IMP  2.2.0
The Integrative Modeling Platform
em2d/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 2.0.12
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 
8 
9 
10 
11 from sys import version_info
12 if version_info >= (2,6,0):
13  def swig_import_helper():
14  from os.path import dirname
15  import imp
16  fp = None
17  try:
18  fp, pathname, description = imp.find_module('_IMP_em2d', [dirname(__file__)])
19  except ImportError:
20  import _IMP_em2d
21  return _IMP_em2d
22  if fp is not None:
23  try:
24  _mod = imp.load_module('_IMP_em2d', fp, pathname, description)
25  finally:
26  fp.close()
27  return _mod
28  _IMP_em2d = swig_import_helper()
29  del swig_import_helper
30 else:
31  import _IMP_em2d
32 del version_info
33 try:
34  _swig_property = property
35 except NameError:
36  pass # Python < 2.2 doesn't have 'property'.
37 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
38  if (name == "thisown"): return self.this.own(value)
39  if (name == "this"):
40  if type(value).__name__ == 'SwigPyObject':
41  self.__dict__[name] = value
42  return
43  method = class_type.__swig_setmethods__.get(name,None)
44  if method: return method(self,value)
45  if (not static):
46  self.__dict__[name] = value
47  else:
48  raise AttributeError("You cannot add attributes to %s" % self)
49 
50 def _swig_setattr(self,class_type,name,value):
51  return _swig_setattr_nondynamic(self,class_type,name,value,0)
52 
53 def _swig_getattr(self,class_type,name):
54  if (name == "thisown"): return self.this.own()
55  method = class_type.__swig_getmethods__.get(name,None)
56  if method: return method(self)
57  raise AttributeError(name)
58 
59 def _swig_repr(self):
60  try: strthis = "proxy of " + self.this.__repr__()
61  except: strthis = ""
62  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
63 
64 try:
65  _object = object
66  _newclass = 1
67 except AttributeError:
68  class _object : pass
69  _newclass = 0
70 
71 
72 try:
73  import weakref
74  weakref_proxy = weakref.proxy
75 except:
76  weakref_proxy = lambda x: x
77 
78 
79 class IMP_EM2D_SwigPyIterator(_object):
80  """Proxy of C++ swig::IMP_EM2D_SwigPyIterator class"""
81  __swig_setmethods__ = {}
82  __setattr__ = lambda self, name, value: _swig_setattr(self, IMP_EM2D_SwigPyIterator, name, value)
83  __swig_getmethods__ = {}
84  __getattr__ = lambda self, name: _swig_getattr(self, IMP_EM2D_SwigPyIterator, name)
85  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
86  __repr__ = _swig_repr
87  __swig_destroy__ = _IMP_em2d.delete_IMP_EM2D_SwigPyIterator
88  __del__ = lambda self : None;
89  def value(self):
90  """value(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
91  return _IMP_em2d.IMP_EM2D_SwigPyIterator_value(self)
92 
93  def incr(self, n=1):
94  """
95  incr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
96  incr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
97  """
98  return _IMP_em2d.IMP_EM2D_SwigPyIterator_incr(self, n)
99 
100  def decr(self, n=1):
101  """
102  decr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
103  decr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
104  """
105  return _IMP_em2d.IMP_EM2D_SwigPyIterator_decr(self, n)
106 
107  def distance(self, *args):
108  """distance(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t"""
109  return _IMP_em2d.IMP_EM2D_SwigPyIterator_distance(self, *args)
110 
111  def equal(self, *args):
112  """equal(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
113  return _IMP_em2d.IMP_EM2D_SwigPyIterator_equal(self, *args)
114 
115  def copy(self):
116  """copy(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator"""
117  return _IMP_em2d.IMP_EM2D_SwigPyIterator_copy(self)
118 
119  def next(self):
120  """next(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
121  return _IMP_em2d.IMP_EM2D_SwigPyIterator_next(self)
122 
123  def __next__(self):
124  """__next__(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
125  return _IMP_em2d.IMP_EM2D_SwigPyIterator___next__(self)
126 
127  def previous(self):
128  """previous(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
129  return _IMP_em2d.IMP_EM2D_SwigPyIterator_previous(self)
130 
131  def advance(self, *args):
132  """advance(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
133  return _IMP_em2d.IMP_EM2D_SwigPyIterator_advance(self, *args)
134 
135  def __eq__(self, *args):
136  """__eq__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
137  return _IMP_em2d.IMP_EM2D_SwigPyIterator___eq__(self, *args)
138 
139  def __ne__(self, *args):
140  """__ne__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
141  return _IMP_em2d.IMP_EM2D_SwigPyIterator___ne__(self, *args)
142 
143  def __iadd__(self, *args):
144  """__iadd__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
145  return _IMP_em2d.IMP_EM2D_SwigPyIterator___iadd__(self, *args)
146 
147  def __isub__(self, *args):
148  """__isub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
149  return _IMP_em2d.IMP_EM2D_SwigPyIterator___isub__(self, *args)
150 
151  def __add__(self, *args):
152  """__add__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
153  return _IMP_em2d.IMP_EM2D_SwigPyIterator___add__(self, *args)
154 
155  def __sub__(self, *args):
156  """
157  __sub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator
158  __sub__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t
159  """
160  return _IMP_em2d.IMP_EM2D_SwigPyIterator___sub__(self, *args)
161 
162  def __iter__(self): return self
163 IMP_EM2D_SwigPyIterator_swigregister = _IMP_em2d.IMP_EM2D_SwigPyIterator_swigregister
164 IMP_EM2D_SwigPyIterator_swigregister(IMP_EM2D_SwigPyIterator)
165 
166 _value_types=[]
167 _object_types=[]
168 _raii_types=[]
169 _plural_types=[]
170 
171 IMP_DEBUG = _IMP_em2d.IMP_DEBUG
172 IMP_RELEASE = _IMP_em2d.IMP_RELEASE
173 IMP_SILENT = _IMP_em2d.IMP_SILENT
174 IMP_PROGRESS = _IMP_em2d.IMP_PROGRESS
175 IMP_TERSE = _IMP_em2d.IMP_TERSE
176 IMP_VERBOSE = _IMP_em2d.IMP_VERBOSE
177 IMP_MEMORY = _IMP_em2d.IMP_MEMORY
178 IMP_NONE = _IMP_em2d.IMP_NONE
179 IMP_USAGE = _IMP_em2d.IMP_USAGE
180 IMP_INTERNAL = _IMP_em2d.IMP_INTERNAL
181 IMP_BASE_HAS_LOG4CXX = _IMP_em2d.IMP_BASE_HAS_LOG4CXX
182 IMP_COMPILER_HAS_AUTO = _IMP_em2d.IMP_COMPILER_HAS_AUTO
183 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em2d.IMP_COMPILER_HAS_DEBUG_VECTOR
184 IMP_BASE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_BASE_HAS_BOOST_RANDOM
185 IMP_BASE_HAS_GPERFTOOLS = _IMP_em2d.IMP_BASE_HAS_GPERFTOOLS
186 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_em2d.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
187 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_em2d.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
188 IMPBASE_SHOW_WARNINGS = _IMP_em2d.IMPBASE_SHOW_WARNINGS
189 import sys
190 class _DirectorObjects(object):
191  """@internal Simple class to keep references to director objects
192  to prevent premature deletion."""
193  def __init__(self):
194  self._objects = []
195  def register(self, obj):
196  """Take a reference to a director object; will only work for
197  refcounted C++ classes"""
198  if hasattr(obj, 'get_ref_count'):
199  self._objects.append(obj)
200  def cleanup(self):
201  """Only drop our reference and allow cleanup by Python if no other
202  Python references exist (we hold 3 references: one in self._objects,
203  one in x, and one in the argument list for getrefcount) *and* no
204  other C++ references exist (the Python object always holds one)"""
205  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
206  or x.get_ref_count() > 1]
207 
208 
209  self._objects = objs
210  def get_object_count(self):
211  """Get number of director objects (useful for testing only)"""
212  return len(self._objects)
213 _director_objects = _DirectorObjects()
214 
215 DEFAULT_CHECK = _IMP_em2d.DEFAULT_CHECK
216 NONE = _IMP_em2d.NONE
217 USAGE = _IMP_em2d.USAGE
218 USAGE_AND_INTERNAL = _IMP_em2d.USAGE_AND_INTERNAL
219 
220 def set_check_level(*args):
221  """set_check_level(IMP::base::CheckLevel tf)"""
222  return _IMP_em2d.set_check_level(*args)
223 
224 def get_check_level():
225  """get_check_level() -> IMP::base::CheckLevel"""
226  return _IMP_em2d.get_check_level()
227 class _ostream(_object):
228  """Proxy of C++ std::ostream class"""
229  __swig_setmethods__ = {}
230  __setattr__ = lambda self, name, value: _swig_setattr(self, _ostream, name, value)
231  __swig_getmethods__ = {}
232  __getattr__ = lambda self, name: _swig_getattr(self, _ostream, name)
233  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
234  __repr__ = _swig_repr
235  def write(self, *args):
236  """write(_ostream self, char const * osa_buf)"""
237  return _IMP_em2d._ostream_write(self, *args)
238 
239 _ostream_swigregister = _IMP_em2d._ostream_swigregister
240 _ostream_swigregister(_ostream)
241 
242 IMP_COMPILER_HAS_OVERRIDE = _IMP_em2d.IMP_COMPILER_HAS_OVERRIDE
243 IMP_COMPILER_HAS_FINAL = _IMP_em2d.IMP_COMPILER_HAS_FINAL
244 IMP_HAS_NOEXCEPT = _IMP_em2d.IMP_HAS_NOEXCEPT
245 import IMP.base
246 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_FILESYSTEM
247 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
248 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CGAL_HAS_BOOST_RANDOM
249 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_SYSTEM
250 IMPCGAL_SHOW_WARNINGS = _IMP_em2d.IMPCGAL_SHOW_WARNINGS
251 import IMP.cgal
252 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_IMP_CGAL
253 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
254 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
255 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_RANDOM
256 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_SYSTEM
257 IMP_ALGEBRA_HAS_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_CGAL
258 IMP_ALGEBRA_HAS_ANN = _IMP_em2d.IMP_ALGEBRA_HAS_ANN
259 IMPALGEBRA_SHOW_WARNINGS = _IMP_em2d.IMPALGEBRA_SHOW_WARNINGS
260 import IMP.algebra
261 IMP_KERNEL_HAS_IMP_CGAL = _IMP_em2d.IMP_KERNEL_HAS_IMP_CGAL
262 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
263 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_KERNEL_HAS_BOOST_RANDOM
264 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_KERNEL_HAS_BOOST_SYSTEM
265 IMP_KERNEL_HAS_CGAL = _IMP_em2d.IMP_KERNEL_HAS_CGAL
266 IMPKERNEL_SHOW_WARNINGS = _IMP_em2d.IMPKERNEL_SHOW_WARNINGS
267 import IMP.kernel
268 IMP_DISPLAY_HAS_IMP_BASE = _IMP_em2d.IMP_DISPLAY_HAS_IMP_BASE
269 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_IMP_CGAL
270 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
271 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
272 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_RANDOM
273 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_SYSTEM
274 IMP_DISPLAY_HAS_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_CGAL
275 IMPDISPLAY_SHOW_WARNINGS = _IMP_em2d.IMPDISPLAY_SHOW_WARNINGS
276 import IMP.display
277 IMP_GSL_HAS_IMP_BASE = _IMP_em2d.IMP_GSL_HAS_IMP_BASE
278 IMP_GSL_HAS_IMP_CGAL = _IMP_em2d.IMP_GSL_HAS_IMP_CGAL
279 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_FILESYSTEM
280 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
281 IMP_GSL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_GSL_HAS_BOOST_RANDOM
282 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_SYSTEM
283 IMP_GSL_HAS_CGAL = _IMP_em2d.IMP_GSL_HAS_CGAL
284 IMPGSL_SHOW_WARNINGS = _IMP_em2d.IMPGSL_SHOW_WARNINGS
285 import IMP.gsl
286 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
287 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
288 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
289 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
290 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
291 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_CGAL
292 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_HDF5
293 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em2d.IMPSCOREFUNCTOR_SHOW_WARNINGS
294 import IMP.score_functor
295 IMP_STATISTICS_HAS_IMP_BASE = _IMP_em2d.IMP_STATISTICS_HAS_IMP_BASE
296 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_IMP_CGAL
297 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
298 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
299 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_RANDOM
300 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_SYSTEM
301 IMP_STATISTICS_HAS_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_CGAL
302 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em2d.IMPSTATISTICS_SHOW_WARNINGS
303 import IMP.statistics
304 IMP_CORE_HAS_IMP_BASE = _IMP_em2d.IMP_CORE_HAS_IMP_BASE
305 IMP_CORE_HAS_IMP_CGAL = _IMP_em2d.IMP_CORE_HAS_IMP_CGAL
306 IMP_CORE_HAS_IMP_KERNEL = _IMP_em2d.IMP_CORE_HAS_IMP_KERNEL
307 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_FILESYSTEM
308 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
309 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CORE_HAS_BOOST_RANDOM
310 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_SYSTEM
311 IMP_CORE_HAS_CGAL = _IMP_em2d.IMP_CORE_HAS_CGAL
312 IMP_CORE_HAS_HDF5 = _IMP_em2d.IMP_CORE_HAS_HDF5
313 IMPCORE_SHOW_WARNINGS = _IMP_em2d.IMPCORE_SHOW_WARNINGS
314 import IMP.core
315 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em2d.IMP_CONTAINER_HAS_IMP_ALGEBRA
316 IMP_CONTAINER_HAS_IMP_BASE = _IMP_em2d.IMP_CONTAINER_HAS_IMP_BASE
317 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_CGAL
318 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em2d.IMP_CONTAINER_HAS_IMP_DISPLAY
319 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_KERNEL
320 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
321 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
322 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
323 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_RANDOM
324 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_SYSTEM
325 IMP_CONTAINER_HAS_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_CGAL
326 IMP_CONTAINER_HAS_HDF5 = _IMP_em2d.IMP_CONTAINER_HAS_HDF5
327 IMPCONTAINER_SHOW_WARNINGS = _IMP_em2d.IMPCONTAINER_SHOW_WARNINGS
328 import IMP.container
329 IMP_ATOM_HAS_IMP_BASE = _IMP_em2d.IMP_ATOM_HAS_IMP_BASE
330 IMP_ATOM_HAS_IMP_CGAL = _IMP_em2d.IMP_ATOM_HAS_IMP_CGAL
331 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em2d.IMP_ATOM_HAS_IMP_KERNEL
332 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
333 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
334 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ATOM_HAS_BOOST_RANDOM
335 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em2d.IMP_ATOM_HAS_BOOST_REGEX
336 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ATOM_HAS_BOOST_SYSTEM
337 IMP_ATOM_HAS_CGAL = _IMP_em2d.IMP_ATOM_HAS_CGAL
338 IMP_ATOM_HAS_HDF5 = _IMP_em2d.IMP_ATOM_HAS_HDF5
339 IMPATOM_SHOW_WARNINGS = _IMP_em2d.IMPATOM_SHOW_WARNINGS
340 IMP_ATOM_TYPE_INDEX = _IMP_em2d.IMP_ATOM_TYPE_INDEX
341 IMP_RESIDUE_TYPE_INDEX = _IMP_em2d.IMP_RESIDUE_TYPE_INDEX
342 IMP_HIERARCHY_TYPE_INDEX = _IMP_em2d.IMP_HIERARCHY_TYPE_INDEX
343 import IMP.atom
344 IMP_EM_HAS_IMP_CGAL = _IMP_em2d.IMP_EM_HAS_IMP_CGAL
345 IMP_EM_HAS_IMP_CONTAINER = _IMP_em2d.IMP_EM_HAS_IMP_CONTAINER
346 IMP_EM_HAS_IMP_DISPLAY = _IMP_em2d.IMP_EM_HAS_IMP_DISPLAY
347 IMP_EM_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM_HAS_IMP_KERNEL
348 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM_HAS_IMP_SCORE_FUNCTOR
349 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_FILESYSTEM
350 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
351 IMP_EM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM_HAS_BOOST_RANDOM
352 IMP_EM_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM_HAS_BOOST_REGEX
353 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_SYSTEM
354 IMP_EM_HAS_CGAL = _IMP_em2d.IMP_EM_HAS_CGAL
355 IMP_EM_HAS_HDF5 = _IMP_em2d.IMP_EM_HAS_HDF5
356 IMPEM_SHOW_WARNINGS = _IMP_em2d.IMPEM_SHOW_WARNINGS
357 import IMP.em
358 IMP_RMF_HAS_IMP_BASE = _IMP_em2d.IMP_RMF_HAS_IMP_BASE
359 IMP_RMF_HAS_IMP_CGAL = _IMP_em2d.IMP_RMF_HAS_IMP_CGAL
360 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
361 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_FILESYSTEM
362 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
363 IMP_RMF_HAS_BOOST_RANDOM = _IMP_em2d.IMP_RMF_HAS_BOOST_RANDOM
364 IMP_RMF_HAS_BOOST_REGEX = _IMP_em2d.IMP_RMF_HAS_BOOST_REGEX
365 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_SYSTEM
366 IMP_RMF_HAS_CGAL = _IMP_em2d.IMP_RMF_HAS_CGAL
367 IMP_RMF_HAS_HDF5 = _IMP_em2d.IMP_RMF_HAS_HDF5
368 IMPRMF_SHOW_WARNINGS = _IMP_em2d.IMPRMF_SHOW_WARNINGS
369 import IMP.rmf
370 import RMF
371 IMP_DOMINO_HAS_IMP_ATOM = _IMP_em2d.IMP_DOMINO_HAS_IMP_ATOM
372 IMP_DOMINO_HAS_IMP_BASE = _IMP_em2d.IMP_DOMINO_HAS_IMP_BASE
373 IMP_DOMINO_HAS_IMP_CGAL = _IMP_em2d.IMP_DOMINO_HAS_IMP_CGAL
374 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_em2d.IMP_DOMINO_HAS_IMP_KERNEL
375 IMP_DOMINO_HAS_IMP_RMF = _IMP_em2d.IMP_DOMINO_HAS_IMP_RMF
376 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
377 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_FILESYSTEM
378 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
379 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_RANDOM
380 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_em2d.IMP_DOMINO_HAS_BOOST_REGEX
381 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_SYSTEM
382 IMP_DOMINO_HAS_CGAL = _IMP_em2d.IMP_DOMINO_HAS_CGAL
383 IMP_DOMINO_HAS_HDF5 = _IMP_em2d.IMP_DOMINO_HAS_HDF5
384 IMP_DOMINO_HAS_RMF = _IMP_em2d.IMP_DOMINO_HAS_RMF
385 IMPDOMINO_SHOW_WARNINGS = _IMP_em2d.IMPDOMINO_SHOW_WARNINGS
386 import RMF_HDF5
387 import IMP.domino
388 IMP_EM2D_HAS_IMP_BASE = _IMP_em2d.IMP_EM2D_HAS_IMP_BASE
389 IMP_EM2D_HAS_IMP_CGAL = _IMP_em2d.IMP_EM2D_HAS_IMP_CGAL
390 IMP_EM2D_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM2D_HAS_IMP_KERNEL
391 IMP_EM2D_HAS_IMP_RMF = _IMP_em2d.IMP_EM2D_HAS_IMP_RMF
392 IMP_EM2D_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM2D_HAS_IMP_SCORE_FUNCTOR
393 IMP_EM2D_HAS_IMP_STATISTICS = _IMP_em2d.IMP_EM2D_HAS_IMP_STATISTICS
394 IMP_EM2D_HAS_BOOST_GRAPH = _IMP_em2d.IMP_EM2D_HAS_BOOST_GRAPH
395 IMP_EM2D_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM2D_HAS_BOOST_RANDOM
396 IMP_EM2D_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM2D_HAS_BOOST_REGEX
397 IMP_EM2D_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM2D_HAS_BOOST_SYSTEM
398 IMP_EM2D_HAS_CGAL = _IMP_em2d.IMP_EM2D_HAS_CGAL
399 IMP_EM2D_HAS_GSL = _IMP_em2d.IMP_EM2D_HAS_GSL
400 IMP_EM2D_HAS_HDF5 = _IMP_em2d.IMP_EM2D_HAS_HDF5
401 IMP_EM2D_HAS_OPENCV22 = _IMP_em2d.IMP_EM2D_HAS_OPENCV22
402 IMP_EM2D_HAS_RMF = _IMP_em2d.IMP_EM2D_HAS_RMF
403 IMP_EM2D_HAS_OPENCV21 = _IMP_em2d.IMP_EM2D_HAS_OPENCV21
404 IMPEM2D_SHOW_WARNINGS = _IMP_em2d.IMPEM2D_SHOW_WARNINGS
405 PolarResamplingParametersList=list
406 _plural_types.append("PolarResamplingParametersList")
407 _value_types.append("PolarResamplingParameters")
408 
409 ProjectionMasks=list
410 _plural_types.append("ProjectionMasks")
411 _value_types.append("ProjectionMask")
412 
413 MasksManagers=list
414 _plural_types.append("MasksManagers")
415 _value_types.append("MasksManager")
416 
417 RegistrationResults=list
418 _plural_types.append("RegistrationResults")
419 _value_types.append("RegistrationResult")
420 
421 ClusterSets=list
422 _plural_types.append("ClusterSets")
423 _value_types.append("ClusterSet")
424 
425 SingleLinkages=list
426 _plural_types.append("SingleLinkages")
427 _value_types.append("SingleLinkage")
428 
429 CompleteLinkages=list
430 _plural_types.append("CompleteLinkages")
431 _value_types.append("CompleteLinkage")
432 
433 AverageDistanceLinkages=list
434 _plural_types.append("AverageDistanceLinkages")
435 _value_types.append("AverageDistanceLinkage")
436 
437 SegmentationParametersList=list
438 _plural_types.append("SegmentationParametersList")
439 _value_types.append("SegmentationParameters")
440 
441 MatchTemplateResults=list
442 _plural_types.append("MatchTemplateResults")
443 _value_types.append("MatchTemplateResult")
444 
445 ProjectingParametersList=list
446 _plural_types.append("ProjectingParametersList")
447 _value_types.append("ProjectingParameters")
448 
449 ProjectingOptionsList=list
450 _plural_types.append("ProjectingOptionsList")
451 _value_types.append("ProjectingOptions")
452 
453 Em2DRestraintParametersList=list
454 _plural_types.append("Em2DRestraintParametersList")
455 _value_types.append("Em2DRestraintParameters")
456 
457 _object_types.append("ProjectionFinder")
458 
459 
460 def _object_cast_to_ProjectionFinder(*args):
461  """_object_cast_to_ProjectionFinder(Object o) -> ProjectionFinder"""
462  return _IMP_em2d._object_cast_to_ProjectionFinder(*args)
463 _object_types.append("ScoreFunction")
464 
465 
466 def _object_cast_to_ScoreFunction(*args):
467  """_object_cast_to_ScoreFunction(Object o) -> ScoreFunction"""
468  return _IMP_em2d._object_cast_to_ScoreFunction(*args)
469 _object_types.append("ChiSquaredScore")
470 
471 
472 def _object_cast_to_ChiSquaredScore(*args):
473  """_object_cast_to_ChiSquaredScore(Object o) -> ChiSquaredScore"""
474  return _IMP_em2d._object_cast_to_ChiSquaredScore(*args)
475 _object_types.append("EM2DScore")
476 
477 
478 def _object_cast_to_EM2DScore(*args):
479  """_object_cast_to_EM2DScore(Object o) -> EM2DScore"""
480  return _IMP_em2d._object_cast_to_EM2DScore(*args)
481 _object_types.append("MeanAbsoluteDifference")
482 
483 
484 def _object_cast_to_MeanAbsoluteDifference(*args):
485  """_object_cast_to_MeanAbsoluteDifference(Object o) -> MeanAbsoluteDifference"""
486  return _IMP_em2d._object_cast_to_MeanAbsoluteDifference(*args)
487 _object_types.append("ProjectionParametersScoreState")
488 
489 
490 def _object_cast_to_ProjectionParametersScoreState(*args):
491  """_object_cast_to_ProjectionParametersScoreState(Object o) -> ProjectionParametersScoreState"""
492  return _IMP_em2d._object_cast_to_ProjectionParametersScoreState(*args)
493 _object_types.append("Em2DRestraint")
494 
495 
496 def _object_cast_to_Em2DRestraint(*args):
497  """_object_cast_to_Em2DRestraint(Object o) -> Em2DRestraint"""
498  return _IMP_em2d._object_cast_to_Em2DRestraint(*args)
499 _object_types.append("Image")
500 
501 
502 def _object_cast_to_Image(*args):
503  """_object_cast_to_Image(Object o) -> Image"""
504  return _IMP_em2d._object_cast_to_Image(*args)
505 _object_types.append("ImageReaderWriter")
506 
507 
508 def _object_cast_to_ImageReaderWriter(*args):
509  """_object_cast_to_ImageReaderWriter(Object o) -> ImageReaderWriter"""
510  return _IMP_em2d._object_cast_to_ImageReaderWriter(*args)
511 _object_types.append("JPGImageReaderWriter")
512 
513 
514 def _object_cast_to_JPGImageReaderWriter(*args):
515  """_object_cast_to_JPGImageReaderWriter(Object o) -> JPGImageReaderWriter"""
516  return _IMP_em2d._object_cast_to_JPGImageReaderWriter(*args)
517 _object_types.append("TIFFImageReaderWriter")
518 
519 
520 def _object_cast_to_TIFFImageReaderWriter(*args):
521  """_object_cast_to_TIFFImageReaderWriter(Object o) -> TIFFImageReaderWriter"""
522  return _IMP_em2d._object_cast_to_TIFFImageReaderWriter(*args)
523 _object_types.append("SpiderImageReaderWriter")
524 
525 
526 def _object_cast_to_SpiderImageReaderWriter(*args):
527  """_object_cast_to_SpiderImageReaderWriter(Object o) -> SpiderImageReaderWriter"""
528  return _IMP_em2d._object_cast_to_SpiderImageReaderWriter(*args)
529 _object_types.append("CollisionCrossSection")
530 
531 
532 def _object_cast_to_CollisionCrossSection(*args):
533  """_object_cast_to_CollisionCrossSection(Object o) -> CollisionCrossSection"""
534  return _IMP_em2d._object_cast_to_CollisionCrossSection(*args)
535 _object_types.append("GridStates")
536 
537 
538 def _object_cast_to_GridStates(*args):
539  """_object_cast_to_GridStates(Object o) -> GridStates"""
540  return _IMP_em2d._object_cast_to_GridStates(*args)
541 _object_types.append("ProjectionStates")
542 
543 
544 def _object_cast_to_ProjectionStates(*args):
545  """_object_cast_to_ProjectionStates(Object o) -> ProjectionStates"""
546  return _IMP_em2d._object_cast_to_ProjectionStates(*args)
547 _object_types.append("DistanceFilter")
548 
549 
550 def _object_cast_to_DistanceFilter(*args):
551  """_object_cast_to_DistanceFilter(Object o) -> DistanceFilter"""
552  return _IMP_em2d._object_cast_to_DistanceFilter(*args)
553 _object_types.append("DistanceFilterTable")
554 
555 
556 def _object_cast_to_DistanceFilterTable(*args):
557  """_object_cast_to_DistanceFilterTable(Object o) -> DistanceFilterTable"""
558  return _IMP_em2d._object_cast_to_DistanceFilterTable(*args)
559 _object_types.append("RigidBodiesImageFitRestraint")
560 
561 
562 def _object_cast_to_RigidBodiesImageFitRestraint(*args):
563  """_object_cast_to_RigidBodiesImageFitRestraint(Object o) -> RigidBodiesImageFitRestraint"""
564  return _IMP_em2d._object_cast_to_RigidBodiesImageFitRestraint(*args)
565 _object_types.append("DummyRestraint")
566 
567 
568 def _object_cast_to_DummyRestraint(*args):
569  """_object_cast_to_DummyRestraint(Object o) -> DummyRestraint"""
570  return _IMP_em2d._object_cast_to_DummyRestraint(*args)
571 _object_types.append("ParticlesDummyRestraint")
572 
573 
574 def _object_cast_to_ParticlesDummyRestraint(*args):
575  """_object_cast_to_ParticlesDummyRestraint(Object o) -> ParticlesDummyRestraint"""
576  return _IMP_em2d._object_cast_to_ParticlesDummyRestraint(*args)
577 _object_types.append("RelativePositionMover")
578 
579 
580 def _object_cast_to_RelativePositionMover(*args):
581  """_object_cast_to_RelativePositionMover(Object o) -> RelativePositionMover"""
582  return _IMP_em2d._object_cast_to_RelativePositionMover(*args)
583 def ProjectionParametersList(l=[]):
584  return [ProjectionParameters(x) for x in l]
585 _plural_types.append("ProjectionParametersList")
586 
587 _value_types.append("ProjectionParameters")
588 
589 
590 def show(*args):
591  """
592  show(cv::Mat const & m, _ostream out=std::cout)
593  show(cv::Mat const & m)
594  """
595  return _IMP_em2d.show(*args)
596 
597 def write_matrix(*args):
598  """write_matrix(cv::Mat & m, std::string name)"""
599  return _IMP_em2d.write_matrix(*args)
600 class ImageReaderWriter(IMP.base.Object):
601  """Proxy of C++ IMP::em2d::ImageReaderWriter class"""
602  __swig_setmethods__ = {}
603  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
604  __setattr__ = lambda self, name, value: _swig_setattr(self, ImageReaderWriter, name, value)
605  __swig_getmethods__ = {}
606  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
607  __getattr__ = lambda self, name: _swig_getattr(self, ImageReaderWriter, name)
608  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
609  def read(self, *args):
610  """read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
611  return _IMP_em2d.ImageReaderWriter_read(self, *args)
612 
613  def read_from_floats(self, *args):
614  """read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
615  return _IMP_em2d.ImageReaderWriter_read_from_floats(self, *args)
616 
617  def read_from_ints(self, *args):
618  """read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
619  return _IMP_em2d.ImageReaderWriter_read_from_ints(self, *args)
620 
621  def write(self, *args):
622  """write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
623  return _IMP_em2d.ImageReaderWriter_write(self, *args)
624 
625  def write_to_floats(self, *args):
626  """write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
627  return _IMP_em2d.ImageReaderWriter_write_to_floats(self, *args)
628 
629  def write_to_ints(self, *args):
630  """write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
631  return _IMP_em2d.ImageReaderWriter_write_to_ints(self, *args)
632 
633  def get_version_info(self):
634  """get_version_info(ImageReaderWriter self) -> VersionInfo"""
635  return _IMP_em2d.ImageReaderWriter_get_version_info(self)
636 
637  def __str__(self):
638  """__str__(ImageReaderWriter self) -> std::string"""
639  return _IMP_em2d.ImageReaderWriter___str__(self)
640 
641  def __repr__(self):
642  """__repr__(ImageReaderWriter self) -> std::string"""
643  return _IMP_em2d.ImageReaderWriter___repr__(self)
644 
645  def get_from(o):
646  return _object_cast_to_ImageReaderWriter(o)
647  get_from = staticmethod(get_from)
648 
649 ImageReaderWriter_swigregister = _IMP_em2d.ImageReaderWriter_swigregister
650 ImageReaderWriter_swigregister(ImageReaderWriter)
651 
652 class PolarResamplingParameters(_object):
653  """Proxy of C++ IMP::em2d::PolarResamplingParameters class"""
654  __swig_setmethods__ = {}
655  __setattr__ = lambda self, name, value: _swig_setattr(self, PolarResamplingParameters, name, value)
656  __swig_getmethods__ = {}
657  __getattr__ = lambda self, name: _swig_getattr(self, PolarResamplingParameters, name)
658  def __init__(self, *args):
659  """
660  __init__(IMP::em2d::PolarResamplingParameters self) -> PolarResamplingParameters
661  __init__(IMP::em2d::PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
662  __init__(IMP::em2d::PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
663  """
664  this = _IMP_em2d.new_PolarResamplingParameters(*args)
665  try: self.this.append(this)
666  except: self.this = this
667  __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
668  __del__ = lambda self : None;
669  def setup(self, *args):
670  """setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
671  return _IMP_em2d.PolarResamplingParameters_setup(self, *args)
672 
673  def get_starting_radius(self):
674  """get_starting_radius(PolarResamplingParameters self) -> double"""
675  return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
676 
677  def get_ending_radius(self):
678  """get_ending_radius(PolarResamplingParameters self) -> double"""
679  return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
680 
681  def get_radius(self, *args):
682  """get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
683  return _IMP_em2d.PolarResamplingParameters_get_radius(self, *args)
684 
685  def get_number_of_rings(self):
686  """get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
687  return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
688 
689  def set_estimated_number_of_angles(self, *args):
690  """set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
691  return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, *args)
692 
693  def get_number_of_angles(self):
694  """get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
695  return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
696 
697  def get_angle_step(self):
698  """get_angle_step(PolarResamplingParameters self) -> double"""
699  return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
700 
701  def get_radius_step(self):
702  """get_radius_step(PolarResamplingParameters self) -> double"""
703  return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
704 
705  def create_maps_for_resampling(self):
706  """create_maps_for_resampling(PolarResamplingParameters self)"""
707  return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
708 
709  def get_resampling_maps(self, *args):
710  """get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
711  return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, *args)
712 
713  def get_resampling_map(self, *args):
714  """get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
715  return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, *args)
716 
717  def show(self, *args):
718  """show(PolarResamplingParameters self, _ostream out)"""
719  return _IMP_em2d.PolarResamplingParameters_show(self, *args)
720 
721  def get_is_setup(self):
722  """get_is_setup(PolarResamplingParameters self) -> bool"""
723  return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
724 
725  def __str__(self):
726  """__str__(PolarResamplingParameters self) -> std::string"""
727  return _IMP_em2d.PolarResamplingParameters___str__(self)
728 
729  def __repr__(self):
730  """__repr__(PolarResamplingParameters self) -> std::string"""
731  return _IMP_em2d.PolarResamplingParameters___repr__(self)
732 
733 PolarResamplingParameters_swigregister = _IMP_em2d.PolarResamplingParameters_swigregister
734 PolarResamplingParameters_swigregister(PolarResamplingParameters)
735 
736 class SegmentationParameters(_object):
737  """Proxy of C++ IMP::em2d::SegmentationParameters class"""
738  __swig_setmethods__ = {}
739  __setattr__ = lambda self, name, value: _swig_setattr(self, SegmentationParameters, name, value)
740  __swig_getmethods__ = {}
741  __getattr__ = lambda self, name: _swig_getattr(self, SegmentationParameters, name)
742  __swig_setmethods__["image_pixel_size"] = _IMP_em2d.SegmentationParameters_image_pixel_size_set
743  __swig_getmethods__["image_pixel_size"] = _IMP_em2d.SegmentationParameters_image_pixel_size_get
744  if _newclass:image_pixel_size = _swig_property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set)
745  __swig_setmethods__["diffusion_beta"] = _IMP_em2d.SegmentationParameters_diffusion_beta_set
746  __swig_getmethods__["diffusion_beta"] = _IMP_em2d.SegmentationParameters_diffusion_beta_get
747  if _newclass:diffusion_beta = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set)
748  __swig_setmethods__["diffusion_timesteps"] = _IMP_em2d.SegmentationParameters_diffusion_timesteps_set
749  __swig_getmethods__["diffusion_timesteps"] = _IMP_em2d.SegmentationParameters_diffusion_timesteps_get
750  if _newclass:diffusion_timesteps = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set)
751  __swig_setmethods__["fill_holes_stddevs"] = _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set
752  __swig_getmethods__["fill_holes_stddevs"] = _IMP_em2d.SegmentationParameters_fill_holes_stddevs_get
753  if _newclass:fill_holes_stddevs = _swig_property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set)
754  __swig_setmethods__["opening_kernel"] = _IMP_em2d.SegmentationParameters_opening_kernel_set
755  __swig_getmethods__["opening_kernel"] = _IMP_em2d.SegmentationParameters_opening_kernel_get
756  if _newclass:opening_kernel = _swig_property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set)
757  __swig_setmethods__["remove_sizing_percentage"] = _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set
758  __swig_getmethods__["remove_sizing_percentage"] = _IMP_em2d.SegmentationParameters_remove_sizing_percentage_get
759  if _newclass:remove_sizing_percentage = _swig_property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set)
760  __swig_setmethods__["binary_background"] = _IMP_em2d.SegmentationParameters_binary_background_set
761  __swig_getmethods__["binary_background"] = _IMP_em2d.SegmentationParameters_binary_background_get
762  if _newclass:binary_background = _swig_property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set)
763  __swig_setmethods__["binary_foreground"] = _IMP_em2d.SegmentationParameters_binary_foreground_set
764  __swig_getmethods__["binary_foreground"] = _IMP_em2d.SegmentationParameters_binary_foreground_get
765  if _newclass:binary_foreground = _swig_property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set)
766  __swig_setmethods__["threshold"] = _IMP_em2d.SegmentationParameters_threshold_set
767  __swig_getmethods__["threshold"] = _IMP_em2d.SegmentationParameters_threshold_get
768  if _newclass:threshold = _swig_property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set)
769  def __init__(self, *args):
770  """
771  __init__(IMP::em2d::SegmentationParameters self) -> SegmentationParameters
772  __init__(IMP::em2d::SegmentationParameters self, double apix, double diff_beta, unsigned int diff_timesteps, double fh_stddevs, cv::Mat const & kr,
773  int background, int foreground) -> SegmentationParameters
774  """
775  this = _IMP_em2d.new_SegmentationParameters(*args)
776  try: self.this.append(this)
777  except: self.this = this
778  def show(self, *args):
779  """
780  show(SegmentationParameters self, _ostream out=std::cout)
781  show(SegmentationParameters self)
782  """
783  return _IMP_em2d.SegmentationParameters_show(self, *args)
784 
785  def __str__(self):
786  """__str__(SegmentationParameters self) -> std::string"""
787  return _IMP_em2d.SegmentationParameters___str__(self)
788 
789  def __repr__(self):
790  """__repr__(SegmentationParameters self) -> std::string"""
791  return _IMP_em2d.SegmentationParameters___repr__(self)
792 
793  __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
794  __del__ = lambda self : None;
795 SegmentationParameters_swigregister = _IMP_em2d.SegmentationParameters_swigregister
796 SegmentationParameters_swigregister(SegmentationParameters)
797 
798 class MatchTemplateResult(_object):
799  """Proxy of C++ IMP::em2d::MatchTemplateResult class"""
800  __swig_setmethods__ = {}
801  __setattr__ = lambda self, name, value: _swig_setattr(self, MatchTemplateResult, name, value)
802  __swig_getmethods__ = {}
803  __getattr__ = lambda self, name: _swig_getattr(self, MatchTemplateResult, name)
804  __swig_setmethods__["pair"] = _IMP_em2d.MatchTemplateResult_pair_set
805  __swig_getmethods__["pair"] = _IMP_em2d.MatchTemplateResult_pair_get
806  if _newclass:pair = _swig_property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set)
807  __swig_setmethods__["cross_correlation"] = _IMP_em2d.MatchTemplateResult_cross_correlation_set
808  __swig_getmethods__["cross_correlation"] = _IMP_em2d.MatchTemplateResult_cross_correlation_get
809  if _newclass:cross_correlation = _swig_property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set)
810  def __init__(self, *args):
811  """__init__(IMP::em2d::MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
812  this = _IMP_em2d.new_MatchTemplateResult(*args)
813  try: self.this.append(this)
814  except: self.this = this
815  def show(self, *args):
816  """
817  show(MatchTemplateResult self, _ostream out=std::cout)
818  show(MatchTemplateResult self)
819  """
820  return _IMP_em2d.MatchTemplateResult_show(self, *args)
821 
822  def __str__(self):
823  """__str__(MatchTemplateResult self) -> std::string"""
824  return _IMP_em2d.MatchTemplateResult___str__(self)
825 
826  def __repr__(self):
827  """__repr__(MatchTemplateResult self) -> std::string"""
828  return _IMP_em2d.MatchTemplateResult___repr__(self)
829 
830  __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
831  __del__ = lambda self : None;
832 MatchTemplateResult_swigregister = _IMP_em2d.MatchTemplateResult_swigregister
833 MatchTemplateResult_swigregister(MatchTemplateResult)
834 
835 
836 def apply_mask(*args):
837  """apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
838  return _IMP_em2d.apply_mask(*args)
839 
840 def apply_circular_mask(*args):
841  """
842  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)
843  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius)
844  """
845  return _IMP_em2d.apply_circular_mask(*args)
846 
847 def get_mean(*args):
848  """get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
849  return _IMP_em2d.get_mean(*args)
850 
851 def create_circular_mask(*args):
852  """create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
853  return _IMP_em2d.create_circular_mask(*args)
854 
855 def do_histogram_stretching(*args):
856  """do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
857  return _IMP_em2d.do_histogram_stretching(*args)
858 
859 def do_dilate_and_shrink_warp(*args):
860  """do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & greyscale, cv::Mat & kernel)"""
861  return _IMP_em2d.do_dilate_and_shrink_warp(*args)
862 
864  """
865  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)
866  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker)
867  """
868  return _IMP_em2d.do_morphologic_reconstruction(*args)
869 
870 def do_labeling(*args):
871  """do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
872  return _IMP_em2d.do_labeling(*args)
873 
875  """get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
876  return _IMP_em2d.get_diffusion_filtering_partial_derivative(*args)
877 
878 def get_domes(*args):
879  """get_domes(cv::Mat & m, cv::Mat & result, double h)"""
880  return _IMP_em2d.get_domes(*args)
881 
882 def my_meanStdDev(*args):
883  """my_meanStdDev(cv::Mat const & m, cv::Scalar & mean, cv::Scalar & stddev)"""
884  return _IMP_em2d.my_meanStdDev(*args)
885 
886 def get_transformed(*args):
887  """get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
888  return _IMP_em2d.get_transformed(*args)
889 
890 def apply_threshold(*args):
891  """
892  apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)
893  apply_threshold(cv::Mat & m, cv::Mat & result)
894  """
895  return _IMP_em2d.apply_threshold(*args)
896 
898  """do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
899  return _IMP_em2d.do_morphologic_contrast_enhancement(*args)
900 
901 def get_morphologic_gradient(*args):
902  """get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
903  return _IMP_em2d.get_morphologic_gradient(*args)
904 
905 def get_overlap_percentage(*args):
906  """get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
907  return _IMP_em2d.get_overlap_percentage(*args)
908 
909 def get_best_template_matches(*args):
910  """get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
911  return _IMP_em2d.get_best_template_matches(*args)
912 class Image(IMP.base.Object):
913  """Proxy of C++ IMP::em2d::Image class"""
914  __swig_setmethods__ = {}
915  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
916  __setattr__ = lambda self, name, value: _swig_setattr(self, Image, name, value)
917  __swig_getmethods__ = {}
918  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
919  __getattr__ = lambda self, name: _swig_getattr(self, Image, name)
920  def __init__(self, *args):
921  """
922  __init__(IMP::em2d::Image self) -> Image
923  __init__(IMP::em2d::Image self, int rows, int cols) -> Image
924  __init__(IMP::em2d::Image self, IMP::String filename, ImageReaderWriter reader) -> Image
925  """
926  this = _IMP_em2d.new_Image(*args)
927  try: self.this.append(this)
928  except: self.this = this
929  def get_data(self):
930  """get_data(Image self) -> cv::Mat &"""
931  return _IMP_em2d.Image_get_data(self)
932 
933  def set_data(self, *args):
934  """set_data(Image self, cv::Mat const & mat)"""
935  return _IMP_em2d.Image_set_data(self, *args)
936 
937  def set_zeros(self):
938  """set_zeros(Image self)"""
939  return _IMP_em2d.Image_set_zeros(self)
940 
941  def set_value(self, *args):
942  """
943  set_value(Image self, double val)
944  set_value(Image self, int i, int j, double val)
945  """
946  return _IMP_em2d.Image_set_value(self, *args)
947 
948  def __call__(self, *args):
949  """__call__(Image self, int i, int j) -> double"""
950  return _IMP_em2d.Image___call__(self, *args)
951 
952  def get_header(self):
953  """get_header(Image self) -> ImageHeader"""
954  return _IMP_em2d.Image_get_header(self)
955 
956  def set_size(self, *args):
957  """
958  set_size(Image self, int rows, int cols)
959  set_size(Image self, Image img)
960  """
961  return _IMP_em2d.Image_set_size(self, *args)
962 
963  def update_header(self):
964  """update_header(Image self)"""
965  return _IMP_em2d.Image_update_header(self)
966 
967  def read(self, *args):
968  """read(Image self, IMP::String filename, ImageReaderWriter reader)"""
969  return _IMP_em2d.Image_read(self, *args)
970 
971  def write(self, *args):
972  """write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
973  return _IMP_em2d.Image_write(self, *args)
974 
975  def show(self, *args):
976  """show(Image self, _ostream out)"""
977  return _IMP_em2d.Image_show(self, *args)
978 
979  def get_version_info(self):
980  """get_version_info(Image self) -> VersionInfo"""
981  return _IMP_em2d.Image_get_version_info(self)
982 
983  def set_name(self, *args):
984  """set_name(Image self, IMP::String const & name)"""
985  return _IMP_em2d.Image_set_name(self, *args)
986 
987  def get_name(self):
988  """get_name(Image self) -> IMP::String"""
989  return _IMP_em2d.Image_get_name(self)
990 
991  def get_min_and_max_values(self):
992  """get_min_and_max_values(Image self) -> IMP::FloatRange"""
993  return _IMP_em2d.Image_get_min_and_max_values(self)
994 
995  def __str__(self):
996  """__str__(Image self) -> std::string"""
997  return _IMP_em2d.Image___str__(self)
998 
999  def __repr__(self):
1000  """__repr__(Image self) -> std::string"""
1001  return _IMP_em2d.Image___repr__(self)
1002 
1003  def get_from(o):
1004  return _object_cast_to_Image(o)
1005  get_from = staticmethod(get_from)
1006 
1007 Image_swigregister = _IMP_em2d.Image_swigregister
1008 Image_swigregister(Image)
1009 
1010 
1011 def read_images(*args):
1012  """read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1013  return _IMP_em2d.read_images(*args)
1014 
1015 def save_images(*args):
1016  """save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1017  return _IMP_em2d.save_images(*args)
1018 
1019 def do_normalize(*args):
1020  """
1021  do_normalize(cv::Mat & m)
1022  do_normalize(Image im, bool force=False)
1023  do_normalize(Image im)
1024  """
1025  return _IMP_em2d.do_normalize(*args)
1026 
1027 def get_histogram(*args):
1028  """
1029  get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1030  get_histogram(Image img, int bins) -> IMP::Floats
1031  """
1032  return _IMP_em2d.get_histogram(*args)
1033 
1034 def apply_variance_filter(*args):
1035  """
1036  apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1037  apply_variance_filter(Image input, Image filtered, int kernelsize)
1038  """
1039  return _IMP_em2d.apply_variance_filter(*args)
1040 
1041 def apply_diffusion_filter(*args):
1042  """
1043  apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1044  apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1045  """
1046  return _IMP_em2d.apply_diffusion_filter(*args)
1047 
1048 def do_fill_holes(*args):
1049  """
1050  do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1051  do_fill_holes(Image input, Image result, double n_stddevs)
1052  """
1053  return _IMP_em2d.do_fill_holes(*args)
1054 
1055 def do_combined_fill_holes_and_threshold(*args):
1056  """
1057  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1058  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs)
1059  do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1060  """
1061  return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1062 
1063 def do_extend_borders(*args):
1064  """
1065  do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1066  do_extend_borders(Image im1, Image im2, unsigned int pix)
1067  """
1068  return _IMP_em2d.do_extend_borders(*args)
1069 
1070 def do_segmentation(*args):
1071  """
1072  do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1073  do_segmentation(Image input, Image result, SegmentationParameters params)
1074  """
1075  return _IMP_em2d.do_segmentation(*args)
1076 
1077 def do_remove_small_objects(*args):
1078  """
1079  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1080  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0)
1081  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage)
1082  do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1083  do_remove_small_objects(Image input, double percentage, int background=0)
1084  do_remove_small_objects(Image input, double percentage)
1085  """
1086  return _IMP_em2d.do_remove_small_objects(*args)
1087 
1088 def do_subtract_images(*args):
1089  """do_subtract_images(Image first, Image second, Image result)"""
1090  return _IMP_em2d.do_subtract_images(*args)
1091 
1092 def add_noise(*args):
1093  """
1094  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode="uniform", double df=3)
1095  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode="uniform")
1096  add_noise(cv::Mat & v, double op1, double op2)
1097  add_noise(Image im1, double op1, double op2, IMP::String const & mode="uniform", double df=3)
1098  add_noise(Image im1, double op1, double op2, IMP::String const & mode="uniform")
1099  add_noise(Image im1, double op1, double op2)
1100  """
1101  return _IMP_em2d.add_noise(*args)
1102 
1103 def do_resample_polar(*args):
1104  """
1105  do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1106  do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1107  """
1108  return _IMP_em2d.do_resample_polar(*args)
1109 
1110 def crop(*args):
1111  """
1112  crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1113  crop(Image img, IMP::IntPair const & center, int size)
1114  """
1115  return _IMP_em2d.crop(*args)
1116 
1117 def apply_mean_outside_mask(*args):
1118  """apply_mean_outside_mask(Image img, double radius)"""
1119  return _IMP_em2d.apply_mean_outside_mask(*args)
1120 class RegistrationResult(_object):
1121  """Proxy of C++ IMP::em2d::RegistrationResult class"""
1122  __swig_setmethods__ = {}
1123  __setattr__ = lambda self, name, value: _swig_setattr(self, RegistrationResult, name, value)
1124  __swig_getmethods__ = {}
1125  __getattr__ = lambda self, name: _swig_getattr(self, RegistrationResult, name)
1126  def __init__(self, *args):
1127  """
1128  __init__(IMP::em2d::RegistrationResult self) -> RegistrationResult
1129  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0,
1130  IMP::String name="") -> RegistrationResult
1131  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1132  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0) -> RegistrationResult
1133  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift) -> RegistrationResult
1134  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.), int projection_index=0,
1135  int image_index=0, IMP::String name="") -> RegistrationResult
1136  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.), int projection_index=0,
1137  int image_index=0) -> RegistrationResult
1138  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.), int projection_index=0) -> RegistrationResult
1139  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.)) -> RegistrationResult
1140  __init__(IMP::em2d::RegistrationResult self, Rotation3D R) -> RegistrationResult
1141  """
1142  this = _IMP_em2d.new_RegistrationResult(*args)
1143  try: self.this.append(this)
1144  except: self.this = this
1145  def get_phi(self):
1146  """get_phi(RegistrationResult self) -> double"""
1147  return _IMP_em2d.RegistrationResult_get_phi(self)
1148 
1149  def get_theta(self):
1150  """get_theta(RegistrationResult self) -> double"""
1151  return _IMP_em2d.RegistrationResult_get_theta(self)
1152 
1153  def get_psi(self):
1154  """get_psi(RegistrationResult self) -> double"""
1155  return _IMP_em2d.RegistrationResult_get_psi(self)
1156 
1157  def get_shift(self):
1158  """get_shift(RegistrationResult self) -> Vector2D"""
1159  return _IMP_em2d.RegistrationResult_get_shift(self)
1160 
1161  def get_shift_3d(self):
1162  """get_shift_3d(RegistrationResult self) -> Vector3D"""
1163  return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1164 
1165  def get_projection_index(self):
1166  """get_projection_index(RegistrationResult self) -> int"""
1167  return _IMP_em2d.RegistrationResult_get_projection_index(self)
1168 
1169  def set_projection_index(self, *args):
1170  """set_projection_index(RegistrationResult self, int index)"""
1171  return _IMP_em2d.RegistrationResult_set_projection_index(self, *args)
1172 
1173  def get_image_index(self):
1174  """get_image_index(RegistrationResult self) -> int"""
1175  return _IMP_em2d.RegistrationResult_get_image_index(self)
1176 
1177  def set_image_index(self, *args):
1178  """set_image_index(RegistrationResult self, int index)"""
1179  return _IMP_em2d.RegistrationResult_set_image_index(self, *args)
1180 
1181  def get_name(self):
1182  """get_name(RegistrationResult self) -> IMP::String"""
1183  return _IMP_em2d.RegistrationResult_get_name(self)
1184 
1185  def get_ccc(self):
1186  """get_ccc(RegistrationResult self) -> double"""
1187  return _IMP_em2d.RegistrationResult_get_ccc(self)
1188 
1189  def set_ccc(self, *args):
1190  """set_ccc(RegistrationResult self, double ccc)"""
1191  return _IMP_em2d.RegistrationResult_set_ccc(self, *args)
1192 
1193  def get_score(self):
1194  """get_score(RegistrationResult self) -> double"""
1195  return _IMP_em2d.RegistrationResult_get_score(self)
1196 
1197  def set_score(self, *args):
1198  """set_score(RegistrationResult self, double Score)"""
1199  return _IMP_em2d.RegistrationResult_set_score(self, *args)
1200 
1201  def set_rotation(self, *args):
1202  """
1203  set_rotation(RegistrationResult self, double phi, double theta, double psi)
1204  set_rotation(RegistrationResult self, Rotation3D R)
1205  """
1206  return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1207 
1208  def set_shift(self, *args):
1209  """set_shift(RegistrationResult self, Vector2D shift)"""
1210  return _IMP_em2d.RegistrationResult_set_shift(self, *args)
1211 
1212  def set_name(self, *args):
1213  """set_name(RegistrationResult self, IMP::String name)"""
1214  return _IMP_em2d.RegistrationResult_set_name(self, *args)
1215 
1216  def add_in_plane_transformation(self, *args):
1217  """add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1218  return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, *args)
1219 
1220  def show(self, *args):
1221  """
1222  show(RegistrationResult self, _ostream out=std::cout)
1223  show(RegistrationResult self)
1224  """
1225  return _IMP_em2d.RegistrationResult_show(self, *args)
1226 
1227  def write(self, *args):
1228  """
1229  write(RegistrationResult self, _ostream out=std::cout)
1230  write(RegistrationResult self)
1231  """
1232  return _IMP_em2d.RegistrationResult_write(self, *args)
1233 
1234  def write_comment_line(self, *args):
1235  """
1236  write_comment_line(RegistrationResult self, _ostream out=std::cout)
1237  write_comment_line(RegistrationResult self)
1238  """
1239  return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1240 
1241  def read(self, *args):
1242  """read(RegistrationResult self, IMP::String const & s)"""
1243  return _IMP_em2d.RegistrationResult_read(self, *args)
1244 
1245  def set_random_registration(self, *args):
1246  """set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1247  return _IMP_em2d.RegistrationResult_set_random_registration(self, *args)
1248 
1249  def get_rotation(self):
1250  """get_rotation(RegistrationResult self) -> Rotation3D"""
1251  return _IMP_em2d.RegistrationResult_get_rotation(self)
1252 
1253  def set_in_image(self, *args):
1254  """set_in_image(RegistrationResult self, ImageHeader header)"""
1255  return _IMP_em2d.RegistrationResult_set_in_image(self, *args)
1256 
1257  def read_from_image(self, *args):
1258  """read_from_image(RegistrationResult self, ImageHeader header)"""
1259  return _IMP_em2d.RegistrationResult_read_from_image(self, *args)
1260 
1261  def get_is_optimized_result(self):
1262  """get_is_optimized_result(RegistrationResult self) -> bool"""
1263  return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1264 
1265  __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1266  __del__ = lambda self : None;
1267  def __str__(self):
1268  """__str__(RegistrationResult self) -> std::string"""
1269  return _IMP_em2d.RegistrationResult___str__(self)
1270 
1271  def __repr__(self):
1272  """__repr__(RegistrationResult self) -> std::string"""
1273  return _IMP_em2d.RegistrationResult___repr__(self)
1274 
1275 RegistrationResult_swigregister = _IMP_em2d.RegistrationResult_swigregister
1276 RegistrationResult_swigregister(RegistrationResult)
1277 
1278 
1279 def read_registration_results(*args):
1280  """read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1281  return _IMP_em2d.read_registration_results(*args)
1282 
1283 def write_registration_results(*args):
1284  """write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1285  return _IMP_em2d.write_registration_results(*args)
1286 
1288  """
1289  get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults
1290  get_random_registration_results(unsigned int n) -> IMP::em2d::RegistrationResults
1291  """
1292  return _IMP_em2d.get_random_registration_results(*args)
1293 
1295  """get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1296  return _IMP_em2d.get_evenly_distributed_registration_results(*args)
1297 
1298 def get_random_between_zero_and_one():
1299  """get_random_between_zero_and_one() -> double"""
1300  return _IMP_em2d.get_random_between_zero_and_one()
1301 class SpiderImageReaderWriter(ImageReaderWriter):
1302  """Proxy of C++ IMP::em2d::SpiderImageReaderWriter class"""
1303  __swig_setmethods__ = {}
1304  for _s in [ImageReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1305  __setattr__ = lambda self, name, value: _swig_setattr(self, SpiderImageReaderWriter, name, value)
1306  __swig_getmethods__ = {}
1307  for _s in [ImageReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1308  __getattr__ = lambda self, name: _swig_getattr(self, SpiderImageReaderWriter, name)
1309  __swig_setmethods__["filename_"] = _IMP_em2d.SpiderImageReaderWriter_filename__set
1310  __swig_getmethods__["filename_"] = _IMP_em2d.SpiderImageReaderWriter_filename__get
1311  if _newclass:filename_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set)
1312  __swig_setmethods__["skip_type_check_"] = _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set
1313  __swig_getmethods__["skip_type_check_"] = _IMP_em2d.SpiderImageReaderWriter_skip_type_check__get
1314  if _newclass:skip_type_check_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set)
1315  __swig_setmethods__["force_reversed_"] = _IMP_em2d.SpiderImageReaderWriter_force_reversed__set
1316  __swig_getmethods__["force_reversed_"] = _IMP_em2d.SpiderImageReaderWriter_force_reversed__get
1317  if _newclass:force_reversed_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set)
1318  __swig_setmethods__["skip_extra_checkings_"] = _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set
1319  __swig_getmethods__["skip_extra_checkings_"] = _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get
1320  if _newclass:skip_extra_checkings_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set)
1321  def __init__(self, *args):
1322  """
1323  __init__(IMP::em2d::SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1324  __init__(IMP::em2d::SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1325  """
1326  this = _IMP_em2d.new_SpiderImageReaderWriter(*args)
1327  try: self.this.append(this)
1328  except: self.this = this
1329  def __str__(self):
1330  """__str__(SpiderImageReaderWriter self) -> std::string"""
1331  return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1332 
1333  def __repr__(self):
1334  """__repr__(SpiderImageReaderWriter self) -> std::string"""
1335  return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1336 
1337  def get_from(o):
1338  return _object_cast_to_SpiderImageReaderWriter(o)
1339  get_from = staticmethod(get_from)
1340 
1341 SpiderImageReaderWriter_swigregister = _IMP_em2d.SpiderImageReaderWriter_swigregister
1342 SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1343 
1344 class JPGImageReaderWriter(ImageReaderWriter):
1345  """Proxy of C++ IMP::em2d::JPGImageReaderWriter class"""
1346  __swig_setmethods__ = {}
1347  for _s in [ImageReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1348  __setattr__ = lambda self, name, value: _swig_setattr(self, JPGImageReaderWriter, name, value)
1349  __swig_getmethods__ = {}
1350  for _s in [ImageReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1351  __getattr__ = lambda self, name: _swig_getattr(self, JPGImageReaderWriter, name)
1352  def __init__(self):
1353  """__init__(IMP::em2d::JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1354  this = _IMP_em2d.new_JPGImageReaderWriter()
1355  try: self.this.append(this)
1356  except: self.this = this
1357  def __str__(self):
1358  """__str__(JPGImageReaderWriter self) -> std::string"""
1359  return _IMP_em2d.JPGImageReaderWriter___str__(self)
1360 
1361  def __repr__(self):
1362  """__repr__(JPGImageReaderWriter self) -> std::string"""
1363  return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1364 
1365  def get_from(o):
1366  return _object_cast_to_JPGImageReaderWriter(o)
1367  get_from = staticmethod(get_from)
1368 
1369 JPGImageReaderWriter_swigregister = _IMP_em2d.JPGImageReaderWriter_swigregister
1370 JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1371 
1372 class TIFFImageReaderWriter(ImageReaderWriter):
1373  """Proxy of C++ IMP::em2d::TIFFImageReaderWriter class"""
1374  __swig_setmethods__ = {}
1375  for _s in [ImageReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1376  __setattr__ = lambda self, name, value: _swig_setattr(self, TIFFImageReaderWriter, name, value)
1377  __swig_getmethods__ = {}
1378  for _s in [ImageReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1379  __getattr__ = lambda self, name: _swig_getattr(self, TIFFImageReaderWriter, name)
1380  def __init__(self):
1381  """__init__(IMP::em2d::TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1382  this = _IMP_em2d.new_TIFFImageReaderWriter()
1383  try: self.this.append(this)
1384  except: self.this = this
1385  def __str__(self):
1386  """__str__(TIFFImageReaderWriter self) -> std::string"""
1387  return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1388 
1389  def __repr__(self):
1390  """__repr__(TIFFImageReaderWriter self) -> std::string"""
1391  return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1392 
1393  def get_from(o):
1394  return _object_cast_to_TIFFImageReaderWriter(o)
1395  get_from = staticmethod(get_from)
1396 
1397 TIFFImageReaderWriter_swigregister = _IMP_em2d.TIFFImageReaderWriter_swigregister
1398 TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1399 
1400 
1401 def do_matrix_to_image_flip(*args):
1402  """do_matrix_to_image_flip(cv::Mat & m)"""
1403  return _IMP_em2d.do_matrix_to_image_flip(*args)
1404 
1406  """get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1407  return _IMP_em2d.get_autocorrelation2d_no_preprocessing(*args)
1408 
1409 def get_autocorrelation2d(*args):
1410  """
1411  get_autocorrelation2d(Image im1, Image im2)
1412  get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1413  """
1414  return _IMP_em2d.get_autocorrelation2d(*args)
1415 
1416 def get_correlation2d(*args):
1417  """
1418  get_correlation2d(Image im1, Image im2, Image corr)
1419  get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1420  """
1421  return _IMP_em2d.get_correlation2d(*args)
1422 
1424  """get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1425  return _IMP_em2d.get_correlation2d_no_preprocessing(*args)
1426 
1427 def get_fft_using_optimal_size(*args):
1428  """get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1429  return _IMP_em2d.get_fft_using_optimal_size(*args)
1430 
1431 def get_spectrum(*args):
1432  """get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1433  return _IMP_em2d.get_spectrum(*args)
1434 
1435 def get_rotation_error(*args):
1436  """get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1437  return _IMP_em2d.get_rotation_error(*args)
1438 
1439 def get_shift_error(*args):
1440  """get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1441  return _IMP_em2d.get_shift_error(*args)
1442 
1443 def get_average_rotation_error(*args):
1444  """get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1445  return _IMP_em2d.get_average_rotation_error(*args)
1446 
1447 def get_average_shift_error(*args):
1448  """get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1449  return _IMP_em2d.get_average_shift_error(*args)
1450 
1452  """
1453  get_cross_correlation_coefficient(Image im1, Image im2) -> double
1454  get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1455  """
1456  return _IMP_em2d.get_cross_correlation_coefficient(*args)
1457 
1458 def get_global_score(*args):
1459  """get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1460  return _IMP_em2d.get_global_score(*args)
1461 class ScoreFunction(IMP.base.Object):
1462  """Proxy of C++ IMP::em2d::ScoreFunction class"""
1463  __swig_setmethods__ = {}
1464  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1465  __setattr__ = lambda self, name, value: _swig_setattr(self, ScoreFunction, name, value)
1466  __swig_getmethods__ = {}
1467  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1468  __getattr__ = lambda self, name: _swig_getattr(self, ScoreFunction, name)
1469  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
1470  def get_score(self, *args):
1471  """get_score(ScoreFunction self, Image image, Image projection) -> double"""
1472  return _IMP_em2d.ScoreFunction_get_score(self, *args)
1473 
1474  def set_variance_image(self, *args):
1475  """set_variance_image(ScoreFunction self, Image var)"""
1476  return _IMP_em2d.ScoreFunction_set_variance_image(self, *args)
1477 
1478  def get_version_info(self):
1479  """get_version_info(ScoreFunction self) -> VersionInfo"""
1480  return _IMP_em2d.ScoreFunction_get_version_info(self)
1481 
1482  def __str__(self):
1483  """__str__(ScoreFunction self) -> std::string"""
1484  return _IMP_em2d.ScoreFunction___str__(self)
1485 
1486  def __repr__(self):
1487  """__repr__(ScoreFunction self) -> std::string"""
1488  return _IMP_em2d.ScoreFunction___repr__(self)
1489 
1490  def get_from(o):
1491  return _object_cast_to_ScoreFunction(o)
1492  get_from = staticmethod(get_from)
1493 
1494 ScoreFunction_swigregister = _IMP_em2d.ScoreFunction_swigregister
1495 ScoreFunction_swigregister(ScoreFunction)
1496 
1497 class ChiSquaredScore(ScoreFunction):
1498  """Proxy of C++ IMP::em2d::ChiSquaredScore class"""
1499  __swig_setmethods__ = {}
1500  for _s in [ScoreFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1501  __setattr__ = lambda self, name, value: _swig_setattr(self, ChiSquaredScore, name, value)
1502  __swig_getmethods__ = {}
1503  for _s in [ScoreFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1504  __getattr__ = lambda self, name: _swig_getattr(self, ChiSquaredScore, name)
1505  def __init__(self):
1506  """__init__(IMP::em2d::ChiSquaredScore self) -> ChiSquaredScore"""
1507  this = _IMP_em2d.new_ChiSquaredScore()
1508  try: self.this.append(this)
1509  except: self.this = this
1510  def __str__(self):
1511  """__str__(ChiSquaredScore self) -> std::string"""
1512  return _IMP_em2d.ChiSquaredScore___str__(self)
1513 
1514  def __repr__(self):
1515  """__repr__(ChiSquaredScore self) -> std::string"""
1516  return _IMP_em2d.ChiSquaredScore___repr__(self)
1517 
1518  def get_from(o):
1519  return _object_cast_to_ChiSquaredScore(o)
1520  get_from = staticmethod(get_from)
1521 
1522  __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1523  __del__ = lambda self : None;
1524 ChiSquaredScore_swigregister = _IMP_em2d.ChiSquaredScore_swigregister
1525 ChiSquaredScore_swigregister(ChiSquaredScore)
1526 
1527 class EM2DScore(ScoreFunction):
1528  """Proxy of C++ IMP::em2d::EM2DScore class"""
1529  __swig_setmethods__ = {}
1530  for _s in [ScoreFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1531  __setattr__ = lambda self, name, value: _swig_setattr(self, EM2DScore, name, value)
1532  __swig_getmethods__ = {}
1533  for _s in [ScoreFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1534  __getattr__ = lambda self, name: _swig_getattr(self, EM2DScore, name)
1535  def __init__(self):
1536  """__init__(IMP::em2d::EM2DScore self) -> EM2DScore"""
1537  this = _IMP_em2d.new_EM2DScore()
1538  try: self.this.append(this)
1539  except: self.this = this
1540  def __str__(self):
1541  """__str__(EM2DScore self) -> std::string"""
1542  return _IMP_em2d.EM2DScore___str__(self)
1543 
1544  def __repr__(self):
1545  """__repr__(EM2DScore self) -> std::string"""
1546  return _IMP_em2d.EM2DScore___repr__(self)
1547 
1548  def get_from(o):
1549  return _object_cast_to_EM2DScore(o)
1550  get_from = staticmethod(get_from)
1551 
1552  __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1553  __del__ = lambda self : None;
1554 EM2DScore_swigregister = _IMP_em2d.EM2DScore_swigregister
1555 EM2DScore_swigregister(EM2DScore)
1556 
1557 class MeanAbsoluteDifference(ScoreFunction):
1558  """Proxy of C++ IMP::em2d::MeanAbsoluteDifference class"""
1559  __swig_setmethods__ = {}
1560  for _s in [ScoreFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1561  __setattr__ = lambda self, name, value: _swig_setattr(self, MeanAbsoluteDifference, name, value)
1562  __swig_getmethods__ = {}
1563  for _s in [ScoreFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1564  __getattr__ = lambda self, name: _swig_getattr(self, MeanAbsoluteDifference, name)
1565  def __init__(self):
1566  """__init__(IMP::em2d::MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1567  this = _IMP_em2d.new_MeanAbsoluteDifference()
1568  try: self.this.append(this)
1569  except: self.this = this
1570  def __str__(self):
1571  """__str__(MeanAbsoluteDifference self) -> std::string"""
1572  return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1573 
1574  def __repr__(self):
1575  """__repr__(MeanAbsoluteDifference self) -> std::string"""
1576  return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1577 
1578  def get_from(o):
1579  return _object_cast_to_MeanAbsoluteDifference(o)
1580  get_from = staticmethod(get_from)
1581 
1582  __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1583  __del__ = lambda self : None;
1584 MeanAbsoluteDifference_swigregister = _IMP_em2d.MeanAbsoluteDifference_swigregister
1585 MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1586 
1587 
1588 def read_selection_file(*args):
1589  """read_selection_file(IMP::String fn) -> IMP::Strings"""
1590  return _IMP_em2d.read_selection_file(*args)
1591 
1592 def create_filenames(*args):
1593  """create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1594  return _IMP_em2d.create_filenames(*args)
1595 class ProjectionParameters(IMP.kernel.Decorator):
1596  """Proxy of C++ IMP::em2d::ProjectionParameters class"""
1597  __swig_setmethods__ = {}
1598  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1599  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionParameters, name, value)
1600  __swig_getmethods__ = {}
1601  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1602  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionParameters, name)
1603  def __init__(self, *args):
1604  """
1605  __init__(IMP::em2d::ProjectionParameters self) -> ProjectionParameters
1606  __init__(IMP::em2d::ProjectionParameters self, Model m, ::IMP::kernel::ParticleIndex id) -> ProjectionParameters
1607  __init__(IMP::em2d::ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1608  """
1609  this = _IMP_em2d.new_ProjectionParameters(*args)
1610  try: self.this.append(this)
1611  except: self.this = this
1612  def decorate_particle(*args):
1613  """decorate_particle(Particle p) -> ProjectionParameters"""
1614  return _IMP_em2d.ProjectionParameters_decorate_particle(*args)
1615 
1616  if _newclass:decorate_particle = staticmethod(decorate_particle)
1617  __swig_getmethods__["decorate_particle"] = lambda x: decorate_particle
1618  def show(self, *args):
1619  """
1620  show(ProjectionParameters self, _ostream out=std::cout)
1621  show(ProjectionParameters self)
1622  """
1623  return _IMP_em2d.ProjectionParameters_show(self, *args)
1624 
1625  def setup_particle(*args):
1626  """
1627  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> ProjectionParameters
1628  setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1629  """
1630  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1631 
1632  if _newclass:setup_particle = staticmethod(setup_particle)
1633  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1634  __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1635  __del__ = lambda self : None;
1636  def get_keys():
1637  """get_keys() -> IMP::kernel::FloatKeys const &"""
1638  return _IMP_em2d.ProjectionParameters_get_keys()
1639 
1640  if _newclass:get_keys = staticmethod(get_keys)
1641  __swig_getmethods__["get_keys"] = lambda x: get_keys
1642  def set_proper_ranges_for_keys(self, *args):
1643  """set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1644  return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, *args)
1645 
1646  def get_is_setup(*args):
1647  """
1648  get_is_setup(_ParticleAdaptor p) -> bool
1649  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1650  """
1651  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1652 
1653  if _newclass:get_is_setup = staticmethod(get_is_setup)
1654  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
1655  def get_parameters_optimized(self):
1656  """get_parameters_optimized(ProjectionParameters self) -> bool"""
1657  return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1658 
1659  def get_translation(self):
1660  """get_translation(ProjectionParameters self) -> Vector3D"""
1661  return _IMP_em2d.ProjectionParameters_get_translation(self)
1662 
1663  def set_translation(self, *args):
1664  """set_translation(ProjectionParameters self, Vector3D v)"""
1665  return _IMP_em2d.ProjectionParameters_set_translation(self, *args)
1666 
1667  def get_rotation(self):
1668  """get_rotation(ProjectionParameters self) -> Rotation3D"""
1669  return _IMP_em2d.ProjectionParameters_get_rotation(self)
1670 
1671  def set_rotation(self, *args):
1672  """set_rotation(ProjectionParameters self, Rotation3D R)"""
1673  return _IMP_em2d.ProjectionParameters_set_rotation(self, *args)
1674 
1675  def set_parameters_optimized(self, *args):
1676  """set_parameters_optimized(ProjectionParameters self, bool tf)"""
1677  return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, *args)
1678 
1679  def get_quaternion_1(self):
1680  """get_quaternion_1(ProjectionParameters self) -> double"""
1681  return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1682 
1683  def set_quaternion_1(self, *args):
1684  """set_quaternion_1(ProjectionParameters self, double t)"""
1685  return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, *args)
1686 
1687  def get_quaternion_2(self):
1688  """get_quaternion_2(ProjectionParameters self) -> double"""
1689  return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1690 
1691  def set_quaternion_2(self, *args):
1692  """set_quaternion_2(ProjectionParameters self, double t)"""
1693  return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, *args)
1694 
1695  def get_quaternion_3(self):
1696  """get_quaternion_3(ProjectionParameters self) -> double"""
1697  return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1698 
1699  def set_quaternion_3(self, *args):
1700  """set_quaternion_3(ProjectionParameters self, double t)"""
1701  return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, *args)
1702 
1703  def get_quaternion_4(self):
1704  """get_quaternion_4(ProjectionParameters self) -> double"""
1705  return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1706 
1707  def set_quaternion_4(self, *args):
1708  """set_quaternion_4(ProjectionParameters self, double t)"""
1709  return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, *args)
1710 
1711  def get_translation_x(self):
1712  """get_translation_x(ProjectionParameters self) -> double"""
1713  return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1714 
1715  def set_translation_x(self, *args):
1716  """set_translation_x(ProjectionParameters self, double t)"""
1717  return _IMP_em2d.ProjectionParameters_set_translation_x(self, *args)
1718 
1719  def get_translation_y(self):
1720  """get_translation_y(ProjectionParameters self) -> double"""
1721  return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1722 
1723  def set_translation_y(self, *args):
1724  """set_translation_y(ProjectionParameters self, double t)"""
1725  return _IMP_em2d.ProjectionParameters_set_translation_y(self, *args)
1726 
1727  def add_attribute(self, *args):
1728  """
1729  add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1730  add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1731  add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1732  add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1733  add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1734  add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1735  """
1736  return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1737 
1738  def get_value(self, *args):
1739  """
1740  get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1741  get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1742  get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1743  get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1744  get_value(ProjectionParameters self, ObjectKey a0) -> Object
1745  """
1746  return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1747 
1748  def set_value(self, *args):
1749  """
1750  set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1751  set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1752  set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1753  set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1754  set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1755  """
1756  return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1757 
1758  def remove_attribute(self, *args):
1759  """
1760  remove_attribute(ProjectionParameters self, FloatKey a0)
1761  remove_attribute(ProjectionParameters self, IntKey a0)
1762  remove_attribute(ProjectionParameters self, StringKey a0)
1763  remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1764  remove_attribute(ProjectionParameters self, ObjectKey a0)
1765  """
1766  return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1767 
1768  def has_attribute(self, *args):
1769  """
1770  has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1771  has_attribute(ProjectionParameters self, IntKey a0) -> bool
1772  has_attribute(ProjectionParameters self, StringKey a0) -> bool
1773  has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
1774  has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
1775  """
1776  return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
1777 
1778  def get_derivative(self, *args):
1779  """get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
1780  return _IMP_em2d.ProjectionParameters_get_derivative(self, *args)
1781 
1782  def get_name(self):
1783  """get_name(ProjectionParameters self) -> std::string"""
1784  return _IMP_em2d.ProjectionParameters_get_name(self)
1785 
1786  def clear_caches(self):
1787  """clear_caches(ProjectionParameters self)"""
1788  return _IMP_em2d.ProjectionParameters_clear_caches(self)
1789 
1790  def set_name(self, *args):
1791  """set_name(ProjectionParameters self, std::string a0)"""
1792  return _IMP_em2d.ProjectionParameters_set_name(self, *args)
1793 
1794  def set_check_level(self, *args):
1795  """set_check_level(ProjectionParameters self, IMP::base::CheckLevel a0)"""
1796  return _IMP_em2d.ProjectionParameters_set_check_level(self, *args)
1797 
1798  def add_to_derivative(self, *args):
1799  """add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1800  return _IMP_em2d.ProjectionParameters_add_to_derivative(self, *args)
1801 
1802  def set_is_optimized(self, *args):
1803  """set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
1804  return _IMP_em2d.ProjectionParameters_set_is_optimized(self, *args)
1805 
1806  def get_is_optimized(self, *args):
1807  """get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
1808  return _IMP_em2d.ProjectionParameters_get_is_optimized(self, *args)
1809 
1810  def get_check_level(self):
1811  """get_check_level(ProjectionParameters self) -> IMP::base::CheckLevel"""
1812  return _IMP_em2d.ProjectionParameters_get_check_level(self)
1813 
1814  def __eq__(self, *args):
1815  """
1816  __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
1817  __eq__(ProjectionParameters self, Particle d) -> bool
1818  """
1819  return _IMP_em2d.ProjectionParameters___eq__(self, *args)
1820 
1821  def __ne__(self, *args):
1822  """
1823  __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
1824  __ne__(ProjectionParameters self, Particle d) -> bool
1825  """
1826  return _IMP_em2d.ProjectionParameters___ne__(self, *args)
1827 
1828  def __le__(self, *args):
1829  """
1830  __le__(ProjectionParameters self, ProjectionParameters o) -> bool
1831  __le__(ProjectionParameters self, Particle d) -> bool
1832  """
1833  return _IMP_em2d.ProjectionParameters___le__(self, *args)
1834 
1835  def __lt__(self, *args):
1836  """
1837  __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
1838  __lt__(ProjectionParameters self, Particle d) -> bool
1839  """
1840  return _IMP_em2d.ProjectionParameters___lt__(self, *args)
1841 
1842  def __ge__(self, *args):
1843  """
1844  __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
1845  __ge__(ProjectionParameters self, Particle d) -> bool
1846  """
1847  return _IMP_em2d.ProjectionParameters___ge__(self, *args)
1848 
1849  def __gt__(self, *args):
1850  """
1851  __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
1852  __gt__(ProjectionParameters self, Particle d) -> bool
1853  """
1854  return _IMP_em2d.ProjectionParameters___gt__(self, *args)
1855 
1856  def __str__(self):
1857  """__str__(ProjectionParameters self) -> std::string"""
1858  return _IMP_em2d.ProjectionParameters___str__(self)
1859 
1860  def __repr__(self):
1861  """__repr__(ProjectionParameters self) -> std::string"""
1862  return _IMP_em2d.ProjectionParameters___repr__(self)
1863 
1864 ProjectionParameters_swigregister = _IMP_em2d.ProjectionParameters_swigregister
1865 ProjectionParameters_swigregister(ProjectionParameters)
1866 
1867 def ProjectionParameters_decorate_particle(*args):
1868  """ProjectionParameters_decorate_particle(Particle p) -> ProjectionParameters"""
1869  return _IMP_em2d.ProjectionParameters_decorate_particle(*args)
1870 
1871 def ProjectionParameters_setup_particle(*args):
1872  """
1873  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> ProjectionParameters
1874  ProjectionParameters_setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1875  """
1876  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1877 
1878 def ProjectionParameters_get_keys():
1879  """ProjectionParameters_get_keys() -> IMP::kernel::FloatKeys const &"""
1880  return _IMP_em2d.ProjectionParameters_get_keys()
1881 
1882 def ProjectionParameters_get_is_setup(*args):
1883  """
1884  get_is_setup(_ParticleAdaptor p) -> bool
1885  ProjectionParameters_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1886  """
1887  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1888 
1889 
1890 def __lshift__(*args):
1891  """__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
1892  return _IMP_em2d.__lshift__(*args)
1893 class ProjectionParametersScoreState(IMP.kernel.ScoreState):
1894  """Proxy of C++ IMP::em2d::ProjectionParametersScoreState class"""
1895  __swig_setmethods__ = {}
1896  for _s in [IMP.kernel.ScoreState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1897  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionParametersScoreState, name, value)
1898  __swig_getmethods__ = {}
1899  for _s in [IMP.kernel.ScoreState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1900  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionParametersScoreState, name)
1901  def __init__(self, *args):
1902  """__init__(IMP::em2d::ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
1903  this = _IMP_em2d.new_ProjectionParametersScoreState(*args)
1904  try: self.this.append(this)
1905  except: self.this = this
1906  def do_before_evaluate(self):
1907  """do_before_evaluate(ProjectionParametersScoreState self)"""
1908  return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
1909 
1910  def do_after_evaluate(self, *args):
1911  """do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
1912  return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, *args)
1913 
1914  def do_get_inputs(self):
1915  """do_get_inputs(ProjectionParametersScoreState self) -> IMP::kernel::ModelObjectsTemp"""
1916  return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
1917 
1918  def do_get_outputs(self):
1919  """do_get_outputs(ProjectionParametersScoreState self) -> IMP::kernel::ModelObjectsTemp"""
1920  return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
1921 
1922  def get_version_info(self):
1923  """get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
1924  return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
1925 
1926  def __str__(self):
1927  """__str__(ProjectionParametersScoreState self) -> std::string"""
1928  return _IMP_em2d.ProjectionParametersScoreState___str__(self)
1929 
1930  def __repr__(self):
1931  """__repr__(ProjectionParametersScoreState self) -> std::string"""
1932  return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
1933 
1934  def get_from(o):
1935  return _object_cast_to_ProjectionParametersScoreState(o)
1936  get_from = staticmethod(get_from)
1937 
1938 ProjectionParametersScoreState_swigregister = _IMP_em2d.ProjectionParametersScoreState_swigregister
1939 ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
1940 
1941 class ProjectionMask(_object):
1942  """Proxy of C++ IMP::em2d::ProjectionMask class"""
1943  __swig_setmethods__ = {}
1944  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionMask, name, value)
1945  __swig_getmethods__ = {}
1946  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionMask, name)
1947  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
1948  def apply(self, *args):
1949  """apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
1950  return _IMP_em2d.ProjectionMask_apply(self, *args)
1951 
1952  def show(self, *args):
1953  """
1954  show(ProjectionMask self, _ostream out=std::cout)
1955  show(ProjectionMask self)
1956  """
1957  return _IMP_em2d.ProjectionMask_show(self, *args)
1958 
1959  __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
1960  __del__ = lambda self : None;
1961  def __str__(self):
1962  """__str__(ProjectionMask self) -> std::string"""
1963  return _IMP_em2d.ProjectionMask___str__(self)
1964 
1965  def __repr__(self):
1966  """__repr__(ProjectionMask self) -> std::string"""
1967  return _IMP_em2d.ProjectionMask___repr__(self)
1968 
1969 ProjectionMask_swigregister = _IMP_em2d.ProjectionMask_swigregister
1970 ProjectionMask_swigregister(ProjectionMask)
1971 
1972 
1973 def do_place(*args):
1974  """do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
1975  return _IMP_em2d.do_place(*args)
1976 class MasksManager(_object):
1977  """Proxy of C++ IMP::em2d::MasksManager class"""
1978  __swig_setmethods__ = {}
1979  __setattr__ = lambda self, name, value: _swig_setattr(self, MasksManager, name, value)
1980  __swig_getmethods__ = {}
1981  __getattr__ = lambda self, name: _swig_getattr(self, MasksManager, name)
1982  def __init__(self, *args):
1983  """
1984  __init__(IMP::em2d::MasksManager self) -> MasksManager
1985  __init__(IMP::em2d::MasksManager self, double resolution, double pixelsize) -> MasksManager
1986  """
1987  this = _IMP_em2d.new_MasksManager(*args)
1988  try: self.this.append(this)
1989  except: self.this = this
1990  def setup_kernel(self, *args):
1991  """setup_kernel(MasksManager self, double resolution, double pixelsize)"""
1992  return _IMP_em2d.MasksManager_setup_kernel(self, *args)
1993 
1994  def create_masks(self, *args):
1995  """create_masks(MasksManager self, IMP::kernel::ParticlesTemp const & ps)"""
1996  return _IMP_em2d.MasksManager_create_masks(self, *args)
1997 
1998  def create_mask(self, *args):
1999  """create_mask(MasksManager self, double radius, double mass)"""
2000  return _IMP_em2d.MasksManager_create_mask(self, *args)
2001 
2002  def find_mask(self, *args):
2003  """find_mask(MasksManager self, double radius) -> IMP::em2d::ProjectionMaskPtr"""
2004  return _IMP_em2d.MasksManager_find_mask(self, *args)
2005 
2006  def show(self, *args):
2007  """
2008  show(MasksManager self, _ostream out=std::cout)
2009  show(MasksManager self)
2010  """
2011  return _IMP_em2d.MasksManager_show(self, *args)
2012 
2013  def get_number_of_masks(self):
2014  """get_number_of_masks(MasksManager self) -> unsigned int"""
2015  return _IMP_em2d.MasksManager_get_number_of_masks(self)
2016 
2017  __swig_destroy__ = _IMP_em2d.delete_MasksManager
2018  __del__ = lambda self : None;
2019  def __str__(self):
2020  """__str__(MasksManager self) -> std::string"""
2021  return _IMP_em2d.MasksManager___str__(self)
2022 
2023  def __repr__(self):
2024  """__repr__(MasksManager self) -> std::string"""
2025  return _IMP_em2d.MasksManager___repr__(self)
2026 
2027 MasksManager_swigregister = _IMP_em2d.MasksManager_swigregister
2028 MasksManager_swigregister(MasksManager)
2029 
2030 class ProjectingParameters(_object):
2031  """Proxy of C++ IMP::em2d::ProjectingParameters class"""
2032  __swig_setmethods__ = {}
2033  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectingParameters, name, value)
2034  __swig_getmethods__ = {}
2035  __getattr__ = lambda self, name: _swig_getattr(self, ProjectingParameters, name)
2036  __swig_setmethods__["pixel_size"] = _IMP_em2d.ProjectingParameters_pixel_size_set
2037  __swig_getmethods__["pixel_size"] = _IMP_em2d.ProjectingParameters_pixel_size_get
2038  if _newclass:pixel_size = _swig_property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set)
2039  __swig_setmethods__["resolution"] = _IMP_em2d.ProjectingParameters_resolution_set
2040  __swig_getmethods__["resolution"] = _IMP_em2d.ProjectingParameters_resolution_get
2041  if _newclass:resolution = _swig_property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set)
2042  def __init__(self, *args):
2043  """
2044  __init__(IMP::em2d::ProjectingParameters self) -> ProjectingParameters
2045  __init__(IMP::em2d::ProjectingParameters self, double ps, double res) -> ProjectingParameters
2046  """
2047  this = _IMP_em2d.new_ProjectingParameters(*args)
2048  try: self.this.append(this)
2049  except: self.this = this
2050  def show(self, *args):
2051  """
2052  show(ProjectingParameters self, _ostream out=std::cout)
2053  show(ProjectingParameters self)
2054  """
2055  return _IMP_em2d.ProjectingParameters_show(self, *args)
2056 
2057  def __str__(self):
2058  """__str__(ProjectingParameters self) -> std::string"""
2059  return _IMP_em2d.ProjectingParameters___str__(self)
2060 
2061  def __repr__(self):
2062  """__repr__(ProjectingParameters self) -> std::string"""
2063  return _IMP_em2d.ProjectingParameters___repr__(self)
2064 
2065  __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2066  __del__ = lambda self : None;
2067 ProjectingParameters_swigregister = _IMP_em2d.ProjectingParameters_swigregister
2068 ProjectingParameters_swigregister(ProjectingParameters)
2069 
2070 class ProjectingOptions(ProjectingParameters):
2071  """Proxy of C++ IMP::em2d::ProjectingOptions class"""
2072  __swig_setmethods__ = {}
2073  for _s in [ProjectingParameters]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2074  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectingOptions, name, value)
2075  __swig_getmethods__ = {}
2076  for _s in [ProjectingParameters]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2077  __getattr__ = lambda self, name: _swig_getattr(self, ProjectingOptions, name)
2078  __swig_setmethods__["save_images"] = _IMP_em2d.ProjectingOptions_save_images_set
2079  __swig_getmethods__["save_images"] = _IMP_em2d.ProjectingOptions_save_images_get
2080  if _newclass:save_images = _swig_property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set)
2081  __swig_setmethods__["normalize"] = _IMP_em2d.ProjectingOptions_normalize_set
2082  __swig_getmethods__["normalize"] = _IMP_em2d.ProjectingOptions_normalize_get
2083  if _newclass:normalize = _swig_property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set)
2084  __swig_setmethods__["clear_matrix_before_projecting"] = _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set
2085  __swig_getmethods__["clear_matrix_before_projecting"] = _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get
2086  if _newclass:clear_matrix_before_projecting = _swig_property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set)
2087  def __init__(self, *args):
2088  """
2089  __init__(IMP::em2d::ProjectingOptions self) -> ProjectingOptions
2090  __init__(IMP::em2d::ProjectingOptions self, double ps, double res) -> ProjectingOptions
2091  __init__(IMP::em2d::ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2092  """
2093  this = _IMP_em2d.new_ProjectingOptions(*args)
2094  try: self.this.append(this)
2095  except: self.this = this
2096  def show(self, *args):
2097  """
2098  show(ProjectingOptions self, _ostream out=std::cout)
2099  show(ProjectingOptions self)
2100  """
2101  return _IMP_em2d.ProjectingOptions_show(self, *args)
2102 
2103  def __str__(self):
2104  """__str__(ProjectingOptions self) -> std::string"""
2105  return _IMP_em2d.ProjectingOptions___str__(self)
2106 
2107  def __repr__(self):
2108  """__repr__(ProjectingOptions self) -> std::string"""
2109  return _IMP_em2d.ProjectingOptions___repr__(self)
2110 
2111  __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2112  __del__ = lambda self : None;
2113 ProjectingOptions_swigregister = _IMP_em2d.ProjectingOptions_swigregister
2114 ProjectingOptions_swigregister(ProjectingOptions)
2115 
2116 
2117 def get_projections(*args):
2118  """
2119  get_projections(IMP::kernel::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs,
2120  int rows, int cols, ProjectingOptions options, IMP::Strings names=IMP::Strings()) -> IMP::em2d::Images
2121  get_projections(IMP::kernel::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs,
2122  int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2123  get_projections(IMP::kernel::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values,
2124  int rows, int cols, ProjectingOptions options, IMP::Strings names=IMP::Strings()) -> IMP::em2d::Images
2125  get_projections(IMP::kernel::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values,
2126  int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2127  """
2128  return _IMP_em2d.get_projections(*args)
2129 
2130 def get_projection(*args):
2131  """
2132  get_projection(Image img, IMP::kernel::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options,
2133  IMP::em2d::MasksManagerPtr masks=IMP::em2d::MasksManagerPtr(),
2134  IMP::String name="")
2135  get_projection(Image img, IMP::kernel::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options,
2136  IMP::em2d::MasksManagerPtr masks=IMP::em2d::MasksManagerPtr())
2137  get_projection(Image img, IMP::kernel::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options)
2138  """
2139  return _IMP_em2d.get_projection(*args)
2140 
2141 def do_project_particles(*args):
2142  """
2143  do_project_particles(IMP::kernel::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation,
2144  ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)
2145  """
2146  return _IMP_em2d.do_project_particles(*args)
2147 
2149  """create_evenly_distributed_projections(IMP::kernel::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2150  return _IMP_em2d.create_evenly_distributed_projections(*args)
2151 
2152 def do_project_vectors(*args):
2153  """
2154  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2155  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2156  """
2157  return _IMP_em2d.do_project_vectors(*args)
2158 
2159 def get_enclosing_image_size(*args):
2160  """get_enclosing_image_size(IMP::kernel::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2161  return _IMP_em2d.get_enclosing_image_size(*args)
2162 
2163 def get_complete_alignment(*args):
2164  """
2165  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2166  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2167  """
2168  return _IMP_em2d.get_complete_alignment(*args)
2169 
2170 def get_rotational_alignment(*args):
2171  """
2172  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2173  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2174  """
2175  return _IMP_em2d.get_rotational_alignment(*args)
2176 
2177 def get_translational_alignment(*args):
2178  """
2179  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2180  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2181  """
2182  return _IMP_em2d.get_translational_alignment(*args)
2183 
2185  """
2186  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align,
2187  cv::Mat const & POLAR2, bool apply=False) -> ResultAlign2D
2188  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align,
2189  cv::Mat const & POLAR2) -> ResultAlign2D
2190  """
2191  return _IMP_em2d.get_complete_alignment_no_preprocessing(*args)
2192 
2194  """get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2195  return _IMP_em2d.get_rotational_alignment_no_preprocessing(*args)
2196 
2198  """get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2199  return _IMP_em2d.get_translational_alignment_no_preprocessing(*args)
2200 
2202  """get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2203  return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(*args)
2204 
2205 def write_vectors_as_pdb(*args):
2206  """
2207  write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2208  write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2209  """
2210  return _IMP_em2d.write_vectors_as_pdb(*args)
2211 class Em2DRestraintParameters(ProjectingParameters):
2212  """Proxy of C++ IMP::em2d::Em2DRestraintParameters class"""
2213  __swig_setmethods__ = {}
2214  for _s in [ProjectingParameters]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2215  __setattr__ = lambda self, name, value: _swig_setattr(self, Em2DRestraintParameters, name, value)
2216  __swig_getmethods__ = {}
2217  for _s in [ProjectingParameters]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2218  __getattr__ = lambda self, name: _swig_getattr(self, Em2DRestraintParameters, name)
2219  __swig_setmethods__["n_projections"] = _IMP_em2d.Em2DRestraintParameters_n_projections_set
2220  __swig_getmethods__["n_projections"] = _IMP_em2d.Em2DRestraintParameters_n_projections_get
2221  if _newclass:n_projections = _swig_property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set)
2222  __swig_setmethods__["coarse_registration_method"] = _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set
2223  __swig_getmethods__["coarse_registration_method"] = _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get
2224  if _newclass:coarse_registration_method = _swig_property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set)
2225  __swig_setmethods__["save_match_images"] = _IMP_em2d.Em2DRestraintParameters_save_match_images_set
2226  __swig_getmethods__["save_match_images"] = _IMP_em2d.Em2DRestraintParameters_save_match_images_get
2227  if _newclass:save_match_images = _swig_property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set)
2228  __swig_setmethods__["optimization_steps"] = _IMP_em2d.Em2DRestraintParameters_optimization_steps_set
2229  __swig_getmethods__["optimization_steps"] = _IMP_em2d.Em2DRestraintParameters_optimization_steps_get
2230  if _newclass:optimization_steps = _swig_property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set)
2231  __swig_setmethods__["simplex_initial_length"] = _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set
2232  __swig_getmethods__["simplex_initial_length"] = _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get
2233  if _newclass:simplex_initial_length = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set)
2234  __swig_setmethods__["simplex_minimum_size"] = _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set
2235  __swig_getmethods__["simplex_minimum_size"] = _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get
2236  if _newclass:simplex_minimum_size = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set)
2237  def __init__(self, *args):
2238  """
2239  __init__(IMP::em2d::Em2DRestraintParameters self) -> Em2DRestraintParameters
2240  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2241  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res) -> Em2DRestraintParameters
2242  """
2243  this = _IMP_em2d.new_Em2DRestraintParameters(*args)
2244  try: self.this.append(this)
2245  except: self.this = this
2246  def show(self, *args):
2247  """
2248  show(Em2DRestraintParameters self, _ostream out=std::cout)
2249  show(Em2DRestraintParameters self)
2250  """
2251  return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2252 
2253  def __str__(self):
2254  """__str__(Em2DRestraintParameters self) -> std::string"""
2255  return _IMP_em2d.Em2DRestraintParameters___str__(self)
2256 
2257  def __repr__(self):
2258  """__repr__(Em2DRestraintParameters self) -> std::string"""
2259  return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2260 
2261  __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2262  __del__ = lambda self : None;
2263 Em2DRestraintParameters_swigregister = _IMP_em2d.Em2DRestraintParameters_swigregister
2264 Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2265 cvar = _IMP_em2d.cvar
2266 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2267 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2268 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2269 
2270 class ProjectionFinder(IMP.base.Object):
2271  """Proxy of C++ IMP::em2d::ProjectionFinder class"""
2272  __swig_setmethods__ = {}
2273  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2274  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionFinder, name, value)
2275  __swig_getmethods__ = {}
2276  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2277  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionFinder, name)
2278  def __init__(self):
2279  """__init__(IMP::em2d::ProjectionFinder self) -> ProjectionFinder"""
2280  this = _IMP_em2d.new_ProjectionFinder()
2281  try: self.this.append(this)
2282  except: self.this = this
2283  def setup(self, *args):
2284  """setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2285  return _IMP_em2d.ProjectionFinder_setup(self, *args)
2286 
2287  def set_subjects(self, *args):
2288  """set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2289  return _IMP_em2d.ProjectionFinder_set_subjects(self, *args)
2290 
2291  def set_projections(self, *args):
2292  """set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2293  return _IMP_em2d.ProjectionFinder_set_projections(self, *args)
2294 
2295  def set_variance_images(self, *args):
2296  """set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2297  return _IMP_em2d.ProjectionFinder_set_variance_images(self, *args)
2298 
2299  def set_model_particles(self, *args):
2300  """set_model_particles(ProjectionFinder self, IMP::kernel::ParticlesTemp const & ps)"""
2301  return _IMP_em2d.ProjectionFinder_set_model_particles(self, *args)
2302 
2303  def set_save_match_images(self, *args):
2304  """set_save_match_images(ProjectionFinder self, bool x)"""
2305  return _IMP_em2d.ProjectionFinder_set_save_match_images(self, *args)
2306 
2307  def get_save_match_images(self):
2308  """get_save_match_images(ProjectionFinder self) -> bool"""
2309  return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2310 
2311  def set_fast_mode(self, *args):
2312  """set_fast_mode(ProjectionFinder self, unsigned int n)"""
2313  return _IMP_em2d.ProjectionFinder_set_fast_mode(self, *args)
2314 
2315  def get_registration_results(self):
2316  """get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2317  return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2318 
2319  def get_coarse_registration(self):
2320  """get_coarse_registration(ProjectionFinder self)"""
2321  return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2322 
2323  def get_complete_registration(self):
2324  """get_complete_registration(ProjectionFinder self)"""
2325  return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2326 
2327  def get_global_score(self):
2328  """get_global_score(ProjectionFinder self) -> double"""
2329  return _IMP_em2d.ProjectionFinder_get_global_score(self)
2330 
2331  def show(self, *args):
2332  """show(ProjectionFinder self, _ostream out)"""
2333  return _IMP_em2d.ProjectionFinder_show(self, *args)
2334 
2335  def get_preprocessing_time(self):
2336  """get_preprocessing_time(ProjectionFinder self) -> double"""
2337  return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2338 
2339  def get_coarse_registration_time(self):
2340  """get_coarse_registration_time(ProjectionFinder self) -> double"""
2341  return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2342 
2343  def get_fine_registration_time(self):
2344  """get_fine_registration_time(ProjectionFinder self) -> double"""
2345  return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2346 
2347  def get_number_of_subjects(self):
2348  """get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2349  return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2350 
2351  def set_number_of_class_averages_members(self, *args):
2352  """set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2353  return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, *args)
2354 
2355  def get_number_of_projections(self):
2356  """get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2357  return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2358 
2359  def get_version_info(self):
2360  """get_version_info(ProjectionFinder self) -> VersionInfo"""
2361  return _IMP_em2d.ProjectionFinder_get_version_info(self)
2362 
2363  def __str__(self):
2364  """__str__(ProjectionFinder self) -> std::string"""
2365  return _IMP_em2d.ProjectionFinder___str__(self)
2366 
2367  def __repr__(self):
2368  """__repr__(ProjectionFinder self) -> std::string"""
2369  return _IMP_em2d.ProjectionFinder___repr__(self)
2370 
2371  def get_from(o):
2372  return _object_cast_to_ProjectionFinder(o)
2373  get_from = staticmethod(get_from)
2374 
2375 ProjectionFinder_swigregister = _IMP_em2d.ProjectionFinder_swigregister
2376 ProjectionFinder_swigregister(ProjectionFinder)
2377 
2378 class Em2DRestraint(IMP.kernel.Restraint):
2379  """Proxy of C++ IMP::em2d::Em2DRestraint class"""
2380  __swig_setmethods__ = {}
2381  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2382  __setattr__ = lambda self, name, value: _swig_setattr(self, Em2DRestraint, name, value)
2383  __swig_getmethods__ = {}
2384  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2385  __getattr__ = lambda self, name: _swig_getattr(self, Em2DRestraint, name)
2386  def __init__(self, *args):
2387  """__init__(IMP::em2d::Em2DRestraint self, Model m) -> Em2DRestraint"""
2388  this = _IMP_em2d.new_Em2DRestraint(*args)
2389  try: self.this.append(this)
2390  except: self.this = this
2391  def setup(self, *args):
2392  """setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2393  return _IMP_em2d.Em2DRestraint_setup(self, *args)
2394 
2395  def set_particles(self, *args):
2396  """set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2397  return _IMP_em2d.Em2DRestraint_set_particles(self, *args)
2398 
2399  def set_images(self, *args):
2400  """set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2401  return _IMP_em2d.Em2DRestraint_set_images(self, *args)
2402 
2403  def set_variance_images(self, *args):
2404  """set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2405  return _IMP_em2d.Em2DRestraint_set_variance_images(self, *args)
2406 
2407  def set_fast_mode(self, *args):
2408  """set_fast_mode(Em2DRestraint self, unsigned int n)"""
2409  return _IMP_em2d.Em2DRestraint_set_fast_mode(self, *args)
2410 
2411  def set_coarse_registration_mode(self, *args):
2412  """set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2413  return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, *args)
2414 
2415  def get_registration_results(self):
2416  """get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2417  return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2418 
2419  def do_get_inputs(self):
2420  """do_get_inputs(Em2DRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2421  return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2422 
2423  def get_version_info(self):
2424  """get_version_info(Em2DRestraint self) -> VersionInfo"""
2425  return _IMP_em2d.Em2DRestraint_get_version_info(self)
2426 
2427  def __str__(self):
2428  """__str__(Em2DRestraint self) -> std::string"""
2429  return _IMP_em2d.Em2DRestraint___str__(self)
2430 
2431  def __repr__(self):
2432  """__repr__(Em2DRestraint self) -> std::string"""
2433  return _IMP_em2d.Em2DRestraint___repr__(self)
2434 
2435  def get_from(o):
2436  return _object_cast_to_Em2DRestraint(o)
2437  get_from = staticmethod(get_from)
2438 
2439 Em2DRestraint_swigregister = _IMP_em2d.Em2DRestraint_swigregister
2440 Em2DRestraint_swigregister(Em2DRestraint)
2441 
2442 class ClusterSet(_object):
2443  """Proxy of C++ IMP::em2d::ClusterSet class"""
2444  __swig_setmethods__ = {}
2445  __setattr__ = lambda self, name, value: _swig_setattr(self, ClusterSet, name, value)
2446  __swig_getmethods__ = {}
2447  __getattr__ = lambda self, name: _swig_getattr(self, ClusterSet, name)
2448  def __init__(self, *args):
2449  """__init__(IMP::em2d::ClusterSet self, unsigned int N) -> ClusterSet"""
2450  this = _IMP_em2d.new_ClusterSet(*args)
2451  try: self.this.append(this)
2452  except: self.this = this
2453  def do_join_clusters(self, *args):
2454  """do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2455  return _IMP_em2d.ClusterSet_do_join_clusters(self, *args)
2456 
2457  def get_cluster_elements(self, *args):
2458  """get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2459  return _IMP_em2d.ClusterSet_get_cluster_elements(self, *args)
2460 
2461  def get_clusters_below_cutoff(self, *args):
2462  """get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2463  return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, *args)
2464 
2465  def get_cluster_formed_at_step(self, *args):
2466  """get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2467  return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, *args)
2468 
2469  def get_distance_at_step(self, *args):
2470  """get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2471  return _IMP_em2d.ClusterSet_get_distance_at_step(self, *args)
2472 
2473  def get_id_for_cluster_at_step(self, *args):
2474  """get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2475  return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, *args)
2476 
2477  def get_linkage_matrix(self):
2478  """get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2479  return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2480 
2481  def get_linkage_matrix_in_matlab_format(self):
2482  """get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2483  return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2484 
2485  def get_number_of_steps(self):
2486  """get_number_of_steps(ClusterSet self) -> unsigned int"""
2487  return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2488 
2489  def show(self, *args):
2490  """show(ClusterSet self, _ostream out)"""
2491  return _IMP_em2d.ClusterSet_show(self, *args)
2492 
2493  def __str__(self):
2494  """__str__(ClusterSet self) -> std::string"""
2495  return _IMP_em2d.ClusterSet___str__(self)
2496 
2497  def __repr__(self):
2498  """__repr__(ClusterSet self) -> std::string"""
2499  return _IMP_em2d.ClusterSet___repr__(self)
2500 
2501  __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2502  __del__ = lambda self : None;
2503 ClusterSet_swigregister = _IMP_em2d.ClusterSet_swigregister
2504 ClusterSet_swigregister(ClusterSet)
2505 
2506 class SingleLinkage(_object):
2507  """Proxy of C++ IMP::em2d::SingleLinkage class"""
2508  __swig_setmethods__ = {}
2509  __setattr__ = lambda self, name, value: _swig_setattr(self, SingleLinkage, name, value)
2510  __swig_getmethods__ = {}
2511  __getattr__ = lambda self, name: _swig_getattr(self, SingleLinkage, name)
2512  def __init__(self):
2513  """__init__(IMP::em2d::SingleLinkage self) -> SingleLinkage"""
2514  this = _IMP_em2d.new_SingleLinkage()
2515  try: self.this.append(this)
2516  except: self.this = this
2517  def __call__(self, *args):
2518  """__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2519  return _IMP_em2d.SingleLinkage___call__(self, *args)
2520 
2521  def show(self, *args):
2522  """show(SingleLinkage self, _ostream out)"""
2523  return _IMP_em2d.SingleLinkage_show(self, *args)
2524 
2525  def __str__(self):
2526  """__str__(SingleLinkage self) -> std::string"""
2527  return _IMP_em2d.SingleLinkage___str__(self)
2528 
2529  def __repr__(self):
2530  """__repr__(SingleLinkage self) -> std::string"""
2531  return _IMP_em2d.SingleLinkage___repr__(self)
2532 
2533  __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2534  __del__ = lambda self : None;
2535 SingleLinkage_swigregister = _IMP_em2d.SingleLinkage_swigregister
2536 SingleLinkage_swigregister(SingleLinkage)
2537 
2538 class CompleteLinkage(_object):
2539  """Proxy of C++ IMP::em2d::CompleteLinkage class"""
2540  __swig_setmethods__ = {}
2541  __setattr__ = lambda self, name, value: _swig_setattr(self, CompleteLinkage, name, value)
2542  __swig_getmethods__ = {}
2543  __getattr__ = lambda self, name: _swig_getattr(self, CompleteLinkage, name)
2544  def __init__(self):
2545  """__init__(IMP::em2d::CompleteLinkage self) -> CompleteLinkage"""
2546  this = _IMP_em2d.new_CompleteLinkage()
2547  try: self.this.append(this)
2548  except: self.this = this
2549  def __call__(self, *args):
2550  """__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2551  return _IMP_em2d.CompleteLinkage___call__(self, *args)
2552 
2553  def show(self, *args):
2554  """show(CompleteLinkage self, _ostream out)"""
2555  return _IMP_em2d.CompleteLinkage_show(self, *args)
2556 
2557  def __str__(self):
2558  """__str__(CompleteLinkage self) -> std::string"""
2559  return _IMP_em2d.CompleteLinkage___str__(self)
2560 
2561  def __repr__(self):
2562  """__repr__(CompleteLinkage self) -> std::string"""
2563  return _IMP_em2d.CompleteLinkage___repr__(self)
2564 
2565  __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2566  __del__ = lambda self : None;
2567 CompleteLinkage_swigregister = _IMP_em2d.CompleteLinkage_swigregister
2568 CompleteLinkage_swigregister(CompleteLinkage)
2569 
2570 class AverageDistanceLinkage(_object):
2571  """Proxy of C++ IMP::em2d::AverageDistanceLinkage class"""
2572  __swig_setmethods__ = {}
2573  __setattr__ = lambda self, name, value: _swig_setattr(self, AverageDistanceLinkage, name, value)
2574  __swig_getmethods__ = {}
2575  __getattr__ = lambda self, name: _swig_getattr(self, AverageDistanceLinkage, name)
2576  def __init__(self):
2577  """__init__(IMP::em2d::AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2578  this = _IMP_em2d.new_AverageDistanceLinkage()
2579  try: self.this.append(this)
2580  except: self.this = this
2581  def __call__(self, *args):
2582  """__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2583  return _IMP_em2d.AverageDistanceLinkage___call__(self, *args)
2584 
2585  def show(self, *args):
2586  """show(AverageDistanceLinkage self, _ostream out)"""
2587  return _IMP_em2d.AverageDistanceLinkage_show(self, *args)
2588 
2589  def __str__(self):
2590  """__str__(AverageDistanceLinkage self) -> std::string"""
2591  return _IMP_em2d.AverageDistanceLinkage___str__(self)
2592 
2593  def __repr__(self):
2594  """__repr__(AverageDistanceLinkage self) -> std::string"""
2595  return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2596 
2597  __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2598  __del__ = lambda self : None;
2599 AverageDistanceLinkage_swigregister = _IMP_em2d.AverageDistanceLinkage_swigregister
2600 AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2601 
2602 class CollisionCrossSection(IMP.base.Object):
2603  """Proxy of C++ IMP::em2d::CollisionCrossSection class"""
2604  __swig_setmethods__ = {}
2605  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2606  __setattr__ = lambda self, name, value: _swig_setattr(self, CollisionCrossSection, name, value)
2607  __swig_getmethods__ = {}
2608  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2609  __getattr__ = lambda self, name: _swig_getattr(self, CollisionCrossSection, name)
2610  def __init__(self, *args):
2611  """__init__(IMP::em2d::CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2612  this = _IMP_em2d.new_CollisionCrossSection(*args)
2613  try: self.this.append(this)
2614  except: self.this = this
2615  def set_model_particles(self, *args):
2616  """set_model_particles(CollisionCrossSection self, IMP::kernel::ParticlesTemp const & ps)"""
2617  return _IMP_em2d.CollisionCrossSection_set_model_particles(self, *args)
2618 
2619  def get_ccs(self):
2620  """get_ccs(CollisionCrossSection self) -> double"""
2621  return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2622 
2623  def show(self, *args):
2624  """show(CollisionCrossSection self, _ostream out)"""
2625  return _IMP_em2d.CollisionCrossSection_show(self, *args)
2626 
2627  def get_version_info(self):
2628  """get_version_info(CollisionCrossSection self) -> VersionInfo"""
2629  return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2630 
2631  def __str__(self):
2632  """__str__(CollisionCrossSection self) -> std::string"""
2633  return _IMP_em2d.CollisionCrossSection___str__(self)
2634 
2635  def __repr__(self):
2636  """__repr__(CollisionCrossSection self) -> std::string"""
2637  return _IMP_em2d.CollisionCrossSection___repr__(self)
2638 
2639  def get_from(o):
2640  return _object_cast_to_CollisionCrossSection(o)
2641  get_from = staticmethod(get_from)
2642 
2643 CollisionCrossSection_swigregister = _IMP_em2d.CollisionCrossSection_swigregister
2644 CollisionCrossSection_swigregister(CollisionCrossSection)
2645 
2646 class GridStates(IMP.domino.ParticleStates):
2647  """Proxy of C++ IMP::em2d::GridStates class"""
2648  __swig_setmethods__ = {}
2649  for _s in [IMP.domino.ParticleStates]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2650  __setattr__ = lambda self, name, value: _swig_setattr(self, GridStates, name, value)
2651  __swig_getmethods__ = {}
2652  for _s in [IMP.domino.ParticleStates]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2653  __getattr__ = lambda self, name: _swig_getattr(self, GridStates, name)
2654  def __init__(self, *args):
2655  """
2656  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations,
2657  IMP::String const & name="GridStates") -> GridStates
2658  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations) -> GridStates
2659  """
2660  this = _IMP_em2d.new_GridStates(*args)
2661  try: self.this.append(this)
2662  except: self.this = this
2663  def get_position(self, *args):
2664  """get_position(GridStates self, unsigned int i) -> Vector3D"""
2665  return _IMP_em2d.GridStates_get_position(self, *args)
2666 
2667  def get_orientation(self, *args):
2668  """get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2669  return _IMP_em2d.GridStates_get_orientation(self, *args)
2670 
2671  def get_version_info(self):
2672  """get_version_info(GridStates self) -> VersionInfo"""
2673  return _IMP_em2d.GridStates_get_version_info(self)
2674 
2675  def do_show(self, *args):
2676  """do_show(GridStates self, _ostream out)"""
2677  return _IMP_em2d.GridStates_do_show(self, *args)
2678 
2679  __swig_destroy__ = _IMP_em2d.delete_GridStates
2680  __del__ = lambda self : None;
2681  def __str__(self):
2682  """__str__(GridStates self) -> std::string"""
2683  return _IMP_em2d.GridStates___str__(self)
2684 
2685  def __repr__(self):
2686  """__repr__(GridStates self) -> std::string"""
2687  return _IMP_em2d.GridStates___repr__(self)
2688 
2689  def get_from(o):
2690  return _object_cast_to_GridStates(o)
2691  get_from = staticmethod(get_from)
2692 
2693 GridStates_swigregister = _IMP_em2d.GridStates_swigregister
2694 GridStates_swigregister(GridStates)
2695 
2696 class ProjectionStates(GridStates):
2697  """Proxy of C++ IMP::em2d::ProjectionStates class"""
2698  __swig_setmethods__ = {}
2699  for _s in [GridStates]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2700  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionStates, name, value)
2701  __swig_getmethods__ = {}
2702  for _s in [GridStates]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2703  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionStates, name)
2704  def __init__(self, *args):
2705  """
2706  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations,
2707  IMP::em2d::Images const & projections, IMP::String const & name="ProjectionStates") -> ProjectionStates
2708  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations,
2709  IMP::em2d::Images const & projections) -> ProjectionStates
2710  """
2711  this = _IMP_em2d.new_ProjectionStates(*args)
2712  try: self.this.append(this)
2713  except: self.this = this
2714  def get_projection(self, *args):
2715  """get_projection(ProjectionStates self, unsigned int i) -> Image"""
2716  return _IMP_em2d.ProjectionStates_get_projection(self, *args)
2717 
2718  def do_show(self, *args):
2719  """do_show(ProjectionStates self, _ostream out)"""
2720  return _IMP_em2d.ProjectionStates_do_show(self, *args)
2721 
2722  __swig_destroy__ = _IMP_em2d.delete_ProjectionStates
2723  __del__ = lambda self : None;
2724  def __str__(self):
2725  """__str__(ProjectionStates self) -> std::string"""
2726  return _IMP_em2d.ProjectionStates___str__(self)
2727 
2728  def __repr__(self):
2729  """__repr__(ProjectionStates self) -> std::string"""
2730  return _IMP_em2d.ProjectionStates___repr__(self)
2731 
2732  def get_from(o):
2733  return _object_cast_to_ProjectionStates(o)
2734  get_from = staticmethod(get_from)
2735 
2736 ProjectionStates_swigregister = _IMP_em2d.ProjectionStates_swigregister
2737 ProjectionStates_swigregister(ProjectionStates)
2738 
2739 class DistanceFilter(IMP.domino.SubsetFilter):
2740  """Proxy of C++ IMP::em2d::DistanceFilter class"""
2741  __swig_setmethods__ = {}
2742  for _s in [IMP.domino.SubsetFilter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2743  __setattr__ = lambda self, name, value: _swig_setattr(self, DistanceFilter, name, value)
2744  __swig_getmethods__ = {}
2745  for _s in [IMP.domino.SubsetFilter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2746  __getattr__ = lambda self, name: _swig_getattr(self, DistanceFilter, name)
2747  def __init__(self, *args):
2748  """
2749  __init__(IMP::em2d::DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table,
2750  double max_distance) -> DistanceFilter
2751  """
2752  this = _IMP_em2d.new_DistanceFilter(*args)
2753  try: self.this.append(this)
2754  except: self.this = this
2755  def show(self, *args):
2756  """
2757  show(DistanceFilter self, _ostream out=std::cout)
2758  show(DistanceFilter self)
2759  """
2760  return _IMP_em2d.DistanceFilter_show(self, *args)
2761 
2762  def get_version_info(self):
2763  """get_version_info(DistanceFilter self) -> VersionInfo"""
2764  return _IMP_em2d.DistanceFilter_get_version_info(self)
2765 
2766  def do_show(self, *args):
2767  """do_show(DistanceFilter self, _ostream out)"""
2768  return _IMP_em2d.DistanceFilter_do_show(self, *args)
2769 
2770  __swig_destroy__ = _IMP_em2d.delete_DistanceFilter
2771  __del__ = lambda self : None;
2772  def __str__(self):
2773  """__str__(DistanceFilter self) -> std::string"""
2774  return _IMP_em2d.DistanceFilter___str__(self)
2775 
2776  def __repr__(self):
2777  """__repr__(DistanceFilter self) -> std::string"""
2778  return _IMP_em2d.DistanceFilter___repr__(self)
2779 
2780  def get_from(o):
2781  return _object_cast_to_DistanceFilter(o)
2782  get_from = staticmethod(get_from)
2783 
2784 DistanceFilter_swigregister = _IMP_em2d.DistanceFilter_swigregister
2785 DistanceFilter_swigregister(DistanceFilter)
2786 
2787 class DistanceFilterTable(IMP.domino.SubsetFilterTable):
2788  """Proxy of C++ IMP::em2d::DistanceFilterTable class"""
2789  __swig_setmethods__ = {}
2790  for _s in [IMP.domino.SubsetFilterTable]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2791  __setattr__ = lambda self, name, value: _swig_setattr(self, DistanceFilterTable, name, value)
2792  __swig_getmethods__ = {}
2793  for _s in [IMP.domino.SubsetFilterTable]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2794  __getattr__ = lambda self, name: _swig_getattr(self, DistanceFilterTable, name)
2795  def __init__(self, *args):
2796  """__init__(IMP::em2d::DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
2797  this = _IMP_em2d.new_DistanceFilterTable(*args)
2798  try: self.this.append(this)
2799  except: self.this = this
2800  def show(self, *args):
2801  """
2802  show(DistanceFilterTable self, _ostream out=std::cout)
2803  show(DistanceFilterTable self)
2804  """
2805  return _IMP_em2d.DistanceFilterTable_show(self, *args)
2806 
2807  def get_version_info(self):
2808  """get_version_info(DistanceFilterTable self) -> VersionInfo"""
2809  return _IMP_em2d.DistanceFilterTable_get_version_info(self)
2810 
2811  def do_show(self, *args):
2812  """do_show(DistanceFilterTable self, _ostream out)"""
2813  return _IMP_em2d.DistanceFilterTable_do_show(self, *args)
2814 
2815  __swig_destroy__ = _IMP_em2d.delete_DistanceFilterTable
2816  __del__ = lambda self : None;
2817  def __str__(self):
2818  """__str__(DistanceFilterTable self) -> std::string"""
2819  return _IMP_em2d.DistanceFilterTable___str__(self)
2820 
2821  def __repr__(self):
2822  """__repr__(DistanceFilterTable self) -> std::string"""
2823  return _IMP_em2d.DistanceFilterTable___repr__(self)
2824 
2825  def get_from(o):
2826  return _object_cast_to_DistanceFilterTable(o)
2827  get_from = staticmethod(get_from)
2828 
2829 DistanceFilterTable_swigregister = _IMP_em2d.DistanceFilterTable_swigregister
2830 DistanceFilterTable_swigregister(DistanceFilterTable)
2831 
2832 class IntsOrder(_object):
2833  """Proxy of C++ IMP::em2d::IntsOrder class"""
2834  __swig_setmethods__ = {}
2835  __setattr__ = lambda self, name, value: _swig_setattr(self, IntsOrder, name, value)
2836  __swig_getmethods__ = {}
2837  __getattr__ = lambda self, name: _swig_getattr(self, IntsOrder, name)
2838  __repr__ = _swig_repr
2839  def __call__(self, *args):
2840  """__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
2841  return _IMP_em2d.IntsOrder___call__(self, *args)
2842 
2843  def __init__(self):
2844  """__init__(IMP::em2d::IntsOrder self) -> IntsOrder"""
2845  this = _IMP_em2d.new_IntsOrder()
2846  try: self.this.append(this)
2847  except: self.this = this
2848  __swig_destroy__ = _IMP_em2d.delete_IntsOrder
2849  __del__ = lambda self : None;
2850 IntsOrder_swigregister = _IMP_em2d.IntsOrder_swigregister
2851 IntsOrder_swigregister(IntsOrder)
2852 
2853 class RigidBodiesImageFitRestraint(IMP.kernel.Restraint):
2854  """Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class"""
2855  __swig_setmethods__ = {}
2856  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2857  __setattr__ = lambda self, name, value: _swig_setattr(self, RigidBodiesImageFitRestraint, name, value)
2858  __swig_getmethods__ = {}
2859  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2860  __getattr__ = lambda self, name: _swig_getattr(self, RigidBodiesImageFitRestraint, name)
2861  def get_version_info(self):
2862  """get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
2863  return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
2864 
2865  def __init__(self, *args):
2866  """__init__(IMP::em2d::RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
2867  this = _IMP_em2d.new_RigidBodiesImageFitRestraint(*args)
2868  try: self.this.append(this)
2869  except: self.this = this
2870  def set_projecting_parameters(self, *args):
2871  """set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
2872  return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, *args)
2873 
2874  def set_orientations(self, *args):
2875  """set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
2876  return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, *args)
2877 
2878  def get_number_of_masks(self, *args):
2879  """get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
2880  return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, *args)
2881 
2882  def __str__(self):
2883  """__str__(RigidBodiesImageFitRestraint self) -> std::string"""
2884  return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
2885 
2886  def __repr__(self):
2887  """__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
2888  return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
2889 
2890  def get_from(o):
2891  return _object_cast_to_RigidBodiesImageFitRestraint(o)
2892  get_from = staticmethod(get_from)
2893 
2894 RigidBodiesImageFitRestraint_swigregister = _IMP_em2d.RigidBodiesImageFitRestraint_swigregister
2895 RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
2896 
2897 
2898 def get_unique_index(*args):
2899  """get_unique_index(Rotation3D rot) -> IMP::Ints"""
2900  return _IMP_em2d.get_unique_index(*args)
2901 class RelativePositionMover(IMP.core.RigidBodyMover):
2902  """Proxy of C++ IMP::em2d::RelativePositionMover class"""
2903  __swig_setmethods__ = {}
2904  for _s in [IMP.core.RigidBodyMover]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2905  __setattr__ = lambda self, name, value: _swig_setattr(self, RelativePositionMover, name, value)
2906  __swig_getmethods__ = {}
2907  for _s in [IMP.core.RigidBodyMover]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2908  __getattr__ = lambda self, name: _swig_getattr(self, RelativePositionMover, name)
2909  def __init__(self, *args):
2910  """__init__(IMP::em2d::RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
2911  this = _IMP_em2d.new_RelativePositionMover(*args)
2912  try: self.this.append(this)
2913  except: self.this = this
2914  def add_internal_transformations(self, *args):
2915  """add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
2916  return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, *args)
2917 
2918  def set_random_move_probability(self, *args):
2919  """set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
2920  return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, *args)
2921 
2922  def __str__(self):
2923  """__str__(RelativePositionMover self) -> std::string"""
2924  return _IMP_em2d.RelativePositionMover___str__(self)
2925 
2926  def __repr__(self):
2927  """__repr__(RelativePositionMover self) -> std::string"""
2928  return _IMP_em2d.RelativePositionMover___repr__(self)
2929 
2930  def get_from(o):
2931  return _object_cast_to_RelativePositionMover(o)
2932  get_from = staticmethod(get_from)
2933 
2934 RelativePositionMover_swigregister = _IMP_em2d.RelativePositionMover_swigregister
2935 RelativePositionMover_swigregister(RelativePositionMover)
2936 
2937 class DummyRestraint(IMP.kernel.Restraint):
2938  """Proxy of C++ IMP::em2d::DummyRestraint class"""
2939  __swig_setmethods__ = {}
2940  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2941  __setattr__ = lambda self, name, value: _swig_setattr(self, DummyRestraint, name, value)
2942  __swig_getmethods__ = {}
2943  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2944  __getattr__ = lambda self, name: _swig_getattr(self, DummyRestraint, name)
2945  def __init__(self, *args):
2946  """__init__(IMP::em2d::DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
2947  this = _IMP_em2d.new_DummyRestraint(*args)
2948  try: self.this.append(this)
2949  except: self.this = this
2950  def show(self, *args):
2951  """
2952  show(DummyRestraint self, _ostream out=std::cout)
2953  show(DummyRestraint self)
2954  """
2955  return _IMP_em2d.DummyRestraint_show(self, *args)
2956 
2957  def do_get_inputs(self):
2958  """do_get_inputs(DummyRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2959  return _IMP_em2d.DummyRestraint_do_get_inputs(self)
2960 
2961  def get_version_info(self):
2962  """get_version_info(DummyRestraint self) -> VersionInfo"""
2963  return _IMP_em2d.DummyRestraint_get_version_info(self)
2964 
2965  def __str__(self):
2966  """__str__(DummyRestraint self) -> std::string"""
2967  return _IMP_em2d.DummyRestraint___str__(self)
2968 
2969  def __repr__(self):
2970  """__repr__(DummyRestraint self) -> std::string"""
2971  return _IMP_em2d.DummyRestraint___repr__(self)
2972 
2973  def get_from(o):
2974  return _object_cast_to_DummyRestraint(o)
2975  get_from = staticmethod(get_from)
2976 
2977 DummyRestraint_swigregister = _IMP_em2d.DummyRestraint_swigregister
2978 DummyRestraint_swigregister(DummyRestraint)
2979 
2980 class ParticlesDummyRestraint(IMP.kernel.Restraint):
2981  """Proxy of C++ IMP::em2d::ParticlesDummyRestraint class"""
2982  __swig_setmethods__ = {}
2983  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2984  __setattr__ = lambda self, name, value: _swig_setattr(self, ParticlesDummyRestraint, name, value)
2985  __swig_getmethods__ = {}
2986  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2987  __getattr__ = lambda self, name: _swig_getattr(self, ParticlesDummyRestraint, name)
2988  def __init__(self, *args):
2989  """__init__(IMP::em2d::ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
2990  this = _IMP_em2d.new_ParticlesDummyRestraint(*args)
2991  try: self.this.append(this)
2992  except: self.this = this
2993  def show(self, *args):
2994  """
2995  show(ParticlesDummyRestraint self, _ostream out=std::cout)
2996  show(ParticlesDummyRestraint self)
2997  """
2998  return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
2999 
3000  def do_get_inputs(self):
3001  """do_get_inputs(ParticlesDummyRestraint self) -> IMP::kernel::ModelObjectsTemp"""
3002  return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3003 
3004  def get_version_info(self):
3005  """get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3006  return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3007 
3008  def __str__(self):
3009  """__str__(ParticlesDummyRestraint self) -> std::string"""
3010  return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3011 
3012  def __repr__(self):
3013  """__repr__(ParticlesDummyRestraint self) -> std::string"""
3014  return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3015 
3016  def get_from(o):
3017  return _object_cast_to_ParticlesDummyRestraint(o)
3018  get_from = staticmethod(get_from)
3019 
3020 ParticlesDummyRestraint_swigregister = _IMP_em2d.ParticlesDummyRestraint_swigregister
3021 ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3022 
3023 class ResultAlign2D(_object):
3024  """Proxy of C++ std::pair<(IMP::algebra::Transformation2D,double)> class"""
3025  __swig_setmethods__ = {}
3026  __setattr__ = lambda self, name, value: _swig_setattr(self, ResultAlign2D, name, value)
3027  __swig_getmethods__ = {}
3028  __getattr__ = lambda self, name: _swig_getattr(self, ResultAlign2D, name)
3029  __repr__ = _swig_repr
3030  def __init__(self, *args):
3031  """
3032  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self) -> ResultAlign2D
3033  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, Transformation2D first, double second) -> ResultAlign2D
3034  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, ResultAlign2D p) -> ResultAlign2D
3035  """
3036  this = _IMP_em2d.new_ResultAlign2D(*args)
3037  try: self.this.append(this)
3038  except: self.this = this
3039  __swig_setmethods__["first"] = _IMP_em2d.ResultAlign2D_first_set
3040  __swig_getmethods__["first"] = _IMP_em2d.ResultAlign2D_first_get
3041  if _newclass:first = _swig_property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set)
3042  __swig_setmethods__["second"] = _IMP_em2d.ResultAlign2D_second_set
3043  __swig_getmethods__["second"] = _IMP_em2d.ResultAlign2D_second_get
3044  if _newclass:second = _swig_property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set)
3045  def __len__(self): return 2
3046  def __repr__(self): return str((self.first, self.second))
3047  def __getitem__(self, index):
3048  if not (index % 2):
3049  return self.first
3050  else:
3051  return self.second
3052  def __setitem__(self, index, val):
3053  if not (index % 2):
3054  self.first = val
3055  else:
3056  self.second = val
3057  __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3058  __del__ = lambda self : None;
3059 ResultAlign2D_swigregister = _IMP_em2d.ResultAlign2D_swigregister
3060 ResultAlign2D_swigregister(ResultAlign2D)
3061 
3062 
3063 def _do_hierarchical_clustering_single_linkage(*args):
3064  """_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3065  return _IMP_em2d._do_hierarchical_clustering_single_linkage(*args)
3066 
3067 def _do_hierarchical_clustering_complete_linkage(*args):
3068  """_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3069  return _IMP_em2d._do_hierarchical_clustering_complete_linkage(*args)
3070 
3071 def _do_hierarchical_clustering_average_distance_linkage(*args):
3072  """_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3073  return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(*args)
3074 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3075 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3076 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3077 
3078 
3079 def get_module_version():
3080  """get_module_version() -> std::string const"""
3081  return _IMP_em2d.get_module_version()
3082 
3083 def get_example_path(*args):
3084  """get_example_path(std::string fname) -> std::string"""
3085  return _IMP_em2d.get_example_path(*args)
3086 
3087 def get_data_path(*args):
3088  """get_data_path(std::string fname) -> std::string"""
3089  return _IMP_em2d.get_data_path(*args)
3090 import _version_check
3091 _version_check.check_version(get_module_version())
3092 
3093 # This file is compatible with both classic and new-style classes.
3094 
3095 
double get_shift_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Distance between the two in-plane translations.
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)
void do_project_particles(const kernel::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.
double get_mean(const cv::Mat &mat, const cvIntMat &mask)
setup
Definition: setup.py:1
void apply_threshold(cv::Mat &m, cv::Mat &result, double threshold=0.0)
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)
See IMP.container for more information.
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.
unsigned int get_enclosing_image_size(const kernel::ParticlesTemp &ps, double pixel_size, unsigned int slack)
Get an automatic size for an image that contains the particles.
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)
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 get_projection(em2d::Image *img, const kernel::ParticlesTemp &ps, const RegistrationResult &reg, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="")
Generates a projection from particles.
void apply_variance_filter(Image *input, Image *filtered, int kernelsize)
Definition: Image.h:265
void apply_diffusion_filter(Image *input, Image *filtered, double beta, double pixelsize, int time_steps)
Definition: Image.h:278
int do_labeling(const cvIntMat &m, cvIntMat &mat_to_label)
Labeling function for a matrix.
See IMP.cgal for more information.
Definition: cgal_config.h:107
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
MatchTemplateResults get_best_template_matches(const cv::Mat &m, const cv::Mat &templ, unsigned int n)
Modify the transformation of a rigid body.
See IMP.base for more information.
Definition: base/Array.h:20
void get_autocorrelation2d(const cv::Mat &m, cv::Mat &corr)
std::string get_data_path(std::string file_name)
Return the full path to installed data.
void apply_mean_outside_mask(Image *img, double radius)
See IMP.gsl for more information.
double get_rotation_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
ScoreStates maintian invariants in the Model.
See IMP.score_functor for more information.
Definition: AddScores.h:14
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:254
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)
See IMP.statistics for more information.
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)
void apply_circular_mask(const cv::Mat &mat, cv::Mat &result, int radius, double value=0.0)
See IMP.kernel for more information.
Images read_images(const Strings &names, const ImageReaderWriter *rw)
A restraint is a term in an IMP ScoringFunction.
void write_registration_results(String filename, const RegistrationResults &results)
Writes a set of registration results.
See IMP.em for more information.
Definition: CoarseCC.h:23
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)
Common base class for heavy weight IMP objects.
Definition: base/Object.h:106
Images create_evenly_distributed_projections(const kernel::ParticlesTemp &ps, unsigned int n, const ProjectingOptions &options)
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)
DensityMap * get_transformed(const DensityMap *input, const algebra::Transformation3D &tr, double threshold)
void do_matrix_to_image_flip(cv::Mat &m)
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)
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
void do_dilate_and_shrink_warp(cv::Mat &m, const cv::Mat &greyscale, cv::Mat &kernel)
(U. Adiga, 2005)
std::pair< algebra::Transformation2D, double > ResultAlign2D
Definition: align2D.h:22
em2d::Images get_projections(const kernel::ParticlesTemp &ps, const algebra::SphericalVector3Ds &vs, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
Generates projections from particles.
void do_resample_polar(Image *im1, Image *im2, const PolarResamplingParameters &polar_params)
See IMP.core for more information.
See IMP.algebra for more information.
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)
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
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)
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)
See IMP.display for more information.
Definition: ChimeraWriter.h:17
CheckLevel get_check_level()
Get the current audit mode.
See IMP.atom for more information.
See IMP.rmf for more information.
Definition: associations.h:20
See IMP.domino for more information.
Definition: analysis.h:15
void get_spectrum(const cv::Mat &m, cv::Mat &real, cv::Mat &imag)