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IMP Reference Guide  2.20.0
The Integrative Modeling Platform
em2d/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.1.1
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 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2023 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_em2d
17 
18 try:
19  import builtins as __builtin__
20 except ImportError:
21  import __builtin__
22 
23 def _swig_repr(self):
24  try:
25  strthis = "proxy of " + self.this.__repr__()
26  except __builtin__.Exception:
27  strthis = ""
28  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
29 
30 
31 def _swig_setattr_nondynamic_instance_variable(set):
32  def set_instance_attr(self, name, value):
33  if name == "this":
34  set(self, name, value)
35  elif name == "thisown":
36  self.this.own(value)
37  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
38  set(self, name, value)
39  else:
40  raise AttributeError("You cannot add instance attributes to %s" % self)
41  return set_instance_attr
42 
43 
44 def _swig_setattr_nondynamic_class_variable(set):
45  def set_class_attr(cls, name, value):
46  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
47  set(cls, name, value)
48  else:
49  raise AttributeError("You cannot add class attributes to %s" % cls)
50  return set_class_attr
51 
52 
53 def _swig_add_metaclass(metaclass):
54  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55  def wrapper(cls):
56  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
57  return wrapper
58 
59 
60 class _SwigNonDynamicMeta(type):
61  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
63 
64 
65 import weakref
66 
67 class IMP_EM2D_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_EM2D_SwigPyIterator class."""
69 
70  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
71 
72  def __init__(self, *args, **kwargs):
73  raise AttributeError("No constructor defined - class is abstract")
74  __repr__ = _swig_repr
75  __swig_destroy__ = _IMP_em2d.delete_IMP_EM2D_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
79  return _IMP_em2d.IMP_EM2D_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator"""
83  return _IMP_em2d.IMP_EM2D_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator"""
87  return _IMP_em2d.IMP_EM2D_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_em2d.IMP_EM2D_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
95  return _IMP_em2d.IMP_EM2D_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator"""
99  return _IMP_em2d.IMP_EM2D_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
103  return _IMP_em2d.IMP_EM2D_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
107  return _IMP_em2d.IMP_EM2D_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
111  return _IMP_em2d.IMP_EM2D_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
115  return _IMP_em2d.IMP_EM2D_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
119  return _IMP_em2d.IMP_EM2D_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
123  return _IMP_em2d.IMP_EM2D_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
127  return _IMP_em2d.IMP_EM2D_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
131  return _IMP_em2d.IMP_EM2D_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
135  return _IMP_em2d.IMP_EM2D_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator
140  __sub__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_em2d.IMP_EM2D_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_EM2D_SwigPyIterator in _IMP_em2d:
147 _IMP_em2d.IMP_EM2D_SwigPyIterator_swigregister(IMP_EM2D_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_em2d.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_em2d.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_em2d.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_em2d.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_em2d.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_em2d.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_em2d.IMP_MEMORY
167 
168 IMP_NONE = _IMP_em2d.IMP_NONE
169 
170 IMP_USAGE = _IMP_em2d.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_em2d.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_em2d.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_em2d.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em2d.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_em2d.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_em2d.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_em2d.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em2d.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_em2d.IMPKERNEL_SHOW_WARNINGS
195 
196 
197 import sys
198 class _DirectorObjects(object):
199  """@internal Simple class to keep references to director objects
200  to prevent premature deletion."""
201  def __init__(self):
202  self._objects = []
203  def register(self, obj):
204  """Take a reference to a director object; will only work for
205  refcounted C++ classes"""
206  if hasattr(obj, 'get_ref_count'):
207  self._objects.append(obj)
208  def cleanup(self):
209  """Only drop our reference and allow cleanup by Python if no other
210  Python references exist (we hold 3 references: one in self._objects,
211  one in x, and one in the argument list for getrefcount) *and* no
212  other C++ references exist (the Python object always holds one)"""
213  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
214  or x.get_ref_count() > 1]
215 # Do in two steps so the references are kept until the end of the
216 # function (deleting references may trigger a fresh call to this method)
217  self._objects = objs
218  def get_object_count(self):
219  """Get number of director objects (useful for testing only)"""
220  return len(self._objects)
221 _director_objects = _DirectorObjects()
222 
223 class _ostream(object):
224  r"""Proxy of C++ std::ostream class."""
225 
226  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
227 
228  def __init__(self, *args, **kwargs):
229  raise AttributeError("No constructor defined")
230  __repr__ = _swig_repr
231 
232  def write(self, osa_buf):
233  r"""write(_ostream self, char const * osa_buf)"""
234  return _IMP_em2d._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_em2d:
237 _IMP_em2d._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_em2d.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_em2d.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_em2d.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_em2d.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_em2d.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_em2d.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_em2d.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_em2d.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_GSL_HAS_IMP_CGAL = _IMP_em2d.IMP_GSL_HAS_IMP_CGAL
291 
292 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_FILESYSTEM
293 
294 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_GSL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_GSL_HAS_BOOST_RANDOM
297 
298 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_SYSTEM
299 
300 IMP_GSL_HAS_CGAL = _IMP_em2d.IMP_GSL_HAS_CGAL
301 
302 IMP_GSL_HAS_NUMPY = _IMP_em2d.IMP_GSL_HAS_NUMPY
303 
304 IMPGSL_SHOW_WARNINGS = _IMP_em2d.IMPGSL_SHOW_WARNINGS
305 
306 import IMP.gsl
307 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
308 
309 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
310 
311 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
312 
313 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
314 
315 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
316 
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_CGAL
318 
319 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_HDF5
320 
321 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_NUMPY
322 
323 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em2d.IMPSCOREFUNCTOR_SHOW_WARNINGS
324 
325 import IMP.score_functor
326 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_IMP_CGAL
327 
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 
330 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
331 
332 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_RANDOM
333 
334 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_SYSTEM
335 
336 IMP_STATISTICS_HAS_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_CGAL
337 
338 IMP_STATISTICS_HAS_NUMPY = _IMP_em2d.IMP_STATISTICS_HAS_NUMPY
339 
340 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em2d.IMPSTATISTICS_SHOW_WARNINGS
341 
342 import IMP.statistics
343 IMP_CORE_HAS_IMP_CGAL = _IMP_em2d.IMP_CORE_HAS_IMP_CGAL
344 
345 IMP_CORE_HAS_IMP_KERNEL = _IMP_em2d.IMP_CORE_HAS_IMP_KERNEL
346 
347 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_FILESYSTEM
348 
349 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
350 
351 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CORE_HAS_BOOST_RANDOM
352 
353 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_SYSTEM
354 
355 IMP_CORE_HAS_CGAL = _IMP_em2d.IMP_CORE_HAS_CGAL
356 
357 IMP_CORE_HAS_HDF5 = _IMP_em2d.IMP_CORE_HAS_HDF5
358 
359 IMP_CORE_HAS_NUMPY = _IMP_em2d.IMP_CORE_HAS_NUMPY
360 
361 IMPCORE_SHOW_WARNINGS = _IMP_em2d.IMPCORE_SHOW_WARNINGS
362 
363 import IMP.core
364 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em2d.IMP_CONTAINER_HAS_IMP_ALGEBRA
365 
366 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_CGAL
367 
368 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em2d.IMP_CONTAINER_HAS_IMP_DISPLAY
369 
370 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_KERNEL
371 
372 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
373 
374 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
375 
376 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
377 
378 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_RANDOM
379 
380 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_SYSTEM
381 
382 IMP_CONTAINER_HAS_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_CGAL
383 
384 IMP_CONTAINER_HAS_HDF5 = _IMP_em2d.IMP_CONTAINER_HAS_HDF5
385 
386 IMP_CONTAINER_HAS_NUMPY = _IMP_em2d.IMP_CONTAINER_HAS_NUMPY
387 
388 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em2d.IMP_CONTAINER_HAS_PYTHON_IHM
389 
390 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em2d.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
391 
392 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em2d.IMP_CONTAINER_HAS_ROBIN_MAP
393 
394 IMPCONTAINER_SHOW_WARNINGS = _IMP_em2d.IMPCONTAINER_SHOW_WARNINGS
395 
396 import IMP.container
397 IMP_ATOM_HAS_IMP_CGAL = _IMP_em2d.IMP_ATOM_HAS_IMP_CGAL
398 
399 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em2d.IMP_ATOM_HAS_IMP_KERNEL
400 
401 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
402 
403 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
404 
405 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ATOM_HAS_BOOST_RANDOM
406 
407 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em2d.IMP_ATOM_HAS_BOOST_REGEX
408 
409 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ATOM_HAS_BOOST_SYSTEM
410 
411 IMP_ATOM_HAS_CGAL = _IMP_em2d.IMP_ATOM_HAS_CGAL
412 
413 IMP_ATOM_HAS_HDF5 = _IMP_em2d.IMP_ATOM_HAS_HDF5
414 
415 IMP_ATOM_HAS_NUMPY = _IMP_em2d.IMP_ATOM_HAS_NUMPY
416 
417 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em2d.IMP_ATOM_HAS_PYTHON_IHM
418 
419 IMPATOM_SHOW_WARNINGS = _IMP_em2d.IMPATOM_SHOW_WARNINGS
420 
421 IMP_ATOM_TYPE_INDEX = _IMP_em2d.IMP_ATOM_TYPE_INDEX
422 
423 IMP_RESIDUE_TYPE_INDEX = _IMP_em2d.IMP_RESIDUE_TYPE_INDEX
424 
425 IMP_HIERARCHY_TYPE_INDEX = _IMP_em2d.IMP_HIERARCHY_TYPE_INDEX
426 
427 IMP_CHAIN_TYPE_INDEX = _IMP_em2d.IMP_CHAIN_TYPE_INDEX
428 
429 import IMP.atom
430 IMP_EM_HAS_IMP_CGAL = _IMP_em2d.IMP_EM_HAS_IMP_CGAL
431 
432 IMP_EM_HAS_IMP_CONTAINER = _IMP_em2d.IMP_EM_HAS_IMP_CONTAINER
433 
434 IMP_EM_HAS_IMP_DISPLAY = _IMP_em2d.IMP_EM_HAS_IMP_DISPLAY
435 
436 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM_HAS_IMP_SCORE_FUNCTOR
437 
438 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_FILESYSTEM
439 
440 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
441 
442 IMP_EM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM_HAS_BOOST_RANDOM
443 
444 IMP_EM_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM_HAS_BOOST_REGEX
445 
446 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_SYSTEM
447 
448 IMP_EM_HAS_CGAL = _IMP_em2d.IMP_EM_HAS_CGAL
449 
450 IMP_EM_HAS_HDF5 = _IMP_em2d.IMP_EM_HAS_HDF5
451 
452 IMP_EM_HAS_NUMPY = _IMP_em2d.IMP_EM_HAS_NUMPY
453 
454 IMP_EM_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM_HAS_PYTHON_IHM
455 
456 IMPEM_SHOW_WARNINGS = _IMP_em2d.IMPEM_SHOW_WARNINGS
457 
458 import IMP.em
459 IMP_SAXS_HAS_IMP_CGAL = _IMP_em2d.IMP_SAXS_HAS_IMP_CGAL
460 
461 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_em2d.IMP_SAXS_HAS_IMP_CONTAINER
462 
463 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_em2d.IMP_SAXS_HAS_IMP_DISPLAY
464 
465 IMP_SAXS_HAS_IMP_KERNEL = _IMP_em2d.IMP_SAXS_HAS_IMP_KERNEL
466 
467 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
468 
469 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SAXS_HAS_BOOST_FILESYSTEM
470 
471 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
472 
473 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SAXS_HAS_BOOST_RANDOM
474 
475 IMP_SAXS_HAS_BOOST_REGEX = _IMP_em2d.IMP_SAXS_HAS_BOOST_REGEX
476 
477 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SAXS_HAS_BOOST_SYSTEM
478 
479 IMP_SAXS_HAS_CGAL = _IMP_em2d.IMP_SAXS_HAS_CGAL
480 
481 IMP_SAXS_HAS_HDF5 = _IMP_em2d.IMP_SAXS_HAS_HDF5
482 
483 IMP_SAXS_HAS_NUMPY = _IMP_em2d.IMP_SAXS_HAS_NUMPY
484 
485 IMP_SAXS_HAS_PYTHON_IHM = _IMP_em2d.IMP_SAXS_HAS_PYTHON_IHM
486 
487 IMPSAXS_SHOW_WARNINGS = _IMP_em2d.IMPSAXS_SHOW_WARNINGS
488 
489 import IMP.saxs
490 IMP_ISD_HAS_IMP_CGAL = _IMP_em2d.IMP_ISD_HAS_IMP_CGAL
491 
492 IMP_ISD_HAS_IMP_DISPLAY = _IMP_em2d.IMP_ISD_HAS_IMP_DISPLAY
493 
494 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
495 
496 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ISD_HAS_BOOST_FILESYSTEM
497 
498 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
499 
500 IMP_ISD_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ISD_HAS_BOOST_RANDOM
501 
502 IMP_ISD_HAS_BOOST_REGEX = _IMP_em2d.IMP_ISD_HAS_BOOST_REGEX
503 
504 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ISD_HAS_BOOST_SYSTEM
505 
506 IMP_ISD_HAS_CGAL = _IMP_em2d.IMP_ISD_HAS_CGAL
507 
508 IMP_ISD_HAS_HDF5 = _IMP_em2d.IMP_ISD_HAS_HDF5
509 
510 IMP_ISD_HAS_NUMPY = _IMP_em2d.IMP_ISD_HAS_NUMPY
511 
512 IMP_ISD_HAS_PYTHON_IHM = _IMP_em2d.IMP_ISD_HAS_PYTHON_IHM
513 
514 IMPISD_SHOW_WARNINGS = _IMP_em2d.IMPISD_SHOW_WARNINGS
515 
516 import IMP.isd
517 IMP_RMF_HAS_IMP_CGAL = _IMP_em2d.IMP_RMF_HAS_IMP_CGAL
518 
519 IMP_RMF_HAS_IMP_EM = _IMP_em2d.IMP_RMF_HAS_IMP_EM
520 
521 IMP_RMF_HAS_IMP_SAXS = _IMP_em2d.IMP_RMF_HAS_IMP_SAXS
522 
523 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
524 
525 IMP_RMF_HAS_IMP_STATISTICS = _IMP_em2d.IMP_RMF_HAS_IMP_STATISTICS
526 
527 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_FILESYSTEM
528 
529 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
530 
531 IMP_RMF_HAS_BOOST_RANDOM = _IMP_em2d.IMP_RMF_HAS_BOOST_RANDOM
532 
533 IMP_RMF_HAS_BOOST_REGEX = _IMP_em2d.IMP_RMF_HAS_BOOST_REGEX
534 
535 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_SYSTEM
536 
537 IMP_RMF_HAS_CGAL = _IMP_em2d.IMP_RMF_HAS_CGAL
538 
539 IMP_RMF_HAS_HDF5 = _IMP_em2d.IMP_RMF_HAS_HDF5
540 
541 IMP_RMF_HAS_NUMPY = _IMP_em2d.IMP_RMF_HAS_NUMPY
542 
543 IMP_RMF_HAS_PYTHON_IHM = _IMP_em2d.IMP_RMF_HAS_PYTHON_IHM
544 
545 IMPRMF_SHOW_WARNINGS = _IMP_em2d.IMPRMF_SHOW_WARNINGS
546 
547 import IMP.rmf
548 import RMF
549 IMP_DOMINO_HAS_IMP_ATOM = _IMP_em2d.IMP_DOMINO_HAS_IMP_ATOM
550 
551 IMP_DOMINO_HAS_IMP_CGAL = _IMP_em2d.IMP_DOMINO_HAS_IMP_CGAL
552 
553 IMP_DOMINO_HAS_IMP_EM = _IMP_em2d.IMP_DOMINO_HAS_IMP_EM
554 
555 IMP_DOMINO_HAS_IMP_ISD = _IMP_em2d.IMP_DOMINO_HAS_IMP_ISD
556 
557 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_em2d.IMP_DOMINO_HAS_IMP_KERNEL
558 
559 IMP_DOMINO_HAS_IMP_RMF = _IMP_em2d.IMP_DOMINO_HAS_IMP_RMF
560 
561 IMP_DOMINO_HAS_IMP_SAXS = _IMP_em2d.IMP_DOMINO_HAS_IMP_SAXS
562 
563 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
564 
565 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_FILESYSTEM
566 
567 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
568 
569 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_RANDOM
570 
571 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_em2d.IMP_DOMINO_HAS_BOOST_REGEX
572 
573 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_SYSTEM
574 
575 IMP_DOMINO_HAS_CGAL = _IMP_em2d.IMP_DOMINO_HAS_CGAL
576 
577 IMP_DOMINO_HAS_HDF5 = _IMP_em2d.IMP_DOMINO_HAS_HDF5
578 
579 IMP_DOMINO_HAS_NUMPY = _IMP_em2d.IMP_DOMINO_HAS_NUMPY
580 
581 IMP_DOMINO_HAS_RMF = _IMP_em2d.IMP_DOMINO_HAS_RMF
582 
583 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_em2d.IMP_DOMINO_HAS_PYTHON_IHM
584 
585 IMPDOMINO_SHOW_WARNINGS = _IMP_em2d.IMPDOMINO_SHOW_WARNINGS
586 
587 import RMF_HDF5
588 import IMP.domino
589 IMP_EM2D_HAS_IMP_CGAL = _IMP_em2d.IMP_EM2D_HAS_IMP_CGAL
590 
591 IMP_EM2D_HAS_IMP_ISD = _IMP_em2d.IMP_EM2D_HAS_IMP_ISD
592 
593 IMP_EM2D_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM2D_HAS_IMP_KERNEL
594 
595 IMP_EM2D_HAS_IMP_RMF = _IMP_em2d.IMP_EM2D_HAS_IMP_RMF
596 
597 IMP_EM2D_HAS_IMP_SAXS = _IMP_em2d.IMP_EM2D_HAS_IMP_SAXS
598 
599 IMP_EM2D_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM2D_HAS_IMP_SCORE_FUNCTOR
600 
601 IMP_EM2D_HAS_IMP_STATISTICS = _IMP_em2d.IMP_EM2D_HAS_IMP_STATISTICS
602 
603 IMP_EM2D_HAS_BOOST_GRAPH = _IMP_em2d.IMP_EM2D_HAS_BOOST_GRAPH
604 
605 IMP_EM2D_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM2D_HAS_BOOST_RANDOM
606 
607 IMP_EM2D_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM2D_HAS_BOOST_REGEX
608 
609 IMP_EM2D_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM2D_HAS_BOOST_SYSTEM
610 
611 IMP_EM2D_HAS_CGAL = _IMP_em2d.IMP_EM2D_HAS_CGAL
612 
613 IMP_EM2D_HAS_GSL = _IMP_em2d.IMP_EM2D_HAS_GSL
614 
615 IMP_EM2D_HAS_HDF5 = _IMP_em2d.IMP_EM2D_HAS_HDF5
616 
617 IMP_EM2D_HAS_NUMPY = _IMP_em2d.IMP_EM2D_HAS_NUMPY
618 
619 IMP_EM2D_HAS_OPENCV3 = _IMP_em2d.IMP_EM2D_HAS_OPENCV3
620 
621 IMP_EM2D_HAS_RMF = _IMP_em2d.IMP_EM2D_HAS_RMF
622 
623 IMP_EM2D_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM2D_HAS_PYTHON_IHM
624 
625 IMP_EM2D_HAS_OPENCV21 = _IMP_em2d.IMP_EM2D_HAS_OPENCV21
626 
627 IMP_EM2D_HAS_OPENCV22 = _IMP_em2d.IMP_EM2D_HAS_OPENCV22
628 
629 IMPEM2D_SHOW_WARNINGS = _IMP_em2d.IMPEM2D_SHOW_WARNINGS
630 
631 
632 PolarResamplingParametersList=list
633 _plural_types.append("PolarResamplingParametersList")
634 _value_types.append("PolarResamplingParameters")
635 
636 
637 ProjectionMasks=list
638 _plural_types.append("ProjectionMasks")
639 _value_types.append("ProjectionMask")
640 
641 
642 MasksManagers=list
643 _plural_types.append("MasksManagers")
644 _value_types.append("MasksManager")
645 
646 
647 RegistrationResults=list
648 _plural_types.append("RegistrationResults")
649 _value_types.append("RegistrationResult")
650 
651 
652 ClusterSets=list
653 _plural_types.append("ClusterSets")
654 _value_types.append("ClusterSet")
655 
656 
657 SingleLinkages=list
658 _plural_types.append("SingleLinkages")
659 _value_types.append("SingleLinkage")
660 
661 
662 CompleteLinkages=list
663 _plural_types.append("CompleteLinkages")
664 _value_types.append("CompleteLinkage")
665 
666 
667 AverageDistanceLinkages=list
668 _plural_types.append("AverageDistanceLinkages")
669 _value_types.append("AverageDistanceLinkage")
670 
671 
672 SegmentationParametersList=list
673 _plural_types.append("SegmentationParametersList")
674 _value_types.append("SegmentationParameters")
675 
676 
677 MatchTemplateResults=list
678 _plural_types.append("MatchTemplateResults")
679 _value_types.append("MatchTemplateResult")
680 
681 
682 ProjectingParametersList=list
683 _plural_types.append("ProjectingParametersList")
684 _value_types.append("ProjectingParameters")
685 
686 
687 ProjectingOptionsList=list
688 _plural_types.append("ProjectingOptionsList")
689 _value_types.append("ProjectingOptions")
690 
691 
692 Em2DRestraintParametersList=list
693 _plural_types.append("Em2DRestraintParametersList")
694 _value_types.append("Em2DRestraintParameters")
695 
696 
697 _object_types.append("ProjectionFinder")
698 
699 
700 def _object_cast_to_ProjectionFinder(o):
701  r"""_object_cast_to_ProjectionFinder(Object o) -> ProjectionFinder"""
702  return _IMP_em2d._object_cast_to_ProjectionFinder(o)
703 
704 _object_types.append("ScoreFunction")
705 
706 
707 def _object_cast_to_ScoreFunction(o):
708  r"""_object_cast_to_ScoreFunction(Object o) -> ScoreFunction"""
709  return _IMP_em2d._object_cast_to_ScoreFunction(o)
710 
711 _object_types.append("ChiSquaredScore")
712 
713 
714 def _object_cast_to_ChiSquaredScore(o):
715  r"""_object_cast_to_ChiSquaredScore(Object o) -> ChiSquaredScore"""
716  return _IMP_em2d._object_cast_to_ChiSquaredScore(o)
717 
718 _object_types.append("EM2DScore")
719 
720 
721 def _object_cast_to_EM2DScore(o):
722  r"""_object_cast_to_EM2DScore(Object o) -> EM2DScore"""
723  return _IMP_em2d._object_cast_to_EM2DScore(o)
724 
725 _object_types.append("MeanAbsoluteDifference")
726 
727 
728 def _object_cast_to_MeanAbsoluteDifference(o):
729  r"""_object_cast_to_MeanAbsoluteDifference(Object o) -> MeanAbsoluteDifference"""
730  return _IMP_em2d._object_cast_to_MeanAbsoluteDifference(o)
731 
732 _object_types.append("ProjectionParametersScoreState")
733 
734 
735 def _object_cast_to_ProjectionParametersScoreState(o):
736  r"""_object_cast_to_ProjectionParametersScoreState(Object o) -> ProjectionParametersScoreState"""
737  return _IMP_em2d._object_cast_to_ProjectionParametersScoreState(o)
738 
739 _object_types.append("Em2DRestraint")
740 
741 
742 def _object_cast_to_Em2DRestraint(o):
743  r"""_object_cast_to_Em2DRestraint(Object o) -> Em2DRestraint"""
744  return _IMP_em2d._object_cast_to_Em2DRestraint(o)
745 
746 _object_types.append("Image")
747 
748 
749 def _object_cast_to_Image(o):
750  r"""_object_cast_to_Image(Object o) -> Image"""
751  return _IMP_em2d._object_cast_to_Image(o)
752 
753 _object_types.append("ImageReaderWriter")
754 
755 
756 def _object_cast_to_ImageReaderWriter(o):
757  r"""_object_cast_to_ImageReaderWriter(Object o) -> ImageReaderWriter"""
758  return _IMP_em2d._object_cast_to_ImageReaderWriter(o)
759 
760 _object_types.append("JPGImageReaderWriter")
761 
762 
763 def _object_cast_to_JPGImageReaderWriter(o):
764  r"""_object_cast_to_JPGImageReaderWriter(Object o) -> JPGImageReaderWriter"""
765  return _IMP_em2d._object_cast_to_JPGImageReaderWriter(o)
766 
767 _object_types.append("TIFFImageReaderWriter")
768 
769 
770 def _object_cast_to_TIFFImageReaderWriter(o):
771  r"""_object_cast_to_TIFFImageReaderWriter(Object o) -> TIFFImageReaderWriter"""
772  return _IMP_em2d._object_cast_to_TIFFImageReaderWriter(o)
773 
774 _object_types.append("SpiderImageReaderWriter")
775 
776 
777 def _object_cast_to_SpiderImageReaderWriter(o):
778  r"""_object_cast_to_SpiderImageReaderWriter(Object o) -> SpiderImageReaderWriter"""
779  return _IMP_em2d._object_cast_to_SpiderImageReaderWriter(o)
780 
781 _object_types.append("CollisionCrossSection")
782 
783 
784 def _object_cast_to_CollisionCrossSection(o):
785  r"""_object_cast_to_CollisionCrossSection(Object o) -> CollisionCrossSection"""
786  return _IMP_em2d._object_cast_to_CollisionCrossSection(o)
787 
788 _object_types.append("GridStates")
789 
790 
791 def _object_cast_to_GridStates(o):
792  r"""_object_cast_to_GridStates(Object o) -> GridStates"""
793  return _IMP_em2d._object_cast_to_GridStates(o)
794 
795 _object_types.append("ProjectionStates")
796 
797 
798 def _object_cast_to_ProjectionStates(o):
799  r"""_object_cast_to_ProjectionStates(Object o) -> ProjectionStates"""
800  return _IMP_em2d._object_cast_to_ProjectionStates(o)
801 
802 _object_types.append("DistanceFilter")
803 
804 
805 def _object_cast_to_DistanceFilter(o):
806  r"""_object_cast_to_DistanceFilter(Object o) -> DistanceFilter"""
807  return _IMP_em2d._object_cast_to_DistanceFilter(o)
808 
809 _object_types.append("DistanceFilterTable")
810 
811 
812 def _object_cast_to_DistanceFilterTable(o):
813  r"""_object_cast_to_DistanceFilterTable(Object o) -> DistanceFilterTable"""
814  return _IMP_em2d._object_cast_to_DistanceFilterTable(o)
815 
816 _object_types.append("RigidBodiesImageFitRestraint")
817 
818 
819 def _object_cast_to_RigidBodiesImageFitRestraint(o):
820  r"""_object_cast_to_RigidBodiesImageFitRestraint(Object o) -> RigidBodiesImageFitRestraint"""
821  return _IMP_em2d._object_cast_to_RigidBodiesImageFitRestraint(o)
822 
823 _object_types.append("DummyRestraint")
824 
825 
826 def _object_cast_to_DummyRestraint(o):
827  r"""_object_cast_to_DummyRestraint(Object o) -> DummyRestraint"""
828  return _IMP_em2d._object_cast_to_DummyRestraint(o)
829 
830 _object_types.append("ParticlesDummyRestraint")
831 
832 
833 def _object_cast_to_ParticlesDummyRestraint(o):
834  r"""_object_cast_to_ParticlesDummyRestraint(Object o) -> ParticlesDummyRestraint"""
835  return _IMP_em2d._object_cast_to_ParticlesDummyRestraint(o)
836 
837 _object_types.append("RelativePositionMover")
838 
839 
840 def _object_cast_to_RelativePositionMover(o):
841  r"""_object_cast_to_RelativePositionMover(Object o) -> RelativePositionMover"""
842  return _IMP_em2d._object_cast_to_RelativePositionMover(o)
843 
844 _object_types.append("PCAFitRestraint")
845 
846 
847 def _object_cast_to_em2dPCAFitRestraint(o):
848  r"""_object_cast_to_em2dPCAFitRestraint(Object o) -> PCAFitRestraint"""
849  return _IMP_em2d._object_cast_to_em2dPCAFitRestraint(o)
850 
851 def ProjectionParametersList(l=[]):
852  return [ProjectionParameters(x) for x in l]
853 _plural_types.append("ProjectionParametersList")
854 
855 
856 _value_types.append("ProjectionParameters")
857 
858 
859 def show(*args):
860  r"""show(cv::Mat const & m, _ostream out=std::cout)"""
861  return _IMP_em2d.show(*args)
862 
863 def write_matrix(m, name):
864  r"""write_matrix(cv::Mat & m, std::string name)"""
865  return _IMP_em2d.write_matrix(m, name)
866 class ImageReaderWriter(IMP.Object):
867  r"""Proxy of C++ IMP::em2d::ImageReaderWriter class."""
868 
869  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
870 
871  def __init__(self, *args, **kwargs):
872  raise AttributeError("No constructor defined - class is abstract")
873 
874  def read(self, filename, header, data):
875  r"""read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
876  return _IMP_em2d.ImageReaderWriter_read(self, filename, header, data)
877 
878  def read_from_floats(self, filename, header, data):
879  r"""read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
880  return _IMP_em2d.ImageReaderWriter_read_from_floats(self, filename, header, data)
881 
882  def read_from_ints(self, filename, header, data):
883  r"""read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
884  return _IMP_em2d.ImageReaderWriter_read_from_ints(self, filename, header, data)
885 
886  def write(self, filename, header, data):
887  r"""write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
888  return _IMP_em2d.ImageReaderWriter_write(self, filename, header, data)
889 
890  def write_to_floats(self, filename, header, data):
891  r"""write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
892  return _IMP_em2d.ImageReaderWriter_write_to_floats(self, filename, header, data)
893 
894  def write_to_ints(self, filename, header, data):
895  r"""write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
896  return _IMP_em2d.ImageReaderWriter_write_to_ints(self, filename, header, data)
897 
898  def get_version_info(self):
899  r"""get_version_info(ImageReaderWriter self) -> VersionInfo"""
900  return _IMP_em2d.ImageReaderWriter_get_version_info(self)
901  __swig_destroy__ = _IMP_em2d.delete_ImageReaderWriter
902 
903  def __str__(self):
904  r"""__str__(ImageReaderWriter self) -> std::string"""
905  return _IMP_em2d.ImageReaderWriter___str__(self)
906 
907  def __repr__(self):
908  r"""__repr__(ImageReaderWriter self) -> std::string"""
909  return _IMP_em2d.ImageReaderWriter___repr__(self)
910 
911  @staticmethod
912  def get_from(o):
913  return _object_cast_to_ImageReaderWriter(o)
914 
915 
916 # Register ImageReaderWriter in _IMP_em2d:
917 _IMP_em2d.ImageReaderWriter_swigregister(ImageReaderWriter)
918 class PolarResamplingParameters(object):
919  r"""Proxy of C++ IMP::em2d::PolarResamplingParameters class."""
920 
921  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
922 
923  def __init__(self, *args):
924  r"""
925  __init__(PolarResamplingParameters self) -> PolarResamplingParameters
926  __init__(PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
927  __init__(PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
928  """
929  _IMP_em2d.PolarResamplingParameters_swiginit(self, _IMP_em2d.new_PolarResamplingParameters(*args))
930  __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
931 
932  def setup(self, rows, cols):
933  r"""setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
934  return _IMP_em2d.PolarResamplingParameters_setup(self, rows, cols)
935 
936  def get_starting_radius(self):
937  r"""get_starting_radius(PolarResamplingParameters self) -> double"""
938  return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
939 
940  def get_ending_radius(self):
941  r"""get_ending_radius(PolarResamplingParameters self) -> double"""
942  return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
943 
944  def get_radius(self, n_ring):
945  r"""get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
946  return _IMP_em2d.PolarResamplingParameters_get_radius(self, n_ring)
947 
948  def get_number_of_rings(self):
949  r"""get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
950  return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
951 
952  def set_estimated_number_of_angles(self, aprox_value):
953  r"""set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
954  return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, aprox_value)
955 
956  def get_number_of_angles(self):
957  r"""get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
958  return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
959 
960  def get_angle_step(self):
961  r"""get_angle_step(PolarResamplingParameters self) -> double"""
962  return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
963 
964  def get_radius_step(self):
965  r"""get_radius_step(PolarResamplingParameters self) -> double"""
966  return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
967 
968  def create_maps_for_resampling(self):
969  r"""create_maps_for_resampling(PolarResamplingParameters self)"""
970  return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
971 
972  def get_resampling_maps(self, m1, m2):
973  r"""get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
974  return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, m1, m2)
975 
976  def get_resampling_map(self, m1):
977  r"""get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
978  return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, m1)
979 
980  def show(self, out):
981  r"""show(PolarResamplingParameters self, _ostream out)"""
982  return _IMP_em2d.PolarResamplingParameters_show(self, out)
983 
984  def get_is_setup(self):
985  r"""get_is_setup(PolarResamplingParameters self) -> bool"""
986  return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
987 
988  def __str__(self):
989  r"""__str__(PolarResamplingParameters self) -> std::string"""
990  return _IMP_em2d.PolarResamplingParameters___str__(self)
991 
992  def __repr__(self):
993  r"""__repr__(PolarResamplingParameters self) -> std::string"""
994  return _IMP_em2d.PolarResamplingParameters___repr__(self)
995 
996  def _get_as_binary(self):
997  r"""_get_as_binary(PolarResamplingParameters self) -> PyObject *"""
998  return _IMP_em2d.PolarResamplingParameters__get_as_binary(self)
999 
1000  def _set_from_binary(self, p):
1001  r"""_set_from_binary(PolarResamplingParameters self, PyObject * p)"""
1002  return _IMP_em2d.PolarResamplingParameters__set_from_binary(self, p)
1003 
1004  def __getstate__(self):
1005  p = self._get_as_binary()
1006  if len(self.__dict__) > 1:
1007  d = self.__dict__.copy()
1008  del d['this']
1009  p = (d, p)
1010  return p
1011 
1012  def __setstate__(self, p):
1013  if not hasattr(self, 'this'):
1014  self.__init__()
1015  if isinstance(p, tuple):
1016  d, p = p
1017  self.__dict__.update(d)
1018  return self._set_from_binary(p)
1019 
1020 
1021 # Register PolarResamplingParameters in _IMP_em2d:
1022 _IMP_em2d.PolarResamplingParameters_swigregister(PolarResamplingParameters)
1023 class SegmentationParameters(object):
1024  r"""Proxy of C++ IMP::em2d::SegmentationParameters class."""
1025 
1026  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1027  image_pixel_size = property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set, doc=r"""image_pixel_size : double""")
1028  diffusion_beta = property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set, doc=r"""diffusion_beta : double""")
1029  diffusion_timesteps = property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set, doc=r"""diffusion_timesteps : double""")
1030  fill_holes_stddevs = property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set, doc=r"""fill_holes_stddevs : double""")
1031  opening_kernel = property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set, doc=r"""opening_kernel : cv::Mat""")
1032  remove_sizing_percentage = property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set, doc=r"""remove_sizing_percentage : double""")
1033  binary_background = property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set, doc=r"""binary_background : int""")
1034  binary_foreground = property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set, doc=r"""binary_foreground : int""")
1035  threshold = property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set, doc=r"""threshold : double""")
1036 
1037  def __init__(self, *args):
1038  r"""
1039  __init__(SegmentationParameters self) -> SegmentationParameters
1040  __init__(SegmentationParameters self, double apix, double diff_beta, unsigned int diff_timesteps, double fh_stddevs, cv::Mat const & kr, int background, int foreground) -> SegmentationParameters
1041  """
1042  _IMP_em2d.SegmentationParameters_swiginit(self, _IMP_em2d.new_SegmentationParameters(*args))
1043 
1044  def show(self, *args):
1045  r"""show(SegmentationParameters self, _ostream out=std::cout)"""
1046  return _IMP_em2d.SegmentationParameters_show(self, *args)
1047 
1048  def __str__(self):
1049  r"""__str__(SegmentationParameters self) -> std::string"""
1050  return _IMP_em2d.SegmentationParameters___str__(self)
1051 
1052  def __repr__(self):
1053  r"""__repr__(SegmentationParameters self) -> std::string"""
1054  return _IMP_em2d.SegmentationParameters___repr__(self)
1055 
1056  def _get_as_binary(self):
1057  r"""_get_as_binary(SegmentationParameters self) -> PyObject *"""
1058  return _IMP_em2d.SegmentationParameters__get_as_binary(self)
1059 
1060  def _set_from_binary(self, p):
1061  r"""_set_from_binary(SegmentationParameters self, PyObject * p)"""
1062  return _IMP_em2d.SegmentationParameters__set_from_binary(self, p)
1063 
1064  def __getstate__(self):
1065  p = self._get_as_binary()
1066  if len(self.__dict__) > 1:
1067  d = self.__dict__.copy()
1068  del d['this']
1069  p = (d, p)
1070  return p
1071 
1072  def __setstate__(self, p):
1073  if not hasattr(self, 'this'):
1074  self.__init__()
1075  if isinstance(p, tuple):
1076  d, p = p
1077  self.__dict__.update(d)
1078  return self._set_from_binary(p)
1079 
1080  __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
1081 
1082 # Register SegmentationParameters in _IMP_em2d:
1083 _IMP_em2d.SegmentationParameters_swigregister(SegmentationParameters)
1084 class MatchTemplateResult(object):
1085  r"""Proxy of C++ IMP::em2d::MatchTemplateResult class."""
1086 
1087  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1088  pair = property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set, doc=r"""pair : IMP::IntPair""")
1089  cross_correlation = property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set, doc=r"""cross_correlation : double""")
1090 
1091  def __init__(self, *args):
1092  r"""
1093  __init__(MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult
1094  __init__(MatchTemplateResult self) -> MatchTemplateResult
1095  """
1096  _IMP_em2d.MatchTemplateResult_swiginit(self, _IMP_em2d.new_MatchTemplateResult(*args))
1097 
1098  def show(self, *args):
1099  r"""show(MatchTemplateResult self, _ostream out=std::cout)"""
1100  return _IMP_em2d.MatchTemplateResult_show(self, *args)
1101 
1102  def __str__(self):
1103  r"""__str__(MatchTemplateResult self) -> std::string"""
1104  return _IMP_em2d.MatchTemplateResult___str__(self)
1105 
1106  def __repr__(self):
1107  r"""__repr__(MatchTemplateResult self) -> std::string"""
1108  return _IMP_em2d.MatchTemplateResult___repr__(self)
1109 
1110  def _get_as_binary(self):
1111  r"""_get_as_binary(MatchTemplateResult self) -> PyObject *"""
1112  return _IMP_em2d.MatchTemplateResult__get_as_binary(self)
1113 
1114  def _set_from_binary(self, p):
1115  r"""_set_from_binary(MatchTemplateResult self, PyObject * p)"""
1116  return _IMP_em2d.MatchTemplateResult__set_from_binary(self, p)
1117 
1118  def __getstate__(self):
1119  p = self._get_as_binary()
1120  if len(self.__dict__) > 1:
1121  d = self.__dict__.copy()
1122  del d['this']
1123  p = (d, p)
1124  return p
1125 
1126  def __setstate__(self, p):
1127  if not hasattr(self, 'this'):
1128  self.__init__()
1129  if isinstance(p, tuple):
1130  d, p = p
1131  self.__dict__.update(d)
1132  return self._set_from_binary(p)
1133 
1134  __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
1135 
1136 # Register MatchTemplateResult in _IMP_em2d:
1137 _IMP_em2d.MatchTemplateResult_swigregister(MatchTemplateResult)
1138 
1139 def apply_mask(m, result, mask, val):
1140  r"""apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
1141  return _IMP_em2d.apply_mask(m, result, mask, val)
1142 
1143 def apply_circular_mask(mat, result, radius, value=0.0):
1144  r"""apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)"""
1145  return _IMP_em2d.apply_circular_mask(mat, result, radius, value)
1146 
1147 def get_mean(mat, mask):
1148  r"""get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
1149  return _IMP_em2d.get_mean(mat, mask)
1150 
1151 def create_circular_mask(rows, cols, radius):
1152  r"""create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
1153  return _IMP_em2d.create_circular_mask(rows, cols, radius)
1154 
1155 def do_histogram_stretching(m, boxes, offset):
1156  r"""do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
1157  return _IMP_em2d.do_histogram_stretching(m, boxes, offset)
1158 
1159 def do_dilate_and_shrink_warp(m, grayscale, kernel):
1160  r"""do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
1161  return _IMP_em2d.do_dilate_and_shrink_warp(m, grayscale, kernel)
1162 
1163 def do_morphologic_reconstruction(mask, marker, neighbors_mode=4):
1164  r"""do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)"""
1165  return _IMP_em2d.do_morphologic_reconstruction(mask, marker, neighbors_mode)
1166 
1167 def do_labeling(m, mat_to_label):
1168  r"""do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
1169  return _IMP_em2d.do_labeling(m, mat_to_label)
1170 
1171 def get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang):
1172  r"""get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
1173  return _IMP_em2d.get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang)
1174 
1175 def get_domes(m, result, h):
1176  r"""get_domes(cv::Mat & m, cv::Mat & result, double h)"""
1177  return _IMP_em2d.get_domes(m, result, h)
1178 
1179 def get_transformed(input, transformed, T):
1180  r"""get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
1181  return _IMP_em2d.get_transformed(input, transformed, T)
1182 
1183 def apply_threshold(m, result, threshold=0.0):
1184  r"""apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)"""
1185  return _IMP_em2d.apply_threshold(m, result, threshold)
1186 
1187 def do_morphologic_contrast_enhancement(m, result, kernel, iterations):
1188  r"""do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
1189  return _IMP_em2d.do_morphologic_contrast_enhancement(m, result, kernel, iterations)
1190 
1191 def get_morphologic_gradient(m, result, kernel):
1192  r"""get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
1193  return _IMP_em2d.get_morphologic_gradient(m, result, kernel)
1194 
1195 def get_overlap_percentage(m1, m2, center):
1196  r"""get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
1197  return _IMP_em2d.get_overlap_percentage(m1, m2, center)
1198 
1199 def get_best_template_matches(m, templ, n):
1200  r"""get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
1201  return _IMP_em2d.get_best_template_matches(m, templ, n)
1202 class Image(IMP.Object):
1203  r"""Proxy of C++ IMP::em2d::Image class."""
1204 
1205  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1206 
1207  def __init__(self, *args):
1208  r"""
1209  __init__(Image self) -> Image
1210  __init__(Image self, int rows, int cols) -> Image
1211  __init__(Image self, IMP::String filename, ImageReaderWriter reader) -> Image
1212  """
1213  _IMP_em2d.Image_swiginit(self, _IMP_em2d.new_Image(*args))
1214 
1215  def get_data(self):
1216  r"""get_data(Image self) -> cv::Mat &"""
1217  return _IMP_em2d.Image_get_data(self)
1218 
1219  def set_data(self, mat):
1220  r"""set_data(Image self, cv::Mat const & mat)"""
1221  return _IMP_em2d.Image_set_data(self, mat)
1222 
1223  def set_zeros(self):
1224  r"""set_zeros(Image self)"""
1225  return _IMP_em2d.Image_set_zeros(self)
1226 
1227  def set_value(self, *args):
1228  r"""
1229  set_value(Image self, double val)
1230  set_value(Image self, int i, int j, double val)
1231  """
1232  return _IMP_em2d.Image_set_value(self, *args)
1233 
1234  def __call__(self, i, j):
1235  r"""__call__(Image self, int i, int j) -> double"""
1236  return _IMP_em2d.Image___call__(self, i, j)
1237 
1238  def get_header(self):
1239  r"""get_header(Image self) -> ImageHeader"""
1240  return _IMP_em2d.Image_get_header(self)
1241 
1242  def set_size(self, *args):
1243  r"""
1244  set_size(Image self, int rows, int cols)
1245  set_size(Image self, Image img)
1246  """
1247  return _IMP_em2d.Image_set_size(self, *args)
1248 
1249  def update_header(self):
1250  r"""update_header(Image self)"""
1251  return _IMP_em2d.Image_update_header(self)
1252 
1253  def read(self, filename, reader):
1254  r"""read(Image self, IMP::String filename, ImageReaderWriter reader)"""
1255  return _IMP_em2d.Image_read(self, filename, reader)
1256 
1257  def write(self, filename, writer):
1258  r"""write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
1259  return _IMP_em2d.Image_write(self, filename, writer)
1260 
1261  def show(self, out):
1262  r"""show(Image self, _ostream out)"""
1263  return _IMP_em2d.Image_show(self, out)
1264 
1265  def get_version_info(self):
1266  r"""get_version_info(Image self) -> VersionInfo"""
1267  return _IMP_em2d.Image_get_version_info(self)
1268  __swig_destroy__ = _IMP_em2d.delete_Image
1269 
1270  def set_name(self, name):
1271  r"""set_name(Image self, IMP::String const & name)"""
1272  return _IMP_em2d.Image_set_name(self, name)
1273 
1274  def get_name(self):
1275  r"""get_name(Image self) -> IMP::String"""
1276  return _IMP_em2d.Image_get_name(self)
1277 
1278  def get_min_and_max_values(self):
1279  r"""get_min_and_max_values(Image self) -> IMP::FloatRange"""
1280  return _IMP_em2d.Image_get_min_and_max_values(self)
1281 
1282  def __str__(self):
1283  r"""__str__(Image self) -> std::string"""
1284  return _IMP_em2d.Image___str__(self)
1285 
1286  def __repr__(self):
1287  r"""__repr__(Image self) -> std::string"""
1288  return _IMP_em2d.Image___repr__(self)
1289 
1290  @staticmethod
1291  def get_from(o):
1292  return _object_cast_to_Image(o)
1293 
1294 
1295 # Register Image in _IMP_em2d:
1296 _IMP_em2d.Image_swigregister(Image)
1297 
1298 def read_images(names, rw):
1299  r"""read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1300  return _IMP_em2d.read_images(names, rw)
1301 
1302 def save_images(images, names, rw):
1303  r"""save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1304  return _IMP_em2d.save_images(images, names, rw)
1305 
1306 def do_normalize(*args):
1307  r"""
1308  do_normalize(cv::Mat & m)
1309  do_normalize(Image im, bool force=False)
1310  """
1311  return _IMP_em2d.do_normalize(*args)
1312 
1313 def get_histogram(*args):
1314  r"""
1315  get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1316  get_histogram(Image img, int bins) -> IMP::Floats
1317  """
1318  return _IMP_em2d.get_histogram(*args)
1319 
1320 def apply_variance_filter(*args):
1321  r"""
1322  apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1323  apply_variance_filter(Image input, Image filtered, int kernelsize)
1324  """
1325  return _IMP_em2d.apply_variance_filter(*args)
1326 
1327 def apply_diffusion_filter(*args):
1328  r"""
1329  apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1330  apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1331  """
1332  return _IMP_em2d.apply_diffusion_filter(*args)
1333 
1334 def do_fill_holes(*args):
1335  r"""
1336  do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1337  do_fill_holes(Image input, Image result, double n_stddevs)
1338  """
1339  return _IMP_em2d.do_fill_holes(*args)
1340 
1341 def do_combined_fill_holes_and_threshold(*args):
1342  r"""
1343  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1344  do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1345  """
1346  return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1347 
1348 def do_extend_borders(*args):
1349  r"""
1350  do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1351  do_extend_borders(Image im1, Image im2, unsigned int pix)
1352  """
1353  return _IMP_em2d.do_extend_borders(*args)
1354 
1355 def do_segmentation(*args):
1356  r"""
1357  do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1358  do_segmentation(Image input, Image result, SegmentationParameters params)
1359  """
1360  return _IMP_em2d.do_segmentation(*args)
1361 
1362 def do_remove_small_objects(*args):
1363  r"""
1364  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1365  do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1366  """
1367  return _IMP_em2d.do_remove_small_objects(*args)
1368 
1369 def do_subtract_images(first, second, result):
1370  r"""do_subtract_images(Image first, Image second, Image result)"""
1371  return _IMP_em2d.do_subtract_images(first, second, result)
1372 
1373 def add_noise(*args):
1374  r"""
1375  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode="uniform", double df=3)
1376  add_noise(Image im1, double op1, double op2, IMP::String const & mode="uniform", double df=3)
1377  """
1378  return _IMP_em2d.add_noise(*args)
1379 
1380 def do_resample_polar(*args):
1381  r"""
1382  do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1383  do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1384  """
1385  return _IMP_em2d.do_resample_polar(*args)
1386 
1387 def crop(*args):
1388  r"""
1389  crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1390  crop(Image img, IMP::IntPair const & center, int size)
1391  """
1392  return _IMP_em2d.crop(*args)
1393 
1394 def apply_mean_outside_mask(img, radius):
1395  r"""apply_mean_outside_mask(Image img, double radius)"""
1396  return _IMP_em2d.apply_mean_outside_mask(img, radius)
1397 class RegistrationResult(object):
1398  r"""Proxy of C++ IMP::em2d::RegistrationResult class."""
1399 
1400  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1401 
1402  def __init__(self, *args):
1403  r"""
1404  __init__(RegistrationResult self) -> RegistrationResult
1405  __init__(RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name="") -> RegistrationResult
1406  __init__(RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.), int projection_index=0, int image_index=0, IMP::String name="") -> RegistrationResult
1407  """
1408  _IMP_em2d.RegistrationResult_swiginit(self, _IMP_em2d.new_RegistrationResult(*args))
1409 
1410  def get_phi(self):
1411  r"""get_phi(RegistrationResult self) -> double"""
1412  return _IMP_em2d.RegistrationResult_get_phi(self)
1413 
1414  def get_theta(self):
1415  r"""get_theta(RegistrationResult self) -> double"""
1416  return _IMP_em2d.RegistrationResult_get_theta(self)
1417 
1418  def get_psi(self):
1419  r"""get_psi(RegistrationResult self) -> double"""
1420  return _IMP_em2d.RegistrationResult_get_psi(self)
1421 
1422  def get_shift(self):
1423  r"""get_shift(RegistrationResult self) -> Vector2D"""
1424  return _IMP_em2d.RegistrationResult_get_shift(self)
1425 
1426  def get_shift_3d(self):
1427  r"""get_shift_3d(RegistrationResult self) -> Vector3D"""
1428  return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1429 
1430  def get_projection_index(self):
1431  r"""get_projection_index(RegistrationResult self) -> int"""
1432  return _IMP_em2d.RegistrationResult_get_projection_index(self)
1433 
1434  def set_projection_index(self, index):
1435  r"""set_projection_index(RegistrationResult self, int index)"""
1436  return _IMP_em2d.RegistrationResult_set_projection_index(self, index)
1437 
1438  def get_image_index(self):
1439  r"""get_image_index(RegistrationResult self) -> int"""
1440  return _IMP_em2d.RegistrationResult_get_image_index(self)
1441 
1442  def set_image_index(self, index):
1443  r"""set_image_index(RegistrationResult self, int index)"""
1444  return _IMP_em2d.RegistrationResult_set_image_index(self, index)
1445 
1446  def get_name(self):
1447  r"""get_name(RegistrationResult self) -> IMP::String"""
1448  return _IMP_em2d.RegistrationResult_get_name(self)
1449 
1450  def get_ccc(self):
1451  r"""get_ccc(RegistrationResult self) -> double"""
1452  return _IMP_em2d.RegistrationResult_get_ccc(self)
1453 
1454  def set_ccc(self, ccc):
1455  r"""set_ccc(RegistrationResult self, double ccc)"""
1456  return _IMP_em2d.RegistrationResult_set_ccc(self, ccc)
1457 
1458  def get_score(self):
1459  r"""get_score(RegistrationResult self) -> double"""
1460  return _IMP_em2d.RegistrationResult_get_score(self)
1461 
1462  def set_score(self, Score):
1463  r"""set_score(RegistrationResult self, double Score)"""
1464  return _IMP_em2d.RegistrationResult_set_score(self, Score)
1465 
1466  def set_rotation(self, *args):
1467  r"""
1468  set_rotation(RegistrationResult self, double phi, double theta, double psi)
1469  set_rotation(RegistrationResult self, Rotation3D R)
1470  """
1471  return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1472 
1473  def set_shift(self, shift):
1474  r"""set_shift(RegistrationResult self, Vector2D shift)"""
1475  return _IMP_em2d.RegistrationResult_set_shift(self, shift)
1476 
1477  def set_name(self, name):
1478  r"""set_name(RegistrationResult self, IMP::String name)"""
1479  return _IMP_em2d.RegistrationResult_set_name(self, name)
1480 
1481  def add_in_plane_transformation(self, t):
1482  r"""add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1483  return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, t)
1484 
1485  def show(self, *args):
1486  r"""show(RegistrationResult self, _ostream out=std::cout)"""
1487  return _IMP_em2d.RegistrationResult_show(self, *args)
1488 
1489  def write(self, *args):
1490  r"""write(RegistrationResult self, _ostream out=std::cout)"""
1491  return _IMP_em2d.RegistrationResult_write(self, *args)
1492 
1493  def write_comment_line(self, *args):
1494  r"""write_comment_line(RegistrationResult self, _ostream out=std::cout)"""
1495  return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1496 
1497  def read(self, s):
1498  r"""read(RegistrationResult self, IMP::String const & s)"""
1499  return _IMP_em2d.RegistrationResult_read(self, s)
1500 
1501  def set_random_registration(self, index, maximum_shift):
1502  r"""set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1503  return _IMP_em2d.RegistrationResult_set_random_registration(self, index, maximum_shift)
1504 
1505  def get_rotation(self):
1506  r"""get_rotation(RegistrationResult self) -> Rotation3D"""
1507  return _IMP_em2d.RegistrationResult_get_rotation(self)
1508 
1509  def set_in_image(self, header):
1510  r"""set_in_image(RegistrationResult self, ImageHeader header)"""
1511  return _IMP_em2d.RegistrationResult_set_in_image(self, header)
1512 
1513  def read_from_image(self, header):
1514  r"""read_from_image(RegistrationResult self, ImageHeader header)"""
1515  return _IMP_em2d.RegistrationResult_read_from_image(self, header)
1516 
1517  def get_is_optimized_result(self):
1518  r"""get_is_optimized_result(RegistrationResult self) -> bool"""
1519  return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1520  __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1521 
1522  def __str__(self):
1523  r"""__str__(RegistrationResult self) -> std::string"""
1524  return _IMP_em2d.RegistrationResult___str__(self)
1525 
1526  def __repr__(self):
1527  r"""__repr__(RegistrationResult self) -> std::string"""
1528  return _IMP_em2d.RegistrationResult___repr__(self)
1529 
1530  def _get_as_binary(self):
1531  r"""_get_as_binary(RegistrationResult self) -> PyObject *"""
1532  return _IMP_em2d.RegistrationResult__get_as_binary(self)
1533 
1534  def _set_from_binary(self, p):
1535  r"""_set_from_binary(RegistrationResult self, PyObject * p)"""
1536  return _IMP_em2d.RegistrationResult__set_from_binary(self, p)
1537 
1538  def __getstate__(self):
1539  p = self._get_as_binary()
1540  if len(self.__dict__) > 1:
1541  d = self.__dict__.copy()
1542  del d['this']
1543  p = (d, p)
1544  return p
1545 
1546  def __setstate__(self, p):
1547  if not hasattr(self, 'this'):
1548  self.__init__()
1549  if isinstance(p, tuple):
1550  d, p = p
1551  self.__dict__.update(d)
1552  return self._set_from_binary(p)
1553 
1554 
1555 # Register RegistrationResult in _IMP_em2d:
1556 _IMP_em2d.RegistrationResult_swigregister(RegistrationResult)
1557 
1558 def read_registration_results(filename):
1559  r"""read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1560  return _IMP_em2d.read_registration_results(filename)
1561 
1562 def write_registration_results(filename, results):
1563  r"""write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1564  return _IMP_em2d.write_registration_results(filename, results)
1565 
1566 def get_random_registration_results(n, maximum_shift=5.0):
1567  r"""get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults"""
1568  return _IMP_em2d.get_random_registration_results(n, maximum_shift)
1569 
1571  r"""get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1572  return _IMP_em2d.get_evenly_distributed_registration_results(n_projections)
1573 class SpiderImageReaderWriter(ImageReaderWriter):
1574  r"""Proxy of C++ IMP::em2d::SpiderImageReaderWriter class."""
1575 
1576  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1577  filename_ = property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set, doc=r"""filename_ : IMP::String""")
1578  skip_type_check_ = property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set, doc=r"""skip_type_check_ : bool""")
1579  force_reversed_ = property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set, doc=r"""force_reversed_ : bool""")
1580  skip_extra_checkings_ = property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set, doc=r"""skip_extra_checkings_ : bool""")
1581 
1582  def __init__(self, *args):
1583  r"""
1584  __init__(SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1585  __init__(SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1586  """
1587  _IMP_em2d.SpiderImageReaderWriter_swiginit(self, _IMP_em2d.new_SpiderImageReaderWriter(*args))
1588  __swig_destroy__ = _IMP_em2d.delete_SpiderImageReaderWriter
1589 
1590  def __str__(self):
1591  r"""__str__(SpiderImageReaderWriter self) -> std::string"""
1592  return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1593 
1594  def __repr__(self):
1595  r"""__repr__(SpiderImageReaderWriter self) -> std::string"""
1596  return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1597 
1598  @staticmethod
1599  def get_from(o):
1600  return _object_cast_to_SpiderImageReaderWriter(o)
1601 
1602 
1603 # Register SpiderImageReaderWriter in _IMP_em2d:
1604 _IMP_em2d.SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1605 class JPGImageReaderWriter(ImageReaderWriter):
1606  r"""Proxy of C++ IMP::em2d::JPGImageReaderWriter class."""
1607 
1608  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1609 
1610  def __init__(self):
1611  r"""__init__(JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1612  _IMP_em2d.JPGImageReaderWriter_swiginit(self, _IMP_em2d.new_JPGImageReaderWriter())
1613  __swig_destroy__ = _IMP_em2d.delete_JPGImageReaderWriter
1614 
1615  def __str__(self):
1616  r"""__str__(JPGImageReaderWriter self) -> std::string"""
1617  return _IMP_em2d.JPGImageReaderWriter___str__(self)
1618 
1619  def __repr__(self):
1620  r"""__repr__(JPGImageReaderWriter self) -> std::string"""
1621  return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1622 
1623  @staticmethod
1624  def get_from(o):
1625  return _object_cast_to_JPGImageReaderWriter(o)
1626 
1627 
1628 # Register JPGImageReaderWriter in _IMP_em2d:
1629 _IMP_em2d.JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1630 class TIFFImageReaderWriter(ImageReaderWriter):
1631  r"""Proxy of C++ IMP::em2d::TIFFImageReaderWriter class."""
1632 
1633  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1634 
1635  def __init__(self):
1636  r"""__init__(TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1637  _IMP_em2d.TIFFImageReaderWriter_swiginit(self, _IMP_em2d.new_TIFFImageReaderWriter())
1638  __swig_destroy__ = _IMP_em2d.delete_TIFFImageReaderWriter
1639 
1640  def __str__(self):
1641  r"""__str__(TIFFImageReaderWriter self) -> std::string"""
1642  return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1643 
1644  def __repr__(self):
1645  r"""__repr__(TIFFImageReaderWriter self) -> std::string"""
1646  return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1647 
1648  @staticmethod
1649  def get_from(o):
1650  return _object_cast_to_TIFFImageReaderWriter(o)
1651 
1652 
1653 # Register TIFFImageReaderWriter in _IMP_em2d:
1654 _IMP_em2d.TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1655 
1657  r"""do_matrix_to_image_flip(cv::Mat & m)"""
1658  return _IMP_em2d.do_matrix_to_image_flip(m)
1659 
1661  r"""get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1662  return _IMP_em2d.get_autocorrelation2d_no_preprocessing(M, corr)
1663 
1664 def get_autocorrelation2d(*args):
1665  r"""
1666  get_autocorrelation2d(Image im1, Image im2)
1667  get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1668  """
1669  return _IMP_em2d.get_autocorrelation2d(*args)
1670 
1671 def get_correlation2d(*args):
1672  r"""
1673  get_correlation2d(Image im1, Image im2, Image corr)
1674  get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1675  """
1676  return _IMP_em2d.get_correlation2d(*args)
1677 
1678 def get_correlation2d_no_preprocessing(M1, M2, corr):
1679  r"""get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1680  return _IMP_em2d.get_correlation2d_no_preprocessing(M1, M2, corr)
1681 
1682 def get_fft_using_optimal_size(m, M):
1683  r"""get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1684  return _IMP_em2d.get_fft_using_optimal_size(m, M)
1685 
1686 def get_spectrum(m, real, imag):
1687  r"""get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1688  return _IMP_em2d.get_spectrum(m, real, imag)
1689 
1690 def get_rotation_error(rr1, rr2):
1691  r"""get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1692  return _IMP_em2d.get_rotation_error(rr1, rr2)
1693 
1694 def get_shift_error(rr1, rr2):
1695  r"""get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1696  return _IMP_em2d.get_shift_error(rr1, rr2)
1697 
1698 def get_average_rotation_error(correct_RRs, computed_RRs):
1699  r"""get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1700  return _IMP_em2d.get_average_rotation_error(correct_RRs, computed_RRs)
1701 
1702 def get_average_shift_error(correct_RRs, computed_RRs):
1703  r"""get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1704  return _IMP_em2d.get_average_shift_error(correct_RRs, computed_RRs)
1705 
1707  r"""
1708  get_cross_correlation_coefficient(Image im1, Image im2) -> double
1709  get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1710  """
1711  return _IMP_em2d.get_cross_correlation_coefficient(*args)
1712 
1713 def get_global_score(RRs):
1714  r"""get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1715  return _IMP_em2d.get_global_score(RRs)
1716 class ScoreFunction(IMP.Object):
1717  r"""Proxy of C++ IMP::em2d::ScoreFunction class."""
1718 
1719  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1720 
1721  def __init__(self, *args, **kwargs):
1722  raise AttributeError("No constructor defined - class is abstract")
1723 
1724  def get_score(self, image, projection):
1725  r"""get_score(ScoreFunction self, Image image, Image projection) -> double"""
1726  return _IMP_em2d.ScoreFunction_get_score(self, image, projection)
1727 
1728  def set_variance_image(self, var):
1729  r"""set_variance_image(ScoreFunction self, Image var)"""
1730  return _IMP_em2d.ScoreFunction_set_variance_image(self, var)
1731 
1732  def get_version_info(self):
1733  r"""get_version_info(ScoreFunction self) -> VersionInfo"""
1734  return _IMP_em2d.ScoreFunction_get_version_info(self)
1735  __swig_destroy__ = _IMP_em2d.delete_ScoreFunction
1736 
1737  def __str__(self):
1738  r"""__str__(ScoreFunction self) -> std::string"""
1739  return _IMP_em2d.ScoreFunction___str__(self)
1740 
1741  def __repr__(self):
1742  r"""__repr__(ScoreFunction self) -> std::string"""
1743  return _IMP_em2d.ScoreFunction___repr__(self)
1744 
1745  @staticmethod
1746  def get_from(o):
1747  return _object_cast_to_ScoreFunction(o)
1748 
1749 
1750 # Register ScoreFunction in _IMP_em2d:
1751 _IMP_em2d.ScoreFunction_swigregister(ScoreFunction)
1752 class ChiSquaredScore(ScoreFunction):
1753  r"""Proxy of C++ IMP::em2d::ChiSquaredScore class."""
1754 
1755  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1756 
1757  def __init__(self):
1758  r"""__init__(ChiSquaredScore self) -> ChiSquaredScore"""
1759  _IMP_em2d.ChiSquaredScore_swiginit(self, _IMP_em2d.new_ChiSquaredScore())
1760 
1761  def __str__(self):
1762  r"""__str__(ChiSquaredScore self) -> std::string"""
1763  return _IMP_em2d.ChiSquaredScore___str__(self)
1764 
1765  def __repr__(self):
1766  r"""__repr__(ChiSquaredScore self) -> std::string"""
1767  return _IMP_em2d.ChiSquaredScore___repr__(self)
1768 
1769  @staticmethod
1770  def get_from(o):
1771  return _object_cast_to_ChiSquaredScore(o)
1772 
1773  __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1774 
1775 # Register ChiSquaredScore in _IMP_em2d:
1776 _IMP_em2d.ChiSquaredScore_swigregister(ChiSquaredScore)
1777 class EM2DScore(ScoreFunction):
1778  r"""Proxy of C++ IMP::em2d::EM2DScore class."""
1779 
1780  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1781 
1782  def __init__(self):
1783  r"""__init__(EM2DScore self) -> EM2DScore"""
1784  _IMP_em2d.EM2DScore_swiginit(self, _IMP_em2d.new_EM2DScore())
1785 
1786  def __str__(self):
1787  r"""__str__(EM2DScore self) -> std::string"""
1788  return _IMP_em2d.EM2DScore___str__(self)
1789 
1790  def __repr__(self):
1791  r"""__repr__(EM2DScore self) -> std::string"""
1792  return _IMP_em2d.EM2DScore___repr__(self)
1793 
1794  @staticmethod
1795  def get_from(o):
1796  return _object_cast_to_EM2DScore(o)
1797 
1798  __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1799 
1800 # Register EM2DScore in _IMP_em2d:
1801 _IMP_em2d.EM2DScore_swigregister(EM2DScore)
1802 class MeanAbsoluteDifference(ScoreFunction):
1803  r"""Proxy of C++ IMP::em2d::MeanAbsoluteDifference class."""
1804 
1805  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1806 
1807  def __init__(self):
1808  r"""__init__(MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1809  _IMP_em2d.MeanAbsoluteDifference_swiginit(self, _IMP_em2d.new_MeanAbsoluteDifference())
1810 
1811  def __str__(self):
1812  r"""__str__(MeanAbsoluteDifference self) -> std::string"""
1813  return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1814 
1815  def __repr__(self):
1816  r"""__repr__(MeanAbsoluteDifference self) -> std::string"""
1817  return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1818 
1819  @staticmethod
1820  def get_from(o):
1821  return _object_cast_to_MeanAbsoluteDifference(o)
1822 
1823  __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1824 
1825 # Register MeanAbsoluteDifference in _IMP_em2d:
1826 _IMP_em2d.MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1827 
1828 def read_selection_file(fn):
1829  r"""read_selection_file(IMP::String fn) -> IMP::Strings"""
1830  return _IMP_em2d.read_selection_file(fn)
1831 
1832 def create_filenames(number, basic_name, extension):
1833  r"""create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1834  return _IMP_em2d.create_filenames(number, basic_name, extension)
1835 class ProjectionParameters(IMP.Decorator):
1836  r"""Proxy of C++ IMP::em2d::ProjectionParameters class."""
1837 
1838  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1839 
1840  def __init__(self, *args):
1841  r"""
1842  __init__(ProjectionParameters self) -> ProjectionParameters
1843  __init__(ProjectionParameters self, Model m, ParticleIndex id) -> ProjectionParameters
1844  __init__(ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1845  """
1846  _IMP_em2d.ProjectionParameters_swiginit(self, _IMP_em2d.new_ProjectionParameters(*args))
1847 
1848  def show(self, *args):
1849  r"""show(ProjectionParameters self, _ostream out=std::cout)"""
1850  return _IMP_em2d.ProjectionParameters_show(self, *args)
1851 
1852  @staticmethod
1853  def setup_particle(*args):
1854  r"""
1855  setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
1856  setup_particle(_ParticleAdaptor pa) -> ProjectionParameters
1857  """
1858  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1859  __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1860 
1861  @staticmethod
1862  def get_keys():
1863  r"""get_keys() -> IMP::FloatKeys const &"""
1864  return _IMP_em2d.ProjectionParameters_get_keys()
1865 
1866  def set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values):
1867  r"""set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1868  return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values)
1869 
1870  @staticmethod
1871  def get_is_setup(*args):
1872  r"""
1873  get_is_setup(_ParticleAdaptor p) -> bool
1874  get_is_setup(Model m, ParticleIndex pi) -> bool
1875  """
1876  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1877 
1878  def get_parameters_optimized(self):
1879  r"""get_parameters_optimized(ProjectionParameters self) -> bool"""
1880  return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1881 
1882  def get_translation(self):
1883  r"""get_translation(ProjectionParameters self) -> Vector3D"""
1884  return _IMP_em2d.ProjectionParameters_get_translation(self)
1885 
1886  def set_translation(self, v):
1887  r"""set_translation(ProjectionParameters self, Vector3D v)"""
1888  return _IMP_em2d.ProjectionParameters_set_translation(self, v)
1889 
1890  def get_rotation(self):
1891  r"""get_rotation(ProjectionParameters self) -> Rotation3D"""
1892  return _IMP_em2d.ProjectionParameters_get_rotation(self)
1893 
1894  def set_rotation(self, R):
1895  r"""set_rotation(ProjectionParameters self, Rotation3D R)"""
1896  return _IMP_em2d.ProjectionParameters_set_rotation(self, R)
1897 
1898  def set_parameters_optimized(self, tf):
1899  r"""set_parameters_optimized(ProjectionParameters self, bool tf)"""
1900  return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, tf)
1901 
1902  def get_quaternion_1(self):
1903  r"""get_quaternion_1(ProjectionParameters self) -> double"""
1904  return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1905 
1906  def set_quaternion_1(self, t):
1907  r"""set_quaternion_1(ProjectionParameters self, double t)"""
1908  return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, t)
1909 
1910  def get_quaternion_2(self):
1911  r"""get_quaternion_2(ProjectionParameters self) -> double"""
1912  return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1913 
1914  def set_quaternion_2(self, t):
1915  r"""set_quaternion_2(ProjectionParameters self, double t)"""
1916  return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, t)
1917 
1918  def get_quaternion_3(self):
1919  r"""get_quaternion_3(ProjectionParameters self) -> double"""
1920  return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1921 
1922  def set_quaternion_3(self, t):
1923  r"""set_quaternion_3(ProjectionParameters self, double t)"""
1924  return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, t)
1925 
1926  def get_quaternion_4(self):
1927  r"""get_quaternion_4(ProjectionParameters self) -> double"""
1928  return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1929 
1930  def set_quaternion_4(self, t):
1931  r"""set_quaternion_4(ProjectionParameters self, double t)"""
1932  return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, t)
1933 
1934  def get_translation_x(self):
1935  r"""get_translation_x(ProjectionParameters self) -> double"""
1936  return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1937 
1938  def set_translation_x(self, t):
1939  r"""set_translation_x(ProjectionParameters self, double t)"""
1940  return _IMP_em2d.ProjectionParameters_set_translation_x(self, t)
1941 
1942  def get_translation_y(self):
1943  r"""get_translation_y(ProjectionParameters self) -> double"""
1944  return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1945 
1946  def set_translation_y(self, t):
1947  r"""set_translation_y(ProjectionParameters self, double t)"""
1948  return _IMP_em2d.ProjectionParameters_set_translation_y(self, t)
1949 
1950  def add_attribute(self, *args):
1951  r"""
1952  add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1953  add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1954  add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1955  add_attribute(ProjectionParameters self, FloatsKey a0, IMP::Floats a1)
1956  add_attribute(ProjectionParameters self, IntsKey a0, IMP::Ints a1)
1957  add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1958  add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1959  add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1960  add_attribute(ProjectionParameters self, SparseFloatKey a0, IMP::Float a1)
1961  add_attribute(ProjectionParameters self, SparseIntKey a0, IMP::Int a1)
1962  add_attribute(ProjectionParameters self, SparseStringKey a0, IMP::String a1)
1963  add_attribute(ProjectionParameters self, SparseParticleIndexKey a0, ParticleIndex a1)
1964  """
1965  return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1966 
1967  def get_value(self, *args):
1968  r"""
1969  get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1970  get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1971  get_value(ProjectionParameters self, FloatsKey a0) -> IMP::Floats
1972  get_value(ProjectionParameters self, IntsKey a0) -> IMP::Ints
1973  get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1974  get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1975  get_value(ProjectionParameters self, ObjectKey a0) -> Object
1976  get_value(ProjectionParameters self, SparseFloatKey a0) -> IMP::Float
1977  get_value(ProjectionParameters self, SparseIntKey a0) -> IMP::Int
1978  get_value(ProjectionParameters self, SparseStringKey a0) -> IMP::String
1979  get_value(ProjectionParameters self, SparseParticleIndexKey a0) -> ParticleIndex
1980  """
1981  return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1982 
1983  def set_value(self, *args):
1984  r"""
1985  set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1986  set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1987  set_value(ProjectionParameters self, FloatsKey a0, IMP::Floats a1)
1988  set_value(ProjectionParameters self, IntsKey a0, IMP::Ints a1)
1989  set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1990  set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1991  set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1992  set_value(ProjectionParameters self, SparseFloatKey a0, IMP::Float a1)
1993  set_value(ProjectionParameters self, SparseIntKey a0, IMP::Int a1)
1994  set_value(ProjectionParameters self, SparseStringKey a0, IMP::String a1)
1995  set_value(ProjectionParameters self, SparseParticleIndexKey a0, ParticleIndex a1)
1996  """
1997  return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1998 
1999  def remove_attribute(self, *args):
2000  r"""
2001  remove_attribute(ProjectionParameters self, FloatKey a0)
2002  remove_attribute(ProjectionParameters self, IntKey a0)
2003  remove_attribute(ProjectionParameters self, FloatsKey a0)
2004  remove_attribute(ProjectionParameters self, IntsKey a0)
2005  remove_attribute(ProjectionParameters self, StringKey a0)
2006  remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
2007  remove_attribute(ProjectionParameters self, ObjectKey a0)
2008  remove_attribute(ProjectionParameters self, SparseFloatKey a0)
2009  remove_attribute(ProjectionParameters self, SparseIntKey a0)
2010  remove_attribute(ProjectionParameters self, SparseStringKey a0)
2011  remove_attribute(ProjectionParameters self, SparseParticleIndexKey a0)
2012  """
2013  return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
2014 
2015  def has_attribute(self, *args):
2016  r"""
2017  has_attribute(ProjectionParameters self, FloatKey a0) -> bool
2018  has_attribute(ProjectionParameters self, IntKey a0) -> bool
2019  has_attribute(ProjectionParameters self, FloatsKey a0) -> bool
2020  has_attribute(ProjectionParameters self, IntsKey a0) -> bool
2021  has_attribute(ProjectionParameters self, StringKey a0) -> bool
2022  has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
2023  has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
2024  has_attribute(ProjectionParameters self, SparseFloatKey a0) -> bool
2025  has_attribute(ProjectionParameters self, SparseIntKey a0) -> bool
2026  has_attribute(ProjectionParameters self, SparseStringKey a0) -> bool
2027  has_attribute(ProjectionParameters self, SparseParticleIndexKey a0) -> bool
2028  """
2029  return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
2030 
2031  def get_derivative(self, a0):
2032  r"""get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
2033  return _IMP_em2d.ProjectionParameters_get_derivative(self, a0)
2034 
2035  def get_name(self):
2036  r"""get_name(ProjectionParameters self) -> std::string"""
2037  return _IMP_em2d.ProjectionParameters_get_name(self)
2038 
2039  def clear_caches(self):
2040  r"""clear_caches(ProjectionParameters self)"""
2041  return _IMP_em2d.ProjectionParameters_clear_caches(self)
2042 
2043  def set_name(self, a0):
2044  r"""set_name(ProjectionParameters self, std::string a0)"""
2045  return _IMP_em2d.ProjectionParameters_set_name(self, a0)
2046 
2047  def set_check_level(self, a0):
2048  r"""set_check_level(ProjectionParameters self, IMP::CheckLevel a0)"""
2049  return _IMP_em2d.ProjectionParameters_set_check_level(self, a0)
2050 
2051  def add_to_derivative(self, a0, a1, a2):
2052  r"""add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2053  return _IMP_em2d.ProjectionParameters_add_to_derivative(self, a0, a1, a2)
2054 
2055  def set_is_optimized(self, a0, a1):
2056  r"""set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
2057  return _IMP_em2d.ProjectionParameters_set_is_optimized(self, a0, a1)
2058 
2059  def get_is_optimized(self, a0):
2060  r"""get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
2061  return _IMP_em2d.ProjectionParameters_get_is_optimized(self, a0)
2062 
2063  def get_check_level(self):
2064  r"""get_check_level(ProjectionParameters self) -> IMP::CheckLevel"""
2065  return _IMP_em2d.ProjectionParameters_get_check_level(self)
2066 
2067  def __eq__(self, *args):
2068  r"""
2069  __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
2070  __eq__(ProjectionParameters self, Particle d) -> bool
2071  """
2072  return _IMP_em2d.ProjectionParameters___eq__(self, *args)
2073 
2074  def __ne__(self, *args):
2075  r"""
2076  __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
2077  __ne__(ProjectionParameters self, Particle d) -> bool
2078  """
2079  return _IMP_em2d.ProjectionParameters___ne__(self, *args)
2080 
2081  def __le__(self, *args):
2082  r"""
2083  __le__(ProjectionParameters self, ProjectionParameters o) -> bool
2084  __le__(ProjectionParameters self, Particle d) -> bool
2085  """
2086  return _IMP_em2d.ProjectionParameters___le__(self, *args)
2087 
2088  def __lt__(self, *args):
2089  r"""
2090  __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
2091  __lt__(ProjectionParameters self, Particle d) -> bool
2092  """
2093  return _IMP_em2d.ProjectionParameters___lt__(self, *args)
2094 
2095  def __ge__(self, *args):
2096  r"""
2097  __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
2098  __ge__(ProjectionParameters self, Particle d) -> bool
2099  """
2100  return _IMP_em2d.ProjectionParameters___ge__(self, *args)
2101 
2102  def __gt__(self, *args):
2103  r"""
2104  __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
2105  __gt__(ProjectionParameters self, Particle d) -> bool
2106  """
2107  return _IMP_em2d.ProjectionParameters___gt__(self, *args)
2108 
2109  def __hash__(self):
2110  r"""__hash__(ProjectionParameters self) -> std::size_t"""
2111  return _IMP_em2d.ProjectionParameters___hash__(self)
2112 
2113  def __str__(self):
2114  r"""__str__(ProjectionParameters self) -> std::string"""
2115  return _IMP_em2d.ProjectionParameters___str__(self)
2116 
2117  def __repr__(self):
2118  r"""__repr__(ProjectionParameters self) -> std::string"""
2119  return _IMP_em2d.ProjectionParameters___repr__(self)
2120 
2121  def _get_as_binary(self):
2122  r"""_get_as_binary(ProjectionParameters self) -> PyObject *"""
2123  return _IMP_em2d.ProjectionParameters__get_as_binary(self)
2124 
2125  def _set_from_binary(self, p):
2126  r"""_set_from_binary(ProjectionParameters self, PyObject * p)"""
2127  return _IMP_em2d.ProjectionParameters__set_from_binary(self, p)
2128 
2129  def __getstate__(self):
2130  p = self._get_as_binary()
2131  if len(self.__dict__) > 1:
2132  d = self.__dict__.copy()
2133  del d['this']
2134  p = (d, p)
2135  return p
2136 
2137  def __setstate__(self, p):
2138  if not hasattr(self, 'this'):
2139  self.__init__()
2140  if isinstance(p, tuple):
2141  d, p = p
2142  self.__dict__.update(d)
2143  return self._set_from_binary(p)
2144 
2145 
2146 # Register ProjectionParameters in _IMP_em2d:
2147 _IMP_em2d.ProjectionParameters_swigregister(ProjectionParameters)
2148 
2149 def __lshift__(out, n):
2150  r"""__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
2151  return _IMP_em2d.__lshift__(out, n)
2152 class ProjectionParametersScoreState(IMP.ScoreState):
2153  r"""Proxy of C++ IMP::em2d::ProjectionParametersScoreState class."""
2154 
2155  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2156 
2157  def __init__(self, p):
2158  r"""__init__(ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
2159  _IMP_em2d.ProjectionParametersScoreState_swiginit(self, _IMP_em2d.new_ProjectionParametersScoreState(p))
2160 
2161  def do_before_evaluate(self):
2162  r"""do_before_evaluate(ProjectionParametersScoreState self)"""
2163  return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
2164 
2165  def do_after_evaluate(self, da):
2166  r"""do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
2167  return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, da)
2168 
2169  def do_get_inputs(self):
2170  r"""do_get_inputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2171  return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
2172 
2173  def do_get_outputs(self):
2174  r"""do_get_outputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2175  return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
2176 
2177  def get_version_info(self):
2178  r"""get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
2179  return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
2180  __swig_destroy__ = _IMP_em2d.delete_ProjectionParametersScoreState
2181 
2182  def __str__(self):
2183  r"""__str__(ProjectionParametersScoreState self) -> std::string"""
2184  return _IMP_em2d.ProjectionParametersScoreState___str__(self)
2185 
2186  def __repr__(self):
2187  r"""__repr__(ProjectionParametersScoreState self) -> std::string"""
2188  return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
2189 
2190  @staticmethod
2191  def get_from(o):
2192  return _object_cast_to_ProjectionParametersScoreState(o)
2193 
2194 
2195 # Register ProjectionParametersScoreState in _IMP_em2d:
2196 _IMP_em2d.ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
2197 class ProjectionMask(object):
2198  r"""Proxy of C++ IMP::em2d::ProjectionMask class."""
2199 
2200  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2201 
2202  def __init__(self):
2203  r"""__init__(ProjectionMask self) -> ProjectionMask"""
2204  _IMP_em2d.ProjectionMask_swiginit(self, _IMP_em2d.new_ProjectionMask())
2205 
2206  def apply(self, m, v):
2207  r"""apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
2208  return _IMP_em2d.ProjectionMask_apply(self, m, v)
2209 
2210  def show(self, *args):
2211  r"""show(ProjectionMask self, _ostream out=std::cout)"""
2212  return _IMP_em2d.ProjectionMask_show(self, *args)
2213  __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
2214 
2215  def __str__(self):
2216  r"""__str__(ProjectionMask self) -> std::string"""
2217  return _IMP_em2d.ProjectionMask___str__(self)
2218 
2219  def __repr__(self):
2220  r"""__repr__(ProjectionMask self) -> std::string"""
2221  return _IMP_em2d.ProjectionMask___repr__(self)
2222 
2223  def _get_as_binary(self):
2224  r"""_get_as_binary(ProjectionMask self) -> PyObject *"""
2225  return _IMP_em2d.ProjectionMask__get_as_binary(self)
2226 
2227  def _set_from_binary(self, p):
2228  r"""_set_from_binary(ProjectionMask self, PyObject * p)"""
2229  return _IMP_em2d.ProjectionMask__set_from_binary(self, p)
2230 
2231  def __getstate__(self):
2232  p = self._get_as_binary()
2233  if len(self.__dict__) > 1:
2234  d = self.__dict__.copy()
2235  del d['this']
2236  p = (d, p)
2237  return p
2238 
2239  def __setstate__(self, p):
2240  if not hasattr(self, 'this'):
2241  self.__init__()
2242  if isinstance(p, tuple):
2243  d, p = p
2244  self.__dict__.update(d)
2245  return self._set_from_binary(p)
2246 
2247 
2248 # Register ProjectionMask in _IMP_em2d:
2249 _IMP_em2d.ProjectionMask_swigregister(ProjectionMask)
2250 
2251 def do_place(mask, m, v):
2252  r"""do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
2253  return _IMP_em2d.do_place(mask, m, v)
2254 class MasksManager(object):
2255  r"""Proxy of C++ IMP::em2d::MasksManager class."""
2256 
2257  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2258 
2259  def __init__(self, *args):
2260  r"""
2261  __init__(MasksManager self) -> MasksManager
2262  __init__(MasksManager self, double resolution, double pixelsize) -> MasksManager
2263  """
2264  _IMP_em2d.MasksManager_swiginit(self, _IMP_em2d.new_MasksManager(*args))
2265 
2266  def setup_kernel(self, resolution, pixelsize):
2267  r"""setup_kernel(MasksManager self, double resolution, double pixelsize)"""
2268  return _IMP_em2d.MasksManager_setup_kernel(self, resolution, pixelsize)
2269 
2270  def create_masks(self, ps):
2271  r"""create_masks(MasksManager self, IMP::ParticlesTemp const & ps)"""
2272  return _IMP_em2d.MasksManager_create_masks(self, ps)
2273 
2274  def create_mask(self, mass):
2275  r"""create_mask(MasksManager self, double mass)"""
2276  return _IMP_em2d.MasksManager_create_mask(self, mass)
2277 
2278  def find_mask(self, mass):
2279  r"""find_mask(MasksManager self, double mass) -> IMP::em2d::ProjectionMaskPtr"""
2280  return _IMP_em2d.MasksManager_find_mask(self, mass)
2281 
2282  def show(self, *args):
2283  r"""show(MasksManager self, _ostream out=std::cout)"""
2284  return _IMP_em2d.MasksManager_show(self, *args)
2285 
2286  def get_number_of_masks(self):
2287  r"""get_number_of_masks(MasksManager self) -> unsigned int"""
2288  return _IMP_em2d.MasksManager_get_number_of_masks(self)
2289  __swig_destroy__ = _IMP_em2d.delete_MasksManager
2290 
2291  def __str__(self):
2292  r"""__str__(MasksManager self) -> std::string"""
2293  return _IMP_em2d.MasksManager___str__(self)
2294 
2295  def __repr__(self):
2296  r"""__repr__(MasksManager self) -> std::string"""
2297  return _IMP_em2d.MasksManager___repr__(self)
2298 
2299  def _get_as_binary(self):
2300  r"""_get_as_binary(MasksManager self) -> PyObject *"""
2301  return _IMP_em2d.MasksManager__get_as_binary(self)
2302 
2303  def _set_from_binary(self, p):
2304  r"""_set_from_binary(MasksManager self, PyObject * p)"""
2305  return _IMP_em2d.MasksManager__set_from_binary(self, p)
2306 
2307  def __getstate__(self):
2308  p = self._get_as_binary()
2309  if len(self.__dict__) > 1:
2310  d = self.__dict__.copy()
2311  del d['this']
2312  p = (d, p)
2313  return p
2314 
2315  def __setstate__(self, p):
2316  if not hasattr(self, 'this'):
2317  self.__init__()
2318  if isinstance(p, tuple):
2319  d, p = p
2320  self.__dict__.update(d)
2321  return self._set_from_binary(p)
2322 
2323 
2324 # Register MasksManager in _IMP_em2d:
2325 _IMP_em2d.MasksManager_swigregister(MasksManager)
2326 class ProjectingParameters(object):
2327  r"""Proxy of C++ IMP::em2d::ProjectingParameters class."""
2328 
2329  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2330  pixel_size = property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set, doc=r"""pixel_size : double""")
2331  resolution = property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set, doc=r"""resolution : double""")
2332 
2333  def __init__(self, *args):
2334  r"""
2335  __init__(ProjectingParameters self) -> ProjectingParameters
2336  __init__(ProjectingParameters self, double ps, double res) -> ProjectingParameters
2337  """
2338  _IMP_em2d.ProjectingParameters_swiginit(self, _IMP_em2d.new_ProjectingParameters(*args))
2339 
2340  def show(self, *args):
2341  r"""show(ProjectingParameters self, _ostream out=std::cout)"""
2342  return _IMP_em2d.ProjectingParameters_show(self, *args)
2343 
2344  def __str__(self):
2345  r"""__str__(ProjectingParameters self) -> std::string"""
2346  return _IMP_em2d.ProjectingParameters___str__(self)
2347 
2348  def __repr__(self):
2349  r"""__repr__(ProjectingParameters self) -> std::string"""
2350  return _IMP_em2d.ProjectingParameters___repr__(self)
2351 
2352  def _get_as_binary(self):
2353  r"""_get_as_binary(ProjectingParameters self) -> PyObject *"""
2354  return _IMP_em2d.ProjectingParameters__get_as_binary(self)
2355 
2356  def _set_from_binary(self, p):
2357  r"""_set_from_binary(ProjectingParameters self, PyObject * p)"""
2358  return _IMP_em2d.ProjectingParameters__set_from_binary(self, p)
2359 
2360  def __getstate__(self):
2361  p = self._get_as_binary()
2362  if len(self.__dict__) > 1:
2363  d = self.__dict__.copy()
2364  del d['this']
2365  p = (d, p)
2366  return p
2367 
2368  def __setstate__(self, p):
2369  if not hasattr(self, 'this'):
2370  self.__init__()
2371  if isinstance(p, tuple):
2372  d, p = p
2373  self.__dict__.update(d)
2374  return self._set_from_binary(p)
2375 
2376  __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2377 
2378 # Register ProjectingParameters in _IMP_em2d:
2379 _IMP_em2d.ProjectingParameters_swigregister(ProjectingParameters)
2380 class ProjectingOptions(ProjectingParameters):
2381  r"""Proxy of C++ IMP::em2d::ProjectingOptions class."""
2382 
2383  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2384  save_images = property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set, doc=r"""save_images : bool""")
2385  normalize = property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set, doc=r"""normalize : bool""")
2386  clear_matrix_before_projecting = property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set, doc=r"""clear_matrix_before_projecting : bool""")
2387 
2388  def __init__(self, *args):
2389  r"""
2390  __init__(ProjectingOptions self) -> ProjectingOptions
2391  __init__(ProjectingOptions self, double ps, double res) -> ProjectingOptions
2392  __init__(ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2393  """
2394  _IMP_em2d.ProjectingOptions_swiginit(self, _IMP_em2d.new_ProjectingOptions(*args))
2395 
2396  def show(self, *args):
2397  r"""show(ProjectingOptions self, _ostream out=std::cout)"""
2398  return _IMP_em2d.ProjectingOptions_show(self, *args)
2399 
2400  def __str__(self):
2401  r"""__str__(ProjectingOptions self) -> std::string"""
2402  return _IMP_em2d.ProjectingOptions___str__(self)
2403 
2404  def __repr__(self):
2405  r"""__repr__(ProjectingOptions self) -> std::string"""
2406  return _IMP_em2d.ProjectingOptions___repr__(self)
2407  __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2408 
2409 # Register ProjectingOptions in _IMP_em2d:
2410 _IMP_em2d.ProjectingOptions_swigregister(ProjectingOptions)
2411 
2412 def get_projections(*args):
2413  r"""
2414  get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options, IMP::Strings names=IMP::Strings()) -> IMP::em2d::Images
2415  get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options, IMP::Strings names=IMP::Strings()) -> IMP::em2d::Images
2416  """
2417  return _IMP_em2d.get_projections(*args)
2418 
2419 def get_projection(*args):
2420  r"""get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks=IMP::em2d::MasksManagerPtr(), IMP::String name="")"""
2421  return _IMP_em2d.get_projection(*args)
2422 
2423 def do_project_particles(ps, m2, R, translation, options, masks):
2424  r"""do_project_particles(IMP::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)"""
2425  return _IMP_em2d.do_project_particles(ps, m2, R, translation, options, masks)
2426 
2427 def create_evenly_distributed_projections(ps, n, options):
2428  r"""create_evenly_distributed_projections(IMP::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2429  return _IMP_em2d.create_evenly_distributed_projections(ps, n, options)
2430 
2431 def do_project_vectors(*args):
2432  r"""
2433  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2434  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2435  """
2436  return _IMP_em2d.do_project_vectors(*args)
2437 
2438 def get_enclosing_image_size(ps, pixel_size, slack):
2439  r"""get_enclosing_image_size(IMP::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2440  return _IMP_em2d.get_enclosing_image_size(ps, pixel_size, slack)
2441 
2442 def get_complete_alignment(input, m_to_align, apply=False):
2443  r"""get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D"""
2444  return _IMP_em2d.get_complete_alignment(input, m_to_align, apply)
2445 
2446 def get_rotational_alignment(input, m_to_align, apply=False):
2447  r"""get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D"""
2448  return _IMP_em2d.get_rotational_alignment(input, m_to_align, apply)
2449 
2450 def get_translational_alignment(input, m_to_align, apply=False):
2451  r"""get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D"""
2452  return _IMP_em2d.get_translational_alignment(input, m_to_align, apply)
2453 
2454 def get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply=False):
2455  r"""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"""
2456  return _IMP_em2d.get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply)
2457 
2458 def get_rotational_alignment_no_preprocessing(POLAR1, POLAR2):
2459  r"""get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2460  return _IMP_em2d.get_rotational_alignment_no_preprocessing(POLAR1, POLAR2)
2461 
2463  r"""get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2464  return _IMP_em2d.get_translational_alignment_no_preprocessing(M1, M2)
2465 
2466 def get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2):
2467  r"""get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2468  return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2)
2469 
2470 def write_vectors_as_pdb(*args):
2471  r"""
2472  write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2473  write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2474  """
2475  return _IMP_em2d.write_vectors_as_pdb(*args)
2476 class Em2DRestraintParameters(ProjectingParameters):
2477  r"""Proxy of C++ IMP::em2d::Em2DRestraintParameters class."""
2478 
2479  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2480  n_projections = property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set, doc=r"""n_projections : unsigned int""")
2481  coarse_registration_method = property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set, doc=r"""coarse_registration_method : unsigned int""")
2482  save_match_images = property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set, doc=r"""save_match_images : bool""")
2483  optimization_steps = property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set, doc=r"""optimization_steps : unsigned int""")
2484  simplex_initial_length = property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set, doc=r"""simplex_initial_length : double""")
2485  simplex_minimum_size = property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set, doc=r"""simplex_minimum_size : double""")
2486 
2487  def __init__(self, *args):
2488  r"""
2489  __init__(Em2DRestraintParameters self) -> Em2DRestraintParameters
2490  __init__(Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2491  """
2492  _IMP_em2d.Em2DRestraintParameters_swiginit(self, _IMP_em2d.new_Em2DRestraintParameters(*args))
2493 
2494  def show(self, *args):
2495  r"""show(Em2DRestraintParameters self, _ostream out=std::cout)"""
2496  return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2497 
2498  def __str__(self):
2499  r"""__str__(Em2DRestraintParameters self) -> std::string"""
2500  return _IMP_em2d.Em2DRestraintParameters___str__(self)
2501 
2502  def __repr__(self):
2503  r"""__repr__(Em2DRestraintParameters self) -> std::string"""
2504  return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2505 
2506  def _get_as_binary(self):
2507  r"""_get_as_binary(Em2DRestraintParameters self) -> PyObject *"""
2508  return _IMP_em2d.Em2DRestraintParameters__get_as_binary(self)
2509 
2510  def _set_from_binary(self, p):
2511  r"""_set_from_binary(Em2DRestraintParameters self, PyObject * p)"""
2512  return _IMP_em2d.Em2DRestraintParameters__set_from_binary(self, p)
2513 
2514  def __getstate__(self):
2515  p = self._get_as_binary()
2516  if len(self.__dict__) > 1:
2517  d = self.__dict__.copy()
2518  del d['this']
2519  p = (d, p)
2520  return p
2521 
2522  def __setstate__(self, p):
2523  if not hasattr(self, 'this'):
2524  self.__init__()
2525  if isinstance(p, tuple):
2526  d, p = p
2527  self.__dict__.update(d)
2528  return self._set_from_binary(p)
2529 
2530  __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2531 
2532 # Register Em2DRestraintParameters in _IMP_em2d:
2533 _IMP_em2d.Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2534 cvar = _IMP_em2d.cvar
2535 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2536 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2537 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2538 
2539 class ProjectionFinder(IMP.Object):
2540  r"""Proxy of C++ IMP::em2d::ProjectionFinder class."""
2541 
2542  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2543 
2544  def __init__(self):
2545  r"""__init__(ProjectionFinder self) -> ProjectionFinder"""
2546  _IMP_em2d.ProjectionFinder_swiginit(self, _IMP_em2d.new_ProjectionFinder())
2547 
2548  def setup(self, score_function, params):
2549  r"""setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2550  return _IMP_em2d.ProjectionFinder_setup(self, score_function, params)
2551 
2552  def set_subjects(self, subjects):
2553  r"""set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2554  return _IMP_em2d.ProjectionFinder_set_subjects(self, subjects)
2555 
2556  def set_projections(self, projections):
2557  r"""set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2558  return _IMP_em2d.ProjectionFinder_set_projections(self, projections)
2559 
2560  def set_variance_images(self, variances):
2561  r"""set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2562  return _IMP_em2d.ProjectionFinder_set_variance_images(self, variances)
2563 
2564  def set_model_particles(self, ps):
2565  r"""set_model_particles(ProjectionFinder self, IMP::ParticlesTemp const & ps)"""
2566  return _IMP_em2d.ProjectionFinder_set_model_particles(self, ps)
2567 
2568  def set_save_match_images(self, x):
2569  r"""set_save_match_images(ProjectionFinder self, bool x)"""
2570  return _IMP_em2d.ProjectionFinder_set_save_match_images(self, x)
2571 
2572  def get_save_match_images(self):
2573  r"""get_save_match_images(ProjectionFinder self) -> bool"""
2574  return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2575 
2576  def set_fast_mode(self, n):
2577  r"""set_fast_mode(ProjectionFinder self, unsigned int n)"""
2578  return _IMP_em2d.ProjectionFinder_set_fast_mode(self, n)
2579 
2580  def get_registration_results(self):
2581  r"""get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2582  return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2583 
2584  def get_coarse_registration(self):
2585  r"""get_coarse_registration(ProjectionFinder self)"""
2586  return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2587 
2588  def get_complete_registration(self):
2589  r"""get_complete_registration(ProjectionFinder self)"""
2590  return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2591 
2592  def get_global_score(self):
2593  r"""get_global_score(ProjectionFinder self) -> double"""
2594  return _IMP_em2d.ProjectionFinder_get_global_score(self)
2595 
2596  def show(self, out):
2597  r"""show(ProjectionFinder self, _ostream out)"""
2598  return _IMP_em2d.ProjectionFinder_show(self, out)
2599 
2600  def get_preprocessing_time(self):
2601  r"""get_preprocessing_time(ProjectionFinder self) -> double"""
2602  return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2603 
2604  def get_coarse_registration_time(self):
2605  r"""get_coarse_registration_time(ProjectionFinder self) -> double"""
2606  return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2607 
2608  def get_fine_registration_time(self):
2609  r"""get_fine_registration_time(ProjectionFinder self) -> double"""
2610  return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2611 
2612  def get_number_of_subjects(self):
2613  r"""get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2614  return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2615 
2616  def set_number_of_class_averages_members(self, n_members):
2617  r"""set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2618  return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, n_members)
2619 
2620  def get_number_of_projections(self):
2621  r"""get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2622  return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2623 
2624  def get_version_info(self):
2625  r"""get_version_info(ProjectionFinder self) -> VersionInfo"""
2626  return _IMP_em2d.ProjectionFinder_get_version_info(self)
2627  __swig_destroy__ = _IMP_em2d.delete_ProjectionFinder
2628 
2629  def __str__(self):
2630  r"""__str__(ProjectionFinder self) -> std::string"""
2631  return _IMP_em2d.ProjectionFinder___str__(self)
2632 
2633  def __repr__(self):
2634  r"""__repr__(ProjectionFinder self) -> std::string"""
2635  return _IMP_em2d.ProjectionFinder___repr__(self)
2636 
2637  @staticmethod
2638  def get_from(o):
2639  return _object_cast_to_ProjectionFinder(o)
2640 
2641 
2642 # Register ProjectionFinder in _IMP_em2d:
2643 _IMP_em2d.ProjectionFinder_swigregister(ProjectionFinder)
2644 class Em2DRestraint(IMP.Restraint):
2645  r"""Proxy of C++ IMP::em2d::Em2DRestraint class."""
2646 
2647  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2648 
2649  def __init__(self, m):
2650  r"""__init__(Em2DRestraint self, Model m) -> Em2DRestraint"""
2651  _IMP_em2d.Em2DRestraint_swiginit(self, _IMP_em2d.new_Em2DRestraint(m))
2652 
2653  def setup(self, score_function, params):
2654  r"""setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2655  return _IMP_em2d.Em2DRestraint_setup(self, score_function, params)
2656 
2657  def set_particles(self, particles_container):
2658  r"""set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2659  return _IMP_em2d.Em2DRestraint_set_particles(self, particles_container)
2660 
2661  def set_images(self, em_images):
2662  r"""set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2663  return _IMP_em2d.Em2DRestraint_set_images(self, em_images)
2664 
2665  def set_variance_images(self, variance_images):
2666  r"""set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2667  return _IMP_em2d.Em2DRestraint_set_variance_images(self, variance_images)
2668 
2669  def set_fast_mode(self, n):
2670  r"""set_fast_mode(Em2DRestraint self, unsigned int n)"""
2671  return _IMP_em2d.Em2DRestraint_set_fast_mode(self, n)
2672 
2673  def set_coarse_registration_mode(self, opt):
2674  r"""set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2675  return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, opt)
2676 
2677  def get_registration_results(self):
2678  r"""get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2679  return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2680 
2681  def do_get_inputs(self):
2682  r"""do_get_inputs(Em2DRestraint self) -> IMP::ModelObjectsTemp"""
2683  return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2684 
2685  def get_version_info(self):
2686  r"""get_version_info(Em2DRestraint self) -> VersionInfo"""
2687  return _IMP_em2d.Em2DRestraint_get_version_info(self)
2688  __swig_destroy__ = _IMP_em2d.delete_Em2DRestraint
2689 
2690  def __str__(self):
2691  r"""__str__(Em2DRestraint self) -> std::string"""
2692  return _IMP_em2d.Em2DRestraint___str__(self)
2693 
2694  def __repr__(self):
2695  r"""__repr__(Em2DRestraint self) -> std::string"""
2696  return _IMP_em2d.Em2DRestraint___repr__(self)
2697 
2698  @staticmethod
2699  def get_from(o):
2700  return _object_cast_to_Em2DRestraint(o)
2701 
2702 
2703 # Register Em2DRestraint in _IMP_em2d:
2704 _IMP_em2d.Em2DRestraint_swigregister(Em2DRestraint)
2705 class ClusterSet(object):
2706  r"""Proxy of C++ IMP::em2d::ClusterSet class."""
2707 
2708  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2709 
2710  def __init__(self, *args):
2711  r"""
2712  __init__(ClusterSet self) -> ClusterSet
2713  __init__(ClusterSet self, unsigned int N) -> ClusterSet
2714  """
2715  _IMP_em2d.ClusterSet_swiginit(self, _IMP_em2d.new_ClusterSet(*args))
2716 
2717  def do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters):
2718  r"""do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2719  return _IMP_em2d.ClusterSet_do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters)
2720 
2721  def get_cluster_elements(self, id):
2722  r"""get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2723  return _IMP_em2d.ClusterSet_get_cluster_elements(self, id)
2724 
2725  def get_clusters_below_cutoff(self, cutoff):
2726  r"""get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2727  return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, cutoff)
2728 
2729  def get_cluster_formed_at_step(self, step):
2730  r"""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  def get_distance_at_step(self, step):
2734  r"""get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2735  return _IMP_em2d.ClusterSet_get_distance_at_step(self, step)
2736 
2737  def get_id_for_cluster_at_step(self, step):
2738  r"""get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2739  return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, step)
2740 
2741  def get_linkage_matrix(self):
2742  r"""get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2743  return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2744 
2745  def get_linkage_matrix_in_matlab_format(self):
2746  r"""get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2747  return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2748 
2749  def get_number_of_steps(self):
2750  r"""get_number_of_steps(ClusterSet self) -> unsigned int"""
2751  return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2752 
2753  def show(self, out):
2754  r"""show(ClusterSet self, _ostream out)"""
2755  return _IMP_em2d.ClusterSet_show(self, out)
2756 
2757  def __str__(self):
2758  r"""__str__(ClusterSet self) -> std::string"""
2759  return _IMP_em2d.ClusterSet___str__(self)
2760 
2761  def __repr__(self):
2762  r"""__repr__(ClusterSet self) -> std::string"""
2763  return _IMP_em2d.ClusterSet___repr__(self)
2764 
2765  def _get_as_binary(self):
2766  r"""_get_as_binary(ClusterSet self) -> PyObject *"""
2767  return _IMP_em2d.ClusterSet__get_as_binary(self)
2768 
2769  def _set_from_binary(self, p):
2770  r"""_set_from_binary(ClusterSet self, PyObject * p)"""
2771  return _IMP_em2d.ClusterSet__set_from_binary(self, p)
2772 
2773  def __getstate__(self):
2774  p = self._get_as_binary()
2775  if len(self.__dict__) > 1:
2776  d = self.__dict__.copy()
2777  del d['this']
2778  p = (d, p)
2779  return p
2780 
2781  def __setstate__(self, p):
2782  if not hasattr(self, 'this'):
2783  self.__init__()
2784  if isinstance(p, tuple):
2785  d, p = p
2786  self.__dict__.update(d)
2787  return self._set_from_binary(p)
2788 
2789  __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2790 
2791 # Register ClusterSet in _IMP_em2d:
2792 _IMP_em2d.ClusterSet_swigregister(ClusterSet)
2793 class SingleLinkage(object):
2794  r"""Proxy of C++ IMP::em2d::SingleLinkage class."""
2795 
2796  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2797 
2798  def __init__(self):
2799  r"""__init__(SingleLinkage self) -> SingleLinkage"""
2800  _IMP_em2d.SingleLinkage_swiginit(self, _IMP_em2d.new_SingleLinkage())
2801 
2802  def __call__(self, id1, id2, cluster_set, distances):
2803  r"""__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2804  return _IMP_em2d.SingleLinkage___call__(self, id1, id2, cluster_set, distances)
2805 
2806  def show(self, out):
2807  r"""show(SingleLinkage self, _ostream out)"""
2808  return _IMP_em2d.SingleLinkage_show(self, out)
2809 
2810  def __str__(self):
2811  r"""__str__(SingleLinkage self) -> std::string"""
2812  return _IMP_em2d.SingleLinkage___str__(self)
2813 
2814  def __repr__(self):
2815  r"""__repr__(SingleLinkage self) -> std::string"""
2816  return _IMP_em2d.SingleLinkage___repr__(self)
2817 
2818  def _get_as_binary(self):
2819  r"""_get_as_binary(SingleLinkage self) -> PyObject *"""
2820  return _IMP_em2d.SingleLinkage__get_as_binary(self)
2821 
2822  def _set_from_binary(self, p):
2823  r"""_set_from_binary(SingleLinkage self, PyObject * p)"""
2824  return _IMP_em2d.SingleLinkage__set_from_binary(self, p)
2825 
2826  def __getstate__(self):
2827  p = self._get_as_binary()
2828  if len(self.__dict__) > 1:
2829  d = self.__dict__.copy()
2830  del d['this']
2831  p = (d, p)
2832  return p
2833 
2834  def __setstate__(self, p):
2835  if not hasattr(self, 'this'):
2836  self.__init__()
2837  if isinstance(p, tuple):
2838  d, p = p
2839  self.__dict__.update(d)
2840  return self._set_from_binary(p)
2841 
2842  __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2843 
2844 # Register SingleLinkage in _IMP_em2d:
2845 _IMP_em2d.SingleLinkage_swigregister(SingleLinkage)
2846 class CompleteLinkage(object):
2847  r"""Proxy of C++ IMP::em2d::CompleteLinkage class."""
2848 
2849  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2850 
2851  def __init__(self):
2852  r"""__init__(CompleteLinkage self) -> CompleteLinkage"""
2853  _IMP_em2d.CompleteLinkage_swiginit(self, _IMP_em2d.new_CompleteLinkage())
2854 
2855  def __call__(self, id1, id2, cluster_set, distances):
2856  r"""__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2857  return _IMP_em2d.CompleteLinkage___call__(self, id1, id2, cluster_set, distances)
2858 
2859  def show(self, out):
2860  r"""show(CompleteLinkage self, _ostream out)"""
2861  return _IMP_em2d.CompleteLinkage_show(self, out)
2862 
2863  def __str__(self):
2864  r"""__str__(CompleteLinkage self) -> std::string"""
2865  return _IMP_em2d.CompleteLinkage___str__(self)
2866 
2867  def __repr__(self):
2868  r"""__repr__(CompleteLinkage self) -> std::string"""
2869  return _IMP_em2d.CompleteLinkage___repr__(self)
2870 
2871  def _get_as_binary(self):
2872  r"""_get_as_binary(CompleteLinkage self) -> PyObject *"""
2873  return _IMP_em2d.CompleteLinkage__get_as_binary(self)
2874 
2875  def _set_from_binary(self, p):
2876  r"""_set_from_binary(CompleteLinkage self, PyObject * p)"""
2877  return _IMP_em2d.CompleteLinkage__set_from_binary(self, p)
2878 
2879  def __getstate__(self):
2880  p = self._get_as_binary()
2881  if len(self.__dict__) > 1:
2882  d = self.__dict__.copy()
2883  del d['this']
2884  p = (d, p)
2885  return p
2886 
2887  def __setstate__(self, p):
2888  if not hasattr(self, 'this'):
2889  self.__init__()
2890  if isinstance(p, tuple):
2891  d, p = p
2892  self.__dict__.update(d)
2893  return self._set_from_binary(p)
2894 
2895  __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2896 
2897 # Register CompleteLinkage in _IMP_em2d:
2898 _IMP_em2d.CompleteLinkage_swigregister(CompleteLinkage)
2899 class AverageDistanceLinkage(object):
2900  r"""Proxy of C++ IMP::em2d::AverageDistanceLinkage class."""
2901 
2902  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2903 
2904  def __init__(self):
2905  r"""__init__(AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2906  _IMP_em2d.AverageDistanceLinkage_swiginit(self, _IMP_em2d.new_AverageDistanceLinkage())
2907 
2908  def __call__(self, id1, id2, cluster_set, distances):
2909  r"""__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2910  return _IMP_em2d.AverageDistanceLinkage___call__(self, id1, id2, cluster_set, distances)
2911 
2912  def show(self, out):
2913  r"""show(AverageDistanceLinkage self, _ostream out)"""
2914  return _IMP_em2d.AverageDistanceLinkage_show(self, out)
2915 
2916  def __str__(self):
2917  r"""__str__(AverageDistanceLinkage self) -> std::string"""
2918  return _IMP_em2d.AverageDistanceLinkage___str__(self)
2919 
2920  def __repr__(self):
2921  r"""__repr__(AverageDistanceLinkage self) -> std::string"""
2922  return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2923 
2924  def _get_as_binary(self):
2925  r"""_get_as_binary(AverageDistanceLinkage self) -> PyObject *"""
2926  return _IMP_em2d.AverageDistanceLinkage__get_as_binary(self)
2927 
2928  def _set_from_binary(self, p):
2929  r"""_set_from_binary(AverageDistanceLinkage self, PyObject * p)"""
2930  return _IMP_em2d.AverageDistanceLinkage__set_from_binary(self, p)
2931 
2932  def __getstate__(self):
2933  p = self._get_as_binary()
2934  if len(self.__dict__) > 1:
2935  d = self.__dict__.copy()
2936  del d['this']
2937  p = (d, p)
2938  return p
2939 
2940  def __setstate__(self, p):
2941  if not hasattr(self, 'this'):
2942  self.__init__()
2943  if isinstance(p, tuple):
2944  d, p = p
2945  self.__dict__.update(d)
2946  return self._set_from_binary(p)
2947 
2948  __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2949 
2950 # Register AverageDistanceLinkage in _IMP_em2d:
2951 _IMP_em2d.AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2952 class CollisionCrossSection(IMP.Object):
2953  r"""Proxy of C++ IMP::em2d::CollisionCrossSection class."""
2954 
2955  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2956 
2957  def __init__(self, n_projections, resolution, pixel_size, projection_image_size):
2958  r"""__init__(CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2959  _IMP_em2d.CollisionCrossSection_swiginit(self, _IMP_em2d.new_CollisionCrossSection(n_projections, resolution, pixel_size, projection_image_size))
2960 
2961  def set_model_particles(self, ps):
2962  r"""set_model_particles(CollisionCrossSection self, IMP::ParticlesTemp const & ps)"""
2963  return _IMP_em2d.CollisionCrossSection_set_model_particles(self, ps)
2964 
2965  def get_ccs(self):
2966  r"""get_ccs(CollisionCrossSection self) -> double"""
2967  return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2968 
2969  def show(self, out):
2970  r"""show(CollisionCrossSection self, _ostream out)"""
2971  return _IMP_em2d.CollisionCrossSection_show(self, out)
2972 
2973  def get_version_info(self):
2974  r"""get_version_info(CollisionCrossSection self) -> VersionInfo"""
2975  return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2976  __swig_destroy__ = _IMP_em2d.delete_CollisionCrossSection
2977 
2978  def __str__(self):
2979  r"""__str__(CollisionCrossSection self) -> std::string"""
2980  return _IMP_em2d.CollisionCrossSection___str__(self)
2981 
2982  def __repr__(self):
2983  r"""__repr__(CollisionCrossSection self) -> std::string"""
2984  return _IMP_em2d.CollisionCrossSection___repr__(self)
2985 
2986  @staticmethod
2987  def get_from(o):
2988  return _object_cast_to_CollisionCrossSection(o)
2989 
2990 
2991 # Register CollisionCrossSection in _IMP_em2d:
2992 _IMP_em2d.CollisionCrossSection_swigregister(CollisionCrossSection)
2993 class GridStates(IMP.domino.ParticleStates):
2994  r"""Proxy of C++ IMP::em2d::GridStates class."""
2995 
2996  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
2997 
2998  def __init__(self, *args):
2999  r"""__init__(GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::String const & name="GridStates") -> GridStates"""
3000  _IMP_em2d.GridStates_swiginit(self, _IMP_em2d.new_GridStates(*args))
3001 
3002  def get_position(self, i):
3003  r"""get_position(GridStates self, unsigned int i) -> Vector3D"""
3004  return _IMP_em2d.GridStates_get_position(self, i)
3005 
3006  def get_orientation(self, i):
3007  r"""get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
3008  return _IMP_em2d.GridStates_get_orientation(self, i)
3009 
3010  def get_version_info(self):
3011  r"""get_version_info(GridStates self) -> VersionInfo"""
3012  return _IMP_em2d.GridStates_get_version_info(self)
3013  __swig_destroy__ = _IMP_em2d.delete_GridStates
3014 
3015  def __str__(self):
3016  r"""__str__(GridStates self) -> std::string"""
3017  return _IMP_em2d.GridStates___str__(self)
3018 
3019  def __repr__(self):
3020  r"""__repr__(GridStates self) -> std::string"""
3021  return _IMP_em2d.GridStates___repr__(self)
3022 
3023  @staticmethod
3024  def get_from(o):
3025  return _object_cast_to_GridStates(o)
3026 
3027 
3028 # Register GridStates in _IMP_em2d:
3029 _IMP_em2d.GridStates_swigregister(GridStates)
3030 class ProjectionStates(GridStates):
3031  r"""Proxy of C++ IMP::em2d::ProjectionStates class."""
3032 
3033  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3034 
3035  def __init__(self, *args):
3036  r"""__init__(ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections, IMP::String const & name="ProjectionStates") -> ProjectionStates"""
3037  _IMP_em2d.ProjectionStates_swiginit(self, _IMP_em2d.new_ProjectionStates(*args))
3038 
3039  def get_projection(self, i):
3040  r"""get_projection(ProjectionStates self, unsigned int i) -> Image"""
3041  return _IMP_em2d.ProjectionStates_get_projection(self, i)
3042  __swig_destroy__ = _IMP_em2d.delete_ProjectionStates
3043 
3044  def __str__(self):
3045  r"""__str__(ProjectionStates self) -> std::string"""
3046  return _IMP_em2d.ProjectionStates___str__(self)
3047 
3048  def __repr__(self):
3049  r"""__repr__(ProjectionStates self) -> std::string"""
3050  return _IMP_em2d.ProjectionStates___repr__(self)
3051 
3052  @staticmethod
3053  def get_from(o):
3054  return _object_cast_to_ProjectionStates(o)
3055 
3056 
3057 # Register ProjectionStates in _IMP_em2d:
3058 _IMP_em2d.ProjectionStates_swigregister(ProjectionStates)
3059 class DistanceFilter(IMP.domino.SubsetFilter):
3060  r"""Proxy of C++ IMP::em2d::DistanceFilter class."""
3061 
3062  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3063 
3064  def __init__(self, subset_to_act_on, subset_to_restrain, ps_table, max_distance):
3065  r"""__init__(DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table, double max_distance) -> DistanceFilter"""
3066  _IMP_em2d.DistanceFilter_swiginit(self, _IMP_em2d.new_DistanceFilter(subset_to_act_on, subset_to_restrain, ps_table, max_distance))
3067 
3068  def show(self, *args):
3069  r"""show(DistanceFilter self, _ostream out=std::cout)"""
3070  return _IMP_em2d.DistanceFilter_show(self, *args)
3071 
3072  def get_version_info(self):
3073  r"""get_version_info(DistanceFilter self) -> VersionInfo"""
3074  return _IMP_em2d.DistanceFilter_get_version_info(self)
3075  __swig_destroy__ = _IMP_em2d.delete_DistanceFilter
3076 
3077  def __str__(self):
3078  r"""__str__(DistanceFilter self) -> std::string"""
3079  return _IMP_em2d.DistanceFilter___str__(self)
3080 
3081  def __repr__(self):
3082  r"""__repr__(DistanceFilter self) -> std::string"""
3083  return _IMP_em2d.DistanceFilter___repr__(self)
3084 
3085  @staticmethod
3086  def get_from(o):
3087  return _object_cast_to_DistanceFilter(o)
3088 
3089 
3090 # Register DistanceFilter in _IMP_em2d:
3091 _IMP_em2d.DistanceFilter_swigregister(DistanceFilter)
3092 class DistanceFilterTable(IMP.domino.SubsetFilterTable):
3093  r"""Proxy of C++ IMP::em2d::DistanceFilterTable class."""
3094 
3095  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3096 
3097  def __init__(self, subset_to_act_on, ps_table, max_distance):
3098  r"""__init__(DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
3099  _IMP_em2d.DistanceFilterTable_swiginit(self, _IMP_em2d.new_DistanceFilterTable(subset_to_act_on, ps_table, max_distance))
3100 
3101  def show(self, *args):
3102  r"""show(DistanceFilterTable self, _ostream out=std::cout)"""
3103  return _IMP_em2d.DistanceFilterTable_show(self, *args)
3104 
3105  def get_version_info(self):
3106  r"""get_version_info(DistanceFilterTable self) -> VersionInfo"""
3107  return _IMP_em2d.DistanceFilterTable_get_version_info(self)
3108  __swig_destroy__ = _IMP_em2d.delete_DistanceFilterTable
3109 
3110  def __str__(self):
3111  r"""__str__(DistanceFilterTable self) -> std::string"""
3112  return _IMP_em2d.DistanceFilterTable___str__(self)
3113 
3114  def __repr__(self):
3115  r"""__repr__(DistanceFilterTable self) -> std::string"""
3116  return _IMP_em2d.DistanceFilterTable___repr__(self)
3117 
3118  @staticmethod
3119  def get_from(o):
3120  return _object_cast_to_DistanceFilterTable(o)
3121 
3122 
3123 # Register DistanceFilterTable in _IMP_em2d:
3124 _IMP_em2d.DistanceFilterTable_swigregister(DistanceFilterTable)
3125 class IntsOrder(object):
3126  r"""Proxy of C++ IMP::em2d::IntsOrder class."""
3127 
3128  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3129  __repr__ = _swig_repr
3130 
3131  def __call__(self, a, b):
3132  r"""__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
3133  return _IMP_em2d.IntsOrder___call__(self, a, b)
3134 
3135  def __init__(self):
3136  r"""__init__(IntsOrder self) -> IntsOrder"""
3137  _IMP_em2d.IntsOrder_swiginit(self, _IMP_em2d.new_IntsOrder())
3138  __swig_destroy__ = _IMP_em2d.delete_IntsOrder
3139 
3140 # Register IntsOrder in _IMP_em2d:
3141 _IMP_em2d.IntsOrder_swigregister(IntsOrder)
3142 class RigidBodiesImageFitRestraint(IMP.Restraint):
3143  r"""Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class."""
3144 
3145  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3146 
3147  def get_version_info(self):
3148  r"""get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
3149  return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
3150  __swig_destroy__ = _IMP_em2d.delete_RigidBodiesImageFitRestraint
3151 
3152  def __init__(self, scf, rbs, img):
3153  r"""__init__(RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
3154  _IMP_em2d.RigidBodiesImageFitRestraint_swiginit(self, _IMP_em2d.new_RigidBodiesImageFitRestraint(scf, rbs, img))
3155 
3156  def set_projecting_parameters(self, p):
3157  r"""set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
3158  return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, p)
3159 
3160  def set_orientations(self, rb, rots):
3161  r"""set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
3162  return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, rb, rots)
3163 
3164  def get_number_of_masks(self, rb):
3165  r"""get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
3166  return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, rb)
3167 
3168  def __str__(self):
3169  r"""__str__(RigidBodiesImageFitRestraint self) -> std::string"""
3170  return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
3171 
3172  def __repr__(self):
3173  r"""__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
3174  return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
3175 
3176  @staticmethod
3177  def get_from(o):
3178  return _object_cast_to_RigidBodiesImageFitRestraint(o)
3179 
3180 
3181 # Register RigidBodiesImageFitRestraint in _IMP_em2d:
3182 _IMP_em2d.RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
3183 
3184 def get_unique_index(rot):
3185  r"""get_unique_index(Rotation3D rot) -> IMP::Ints"""
3186  return _IMP_em2d.get_unique_index(rot)
3187 class RelativePositionMover(IMP.core.RigidBodyMover):
3188  r"""Proxy of C++ IMP::em2d::RelativePositionMover class."""
3189 
3190  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3191 
3192  def __init__(self, d, max_translation, max_rotation):
3193  r"""__init__(RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
3194  _IMP_em2d.RelativePositionMover_swiginit(self, _IMP_em2d.new_RelativePositionMover(d, max_translation, max_rotation))
3195 
3196  def add_internal_transformations(self, d, transforms):
3197  r"""add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
3198  return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, d, transforms)
3199 
3200  def set_random_move_probability(self, p):
3201  r"""set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
3202  return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, p)
3203  __swig_destroy__ = _IMP_em2d.delete_RelativePositionMover
3204 
3205  def __str__(self):
3206  r"""__str__(RelativePositionMover self) -> std::string"""
3207  return _IMP_em2d.RelativePositionMover___str__(self)
3208 
3209  def __repr__(self):
3210  r"""__repr__(RelativePositionMover self) -> std::string"""
3211  return _IMP_em2d.RelativePositionMover___repr__(self)
3212 
3213  @staticmethod
3214  def get_from(o):
3215  return _object_cast_to_RelativePositionMover(o)
3216 
3217 
3218 # Register RelativePositionMover in _IMP_em2d:
3219 _IMP_em2d.RelativePositionMover_swigregister(RelativePositionMover)
3220 class DummyRestraint(IMP.Restraint):
3221  r"""Proxy of C++ IMP::em2d::DummyRestraint class."""
3222 
3223  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3224 
3225  def __init__(self, p, q):
3226  r"""__init__(DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
3227  _IMP_em2d.DummyRestraint_swiginit(self, _IMP_em2d.new_DummyRestraint(p, q))
3228 
3229  def show(self, *args):
3230  r"""show(DummyRestraint self, _ostream out=std::cout)"""
3231  return _IMP_em2d.DummyRestraint_show(self, *args)
3232 
3233  def do_get_inputs(self):
3234  r"""do_get_inputs(DummyRestraint self) -> IMP::ModelObjectsTemp"""
3235  return _IMP_em2d.DummyRestraint_do_get_inputs(self)
3236 
3237  def get_version_info(self):
3238  r"""get_version_info(DummyRestraint self) -> VersionInfo"""
3239  return _IMP_em2d.DummyRestraint_get_version_info(self)
3240  __swig_destroy__ = _IMP_em2d.delete_DummyRestraint
3241 
3242  def __str__(self):
3243  r"""__str__(DummyRestraint self) -> std::string"""
3244  return _IMP_em2d.DummyRestraint___str__(self)
3245 
3246  def __repr__(self):
3247  r"""__repr__(DummyRestraint self) -> std::string"""
3248  return _IMP_em2d.DummyRestraint___repr__(self)
3249 
3250  @staticmethod
3251  def get_from(o):
3252  return _object_cast_to_DummyRestraint(o)
3253 
3254 
3255 # Register DummyRestraint in _IMP_em2d:
3256 _IMP_em2d.DummyRestraint_swigregister(DummyRestraint)
3257 class ParticlesDummyRestraint(IMP.Restraint):
3258  r"""Proxy of C++ IMP::em2d::ParticlesDummyRestraint class."""
3259 
3260  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3261 
3262  def __init__(self, sc):
3263  r"""__init__(ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
3264  _IMP_em2d.ParticlesDummyRestraint_swiginit(self, _IMP_em2d.new_ParticlesDummyRestraint(sc))
3265 
3266  def show(self, *args):
3267  r"""show(ParticlesDummyRestraint self, _ostream out=std::cout)"""
3268  return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
3269 
3270  def do_get_inputs(self):
3271  r"""do_get_inputs(ParticlesDummyRestraint self) -> IMP::ModelObjectsTemp"""
3272  return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3273 
3274  def get_version_info(self):
3275  r"""get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3276  return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3277  __swig_destroy__ = _IMP_em2d.delete_ParticlesDummyRestraint
3278 
3279  def __str__(self):
3280  r"""__str__(ParticlesDummyRestraint self) -> std::string"""
3281  return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3282 
3283  def __repr__(self):
3284  r"""__repr__(ParticlesDummyRestraint self) -> std::string"""
3285  return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3286 
3287  @staticmethod
3288  def get_from(o):
3289  return _object_cast_to_ParticlesDummyRestraint(o)
3290 
3291 
3292 # Register ParticlesDummyRestraint in _IMP_em2d:
3293 _IMP_em2d.ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3294 class PCAFitRestraint(IMP.Restraint):
3295  r"""Proxy of C++ IMP::em2d::PCAFitRestraint class."""
3296 
3297  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3298 
3299  def __init__(self, particles, image_files, pixel_size, resolution=10.0, projection_number=100, reuse_direction=False, n_components=1, micrographs_number=0):
3300  r"""__init__(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, unsigned int micrographs_number=0) -> PCAFitRestraint"""
3301  _IMP_em2d.PCAFitRestraint_swiginit(self, _IMP_em2d.new_PCAFitRestraint(particles, image_files, pixel_size, resolution, projection_number, reuse_direction, n_components, micrographs_number))
3302 
3303  def get_projection_number(self):
3304  r"""get_projection_number(PCAFitRestraint self) -> unsigned int"""
3305  return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3306 
3307  def set_projection_number(self, n):
3308  r"""set_projection_number(PCAFitRestraint self, unsigned int n)"""
3309  return _IMP_em2d.PCAFitRestraint_set_projection_number(self, n)
3310 
3311  def get_micrographs_number(self):
3312  r"""get_micrographs_number(PCAFitRestraint self) -> unsigned int"""
3313  return _IMP_em2d.PCAFitRestraint_get_micrographs_number(self)
3314 
3315  def set_micrographs_number(self, n):
3316  r"""set_micrographs_number(PCAFitRestraint self, unsigned int n)"""
3317  return _IMP_em2d.PCAFitRestraint_set_micrographs_number(self, n)
3318 
3319  def get_transformation(self, image_number):
3320  r"""get_transformation(PCAFitRestraint self, unsigned int image_number) -> Transformation3D"""
3321  return _IMP_em2d.PCAFitRestraint_get_transformation(self, image_number)
3322 
3323  def get_cross_correlation_coefficient(self, image_number):
3324  r"""get_cross_correlation_coefficient(PCAFitRestraint self, unsigned int image_number) -> double"""
3325  return _IMP_em2d.PCAFitRestraint_get_cross_correlation_coefficient(self, image_number)
3326 
3327  def write_best_projections(self, file_name, evaluate=False):
3328  r"""write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)"""
3329  return _IMP_em2d.PCAFitRestraint_write_best_projections(self, file_name, evaluate)
3330 
3331  def do_get_inputs(self):
3332  r"""do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
3333  return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3334 
3335  def get_version_info(self):
3336  r"""get_version_info(PCAFitRestraint self) -> VersionInfo"""
3337  return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3338  __swig_destroy__ = _IMP_em2d.delete_PCAFitRestraint
3339 
3340  def __str__(self):
3341  r"""__str__(PCAFitRestraint self) -> std::string"""
3342  return _IMP_em2d.PCAFitRestraint___str__(self)
3343 
3344  def __repr__(self):
3345  r"""__repr__(PCAFitRestraint self) -> std::string"""
3346  return _IMP_em2d.PCAFitRestraint___repr__(self)
3347 
3348  @staticmethod
3349  def get_from(o):
3350  return _object_cast_to_em2dPCAFitRestraint(o)
3351 
3352 
3353 # Register PCAFitRestraint in _IMP_em2d:
3354 _IMP_em2d.PCAFitRestraint_swigregister(PCAFitRestraint)
3355 class ResultAlign2D(object):
3356  r"""Proxy of C++ std::pair< IMP::algebra::Transformation2D,double > class."""
3357 
3358  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
3359  __repr__ = _swig_repr
3360 
3361  def __init__(self, *args):
3362  r"""
3363  __init__(ResultAlign2D self) -> ResultAlign2D
3364  __init__(ResultAlign2D self, Transformation2D first, double second) -> ResultAlign2D
3365  __init__(ResultAlign2D self, ResultAlign2D other) -> ResultAlign2D
3366  """
3367  _IMP_em2d.ResultAlign2D_swiginit(self, _IMP_em2d.new_ResultAlign2D(*args))
3368  first = property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set, doc=r"""first : IMP::algebra::Transformation2D""")
3369  second = property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set, doc=r"""second : double""")
3370  def __len__(self):
3371  return 2
3372  def __repr__(self):
3373  return str((self.first, self.second))
3374  def __getitem__(self, index):
3375  if not (index % 2):
3376  return self.first
3377  else:
3378  return self.second
3379  def __setitem__(self, index, val):
3380  if not (index % 2):
3381  self.first = val
3382  else:
3383  self.second = val
3384  __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3385 
3386 # Register ResultAlign2D in _IMP_em2d:
3387 _IMP_em2d.ResultAlign2D_swigregister(ResultAlign2D)
3388 
3389 def _do_hierarchical_clustering_single_linkage(distances):
3390  r"""_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3391  return _IMP_em2d._do_hierarchical_clustering_single_linkage(distances)
3392 
3393 def _do_hierarchical_clustering_complete_linkage(distances):
3394  r"""_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3395  return _IMP_em2d._do_hierarchical_clustering_complete_linkage(distances)
3396 
3397 def _do_hierarchical_clustering_average_distance_linkage(distances):
3398  r"""_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3399  return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(distances)
3400 
3401 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3402 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3403 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3404 
3405 
3406 def get_module_version():
3407  r"""get_module_version() -> std::string const"""
3408  return _IMP_em2d.get_module_version()
3409 
3410 def get_example_path(fname):
3411  r"""get_example_path(std::string fname) -> std::string"""
3412  return _IMP_em2d.get_example_path(fname)
3413 
3414 def get_data_path(fname):
3415  r"""get_data_path(std::string fname) -> std::string"""
3416  return _IMP_em2d.get_data_path(fname)
3417 
3418 from . import _version_check
3419 _version_check.check_version(get_module_version())
3420 __version__ = get_module_version()
3421 
3422 
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:80
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:111
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:56
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:119
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:72
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:56
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.