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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
em2d/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 # This wrapper is part of IMP,
8 # Copyright 2007-2017 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_em2d')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_em2d')
25  _IMP_em2d = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_em2d', [dirname(__file__)])
34  except ImportError:
35  import _IMP_em2d
36  return _IMP_em2d
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_em2d', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_em2d = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_em2d
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_EM2D_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_EM2D_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_em2d.delete_IMP_EM2D_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
126  return _IMP_em2d.IMP_EM2D_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
132  incr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
133  """
134  return _IMP_em2d.IMP_EM2D_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
140  decr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
141  """
142  return _IMP_em2d.IMP_EM2D_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_em2d.IMP_EM2D_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
152  return _IMP_em2d.IMP_EM2D_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator"""
157  return _IMP_em2d.IMP_EM2D_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
162  return _IMP_em2d.IMP_EM2D_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
167  return _IMP_em2d.IMP_EM2D_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
172  return _IMP_em2d.IMP_EM2D_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
177  return _IMP_em2d.IMP_EM2D_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
182  return _IMP_em2d.IMP_EM2D_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
187  return _IMP_em2d.IMP_EM2D_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
192  return _IMP_em2d.IMP_EM2D_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
197  return _IMP_em2d.IMP_EM2D_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
202  return _IMP_em2d.IMP_EM2D_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator
208  __sub__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_em2d.IMP_EM2D_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_EM2D_SwigPyIterator_swigregister = _IMP_em2d.IMP_EM2D_SwigPyIterator_swigregister
215 IMP_EM2D_SwigPyIterator_swigregister(IMP_EM2D_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_em2d.IMP_DEBUG
224 IMP_RELEASE = _IMP_em2d.IMP_RELEASE
225 IMP_SILENT = _IMP_em2d.IMP_SILENT
226 IMP_PROGRESS = _IMP_em2d.IMP_PROGRESS
227 IMP_TERSE = _IMP_em2d.IMP_TERSE
228 IMP_VERBOSE = _IMP_em2d.IMP_VERBOSE
229 IMP_MEMORY = _IMP_em2d.IMP_MEMORY
230 IMP_NONE = _IMP_em2d.IMP_NONE
231 IMP_USAGE = _IMP_em2d.IMP_USAGE
232 IMP_INTERNAL = _IMP_em2d.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_em2d.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_em2d.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em2d.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_em2d.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em2d.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_em2d.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_em2d._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_em2d._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_em2d.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_em2d.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_em2d.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_em2d.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_em2d.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_em2d.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_em2d.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_GSL_HAS_IMP_CGAL = _IMP_em2d.IMP_GSL_HAS_IMP_CGAL
313 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_FILESYSTEM
314 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
315 IMP_GSL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_GSL_HAS_BOOST_RANDOM
316 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_SYSTEM
317 IMP_GSL_HAS_CGAL = _IMP_em2d.IMP_GSL_HAS_CGAL
318 IMPGSL_SHOW_WARNINGS = _IMP_em2d.IMPGSL_SHOW_WARNINGS
319 import IMP.gsl
320 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
321 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
322 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
323 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
324 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
325 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_CGAL
326 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_HDF5
327 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em2d.IMPSCOREFUNCTOR_SHOW_WARNINGS
328 import IMP.score_functor
329 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_IMP_CGAL
330 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
331 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
332 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_RANDOM
333 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_SYSTEM
334 IMP_STATISTICS_HAS_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_CGAL
335 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em2d.IMPSTATISTICS_SHOW_WARNINGS
336 import IMP.statistics
337 IMP_CORE_HAS_IMP_CGAL = _IMP_em2d.IMP_CORE_HAS_IMP_CGAL
338 IMP_CORE_HAS_IMP_KERNEL = _IMP_em2d.IMP_CORE_HAS_IMP_KERNEL
339 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_FILESYSTEM
340 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
341 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CORE_HAS_BOOST_RANDOM
342 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_SYSTEM
343 IMP_CORE_HAS_CGAL = _IMP_em2d.IMP_CORE_HAS_CGAL
344 IMP_CORE_HAS_HDF5 = _IMP_em2d.IMP_CORE_HAS_HDF5
345 IMPCORE_SHOW_WARNINGS = _IMP_em2d.IMPCORE_SHOW_WARNINGS
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em2d.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em2d.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_em2d.IMP_CONTAINER_HAS_HDF5
358 IMPCONTAINER_SHOW_WARNINGS = _IMP_em2d.IMPCONTAINER_SHOW_WARNINGS
359 import IMP.container
360 IMP_ATOM_HAS_IMP_CGAL = _IMP_em2d.IMP_ATOM_HAS_IMP_CGAL
361 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em2d.IMP_ATOM_HAS_IMP_KERNEL
362 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
363 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
364 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ATOM_HAS_BOOST_RANDOM
365 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em2d.IMP_ATOM_HAS_BOOST_REGEX
366 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ATOM_HAS_BOOST_SYSTEM
367 IMP_ATOM_HAS_CGAL = _IMP_em2d.IMP_ATOM_HAS_CGAL
368 IMP_ATOM_HAS_HDF5 = _IMP_em2d.IMP_ATOM_HAS_HDF5
369 IMPATOM_SHOW_WARNINGS = _IMP_em2d.IMPATOM_SHOW_WARNINGS
370 IMP_ATOM_TYPE_INDEX = _IMP_em2d.IMP_ATOM_TYPE_INDEX
371 IMP_RESIDUE_TYPE_INDEX = _IMP_em2d.IMP_RESIDUE_TYPE_INDEX
372 IMP_HIERARCHY_TYPE_INDEX = _IMP_em2d.IMP_HIERARCHY_TYPE_INDEX
373 import IMP.atom
374 IMP_EM_HAS_IMP_CGAL = _IMP_em2d.IMP_EM_HAS_IMP_CGAL
375 IMP_EM_HAS_IMP_CONTAINER = _IMP_em2d.IMP_EM_HAS_IMP_CONTAINER
376 IMP_EM_HAS_IMP_DISPLAY = _IMP_em2d.IMP_EM_HAS_IMP_DISPLAY
377 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM_HAS_IMP_SCORE_FUNCTOR
378 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_FILESYSTEM
379 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
380 IMP_EM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM_HAS_BOOST_RANDOM
381 IMP_EM_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM_HAS_BOOST_REGEX
382 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_SYSTEM
383 IMP_EM_HAS_CGAL = _IMP_em2d.IMP_EM_HAS_CGAL
384 IMP_EM_HAS_HDF5 = _IMP_em2d.IMP_EM_HAS_HDF5
385 IMPEM_SHOW_WARNINGS = _IMP_em2d.IMPEM_SHOW_WARNINGS
386 import IMP.em
387 IMP_RMF_HAS_IMP_CGAL = _IMP_em2d.IMP_RMF_HAS_IMP_CGAL
388 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
389 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_FILESYSTEM
390 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
391 IMP_RMF_HAS_BOOST_RANDOM = _IMP_em2d.IMP_RMF_HAS_BOOST_RANDOM
392 IMP_RMF_HAS_BOOST_REGEX = _IMP_em2d.IMP_RMF_HAS_BOOST_REGEX
393 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_SYSTEM
394 IMP_RMF_HAS_CGAL = _IMP_em2d.IMP_RMF_HAS_CGAL
395 IMP_RMF_HAS_HDF5 = _IMP_em2d.IMP_RMF_HAS_HDF5
396 IMPRMF_SHOW_WARNINGS = _IMP_em2d.IMPRMF_SHOW_WARNINGS
397 import IMP.rmf
398 import RMF
399 IMP_DOMINO_HAS_IMP_ATOM = _IMP_em2d.IMP_DOMINO_HAS_IMP_ATOM
400 IMP_DOMINO_HAS_IMP_CGAL = _IMP_em2d.IMP_DOMINO_HAS_IMP_CGAL
401 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_em2d.IMP_DOMINO_HAS_IMP_KERNEL
402 IMP_DOMINO_HAS_IMP_RMF = _IMP_em2d.IMP_DOMINO_HAS_IMP_RMF
403 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
404 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_FILESYSTEM
405 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
406 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_RANDOM
407 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_em2d.IMP_DOMINO_HAS_BOOST_REGEX
408 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_SYSTEM
409 IMP_DOMINO_HAS_CGAL = _IMP_em2d.IMP_DOMINO_HAS_CGAL
410 IMP_DOMINO_HAS_HDF5 = _IMP_em2d.IMP_DOMINO_HAS_HDF5
411 IMP_DOMINO_HAS_RMF = _IMP_em2d.IMP_DOMINO_HAS_RMF
412 IMPDOMINO_SHOW_WARNINGS = _IMP_em2d.IMPDOMINO_SHOW_WARNINGS
413 import RMF_HDF5
414 import IMP.domino
415 IMP_EM2D_HAS_IMP_CGAL = _IMP_em2d.IMP_EM2D_HAS_IMP_CGAL
416 IMP_EM2D_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM2D_HAS_IMP_KERNEL
417 IMP_EM2D_HAS_IMP_RMF = _IMP_em2d.IMP_EM2D_HAS_IMP_RMF
418 IMP_EM2D_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM2D_HAS_IMP_SCORE_FUNCTOR
419 IMP_EM2D_HAS_IMP_STATISTICS = _IMP_em2d.IMP_EM2D_HAS_IMP_STATISTICS
420 IMP_EM2D_HAS_BOOST_GRAPH = _IMP_em2d.IMP_EM2D_HAS_BOOST_GRAPH
421 IMP_EM2D_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM2D_HAS_BOOST_RANDOM
422 IMP_EM2D_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM2D_HAS_BOOST_REGEX
423 IMP_EM2D_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM2D_HAS_BOOST_SYSTEM
424 IMP_EM2D_HAS_CGAL = _IMP_em2d.IMP_EM2D_HAS_CGAL
425 IMP_EM2D_HAS_GSL = _IMP_em2d.IMP_EM2D_HAS_GSL
426 IMP_EM2D_HAS_HDF5 = _IMP_em2d.IMP_EM2D_HAS_HDF5
427 IMP_EM2D_HAS_OPENCV22 = _IMP_em2d.IMP_EM2D_HAS_OPENCV22
428 IMP_EM2D_HAS_RMF = _IMP_em2d.IMP_EM2D_HAS_RMF
429 IMP_EM2D_HAS_OPENCV21 = _IMP_em2d.IMP_EM2D_HAS_OPENCV21
430 IMP_EM2D_HAS_OPENCV3 = _IMP_em2d.IMP_EM2D_HAS_OPENCV3
431 IMPEM2D_SHOW_WARNINGS = _IMP_em2d.IMPEM2D_SHOW_WARNINGS
432 
433 PolarResamplingParametersList=list
434 _plural_types.append("PolarResamplingParametersList")
435 _value_types.append("PolarResamplingParameters")
436 
437 
438 ProjectionMasks=list
439 _plural_types.append("ProjectionMasks")
440 _value_types.append("ProjectionMask")
441 
442 
443 MasksManagers=list
444 _plural_types.append("MasksManagers")
445 _value_types.append("MasksManager")
446 
447 
448 RegistrationResults=list
449 _plural_types.append("RegistrationResults")
450 _value_types.append("RegistrationResult")
451 
452 
453 ClusterSets=list
454 _plural_types.append("ClusterSets")
455 _value_types.append("ClusterSet")
456 
457 
458 SingleLinkages=list
459 _plural_types.append("SingleLinkages")
460 _value_types.append("SingleLinkage")
461 
462 
463 CompleteLinkages=list
464 _plural_types.append("CompleteLinkages")
465 _value_types.append("CompleteLinkage")
466 
467 
468 AverageDistanceLinkages=list
469 _plural_types.append("AverageDistanceLinkages")
470 _value_types.append("AverageDistanceLinkage")
471 
472 
473 SegmentationParametersList=list
474 _plural_types.append("SegmentationParametersList")
475 _value_types.append("SegmentationParameters")
476 
477 
478 MatchTemplateResults=list
479 _plural_types.append("MatchTemplateResults")
480 _value_types.append("MatchTemplateResult")
481 
482 
483 ProjectingParametersList=list
484 _plural_types.append("ProjectingParametersList")
485 _value_types.append("ProjectingParameters")
486 
487 
488 ProjectingOptionsList=list
489 _plural_types.append("ProjectingOptionsList")
490 _value_types.append("ProjectingOptions")
491 
492 
493 Em2DRestraintParametersList=list
494 _plural_types.append("Em2DRestraintParametersList")
495 _value_types.append("Em2DRestraintParameters")
496 
497 
498 _object_types.append("ProjectionFinder")
499 
500 
501 def _object_cast_to_ProjectionFinder(o):
502  """_object_cast_to_ProjectionFinder(Object o) -> ProjectionFinder"""
503  return _IMP_em2d._object_cast_to_ProjectionFinder(o)
504 
505 _object_types.append("ScoreFunction")
506 
507 
508 def _object_cast_to_ScoreFunction(o):
509  """_object_cast_to_ScoreFunction(Object o) -> ScoreFunction"""
510  return _IMP_em2d._object_cast_to_ScoreFunction(o)
511 
512 _object_types.append("ChiSquaredScore")
513 
514 
515 def _object_cast_to_ChiSquaredScore(o):
516  """_object_cast_to_ChiSquaredScore(Object o) -> ChiSquaredScore"""
517  return _IMP_em2d._object_cast_to_ChiSquaredScore(o)
518 
519 _object_types.append("EM2DScore")
520 
521 
522 def _object_cast_to_EM2DScore(o):
523  """_object_cast_to_EM2DScore(Object o) -> EM2DScore"""
524  return _IMP_em2d._object_cast_to_EM2DScore(o)
525 
526 _object_types.append("MeanAbsoluteDifference")
527 
528 
529 def _object_cast_to_MeanAbsoluteDifference(o):
530  """_object_cast_to_MeanAbsoluteDifference(Object o) -> MeanAbsoluteDifference"""
531  return _IMP_em2d._object_cast_to_MeanAbsoluteDifference(o)
532 
533 _object_types.append("ProjectionParametersScoreState")
534 
535 
536 def _object_cast_to_ProjectionParametersScoreState(o):
537  """_object_cast_to_ProjectionParametersScoreState(Object o) -> ProjectionParametersScoreState"""
538  return _IMP_em2d._object_cast_to_ProjectionParametersScoreState(o)
539 
540 _object_types.append("Em2DRestraint")
541 
542 
543 def _object_cast_to_Em2DRestraint(o):
544  """_object_cast_to_Em2DRestraint(Object o) -> Em2DRestraint"""
545  return _IMP_em2d._object_cast_to_Em2DRestraint(o)
546 
547 _object_types.append("Image")
548 
549 
550 def _object_cast_to_Image(o):
551  """_object_cast_to_Image(Object o) -> Image"""
552  return _IMP_em2d._object_cast_to_Image(o)
553 
554 _object_types.append("ImageReaderWriter")
555 
556 
557 def _object_cast_to_ImageReaderWriter(o):
558  """_object_cast_to_ImageReaderWriter(Object o) -> ImageReaderWriter"""
559  return _IMP_em2d._object_cast_to_ImageReaderWriter(o)
560 
561 _object_types.append("JPGImageReaderWriter")
562 
563 
564 def _object_cast_to_JPGImageReaderWriter(o):
565  """_object_cast_to_JPGImageReaderWriter(Object o) -> JPGImageReaderWriter"""
566  return _IMP_em2d._object_cast_to_JPGImageReaderWriter(o)
567 
568 _object_types.append("TIFFImageReaderWriter")
569 
570 
571 def _object_cast_to_TIFFImageReaderWriter(o):
572  """_object_cast_to_TIFFImageReaderWriter(Object o) -> TIFFImageReaderWriter"""
573  return _IMP_em2d._object_cast_to_TIFFImageReaderWriter(o)
574 
575 _object_types.append("SpiderImageReaderWriter")
576 
577 
578 def _object_cast_to_SpiderImageReaderWriter(o):
579  """_object_cast_to_SpiderImageReaderWriter(Object o) -> SpiderImageReaderWriter"""
580  return _IMP_em2d._object_cast_to_SpiderImageReaderWriter(o)
581 
582 _object_types.append("CollisionCrossSection")
583 
584 
585 def _object_cast_to_CollisionCrossSection(o):
586  """_object_cast_to_CollisionCrossSection(Object o) -> CollisionCrossSection"""
587  return _IMP_em2d._object_cast_to_CollisionCrossSection(o)
588 
589 _object_types.append("GridStates")
590 
591 
592 def _object_cast_to_GridStates(o):
593  """_object_cast_to_GridStates(Object o) -> GridStates"""
594  return _IMP_em2d._object_cast_to_GridStates(o)
595 
596 _object_types.append("ProjectionStates")
597 
598 
599 def _object_cast_to_ProjectionStates(o):
600  """_object_cast_to_ProjectionStates(Object o) -> ProjectionStates"""
601  return _IMP_em2d._object_cast_to_ProjectionStates(o)
602 
603 _object_types.append("DistanceFilter")
604 
605 
606 def _object_cast_to_DistanceFilter(o):
607  """_object_cast_to_DistanceFilter(Object o) -> DistanceFilter"""
608  return _IMP_em2d._object_cast_to_DistanceFilter(o)
609 
610 _object_types.append("DistanceFilterTable")
611 
612 
613 def _object_cast_to_DistanceFilterTable(o):
614  """_object_cast_to_DistanceFilterTable(Object o) -> DistanceFilterTable"""
615  return _IMP_em2d._object_cast_to_DistanceFilterTable(o)
616 
617 _object_types.append("RigidBodiesImageFitRestraint")
618 
619 
620 def _object_cast_to_RigidBodiesImageFitRestraint(o):
621  """_object_cast_to_RigidBodiesImageFitRestraint(Object o) -> RigidBodiesImageFitRestraint"""
622  return _IMP_em2d._object_cast_to_RigidBodiesImageFitRestraint(o)
623 
624 _object_types.append("DummyRestraint")
625 
626 
627 def _object_cast_to_DummyRestraint(o):
628  """_object_cast_to_DummyRestraint(Object o) -> DummyRestraint"""
629  return _IMP_em2d._object_cast_to_DummyRestraint(o)
630 
631 _object_types.append("ParticlesDummyRestraint")
632 
633 
634 def _object_cast_to_ParticlesDummyRestraint(o):
635  """_object_cast_to_ParticlesDummyRestraint(Object o) -> ParticlesDummyRestraint"""
636  return _IMP_em2d._object_cast_to_ParticlesDummyRestraint(o)
637 
638 _object_types.append("RelativePositionMover")
639 
640 
641 def _object_cast_to_RelativePositionMover(o):
642  """_object_cast_to_RelativePositionMover(Object o) -> RelativePositionMover"""
643  return _IMP_em2d._object_cast_to_RelativePositionMover(o)
644 
645 _object_types.append("PCAFitRestraint")
646 
647 
648 def _object_cast_to_em2dPCAFitRestraint(o):
649  """_object_cast_to_em2dPCAFitRestraint(Object o) -> PCAFitRestraint"""
650  return _IMP_em2d._object_cast_to_em2dPCAFitRestraint(o)
651 
652 def ProjectionParametersList(l=[]):
653  return [ProjectionParameters(x) for x in l]
654 _plural_types.append("ProjectionParametersList")
655 
656 
657 _value_types.append("ProjectionParameters")
658 
659 
660 def show(*args):
661  """
662  show(cv::Mat const & m, _ostream out)
663  show(cv::Mat const & m)
664  """
665  return _IMP_em2d.show(*args)
666 
667 def write_matrix(m, name):
668  """write_matrix(cv::Mat & m, std::string name)"""
669  return _IMP_em2d.write_matrix(m, name)
670 class ImageReaderWriter(IMP.Object):
671  """Proxy of C++ IMP::em2d::ImageReaderWriter class."""
672 
673  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
674 
675  def __init__(self, *args, **kwargs):
676  raise AttributeError("No constructor defined - class is abstract")
677 
678  def read(self, filename, header, data):
679  """read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
680  return _IMP_em2d.ImageReaderWriter_read(self, filename, header, data)
681 
682 
683  def read_from_floats(self, filename, header, data):
684  """read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
685  return _IMP_em2d.ImageReaderWriter_read_from_floats(self, filename, header, data)
686 
687 
688  def read_from_ints(self, filename, header, data):
689  """read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
690  return _IMP_em2d.ImageReaderWriter_read_from_ints(self, filename, header, data)
691 
692 
693  def write(self, filename, header, data):
694  """write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
695  return _IMP_em2d.ImageReaderWriter_write(self, filename, header, data)
696 
697 
698  def write_to_floats(self, filename, header, data):
699  """write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
700  return _IMP_em2d.ImageReaderWriter_write_to_floats(self, filename, header, data)
701 
702 
703  def write_to_ints(self, filename, header, data):
704  """write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
705  return _IMP_em2d.ImageReaderWriter_write_to_ints(self, filename, header, data)
706 
707 
708  def get_version_info(self):
709  """get_version_info(ImageReaderWriter self) -> VersionInfo"""
710  return _IMP_em2d.ImageReaderWriter_get_version_info(self)
711 
712 
713  def __str__(self):
714  """__str__(ImageReaderWriter self) -> std::string"""
715  return _IMP_em2d.ImageReaderWriter___str__(self)
716 
717 
718  def __repr__(self):
719  """__repr__(ImageReaderWriter self) -> std::string"""
720  return _IMP_em2d.ImageReaderWriter___repr__(self)
721 
722 
723  @staticmethod
724  def get_from(o):
725  return _object_cast_to_ImageReaderWriter(o)
726 
727 ImageReaderWriter_swigregister = _IMP_em2d.ImageReaderWriter_swigregister
728 ImageReaderWriter_swigregister(ImageReaderWriter)
729 
730 class PolarResamplingParameters(object):
731  """Proxy of C++ IMP::em2d::PolarResamplingParameters class."""
732 
733  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
734 
735  def __init__(self, *args):
736  """
737  __init__(IMP::em2d::PolarResamplingParameters self) -> PolarResamplingParameters
738  __init__(IMP::em2d::PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
739  __init__(IMP::em2d::PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
740  """
741  this = _IMP_em2d.new_PolarResamplingParameters(*args)
742  try:
743  self.this.append(this)
744  except __builtin__.Exception:
745  self.this = this
746  __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
747  __del__ = lambda self: None
748 
749  def setup(self, rows, cols):
750  """setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
751  return _IMP_em2d.PolarResamplingParameters_setup(self, rows, cols)
752 
753 
754  def get_starting_radius(self):
755  """get_starting_radius(PolarResamplingParameters self) -> double"""
756  return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
757 
758 
759  def get_ending_radius(self):
760  """get_ending_radius(PolarResamplingParameters self) -> double"""
761  return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
762 
763 
764  def get_radius(self, n_ring):
765  """get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
766  return _IMP_em2d.PolarResamplingParameters_get_radius(self, n_ring)
767 
768 
769  def get_number_of_rings(self):
770  """get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
771  return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
772 
773 
774  def set_estimated_number_of_angles(self, aprox_value):
775  """set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
776  return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, aprox_value)
777 
778 
779  def get_number_of_angles(self):
780  """get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
781  return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
782 
783 
784  def get_angle_step(self):
785  """get_angle_step(PolarResamplingParameters self) -> double"""
786  return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
787 
788 
789  def get_radius_step(self):
790  """get_radius_step(PolarResamplingParameters self) -> double"""
791  return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
792 
793 
794  def create_maps_for_resampling(self):
795  """create_maps_for_resampling(PolarResamplingParameters self)"""
796  return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
797 
798 
799  def get_resampling_maps(self, m1, m2):
800  """get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
801  return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, m1, m2)
802 
803 
804  def get_resampling_map(self, m1):
805  """get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
806  return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, m1)
807 
808 
809  def show(self, out):
810  """show(PolarResamplingParameters self, _ostream out)"""
811  return _IMP_em2d.PolarResamplingParameters_show(self, out)
812 
813 
814  def get_is_setup(self):
815  """get_is_setup(PolarResamplingParameters self) -> bool"""
816  return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
817 
818 
819  def __str__(self):
820  """__str__(PolarResamplingParameters self) -> std::string"""
821  return _IMP_em2d.PolarResamplingParameters___str__(self)
822 
823 
824  def __repr__(self):
825  """__repr__(PolarResamplingParameters self) -> std::string"""
826  return _IMP_em2d.PolarResamplingParameters___repr__(self)
827 
828 PolarResamplingParameters_swigregister = _IMP_em2d.PolarResamplingParameters_swigregister
829 PolarResamplingParameters_swigregister(PolarResamplingParameters)
830 
831 class SegmentationParameters(object):
832  """Proxy of C++ IMP::em2d::SegmentationParameters class."""
833 
834  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
835  image_pixel_size = _swig_property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set)
836  diffusion_beta = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set)
837  diffusion_timesteps = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set)
838  fill_holes_stddevs = _swig_property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set)
839  opening_kernel = _swig_property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set)
840  remove_sizing_percentage = _swig_property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set)
841  binary_background = _swig_property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set)
842  binary_foreground = _swig_property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set)
843  threshold = _swig_property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set)
844 
845  def __init__(self, *args):
846  """
847  __init__(IMP::em2d::SegmentationParameters self) -> SegmentationParameters
848  __init__(IMP::em2d::SegmentationParameters self, double apix, double diff_beta, unsigned int diff_timesteps, double fh_stddevs, cv::Mat const & kr, int background, int foreground) -> SegmentationParameters
849  """
850  this = _IMP_em2d.new_SegmentationParameters(*args)
851  try:
852  self.this.append(this)
853  except __builtin__.Exception:
854  self.this = this
855 
856  def show(self, *args):
857  """
858  show(SegmentationParameters self, _ostream out)
859  show(SegmentationParameters self)
860  """
861  return _IMP_em2d.SegmentationParameters_show(self, *args)
862 
863 
864  def __str__(self):
865  """__str__(SegmentationParameters self) -> std::string"""
866  return _IMP_em2d.SegmentationParameters___str__(self)
867 
868 
869  def __repr__(self):
870  """__repr__(SegmentationParameters self) -> std::string"""
871  return _IMP_em2d.SegmentationParameters___repr__(self)
872 
873  __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
874  __del__ = lambda self: None
875 SegmentationParameters_swigregister = _IMP_em2d.SegmentationParameters_swigregister
876 SegmentationParameters_swigregister(SegmentationParameters)
877 
878 class MatchTemplateResult(object):
879  """Proxy of C++ IMP::em2d::MatchTemplateResult class."""
880 
881  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
882  pair = _swig_property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set)
883  cross_correlation = _swig_property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set)
884 
885  def __init__(self, p, cc):
886  """__init__(IMP::em2d::MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
887  this = _IMP_em2d.new_MatchTemplateResult(p, cc)
888  try:
889  self.this.append(this)
890  except __builtin__.Exception:
891  self.this = this
892 
893  def show(self, *args):
894  """
895  show(MatchTemplateResult self, _ostream out)
896  show(MatchTemplateResult self)
897  """
898  return _IMP_em2d.MatchTemplateResult_show(self, *args)
899 
900 
901  def __str__(self):
902  """__str__(MatchTemplateResult self) -> std::string"""
903  return _IMP_em2d.MatchTemplateResult___str__(self)
904 
905 
906  def __repr__(self):
907  """__repr__(MatchTemplateResult self) -> std::string"""
908  return _IMP_em2d.MatchTemplateResult___repr__(self)
909 
910  __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
911  __del__ = lambda self: None
912 MatchTemplateResult_swigregister = _IMP_em2d.MatchTemplateResult_swigregister
913 MatchTemplateResult_swigregister(MatchTemplateResult)
914 
915 
916 def apply_mask(m, result, mask, val):
917  """apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
918  return _IMP_em2d.apply_mask(m, result, mask, val)
919 
920 def apply_circular_mask(mat, result, radius, value=0.0):
921  """
922  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)
923  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius)
924  """
925  return _IMP_em2d.apply_circular_mask(mat, result, radius, value)
926 
927 def get_mean(mat, mask):
928  """get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
929  return _IMP_em2d.get_mean(mat, mask)
930 
931 def create_circular_mask(rows, cols, radius):
932  """create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
933  return _IMP_em2d.create_circular_mask(rows, cols, radius)
934 
935 def do_histogram_stretching(m, boxes, offset):
936  """do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
937  return _IMP_em2d.do_histogram_stretching(m, boxes, offset)
938 
939 def do_dilate_and_shrink_warp(m, grayscale, kernel):
940  """do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
941  return _IMP_em2d.do_dilate_and_shrink_warp(m, grayscale, kernel)
942 
943 def do_morphologic_reconstruction(mask, marker, neighbors_mode=4):
944  """
945  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)
946  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker)
947  """
948  return _IMP_em2d.do_morphologic_reconstruction(mask, marker, neighbors_mode)
949 
950 def do_labeling(m, mat_to_label):
951  """do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
952  return _IMP_em2d.do_labeling(m, mat_to_label)
953 
954 def get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang):
955  """get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
956  return _IMP_em2d.get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang)
957 
958 def get_domes(m, result, h):
959  """get_domes(cv::Mat & m, cv::Mat & result, double h)"""
960  return _IMP_em2d.get_domes(m, result, h)
961 
962 def get_transformed(input, transformed, T):
963  """get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
964  return _IMP_em2d.get_transformed(input, transformed, T)
965 
966 def apply_threshold(m, result, threshold=0.0):
967  """
968  apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)
969  apply_threshold(cv::Mat & m, cv::Mat & result)
970  """
971  return _IMP_em2d.apply_threshold(m, result, threshold)
972 
973 def do_morphologic_contrast_enhancement(m, result, kernel, iterations):
974  """do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
975  return _IMP_em2d.do_morphologic_contrast_enhancement(m, result, kernel, iterations)
976 
977 def get_morphologic_gradient(m, result, kernel):
978  """get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
979  return _IMP_em2d.get_morphologic_gradient(m, result, kernel)
980 
981 def get_overlap_percentage(m1, m2, center):
982  """get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
983  return _IMP_em2d.get_overlap_percentage(m1, m2, center)
984 
985 def get_best_template_matches(m, templ, n):
986  """get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
987  return _IMP_em2d.get_best_template_matches(m, templ, n)
988 class Image(IMP.Object):
989  """Proxy of C++ IMP::em2d::Image class."""
990 
991  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
992 
993  def __init__(self, *args):
994  """
995  __init__(IMP::em2d::Image self) -> Image
996  __init__(IMP::em2d::Image self, int rows, int cols) -> Image
997  __init__(IMP::em2d::Image self, IMP::String filename, ImageReaderWriter reader) -> Image
998  """
999  this = _IMP_em2d.new_Image(*args)
1000  try:
1001  self.this.append(this)
1002  except __builtin__.Exception:
1003  self.this = this
1004 
1005  def get_data(self):
1006  """get_data(Image self) -> cv::Mat &"""
1007  return _IMP_em2d.Image_get_data(self)
1008 
1009 
1010  def set_data(self, mat):
1011  """set_data(Image self, cv::Mat const & mat)"""
1012  return _IMP_em2d.Image_set_data(self, mat)
1013 
1014 
1015  def set_zeros(self):
1016  """set_zeros(Image self)"""
1017  return _IMP_em2d.Image_set_zeros(self)
1018 
1019 
1020  def set_value(self, *args):
1021  """
1022  set_value(Image self, double val)
1023  set_value(Image self, int i, int j, double val)
1024  """
1025  return _IMP_em2d.Image_set_value(self, *args)
1026 
1027 
1028  def __call__(self, i, j):
1029  """__call__(Image self, int i, int j) -> double"""
1030  return _IMP_em2d.Image___call__(self, i, j)
1031 
1032 
1033  def get_header(self):
1034  """get_header(Image self) -> ImageHeader"""
1035  return _IMP_em2d.Image_get_header(self)
1036 
1037 
1038  def set_size(self, *args):
1039  """
1040  set_size(Image self, int rows, int cols)
1041  set_size(Image self, Image img)
1042  """
1043  return _IMP_em2d.Image_set_size(self, *args)
1044 
1045 
1046  def update_header(self):
1047  """update_header(Image self)"""
1048  return _IMP_em2d.Image_update_header(self)
1049 
1050 
1051  def read(self, filename, reader):
1052  """read(Image self, IMP::String filename, ImageReaderWriter reader)"""
1053  return _IMP_em2d.Image_read(self, filename, reader)
1054 
1055 
1056  def write(self, filename, writer):
1057  """write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
1058  return _IMP_em2d.Image_write(self, filename, writer)
1059 
1060 
1061  def show(self, out):
1062  """show(Image self, _ostream out)"""
1063  return _IMP_em2d.Image_show(self, out)
1064 
1065 
1066  def get_version_info(self):
1067  """get_version_info(Image self) -> VersionInfo"""
1068  return _IMP_em2d.Image_get_version_info(self)
1069 
1070 
1071  def set_name(self, name):
1072  """set_name(Image self, IMP::String const & name)"""
1073  return _IMP_em2d.Image_set_name(self, name)
1074 
1075 
1076  def get_name(self):
1077  """get_name(Image self) -> IMP::String"""
1078  return _IMP_em2d.Image_get_name(self)
1079 
1080 
1081  def get_min_and_max_values(self):
1082  """get_min_and_max_values(Image self) -> IMP::FloatRange"""
1083  return _IMP_em2d.Image_get_min_and_max_values(self)
1084 
1085 
1086  def __str__(self):
1087  """__str__(Image self) -> std::string"""
1088  return _IMP_em2d.Image___str__(self)
1089 
1090 
1091  def __repr__(self):
1092  """__repr__(Image self) -> std::string"""
1093  return _IMP_em2d.Image___repr__(self)
1094 
1095 
1096  @staticmethod
1097  def get_from(o):
1098  return _object_cast_to_Image(o)
1099 
1100 Image_swigregister = _IMP_em2d.Image_swigregister
1101 Image_swigregister(Image)
1102 
1103 
1104 def read_images(names, rw):
1105  """read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1106  return _IMP_em2d.read_images(names, rw)
1107 
1108 def save_images(images, names, rw):
1109  """save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1110  return _IMP_em2d.save_images(images, names, rw)
1111 
1112 def do_normalize(*args):
1113  """
1114  do_normalize(cv::Mat & m)
1115  do_normalize(Image im, bool force=False)
1116  do_normalize(Image im)
1117  """
1118  return _IMP_em2d.do_normalize(*args)
1119 
1120 def get_histogram(*args):
1121  """
1122  get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1123  get_histogram(Image img, int bins) -> IMP::Floats
1124  """
1125  return _IMP_em2d.get_histogram(*args)
1126 
1127 def apply_variance_filter(*args):
1128  """
1129  apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1130  apply_variance_filter(Image input, Image filtered, int kernelsize)
1131  """
1132  return _IMP_em2d.apply_variance_filter(*args)
1133 
1134 def apply_diffusion_filter(*args):
1135  """
1136  apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1137  apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1138  """
1139  return _IMP_em2d.apply_diffusion_filter(*args)
1140 
1141 def do_fill_holes(*args):
1142  """
1143  do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1144  do_fill_holes(Image input, Image result, double n_stddevs)
1145  """
1146  return _IMP_em2d.do_fill_holes(*args)
1147 
1148 def do_combined_fill_holes_and_threshold(*args):
1149  """
1150  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1151  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs)
1152  do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1153  """
1154  return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1155 
1156 def do_extend_borders(*args):
1157  """
1158  do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1159  do_extend_borders(Image im1, Image im2, unsigned int pix)
1160  """
1161  return _IMP_em2d.do_extend_borders(*args)
1162 
1163 def do_segmentation(*args):
1164  """
1165  do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1166  do_segmentation(Image input, Image result, SegmentationParameters params)
1167  """
1168  return _IMP_em2d.do_segmentation(*args)
1169 
1170 def do_remove_small_objects(*args):
1171  """
1172  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1173  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0)
1174  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage)
1175  do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1176  do_remove_small_objects(Image input, double percentage, int background=0)
1177  do_remove_small_objects(Image input, double percentage)
1178  """
1179  return _IMP_em2d.do_remove_small_objects(*args)
1180 
1181 def do_subtract_images(first, second, result):
1182  """do_subtract_images(Image first, Image second, Image result)"""
1183  return _IMP_em2d.do_subtract_images(first, second, result)
1184 
1185 def add_noise(*args):
1186  """
1187  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode, double df=3)
1188  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode)
1189  add_noise(cv::Mat & v, double op1, double op2)
1190  add_noise(Image im1, double op1, double op2, IMP::String const & mode, double df=3)
1191  add_noise(Image im1, double op1, double op2, IMP::String const & mode)
1192  add_noise(Image im1, double op1, double op2)
1193  """
1194  return _IMP_em2d.add_noise(*args)
1195 
1196 def do_resample_polar(*args):
1197  """
1198  do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1199  do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1200  """
1201  return _IMP_em2d.do_resample_polar(*args)
1202 
1203 def crop(*args):
1204  """
1205  crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1206  crop(Image img, IMP::IntPair const & center, int size)
1207  """
1208  return _IMP_em2d.crop(*args)
1209 
1210 def apply_mean_outside_mask(img, radius):
1211  """apply_mean_outside_mask(Image img, double radius)"""
1212  return _IMP_em2d.apply_mean_outside_mask(img, radius)
1213 class RegistrationResult(object):
1214  """Proxy of C++ IMP::em2d::RegistrationResult class."""
1215 
1216  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1217 
1218  def __init__(self, *args):
1219  """
1220  __init__(IMP::em2d::RegistrationResult self) -> RegistrationResult
1221  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1222  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1223  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0) -> RegistrationResult
1224  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift) -> RegistrationResult
1225  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1226  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1227  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0) -> RegistrationResult
1228  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift) -> RegistrationResult
1229  __init__(IMP::em2d::RegistrationResult self, Rotation3D R) -> RegistrationResult
1230  """
1231  this = _IMP_em2d.new_RegistrationResult(*args)
1232  try:
1233  self.this.append(this)
1234  except __builtin__.Exception:
1235  self.this = this
1236 
1237  def get_phi(self):
1238  """get_phi(RegistrationResult self) -> double"""
1239  return _IMP_em2d.RegistrationResult_get_phi(self)
1240 
1241 
1242  def get_theta(self):
1243  """get_theta(RegistrationResult self) -> double"""
1244  return _IMP_em2d.RegistrationResult_get_theta(self)
1245 
1246 
1247  def get_psi(self):
1248  """get_psi(RegistrationResult self) -> double"""
1249  return _IMP_em2d.RegistrationResult_get_psi(self)
1250 
1251 
1252  def get_shift(self):
1253  """get_shift(RegistrationResult self) -> Vector2D"""
1254  return _IMP_em2d.RegistrationResult_get_shift(self)
1255 
1256 
1257  def get_shift_3d(self):
1258  """get_shift_3d(RegistrationResult self) -> Vector3D"""
1259  return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1260 
1261 
1262  def get_projection_index(self):
1263  """get_projection_index(RegistrationResult self) -> int"""
1264  return _IMP_em2d.RegistrationResult_get_projection_index(self)
1265 
1266 
1267  def set_projection_index(self, index):
1268  """set_projection_index(RegistrationResult self, int index)"""
1269  return _IMP_em2d.RegistrationResult_set_projection_index(self, index)
1270 
1271 
1272  def get_image_index(self):
1273  """get_image_index(RegistrationResult self) -> int"""
1274  return _IMP_em2d.RegistrationResult_get_image_index(self)
1275 
1276 
1277  def set_image_index(self, index):
1278  """set_image_index(RegistrationResult self, int index)"""
1279  return _IMP_em2d.RegistrationResult_set_image_index(self, index)
1280 
1281 
1282  def get_name(self):
1283  """get_name(RegistrationResult self) -> IMP::String"""
1284  return _IMP_em2d.RegistrationResult_get_name(self)
1285 
1286 
1287  def get_ccc(self):
1288  """get_ccc(RegistrationResult self) -> double"""
1289  return _IMP_em2d.RegistrationResult_get_ccc(self)
1290 
1291 
1292  def set_ccc(self, ccc):
1293  """set_ccc(RegistrationResult self, double ccc)"""
1294  return _IMP_em2d.RegistrationResult_set_ccc(self, ccc)
1295 
1296 
1297  def get_score(self):
1298  """get_score(RegistrationResult self) -> double"""
1299  return _IMP_em2d.RegistrationResult_get_score(self)
1300 
1301 
1302  def set_score(self, Score):
1303  """set_score(RegistrationResult self, double Score)"""
1304  return _IMP_em2d.RegistrationResult_set_score(self, Score)
1305 
1306 
1307  def set_rotation(self, *args):
1308  """
1309  set_rotation(RegistrationResult self, double phi, double theta, double psi)
1310  set_rotation(RegistrationResult self, Rotation3D R)
1311  """
1312  return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1313 
1314 
1315  def set_shift(self, shift):
1316  """set_shift(RegistrationResult self, Vector2D shift)"""
1317  return _IMP_em2d.RegistrationResult_set_shift(self, shift)
1318 
1319 
1320  def set_name(self, name):
1321  """set_name(RegistrationResult self, IMP::String name)"""
1322  return _IMP_em2d.RegistrationResult_set_name(self, name)
1323 
1324 
1325  def add_in_plane_transformation(self, t):
1326  """add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1327  return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, t)
1328 
1329 
1330  def show(self, *args):
1331  """
1332  show(RegistrationResult self, _ostream out)
1333  show(RegistrationResult self)
1334  """
1335  return _IMP_em2d.RegistrationResult_show(self, *args)
1336 
1337 
1338  def write(self, *args):
1339  """
1340  write(RegistrationResult self, _ostream out)
1341  write(RegistrationResult self)
1342  """
1343  return _IMP_em2d.RegistrationResult_write(self, *args)
1344 
1345 
1346  def write_comment_line(self, *args):
1347  """
1348  write_comment_line(RegistrationResult self, _ostream out)
1349  write_comment_line(RegistrationResult self)
1350  """
1351  return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1352 
1353 
1354  def read(self, s):
1355  """read(RegistrationResult self, IMP::String const & s)"""
1356  return _IMP_em2d.RegistrationResult_read(self, s)
1357 
1358 
1359  def set_random_registration(self, index, maximum_shift):
1360  """set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1361  return _IMP_em2d.RegistrationResult_set_random_registration(self, index, maximum_shift)
1362 
1363 
1364  def get_rotation(self):
1365  """get_rotation(RegistrationResult self) -> Rotation3D"""
1366  return _IMP_em2d.RegistrationResult_get_rotation(self)
1367 
1368 
1369  def set_in_image(self, header):
1370  """set_in_image(RegistrationResult self, ImageHeader header)"""
1371  return _IMP_em2d.RegistrationResult_set_in_image(self, header)
1372 
1373 
1374  def read_from_image(self, header):
1375  """read_from_image(RegistrationResult self, ImageHeader header)"""
1376  return _IMP_em2d.RegistrationResult_read_from_image(self, header)
1377 
1378 
1379  def get_is_optimized_result(self):
1380  """get_is_optimized_result(RegistrationResult self) -> bool"""
1381  return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1382 
1383  __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1384  __del__ = lambda self: None
1385 
1386  def __str__(self):
1387  """__str__(RegistrationResult self) -> std::string"""
1388  return _IMP_em2d.RegistrationResult___str__(self)
1389 
1390 
1391  def __repr__(self):
1392  """__repr__(RegistrationResult self) -> std::string"""
1393  return _IMP_em2d.RegistrationResult___repr__(self)
1394 
1395 RegistrationResult_swigregister = _IMP_em2d.RegistrationResult_swigregister
1396 RegistrationResult_swigregister(RegistrationResult)
1397 
1398 
1399 def read_registration_results(filename):
1400  """read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1401  return _IMP_em2d.read_registration_results(filename)
1402 
1403 def write_registration_results(filename, results):
1404  """write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1405  return _IMP_em2d.write_registration_results(filename, results)
1406 
1407 def get_random_registration_results(n, maximum_shift=5.0):
1408  """
1409  get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults
1410  get_random_registration_results(unsigned int n) -> IMP::em2d::RegistrationResults
1411  """
1412  return _IMP_em2d.get_random_registration_results(n, maximum_shift)
1413 
1415  """get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1416  return _IMP_em2d.get_evenly_distributed_registration_results(n_projections)
1417 class SpiderImageReaderWriter(ImageReaderWriter):
1418  """Proxy of C++ IMP::em2d::SpiderImageReaderWriter class."""
1419 
1420  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1421  filename_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set)
1422  skip_type_check_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set)
1423  force_reversed_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set)
1424  skip_extra_checkings_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set)
1425 
1426  def __init__(self, *args):
1427  """
1428  __init__(IMP::em2d::SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1429  __init__(IMP::em2d::SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1430  """
1431  this = _IMP_em2d.new_SpiderImageReaderWriter(*args)
1432  try:
1433  self.this.append(this)
1434  except __builtin__.Exception:
1435  self.this = this
1436 
1437  def __str__(self):
1438  """__str__(SpiderImageReaderWriter self) -> std::string"""
1439  return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1440 
1441 
1442  def __repr__(self):
1443  """__repr__(SpiderImageReaderWriter self) -> std::string"""
1444  return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1445 
1446 
1447  @staticmethod
1448  def get_from(o):
1449  return _object_cast_to_SpiderImageReaderWriter(o)
1450 
1451 SpiderImageReaderWriter_swigregister = _IMP_em2d.SpiderImageReaderWriter_swigregister
1452 SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1453 
1454 class JPGImageReaderWriter(ImageReaderWriter):
1455  """Proxy of C++ IMP::em2d::JPGImageReaderWriter class."""
1456 
1457  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1458 
1459  def __init__(self):
1460  """__init__(IMP::em2d::JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1461  this = _IMP_em2d.new_JPGImageReaderWriter()
1462  try:
1463  self.this.append(this)
1464  except __builtin__.Exception:
1465  self.this = this
1466 
1467  def __str__(self):
1468  """__str__(JPGImageReaderWriter self) -> std::string"""
1469  return _IMP_em2d.JPGImageReaderWriter___str__(self)
1470 
1471 
1472  def __repr__(self):
1473  """__repr__(JPGImageReaderWriter self) -> std::string"""
1474  return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1475 
1476 
1477  @staticmethod
1478  def get_from(o):
1479  return _object_cast_to_JPGImageReaderWriter(o)
1480 
1481 JPGImageReaderWriter_swigregister = _IMP_em2d.JPGImageReaderWriter_swigregister
1482 JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1483 
1484 class TIFFImageReaderWriter(ImageReaderWriter):
1485  """Proxy of C++ IMP::em2d::TIFFImageReaderWriter class."""
1486 
1487  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1488 
1489  def __init__(self):
1490  """__init__(IMP::em2d::TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1491  this = _IMP_em2d.new_TIFFImageReaderWriter()
1492  try:
1493  self.this.append(this)
1494  except __builtin__.Exception:
1495  self.this = this
1496 
1497  def __str__(self):
1498  """__str__(TIFFImageReaderWriter self) -> std::string"""
1499  return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1500 
1501 
1502  def __repr__(self):
1503  """__repr__(TIFFImageReaderWriter self) -> std::string"""
1504  return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1505 
1506 
1507  @staticmethod
1508  def get_from(o):
1509  return _object_cast_to_TIFFImageReaderWriter(o)
1510 
1511 TIFFImageReaderWriter_swigregister = _IMP_em2d.TIFFImageReaderWriter_swigregister
1512 TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1513 
1514 
1516  """do_matrix_to_image_flip(cv::Mat & m)"""
1517  return _IMP_em2d.do_matrix_to_image_flip(m)
1518 
1520  """get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1521  return _IMP_em2d.get_autocorrelation2d_no_preprocessing(M, corr)
1522 
1523 def get_autocorrelation2d(*args):
1524  """
1525  get_autocorrelation2d(Image im1, Image im2)
1526  get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1527  """
1528  return _IMP_em2d.get_autocorrelation2d(*args)
1529 
1530 def get_correlation2d(*args):
1531  """
1532  get_correlation2d(Image im1, Image im2, Image corr)
1533  get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1534  """
1535  return _IMP_em2d.get_correlation2d(*args)
1536 
1537 def get_correlation2d_no_preprocessing(M1, M2, corr):
1538  """get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1539  return _IMP_em2d.get_correlation2d_no_preprocessing(M1, M2, corr)
1540 
1541 def get_fft_using_optimal_size(m, M):
1542  """get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1543  return _IMP_em2d.get_fft_using_optimal_size(m, M)
1544 
1545 def get_spectrum(m, real, imag):
1546  """get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1547  return _IMP_em2d.get_spectrum(m, real, imag)
1548 
1549 def get_rotation_error(rr1, rr2):
1550  """get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1551  return _IMP_em2d.get_rotation_error(rr1, rr2)
1552 
1553 def get_shift_error(rr1, rr2):
1554  """get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1555  return _IMP_em2d.get_shift_error(rr1, rr2)
1556 
1557 def get_average_rotation_error(correct_RRs, computed_RRs):
1558  """get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1559  return _IMP_em2d.get_average_rotation_error(correct_RRs, computed_RRs)
1560 
1561 def get_average_shift_error(correct_RRs, computed_RRs):
1562  """get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1563  return _IMP_em2d.get_average_shift_error(correct_RRs, computed_RRs)
1564 
1566  """
1567  get_cross_correlation_coefficient(Image im1, Image im2) -> double
1568  get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1569  """
1570  return _IMP_em2d.get_cross_correlation_coefficient(*args)
1571 
1572 def get_global_score(RRs):
1573  """get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1574  return _IMP_em2d.get_global_score(RRs)
1575 class ScoreFunction(IMP.Object):
1576  """Proxy of C++ IMP::em2d::ScoreFunction class."""
1577 
1578  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1579 
1580  def __init__(self, *args, **kwargs):
1581  raise AttributeError("No constructor defined - class is abstract")
1582 
1583  def get_score(self, image, projection):
1584  """get_score(ScoreFunction self, Image image, Image projection) -> double"""
1585  return _IMP_em2d.ScoreFunction_get_score(self, image, projection)
1586 
1587 
1588  def set_variance_image(self, var):
1589  """set_variance_image(ScoreFunction self, Image var)"""
1590  return _IMP_em2d.ScoreFunction_set_variance_image(self, var)
1591 
1592 
1593  def get_version_info(self):
1594  """get_version_info(ScoreFunction self) -> VersionInfo"""
1595  return _IMP_em2d.ScoreFunction_get_version_info(self)
1596 
1597 
1598  def __str__(self):
1599  """__str__(ScoreFunction self) -> std::string"""
1600  return _IMP_em2d.ScoreFunction___str__(self)
1601 
1602 
1603  def __repr__(self):
1604  """__repr__(ScoreFunction self) -> std::string"""
1605  return _IMP_em2d.ScoreFunction___repr__(self)
1606 
1607 
1608  @staticmethod
1609  def get_from(o):
1610  return _object_cast_to_ScoreFunction(o)
1611 
1612 ScoreFunction_swigregister = _IMP_em2d.ScoreFunction_swigregister
1613 ScoreFunction_swigregister(ScoreFunction)
1614 
1615 class ChiSquaredScore(ScoreFunction):
1616  """Proxy of C++ IMP::em2d::ChiSquaredScore class."""
1617 
1618  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1619 
1620  def __init__(self):
1621  """__init__(IMP::em2d::ChiSquaredScore self) -> ChiSquaredScore"""
1622  this = _IMP_em2d.new_ChiSquaredScore()
1623  try:
1624  self.this.append(this)
1625  except __builtin__.Exception:
1626  self.this = this
1627 
1628  def __str__(self):
1629  """__str__(ChiSquaredScore self) -> std::string"""
1630  return _IMP_em2d.ChiSquaredScore___str__(self)
1631 
1632 
1633  def __repr__(self):
1634  """__repr__(ChiSquaredScore self) -> std::string"""
1635  return _IMP_em2d.ChiSquaredScore___repr__(self)
1636 
1637 
1638  @staticmethod
1639  def get_from(o):
1640  return _object_cast_to_ChiSquaredScore(o)
1641 
1642  __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1643  __del__ = lambda self: None
1644 ChiSquaredScore_swigregister = _IMP_em2d.ChiSquaredScore_swigregister
1645 ChiSquaredScore_swigregister(ChiSquaredScore)
1646 
1647 class EM2DScore(ScoreFunction):
1648  """Proxy of C++ IMP::em2d::EM2DScore class."""
1649 
1650  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1651 
1652  def __init__(self):
1653  """__init__(IMP::em2d::EM2DScore self) -> EM2DScore"""
1654  this = _IMP_em2d.new_EM2DScore()
1655  try:
1656  self.this.append(this)
1657  except __builtin__.Exception:
1658  self.this = this
1659 
1660  def __str__(self):
1661  """__str__(EM2DScore self) -> std::string"""
1662  return _IMP_em2d.EM2DScore___str__(self)
1663 
1664 
1665  def __repr__(self):
1666  """__repr__(EM2DScore self) -> std::string"""
1667  return _IMP_em2d.EM2DScore___repr__(self)
1668 
1669 
1670  @staticmethod
1671  def get_from(o):
1672  return _object_cast_to_EM2DScore(o)
1673 
1674  __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1675  __del__ = lambda self: None
1676 EM2DScore_swigregister = _IMP_em2d.EM2DScore_swigregister
1677 EM2DScore_swigregister(EM2DScore)
1678 
1679 class MeanAbsoluteDifference(ScoreFunction):
1680  """Proxy of C++ IMP::em2d::MeanAbsoluteDifference class."""
1681 
1682  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1683 
1684  def __init__(self):
1685  """__init__(IMP::em2d::MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1686  this = _IMP_em2d.new_MeanAbsoluteDifference()
1687  try:
1688  self.this.append(this)
1689  except __builtin__.Exception:
1690  self.this = this
1691 
1692  def __str__(self):
1693  """__str__(MeanAbsoluteDifference self) -> std::string"""
1694  return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1695 
1696 
1697  def __repr__(self):
1698  """__repr__(MeanAbsoluteDifference self) -> std::string"""
1699  return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1700 
1701 
1702  @staticmethod
1703  def get_from(o):
1704  return _object_cast_to_MeanAbsoluteDifference(o)
1705 
1706  __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1707  __del__ = lambda self: None
1708 MeanAbsoluteDifference_swigregister = _IMP_em2d.MeanAbsoluteDifference_swigregister
1709 MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1710 
1711 
1712 def read_selection_file(fn):
1713  """read_selection_file(IMP::String fn) -> IMP::Strings"""
1714  return _IMP_em2d.read_selection_file(fn)
1715 
1716 def create_filenames(number, basic_name, extension):
1717  """create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1718  return _IMP_em2d.create_filenames(number, basic_name, extension)
1719 class ProjectionParameters(IMP.Decorator):
1720  """Proxy of C++ IMP::em2d::ProjectionParameters class."""
1721 
1722  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1723 
1724  def __init__(self, *args):
1725  """
1726  __init__(IMP::em2d::ProjectionParameters self) -> ProjectionParameters
1727  __init__(IMP::em2d::ProjectionParameters self, Model m, ParticleIndex id) -> ProjectionParameters
1728  __init__(IMP::em2d::ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1729  """
1730  this = _IMP_em2d.new_ProjectionParameters(*args)
1731  try:
1732  self.this.append(this)
1733  except __builtin__.Exception:
1734  self.this = this
1735 
1736  def show(self, *args):
1737  """
1738  show(ProjectionParameters self, _ostream out)
1739  show(ProjectionParameters self)
1740  """
1741  return _IMP_em2d.ProjectionParameters_show(self, *args)
1742 
1743 
1744  def setup_particle(*args):
1745  """
1746  setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
1747  setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1748  """
1749  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1750 
1751  setup_particle = staticmethod(setup_particle)
1752  __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1753  __del__ = lambda self: None
1754 
1755  def get_keys():
1756  """get_keys() -> IMP::FloatKeys const &"""
1757  return _IMP_em2d.ProjectionParameters_get_keys()
1758 
1759  get_keys = staticmethod(get_keys)
1760 
1761  def set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values):
1762  """set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1763  return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values)
1764 
1765 
1766  def get_is_setup(*args):
1767  """
1768  get_is_setup(_ParticleAdaptor p) -> bool
1769  get_is_setup(Model m, ParticleIndex pi) -> bool
1770  """
1771  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1772 
1773  get_is_setup = staticmethod(get_is_setup)
1774 
1775  def get_parameters_optimized(self):
1776  """get_parameters_optimized(ProjectionParameters self) -> bool"""
1777  return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1778 
1779 
1780  def get_translation(self):
1781  """get_translation(ProjectionParameters self) -> Vector3D"""
1782  return _IMP_em2d.ProjectionParameters_get_translation(self)
1783 
1784 
1785  def set_translation(self, v):
1786  """set_translation(ProjectionParameters self, Vector3D v)"""
1787  return _IMP_em2d.ProjectionParameters_set_translation(self, v)
1788 
1789 
1790  def get_rotation(self):
1791  """get_rotation(ProjectionParameters self) -> Rotation3D"""
1792  return _IMP_em2d.ProjectionParameters_get_rotation(self)
1793 
1794 
1795  def set_rotation(self, R):
1796  """set_rotation(ProjectionParameters self, Rotation3D R)"""
1797  return _IMP_em2d.ProjectionParameters_set_rotation(self, R)
1798 
1799 
1800  def set_parameters_optimized(self, tf):
1801  """set_parameters_optimized(ProjectionParameters self, bool tf)"""
1802  return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, tf)
1803 
1804 
1805  def get_quaternion_1(self):
1806  """get_quaternion_1(ProjectionParameters self) -> double"""
1807  return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1808 
1809 
1810  def set_quaternion_1(self, t):
1811  """set_quaternion_1(ProjectionParameters self, double t)"""
1812  return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, t)
1813 
1814 
1815  def get_quaternion_2(self):
1816  """get_quaternion_2(ProjectionParameters self) -> double"""
1817  return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1818 
1819 
1820  def set_quaternion_2(self, t):
1821  """set_quaternion_2(ProjectionParameters self, double t)"""
1822  return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, t)
1823 
1824 
1825  def get_quaternion_3(self):
1826  """get_quaternion_3(ProjectionParameters self) -> double"""
1827  return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1828 
1829 
1830  def set_quaternion_3(self, t):
1831  """set_quaternion_3(ProjectionParameters self, double t)"""
1832  return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, t)
1833 
1834 
1835  def get_quaternion_4(self):
1836  """get_quaternion_4(ProjectionParameters self) -> double"""
1837  return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1838 
1839 
1840  def set_quaternion_4(self, t):
1841  """set_quaternion_4(ProjectionParameters self, double t)"""
1842  return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, t)
1843 
1844 
1845  def get_translation_x(self):
1846  """get_translation_x(ProjectionParameters self) -> double"""
1847  return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1848 
1849 
1850  def set_translation_x(self, t):
1851  """set_translation_x(ProjectionParameters self, double t)"""
1852  return _IMP_em2d.ProjectionParameters_set_translation_x(self, t)
1853 
1854 
1855  def get_translation_y(self):
1856  """get_translation_y(ProjectionParameters self) -> double"""
1857  return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1858 
1859 
1860  def set_translation_y(self, t):
1861  """set_translation_y(ProjectionParameters self, double t)"""
1862  return _IMP_em2d.ProjectionParameters_set_translation_y(self, t)
1863 
1864 
1865  def add_attribute(self, *args):
1866  """
1867  add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1868  add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1869  add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1870  add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1871  add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1872  add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1873  """
1874  return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1875 
1876 
1877  def get_value(self, *args):
1878  """
1879  get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1880  get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1881  get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1882  get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1883  get_value(ProjectionParameters self, ObjectKey a0) -> Object
1884  """
1885  return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1886 
1887 
1888  def set_value(self, *args):
1889  """
1890  set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1891  set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1892  set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1893  set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1894  set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1895  """
1896  return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1897 
1898 
1899  def remove_attribute(self, *args):
1900  """
1901  remove_attribute(ProjectionParameters self, FloatKey a0)
1902  remove_attribute(ProjectionParameters self, IntKey a0)
1903  remove_attribute(ProjectionParameters self, StringKey a0)
1904  remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1905  remove_attribute(ProjectionParameters self, ObjectKey a0)
1906  """
1907  return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1908 
1909 
1910  def has_attribute(self, *args):
1911  """
1912  has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1913  has_attribute(ProjectionParameters self, IntKey a0) -> bool
1914  has_attribute(ProjectionParameters self, StringKey a0) -> bool
1915  has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
1916  has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
1917  """
1918  return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
1919 
1920 
1921  def get_derivative(self, a0):
1922  """get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
1923  return _IMP_em2d.ProjectionParameters_get_derivative(self, a0)
1924 
1925 
1926  def get_name(self):
1927  """get_name(ProjectionParameters self) -> std::string"""
1928  return _IMP_em2d.ProjectionParameters_get_name(self)
1929 
1930 
1931  def clear_caches(self):
1932  """clear_caches(ProjectionParameters self)"""
1933  return _IMP_em2d.ProjectionParameters_clear_caches(self)
1934 
1935 
1936  def set_name(self, a0):
1937  """set_name(ProjectionParameters self, std::string a0)"""
1938  return _IMP_em2d.ProjectionParameters_set_name(self, a0)
1939 
1940 
1941  def set_check_level(self, a0):
1942  """set_check_level(ProjectionParameters self, IMP::CheckLevel a0)"""
1943  return _IMP_em2d.ProjectionParameters_set_check_level(self, a0)
1944 
1945 
1946  def add_to_derivative(self, a0, a1, a2):
1947  """add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1948  return _IMP_em2d.ProjectionParameters_add_to_derivative(self, a0, a1, a2)
1949 
1950 
1951  def set_is_optimized(self, a0, a1):
1952  """set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
1953  return _IMP_em2d.ProjectionParameters_set_is_optimized(self, a0, a1)
1954 
1955 
1956  def get_is_optimized(self, a0):
1957  """get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
1958  return _IMP_em2d.ProjectionParameters_get_is_optimized(self, a0)
1959 
1960 
1961  def get_check_level(self):
1962  """get_check_level(ProjectionParameters self) -> IMP::CheckLevel"""
1963  return _IMP_em2d.ProjectionParameters_get_check_level(self)
1964 
1965 
1966  def __eq__(self, *args):
1967  """
1968  __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
1969  __eq__(ProjectionParameters self, Particle d) -> bool
1970  """
1971  return _IMP_em2d.ProjectionParameters___eq__(self, *args)
1972 
1973 
1974  def __ne__(self, *args):
1975  """
1976  __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
1977  __ne__(ProjectionParameters self, Particle d) -> bool
1978  """
1979  return _IMP_em2d.ProjectionParameters___ne__(self, *args)
1980 
1981 
1982  def __le__(self, *args):
1983  """
1984  __le__(ProjectionParameters self, ProjectionParameters o) -> bool
1985  __le__(ProjectionParameters self, Particle d) -> bool
1986  """
1987  return _IMP_em2d.ProjectionParameters___le__(self, *args)
1988 
1989 
1990  def __lt__(self, *args):
1991  """
1992  __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
1993  __lt__(ProjectionParameters self, Particle d) -> bool
1994  """
1995  return _IMP_em2d.ProjectionParameters___lt__(self, *args)
1996 
1997 
1998  def __ge__(self, *args):
1999  """
2000  __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
2001  __ge__(ProjectionParameters self, Particle d) -> bool
2002  """
2003  return _IMP_em2d.ProjectionParameters___ge__(self, *args)
2004 
2005 
2006  def __gt__(self, *args):
2007  """
2008  __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
2009  __gt__(ProjectionParameters self, Particle d) -> bool
2010  """
2011  return _IMP_em2d.ProjectionParameters___gt__(self, *args)
2012 
2013 
2014  def __hash__(self):
2015  """__hash__(ProjectionParameters self) -> std::size_t"""
2016  return _IMP_em2d.ProjectionParameters___hash__(self)
2017 
2018 
2019  def __str__(self):
2020  """__str__(ProjectionParameters self) -> std::string"""
2021  return _IMP_em2d.ProjectionParameters___str__(self)
2022 
2023 
2024  def __repr__(self):
2025  """__repr__(ProjectionParameters self) -> std::string"""
2026  return _IMP_em2d.ProjectionParameters___repr__(self)
2027 
2028 ProjectionParameters_swigregister = _IMP_em2d.ProjectionParameters_swigregister
2029 ProjectionParameters_swigregister(ProjectionParameters)
2030 
2031 def ProjectionParameters_setup_particle(*args):
2032  """
2033  setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
2034  ProjectionParameters_setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
2035  """
2036  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
2037 
2038 def ProjectionParameters_get_keys():
2039  """ProjectionParameters_get_keys() -> IMP::FloatKeys const &"""
2040  return _IMP_em2d.ProjectionParameters_get_keys()
2041 
2042 def ProjectionParameters_get_is_setup(*args):
2043  """
2044  get_is_setup(_ParticleAdaptor p) -> bool
2045  ProjectionParameters_get_is_setup(Model m, ParticleIndex pi) -> bool
2046  """
2047  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
2048 
2049 
2050 def __lshift__(out, n):
2051  """__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
2052  return _IMP_em2d.__lshift__(out, n)
2053 class ProjectionParametersScoreState(IMP.ScoreState):
2054  """Proxy of C++ IMP::em2d::ProjectionParametersScoreState class."""
2055 
2056  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2057 
2058  def __init__(self, p):
2059  """__init__(IMP::em2d::ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
2060  this = _IMP_em2d.new_ProjectionParametersScoreState(p)
2061  try:
2062  self.this.append(this)
2063  except __builtin__.Exception:
2064  self.this = this
2065 
2066  def do_before_evaluate(self):
2067  """do_before_evaluate(ProjectionParametersScoreState self)"""
2068  return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
2069 
2070 
2071  def do_after_evaluate(self, da):
2072  """do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
2073  return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, da)
2074 
2075 
2076  def do_get_inputs(self):
2077  """do_get_inputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2078  return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
2079 
2080 
2081  def do_get_outputs(self):
2082  """do_get_outputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2083  return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
2084 
2085 
2086  def get_version_info(self):
2087  """get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
2088  return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
2089 
2090 
2091  def __str__(self):
2092  """__str__(ProjectionParametersScoreState self) -> std::string"""
2093  return _IMP_em2d.ProjectionParametersScoreState___str__(self)
2094 
2095 
2096  def __repr__(self):
2097  """__repr__(ProjectionParametersScoreState self) -> std::string"""
2098  return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
2099 
2100 
2101  @staticmethod
2102  def get_from(o):
2103  return _object_cast_to_ProjectionParametersScoreState(o)
2104 
2105 ProjectionParametersScoreState_swigregister = _IMP_em2d.ProjectionParametersScoreState_swigregister
2106 ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
2107 
2108 class ProjectionMask(object):
2109  """Proxy of C++ IMP::em2d::ProjectionMask class."""
2110 
2111  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2112 
2113  def __init__(self, *args, **kwargs):
2114  raise AttributeError("No constructor defined")
2115 
2116  def apply(self, m, v):
2117  """apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
2118  return _IMP_em2d.ProjectionMask_apply(self, m, v)
2119 
2120 
2121  def show(self, *args):
2122  """
2123  show(ProjectionMask self, _ostream out)
2124  show(ProjectionMask self)
2125  """
2126  return _IMP_em2d.ProjectionMask_show(self, *args)
2127 
2128  __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
2129  __del__ = lambda self: None
2130 
2131  def __str__(self):
2132  """__str__(ProjectionMask self) -> std::string"""
2133  return _IMP_em2d.ProjectionMask___str__(self)
2134 
2135 
2136  def __repr__(self):
2137  """__repr__(ProjectionMask self) -> std::string"""
2138  return _IMP_em2d.ProjectionMask___repr__(self)
2139 
2140 ProjectionMask_swigregister = _IMP_em2d.ProjectionMask_swigregister
2141 ProjectionMask_swigregister(ProjectionMask)
2142 
2143 
2144 def do_place(mask, m, v):
2145  """do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
2146  return _IMP_em2d.do_place(mask, m, v)
2147 class MasksManager(object):
2148  """Proxy of C++ IMP::em2d::MasksManager class."""
2149 
2150  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2151 
2152  def __init__(self, *args):
2153  """
2154  __init__(IMP::em2d::MasksManager self) -> MasksManager
2155  __init__(IMP::em2d::MasksManager self, double resolution, double pixelsize) -> MasksManager
2156  """
2157  this = _IMP_em2d.new_MasksManager(*args)
2158  try:
2159  self.this.append(this)
2160  except __builtin__.Exception:
2161  self.this = this
2162 
2163  def setup_kernel(self, resolution, pixelsize):
2164  """setup_kernel(MasksManager self, double resolution, double pixelsize)"""
2165  return _IMP_em2d.MasksManager_setup_kernel(self, resolution, pixelsize)
2166 
2167 
2168  def create_masks(self, ps):
2169  """create_masks(MasksManager self, IMP::ParticlesTemp const & ps)"""
2170  return _IMP_em2d.MasksManager_create_masks(self, ps)
2171 
2172 
2173  def create_mask(self, mass):
2174  """create_mask(MasksManager self, double mass)"""
2175  return _IMP_em2d.MasksManager_create_mask(self, mass)
2176 
2177 
2178  def find_mask(self, mass):
2179  """find_mask(MasksManager self, double mass) -> IMP::em2d::ProjectionMaskPtr"""
2180  return _IMP_em2d.MasksManager_find_mask(self, mass)
2181 
2182 
2183  def show(self, *args):
2184  """
2185  show(MasksManager self, _ostream out)
2186  show(MasksManager self)
2187  """
2188  return _IMP_em2d.MasksManager_show(self, *args)
2189 
2190 
2191  def get_number_of_masks(self):
2192  """get_number_of_masks(MasksManager self) -> unsigned int"""
2193  return _IMP_em2d.MasksManager_get_number_of_masks(self)
2194 
2195  __swig_destroy__ = _IMP_em2d.delete_MasksManager
2196  __del__ = lambda self: None
2197 
2198  def __str__(self):
2199  """__str__(MasksManager self) -> std::string"""
2200  return _IMP_em2d.MasksManager___str__(self)
2201 
2202 
2203  def __repr__(self):
2204  """__repr__(MasksManager self) -> std::string"""
2205  return _IMP_em2d.MasksManager___repr__(self)
2206 
2207 MasksManager_swigregister = _IMP_em2d.MasksManager_swigregister
2208 MasksManager_swigregister(MasksManager)
2209 
2210 class ProjectingParameters(object):
2211  """Proxy of C++ IMP::em2d::ProjectingParameters class."""
2212 
2213  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2214  pixel_size = _swig_property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set)
2215  resolution = _swig_property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set)
2216 
2217  def __init__(self, *args):
2218  """
2219  __init__(IMP::em2d::ProjectingParameters self) -> ProjectingParameters
2220  __init__(IMP::em2d::ProjectingParameters self, double ps, double res) -> ProjectingParameters
2221  """
2222  this = _IMP_em2d.new_ProjectingParameters(*args)
2223  try:
2224  self.this.append(this)
2225  except __builtin__.Exception:
2226  self.this = this
2227 
2228  def show(self, *args):
2229  """
2230  show(ProjectingParameters self, _ostream out)
2231  show(ProjectingParameters self)
2232  """
2233  return _IMP_em2d.ProjectingParameters_show(self, *args)
2234 
2235 
2236  def __str__(self):
2237  """__str__(ProjectingParameters self) -> std::string"""
2238  return _IMP_em2d.ProjectingParameters___str__(self)
2239 
2240 
2241  def __repr__(self):
2242  """__repr__(ProjectingParameters self) -> std::string"""
2243  return _IMP_em2d.ProjectingParameters___repr__(self)
2244 
2245  __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2246  __del__ = lambda self: None
2247 ProjectingParameters_swigregister = _IMP_em2d.ProjectingParameters_swigregister
2248 ProjectingParameters_swigregister(ProjectingParameters)
2249 
2250 class ProjectingOptions(ProjectingParameters):
2251  """Proxy of C++ IMP::em2d::ProjectingOptions class."""
2252 
2253  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2254  save_images = _swig_property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set)
2255  normalize = _swig_property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set)
2256  clear_matrix_before_projecting = _swig_property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set)
2257 
2258  def __init__(self, *args):
2259  """
2260  __init__(IMP::em2d::ProjectingOptions self) -> ProjectingOptions
2261  __init__(IMP::em2d::ProjectingOptions self, double ps, double res) -> ProjectingOptions
2262  __init__(IMP::em2d::ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2263  """
2264  this = _IMP_em2d.new_ProjectingOptions(*args)
2265  try:
2266  self.this.append(this)
2267  except __builtin__.Exception:
2268  self.this = this
2269 
2270  def show(self, *args):
2271  """
2272  show(ProjectingOptions self, _ostream out)
2273  show(ProjectingOptions self)
2274  """
2275  return _IMP_em2d.ProjectingOptions_show(self, *args)
2276 
2277 
2278  def __str__(self):
2279  """__str__(ProjectingOptions self) -> std::string"""
2280  return _IMP_em2d.ProjectingOptions___str__(self)
2281 
2282 
2283  def __repr__(self):
2284  """__repr__(ProjectingOptions self) -> std::string"""
2285  return _IMP_em2d.ProjectingOptions___repr__(self)
2286 
2287  __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2288  __del__ = lambda self: None
2289 ProjectingOptions_swigregister = _IMP_em2d.ProjectingOptions_swigregister
2290 ProjectingOptions_swigregister(ProjectingOptions)
2291 
2292 
2293 def get_projections(*args):
2294  """
2295  get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2296  get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2297  get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2298  get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2299  """
2300  return _IMP_em2d.get_projections(*args)
2301 
2302 def get_projection(*args):
2303  """
2304  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks, IMP::String name)
2305  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)
2306  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options)
2307  """
2308  return _IMP_em2d.get_projection(*args)
2309 
2310 def do_project_particles(ps, m2, R, translation, options, masks):
2311  """do_project_particles(IMP::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)"""
2312  return _IMP_em2d.do_project_particles(ps, m2, R, translation, options, masks)
2313 
2314 def create_evenly_distributed_projections(ps, n, options):
2315  """create_evenly_distributed_projections(IMP::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2316  return _IMP_em2d.create_evenly_distributed_projections(ps, n, options)
2317 
2318 def do_project_vectors(*args):
2319  """
2320  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2321  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2322  """
2323  return _IMP_em2d.do_project_vectors(*args)
2324 
2325 def get_enclosing_image_size(ps, pixel_size, slack):
2326  """get_enclosing_image_size(IMP::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2327  return _IMP_em2d.get_enclosing_image_size(ps, pixel_size, slack)
2328 
2329 def get_complete_alignment(input, m_to_align, apply=False):
2330  """
2331  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2332  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2333  """
2334  return _IMP_em2d.get_complete_alignment(input, m_to_align, apply)
2335 
2336 def get_rotational_alignment(input, m_to_align, apply=False):
2337  """
2338  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2339  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2340  """
2341  return _IMP_em2d.get_rotational_alignment(input, m_to_align, apply)
2342 
2343 def get_translational_alignment(input, m_to_align, apply=False):
2344  """
2345  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2346  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2347  """
2348  return _IMP_em2d.get_translational_alignment(input, m_to_align, apply)
2349 
2350 def get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply=False):
2351  """
2352  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
2353  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align, cv::Mat const & POLAR2) -> ResultAlign2D
2354  """
2355  return _IMP_em2d.get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply)
2356 
2357 def get_rotational_alignment_no_preprocessing(POLAR1, POLAR2):
2358  """get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2359  return _IMP_em2d.get_rotational_alignment_no_preprocessing(POLAR1, POLAR2)
2360 
2362  """get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2363  return _IMP_em2d.get_translational_alignment_no_preprocessing(M1, M2)
2364 
2365 def get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2):
2366  """get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2367  return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2)
2368 
2369 def write_vectors_as_pdb(*args):
2370  """
2371  write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2372  write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2373  """
2374  return _IMP_em2d.write_vectors_as_pdb(*args)
2375 class Em2DRestraintParameters(ProjectingParameters):
2376  """Proxy of C++ IMP::em2d::Em2DRestraintParameters class."""
2377 
2378  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2379  n_projections = _swig_property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set)
2380  coarse_registration_method = _swig_property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set)
2381  save_match_images = _swig_property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set)
2382  optimization_steps = _swig_property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set)
2383  simplex_initial_length = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set)
2384  simplex_minimum_size = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set)
2385 
2386  def __init__(self, *args):
2387  """
2388  __init__(IMP::em2d::Em2DRestraintParameters self) -> Em2DRestraintParameters
2389  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2390  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res) -> Em2DRestraintParameters
2391  """
2392  this = _IMP_em2d.new_Em2DRestraintParameters(*args)
2393  try:
2394  self.this.append(this)
2395  except __builtin__.Exception:
2396  self.this = this
2397 
2398  def show(self, *args):
2399  """
2400  show(Em2DRestraintParameters self, _ostream out)
2401  show(Em2DRestraintParameters self)
2402  """
2403  return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2404 
2405 
2406  def __str__(self):
2407  """__str__(Em2DRestraintParameters self) -> std::string"""
2408  return _IMP_em2d.Em2DRestraintParameters___str__(self)
2409 
2410 
2411  def __repr__(self):
2412  """__repr__(Em2DRestraintParameters self) -> std::string"""
2413  return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2414 
2415  __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2416  __del__ = lambda self: None
2417 Em2DRestraintParameters_swigregister = _IMP_em2d.Em2DRestraintParameters_swigregister
2418 Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2419 cvar = _IMP_em2d.cvar
2420 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2421 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2422 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2423 
2424 class ProjectionFinder(IMP.Object):
2425  """Proxy of C++ IMP::em2d::ProjectionFinder class."""
2426 
2427  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2428 
2429  def __init__(self):
2430  """__init__(IMP::em2d::ProjectionFinder self) -> ProjectionFinder"""
2431  this = _IMP_em2d.new_ProjectionFinder()
2432  try:
2433  self.this.append(this)
2434  except __builtin__.Exception:
2435  self.this = this
2436 
2437  def setup(self, score_function, params):
2438  """setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2439  return _IMP_em2d.ProjectionFinder_setup(self, score_function, params)
2440 
2441 
2442  def set_subjects(self, subjects):
2443  """set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2444  return _IMP_em2d.ProjectionFinder_set_subjects(self, subjects)
2445 
2446 
2447  def set_projections(self, projections):
2448  """set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2449  return _IMP_em2d.ProjectionFinder_set_projections(self, projections)
2450 
2451 
2452  def set_variance_images(self, variances):
2453  """set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2454  return _IMP_em2d.ProjectionFinder_set_variance_images(self, variances)
2455 
2456 
2457  def set_model_particles(self, ps):
2458  """set_model_particles(ProjectionFinder self, IMP::ParticlesTemp const & ps)"""
2459  return _IMP_em2d.ProjectionFinder_set_model_particles(self, ps)
2460 
2461 
2462  def set_save_match_images(self, x):
2463  """set_save_match_images(ProjectionFinder self, bool x)"""
2464  return _IMP_em2d.ProjectionFinder_set_save_match_images(self, x)
2465 
2466 
2467  def get_save_match_images(self):
2468  """get_save_match_images(ProjectionFinder self) -> bool"""
2469  return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2470 
2471 
2472  def set_fast_mode(self, n):
2473  """set_fast_mode(ProjectionFinder self, unsigned int n)"""
2474  return _IMP_em2d.ProjectionFinder_set_fast_mode(self, n)
2475 
2476 
2477  def get_registration_results(self):
2478  """get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2479  return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2480 
2481 
2482  def get_coarse_registration(self):
2483  """get_coarse_registration(ProjectionFinder self)"""
2484  return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2485 
2486 
2487  def get_complete_registration(self):
2488  """get_complete_registration(ProjectionFinder self)"""
2489  return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2490 
2491 
2492  def get_global_score(self):
2493  """get_global_score(ProjectionFinder self) -> double"""
2494  return _IMP_em2d.ProjectionFinder_get_global_score(self)
2495 
2496 
2497  def show(self, out):
2498  """show(ProjectionFinder self, _ostream out)"""
2499  return _IMP_em2d.ProjectionFinder_show(self, out)
2500 
2501 
2502  def get_preprocessing_time(self):
2503  """get_preprocessing_time(ProjectionFinder self) -> double"""
2504  return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2505 
2506 
2507  def get_coarse_registration_time(self):
2508  """get_coarse_registration_time(ProjectionFinder self) -> double"""
2509  return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2510 
2511 
2512  def get_fine_registration_time(self):
2513  """get_fine_registration_time(ProjectionFinder self) -> double"""
2514  return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2515 
2516 
2517  def get_number_of_subjects(self):
2518  """get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2519  return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2520 
2521 
2522  def set_number_of_class_averages_members(self, n_members):
2523  """set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2524  return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, n_members)
2525 
2526 
2527  def get_number_of_projections(self):
2528  """get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2529  return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2530 
2531 
2532  def get_version_info(self):
2533  """get_version_info(ProjectionFinder self) -> VersionInfo"""
2534  return _IMP_em2d.ProjectionFinder_get_version_info(self)
2535 
2536 
2537  def __str__(self):
2538  """__str__(ProjectionFinder self) -> std::string"""
2539  return _IMP_em2d.ProjectionFinder___str__(self)
2540 
2541 
2542  def __repr__(self):
2543  """__repr__(ProjectionFinder self) -> std::string"""
2544  return _IMP_em2d.ProjectionFinder___repr__(self)
2545 
2546 
2547  @staticmethod
2548  def get_from(o):
2549  return _object_cast_to_ProjectionFinder(o)
2550 
2551 ProjectionFinder_swigregister = _IMP_em2d.ProjectionFinder_swigregister
2552 ProjectionFinder_swigregister(ProjectionFinder)
2553 
2554 class Em2DRestraint(IMP.Restraint):
2555  """Proxy of C++ IMP::em2d::Em2DRestraint class."""
2556 
2557  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2558 
2559  def __init__(self, m):
2560  """__init__(IMP::em2d::Em2DRestraint self, Model m) -> Em2DRestraint"""
2561  this = _IMP_em2d.new_Em2DRestraint(m)
2562  try:
2563  self.this.append(this)
2564  except __builtin__.Exception:
2565  self.this = this
2566 
2567  def setup(self, score_function, params):
2568  """setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2569  return _IMP_em2d.Em2DRestraint_setup(self, score_function, params)
2570 
2571 
2572  def set_particles(self, particles_container):
2573  """set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2574  return _IMP_em2d.Em2DRestraint_set_particles(self, particles_container)
2575 
2576 
2577  def set_images(self, em_images):
2578  """set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2579  return _IMP_em2d.Em2DRestraint_set_images(self, em_images)
2580 
2581 
2582  def set_variance_images(self, variance_images):
2583  """set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2584  return _IMP_em2d.Em2DRestraint_set_variance_images(self, variance_images)
2585 
2586 
2587  def set_fast_mode(self, n):
2588  """set_fast_mode(Em2DRestraint self, unsigned int n)"""
2589  return _IMP_em2d.Em2DRestraint_set_fast_mode(self, n)
2590 
2591 
2592  def set_coarse_registration_mode(self, opt):
2593  """set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2594  return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, opt)
2595 
2596 
2597  def get_registration_results(self):
2598  """get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2599  return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2600 
2601 
2602  def do_get_inputs(self):
2603  """do_get_inputs(Em2DRestraint self) -> IMP::ModelObjectsTemp"""
2604  return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2605 
2606 
2607  def get_version_info(self):
2608  """get_version_info(Em2DRestraint self) -> VersionInfo"""
2609  return _IMP_em2d.Em2DRestraint_get_version_info(self)
2610 
2611 
2612  def __str__(self):
2613  """__str__(Em2DRestraint self) -> std::string"""
2614  return _IMP_em2d.Em2DRestraint___str__(self)
2615 
2616 
2617  def __repr__(self):
2618  """__repr__(Em2DRestraint self) -> std::string"""
2619  return _IMP_em2d.Em2DRestraint___repr__(self)
2620 
2621 
2622  @staticmethod
2623  def get_from(o):
2624  return _object_cast_to_Em2DRestraint(o)
2625 
2626 Em2DRestraint_swigregister = _IMP_em2d.Em2DRestraint_swigregister
2627 Em2DRestraint_swigregister(Em2DRestraint)
2628 
2629 class ClusterSet(object):
2630  """Proxy of C++ IMP::em2d::ClusterSet class."""
2631 
2632  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2633 
2634  def __init__(self, N):
2635  """__init__(IMP::em2d::ClusterSet self, unsigned int N) -> ClusterSet"""
2636  this = _IMP_em2d.new_ClusterSet(N)
2637  try:
2638  self.this.append(this)
2639  except __builtin__.Exception:
2640  self.this = this
2641 
2642  def do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters):
2643  """do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2644  return _IMP_em2d.ClusterSet_do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters)
2645 
2646 
2647  def get_cluster_elements(self, id):
2648  """get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2649  return _IMP_em2d.ClusterSet_get_cluster_elements(self, id)
2650 
2651 
2652  def get_clusters_below_cutoff(self, cutoff):
2653  """get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2654  return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, cutoff)
2655 
2656 
2657  def get_cluster_formed_at_step(self, step):
2658  """get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2659  return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, step)
2660 
2661 
2662  def get_distance_at_step(self, step):
2663  """get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2664  return _IMP_em2d.ClusterSet_get_distance_at_step(self, step)
2665 
2666 
2667  def get_id_for_cluster_at_step(self, step):
2668  """get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2669  return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, step)
2670 
2671 
2672  def get_linkage_matrix(self):
2673  """get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2674  return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2675 
2676 
2677  def get_linkage_matrix_in_matlab_format(self):
2678  """get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2679  return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2680 
2681 
2682  def get_number_of_steps(self):
2683  """get_number_of_steps(ClusterSet self) -> unsigned int"""
2684  return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2685 
2686 
2687  def show(self, out):
2688  """show(ClusterSet self, _ostream out)"""
2689  return _IMP_em2d.ClusterSet_show(self, out)
2690 
2691 
2692  def __str__(self):
2693  """__str__(ClusterSet self) -> std::string"""
2694  return _IMP_em2d.ClusterSet___str__(self)
2695 
2696 
2697  def __repr__(self):
2698  """__repr__(ClusterSet self) -> std::string"""
2699  return _IMP_em2d.ClusterSet___repr__(self)
2700 
2701  __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2702  __del__ = lambda self: None
2703 ClusterSet_swigregister = _IMP_em2d.ClusterSet_swigregister
2704 ClusterSet_swigregister(ClusterSet)
2705 
2706 class SingleLinkage(object):
2707  """Proxy of C++ IMP::em2d::SingleLinkage class."""
2708 
2709  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2710 
2711  def __init__(self):
2712  """__init__(IMP::em2d::SingleLinkage self) -> SingleLinkage"""
2713  this = _IMP_em2d.new_SingleLinkage()
2714  try:
2715  self.this.append(this)
2716  except __builtin__.Exception:
2717  self.this = this
2718 
2719  def __call__(self, id1, id2, cluster_set, distances):
2720  """__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2721  return _IMP_em2d.SingleLinkage___call__(self, id1, id2, cluster_set, distances)
2722 
2723 
2724  def show(self, out):
2725  """show(SingleLinkage self, _ostream out)"""
2726  return _IMP_em2d.SingleLinkage_show(self, out)
2727 
2728 
2729  def __str__(self):
2730  """__str__(SingleLinkage self) -> std::string"""
2731  return _IMP_em2d.SingleLinkage___str__(self)
2732 
2733 
2734  def __repr__(self):
2735  """__repr__(SingleLinkage self) -> std::string"""
2736  return _IMP_em2d.SingleLinkage___repr__(self)
2737 
2738  __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2739  __del__ = lambda self: None
2740 SingleLinkage_swigregister = _IMP_em2d.SingleLinkage_swigregister
2741 SingleLinkage_swigregister(SingleLinkage)
2742 
2743 class CompleteLinkage(object):
2744  """Proxy of C++ IMP::em2d::CompleteLinkage class."""
2745 
2746  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2747 
2748  def __init__(self):
2749  """__init__(IMP::em2d::CompleteLinkage self) -> CompleteLinkage"""
2750  this = _IMP_em2d.new_CompleteLinkage()
2751  try:
2752  self.this.append(this)
2753  except __builtin__.Exception:
2754  self.this = this
2755 
2756  def __call__(self, id1, id2, cluster_set, distances):
2757  """__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2758  return _IMP_em2d.CompleteLinkage___call__(self, id1, id2, cluster_set, distances)
2759 
2760 
2761  def show(self, out):
2762  """show(CompleteLinkage self, _ostream out)"""
2763  return _IMP_em2d.CompleteLinkage_show(self, out)
2764 
2765 
2766  def __str__(self):
2767  """__str__(CompleteLinkage self) -> std::string"""
2768  return _IMP_em2d.CompleteLinkage___str__(self)
2769 
2770 
2771  def __repr__(self):
2772  """__repr__(CompleteLinkage self) -> std::string"""
2773  return _IMP_em2d.CompleteLinkage___repr__(self)
2774 
2775  __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2776  __del__ = lambda self: None
2777 CompleteLinkage_swigregister = _IMP_em2d.CompleteLinkage_swigregister
2778 CompleteLinkage_swigregister(CompleteLinkage)
2779 
2780 class AverageDistanceLinkage(object):
2781  """Proxy of C++ IMP::em2d::AverageDistanceLinkage class."""
2782 
2783  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2784 
2785  def __init__(self):
2786  """__init__(IMP::em2d::AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2787  this = _IMP_em2d.new_AverageDistanceLinkage()
2788  try:
2789  self.this.append(this)
2790  except __builtin__.Exception:
2791  self.this = this
2792 
2793  def __call__(self, id1, id2, cluster_set, distances):
2794  """__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2795  return _IMP_em2d.AverageDistanceLinkage___call__(self, id1, id2, cluster_set, distances)
2796 
2797 
2798  def show(self, out):
2799  """show(AverageDistanceLinkage self, _ostream out)"""
2800  return _IMP_em2d.AverageDistanceLinkage_show(self, out)
2801 
2802 
2803  def __str__(self):
2804  """__str__(AverageDistanceLinkage self) -> std::string"""
2805  return _IMP_em2d.AverageDistanceLinkage___str__(self)
2806 
2807 
2808  def __repr__(self):
2809  """__repr__(AverageDistanceLinkage self) -> std::string"""
2810  return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2811 
2812  __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2813  __del__ = lambda self: None
2814 AverageDistanceLinkage_swigregister = _IMP_em2d.AverageDistanceLinkage_swigregister
2815 AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2816 
2817 class CollisionCrossSection(IMP.Object):
2818  """Proxy of C++ IMP::em2d::CollisionCrossSection class."""
2819 
2820  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2821 
2822  def __init__(self, n_projections, resolution, pixel_size, projection_image_size):
2823  """__init__(IMP::em2d::CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2824  this = _IMP_em2d.new_CollisionCrossSection(n_projections, resolution, pixel_size, projection_image_size)
2825  try:
2826  self.this.append(this)
2827  except __builtin__.Exception:
2828  self.this = this
2829 
2830  def set_model_particles(self, ps):
2831  """set_model_particles(CollisionCrossSection self, IMP::ParticlesTemp const & ps)"""
2832  return _IMP_em2d.CollisionCrossSection_set_model_particles(self, ps)
2833 
2834 
2835  def get_ccs(self):
2836  """get_ccs(CollisionCrossSection self) -> double"""
2837  return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2838 
2839 
2840  def show(self, out):
2841  """show(CollisionCrossSection self, _ostream out)"""
2842  return _IMP_em2d.CollisionCrossSection_show(self, out)
2843 
2844 
2845  def get_version_info(self):
2846  """get_version_info(CollisionCrossSection self) -> VersionInfo"""
2847  return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2848 
2849 
2850  def __str__(self):
2851  """__str__(CollisionCrossSection self) -> std::string"""
2852  return _IMP_em2d.CollisionCrossSection___str__(self)
2853 
2854 
2855  def __repr__(self):
2856  """__repr__(CollisionCrossSection self) -> std::string"""
2857  return _IMP_em2d.CollisionCrossSection___repr__(self)
2858 
2859 
2860  @staticmethod
2861  def get_from(o):
2862  return _object_cast_to_CollisionCrossSection(o)
2863 
2864 CollisionCrossSection_swigregister = _IMP_em2d.CollisionCrossSection_swigregister
2865 CollisionCrossSection_swigregister(CollisionCrossSection)
2866 
2867 class GridStates(IMP.domino.ParticleStates):
2868  """Proxy of C++ IMP::em2d::GridStates class."""
2869 
2870  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2871 
2872  def __init__(self, *args):
2873  """
2874  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::String const & name) -> GridStates
2875  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations) -> GridStates
2876  """
2877  this = _IMP_em2d.new_GridStates(*args)
2878  try:
2879  self.this.append(this)
2880  except __builtin__.Exception:
2881  self.this = this
2882 
2883  def get_position(self, i):
2884  """get_position(GridStates self, unsigned int i) -> Vector3D"""
2885  return _IMP_em2d.GridStates_get_position(self, i)
2886 
2887 
2888  def get_orientation(self, i):
2889  """get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2890  return _IMP_em2d.GridStates_get_orientation(self, i)
2891 
2892 
2893  def get_version_info(self):
2894  """get_version_info(GridStates self) -> VersionInfo"""
2895  return _IMP_em2d.GridStates_get_version_info(self)
2896 
2897 
2898  def __str__(self):
2899  """__str__(GridStates self) -> std::string"""
2900  return _IMP_em2d.GridStates___str__(self)
2901 
2902 
2903  def __repr__(self):
2904  """__repr__(GridStates self) -> std::string"""
2905  return _IMP_em2d.GridStates___repr__(self)
2906 
2907 
2908  @staticmethod
2909  def get_from(o):
2910  return _object_cast_to_GridStates(o)
2911 
2912 GridStates_swigregister = _IMP_em2d.GridStates_swigregister
2913 GridStates_swigregister(GridStates)
2914 
2915 class ProjectionStates(GridStates):
2916  """Proxy of C++ IMP::em2d::ProjectionStates class."""
2917 
2918  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2919 
2920  def __init__(self, *args):
2921  """
2922  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections, IMP::String const & name) -> ProjectionStates
2923  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections) -> ProjectionStates
2924  """
2925  this = _IMP_em2d.new_ProjectionStates(*args)
2926  try:
2927  self.this.append(this)
2928  except __builtin__.Exception:
2929  self.this = this
2930 
2931  def get_projection(self, i):
2932  """get_projection(ProjectionStates self, unsigned int i) -> Image"""
2933  return _IMP_em2d.ProjectionStates_get_projection(self, i)
2934 
2935 
2936  def __str__(self):
2937  """__str__(ProjectionStates self) -> std::string"""
2938  return _IMP_em2d.ProjectionStates___str__(self)
2939 
2940 
2941  def __repr__(self):
2942  """__repr__(ProjectionStates self) -> std::string"""
2943  return _IMP_em2d.ProjectionStates___repr__(self)
2944 
2945 
2946  @staticmethod
2947  def get_from(o):
2948  return _object_cast_to_ProjectionStates(o)
2949 
2950 ProjectionStates_swigregister = _IMP_em2d.ProjectionStates_swigregister
2951 ProjectionStates_swigregister(ProjectionStates)
2952 
2953 class DistanceFilter(IMP.domino.SubsetFilter):
2954  """Proxy of C++ IMP::em2d::DistanceFilter class."""
2955 
2956  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2957 
2958  def __init__(self, subset_to_act_on, subset_to_restrain, ps_table, max_distance):
2959  """__init__(IMP::em2d::DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table, double max_distance) -> DistanceFilter"""
2960  this = _IMP_em2d.new_DistanceFilter(subset_to_act_on, subset_to_restrain, ps_table, max_distance)
2961  try:
2962  self.this.append(this)
2963  except __builtin__.Exception:
2964  self.this = this
2965 
2966  def show(self, *args):
2967  """
2968  show(DistanceFilter self, _ostream out)
2969  show(DistanceFilter self)
2970  """
2971  return _IMP_em2d.DistanceFilter_show(self, *args)
2972 
2973 
2974  def get_version_info(self):
2975  """get_version_info(DistanceFilter self) -> VersionInfo"""
2976  return _IMP_em2d.DistanceFilter_get_version_info(self)
2977 
2978 
2979  def __str__(self):
2980  """__str__(DistanceFilter self) -> std::string"""
2981  return _IMP_em2d.DistanceFilter___str__(self)
2982 
2983 
2984  def __repr__(self):
2985  """__repr__(DistanceFilter self) -> std::string"""
2986  return _IMP_em2d.DistanceFilter___repr__(self)
2987 
2988 
2989  @staticmethod
2990  def get_from(o):
2991  return _object_cast_to_DistanceFilter(o)
2992 
2993 DistanceFilter_swigregister = _IMP_em2d.DistanceFilter_swigregister
2994 DistanceFilter_swigregister(DistanceFilter)
2995 
2996 class DistanceFilterTable(IMP.domino.SubsetFilterTable):
2997  """Proxy of C++ IMP::em2d::DistanceFilterTable class."""
2998 
2999  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3000 
3001  def __init__(self, subset_to_act_on, ps_table, max_distance):
3002  """__init__(IMP::em2d::DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
3003  this = _IMP_em2d.new_DistanceFilterTable(subset_to_act_on, ps_table, max_distance)
3004  try:
3005  self.this.append(this)
3006  except __builtin__.Exception:
3007  self.this = this
3008 
3009  def show(self, *args):
3010  """
3011  show(DistanceFilterTable self, _ostream out)
3012  show(DistanceFilterTable self)
3013  """
3014  return _IMP_em2d.DistanceFilterTable_show(self, *args)
3015 
3016 
3017  def get_version_info(self):
3018  """get_version_info(DistanceFilterTable self) -> VersionInfo"""
3019  return _IMP_em2d.DistanceFilterTable_get_version_info(self)
3020 
3021 
3022  def __str__(self):
3023  """__str__(DistanceFilterTable self) -> std::string"""
3024  return _IMP_em2d.DistanceFilterTable___str__(self)
3025 
3026 
3027  def __repr__(self):
3028  """__repr__(DistanceFilterTable self) -> std::string"""
3029  return _IMP_em2d.DistanceFilterTable___repr__(self)
3030 
3031 
3032  @staticmethod
3033  def get_from(o):
3034  return _object_cast_to_DistanceFilterTable(o)
3035 
3036 DistanceFilterTable_swigregister = _IMP_em2d.DistanceFilterTable_swigregister
3037 DistanceFilterTable_swigregister(DistanceFilterTable)
3038 
3039 class IntsOrder(object):
3040  """Proxy of C++ IMP::em2d::IntsOrder class."""
3041 
3042  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3043  __repr__ = _swig_repr
3044 
3045  def __call__(self, a, b):
3046  """__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
3047  return _IMP_em2d.IntsOrder___call__(self, a, b)
3048 
3049 
3050  def __init__(self):
3051  """__init__(IMP::em2d::IntsOrder self) -> IntsOrder"""
3052  this = _IMP_em2d.new_IntsOrder()
3053  try:
3054  self.this.append(this)
3055  except __builtin__.Exception:
3056  self.this = this
3057  __swig_destroy__ = _IMP_em2d.delete_IntsOrder
3058  __del__ = lambda self: None
3059 IntsOrder_swigregister = _IMP_em2d.IntsOrder_swigregister
3060 IntsOrder_swigregister(IntsOrder)
3061 
3062 class RigidBodiesImageFitRestraint(IMP.Restraint):
3063  """Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class."""
3064 
3065  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3066 
3067  def get_version_info(self):
3068  """get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
3069  return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
3070 
3071 
3072  def __init__(self, scf, rbs, img):
3073  """__init__(IMP::em2d::RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
3074  this = _IMP_em2d.new_RigidBodiesImageFitRestraint(scf, rbs, img)
3075  try:
3076  self.this.append(this)
3077  except __builtin__.Exception:
3078  self.this = this
3079 
3080  def set_projecting_parameters(self, p):
3081  """set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
3082  return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, p)
3083 
3084 
3085  def set_orientations(self, rb, rots):
3086  """set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
3087  return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, rb, rots)
3088 
3089 
3090  def get_number_of_masks(self, rb):
3091  """get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
3092  return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, rb)
3093 
3094 
3095  def __str__(self):
3096  """__str__(RigidBodiesImageFitRestraint self) -> std::string"""
3097  return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
3098 
3099 
3100  def __repr__(self):
3101  """__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
3102  return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
3103 
3104 
3105  @staticmethod
3106  def get_from(o):
3107  return _object_cast_to_RigidBodiesImageFitRestraint(o)
3108 
3109 RigidBodiesImageFitRestraint_swigregister = _IMP_em2d.RigidBodiesImageFitRestraint_swigregister
3110 RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
3111 
3112 
3113 def get_unique_index(rot):
3114  """get_unique_index(Rotation3D rot) -> IMP::Ints"""
3115  return _IMP_em2d.get_unique_index(rot)
3116 class RelativePositionMover(IMP.core.RigidBodyMover):
3117  """Proxy of C++ IMP::em2d::RelativePositionMover class."""
3118 
3119  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3120 
3121  def __init__(self, d, max_translation, max_rotation):
3122  """__init__(IMP::em2d::RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
3123  this = _IMP_em2d.new_RelativePositionMover(d, max_translation, max_rotation)
3124  try:
3125  self.this.append(this)
3126  except __builtin__.Exception:
3127  self.this = this
3128 
3129  def add_internal_transformations(self, d, transforms):
3130  """add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
3131  return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, d, transforms)
3132 
3133 
3134  def set_random_move_probability(self, p):
3135  """set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
3136  return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, p)
3137 
3138 
3139  def __str__(self):
3140  """__str__(RelativePositionMover self) -> std::string"""
3141  return _IMP_em2d.RelativePositionMover___str__(self)
3142 
3143 
3144  def __repr__(self):
3145  """__repr__(RelativePositionMover self) -> std::string"""
3146  return _IMP_em2d.RelativePositionMover___repr__(self)
3147 
3148 
3149  @staticmethod
3150  def get_from(o):
3151  return _object_cast_to_RelativePositionMover(o)
3152 
3153 RelativePositionMover_swigregister = _IMP_em2d.RelativePositionMover_swigregister
3154 RelativePositionMover_swigregister(RelativePositionMover)
3155 
3156 class DummyRestraint(IMP.Restraint):
3157  """Proxy of C++ IMP::em2d::DummyRestraint class."""
3158 
3159  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3160 
3161  def __init__(self, p, q):
3162  """__init__(IMP::em2d::DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
3163  this = _IMP_em2d.new_DummyRestraint(p, q)
3164  try:
3165  self.this.append(this)
3166  except __builtin__.Exception:
3167  self.this = this
3168 
3169  def show(self, *args):
3170  """
3171  show(DummyRestraint self, _ostream out)
3172  show(DummyRestraint self)
3173  """
3174  return _IMP_em2d.DummyRestraint_show(self, *args)
3175 
3176 
3177  def do_get_inputs(self):
3178  """do_get_inputs(DummyRestraint self) -> IMP::ModelObjectsTemp"""
3179  return _IMP_em2d.DummyRestraint_do_get_inputs(self)
3180 
3181 
3182  def get_version_info(self):
3183  """get_version_info(DummyRestraint self) -> VersionInfo"""
3184  return _IMP_em2d.DummyRestraint_get_version_info(self)
3185 
3186 
3187  def __str__(self):
3188  """__str__(DummyRestraint self) -> std::string"""
3189  return _IMP_em2d.DummyRestraint___str__(self)
3190 
3191 
3192  def __repr__(self):
3193  """__repr__(DummyRestraint self) -> std::string"""
3194  return _IMP_em2d.DummyRestraint___repr__(self)
3195 
3196 
3197  @staticmethod
3198  def get_from(o):
3199  return _object_cast_to_DummyRestraint(o)
3200 
3201 DummyRestraint_swigregister = _IMP_em2d.DummyRestraint_swigregister
3202 DummyRestraint_swigregister(DummyRestraint)
3203 
3204 class ParticlesDummyRestraint(IMP.Restraint):
3205  """Proxy of C++ IMP::em2d::ParticlesDummyRestraint class."""
3206 
3207  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3208 
3209  def __init__(self, sc):
3210  """__init__(IMP::em2d::ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
3211  this = _IMP_em2d.new_ParticlesDummyRestraint(sc)
3212  try:
3213  self.this.append(this)
3214  except __builtin__.Exception:
3215  self.this = this
3216 
3217  def show(self, *args):
3218  """
3219  show(ParticlesDummyRestraint self, _ostream out)
3220  show(ParticlesDummyRestraint self)
3221  """
3222  return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
3223 
3224 
3225  def do_get_inputs(self):
3226  """do_get_inputs(ParticlesDummyRestraint self) -> IMP::ModelObjectsTemp"""
3227  return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3228 
3229 
3230  def get_version_info(self):
3231  """get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3232  return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3233 
3234 
3235  def __str__(self):
3236  """__str__(ParticlesDummyRestraint self) -> std::string"""
3237  return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3238 
3239 
3240  def __repr__(self):
3241  """__repr__(ParticlesDummyRestraint self) -> std::string"""
3242  return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3243 
3244 
3245  @staticmethod
3246  def get_from(o):
3247  return _object_cast_to_ParticlesDummyRestraint(o)
3248 
3249 ParticlesDummyRestraint_swigregister = _IMP_em2d.ParticlesDummyRestraint_swigregister
3250 ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3251 
3252 class PCAFitRestraint(IMP.Restraint):
3253  """Proxy of C++ IMP::em2d::PCAFitRestraint class."""
3254 
3255  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3256 
3257  def __init__(self, particles, image_files, pixel_size, resolution=10.0, projection_number=100, reuse_direction=False, n_components=1):
3258  """
3259  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False, unsigned int n_components=1) -> PCAFitRestraint
3260  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False) -> PCAFitRestraint
3261  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100) -> PCAFitRestraint
3262  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0) -> PCAFitRestraint
3263  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size) -> PCAFitRestraint
3264  """
3265  this = _IMP_em2d.new_PCAFitRestraint(particles, image_files, pixel_size, resolution, projection_number, reuse_direction, n_components)
3266  try:
3267  self.this.append(this)
3268  except __builtin__.Exception:
3269  self.this = this
3270 
3271  def get_projection_number(self):
3272  """get_projection_number(PCAFitRestraint self) -> unsigned int"""
3273  return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3274 
3275 
3276  def set_projection_number(self, n):
3277  """set_projection_number(PCAFitRestraint self, unsigned int n)"""
3278  return _IMP_em2d.PCAFitRestraint_set_projection_number(self, n)
3279 
3280 
3281  def get_transformation(self, image_number):
3282  """get_transformation(PCAFitRestraint self, unsigned int image_number) -> Transformation3D"""
3283  return _IMP_em2d.PCAFitRestraint_get_transformation(self, image_number)
3284 
3285 
3286  def get_cross_correlation_coefficient(self, image_number):
3287  """get_cross_correlation_coefficient(PCAFitRestraint self, unsigned int image_number) -> double"""
3288  return _IMP_em2d.PCAFitRestraint_get_cross_correlation_coefficient(self, image_number)
3289 
3290 
3291  def write_best_projections(self, file_name, evaluate=False):
3292  """
3293  write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)
3294  write_best_projections(PCAFitRestraint self, std::string file_name)
3295  """
3296  return _IMP_em2d.PCAFitRestraint_write_best_projections(self, file_name, evaluate)
3297 
3298 
3299  def do_get_inputs(self):
3300  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
3301  return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3302 
3303 
3304  def get_version_info(self):
3305  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
3306  return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3307 
3308 
3309  def __str__(self):
3310  """__str__(PCAFitRestraint self) -> std::string"""
3311  return _IMP_em2d.PCAFitRestraint___str__(self)
3312 
3313 
3314  def __repr__(self):
3315  """__repr__(PCAFitRestraint self) -> std::string"""
3316  return _IMP_em2d.PCAFitRestraint___repr__(self)
3317 
3318 
3319  @staticmethod
3320  def get_from(o):
3321  return _object_cast_to_em2dPCAFitRestraint(o)
3322 
3323 PCAFitRestraint_swigregister = _IMP_em2d.PCAFitRestraint_swigregister
3324 PCAFitRestraint_swigregister(PCAFitRestraint)
3325 
3326 class ResultAlign2D(object):
3327  """Proxy of C++ std::pair<(IMP::algebra::Transformation2D,double)> class."""
3328 
3329  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3330  __repr__ = _swig_repr
3331 
3332  def __init__(self, *args):
3333  """
3334  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self) -> ResultAlign2D
3335  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, Transformation2D first, double second) -> ResultAlign2D
3336  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, ResultAlign2D p) -> ResultAlign2D
3337  """
3338  this = _IMP_em2d.new_ResultAlign2D(*args)
3339  try:
3340  self.this.append(this)
3341  except __builtin__.Exception:
3342  self.this = this
3343  first = _swig_property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set)
3344  second = _swig_property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set)
3345  def __len__(self):
3346  return 2
3347  def __repr__(self):
3348  return str((self.first, self.second))
3349  def __getitem__(self, index):
3350  if not (index % 2):
3351  return self.first
3352  else:
3353  return self.second
3354  def __setitem__(self, index, val):
3355  if not (index % 2):
3356  self.first = val
3357  else:
3358  self.second = val
3359  __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3360  __del__ = lambda self: None
3361 ResultAlign2D_swigregister = _IMP_em2d.ResultAlign2D_swigregister
3362 ResultAlign2D_swigregister(ResultAlign2D)
3363 
3364 
3365 def _do_hierarchical_clustering_single_linkage(distances):
3366  """_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3367  return _IMP_em2d._do_hierarchical_clustering_single_linkage(distances)
3368 
3369 def _do_hierarchical_clustering_complete_linkage(distances):
3370  """_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3371  return _IMP_em2d._do_hierarchical_clustering_complete_linkage(distances)
3372 
3373 def _do_hierarchical_clustering_average_distance_linkage(distances):
3374  """_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3375  return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(distances)
3376 
3377 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3378 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3379 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3380 
3381 
3382 def get_module_version():
3383  """get_module_version() -> std::string const"""
3384  return _IMP_em2d.get_module_version()
3385 
3386 def get_example_path(fname):
3387  """get_example_path(std::string fname) -> std::string"""
3388  return _IMP_em2d.get_example_path(fname)
3389 
3390 def get_data_path(fname):
3391  """get_data_path(std::string fname) -> std::string"""
3392  return _IMP_em2d.get_data_path(fname)
3393 
3394 from . import _version_check
3395 _version_check.check_version(get_module_version())
3396 __version__ = get_module_version()
3397 
3398 
3399 
double get_shift_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Distance between the two in-plane translations.
Images create_evenly_distributed_projections(const ParticlesTemp &ps, unsigned int n, const ProjectingOptions &options)
void get_autocorrelation2d_no_preprocessing(const cv::Mat &M, cv::Mat &corr)
Autocorrelation without preprocessing.
void do_morphologic_contrast_enhancement(const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel, unsigned int iterations)
double get_mean(const cv::Mat &mat, const cvIntMat &mask)
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
setup
Definition: setup.py:1
void apply_threshold(cv::Mat &m, cv::Mat &result, double threshold=0.0)
em2d::Images get_projections(const ParticlesTemp &ps, const algebra::SphericalVector3Ds &vs, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
Generates projections from particles.
IMPEM2D_BEGIN_NAMESPACE Strings read_selection_file(String fn)
Reads a selection file.
ResultAlign2D get_complete_alignment_with_centers_no_preprocessing(const algebra::Vector2D &center1, const algebra::Vector2D &center2, const cv::Mat &AUTOC_POLAR1, const cv::Mat &AUTOC_POLAR2)
Strings create_filenames(unsigned long number, String basic_name, String extension)
Various classes to hold sets of particles.
ResultAlign2D get_translational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
Aligns two matrices translationally.
void get_correlation2d(const cv::Mat &A, const cv::Mat &B, cv::Mat &corr)
Correlation matrix between two 2D matrices using FFT.
cvIntMat create_circular_mask(int rows, int cols, int radius)
ResultAlign2D get_complete_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
void do_dilate_and_shrink_warp(cv::Mat &m, const cv::Mat &grayscale, cv::Mat &kernel)
(U. Adiga, 2005)
em2d::ResultAlign2D get_rotational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
RegistrationResults get_evenly_distributed_registration_results(unsigned int n_projections)
void apply_variance_filter(Image *input, Image *filtered, int kernelsize)
Definition: Image.h:266
void apply_diffusion_filter(Image *input, Image *filtered, double beta, double pixelsize, int time_steps)
Definition: Image.h:279
int do_labeling(const cvIntMat &m, cvIntMat &mat_to_label)
Labeling function for a matrix.
Make CGAL functionality available to IMP.
MatchTemplateResults get_best_template_matches(const cv::Mat &m, const cv::Mat &templ, unsigned int n)
Modify the transformation of a rigid body.
void do_project_particles(const ParticlesTemp &ps, cv::Mat &m2, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const ProjectingOptions &options, MasksManagerPtr masks)
Projects a set of particles. This is the core function that others call.
void get_autocorrelation2d(const cv::Mat &m, cv::Mat &corr)
Computes the autocorrelation matrix.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
void apply_mean_outside_mask(Image *img, double radius)
Several general purpose optimizers from the GNU Scientific Library (GSL).
double get_rotation_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Composable functors to implement scores via compile-time composition.
ResultAlign2D get_rotational_alignment_no_preprocessing(const cv::Mat &POLAR1, const cv::Mat &POLAR2)
void get_fft_using_optimal_size(const cv::Mat &m, cv::Mat &M)
Floats get_histogram(Image *img, int bins)
Definition: Image.h:255
void write_matrix(cv::Mat &m, std::string name)
Quick and dirty way of writing a OpenCV matrix to a Spider image.
void do_subtract_images(Image *first, Image *second, Image *result)
Code to compute statistical measures.
RegistrationResults get_random_registration_results(unsigned int n, double maximum_shift=5.0)
Provides a set of random registration results (or parameters)
algebra::Vector2Ds do_project_vectors(const algebra::Vector3Ds &ps, const algebra::Rotation3D &R, const algebra::Vector3D &translation)
Project the points contained in Vector3Ds to gen vectors in 2D.
void write_vectors_as_pdb(const algebra::Vector2Ds vs, const String filename)
Common base class for heavy weight IMP objects.
Definition: Object.h:106
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:53
void apply_circular_mask(const cv::Mat &mat, cv::Mat &result, int radius, double value=0.0)
Images read_images(const Strings &names, const ImageReaderWriter *rw)
void write_registration_results(String filename, const RegistrationResults &results)
Writes a set of registration results.
Basic utilities for handling cryo-electron microscopy 3D density maps.
void crop(Image *img, const IntPair &center, int size)
void get_morphologic_gradient(const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel)
void apply_mask(const cv::Mat &m, cv::Mat &result, const cvIntMat &mask, double val)
Applies a binary mask to an image.
double get_cross_correlation_coefficient(Image *im1, Image *im2)
Cross correlation between two images.
void save_images(Images images, const Strings &names, const ImageReaderWriter *rw)
void get_domes(cv::Mat &m, cv::Mat &result, double h)
Gets the domes of m with height h.
void do_normalize(Image *im, bool force=false)
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:118
void do_matrix_to_image_flip(cv::Mat &m)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
ResultAlign2D get_translational_alignment_no_preprocessing(const cv::Mat &M1, const cv::Mat &M2)
void get_correlation2d_no_preprocessing(const cv::Mat &M1, const cv::Mat &M2, cv::Mat &corr)
Correlation without preprocessing.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
unsigned int get_enclosing_image_size(const ParticlesTemp &ps, double pixel_size, unsigned int slack)
Get an automatic size for an image that contains the particles.
std::pair< algebra::Transformation2D, double > ResultAlign2D
Definition: align2D.h:22
void do_resample_polar(Image *im1, Image *im2, const PolarResamplingParameters &polar_params)
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
em2d::ResultAlign2D get_complete_alignment_no_preprocessing(const cv::Mat &input, const cv::Mat &INPUT, const cv::Mat &POLAR1, cv::Mat &m_to_align, const cv::Mat &POLAR2, bool apply=false)
double get_overlap_percentage(cv::Mat &m1, cv::Mat &m2, const IntPair &center)
RegistrationResults read_registration_results(const String &filename)
Reads a set of registration results.
void get_diffusion_filtering_partial_derivative(const cv::Mat &m, cv::Mat &der, double dx, double dy, double ang)
Ints get_unique_index(const algebra::Rotation3D &rot)
Map a rotation to a list of 4 "unique" integers.
double get_global_score(const RegistrationResults &RRs)
void do_place(cv::Mat &mask, cv::Mat &m, const algebra::Vector2D &v)
void do_morphologic_reconstruction(const cv::Mat &mask, cv::Mat &marker, int neighbors_mode=4)
morphologic grayscale reconstruction (L Vincent, 1993)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
void get_projection(em2d::Image *img, const ParticlesTemp &ps, const RegistrationResult &reg, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="")
Generates a projection from particles.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52
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.