRestraint(o)
3272 
3273 DummyRestraint_swigregister = _IMP_em2d.DummyRestraint_swigregister
3274 DummyRestraint_swigregister(DummyRestraint)
3275 
3276 class ParticlesDummyRestraint(IMP.Restraint):
3277  """Proxy of C++ IMP::em2d::ParticlesDummyRestraint class."""
3278 
3279  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3280 
3281  def __init__(self, sc):
3282  """__init__(IMP::em2d::ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
3283  this = _IMP_em2d.new_ParticlesDummyRestraint(sc)
3284  try:
3285  self.this.append(this)
3286  except __builtin__.Exception:
3287  self.this = this
3288 
3289  def show(self, *args):
3290  """
3291  show(ParticlesDummyRestraint self, _ostream out)
3292  show(ParticlesDummyRestraint self)
3293  """
3294  return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
3295 
3296 
3297  def do_get_inputs(self):
3298  """do_get_inputs(ParticlesDummyRestraint self) -> IMP::ModelObjectsTemp"""
3299  return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3300 
3301 
3302  def get_version_info(self):
3303  """get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3304  return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3305 
3306 
3307  def __str__(self):
3308  """__str__(ParticlesDummyRestraint self) -> std::string"""
3309  return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3310 
3311 
3312  def __repr__(self):
3313  """__repr__(ParticlesDummyRestraint self) -> std::string"""
3314  return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3315 
3316 
3317  @staticmethod
3318  def get_from(o):
3319  return _object_cast_to_ParticlesDummyRestraint(o)
3320 
3321 ParticlesDummyRestraint_swigregister = _IMP_em2d.ParticlesDummyRestraint_swigregister
3322 ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3323 
3324 class PCAFitRestraint(IMP.Restraint):
3325  """Proxy of C++ IMP::em2d::PCAFitRestraint class."""
3326 
3327  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3328 
3329  def __init__(self, particles, image_files, pixel_size, resolution=10.0, projection_number=100, reuse_direction=False, n_components=1):
3330  """
3331  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False, unsigned int n_components=1) -> PCAFitRestraint
3332  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False) -> PCAFitRestraint
3333  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100) -> PCAFitRestraint
3334  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0) -> PCAFitRestraint
3335  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size) -> PCAFitRestraint
3336  """
3337  this = _IMP_em2d.new_PCAFitRestraint(particles, image_files, pixel_size, resolution, projection_number, reuse_direction, n_components)
3338  try:
3339  self.this.append(this)
3340  except __builtin__.Exception:
3341  self.this = this
3342 
3343  def get_projection_number(self):
3344  """get_projection_number(PCAFitRestraint self) -> unsigned int"""
3345  return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3346 
3347 
3348  def set_projection_number(self, n):
3349  """set_projection_number(PCAFitRestraint self, unsigned int n)"""
3350  return _IMP_em2d.PCAFitRestraint_set_projection_number(self, n)
3351 
3352 
3353  def get_transformation(self, image_number):
3354  """get_transformation(PCAFitRestraint self, unsigned int image_number) -> Transformation3D"""
3355  return _IMP_em2d.PCAFitRestraint_get_transformation(self, image_number)
3356 
3357 
3358  def get_cross_correlation_coefficient(self, image_number):
3359  """get_cross_correlation_coefficient(PCAFitRestraint self, unsigned int image_number) -> double"""
3360  return _IMP_em2d.PCAFitRestraint_get_cross_correlation_coefficient(self, image_number)
3361 
3362 
3363  def write_best_projections(self, file_name, evaluate=False):
3364  """
3365  write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)
3366  write_best_projections(PCAFitRestraint self, std::string file_name)
3367  """
3368  return _IMP_em2d.PCAFitRestraint_write_best_projections(self, file_name, evaluate)
3369 
3370 
3371  def do_get_inputs(self):
3372  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
3373  return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3374 
3375 
3376  def get_version_info(self):
3377  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
3378  return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3379 
3380 
3381  def __str__(self):
3382  """__str__(PCAFitRestraint self) -> std::string"""
3383  return _IMP_em2d.PCAFitRestraint___str__(self)
3384 
3385 
3386  def __repr__(self):
3387  """__repr__(PCAFitRestraint self) -> std::string"""
3388  return _IMP_em2d.PCAFitRestraint___repr__(self)
3389 
3390 
3391  @staticmethod
3392  def get_from(o):
3393  return _object_cast_to_em2dPCAFitRestraint(o)
3394 
3395 PCAFitRestraint_swigregister = _IMP_em2d.PCAFitRestraint_swigregister
3396 PCAFitRestraint_swigregister(PCAFitRestraint)
3397 
3398 class ResultAlign2D(object):
3399  """Proxy of C++ std::pair<(IMP::algebra::Transformation2D,double)> class."""
3400 
3401  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3402  __repr__ = _swig_repr
3403 
3404  def __init__(self, *args):
3405  """
3406  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self) -> ResultAlign2D
3407  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, Transformation2D first, double second) -> ResultAlign2D
3408  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, ResultAlign2D p) -> ResultAlign2D
3409  """
3410  this = _IMP_em2d.new_ResultAlign2D(*args)
3411  try:
3412  self.this.append(this)
3413  except __builtin__.Exception:
3414  self.this = this
3415  first = _swig_property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set)
3416  second = _swig_property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set)
3417  def __len__(self):
3418  return 2
3419  def __repr__(self):
3420  return str((self.first, self.second))
3421  def __getitem__(self, index):
3422  if not (index % 2):
3423  return self.first
3424  else:
3425  return self.second
3426  def __setitem__(self, index, val):
3427  if not (index % 2):
3428  self.first = val
3429  else:
3430  self.second = val
3431  __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3432  __del__ = lambda self: None
3433 ResultAlign2D_swigregister = _IMP_em2d.ResultAlign2D_swigregister
3434 ResultAlign2D_swigregister(ResultAlign2D)
3435 
3436 
3437 def _do_hierarchical_clustering_single_linkage(distances):
3438  """_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3439  return _IMP_em2d._do_hierarchical_clustering_single_linkage(distances)
3440 
3441 def _do_hierarchical_clustering_complete_linkage(distances):
3442  """_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3443  return _IMP_em2d._do_hierarchical_clustering_complete_linkage(distances)
3444 
3445 def _do_hierarchical_clustering_average_distance_linkage(distances):
3446  """_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3447  return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(distances)
3448 
3449 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3450 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3451 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3452 
3453 
3454 def get_module_version():
3455  """get_module_version() -> std::string const"""
3456  return _IMP_em2d.get_module_version()
3457 
3458 def get_example_path(fname):
3459  """get_example_path(std::string fname) -> std::string"""
3460  return _IMP_em2d.get_example_path(fname)
3461 
3462 def get_data_path(fname):
3463  """get_data_path(std::string fname) -> std::string"""
3464  return _IMP_em2d.get_data_path(fname)
3465 
3466 from . import _version_check
3467 _version_check.check_version(get_module_version())
3468 __version__ = get_module_version()
3469 
3470 
3471 
double get_shift_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Distance between the two in-plane translations.
Images create_evenly_distributed_projections(const ParticlesTemp &ps, unsigned int n, const ProjectingOptions &options)
void get_autocorrelation2d_no_preprocessing(const cv::Mat &M, cv::Mat &corr)
Autocorrelation without preprocessing.
void do_morphologic_contrast_enhancement(const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel, unsigned int iterations)
double get_mean(const cv::Mat &mat, const cvIntMat &mask)
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
setup
Definition: setup.py:1
void apply_threshold(cv::Mat &m, cv::Mat &result, double threshold=0.0)
em2d::Images get_projections(const ParticlesTemp &ps, const algebra::SphericalVector3Ds &vs, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
Generates projections from particles.
std::string get_module_version()
Return the version of this module, as a string.
IMPEM2D_BEGIN_NAMESPACE Strings read_selection_file(String fn)
Reads a selection file.
ResultAlign2D get_complete_alignment_with_centers_no_preprocessing(const algebra::Vector2D &center1, const algebra::Vector2D &center2, const cv::Mat &AUTOC_POLAR1, const cv::Mat &AUTOC_POLAR2)
Strings create_filenames(unsigned long number, String basic_name, String extension)
Various classes to hold sets of particles.
ResultAlign2D get_translational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
Aligns two matrices translationally.
void get_correlation2d(const cv::Mat &A, const cv::Mat &B, cv::Mat &corr)
Correlation matrix between two 2D matrices using FFT.
cvIntMat create_circular_mask(int rows, int cols, int radius)
ResultAlign2D get_complete_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
void do_dilate_and_shrink_warp(cv::Mat &m, const cv::Mat &grayscale, cv::Mat &kernel)
(U. Adiga, 2005)
em2d::ResultAlign2D get_rotational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
RegistrationResults get_evenly_distributed_registration_results(unsigned int n_projections)
void apply_variance_filter(Image *input, Image *filtered, int kernelsize)
Definition: Image.h:266
void apply_diffusion_filter(Image *input, Image *filtered, double beta, double pixelsize, int time_steps)
Definition: Image.h:279
int do_labeling(const cvIntMat &m, cvIntMat &mat_to_label)
Labeling function for a matrix.
Make CGAL functionality available to IMP.
MatchTemplateResults get_best_template_matches(const cv::Mat &m, const cv::Mat &templ, unsigned int n)
Modify the transformation of a rigid body.
void do_project_particles(const ParticlesTemp &ps, cv::Mat &m2, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const ProjectingOptions &options, MasksManagerPtr masks)
Projects a set of particles. This is the core function that others call.
void get_autocorrelation2d(const cv::Mat &m, cv::Mat &corr)
Computes the autocorrelation matrix.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
void apply_mean_outside_mask(Image *img, double radius)
Several general purpose optimizers from the GNU Scientific Library (GSL).
double get_rotation_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Composable functors to implement scores via compile-time composition.
ResultAlign2D get_rotational_alignment_no_preprocessing(const cv::Mat &POLAR1, const cv::Mat &POLAR2)
void get_fft_using_optimal_size(const cv::Mat &m, cv::Mat &M)
Floats get_histogram(Image *img, int bins)
Definition: Image.h:255
void write_matrix(cv::Mat &m, std::string name)
Quick and dirty way of writing a OpenCV matrix to a Spider image.
void do_subtract_images(Image *first, Image *second, Image *result)
Code to compute statistical measures.
RegistrationResults get_random_registration_results(unsigned int n, double maximum_shift=5.0)
Provides a set of random registration results (or parameters)
algebra::Vector2Ds do_project_vectors(const algebra::Vector3Ds &ps, const algebra::Rotation3D &R, const algebra::Vector3D &translation)
Project the points contained in Vector3Ds to gen vectors in 2D.
void write_vectors_as_pdb(const algebra::Vector2Ds vs, const String filename)
Common base class for heavy weight IMP objects.
Definition: Object.h:106
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:53
void apply_circular_mask(const cv::Mat &mat, cv::Mat &result, int radius, double value=0.0)
Images read_images(const Strings &names, const ImageReaderWriter *rw)
void write_registration_results(String filename, const RegistrationResults &results)
Writes a set of registration results.
Basic utilities for handling cryo-electron microscopy 3D density maps.
void crop(Image *img, const IntPair &center, int size)
void get_morphologic_gradient(const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel)
void apply_mask(const cv::Mat &m, cv::Mat &result, const cvIntMat &mask, double val)
Applies a binary mask to an image.
double get_cross_correlation_coefficient(Image *im1, Image *im2)
Cross correlation between two images.
void save_images(Images images, const Strings &names, const ImageReaderWriter *rw)
void get_domes(cv::Mat &m, cv::Mat &result, double h)
Gets the domes of m with height h.
void do_normalize(Image *im, bool force=false)
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:118
void do_matrix_to_image_flip(cv::Mat &m)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
ResultAlign2D get_translational_alignment_no_preprocessing(const cv::Mat &M1, const cv::Mat &M2)
void get_correlation2d_no_preprocessing(const cv::Mat &M1, const cv::Mat &M2, cv::Mat &corr)
Correlation without preprocessing.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
unsigned int get_enclosing_image_size(const ParticlesTemp &ps, double pixel_size, unsigned int slack)
Get an automatic size for an image that contains the particles.
std::pair< algebra::Transformation2D, double > ResultAlign2D
Definition: align2D.h:22
void do_resample_polar(Image *im1, Image *im2, const PolarResamplingParameters &polar_params)
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
em2d::ResultAlign2D get_complete_alignment_no_preprocessing(const cv::Mat &input, const cv::Mat &INPUT, const cv::Mat &POLAR1, cv::Mat &m_to_align, const cv::Mat &POLAR2, bool apply=false)
double get_overlap_percentage(cv::Mat &m1, cv::Mat &m2, const IntPair &center)
RegistrationResults read_registration_results(const String &filename)
Reads a set of registration results.
void get_diffusion_filtering_partial_derivative(const cv::Mat &m, cv::Mat &der, double dx, double dy, double ang)
Ints get_unique_index(const algebra::Rotation3D &rot)
Map a rotation to a list of 4 "unique" integers.
double get_global_score(const RegistrationResults &RRs)
void do_place(cv::Mat &mask, cv::Mat &m, const algebra::Vector2D &v)
void do_morphologic_reconstruction(const cv::Mat &mask, cv::Mat &marker, int neighbors_mode=4)
morphologic grayscale reconstruction (L Vincent, 1993)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.
Support for small angle X-ray scattering (SAXS) data.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
void get_projection(em2d::Image *img, const ParticlesTemp &ps, const RegistrationResult &reg, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="")
Generates a projection from particles.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54
void get_spectrum(const cv::Mat &m, cv::Mat &real, cv::Mat &imag)
Computes the fft of a matrix and returns the real and imaginary matrices.