IMP  2.3.0
The Integrative Modeling Platform
em2d/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.2
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 _object_types.append("PCAFitRestraint")
584 
585 def ProjectionParametersList(l=[]):
586  return [ProjectionParameters(x) for x in l]
587 _plural_types.append("ProjectionParametersList")
588 
589 _value_types.append("ProjectionParameters")
590 
591 
592 def show(*args):
593  """
594  show(cv::Mat const & m, _ostream out=std::cout)
595  show(cv::Mat const & m)
596  """
597  return _IMP_em2d.show(*args)
598 
599 def write_matrix(*args):
600  """write_matrix(cv::Mat & m, std::string name)"""
601  return _IMP_em2d.write_matrix(*args)
602 class ImageReaderWriter(IMP.base.Object):
603  """Proxy of C++ IMP::em2d::ImageReaderWriter class"""
604  __swig_setmethods__ = {}
605  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
606  __setattr__ = lambda self, name, value: _swig_setattr(self, ImageReaderWriter, name, value)
607  __swig_getmethods__ = {}
608  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
609  __getattr__ = lambda self, name: _swig_getattr(self, ImageReaderWriter, name)
610  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
611  def read(self, *args):
612  """read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
613  return _IMP_em2d.ImageReaderWriter_read(self, *args)
614 
615  def read_from_floats(self, *args):
616  """read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
617  return _IMP_em2d.ImageReaderWriter_read_from_floats(self, *args)
618 
619  def read_from_ints(self, *args):
620  """read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
621  return _IMP_em2d.ImageReaderWriter_read_from_ints(self, *args)
622 
623  def write(self, *args):
624  """write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
625  return _IMP_em2d.ImageReaderWriter_write(self, *args)
626 
627  def write_to_floats(self, *args):
628  """write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
629  return _IMP_em2d.ImageReaderWriter_write_to_floats(self, *args)
630 
631  def write_to_ints(self, *args):
632  """write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
633  return _IMP_em2d.ImageReaderWriter_write_to_ints(self, *args)
634 
635  def get_version_info(self):
636  """get_version_info(ImageReaderWriter self) -> VersionInfo"""
637  return _IMP_em2d.ImageReaderWriter_get_version_info(self)
638 
639  def __str__(self):
640  """__str__(ImageReaderWriter self) -> std::string"""
641  return _IMP_em2d.ImageReaderWriter___str__(self)
642 
643  def __repr__(self):
644  """__repr__(ImageReaderWriter self) -> std::string"""
645  return _IMP_em2d.ImageReaderWriter___repr__(self)
646 
647  def get_from(o):
648  return _object_cast_to_ImageReaderWriter(o)
649  get_from = staticmethod(get_from)
650 
651 ImageReaderWriter_swigregister = _IMP_em2d.ImageReaderWriter_swigregister
652 ImageReaderWriter_swigregister(ImageReaderWriter)
653 
654 class PolarResamplingParameters(_object):
655  """Proxy of C++ IMP::em2d::PolarResamplingParameters class"""
656  __swig_setmethods__ = {}
657  __setattr__ = lambda self, name, value: _swig_setattr(self, PolarResamplingParameters, name, value)
658  __swig_getmethods__ = {}
659  __getattr__ = lambda self, name: _swig_getattr(self, PolarResamplingParameters, name)
660  def __init__(self, *args):
661  """
662  __init__(IMP::em2d::PolarResamplingParameters self) -> PolarResamplingParameters
663  __init__(IMP::em2d::PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
664  __init__(IMP::em2d::PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
665  """
666  this = _IMP_em2d.new_PolarResamplingParameters(*args)
667  try: self.this.append(this)
668  except: self.this = this
669  __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
670  __del__ = lambda self : None;
671  def setup(self, *args):
672  """setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
673  return _IMP_em2d.PolarResamplingParameters_setup(self, *args)
674 
675  def get_starting_radius(self):
676  """get_starting_radius(PolarResamplingParameters self) -> double"""
677  return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
678 
679  def get_ending_radius(self):
680  """get_ending_radius(PolarResamplingParameters self) -> double"""
681  return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
682 
683  def get_radius(self, *args):
684  """get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
685  return _IMP_em2d.PolarResamplingParameters_get_radius(self, *args)
686 
687  def get_number_of_rings(self):
688  """get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
689  return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
690 
691  def set_estimated_number_of_angles(self, *args):
692  """set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
693  return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, *args)
694 
695  def get_number_of_angles(self):
696  """get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
697  return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
698 
699  def get_angle_step(self):
700  """get_angle_step(PolarResamplingParameters self) -> double"""
701  return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
702 
703  def get_radius_step(self):
704  """get_radius_step(PolarResamplingParameters self) -> double"""
705  return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
706 
707  def create_maps_for_resampling(self):
708  """create_maps_for_resampling(PolarResamplingParameters self)"""
709  return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
710 
711  def get_resampling_maps(self, *args):
712  """get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
713  return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, *args)
714 
715  def get_resampling_map(self, *args):
716  """get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
717  return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, *args)
718 
719  def show(self, *args):
720  """show(PolarResamplingParameters self, _ostream out)"""
721  return _IMP_em2d.PolarResamplingParameters_show(self, *args)
722 
723  def get_is_setup(self):
724  """get_is_setup(PolarResamplingParameters self) -> bool"""
725  return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
726 
727  def __str__(self):
728  """__str__(PolarResamplingParameters self) -> std::string"""
729  return _IMP_em2d.PolarResamplingParameters___str__(self)
730 
731  def __repr__(self):
732  """__repr__(PolarResamplingParameters self) -> std::string"""
733  return _IMP_em2d.PolarResamplingParameters___repr__(self)
734 
735 PolarResamplingParameters_swigregister = _IMP_em2d.PolarResamplingParameters_swigregister
736 PolarResamplingParameters_swigregister(PolarResamplingParameters)
737 
738 class SegmentationParameters(_object):
739  """Proxy of C++ IMP::em2d::SegmentationParameters class"""
740  __swig_setmethods__ = {}
741  __setattr__ = lambda self, name, value: _swig_setattr(self, SegmentationParameters, name, value)
742  __swig_getmethods__ = {}
743  __getattr__ = lambda self, name: _swig_getattr(self, SegmentationParameters, name)
744  __swig_setmethods__["image_pixel_size"] = _IMP_em2d.SegmentationParameters_image_pixel_size_set
745  __swig_getmethods__["image_pixel_size"] = _IMP_em2d.SegmentationParameters_image_pixel_size_get
746  if _newclass:image_pixel_size = _swig_property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set)
747  __swig_setmethods__["diffusion_beta"] = _IMP_em2d.SegmentationParameters_diffusion_beta_set
748  __swig_getmethods__["diffusion_beta"] = _IMP_em2d.SegmentationParameters_diffusion_beta_get
749  if _newclass:diffusion_beta = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set)
750  __swig_setmethods__["diffusion_timesteps"] = _IMP_em2d.SegmentationParameters_diffusion_timesteps_set
751  __swig_getmethods__["diffusion_timesteps"] = _IMP_em2d.SegmentationParameters_diffusion_timesteps_get
752  if _newclass:diffusion_timesteps = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set)
753  __swig_setmethods__["fill_holes_stddevs"] = _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set
754  __swig_getmethods__["fill_holes_stddevs"] = _IMP_em2d.SegmentationParameters_fill_holes_stddevs_get
755  if _newclass:fill_holes_stddevs = _swig_property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set)
756  __swig_setmethods__["opening_kernel"] = _IMP_em2d.SegmentationParameters_opening_kernel_set
757  __swig_getmethods__["opening_kernel"] = _IMP_em2d.SegmentationParameters_opening_kernel_get
758  if _newclass:opening_kernel = _swig_property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set)
759  __swig_setmethods__["remove_sizing_percentage"] = _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set
760  __swig_getmethods__["remove_sizing_percentage"] = _IMP_em2d.SegmentationParameters_remove_sizing_percentage_get
761  if _newclass:remove_sizing_percentage = _swig_property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set)
762  __swig_setmethods__["binary_background"] = _IMP_em2d.SegmentationParameters_binary_background_set
763  __swig_getmethods__["binary_background"] = _IMP_em2d.SegmentationParameters_binary_background_get
764  if _newclass:binary_background = _swig_property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set)
765  __swig_setmethods__["binary_foreground"] = _IMP_em2d.SegmentationParameters_binary_foreground_set
766  __swig_getmethods__["binary_foreground"] = _IMP_em2d.SegmentationParameters_binary_foreground_get
767  if _newclass:binary_foreground = _swig_property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set)
768  __swig_setmethods__["threshold"] = _IMP_em2d.SegmentationParameters_threshold_set
769  __swig_getmethods__["threshold"] = _IMP_em2d.SegmentationParameters_threshold_get
770  if _newclass:threshold = _swig_property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set)
771  def __init__(self, *args):
772  """
773  __init__(IMP::em2d::SegmentationParameters self) -> SegmentationParameters
774  __init__(IMP::em2d::SegmentationParameters self, double apix, double diff_beta, unsigned int diff_timesteps, double fh_stddevs, cv::Mat const & kr,
775  int background, int foreground) -> SegmentationParameters
776  """
777  this = _IMP_em2d.new_SegmentationParameters(*args)
778  try: self.this.append(this)
779  except: self.this = this
780  def show(self, *args):
781  """
782  show(SegmentationParameters self, _ostream out=std::cout)
783  show(SegmentationParameters self)
784  """
785  return _IMP_em2d.SegmentationParameters_show(self, *args)
786 
787  def __str__(self):
788  """__str__(SegmentationParameters self) -> std::string"""
789  return _IMP_em2d.SegmentationParameters___str__(self)
790 
791  def __repr__(self):
792  """__repr__(SegmentationParameters self) -> std::string"""
793  return _IMP_em2d.SegmentationParameters___repr__(self)
794 
795  __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
796  __del__ = lambda self : None;
797 SegmentationParameters_swigregister = _IMP_em2d.SegmentationParameters_swigregister
798 SegmentationParameters_swigregister(SegmentationParameters)
799 
800 class MatchTemplateResult(_object):
801  """Proxy of C++ IMP::em2d::MatchTemplateResult class"""
802  __swig_setmethods__ = {}
803  __setattr__ = lambda self, name, value: _swig_setattr(self, MatchTemplateResult, name, value)
804  __swig_getmethods__ = {}
805  __getattr__ = lambda self, name: _swig_getattr(self, MatchTemplateResult, name)
806  __swig_setmethods__["pair"] = _IMP_em2d.MatchTemplateResult_pair_set
807  __swig_getmethods__["pair"] = _IMP_em2d.MatchTemplateResult_pair_get
808  if _newclass:pair = _swig_property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set)
809  __swig_setmethods__["cross_correlation"] = _IMP_em2d.MatchTemplateResult_cross_correlation_set
810  __swig_getmethods__["cross_correlation"] = _IMP_em2d.MatchTemplateResult_cross_correlation_get
811  if _newclass:cross_correlation = _swig_property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set)
812  def __init__(self, *args):
813  """__init__(IMP::em2d::MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
814  this = _IMP_em2d.new_MatchTemplateResult(*args)
815  try: self.this.append(this)
816  except: self.this = this
817  def show(self, *args):
818  """
819  show(MatchTemplateResult self, _ostream out=std::cout)
820  show(MatchTemplateResult self)
821  """
822  return _IMP_em2d.MatchTemplateResult_show(self, *args)
823 
824  def __str__(self):
825  """__str__(MatchTemplateResult self) -> std::string"""
826  return _IMP_em2d.MatchTemplateResult___str__(self)
827 
828  def __repr__(self):
829  """__repr__(MatchTemplateResult self) -> std::string"""
830  return _IMP_em2d.MatchTemplateResult___repr__(self)
831 
832  __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
833  __del__ = lambda self : None;
834 MatchTemplateResult_swigregister = _IMP_em2d.MatchTemplateResult_swigregister
835 MatchTemplateResult_swigregister(MatchTemplateResult)
836 
837 
838 def apply_mask(*args):
839  """apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
840  return _IMP_em2d.apply_mask(*args)
841 
842 def apply_circular_mask(*args):
843  """
844  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)
845  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius)
846  """
847  return _IMP_em2d.apply_circular_mask(*args)
848 
849 def get_mean(*args):
850  """get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
851  return _IMP_em2d.get_mean(*args)
852 
853 def create_circular_mask(*args):
854  """create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
855  return _IMP_em2d.create_circular_mask(*args)
856 
857 def do_histogram_stretching(*args):
858  """do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
859  return _IMP_em2d.do_histogram_stretching(*args)
860 
861 def do_dilate_and_shrink_warp(*args):
862  """do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
863  return _IMP_em2d.do_dilate_and_shrink_warp(*args)
864 
866  """
867  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)
868  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker)
869  """
870  return _IMP_em2d.do_morphologic_reconstruction(*args)
871 
872 def do_labeling(*args):
873  """do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
874  return _IMP_em2d.do_labeling(*args)
875 
877  """get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
878  return _IMP_em2d.get_diffusion_filtering_partial_derivative(*args)
879 
880 def get_domes(*args):
881  """get_domes(cv::Mat & m, cv::Mat & result, double h)"""
882  return _IMP_em2d.get_domes(*args)
883 
884 def get_transformed(*args):
885  """get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
886  return _IMP_em2d.get_transformed(*args)
887 
888 def apply_threshold(*args):
889  """
890  apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)
891  apply_threshold(cv::Mat & m, cv::Mat & result)
892  """
893  return _IMP_em2d.apply_threshold(*args)
894 
896  """do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
897  return _IMP_em2d.do_morphologic_contrast_enhancement(*args)
898 
899 def get_morphologic_gradient(*args):
900  """get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
901  return _IMP_em2d.get_morphologic_gradient(*args)
902 
903 def get_overlap_percentage(*args):
904  """get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
905  return _IMP_em2d.get_overlap_percentage(*args)
906 
907 def get_best_template_matches(*args):
908  """get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
909  return _IMP_em2d.get_best_template_matches(*args)
910 class Image(IMP.base.Object):
911  """Proxy of C++ IMP::em2d::Image class"""
912  __swig_setmethods__ = {}
913  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
914  __setattr__ = lambda self, name, value: _swig_setattr(self, Image, name, value)
915  __swig_getmethods__ = {}
916  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
917  __getattr__ = lambda self, name: _swig_getattr(self, Image, name)
918  def __init__(self, *args):
919  """
920  __init__(IMP::em2d::Image self) -> Image
921  __init__(IMP::em2d::Image self, int rows, int cols) -> Image
922  __init__(IMP::em2d::Image self, IMP::String filename, ImageReaderWriter reader) -> Image
923  """
924  this = _IMP_em2d.new_Image(*args)
925  try: self.this.append(this)
926  except: self.this = this
927  def get_data(self):
928  """get_data(Image self) -> cv::Mat &"""
929  return _IMP_em2d.Image_get_data(self)
930 
931  def set_data(self, *args):
932  """set_data(Image self, cv::Mat const & mat)"""
933  return _IMP_em2d.Image_set_data(self, *args)
934 
935  def set_zeros(self):
936  """set_zeros(Image self)"""
937  return _IMP_em2d.Image_set_zeros(self)
938 
939  def set_value(self, *args):
940  """
941  set_value(Image self, double val)
942  set_value(Image self, int i, int j, double val)
943  """
944  return _IMP_em2d.Image_set_value(self, *args)
945 
946  def __call__(self, *args):
947  """__call__(Image self, int i, int j) -> double"""
948  return _IMP_em2d.Image___call__(self, *args)
949 
950  def get_header(self):
951  """get_header(Image self) -> ImageHeader"""
952  return _IMP_em2d.Image_get_header(self)
953 
954  def set_size(self, *args):
955  """
956  set_size(Image self, int rows, int cols)
957  set_size(Image self, Image img)
958  """
959  return _IMP_em2d.Image_set_size(self, *args)
960 
961  def update_header(self):
962  """update_header(Image self)"""
963  return _IMP_em2d.Image_update_header(self)
964 
965  def read(self, *args):
966  """read(Image self, IMP::String filename, ImageReaderWriter reader)"""
967  return _IMP_em2d.Image_read(self, *args)
968 
969  def write(self, *args):
970  """write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
971  return _IMP_em2d.Image_write(self, *args)
972 
973  def show(self, *args):
974  """show(Image self, _ostream out)"""
975  return _IMP_em2d.Image_show(self, *args)
976 
977  def get_version_info(self):
978  """get_version_info(Image self) -> VersionInfo"""
979  return _IMP_em2d.Image_get_version_info(self)
980 
981  def set_name(self, *args):
982  """set_name(Image self, IMP::String const & name)"""
983  return _IMP_em2d.Image_set_name(self, *args)
984 
985  def get_name(self):
986  """get_name(Image self) -> IMP::String"""
987  return _IMP_em2d.Image_get_name(self)
988 
989  def get_min_and_max_values(self):
990  """get_min_and_max_values(Image self) -> IMP::FloatRange"""
991  return _IMP_em2d.Image_get_min_and_max_values(self)
992 
993  def __str__(self):
994  """__str__(Image self) -> std::string"""
995  return _IMP_em2d.Image___str__(self)
996 
997  def __repr__(self):
998  """__repr__(Image self) -> std::string"""
999  return _IMP_em2d.Image___repr__(self)
1000 
1001  def get_from(o):
1002  return _object_cast_to_Image(o)
1003  get_from = staticmethod(get_from)
1004 
1005 Image_swigregister = _IMP_em2d.Image_swigregister
1006 Image_swigregister(Image)
1007 
1008 
1009 def read_images(*args):
1010  """read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1011  return _IMP_em2d.read_images(*args)
1012 
1013 def save_images(*args):
1014  """save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1015  return _IMP_em2d.save_images(*args)
1016 
1017 def do_normalize(*args):
1018  """
1019  do_normalize(cv::Mat & m)
1020  do_normalize(Image im, bool force=False)
1021  do_normalize(Image im)
1022  """
1023  return _IMP_em2d.do_normalize(*args)
1024 
1025 def get_histogram(*args):
1026  """
1027  get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1028  get_histogram(Image img, int bins) -> IMP::Floats
1029  """
1030  return _IMP_em2d.get_histogram(*args)
1031 
1032 def apply_variance_filter(*args):
1033  """
1034  apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1035  apply_variance_filter(Image input, Image filtered, int kernelsize)
1036  """
1037  return _IMP_em2d.apply_variance_filter(*args)
1038 
1039 def apply_diffusion_filter(*args):
1040  """
1041  apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1042  apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1043  """
1044  return _IMP_em2d.apply_diffusion_filter(*args)
1045 
1046 def do_fill_holes(*args):
1047  """
1048  do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1049  do_fill_holes(Image input, Image result, double n_stddevs)
1050  """
1051  return _IMP_em2d.do_fill_holes(*args)
1052 
1053 def do_combined_fill_holes_and_threshold(*args):
1054  """
1055  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1056  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs)
1057  do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1058  """
1059  return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1060 
1061 def do_extend_borders(*args):
1062  """
1063  do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1064  do_extend_borders(Image im1, Image im2, unsigned int pix)
1065  """
1066  return _IMP_em2d.do_extend_borders(*args)
1067 
1068 def do_segmentation(*args):
1069  """
1070  do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1071  do_segmentation(Image input, Image result, SegmentationParameters params)
1072  """
1073  return _IMP_em2d.do_segmentation(*args)
1074 
1075 def do_remove_small_objects(*args):
1076  """
1077  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1078  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0)
1079  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage)
1080  do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1081  do_remove_small_objects(Image input, double percentage, int background=0)
1082  do_remove_small_objects(Image input, double percentage)
1083  """
1084  return _IMP_em2d.do_remove_small_objects(*args)
1085 
1086 def do_subtract_images(*args):
1087  """do_subtract_images(Image first, Image second, Image result)"""
1088  return _IMP_em2d.do_subtract_images(*args)
1089 
1090 def add_noise(*args):
1091  """
1092  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode="uniform", double df=3)
1093  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode="uniform")
1094  add_noise(cv::Mat & v, double op1, double op2)
1095  add_noise(Image im1, double op1, double op2, IMP::String const & mode="uniform", double df=3)
1096  add_noise(Image im1, double op1, double op2, IMP::String const & mode="uniform")
1097  add_noise(Image im1, double op1, double op2)
1098  """
1099  return _IMP_em2d.add_noise(*args)
1100 
1101 def do_resample_polar(*args):
1102  """
1103  do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1104  do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1105  """
1106  return _IMP_em2d.do_resample_polar(*args)
1107 
1108 def crop(*args):
1109  """
1110  crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1111  crop(Image img, IMP::IntPair const & center, int size)
1112  """
1113  return _IMP_em2d.crop(*args)
1114 
1115 def apply_mean_outside_mask(*args):
1116  """apply_mean_outside_mask(Image img, double radius)"""
1117  return _IMP_em2d.apply_mean_outside_mask(*args)
1118 class RegistrationResult(_object):
1119  """Proxy of C++ IMP::em2d::RegistrationResult class"""
1120  __swig_setmethods__ = {}
1121  __setattr__ = lambda self, name, value: _swig_setattr(self, RegistrationResult, name, value)
1122  __swig_getmethods__ = {}
1123  __getattr__ = lambda self, name: _swig_getattr(self, RegistrationResult, name)
1124  def __init__(self, *args):
1125  """
1126  __init__(IMP::em2d::RegistrationResult self) -> RegistrationResult
1127  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0,
1128  IMP::String name="") -> RegistrationResult
1129  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1130  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0) -> RegistrationResult
1131  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift) -> RegistrationResult
1132  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.), int projection_index=0,
1133  int image_index=0, IMP::String name="") -> 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) -> RegistrationResult
1136  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.), int projection_index=0) -> RegistrationResult
1137  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.)) -> RegistrationResult
1138  __init__(IMP::em2d::RegistrationResult self, Rotation3D R) -> RegistrationResult
1139  """
1140  this = _IMP_em2d.new_RegistrationResult(*args)
1141  try: self.this.append(this)
1142  except: self.this = this
1143  def get_phi(self):
1144  """get_phi(RegistrationResult self) -> double"""
1145  return _IMP_em2d.RegistrationResult_get_phi(self)
1146 
1147  def get_theta(self):
1148  """get_theta(RegistrationResult self) -> double"""
1149  return _IMP_em2d.RegistrationResult_get_theta(self)
1150 
1151  def get_psi(self):
1152  """get_psi(RegistrationResult self) -> double"""
1153  return _IMP_em2d.RegistrationResult_get_psi(self)
1154 
1155  def get_shift(self):
1156  """get_shift(RegistrationResult self) -> Vector2D"""
1157  return _IMP_em2d.RegistrationResult_get_shift(self)
1158 
1159  def get_shift_3d(self):
1160  """get_shift_3d(RegistrationResult self) -> Vector3D"""
1161  return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1162 
1163  def get_projection_index(self):
1164  """get_projection_index(RegistrationResult self) -> int"""
1165  return _IMP_em2d.RegistrationResult_get_projection_index(self)
1166 
1167  def set_projection_index(self, *args):
1168  """set_projection_index(RegistrationResult self, int index)"""
1169  return _IMP_em2d.RegistrationResult_set_projection_index(self, *args)
1170 
1171  def get_image_index(self):
1172  """get_image_index(RegistrationResult self) -> int"""
1173  return _IMP_em2d.RegistrationResult_get_image_index(self)
1174 
1175  def set_image_index(self, *args):
1176  """set_image_index(RegistrationResult self, int index)"""
1177  return _IMP_em2d.RegistrationResult_set_image_index(self, *args)
1178 
1179  def get_name(self):
1180  """get_name(RegistrationResult self) -> IMP::String"""
1181  return _IMP_em2d.RegistrationResult_get_name(self)
1182 
1183  def get_ccc(self):
1184  """get_ccc(RegistrationResult self) -> double"""
1185  return _IMP_em2d.RegistrationResult_get_ccc(self)
1186 
1187  def set_ccc(self, *args):
1188  """set_ccc(RegistrationResult self, double ccc)"""
1189  return _IMP_em2d.RegistrationResult_set_ccc(self, *args)
1190 
1191  def get_score(self):
1192  """get_score(RegistrationResult self) -> double"""
1193  return _IMP_em2d.RegistrationResult_get_score(self)
1194 
1195  def set_score(self, *args):
1196  """set_score(RegistrationResult self, double Score)"""
1197  return _IMP_em2d.RegistrationResult_set_score(self, *args)
1198 
1199  def set_rotation(self, *args):
1200  """
1201  set_rotation(RegistrationResult self, double phi, double theta, double psi)
1202  set_rotation(RegistrationResult self, Rotation3D R)
1203  """
1204  return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1205 
1206  def set_shift(self, *args):
1207  """set_shift(RegistrationResult self, Vector2D shift)"""
1208  return _IMP_em2d.RegistrationResult_set_shift(self, *args)
1209 
1210  def set_name(self, *args):
1211  """set_name(RegistrationResult self, IMP::String name)"""
1212  return _IMP_em2d.RegistrationResult_set_name(self, *args)
1213 
1214  def add_in_plane_transformation(self, *args):
1215  """add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1216  return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, *args)
1217 
1218  def show(self, *args):
1219  """
1220  show(RegistrationResult self, _ostream out=std::cout)
1221  show(RegistrationResult self)
1222  """
1223  return _IMP_em2d.RegistrationResult_show(self, *args)
1224 
1225  def write(self, *args):
1226  """
1227  write(RegistrationResult self, _ostream out=std::cout)
1228  write(RegistrationResult self)
1229  """
1230  return _IMP_em2d.RegistrationResult_write(self, *args)
1231 
1232  def write_comment_line(self, *args):
1233  """
1234  write_comment_line(RegistrationResult self, _ostream out=std::cout)
1235  write_comment_line(RegistrationResult self)
1236  """
1237  return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1238 
1239  def read(self, *args):
1240  """read(RegistrationResult self, IMP::String const & s)"""
1241  return _IMP_em2d.RegistrationResult_read(self, *args)
1242 
1243  def set_random_registration(self, *args):
1244  """set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1245  return _IMP_em2d.RegistrationResult_set_random_registration(self, *args)
1246 
1247  def get_rotation(self):
1248  """get_rotation(RegistrationResult self) -> Rotation3D"""
1249  return _IMP_em2d.RegistrationResult_get_rotation(self)
1250 
1251  def set_in_image(self, *args):
1252  """set_in_image(RegistrationResult self, ImageHeader header)"""
1253  return _IMP_em2d.RegistrationResult_set_in_image(self, *args)
1254 
1255  def read_from_image(self, *args):
1256  """read_from_image(RegistrationResult self, ImageHeader header)"""
1257  return _IMP_em2d.RegistrationResult_read_from_image(self, *args)
1258 
1259  def get_is_optimized_result(self):
1260  """get_is_optimized_result(RegistrationResult self) -> bool"""
1261  return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1262 
1263  __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1264  __del__ = lambda self : None;
1265  def __str__(self):
1266  """__str__(RegistrationResult self) -> std::string"""
1267  return _IMP_em2d.RegistrationResult___str__(self)
1268 
1269  def __repr__(self):
1270  """__repr__(RegistrationResult self) -> std::string"""
1271  return _IMP_em2d.RegistrationResult___repr__(self)
1272 
1273 RegistrationResult_swigregister = _IMP_em2d.RegistrationResult_swigregister
1274 RegistrationResult_swigregister(RegistrationResult)
1275 
1276 
1277 def read_registration_results(*args):
1278  """read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1279  return _IMP_em2d.read_registration_results(*args)
1280 
1281 def write_registration_results(*args):
1282  """write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1283  return _IMP_em2d.write_registration_results(*args)
1284 
1286  """
1287  get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults
1288  get_random_registration_results(unsigned int n) -> IMP::em2d::RegistrationResults
1289  """
1290  return _IMP_em2d.get_random_registration_results(*args)
1291 
1293  """get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1294  return _IMP_em2d.get_evenly_distributed_registration_results(*args)
1295 
1296 def get_random_between_zero_and_one():
1297  """get_random_between_zero_and_one() -> double"""
1298  return _IMP_em2d.get_random_between_zero_and_one()
1299 class SpiderImageReaderWriter(ImageReaderWriter):
1300  """Proxy of C++ IMP::em2d::SpiderImageReaderWriter class"""
1301  __swig_setmethods__ = {}
1302  for _s in [ImageReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1303  __setattr__ = lambda self, name, value: _swig_setattr(self, SpiderImageReaderWriter, name, value)
1304  __swig_getmethods__ = {}
1305  for _s in [ImageReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1306  __getattr__ = lambda self, name: _swig_getattr(self, SpiderImageReaderWriter, name)
1307  __swig_setmethods__["filename_"] = _IMP_em2d.SpiderImageReaderWriter_filename__set
1308  __swig_getmethods__["filename_"] = _IMP_em2d.SpiderImageReaderWriter_filename__get
1309  if _newclass:filename_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set)
1310  __swig_setmethods__["skip_type_check_"] = _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set
1311  __swig_getmethods__["skip_type_check_"] = _IMP_em2d.SpiderImageReaderWriter_skip_type_check__get
1312  if _newclass:skip_type_check_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set)
1313  __swig_setmethods__["force_reversed_"] = _IMP_em2d.SpiderImageReaderWriter_force_reversed__set
1314  __swig_getmethods__["force_reversed_"] = _IMP_em2d.SpiderImageReaderWriter_force_reversed__get
1315  if _newclass:force_reversed_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set)
1316  __swig_setmethods__["skip_extra_checkings_"] = _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set
1317  __swig_getmethods__["skip_extra_checkings_"] = _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get
1318  if _newclass:skip_extra_checkings_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set)
1319  def __init__(self, *args):
1320  """
1321  __init__(IMP::em2d::SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1322  __init__(IMP::em2d::SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1323  """
1324  this = _IMP_em2d.new_SpiderImageReaderWriter(*args)
1325  try: self.this.append(this)
1326  except: self.this = this
1327  def __str__(self):
1328  """__str__(SpiderImageReaderWriter self) -> std::string"""
1329  return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1330 
1331  def __repr__(self):
1332  """__repr__(SpiderImageReaderWriter self) -> std::string"""
1333  return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1334 
1335  def get_from(o):
1336  return _object_cast_to_SpiderImageReaderWriter(o)
1337  get_from = staticmethod(get_from)
1338 
1339 SpiderImageReaderWriter_swigregister = _IMP_em2d.SpiderImageReaderWriter_swigregister
1340 SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1341 
1342 class JPGImageReaderWriter(ImageReaderWriter):
1343  """Proxy of C++ IMP::em2d::JPGImageReaderWriter class"""
1344  __swig_setmethods__ = {}
1345  for _s in [ImageReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1346  __setattr__ = lambda self, name, value: _swig_setattr(self, JPGImageReaderWriter, name, value)
1347  __swig_getmethods__ = {}
1348  for _s in [ImageReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1349  __getattr__ = lambda self, name: _swig_getattr(self, JPGImageReaderWriter, name)
1350  def __init__(self):
1351  """__init__(IMP::em2d::JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1352  this = _IMP_em2d.new_JPGImageReaderWriter()
1353  try: self.this.append(this)
1354  except: self.this = this
1355  def __str__(self):
1356  """__str__(JPGImageReaderWriter self) -> std::string"""
1357  return _IMP_em2d.JPGImageReaderWriter___str__(self)
1358 
1359  def __repr__(self):
1360  """__repr__(JPGImageReaderWriter self) -> std::string"""
1361  return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1362 
1363  def get_from(o):
1364  return _object_cast_to_JPGImageReaderWriter(o)
1365  get_from = staticmethod(get_from)
1366 
1367 JPGImageReaderWriter_swigregister = _IMP_em2d.JPGImageReaderWriter_swigregister
1368 JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1369 
1370 class TIFFImageReaderWriter(ImageReaderWriter):
1371  """Proxy of C++ IMP::em2d::TIFFImageReaderWriter class"""
1372  __swig_setmethods__ = {}
1373  for _s in [ImageReaderWriter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1374  __setattr__ = lambda self, name, value: _swig_setattr(self, TIFFImageReaderWriter, name, value)
1375  __swig_getmethods__ = {}
1376  for _s in [ImageReaderWriter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1377  __getattr__ = lambda self, name: _swig_getattr(self, TIFFImageReaderWriter, name)
1378  def __init__(self):
1379  """__init__(IMP::em2d::TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1380  this = _IMP_em2d.new_TIFFImageReaderWriter()
1381  try: self.this.append(this)
1382  except: self.this = this
1383  def __str__(self):
1384  """__str__(TIFFImageReaderWriter self) -> std::string"""
1385  return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1386 
1387  def __repr__(self):
1388  """__repr__(TIFFImageReaderWriter self) -> std::string"""
1389  return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1390 
1391  def get_from(o):
1392  return _object_cast_to_TIFFImageReaderWriter(o)
1393  get_from = staticmethod(get_from)
1394 
1395 TIFFImageReaderWriter_swigregister = _IMP_em2d.TIFFImageReaderWriter_swigregister
1396 TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1397 
1398 
1399 def do_matrix_to_image_flip(*args):
1400  """do_matrix_to_image_flip(cv::Mat & m)"""
1401  return _IMP_em2d.do_matrix_to_image_flip(*args)
1402 
1404  """get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1405  return _IMP_em2d.get_autocorrelation2d_no_preprocessing(*args)
1406 
1407 def get_autocorrelation2d(*args):
1408  """
1409  get_autocorrelation2d(Image im1, Image im2)
1410  get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1411  """
1412  return _IMP_em2d.get_autocorrelation2d(*args)
1413 
1414 def get_correlation2d(*args):
1415  """
1416  get_correlation2d(Image im1, Image im2, Image corr)
1417  get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1418  """
1419  return _IMP_em2d.get_correlation2d(*args)
1420 
1422  """get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1423  return _IMP_em2d.get_correlation2d_no_preprocessing(*args)
1424 
1425 def get_fft_using_optimal_size(*args):
1426  """get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1427  return _IMP_em2d.get_fft_using_optimal_size(*args)
1428 
1429 def get_spectrum(*args):
1430  """get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1431  return _IMP_em2d.get_spectrum(*args)
1432 
1433 def get_rotation_error(*args):
1434  """get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1435  return _IMP_em2d.get_rotation_error(*args)
1436 
1437 def get_shift_error(*args):
1438  """get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1439  return _IMP_em2d.get_shift_error(*args)
1440 
1441 def get_average_rotation_error(*args):
1442  """get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1443  return _IMP_em2d.get_average_rotation_error(*args)
1444 
1445 def get_average_shift_error(*args):
1446  """get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1447  return _IMP_em2d.get_average_shift_error(*args)
1448 
1450  """
1451  get_cross_correlation_coefficient(Image im1, Image im2) -> double
1452  get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1453  """
1454  return _IMP_em2d.get_cross_correlation_coefficient(*args)
1455 
1456 def get_global_score(*args):
1457  """get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1458  return _IMP_em2d.get_global_score(*args)
1459 class ScoreFunction(IMP.base.Object):
1460  """Proxy of C++ IMP::em2d::ScoreFunction class"""
1461  __swig_setmethods__ = {}
1462  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1463  __setattr__ = lambda self, name, value: _swig_setattr(self, ScoreFunction, name, value)
1464  __swig_getmethods__ = {}
1465  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1466  __getattr__ = lambda self, name: _swig_getattr(self, ScoreFunction, name)
1467  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
1468  def get_score(self, *args):
1469  """get_score(ScoreFunction self, Image image, Image projection) -> double"""
1470  return _IMP_em2d.ScoreFunction_get_score(self, *args)
1471 
1472  def set_variance_image(self, *args):
1473  """set_variance_image(ScoreFunction self, Image var)"""
1474  return _IMP_em2d.ScoreFunction_set_variance_image(self, *args)
1475 
1476  def get_version_info(self):
1477  """get_version_info(ScoreFunction self) -> VersionInfo"""
1478  return _IMP_em2d.ScoreFunction_get_version_info(self)
1479 
1480  def __str__(self):
1481  """__str__(ScoreFunction self) -> std::string"""
1482  return _IMP_em2d.ScoreFunction___str__(self)
1483 
1484  def __repr__(self):
1485  """__repr__(ScoreFunction self) -> std::string"""
1486  return _IMP_em2d.ScoreFunction___repr__(self)
1487 
1488  def get_from(o):
1489  return _object_cast_to_ScoreFunction(o)
1490  get_from = staticmethod(get_from)
1491 
1492 ScoreFunction_swigregister = _IMP_em2d.ScoreFunction_swigregister
1493 ScoreFunction_swigregister(ScoreFunction)
1494 
1495 class ChiSquaredScore(ScoreFunction):
1496  """Proxy of C++ IMP::em2d::ChiSquaredScore class"""
1497  __swig_setmethods__ = {}
1498  for _s in [ScoreFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1499  __setattr__ = lambda self, name, value: _swig_setattr(self, ChiSquaredScore, name, value)
1500  __swig_getmethods__ = {}
1501  for _s in [ScoreFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1502  __getattr__ = lambda self, name: _swig_getattr(self, ChiSquaredScore, name)
1503  def __init__(self):
1504  """__init__(IMP::em2d::ChiSquaredScore self) -> ChiSquaredScore"""
1505  this = _IMP_em2d.new_ChiSquaredScore()
1506  try: self.this.append(this)
1507  except: self.this = this
1508  def __str__(self):
1509  """__str__(ChiSquaredScore self) -> std::string"""
1510  return _IMP_em2d.ChiSquaredScore___str__(self)
1511 
1512  def __repr__(self):
1513  """__repr__(ChiSquaredScore self) -> std::string"""
1514  return _IMP_em2d.ChiSquaredScore___repr__(self)
1515 
1516  def get_from(o):
1517  return _object_cast_to_ChiSquaredScore(o)
1518  get_from = staticmethod(get_from)
1519 
1520  __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1521  __del__ = lambda self : None;
1522 ChiSquaredScore_swigregister = _IMP_em2d.ChiSquaredScore_swigregister
1523 ChiSquaredScore_swigregister(ChiSquaredScore)
1524 
1525 class EM2DScore(ScoreFunction):
1526  """Proxy of C++ IMP::em2d::EM2DScore class"""
1527  __swig_setmethods__ = {}
1528  for _s in [ScoreFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1529  __setattr__ = lambda self, name, value: _swig_setattr(self, EM2DScore, name, value)
1530  __swig_getmethods__ = {}
1531  for _s in [ScoreFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1532  __getattr__ = lambda self, name: _swig_getattr(self, EM2DScore, name)
1533  def __init__(self):
1534  """__init__(IMP::em2d::EM2DScore self) -> EM2DScore"""
1535  this = _IMP_em2d.new_EM2DScore()
1536  try: self.this.append(this)
1537  except: self.this = this
1538  def __str__(self):
1539  """__str__(EM2DScore self) -> std::string"""
1540  return _IMP_em2d.EM2DScore___str__(self)
1541 
1542  def __repr__(self):
1543  """__repr__(EM2DScore self) -> std::string"""
1544  return _IMP_em2d.EM2DScore___repr__(self)
1545 
1546  def get_from(o):
1547  return _object_cast_to_EM2DScore(o)
1548  get_from = staticmethod(get_from)
1549 
1550  __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1551  __del__ = lambda self : None;
1552 EM2DScore_swigregister = _IMP_em2d.EM2DScore_swigregister
1553 EM2DScore_swigregister(EM2DScore)
1554 
1555 class MeanAbsoluteDifference(ScoreFunction):
1556  """Proxy of C++ IMP::em2d::MeanAbsoluteDifference class"""
1557  __swig_setmethods__ = {}
1558  for _s in [ScoreFunction]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1559  __setattr__ = lambda self, name, value: _swig_setattr(self, MeanAbsoluteDifference, name, value)
1560  __swig_getmethods__ = {}
1561  for _s in [ScoreFunction]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1562  __getattr__ = lambda self, name: _swig_getattr(self, MeanAbsoluteDifference, name)
1563  def __init__(self):
1564  """__init__(IMP::em2d::MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1565  this = _IMP_em2d.new_MeanAbsoluteDifference()
1566  try: self.this.append(this)
1567  except: self.this = this
1568  def __str__(self):
1569  """__str__(MeanAbsoluteDifference self) -> std::string"""
1570  return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1571 
1572  def __repr__(self):
1573  """__repr__(MeanAbsoluteDifference self) -> std::string"""
1574  return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1575 
1576  def get_from(o):
1577  return _object_cast_to_MeanAbsoluteDifference(o)
1578  get_from = staticmethod(get_from)
1579 
1580  __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1581  __del__ = lambda self : None;
1582 MeanAbsoluteDifference_swigregister = _IMP_em2d.MeanAbsoluteDifference_swigregister
1583 MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1584 
1585 
1586 def read_selection_file(*args):
1587  """read_selection_file(IMP::String fn) -> IMP::Strings"""
1588  return _IMP_em2d.read_selection_file(*args)
1589 
1590 def create_filenames(*args):
1591  """create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1592  return _IMP_em2d.create_filenames(*args)
1593 class ProjectionParameters(IMP.kernel.Decorator):
1594  """Proxy of C++ IMP::em2d::ProjectionParameters class"""
1595  __swig_setmethods__ = {}
1596  for _s in [IMP.kernel.Decorator]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1597  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionParameters, name, value)
1598  __swig_getmethods__ = {}
1599  for _s in [IMP.kernel.Decorator]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1600  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionParameters, name)
1601  def __init__(self, *args):
1602  """
1603  __init__(IMP::em2d::ProjectionParameters self) -> ProjectionParameters
1604  __init__(IMP::em2d::ProjectionParameters self, Model m, ::IMP::kernel::ParticleIndex id) -> ProjectionParameters
1605  __init__(IMP::em2d::ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1606  """
1607  this = _IMP_em2d.new_ProjectionParameters(*args)
1608  try: self.this.append(this)
1609  except: self.this = this
1610  def show(self, *args):
1611  """
1612  show(ProjectionParameters self, _ostream out=std::cout)
1613  show(ProjectionParameters self)
1614  """
1615  return _IMP_em2d.ProjectionParameters_show(self, *args)
1616 
1617  def setup_particle(*args):
1618  """
1619  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> ProjectionParameters
1620  setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1621  """
1622  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1623 
1624  if _newclass:setup_particle = staticmethod(setup_particle)
1625  __swig_getmethods__["setup_particle"] = lambda x: setup_particle
1626  __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1627  __del__ = lambda self : None;
1628  def get_keys():
1629  """get_keys() -> IMP::kernel::FloatKeys const &"""
1630  return _IMP_em2d.ProjectionParameters_get_keys()
1631 
1632  if _newclass:get_keys = staticmethod(get_keys)
1633  __swig_getmethods__["get_keys"] = lambda x: get_keys
1634  def set_proper_ranges_for_keys(self, *args):
1635  """set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1636  return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, *args)
1637 
1638  def get_is_setup(*args):
1639  """
1640  get_is_setup(_ParticleAdaptor p) -> bool
1641  get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1642  """
1643  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1644 
1645  if _newclass:get_is_setup = staticmethod(get_is_setup)
1646  __swig_getmethods__["get_is_setup"] = lambda x: get_is_setup
1647  def get_parameters_optimized(self):
1648  """get_parameters_optimized(ProjectionParameters self) -> bool"""
1649  return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1650 
1651  def get_translation(self):
1652  """get_translation(ProjectionParameters self) -> Vector3D"""
1653  return _IMP_em2d.ProjectionParameters_get_translation(self)
1654 
1655  def set_translation(self, *args):
1656  """set_translation(ProjectionParameters self, Vector3D v)"""
1657  return _IMP_em2d.ProjectionParameters_set_translation(self, *args)
1658 
1659  def get_rotation(self):
1660  """get_rotation(ProjectionParameters self) -> Rotation3D"""
1661  return _IMP_em2d.ProjectionParameters_get_rotation(self)
1662 
1663  def set_rotation(self, *args):
1664  """set_rotation(ProjectionParameters self, Rotation3D R)"""
1665  return _IMP_em2d.ProjectionParameters_set_rotation(self, *args)
1666 
1667  def set_parameters_optimized(self, *args):
1668  """set_parameters_optimized(ProjectionParameters self, bool tf)"""
1669  return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, *args)
1670 
1671  def get_quaternion_1(self):
1672  """get_quaternion_1(ProjectionParameters self) -> double"""
1673  return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1674 
1675  def set_quaternion_1(self, *args):
1676  """set_quaternion_1(ProjectionParameters self, double t)"""
1677  return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, *args)
1678 
1679  def get_quaternion_2(self):
1680  """get_quaternion_2(ProjectionParameters self) -> double"""
1681  return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1682 
1683  def set_quaternion_2(self, *args):
1684  """set_quaternion_2(ProjectionParameters self, double t)"""
1685  return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, *args)
1686 
1687  def get_quaternion_3(self):
1688  """get_quaternion_3(ProjectionParameters self) -> double"""
1689  return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1690 
1691  def set_quaternion_3(self, *args):
1692  """set_quaternion_3(ProjectionParameters self, double t)"""
1693  return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, *args)
1694 
1695  def get_quaternion_4(self):
1696  """get_quaternion_4(ProjectionParameters self) -> double"""
1697  return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1698 
1699  def set_quaternion_4(self, *args):
1700  """set_quaternion_4(ProjectionParameters self, double t)"""
1701  return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, *args)
1702 
1703  def get_translation_x(self):
1704  """get_translation_x(ProjectionParameters self) -> double"""
1705  return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1706 
1707  def set_translation_x(self, *args):
1708  """set_translation_x(ProjectionParameters self, double t)"""
1709  return _IMP_em2d.ProjectionParameters_set_translation_x(self, *args)
1710 
1711  def get_translation_y(self):
1712  """get_translation_y(ProjectionParameters self) -> double"""
1713  return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1714 
1715  def set_translation_y(self, *args):
1716  """set_translation_y(ProjectionParameters self, double t)"""
1717  return _IMP_em2d.ProjectionParameters_set_translation_y(self, *args)
1718 
1719  def add_attribute(self, *args):
1720  """
1721  add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1722  add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1723  add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1724  add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1725  add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1726  add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1727  """
1728  return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1729 
1730  def get_value(self, *args):
1731  """
1732  get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1733  get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1734  get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1735  get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1736  get_value(ProjectionParameters self, ObjectKey a0) -> Object
1737  """
1738  return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1739 
1740  def set_value(self, *args):
1741  """
1742  set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1743  set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1744  set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1745  set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1746  set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1747  """
1748  return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1749 
1750  def remove_attribute(self, *args):
1751  """
1752  remove_attribute(ProjectionParameters self, FloatKey a0)
1753  remove_attribute(ProjectionParameters self, IntKey a0)
1754  remove_attribute(ProjectionParameters self, StringKey a0)
1755  remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1756  remove_attribute(ProjectionParameters self, ObjectKey a0)
1757  """
1758  return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1759 
1760  def has_attribute(self, *args):
1761  """
1762  has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1763  has_attribute(ProjectionParameters self, IntKey a0) -> bool
1764  has_attribute(ProjectionParameters self, StringKey a0) -> bool
1765  has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
1766  has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
1767  """
1768  return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
1769 
1770  def get_derivative(self, *args):
1771  """get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
1772  return _IMP_em2d.ProjectionParameters_get_derivative(self, *args)
1773 
1774  def get_name(self):
1775  """get_name(ProjectionParameters self) -> std::string"""
1776  return _IMP_em2d.ProjectionParameters_get_name(self)
1777 
1778  def clear_caches(self):
1779  """clear_caches(ProjectionParameters self)"""
1780  return _IMP_em2d.ProjectionParameters_clear_caches(self)
1781 
1782  def set_name(self, *args):
1783  """set_name(ProjectionParameters self, std::string a0)"""
1784  return _IMP_em2d.ProjectionParameters_set_name(self, *args)
1785 
1786  def set_check_level(self, *args):
1787  """set_check_level(ProjectionParameters self, IMP::base::CheckLevel a0)"""
1788  return _IMP_em2d.ProjectionParameters_set_check_level(self, *args)
1789 
1790  def add_to_derivative(self, *args):
1791  """add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1792  return _IMP_em2d.ProjectionParameters_add_to_derivative(self, *args)
1793 
1794  def set_is_optimized(self, *args):
1795  """set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
1796  return _IMP_em2d.ProjectionParameters_set_is_optimized(self, *args)
1797 
1798  def get_is_optimized(self, *args):
1799  """get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
1800  return _IMP_em2d.ProjectionParameters_get_is_optimized(self, *args)
1801 
1802  def get_check_level(self):
1803  """get_check_level(ProjectionParameters self) -> IMP::base::CheckLevel"""
1804  return _IMP_em2d.ProjectionParameters_get_check_level(self)
1805 
1806  def __eq__(self, *args):
1807  """
1808  __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
1809  __eq__(ProjectionParameters self, Particle d) -> bool
1810  """
1811  return _IMP_em2d.ProjectionParameters___eq__(self, *args)
1812 
1813  def __ne__(self, *args):
1814  """
1815  __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
1816  __ne__(ProjectionParameters self, Particle d) -> bool
1817  """
1818  return _IMP_em2d.ProjectionParameters___ne__(self, *args)
1819 
1820  def __le__(self, *args):
1821  """
1822  __le__(ProjectionParameters self, ProjectionParameters o) -> bool
1823  __le__(ProjectionParameters self, Particle d) -> bool
1824  """
1825  return _IMP_em2d.ProjectionParameters___le__(self, *args)
1826 
1827  def __lt__(self, *args):
1828  """
1829  __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
1830  __lt__(ProjectionParameters self, Particle d) -> bool
1831  """
1832  return _IMP_em2d.ProjectionParameters___lt__(self, *args)
1833 
1834  def __ge__(self, *args):
1835  """
1836  __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
1837  __ge__(ProjectionParameters self, Particle d) -> bool
1838  """
1839  return _IMP_em2d.ProjectionParameters___ge__(self, *args)
1840 
1841  def __gt__(self, *args):
1842  """
1843  __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
1844  __gt__(ProjectionParameters self, Particle d) -> bool
1845  """
1846  return _IMP_em2d.ProjectionParameters___gt__(self, *args)
1847 
1848  def __str__(self):
1849  """__str__(ProjectionParameters self) -> std::string"""
1850  return _IMP_em2d.ProjectionParameters___str__(self)
1851 
1852  def __repr__(self):
1853  """__repr__(ProjectionParameters self) -> std::string"""
1854  return _IMP_em2d.ProjectionParameters___repr__(self)
1855 
1856 ProjectionParameters_swigregister = _IMP_em2d.ProjectionParameters_swigregister
1857 ProjectionParameters_swigregister(ProjectionParameters)
1858 
1859 def ProjectionParameters_setup_particle(*args):
1860  """
1861  setup_particle(Model m, IMP::kernel::ParticleIndex pi) -> ProjectionParameters
1862  ProjectionParameters_setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1863  """
1864  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1865 
1866 def ProjectionParameters_get_keys():
1867  """ProjectionParameters_get_keys() -> IMP::kernel::FloatKeys const &"""
1868  return _IMP_em2d.ProjectionParameters_get_keys()
1869 
1870 def ProjectionParameters_get_is_setup(*args):
1871  """
1872  get_is_setup(_ParticleAdaptor p) -> bool
1873  ProjectionParameters_get_is_setup(Model m, IMP::kernel::ParticleIndex pi) -> bool
1874  """
1875  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1876 
1877 
1878 def __lshift__(*args):
1879  """__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
1880  return _IMP_em2d.__lshift__(*args)
1881 class ProjectionParametersScoreState(IMP.kernel.ScoreState):
1882  """Proxy of C++ IMP::em2d::ProjectionParametersScoreState class"""
1883  __swig_setmethods__ = {}
1884  for _s in [IMP.kernel.ScoreState]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
1885  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionParametersScoreState, name, value)
1886  __swig_getmethods__ = {}
1887  for _s in [IMP.kernel.ScoreState]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
1888  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionParametersScoreState, name)
1889  def __init__(self, *args):
1890  """__init__(IMP::em2d::ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
1891  this = _IMP_em2d.new_ProjectionParametersScoreState(*args)
1892  try: self.this.append(this)
1893  except: self.this = this
1894  def do_before_evaluate(self):
1895  """do_before_evaluate(ProjectionParametersScoreState self)"""
1896  return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
1897 
1898  def do_after_evaluate(self, *args):
1899  """do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
1900  return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, *args)
1901 
1902  def do_get_inputs(self):
1903  """do_get_inputs(ProjectionParametersScoreState self) -> IMP::kernel::ModelObjectsTemp"""
1904  return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
1905 
1906  def do_get_outputs(self):
1907  """do_get_outputs(ProjectionParametersScoreState self) -> IMP::kernel::ModelObjectsTemp"""
1908  return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
1909 
1910  def get_version_info(self):
1911  """get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
1912  return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
1913 
1914  def __str__(self):
1915  """__str__(ProjectionParametersScoreState self) -> std::string"""
1916  return _IMP_em2d.ProjectionParametersScoreState___str__(self)
1917 
1918  def __repr__(self):
1919  """__repr__(ProjectionParametersScoreState self) -> std::string"""
1920  return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
1921 
1922  def get_from(o):
1923  return _object_cast_to_ProjectionParametersScoreState(o)
1924  get_from = staticmethod(get_from)
1925 
1926 ProjectionParametersScoreState_swigregister = _IMP_em2d.ProjectionParametersScoreState_swigregister
1927 ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
1928 
1929 class ProjectionMask(_object):
1930  """Proxy of C++ IMP::em2d::ProjectionMask class"""
1931  __swig_setmethods__ = {}
1932  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionMask, name, value)
1933  __swig_getmethods__ = {}
1934  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionMask, name)
1935  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
1936  def apply(self, *args):
1937  """apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
1938  return _IMP_em2d.ProjectionMask_apply(self, *args)
1939 
1940  def show(self, *args):
1941  """
1942  show(ProjectionMask self, _ostream out=std::cout)
1943  show(ProjectionMask self)
1944  """
1945  return _IMP_em2d.ProjectionMask_show(self, *args)
1946 
1947  __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
1948  __del__ = lambda self : None;
1949  def __str__(self):
1950  """__str__(ProjectionMask self) -> std::string"""
1951  return _IMP_em2d.ProjectionMask___str__(self)
1952 
1953  def __repr__(self):
1954  """__repr__(ProjectionMask self) -> std::string"""
1955  return _IMP_em2d.ProjectionMask___repr__(self)
1956 
1957 ProjectionMask_swigregister = _IMP_em2d.ProjectionMask_swigregister
1958 ProjectionMask_swigregister(ProjectionMask)
1959 
1960 
1961 def do_place(*args):
1962  """do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
1963  return _IMP_em2d.do_place(*args)
1964 class MasksManager(_object):
1965  """Proxy of C++ IMP::em2d::MasksManager class"""
1966  __swig_setmethods__ = {}
1967  __setattr__ = lambda self, name, value: _swig_setattr(self, MasksManager, name, value)
1968  __swig_getmethods__ = {}
1969  __getattr__ = lambda self, name: _swig_getattr(self, MasksManager, name)
1970  def __init__(self, *args):
1971  """
1972  __init__(IMP::em2d::MasksManager self) -> MasksManager
1973  __init__(IMP::em2d::MasksManager self, double resolution, double pixelsize) -> MasksManager
1974  """
1975  this = _IMP_em2d.new_MasksManager(*args)
1976  try: self.this.append(this)
1977  except: self.this = this
1978  def setup_kernel(self, *args):
1979  """setup_kernel(MasksManager self, double resolution, double pixelsize)"""
1980  return _IMP_em2d.MasksManager_setup_kernel(self, *args)
1981 
1982  def create_masks(self, *args):
1983  """create_masks(MasksManager self, IMP::kernel::ParticlesTemp const & ps)"""
1984  return _IMP_em2d.MasksManager_create_masks(self, *args)
1985 
1986  def create_mask(self, *args):
1987  """create_mask(MasksManager self, double radius, double mass)"""
1988  return _IMP_em2d.MasksManager_create_mask(self, *args)
1989 
1990  def find_mask(self, *args):
1991  """find_mask(MasksManager self, double radius) -> IMP::em2d::ProjectionMaskPtr"""
1992  return _IMP_em2d.MasksManager_find_mask(self, *args)
1993 
1994  def show(self, *args):
1995  """
1996  show(MasksManager self, _ostream out=std::cout)
1997  show(MasksManager self)
1998  """
1999  return _IMP_em2d.MasksManager_show(self, *args)
2000 
2001  def get_number_of_masks(self):
2002  """get_number_of_masks(MasksManager self) -> unsigned int"""
2003  return _IMP_em2d.MasksManager_get_number_of_masks(self)
2004 
2005  __swig_destroy__ = _IMP_em2d.delete_MasksManager
2006  __del__ = lambda self : None;
2007  def __str__(self):
2008  """__str__(MasksManager self) -> std::string"""
2009  return _IMP_em2d.MasksManager___str__(self)
2010 
2011  def __repr__(self):
2012  """__repr__(MasksManager self) -> std::string"""
2013  return _IMP_em2d.MasksManager___repr__(self)
2014 
2015 MasksManager_swigregister = _IMP_em2d.MasksManager_swigregister
2016 MasksManager_swigregister(MasksManager)
2017 
2018 class ProjectingParameters(_object):
2019  """Proxy of C++ IMP::em2d::ProjectingParameters class"""
2020  __swig_setmethods__ = {}
2021  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectingParameters, name, value)
2022  __swig_getmethods__ = {}
2023  __getattr__ = lambda self, name: _swig_getattr(self, ProjectingParameters, name)
2024  __swig_setmethods__["pixel_size"] = _IMP_em2d.ProjectingParameters_pixel_size_set
2025  __swig_getmethods__["pixel_size"] = _IMP_em2d.ProjectingParameters_pixel_size_get
2026  if _newclass:pixel_size = _swig_property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set)
2027  __swig_setmethods__["resolution"] = _IMP_em2d.ProjectingParameters_resolution_set
2028  __swig_getmethods__["resolution"] = _IMP_em2d.ProjectingParameters_resolution_get
2029  if _newclass:resolution = _swig_property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set)
2030  def __init__(self, *args):
2031  """
2032  __init__(IMP::em2d::ProjectingParameters self) -> ProjectingParameters
2033  __init__(IMP::em2d::ProjectingParameters self, double ps, double res) -> ProjectingParameters
2034  """
2035  this = _IMP_em2d.new_ProjectingParameters(*args)
2036  try: self.this.append(this)
2037  except: self.this = this
2038  def show(self, *args):
2039  """
2040  show(ProjectingParameters self, _ostream out=std::cout)
2041  show(ProjectingParameters self)
2042  """
2043  return _IMP_em2d.ProjectingParameters_show(self, *args)
2044 
2045  def __str__(self):
2046  """__str__(ProjectingParameters self) -> std::string"""
2047  return _IMP_em2d.ProjectingParameters___str__(self)
2048 
2049  def __repr__(self):
2050  """__repr__(ProjectingParameters self) -> std::string"""
2051  return _IMP_em2d.ProjectingParameters___repr__(self)
2052 
2053  __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2054  __del__ = lambda self : None;
2055 ProjectingParameters_swigregister = _IMP_em2d.ProjectingParameters_swigregister
2056 ProjectingParameters_swigregister(ProjectingParameters)
2057 
2058 class ProjectingOptions(ProjectingParameters):
2059  """Proxy of C++ IMP::em2d::ProjectingOptions class"""
2060  __swig_setmethods__ = {}
2061  for _s in [ProjectingParameters]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2062  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectingOptions, name, value)
2063  __swig_getmethods__ = {}
2064  for _s in [ProjectingParameters]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2065  __getattr__ = lambda self, name: _swig_getattr(self, ProjectingOptions, name)
2066  __swig_setmethods__["save_images"] = _IMP_em2d.ProjectingOptions_save_images_set
2067  __swig_getmethods__["save_images"] = _IMP_em2d.ProjectingOptions_save_images_get
2068  if _newclass:save_images = _swig_property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set)
2069  __swig_setmethods__["normalize"] = _IMP_em2d.ProjectingOptions_normalize_set
2070  __swig_getmethods__["normalize"] = _IMP_em2d.ProjectingOptions_normalize_get
2071  if _newclass:normalize = _swig_property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set)
2072  __swig_setmethods__["clear_matrix_before_projecting"] = _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set
2073  __swig_getmethods__["clear_matrix_before_projecting"] = _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get
2074  if _newclass:clear_matrix_before_projecting = _swig_property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set)
2075  def __init__(self, *args):
2076  """
2077  __init__(IMP::em2d::ProjectingOptions self) -> ProjectingOptions
2078  __init__(IMP::em2d::ProjectingOptions self, double ps, double res) -> ProjectingOptions
2079  __init__(IMP::em2d::ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2080  """
2081  this = _IMP_em2d.new_ProjectingOptions(*args)
2082  try: self.this.append(this)
2083  except: self.this = this
2084  def show(self, *args):
2085  """
2086  show(ProjectingOptions self, _ostream out=std::cout)
2087  show(ProjectingOptions self)
2088  """
2089  return _IMP_em2d.ProjectingOptions_show(self, *args)
2090 
2091  def __str__(self):
2092  """__str__(ProjectingOptions self) -> std::string"""
2093  return _IMP_em2d.ProjectingOptions___str__(self)
2094 
2095  def __repr__(self):
2096  """__repr__(ProjectingOptions self) -> std::string"""
2097  return _IMP_em2d.ProjectingOptions___repr__(self)
2098 
2099  __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2100  __del__ = lambda self : None;
2101 ProjectingOptions_swigregister = _IMP_em2d.ProjectingOptions_swigregister
2102 ProjectingOptions_swigregister(ProjectingOptions)
2103 
2104 
2105 def get_projections(*args):
2106  """
2107  get_projections(IMP::kernel::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs,
2108  int rows, int cols, ProjectingOptions options, IMP::Strings names=IMP::Strings()) -> IMP::em2d::Images
2109  get_projections(IMP::kernel::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs,
2110  int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2111  get_projections(IMP::kernel::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values,
2112  int rows, int cols, ProjectingOptions options, IMP::Strings names=IMP::Strings()) -> IMP::em2d::Images
2113  get_projections(IMP::kernel::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values,
2114  int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2115  """
2116  return _IMP_em2d.get_projections(*args)
2117 
2118 def get_projection(*args):
2119  """
2120  get_projection(Image img, IMP::kernel::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options,
2121  IMP::em2d::MasksManagerPtr masks=IMP::em2d::MasksManagerPtr(),
2122  IMP::String name="")
2123  get_projection(Image img, IMP::kernel::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options,
2124  IMP::em2d::MasksManagerPtr masks=IMP::em2d::MasksManagerPtr())
2125  get_projection(Image img, IMP::kernel::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options)
2126  """
2127  return _IMP_em2d.get_projection(*args)
2128 
2129 def do_project_particles(*args):
2130  """
2131  do_project_particles(IMP::kernel::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation,
2132  ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)
2133  """
2134  return _IMP_em2d.do_project_particles(*args)
2135 
2137  """create_evenly_distributed_projections(IMP::kernel::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2138  return _IMP_em2d.create_evenly_distributed_projections(*args)
2139 
2140 def do_project_vectors(*args):
2141  """
2142  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2143  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2144  """
2145  return _IMP_em2d.do_project_vectors(*args)
2146 
2147 def get_enclosing_image_size(*args):
2148  """get_enclosing_image_size(IMP::kernel::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2149  return _IMP_em2d.get_enclosing_image_size(*args)
2150 
2151 def get_complete_alignment(*args):
2152  """
2153  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2154  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2155  """
2156  return _IMP_em2d.get_complete_alignment(*args)
2157 
2158 def get_rotational_alignment(*args):
2159  """
2160  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2161  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2162  """
2163  return _IMP_em2d.get_rotational_alignment(*args)
2164 
2165 def get_translational_alignment(*args):
2166  """
2167  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2168  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2169  """
2170  return _IMP_em2d.get_translational_alignment(*args)
2171 
2173  """
2174  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align,
2175  cv::Mat const & POLAR2, bool apply=False) -> ResultAlign2D
2176  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align,
2177  cv::Mat const & POLAR2) -> ResultAlign2D
2178  """
2179  return _IMP_em2d.get_complete_alignment_no_preprocessing(*args)
2180 
2182  """get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2183  return _IMP_em2d.get_rotational_alignment_no_preprocessing(*args)
2184 
2186  """get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2187  return _IMP_em2d.get_translational_alignment_no_preprocessing(*args)
2188 
2190  """get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2191  return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(*args)
2192 
2193 def write_vectors_as_pdb(*args):
2194  """
2195  write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2196  write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2197  """
2198  return _IMP_em2d.write_vectors_as_pdb(*args)
2199 class Em2DRestraintParameters(ProjectingParameters):
2200  """Proxy of C++ IMP::em2d::Em2DRestraintParameters class"""
2201  __swig_setmethods__ = {}
2202  for _s in [ProjectingParameters]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2203  __setattr__ = lambda self, name, value: _swig_setattr(self, Em2DRestraintParameters, name, value)
2204  __swig_getmethods__ = {}
2205  for _s in [ProjectingParameters]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2206  __getattr__ = lambda self, name: _swig_getattr(self, Em2DRestraintParameters, name)
2207  __swig_setmethods__["n_projections"] = _IMP_em2d.Em2DRestraintParameters_n_projections_set
2208  __swig_getmethods__["n_projections"] = _IMP_em2d.Em2DRestraintParameters_n_projections_get
2209  if _newclass:n_projections = _swig_property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set)
2210  __swig_setmethods__["coarse_registration_method"] = _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set
2211  __swig_getmethods__["coarse_registration_method"] = _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get
2212  if _newclass:coarse_registration_method = _swig_property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set)
2213  __swig_setmethods__["save_match_images"] = _IMP_em2d.Em2DRestraintParameters_save_match_images_set
2214  __swig_getmethods__["save_match_images"] = _IMP_em2d.Em2DRestraintParameters_save_match_images_get
2215  if _newclass:save_match_images = _swig_property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set)
2216  __swig_setmethods__["optimization_steps"] = _IMP_em2d.Em2DRestraintParameters_optimization_steps_set
2217  __swig_getmethods__["optimization_steps"] = _IMP_em2d.Em2DRestraintParameters_optimization_steps_get
2218  if _newclass:optimization_steps = _swig_property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set)
2219  __swig_setmethods__["simplex_initial_length"] = _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set
2220  __swig_getmethods__["simplex_initial_length"] = _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get
2221  if _newclass:simplex_initial_length = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set)
2222  __swig_setmethods__["simplex_minimum_size"] = _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set
2223  __swig_getmethods__["simplex_minimum_size"] = _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get
2224  if _newclass:simplex_minimum_size = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set)
2225  def __init__(self, *args):
2226  """
2227  __init__(IMP::em2d::Em2DRestraintParameters self) -> Em2DRestraintParameters
2228  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2229  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res) -> Em2DRestraintParameters
2230  """
2231  this = _IMP_em2d.new_Em2DRestraintParameters(*args)
2232  try: self.this.append(this)
2233  except: self.this = this
2234  def show(self, *args):
2235  """
2236  show(Em2DRestraintParameters self, _ostream out=std::cout)
2237  show(Em2DRestraintParameters self)
2238  """
2239  return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2240 
2241  def __str__(self):
2242  """__str__(Em2DRestraintParameters self) -> std::string"""
2243  return _IMP_em2d.Em2DRestraintParameters___str__(self)
2244 
2245  def __repr__(self):
2246  """__repr__(Em2DRestraintParameters self) -> std::string"""
2247  return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2248 
2249  __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2250  __del__ = lambda self : None;
2251 Em2DRestraintParameters_swigregister = _IMP_em2d.Em2DRestraintParameters_swigregister
2252 Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2253 cvar = _IMP_em2d.cvar
2254 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2255 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2256 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2257 
2258 class ProjectionFinder(IMP.base.Object):
2259  """Proxy of C++ IMP::em2d::ProjectionFinder class"""
2260  __swig_setmethods__ = {}
2261  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2262  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionFinder, name, value)
2263  __swig_getmethods__ = {}
2264  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2265  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionFinder, name)
2266  def __init__(self):
2267  """__init__(IMP::em2d::ProjectionFinder self) -> ProjectionFinder"""
2268  this = _IMP_em2d.new_ProjectionFinder()
2269  try: self.this.append(this)
2270  except: self.this = this
2271  def setup(self, *args):
2272  """setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2273  return _IMP_em2d.ProjectionFinder_setup(self, *args)
2274 
2275  def set_subjects(self, *args):
2276  """set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2277  return _IMP_em2d.ProjectionFinder_set_subjects(self, *args)
2278 
2279  def set_projections(self, *args):
2280  """set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2281  return _IMP_em2d.ProjectionFinder_set_projections(self, *args)
2282 
2283  def set_variance_images(self, *args):
2284  """set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2285  return _IMP_em2d.ProjectionFinder_set_variance_images(self, *args)
2286 
2287  def set_model_particles(self, *args):
2288  """set_model_particles(ProjectionFinder self, IMP::kernel::ParticlesTemp const & ps)"""
2289  return _IMP_em2d.ProjectionFinder_set_model_particles(self, *args)
2290 
2291  def set_save_match_images(self, *args):
2292  """set_save_match_images(ProjectionFinder self, bool x)"""
2293  return _IMP_em2d.ProjectionFinder_set_save_match_images(self, *args)
2294 
2295  def get_save_match_images(self):
2296  """get_save_match_images(ProjectionFinder self) -> bool"""
2297  return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2298 
2299  def set_fast_mode(self, *args):
2300  """set_fast_mode(ProjectionFinder self, unsigned int n)"""
2301  return _IMP_em2d.ProjectionFinder_set_fast_mode(self, *args)
2302 
2303  def get_registration_results(self):
2304  """get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2305  return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2306 
2307  def get_coarse_registration(self):
2308  """get_coarse_registration(ProjectionFinder self)"""
2309  return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2310 
2311  def get_complete_registration(self):
2312  """get_complete_registration(ProjectionFinder self)"""
2313  return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2314 
2315  def get_global_score(self):
2316  """get_global_score(ProjectionFinder self) -> double"""
2317  return _IMP_em2d.ProjectionFinder_get_global_score(self)
2318 
2319  def show(self, *args):
2320  """show(ProjectionFinder self, _ostream out)"""
2321  return _IMP_em2d.ProjectionFinder_show(self, *args)
2322 
2323  def get_preprocessing_time(self):
2324  """get_preprocessing_time(ProjectionFinder self) -> double"""
2325  return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2326 
2327  def get_coarse_registration_time(self):
2328  """get_coarse_registration_time(ProjectionFinder self) -> double"""
2329  return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2330 
2331  def get_fine_registration_time(self):
2332  """get_fine_registration_time(ProjectionFinder self) -> double"""
2333  return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2334 
2335  def get_number_of_subjects(self):
2336  """get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2337  return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2338 
2339  def set_number_of_class_averages_members(self, *args):
2340  """set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2341  return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, *args)
2342 
2343  def get_number_of_projections(self):
2344  """get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2345  return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2346 
2347  def get_version_info(self):
2348  """get_version_info(ProjectionFinder self) -> VersionInfo"""
2349  return _IMP_em2d.ProjectionFinder_get_version_info(self)
2350 
2351  def __str__(self):
2352  """__str__(ProjectionFinder self) -> std::string"""
2353  return _IMP_em2d.ProjectionFinder___str__(self)
2354 
2355  def __repr__(self):
2356  """__repr__(ProjectionFinder self) -> std::string"""
2357  return _IMP_em2d.ProjectionFinder___repr__(self)
2358 
2359  def get_from(o):
2360  return _object_cast_to_ProjectionFinder(o)
2361  get_from = staticmethod(get_from)
2362 
2363 ProjectionFinder_swigregister = _IMP_em2d.ProjectionFinder_swigregister
2364 ProjectionFinder_swigregister(ProjectionFinder)
2365 
2366 class Em2DRestraint(IMP.kernel.Restraint):
2367  """Proxy of C++ IMP::em2d::Em2DRestraint class"""
2368  __swig_setmethods__ = {}
2369  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2370  __setattr__ = lambda self, name, value: _swig_setattr(self, Em2DRestraint, name, value)
2371  __swig_getmethods__ = {}
2372  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2373  __getattr__ = lambda self, name: _swig_getattr(self, Em2DRestraint, name)
2374  def __init__(self, *args):
2375  """__init__(IMP::em2d::Em2DRestraint self, Model m) -> Em2DRestraint"""
2376  this = _IMP_em2d.new_Em2DRestraint(*args)
2377  try: self.this.append(this)
2378  except: self.this = this
2379  def setup(self, *args):
2380  """setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2381  return _IMP_em2d.Em2DRestraint_setup(self, *args)
2382 
2383  def set_particles(self, *args):
2384  """set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2385  return _IMP_em2d.Em2DRestraint_set_particles(self, *args)
2386 
2387  def set_images(self, *args):
2388  """set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2389  return _IMP_em2d.Em2DRestraint_set_images(self, *args)
2390 
2391  def set_variance_images(self, *args):
2392  """set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2393  return _IMP_em2d.Em2DRestraint_set_variance_images(self, *args)
2394 
2395  def set_fast_mode(self, *args):
2396  """set_fast_mode(Em2DRestraint self, unsigned int n)"""
2397  return _IMP_em2d.Em2DRestraint_set_fast_mode(self, *args)
2398 
2399  def set_coarse_registration_mode(self, *args):
2400  """set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2401  return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, *args)
2402 
2403  def get_registration_results(self):
2404  """get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2405  return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2406 
2407  def do_get_inputs(self):
2408  """do_get_inputs(Em2DRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2409  return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2410 
2411  def get_version_info(self):
2412  """get_version_info(Em2DRestraint self) -> VersionInfo"""
2413  return _IMP_em2d.Em2DRestraint_get_version_info(self)
2414 
2415  def __str__(self):
2416  """__str__(Em2DRestraint self) -> std::string"""
2417  return _IMP_em2d.Em2DRestraint___str__(self)
2418 
2419  def __repr__(self):
2420  """__repr__(Em2DRestraint self) -> std::string"""
2421  return _IMP_em2d.Em2DRestraint___repr__(self)
2422 
2423  def get_from(o):
2424  return _object_cast_to_Em2DRestraint(o)
2425  get_from = staticmethod(get_from)
2426 
2427 Em2DRestraint_swigregister = _IMP_em2d.Em2DRestraint_swigregister
2428 Em2DRestraint_swigregister(Em2DRestraint)
2429 
2430 class ClusterSet(_object):
2431  """Proxy of C++ IMP::em2d::ClusterSet class"""
2432  __swig_setmethods__ = {}
2433  __setattr__ = lambda self, name, value: _swig_setattr(self, ClusterSet, name, value)
2434  __swig_getmethods__ = {}
2435  __getattr__ = lambda self, name: _swig_getattr(self, ClusterSet, name)
2436  def __init__(self, *args):
2437  """__init__(IMP::em2d::ClusterSet self, unsigned int N) -> ClusterSet"""
2438  this = _IMP_em2d.new_ClusterSet(*args)
2439  try: self.this.append(this)
2440  except: self.this = this
2441  def do_join_clusters(self, *args):
2442  """do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2443  return _IMP_em2d.ClusterSet_do_join_clusters(self, *args)
2444 
2445  def get_cluster_elements(self, *args):
2446  """get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2447  return _IMP_em2d.ClusterSet_get_cluster_elements(self, *args)
2448 
2449  def get_clusters_below_cutoff(self, *args):
2450  """get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2451  return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, *args)
2452 
2453  def get_cluster_formed_at_step(self, *args):
2454  """get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2455  return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, *args)
2456 
2457  def get_distance_at_step(self, *args):
2458  """get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2459  return _IMP_em2d.ClusterSet_get_distance_at_step(self, *args)
2460 
2461  def get_id_for_cluster_at_step(self, *args):
2462  """get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2463  return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, *args)
2464 
2465  def get_linkage_matrix(self):
2466  """get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2467  return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2468 
2469  def get_linkage_matrix_in_matlab_format(self):
2470  """get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2471  return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2472 
2473  def get_number_of_steps(self):
2474  """get_number_of_steps(ClusterSet self) -> unsigned int"""
2475  return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2476 
2477  def show(self, *args):
2478  """show(ClusterSet self, _ostream out)"""
2479  return _IMP_em2d.ClusterSet_show(self, *args)
2480 
2481  def __str__(self):
2482  """__str__(ClusterSet self) -> std::string"""
2483  return _IMP_em2d.ClusterSet___str__(self)
2484 
2485  def __repr__(self):
2486  """__repr__(ClusterSet self) -> std::string"""
2487  return _IMP_em2d.ClusterSet___repr__(self)
2488 
2489  __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2490  __del__ = lambda self : None;
2491 ClusterSet_swigregister = _IMP_em2d.ClusterSet_swigregister
2492 ClusterSet_swigregister(ClusterSet)
2493 
2494 class SingleLinkage(_object):
2495  """Proxy of C++ IMP::em2d::SingleLinkage class"""
2496  __swig_setmethods__ = {}
2497  __setattr__ = lambda self, name, value: _swig_setattr(self, SingleLinkage, name, value)
2498  __swig_getmethods__ = {}
2499  __getattr__ = lambda self, name: _swig_getattr(self, SingleLinkage, name)
2500  def __init__(self):
2501  """__init__(IMP::em2d::SingleLinkage self) -> SingleLinkage"""
2502  this = _IMP_em2d.new_SingleLinkage()
2503  try: self.this.append(this)
2504  except: self.this = this
2505  def __call__(self, *args):
2506  """__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2507  return _IMP_em2d.SingleLinkage___call__(self, *args)
2508 
2509  def show(self, *args):
2510  """show(SingleLinkage self, _ostream out)"""
2511  return _IMP_em2d.SingleLinkage_show(self, *args)
2512 
2513  def __str__(self):
2514  """__str__(SingleLinkage self) -> std::string"""
2515  return _IMP_em2d.SingleLinkage___str__(self)
2516 
2517  def __repr__(self):
2518  """__repr__(SingleLinkage self) -> std::string"""
2519  return _IMP_em2d.SingleLinkage___repr__(self)
2520 
2521  __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2522  __del__ = lambda self : None;
2523 SingleLinkage_swigregister = _IMP_em2d.SingleLinkage_swigregister
2524 SingleLinkage_swigregister(SingleLinkage)
2525 
2526 class CompleteLinkage(_object):
2527  """Proxy of C++ IMP::em2d::CompleteLinkage class"""
2528  __swig_setmethods__ = {}
2529  __setattr__ = lambda self, name, value: _swig_setattr(self, CompleteLinkage, name, value)
2530  __swig_getmethods__ = {}
2531  __getattr__ = lambda self, name: _swig_getattr(self, CompleteLinkage, name)
2532  def __init__(self):
2533  """__init__(IMP::em2d::CompleteLinkage self) -> CompleteLinkage"""
2534  this = _IMP_em2d.new_CompleteLinkage()
2535  try: self.this.append(this)
2536  except: self.this = this
2537  def __call__(self, *args):
2538  """__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2539  return _IMP_em2d.CompleteLinkage___call__(self, *args)
2540 
2541  def show(self, *args):
2542  """show(CompleteLinkage self, _ostream out)"""
2543  return _IMP_em2d.CompleteLinkage_show(self, *args)
2544 
2545  def __str__(self):
2546  """__str__(CompleteLinkage self) -> std::string"""
2547  return _IMP_em2d.CompleteLinkage___str__(self)
2548 
2549  def __repr__(self):
2550  """__repr__(CompleteLinkage self) -> std::string"""
2551  return _IMP_em2d.CompleteLinkage___repr__(self)
2552 
2553  __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2554  __del__ = lambda self : None;
2555 CompleteLinkage_swigregister = _IMP_em2d.CompleteLinkage_swigregister
2556 CompleteLinkage_swigregister(CompleteLinkage)
2557 
2558 class AverageDistanceLinkage(_object):
2559  """Proxy of C++ IMP::em2d::AverageDistanceLinkage class"""
2560  __swig_setmethods__ = {}
2561  __setattr__ = lambda self, name, value: _swig_setattr(self, AverageDistanceLinkage, name, value)
2562  __swig_getmethods__ = {}
2563  __getattr__ = lambda self, name: _swig_getattr(self, AverageDistanceLinkage, name)
2564  def __init__(self):
2565  """__init__(IMP::em2d::AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2566  this = _IMP_em2d.new_AverageDistanceLinkage()
2567  try: self.this.append(this)
2568  except: self.this = this
2569  def __call__(self, *args):
2570  """__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2571  return _IMP_em2d.AverageDistanceLinkage___call__(self, *args)
2572 
2573  def show(self, *args):
2574  """show(AverageDistanceLinkage self, _ostream out)"""
2575  return _IMP_em2d.AverageDistanceLinkage_show(self, *args)
2576 
2577  def __str__(self):
2578  """__str__(AverageDistanceLinkage self) -> std::string"""
2579  return _IMP_em2d.AverageDistanceLinkage___str__(self)
2580 
2581  def __repr__(self):
2582  """__repr__(AverageDistanceLinkage self) -> std::string"""
2583  return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2584 
2585  __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2586  __del__ = lambda self : None;
2587 AverageDistanceLinkage_swigregister = _IMP_em2d.AverageDistanceLinkage_swigregister
2588 AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2589 
2590 class CollisionCrossSection(IMP.base.Object):
2591  """Proxy of C++ IMP::em2d::CollisionCrossSection class"""
2592  __swig_setmethods__ = {}
2593  for _s in [IMP.base.Object]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2594  __setattr__ = lambda self, name, value: _swig_setattr(self, CollisionCrossSection, name, value)
2595  __swig_getmethods__ = {}
2596  for _s in [IMP.base.Object]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2597  __getattr__ = lambda self, name: _swig_getattr(self, CollisionCrossSection, name)
2598  def __init__(self, *args):
2599  """__init__(IMP::em2d::CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2600  this = _IMP_em2d.new_CollisionCrossSection(*args)
2601  try: self.this.append(this)
2602  except: self.this = this
2603  def set_model_particles(self, *args):
2604  """set_model_particles(CollisionCrossSection self, IMP::kernel::ParticlesTemp const & ps)"""
2605  return _IMP_em2d.CollisionCrossSection_set_model_particles(self, *args)
2606 
2607  def get_ccs(self):
2608  """get_ccs(CollisionCrossSection self) -> double"""
2609  return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2610 
2611  def show(self, *args):
2612  """show(CollisionCrossSection self, _ostream out)"""
2613  return _IMP_em2d.CollisionCrossSection_show(self, *args)
2614 
2615  def get_version_info(self):
2616  """get_version_info(CollisionCrossSection self) -> VersionInfo"""
2617  return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2618 
2619  def __str__(self):
2620  """__str__(CollisionCrossSection self) -> std::string"""
2621  return _IMP_em2d.CollisionCrossSection___str__(self)
2622 
2623  def __repr__(self):
2624  """__repr__(CollisionCrossSection self) -> std::string"""
2625  return _IMP_em2d.CollisionCrossSection___repr__(self)
2626 
2627  def get_from(o):
2628  return _object_cast_to_CollisionCrossSection(o)
2629  get_from = staticmethod(get_from)
2630 
2631 CollisionCrossSection_swigregister = _IMP_em2d.CollisionCrossSection_swigregister
2632 CollisionCrossSection_swigregister(CollisionCrossSection)
2633 
2634 class GridStates(IMP.domino.ParticleStates):
2635  """Proxy of C++ IMP::em2d::GridStates class"""
2636  __swig_setmethods__ = {}
2637  for _s in [IMP.domino.ParticleStates]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2638  __setattr__ = lambda self, name, value: _swig_setattr(self, GridStates, name, value)
2639  __swig_getmethods__ = {}
2640  for _s in [IMP.domino.ParticleStates]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2641  __getattr__ = lambda self, name: _swig_getattr(self, GridStates, name)
2642  def __init__(self, *args):
2643  """
2644  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations,
2645  IMP::String const & name="GridStates") -> GridStates
2646  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations) -> GridStates
2647  """
2648  this = _IMP_em2d.new_GridStates(*args)
2649  try: self.this.append(this)
2650  except: self.this = this
2651  def get_position(self, *args):
2652  """get_position(GridStates self, unsigned int i) -> Vector3D"""
2653  return _IMP_em2d.GridStates_get_position(self, *args)
2654 
2655  def get_orientation(self, *args):
2656  """get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2657  return _IMP_em2d.GridStates_get_orientation(self, *args)
2658 
2659  def get_version_info(self):
2660  """get_version_info(GridStates self) -> VersionInfo"""
2661  return _IMP_em2d.GridStates_get_version_info(self)
2662 
2663  def do_show(self, *args):
2664  """do_show(GridStates self, _ostream out)"""
2665  return _IMP_em2d.GridStates_do_show(self, *args)
2666 
2667  __swig_destroy__ = _IMP_em2d.delete_GridStates
2668  __del__ = lambda self : None;
2669  def __str__(self):
2670  """__str__(GridStates self) -> std::string"""
2671  return _IMP_em2d.GridStates___str__(self)
2672 
2673  def __repr__(self):
2674  """__repr__(GridStates self) -> std::string"""
2675  return _IMP_em2d.GridStates___repr__(self)
2676 
2677  def get_from(o):
2678  return _object_cast_to_GridStates(o)
2679  get_from = staticmethod(get_from)
2680 
2681 GridStates_swigregister = _IMP_em2d.GridStates_swigregister
2682 GridStates_swigregister(GridStates)
2683 
2684 class ProjectionStates(GridStates):
2685  """Proxy of C++ IMP::em2d::ProjectionStates class"""
2686  __swig_setmethods__ = {}
2687  for _s in [GridStates]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2688  __setattr__ = lambda self, name, value: _swig_setattr(self, ProjectionStates, name, value)
2689  __swig_getmethods__ = {}
2690  for _s in [GridStates]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2691  __getattr__ = lambda self, name: _swig_getattr(self, ProjectionStates, name)
2692  def __init__(self, *args):
2693  """
2694  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations,
2695  IMP::em2d::Images const & projections, IMP::String const & name="ProjectionStates") -> ProjectionStates
2696  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations,
2697  IMP::em2d::Images const & projections) -> ProjectionStates
2698  """
2699  this = _IMP_em2d.new_ProjectionStates(*args)
2700  try: self.this.append(this)
2701  except: self.this = this
2702  def get_projection(self, *args):
2703  """get_projection(ProjectionStates self, unsigned int i) -> Image"""
2704  return _IMP_em2d.ProjectionStates_get_projection(self, *args)
2705 
2706  def do_show(self, *args):
2707  """do_show(ProjectionStates self, _ostream out)"""
2708  return _IMP_em2d.ProjectionStates_do_show(self, *args)
2709 
2710  __swig_destroy__ = _IMP_em2d.delete_ProjectionStates
2711  __del__ = lambda self : None;
2712  def __str__(self):
2713  """__str__(ProjectionStates self) -> std::string"""
2714  return _IMP_em2d.ProjectionStates___str__(self)
2715 
2716  def __repr__(self):
2717  """__repr__(ProjectionStates self) -> std::string"""
2718  return _IMP_em2d.ProjectionStates___repr__(self)
2719 
2720  def get_from(o):
2721  return _object_cast_to_ProjectionStates(o)
2722  get_from = staticmethod(get_from)
2723 
2724 ProjectionStates_swigregister = _IMP_em2d.ProjectionStates_swigregister
2725 ProjectionStates_swigregister(ProjectionStates)
2726 
2727 class DistanceFilter(IMP.domino.SubsetFilter):
2728  """Proxy of C++ IMP::em2d::DistanceFilter class"""
2729  __swig_setmethods__ = {}
2730  for _s in [IMP.domino.SubsetFilter]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2731  __setattr__ = lambda self, name, value: _swig_setattr(self, DistanceFilter, name, value)
2732  __swig_getmethods__ = {}
2733  for _s in [IMP.domino.SubsetFilter]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2734  __getattr__ = lambda self, name: _swig_getattr(self, DistanceFilter, name)
2735  def __init__(self, *args):
2736  """
2737  __init__(IMP::em2d::DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table,
2738  double max_distance) -> DistanceFilter
2739  """
2740  this = _IMP_em2d.new_DistanceFilter(*args)
2741  try: self.this.append(this)
2742  except: self.this = this
2743  def show(self, *args):
2744  """
2745  show(DistanceFilter self, _ostream out=std::cout)
2746  show(DistanceFilter self)
2747  """
2748  return _IMP_em2d.DistanceFilter_show(self, *args)
2749 
2750  def get_version_info(self):
2751  """get_version_info(DistanceFilter self) -> VersionInfo"""
2752  return _IMP_em2d.DistanceFilter_get_version_info(self)
2753 
2754  def do_show(self, *args):
2755  """do_show(DistanceFilter self, _ostream out)"""
2756  return _IMP_em2d.DistanceFilter_do_show(self, *args)
2757 
2758  __swig_destroy__ = _IMP_em2d.delete_DistanceFilter
2759  __del__ = lambda self : None;
2760  def __str__(self):
2761  """__str__(DistanceFilter self) -> std::string"""
2762  return _IMP_em2d.DistanceFilter___str__(self)
2763 
2764  def __repr__(self):
2765  """__repr__(DistanceFilter self) -> std::string"""
2766  return _IMP_em2d.DistanceFilter___repr__(self)
2767 
2768  def get_from(o):
2769  return _object_cast_to_DistanceFilter(o)
2770  get_from = staticmethod(get_from)
2771 
2772 DistanceFilter_swigregister = _IMP_em2d.DistanceFilter_swigregister
2773 DistanceFilter_swigregister(DistanceFilter)
2774 
2775 class DistanceFilterTable(IMP.domino.SubsetFilterTable):
2776  """Proxy of C++ IMP::em2d::DistanceFilterTable class"""
2777  __swig_setmethods__ = {}
2778  for _s in [IMP.domino.SubsetFilterTable]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2779  __setattr__ = lambda self, name, value: _swig_setattr(self, DistanceFilterTable, name, value)
2780  __swig_getmethods__ = {}
2781  for _s in [IMP.domino.SubsetFilterTable]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2782  __getattr__ = lambda self, name: _swig_getattr(self, DistanceFilterTable, name)
2783  def __init__(self, *args):
2784  """__init__(IMP::em2d::DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
2785  this = _IMP_em2d.new_DistanceFilterTable(*args)
2786  try: self.this.append(this)
2787  except: self.this = this
2788  def show(self, *args):
2789  """
2790  show(DistanceFilterTable self, _ostream out=std::cout)
2791  show(DistanceFilterTable self)
2792  """
2793  return _IMP_em2d.DistanceFilterTable_show(self, *args)
2794 
2795  def get_version_info(self):
2796  """get_version_info(DistanceFilterTable self) -> VersionInfo"""
2797  return _IMP_em2d.DistanceFilterTable_get_version_info(self)
2798 
2799  def do_show(self, *args):
2800  """do_show(DistanceFilterTable self, _ostream out)"""
2801  return _IMP_em2d.DistanceFilterTable_do_show(self, *args)
2802 
2803  __swig_destroy__ = _IMP_em2d.delete_DistanceFilterTable
2804  __del__ = lambda self : None;
2805  def __str__(self):
2806  """__str__(DistanceFilterTable self) -> std::string"""
2807  return _IMP_em2d.DistanceFilterTable___str__(self)
2808 
2809  def __repr__(self):
2810  """__repr__(DistanceFilterTable self) -> std::string"""
2811  return _IMP_em2d.DistanceFilterTable___repr__(self)
2812 
2813  def get_from(o):
2814  return _object_cast_to_DistanceFilterTable(o)
2815  get_from = staticmethod(get_from)
2816 
2817 DistanceFilterTable_swigregister = _IMP_em2d.DistanceFilterTable_swigregister
2818 DistanceFilterTable_swigregister(DistanceFilterTable)
2819 
2820 class IntsOrder(_object):
2821  """Proxy of C++ IMP::em2d::IntsOrder class"""
2822  __swig_setmethods__ = {}
2823  __setattr__ = lambda self, name, value: _swig_setattr(self, IntsOrder, name, value)
2824  __swig_getmethods__ = {}
2825  __getattr__ = lambda self, name: _swig_getattr(self, IntsOrder, name)
2826  __repr__ = _swig_repr
2827  def __call__(self, *args):
2828  """__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
2829  return _IMP_em2d.IntsOrder___call__(self, *args)
2830 
2831  def __init__(self):
2832  """__init__(IMP::em2d::IntsOrder self) -> IntsOrder"""
2833  this = _IMP_em2d.new_IntsOrder()
2834  try: self.this.append(this)
2835  except: self.this = this
2836  __swig_destroy__ = _IMP_em2d.delete_IntsOrder
2837  __del__ = lambda self : None;
2838 IntsOrder_swigregister = _IMP_em2d.IntsOrder_swigregister
2839 IntsOrder_swigregister(IntsOrder)
2840 
2841 class RigidBodiesImageFitRestraint(IMP.kernel.Restraint):
2842  """Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class"""
2843  __swig_setmethods__ = {}
2844  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2845  __setattr__ = lambda self, name, value: _swig_setattr(self, RigidBodiesImageFitRestraint, name, value)
2846  __swig_getmethods__ = {}
2847  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2848  __getattr__ = lambda self, name: _swig_getattr(self, RigidBodiesImageFitRestraint, name)
2849  def get_version_info(self):
2850  """get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
2851  return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
2852 
2853  def __init__(self, *args):
2854  """__init__(IMP::em2d::RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
2855  this = _IMP_em2d.new_RigidBodiesImageFitRestraint(*args)
2856  try: self.this.append(this)
2857  except: self.this = this
2858  def set_projecting_parameters(self, *args):
2859  """set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
2860  return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, *args)
2861 
2862  def set_orientations(self, *args):
2863  """set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
2864  return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, *args)
2865 
2866  def get_number_of_masks(self, *args):
2867  """get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
2868  return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, *args)
2869 
2870  def __str__(self):
2871  """__str__(RigidBodiesImageFitRestraint self) -> std::string"""
2872  return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
2873 
2874  def __repr__(self):
2875  """__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
2876  return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
2877 
2878  def get_from(o):
2879  return _object_cast_to_RigidBodiesImageFitRestraint(o)
2880  get_from = staticmethod(get_from)
2881 
2882 RigidBodiesImageFitRestraint_swigregister = _IMP_em2d.RigidBodiesImageFitRestraint_swigregister
2883 RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
2884 
2885 
2886 def get_unique_index(*args):
2887  """get_unique_index(Rotation3D rot) -> IMP::Ints"""
2888  return _IMP_em2d.get_unique_index(*args)
2889 class RelativePositionMover(IMP.core.RigidBodyMover):
2890  """Proxy of C++ IMP::em2d::RelativePositionMover class"""
2891  __swig_setmethods__ = {}
2892  for _s in [IMP.core.RigidBodyMover]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2893  __setattr__ = lambda self, name, value: _swig_setattr(self, RelativePositionMover, name, value)
2894  __swig_getmethods__ = {}
2895  for _s in [IMP.core.RigidBodyMover]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2896  __getattr__ = lambda self, name: _swig_getattr(self, RelativePositionMover, name)
2897  def __init__(self, *args):
2898  """__init__(IMP::em2d::RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
2899  this = _IMP_em2d.new_RelativePositionMover(*args)
2900  try: self.this.append(this)
2901  except: self.this = this
2902  def add_internal_transformations(self, *args):
2903  """add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
2904  return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, *args)
2905 
2906  def set_random_move_probability(self, *args):
2907  """set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
2908  return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, *args)
2909 
2910  def __str__(self):
2911  """__str__(RelativePositionMover self) -> std::string"""
2912  return _IMP_em2d.RelativePositionMover___str__(self)
2913 
2914  def __repr__(self):
2915  """__repr__(RelativePositionMover self) -> std::string"""
2916  return _IMP_em2d.RelativePositionMover___repr__(self)
2917 
2918  def get_from(o):
2919  return _object_cast_to_RelativePositionMover(o)
2920  get_from = staticmethod(get_from)
2921 
2922 RelativePositionMover_swigregister = _IMP_em2d.RelativePositionMover_swigregister
2923 RelativePositionMover_swigregister(RelativePositionMover)
2924 
2925 class DummyRestraint(IMP.kernel.Restraint):
2926  """Proxy of C++ IMP::em2d::DummyRestraint class"""
2927  __swig_setmethods__ = {}
2928  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2929  __setattr__ = lambda self, name, value: _swig_setattr(self, DummyRestraint, name, value)
2930  __swig_getmethods__ = {}
2931  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2932  __getattr__ = lambda self, name: _swig_getattr(self, DummyRestraint, name)
2933  def __init__(self, *args):
2934  """__init__(IMP::em2d::DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
2935  this = _IMP_em2d.new_DummyRestraint(*args)
2936  try: self.this.append(this)
2937  except: self.this = this
2938  def show(self, *args):
2939  """
2940  show(DummyRestraint self, _ostream out=std::cout)
2941  show(DummyRestraint self)
2942  """
2943  return _IMP_em2d.DummyRestraint_show(self, *args)
2944 
2945  def do_get_inputs(self):
2946  """do_get_inputs(DummyRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2947  return _IMP_em2d.DummyRestraint_do_get_inputs(self)
2948 
2949  def get_version_info(self):
2950  """get_version_info(DummyRestraint self) -> VersionInfo"""
2951  return _IMP_em2d.DummyRestraint_get_version_info(self)
2952 
2953  def __str__(self):
2954  """__str__(DummyRestraint self) -> std::string"""
2955  return _IMP_em2d.DummyRestraint___str__(self)
2956 
2957  def __repr__(self):
2958  """__repr__(DummyRestraint self) -> std::string"""
2959  return _IMP_em2d.DummyRestraint___repr__(self)
2960 
2961  def get_from(o):
2962  return _object_cast_to_DummyRestraint(o)
2963  get_from = staticmethod(get_from)
2964 
2965 DummyRestraint_swigregister = _IMP_em2d.DummyRestraint_swigregister
2966 DummyRestraint_swigregister(DummyRestraint)
2967 
2968 class ParticlesDummyRestraint(IMP.kernel.Restraint):
2969  """Proxy of C++ IMP::em2d::ParticlesDummyRestraint class"""
2970  __swig_setmethods__ = {}
2971  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
2972  __setattr__ = lambda self, name, value: _swig_setattr(self, ParticlesDummyRestraint, name, value)
2973  __swig_getmethods__ = {}
2974  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
2975  __getattr__ = lambda self, name: _swig_getattr(self, ParticlesDummyRestraint, name)
2976  def __init__(self, *args):
2977  """__init__(IMP::em2d::ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
2978  this = _IMP_em2d.new_ParticlesDummyRestraint(*args)
2979  try: self.this.append(this)
2980  except: self.this = this
2981  def show(self, *args):
2982  """
2983  show(ParticlesDummyRestraint self, _ostream out=std::cout)
2984  show(ParticlesDummyRestraint self)
2985  """
2986  return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
2987 
2988  def do_get_inputs(self):
2989  """do_get_inputs(ParticlesDummyRestraint self) -> IMP::kernel::ModelObjectsTemp"""
2990  return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
2991 
2992  def get_version_info(self):
2993  """get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
2994  return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
2995 
2996  def __str__(self):
2997  """__str__(ParticlesDummyRestraint self) -> std::string"""
2998  return _IMP_em2d.ParticlesDummyRestraint___str__(self)
2999 
3000  def __repr__(self):
3001  """__repr__(ParticlesDummyRestraint self) -> std::string"""
3002  return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3003 
3004  def get_from(o):
3005  return _object_cast_to_ParticlesDummyRestraint(o)
3006  get_from = staticmethod(get_from)
3007 
3008 ParticlesDummyRestraint_swigregister = _IMP_em2d.ParticlesDummyRestraint_swigregister
3009 ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3010 
3011 class PCAFitRestraint(IMP.kernel.Restraint):
3012  """Proxy of C++ IMP::em2d::PCAFitRestraint class"""
3013  __swig_setmethods__ = {}
3014  for _s in [IMP.kernel.Restraint]: __swig_setmethods__.update(getattr(_s,'__swig_setmethods__',{}))
3015  __setattr__ = lambda self, name, value: _swig_setattr(self, PCAFitRestraint, name, value)
3016  __swig_getmethods__ = {}
3017  for _s in [IMP.kernel.Restraint]: __swig_getmethods__.update(getattr(_s,'__swig_getmethods__',{}))
3018  __getattr__ = lambda self, name: _swig_getattr(self, PCAFitRestraint, name)
3019  def __init__(self, *args):
3020  """
3021  __init__(IMP::em2d::PCAFitRestraint self, IMP::kernel::Particles particles, Strings image_files, double pixel_size, double resolution=10.0,
3022  unsigned int projection_number=100, bool reuse_direction=False) -> PCAFitRestraint
3023  __init__(IMP::em2d::PCAFitRestraint self, IMP::kernel::Particles particles, Strings image_files, double pixel_size, double resolution=10.0,
3024  unsigned int projection_number=100) -> PCAFitRestraint
3025  __init__(IMP::em2d::PCAFitRestraint self, IMP::kernel::Particles particles, Strings image_files, double pixel_size, double resolution=10.0) -> PCAFitRestraint
3026  __init__(IMP::em2d::PCAFitRestraint self, IMP::kernel::Particles particles, Strings image_files, double pixel_size) -> PCAFitRestraint
3027  """
3028  this = _IMP_em2d.new_PCAFitRestraint(*args)
3029  try: self.this.append(this)
3030  except: self.this = this
3031  def get_projection_number(self):
3032  """get_projection_number(PCAFitRestraint self) -> unsigned int"""
3033  return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3034 
3035  def set_projection_number(self, *args):
3036  """set_projection_number(PCAFitRestraint self, unsigned int n)"""
3037  return _IMP_em2d.PCAFitRestraint_set_projection_number(self, *args)
3038 
3039  def write_best_projections(self, *args):
3040  """
3041  write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)
3042  write_best_projections(PCAFitRestraint self, std::string file_name)
3043  """
3044  return _IMP_em2d.PCAFitRestraint_write_best_projections(self, *args)
3045 
3046  def do_get_inputs(self):
3047  """do_get_inputs(PCAFitRestraint self) -> IMP::kernel::ModelObjectsTemp"""
3048  return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3049 
3050  def get_version_info(self):
3051  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
3052  return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3053 
3054  def __str__(self):
3055  """__str__(PCAFitRestraint self) -> std::string"""
3056  return _IMP_em2d.PCAFitRestraint___str__(self)
3057 
3058  def __repr__(self):
3059  """__repr__(PCAFitRestraint self) -> std::string"""
3060  return _IMP_em2d.PCAFitRestraint___repr__(self)
3061 
3062  def get_from(o):
3063  return _object_cast_to_PCAFitRestraint(o)
3064  get_from = staticmethod(get_from)
3065 
3066 PCAFitRestraint_swigregister = _IMP_em2d.PCAFitRestraint_swigregister
3067 PCAFitRestraint_swigregister(PCAFitRestraint)
3068 
3069 class ResultAlign2D(_object):
3070  """Proxy of C++ std::pair<(IMP::algebra::Transformation2D,double)> class"""
3071  __swig_setmethods__ = {}
3072  __setattr__ = lambda self, name, value: _swig_setattr(self, ResultAlign2D, name, value)
3073  __swig_getmethods__ = {}
3074  __getattr__ = lambda self, name: _swig_getattr(self, ResultAlign2D, name)
3075  __repr__ = _swig_repr
3076  def __init__(self, *args):
3077  """
3078  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self) -> ResultAlign2D
3079  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, Transformation2D first, double second) -> ResultAlign2D
3080  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, ResultAlign2D p) -> ResultAlign2D
3081  """
3082  this = _IMP_em2d.new_ResultAlign2D(*args)
3083  try: self.this.append(this)
3084  except: self.this = this
3085  __swig_setmethods__["first"] = _IMP_em2d.ResultAlign2D_first_set
3086  __swig_getmethods__["first"] = _IMP_em2d.ResultAlign2D_first_get
3087  if _newclass:first = _swig_property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set)
3088  __swig_setmethods__["second"] = _IMP_em2d.ResultAlign2D_second_set
3089  __swig_getmethods__["second"] = _IMP_em2d.ResultAlign2D_second_get
3090  if _newclass:second = _swig_property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set)
3091  def __len__(self): return 2
3092  def __repr__(self): return str((self.first, self.second))
3093  def __getitem__(self, index):
3094  if not (index % 2):
3095  return self.first
3096  else:
3097  return self.second
3098  def __setitem__(self, index, val):
3099  if not (index % 2):
3100  self.first = val
3101  else:
3102  self.second = val
3103  __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3104  __del__ = lambda self : None;
3105 ResultAlign2D_swigregister = _IMP_em2d.ResultAlign2D_swigregister
3106 ResultAlign2D_swigregister(ResultAlign2D)
3107 
3108 
3109 def _do_hierarchical_clustering_single_linkage(*args):
3110  """_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3111  return _IMP_em2d._do_hierarchical_clustering_single_linkage(*args)
3112 
3113 def _do_hierarchical_clustering_complete_linkage(*args):
3114  """_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3115  return _IMP_em2d._do_hierarchical_clustering_complete_linkage(*args)
3116 
3117 def _do_hierarchical_clustering_average_distance_linkage(*args):
3118  """_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3119  return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(*args)
3120 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3121 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3122 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3123 
3124 
3125 def get_module_version():
3126  """get_module_version() -> std::string const"""
3127  return _IMP_em2d.get_module_version()
3128 
3129 def get_example_path(*args):
3130  """get_example_path(std::string fname) -> std::string"""
3131  return _IMP_em2d.get_example_path(*args)
3132 
3133 def get_data_path(*args):
3134  """get_data_path(std::string fname) -> std::string"""
3135  return _IMP_em2d.get_data_path(*args)
3136 import _version_check
3137 _version_check.check_version(get_module_version())
3138 
3139 # This file is compatible with both classic and new-style classes.
3140 
3141 
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)
Various classes to hold sets of particles.
ResultAlign2D get_translational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
Aligns two matrices translationally.
void get_correlation2d(const cv::Mat &A, const cv::Mat &B, cv::Mat &corr)
Correlation matrix between two 2D matrices using FFT.
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)
void do_dilate_and_shrink_warp(cv::Mat &m, const cv::Mat &grayscale, cv::Mat &kernel)
(U. Adiga, 2005)
em2d::ResultAlign2D get_rotational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
RegistrationResults get_evenly_distributed_registration_results(unsigned int n_projections)
void 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.
Make CGAL functionality available to IMP.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
MatchTemplateResults get_best_template_matches(const cv::Mat &m, const cv::Mat &templ, unsigned int n)
Modify the transformation of a rigid body.
Low level functionality (logging, error handling, profiling, command line flags etc) that is used by ...
void get_autocorrelation2d(const cv::Mat &m, cv::Mat &corr)
Computes the autocorrelation matrix.
std::string get_data_path(std::string file_name)
Return the full path to installed data.
void apply_mean_outside_mask(Image *img, double radius)
Several general purpose optimizers from the GNU Scientific Library (GSL).
double get_rotation_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
ScoreStates maintain invariants in the Model.
Composable functors to implement scores via compile-time composition.
ResultAlign2D get_rotational_alignment_no_preprocessing(const cv::Mat &POLAR1, const cv::Mat &POLAR2)
void get_fft_using_optimal_size(const cv::Mat &m, cv::Mat &M)
Floats get_histogram(Image *img, int bins)
Definition: Image.h: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)
Code to compute statistical measures.
RegistrationResults get_random_registration_results(unsigned int n, double maximum_shift=5.0)
Provides a set of random registration results (or parameters)
algebra::Vector2Ds do_project_vectors(const algebra::Vector3Ds &ps, const algebra::Rotation3D &R, const algebra::Vector3D &translation)
Project the points contained in Vector3Ds to gen vectors in 2D.
void write_vectors_as_pdb(const algebra::Vector2Ds vs, const String filename)
void apply_circular_mask(const cv::Mat &mat, cv::Mat &result, int radius, double value=0.0)
Base functionality and abstract base classes for representation, scoring and sampling.
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.
Basic utilities for handling cryo-electron microscopy 3D density maps.
void crop(Image *img, const IntPair &center, int size)
void get_morphologic_gradient(const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel)
void apply_mask(const cv::Mat &m, cv::Mat &result, const cvIntMat &mask, double val)
Applies a binary mask to an image.
double get_cross_correlation_coefficient(Image *im1, Image *im2)
Cross correlation between two images.
void save_images(Images images, const Strings &names, const ImageReaderWriter *rw)
Common base class for heavy weight IMP objects.
Definition: 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)
Return a new density map containing a rotated version of the old one.
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)
Correlation without preprocessing.
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
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)
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
em2d::ResultAlign2D get_complete_alignment_no_preprocessing(const cv::Mat &input, const cv::Mat &INPUT, const cv::Mat &POLAR1, cv::Mat &m_to_align, const cv::Mat &POLAR2, bool apply=false)
double get_overlap_percentage(cv::Mat &m1, cv::Mat &m2, const IntPair &center)
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)
Ints get_unique_index(const algebra::Rotation3D &rot)
For a unique 4 ints ( 2 first decimal positions) for a rotation.
double get_global_score(const RegistrationResults &RRs)
void do_place(cv::Mat &mask, cv::Mat &m, const algebra::Vector2D &v)
void do_morphologic_reconstruction(const cv::Mat &mask, cv::Mat &marker, int neighbors_mode=4)
morphologic grayscale reconstruction (L Vincent, 1993)
Output IMP model data in various file formats.
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.
void get_spectrum(const cv::Mat &m, cv::Mat &real, cv::Mat &imag)
Computes the fft of a matrix and returns the real and imaginary matrices.