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IMP Reference Guide  2.10.0
The Integrative Modeling Platform
em2d/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
3 #
4 # Do not make changes to this file unless you know what you are doing--modify
5 # the SWIG interface file instead.
6 
7 # This wrapper is part of IMP,
8 # Copyright 2007-2018 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_em2d')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_em2d')
25  _IMP_em2d = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_em2d', [dirname(__file__)])
34  except ImportError:
35  import _IMP_em2d
36  return _IMP_em2d
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_em2d', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_em2d = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_em2d
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_EM2D_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_EM2D_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_em2d.delete_IMP_EM2D_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
126  return _IMP_em2d.IMP_EM2D_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
132  incr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
133  """
134  return _IMP_em2d.IMP_EM2D_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
140  decr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
141  """
142  return _IMP_em2d.IMP_EM2D_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_em2d.IMP_EM2D_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
152  return _IMP_em2d.IMP_EM2D_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator"""
157  return _IMP_em2d.IMP_EM2D_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
162  return _IMP_em2d.IMP_EM2D_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
167  return _IMP_em2d.IMP_EM2D_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
172  return _IMP_em2d.IMP_EM2D_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
177  return _IMP_em2d.IMP_EM2D_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
182  return _IMP_em2d.IMP_EM2D_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
187  return _IMP_em2d.IMP_EM2D_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
192  return _IMP_em2d.IMP_EM2D_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
197  return _IMP_em2d.IMP_EM2D_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
202  return _IMP_em2d.IMP_EM2D_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator
208  __sub__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_em2d.IMP_EM2D_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_EM2D_SwigPyIterator_swigregister = _IMP_em2d.IMP_EM2D_SwigPyIterator_swigregister
215 IMP_EM2D_SwigPyIterator_swigregister(IMP_EM2D_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_em2d.IMP_DEBUG
224 IMP_RELEASE = _IMP_em2d.IMP_RELEASE
225 IMP_SILENT = _IMP_em2d.IMP_SILENT
226 IMP_PROGRESS = _IMP_em2d.IMP_PROGRESS
227 IMP_TERSE = _IMP_em2d.IMP_TERSE
228 IMP_VERBOSE = _IMP_em2d.IMP_VERBOSE
229 IMP_MEMORY = _IMP_em2d.IMP_MEMORY
230 IMP_NONE = _IMP_em2d.IMP_NONE
231 IMP_USAGE = _IMP_em2d.IMP_USAGE
232 IMP_INTERNAL = _IMP_em2d.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_em2d.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_em2d.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em2d.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_em2d.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em2d.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_em2d.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_em2d._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_em2d._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_em2d.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_em2d.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_em2d.IMP_HAS_NOEXCEPT
288 IMP_C_OPEN_BINARY = _IMP_em2d.IMP_C_OPEN_BINARY
289 import IMP
290 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_FILESYSTEM
291 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
292 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CGAL_HAS_BOOST_RANDOM
293 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_SYSTEM
294 IMPCGAL_SHOW_WARNINGS = _IMP_em2d.IMPCGAL_SHOW_WARNINGS
295 import IMP.cgal
296 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_IMP_CGAL
297 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
298 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
299 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_RANDOM
300 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_SYSTEM
301 IMP_ALGEBRA_HAS_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_CGAL
302 IMP_ALGEBRA_HAS_ANN = _IMP_em2d.IMP_ALGEBRA_HAS_ANN
303 IMPALGEBRA_SHOW_WARNINGS = _IMP_em2d.IMPALGEBRA_SHOW_WARNINGS
304 import IMP.algebra
305 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_IMP_CGAL
306 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
307 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
308 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_RANDOM
309 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_SYSTEM
310 IMP_DISPLAY_HAS_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_CGAL
311 IMPDISPLAY_SHOW_WARNINGS = _IMP_em2d.IMPDISPLAY_SHOW_WARNINGS
312 import IMP.display
313 IMP_GSL_HAS_IMP_CGAL = _IMP_em2d.IMP_GSL_HAS_IMP_CGAL
314 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_FILESYSTEM
315 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
316 IMP_GSL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_GSL_HAS_BOOST_RANDOM
317 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_SYSTEM
318 IMP_GSL_HAS_CGAL = _IMP_em2d.IMP_GSL_HAS_CGAL
319 IMPGSL_SHOW_WARNINGS = _IMP_em2d.IMPGSL_SHOW_WARNINGS
320 import IMP.gsl
321 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
322 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
323 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
324 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
325 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
326 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_CGAL
327 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_HDF5
328 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em2d.IMPSCOREFUNCTOR_SHOW_WARNINGS
329 import IMP.score_functor
330 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_IMP_CGAL
331 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
332 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
333 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_RANDOM
334 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_SYSTEM
335 IMP_STATISTICS_HAS_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_CGAL
336 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em2d.IMPSTATISTICS_SHOW_WARNINGS
337 import IMP.statistics
338 IMP_CORE_HAS_IMP_CGAL = _IMP_em2d.IMP_CORE_HAS_IMP_CGAL
339 IMP_CORE_HAS_IMP_KERNEL = _IMP_em2d.IMP_CORE_HAS_IMP_KERNEL
340 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_FILESYSTEM
341 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
342 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CORE_HAS_BOOST_RANDOM
343 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_SYSTEM
344 IMP_CORE_HAS_CGAL = _IMP_em2d.IMP_CORE_HAS_CGAL
345 IMP_CORE_HAS_HDF5 = _IMP_em2d.IMP_CORE_HAS_HDF5
346 IMPCORE_SHOW_WARNINGS = _IMP_em2d.IMPCORE_SHOW_WARNINGS
347 import IMP.core
348 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em2d.IMP_CONTAINER_HAS_IMP_ALGEBRA
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_CGAL
350 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em2d.IMP_CONTAINER_HAS_IMP_DISPLAY
351 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_KERNEL
352 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
353 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
354 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
355 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_RANDOM
356 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_SYSTEM
357 IMP_CONTAINER_HAS_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_CGAL
358 IMP_CONTAINER_HAS_HDF5 = _IMP_em2d.IMP_CONTAINER_HAS_HDF5
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em2d.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em2d.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em2d.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_em2d.IMPCONTAINER_SHOW_WARNINGS
363 import IMP.container
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_em2d.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em2d.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em2d.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_em2d.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_em2d.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em2d.IMP_ATOM_HAS_PYTHON_IHM
374 IMPATOM_SHOW_WARNINGS = _IMP_em2d.IMPATOM_SHOW_WARNINGS
375 IMP_ATOM_TYPE_INDEX = _IMP_em2d.IMP_ATOM_TYPE_INDEX
376 IMP_RESIDUE_TYPE_INDEX = _IMP_em2d.IMP_RESIDUE_TYPE_INDEX
377 IMP_HIERARCHY_TYPE_INDEX = _IMP_em2d.IMP_HIERARCHY_TYPE_INDEX
378 IMP_CHAIN_TYPE_INDEX = _IMP_em2d.IMP_CHAIN_TYPE_INDEX
379 import IMP.atom
380 IMP_EM_HAS_IMP_CGAL = _IMP_em2d.IMP_EM_HAS_IMP_CGAL
381 IMP_EM_HAS_IMP_CONTAINER = _IMP_em2d.IMP_EM_HAS_IMP_CONTAINER
382 IMP_EM_HAS_IMP_DISPLAY = _IMP_em2d.IMP_EM_HAS_IMP_DISPLAY
383 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM_HAS_IMP_SCORE_FUNCTOR
384 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_FILESYSTEM
385 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
386 IMP_EM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM_HAS_BOOST_RANDOM
387 IMP_EM_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM_HAS_BOOST_REGEX
388 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_SYSTEM
389 IMP_EM_HAS_CGAL = _IMP_em2d.IMP_EM_HAS_CGAL
390 IMP_EM_HAS_HDF5 = _IMP_em2d.IMP_EM_HAS_HDF5
391 IMP_EM_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM_HAS_PYTHON_IHM
392 IMPEM_SHOW_WARNINGS = _IMP_em2d.IMPEM_SHOW_WARNINGS
393 import IMP.em
394 IMP_RMF_HAS_IMP_CGAL = _IMP_em2d.IMP_RMF_HAS_IMP_CGAL
395 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
396 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_FILESYSTEM
397 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
398 IMP_RMF_HAS_BOOST_RANDOM = _IMP_em2d.IMP_RMF_HAS_BOOST_RANDOM
399 IMP_RMF_HAS_BOOST_REGEX = _IMP_em2d.IMP_RMF_HAS_BOOST_REGEX
400 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_SYSTEM
401 IMP_RMF_HAS_CGAL = _IMP_em2d.IMP_RMF_HAS_CGAL
402 IMP_RMF_HAS_HDF5 = _IMP_em2d.IMP_RMF_HAS_HDF5
403 IMP_RMF_HAS_PYTHON_IHM = _IMP_em2d.IMP_RMF_HAS_PYTHON_IHM
404 IMPRMF_SHOW_WARNINGS = _IMP_em2d.IMPRMF_SHOW_WARNINGS
405 import IMP.rmf
406 import RMF
407 IMP_DOMINO_HAS_IMP_ATOM = _IMP_em2d.IMP_DOMINO_HAS_IMP_ATOM
408 IMP_DOMINO_HAS_IMP_CGAL = _IMP_em2d.IMP_DOMINO_HAS_IMP_CGAL
409 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_em2d.IMP_DOMINO_HAS_IMP_KERNEL
410 IMP_DOMINO_HAS_IMP_RMF = _IMP_em2d.IMP_DOMINO_HAS_IMP_RMF
411 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
412 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_FILESYSTEM
413 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
414 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_RANDOM
415 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_em2d.IMP_DOMINO_HAS_BOOST_REGEX
416 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_SYSTEM
417 IMP_DOMINO_HAS_CGAL = _IMP_em2d.IMP_DOMINO_HAS_CGAL
418 IMP_DOMINO_HAS_HDF5 = _IMP_em2d.IMP_DOMINO_HAS_HDF5
419 IMP_DOMINO_HAS_RMF = _IMP_em2d.IMP_DOMINO_HAS_RMF
420 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_em2d.IMP_DOMINO_HAS_PYTHON_IHM
421 IMPDOMINO_SHOW_WARNINGS = _IMP_em2d.IMPDOMINO_SHOW_WARNINGS
422 import RMF_HDF5
423 import IMP.domino
424 IMP_EM2D_HAS_IMP_CGAL = _IMP_em2d.IMP_EM2D_HAS_IMP_CGAL
425 IMP_EM2D_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM2D_HAS_IMP_KERNEL
426 IMP_EM2D_HAS_IMP_RMF = _IMP_em2d.IMP_EM2D_HAS_IMP_RMF
427 IMP_EM2D_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM2D_HAS_IMP_SCORE_FUNCTOR
428 IMP_EM2D_HAS_IMP_STATISTICS = _IMP_em2d.IMP_EM2D_HAS_IMP_STATISTICS
429 IMP_EM2D_HAS_BOOST_GRAPH = _IMP_em2d.IMP_EM2D_HAS_BOOST_GRAPH
430 IMP_EM2D_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM2D_HAS_BOOST_RANDOM
431 IMP_EM2D_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM2D_HAS_BOOST_REGEX
432 IMP_EM2D_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM2D_HAS_BOOST_SYSTEM
433 IMP_EM2D_HAS_CGAL = _IMP_em2d.IMP_EM2D_HAS_CGAL
434 IMP_EM2D_HAS_GSL = _IMP_em2d.IMP_EM2D_HAS_GSL
435 IMP_EM2D_HAS_HDF5 = _IMP_em2d.IMP_EM2D_HAS_HDF5
436 IMP_EM2D_HAS_OPENCV22 = _IMP_em2d.IMP_EM2D_HAS_OPENCV22
437 IMP_EM2D_HAS_RMF = _IMP_em2d.IMP_EM2D_HAS_RMF
438 IMP_EM2D_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM2D_HAS_PYTHON_IHM
439 IMP_EM2D_HAS_OPENCV21 = _IMP_em2d.IMP_EM2D_HAS_OPENCV21
440 IMP_EM2D_HAS_OPENCV3 = _IMP_em2d.IMP_EM2D_HAS_OPENCV3
441 IMPEM2D_SHOW_WARNINGS = _IMP_em2d.IMPEM2D_SHOW_WARNINGS
442 
443 PolarResamplingParametersList=list
444 _plural_types.append("PolarResamplingParametersList")
445 _value_types.append("PolarResamplingParameters")
446 
447 
448 ProjectionMasks=list
449 _plural_types.append("ProjectionMasks")
450 _value_types.append("ProjectionMask")
451 
452 
453 MasksManagers=list
454 _plural_types.append("MasksManagers")
455 _value_types.append("MasksManager")
456 
457 
458 RegistrationResults=list
459 _plural_types.append("RegistrationResults")
460 _value_types.append("RegistrationResult")
461 
462 
463 ClusterSets=list
464 _plural_types.append("ClusterSets")
465 _value_types.append("ClusterSet")
466 
467 
468 SingleLinkages=list
469 _plural_types.append("SingleLinkages")
470 _value_types.append("SingleLinkage")
471 
472 
473 CompleteLinkages=list
474 _plural_types.append("CompleteLinkages")
475 _value_types.append("CompleteLinkage")
476 
477 
478 AverageDistanceLinkages=list
479 _plural_types.append("AverageDistanceLinkages")
480 _value_types.append("AverageDistanceLinkage")
481 
482 
483 SegmentationParametersList=list
484 _plural_types.append("SegmentationParametersList")
485 _value_types.append("SegmentationParameters")
486 
487 
488 MatchTemplateResults=list
489 _plural_types.append("MatchTemplateResults")
490 _value_types.append("MatchTemplateResult")
491 
492 
493 ProjectingParametersList=list
494 _plural_types.append("ProjectingParametersList")
495 _value_types.append("ProjectingParameters")
496 
497 
498 ProjectingOptionsList=list
499 _plural_types.append("ProjectingOptionsList")
500 _value_types.append("ProjectingOptions")
501 
502 
503 Em2DRestraintParametersList=list
504 _plural_types.append("Em2DRestraintParametersList")
505 _value_types.append("Em2DRestraintParameters")
506 
507 
508 _object_types.append("ProjectionFinder")
509 
510 
511 def _object_cast_to_ProjectionFinder(o):
512  """_object_cast_to_ProjectionFinder(Object o) -> ProjectionFinder"""
513  return _IMP_em2d._object_cast_to_ProjectionFinder(o)
514 
515 _object_types.append("ScoreFunction")
516 
517 
518 def _object_cast_to_ScoreFunction(o):
519  """_object_cast_to_ScoreFunction(Object o) -> ScoreFunction"""
520  return _IMP_em2d._object_cast_to_ScoreFunction(o)
521 
522 _object_types.append("ChiSquaredScore")
523 
524 
525 def _object_cast_to_ChiSquaredScore(o):
526  """_object_cast_to_ChiSquaredScore(Object o) -> ChiSquaredScore"""
527  return _IMP_em2d._object_cast_to_ChiSquaredScore(o)
528 
529 _object_types.append("EM2DScore")
530 
531 
532 def _object_cast_to_EM2DScore(o):
533  """_object_cast_to_EM2DScore(Object o) -> EM2DScore"""
534  return _IMP_em2d._object_cast_to_EM2DScore(o)
535 
536 _object_types.append("MeanAbsoluteDifference")
537 
538 
539 def _object_cast_to_MeanAbsoluteDifference(o):
540  """_object_cast_to_MeanAbsoluteDifference(Object o) -> MeanAbsoluteDifference"""
541  return _IMP_em2d._object_cast_to_MeanAbsoluteDifference(o)
542 
543 _object_types.append("ProjectionParametersScoreState")
544 
545 
546 def _object_cast_to_ProjectionParametersScoreState(o):
547  """_object_cast_to_ProjectionParametersScoreState(Object o) -> ProjectionParametersScoreState"""
548  return _IMP_em2d._object_cast_to_ProjectionParametersScoreState(o)
549 
550 _object_types.append("Em2DRestraint")
551 
552 
553 def _object_cast_to_Em2DRestraint(o):
554  """_object_cast_to_Em2DRestraint(Object o) -> Em2DRestraint"""
555  return _IMP_em2d._object_cast_to_Em2DRestraint(o)
556 
557 _object_types.append("Image")
558 
559 
560 def _object_cast_to_Image(o):
561  """_object_cast_to_Image(Object o) -> Image"""
562  return _IMP_em2d._object_cast_to_Image(o)
563 
564 _object_types.append("ImageReaderWriter")
565 
566 
567 def _object_cast_to_ImageReaderWriter(o):
568  """_object_cast_to_ImageReaderWriter(Object o) -> ImageReaderWriter"""
569  return _IMP_em2d._object_cast_to_ImageReaderWriter(o)
570 
571 _object_types.append("JPGImageReaderWriter")
572 
573 
574 def _object_cast_to_JPGImageReaderWriter(o):
575  """_object_cast_to_JPGImageReaderWriter(Object o) -> JPGImageReaderWriter"""
576  return _IMP_em2d._object_cast_to_JPGImageReaderWriter(o)
577 
578 _object_types.append("TIFFImageReaderWriter")
579 
580 
581 def _object_cast_to_TIFFImageReaderWriter(o):
582  """_object_cast_to_TIFFImageReaderWriter(Object o) -> TIFFImageReaderWriter"""
583  return _IMP_em2d._object_cast_to_TIFFImageReaderWriter(o)
584 
585 _object_types.append("SpiderImageReaderWriter")
586 
587 
588 def _object_cast_to_SpiderImageReaderWriter(o):
589  """_object_cast_to_SpiderImageReaderWriter(Object o) -> SpiderImageReaderWriter"""
590  return _IMP_em2d._object_cast_to_SpiderImageReaderWriter(o)
591 
592 _object_types.append("CollisionCrossSection")
593 
594 
595 def _object_cast_to_CollisionCrossSection(o):
596  """_object_cast_to_CollisionCrossSection(Object o) -> CollisionCrossSection"""
597  return _IMP_em2d._object_cast_to_CollisionCrossSection(o)
598 
599 _object_types.append("GridStates")
600 
601 
602 def _object_cast_to_GridStates(o):
603  """_object_cast_to_GridStates(Object o) -> GridStates"""
604  return _IMP_em2d._object_cast_to_GridStates(o)
605 
606 _object_types.append("ProjectionStates")
607 
608 
609 def _object_cast_to_ProjectionStates(o):
610  """_object_cast_to_ProjectionStates(Object o) -> ProjectionStates"""
611  return _IMP_em2d._object_cast_to_ProjectionStates(o)
612 
613 _object_types.append("DistanceFilter")
614 
615 
616 def _object_cast_to_DistanceFilter(o):
617  """_object_cast_to_DistanceFilter(Object o) -> DistanceFilter"""
618  return _IMP_em2d._object_cast_to_DistanceFilter(o)
619 
620 _object_types.append("DistanceFilterTable")
621 
622 
623 def _object_cast_to_DistanceFilterTable(o):
624  """_object_cast_to_DistanceFilterTable(Object o) -> DistanceFilterTable"""
625  return _IMP_em2d._object_cast_to_DistanceFilterTable(o)
626 
627 _object_types.append("RigidBodiesImageFitRestraint")
628 
629 
630 def _object_cast_to_RigidBodiesImageFitRestraint(o):
631  """_object_cast_to_RigidBodiesImageFitRestraint(Object o) -> RigidBodiesImageFitRestraint"""
632  return _IMP_em2d._object_cast_to_RigidBodiesImageFitRestraint(o)
633 
634 _object_types.append("DummyRestraint")
635 
636 
637 def _object_cast_to_DummyRestraint(o):
638  """_object_cast_to_DummyRestraint(Object o) -> DummyRestraint"""
639  return _IMP_em2d._object_cast_to_DummyRestraint(o)
640 
641 _object_types.append("ParticlesDummyRestraint")
642 
643 
644 def _object_cast_to_ParticlesDummyRestraint(o):
645  """_object_cast_to_ParticlesDummyRestraint(Object o) -> ParticlesDummyRestraint"""
646  return _IMP_em2d._object_cast_to_ParticlesDummyRestraint(o)
647 
648 _object_types.append("RelativePositionMover")
649 
650 
651 def _object_cast_to_RelativePositionMover(o):
652  """_object_cast_to_RelativePositionMover(Object o) -> RelativePositionMover"""
653  return _IMP_em2d._object_cast_to_RelativePositionMover(o)
654 
655 _object_types.append("PCAFitRestraint")
656 
657 
658 def _object_cast_to_em2dPCAFitRestraint(o):
659  """_object_cast_to_em2dPCAFitRestraint(Object o) -> PCAFitRestraint"""
660  return _IMP_em2d._object_cast_to_em2dPCAFitRestraint(o)
661 
662 def ProjectionParametersList(l=[]):
663  return [ProjectionParameters(x) for x in l]
664 _plural_types.append("ProjectionParametersList")
665 
666 
667 _value_types.append("ProjectionParameters")
668 
669 
670 def show(*args):
671  """
672  show(cv::Mat const & m, _ostream out)
673  show(cv::Mat const & m)
674  """
675  return _IMP_em2d.show(*args)
676 
677 def write_matrix(m, name):
678  """write_matrix(cv::Mat & m, std::string name)"""
679  return _IMP_em2d.write_matrix(m, name)
680 class ImageReaderWriter(IMP.Object):
681  """Proxy of C++ IMP::em2d::ImageReaderWriter class."""
682 
683  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
684 
685  def __init__(self, *args, **kwargs):
686  raise AttributeError("No constructor defined - class is abstract")
687 
688  def read(self, filename, header, data):
689  """read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
690  return _IMP_em2d.ImageReaderWriter_read(self, filename, header, data)
691 
692 
693  def read_from_floats(self, filename, header, data):
694  """read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
695  return _IMP_em2d.ImageReaderWriter_read_from_floats(self, filename, header, data)
696 
697 
698  def read_from_ints(self, filename, header, data):
699  """read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
700  return _IMP_em2d.ImageReaderWriter_read_from_ints(self, filename, header, data)
701 
702 
703  def write(self, filename, header, data):
704  """write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
705  return _IMP_em2d.ImageReaderWriter_write(self, filename, header, data)
706 
707 
708  def write_to_floats(self, filename, header, data):
709  """write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
710  return _IMP_em2d.ImageReaderWriter_write_to_floats(self, filename, header, data)
711 
712 
713  def write_to_ints(self, filename, header, data):
714  """write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
715  return _IMP_em2d.ImageReaderWriter_write_to_ints(self, filename, header, data)
716 
717 
718  def get_version_info(self):
719  """get_version_info(ImageReaderWriter self) -> VersionInfo"""
720  return _IMP_em2d.ImageReaderWriter_get_version_info(self)
721 
722 
723  def __str__(self):
724  """__str__(ImageReaderWriter self) -> std::string"""
725  return _IMP_em2d.ImageReaderWriter___str__(self)
726 
727 
728  def __repr__(self):
729  """__repr__(ImageReaderWriter self) -> std::string"""
730  return _IMP_em2d.ImageReaderWriter___repr__(self)
731 
732 
733  @staticmethod
734  def get_from(o):
735  return _object_cast_to_ImageReaderWriter(o)
736 
737 ImageReaderWriter_swigregister = _IMP_em2d.ImageReaderWriter_swigregister
738 ImageReaderWriter_swigregister(ImageReaderWriter)
739 
740 class PolarResamplingParameters(object):
741  """Proxy of C++ IMP::em2d::PolarResamplingParameters class."""
742 
743  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
744 
745  def __init__(self, *args):
746  """
747  __init__(IMP::em2d::PolarResamplingParameters self) -> PolarResamplingParameters
748  __init__(IMP::em2d::PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
749  __init__(IMP::em2d::PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
750  """
751  this = _IMP_em2d.new_PolarResamplingParameters(*args)
752  try:
753  self.this.append(this)
754  except __builtin__.Exception:
755  self.this = this
756  __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
757  __del__ = lambda self: None
758 
759  def setup(self, rows, cols):
760  """setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
761  return _IMP_em2d.PolarResamplingParameters_setup(self, rows, cols)
762 
763 
764  def get_starting_radius(self):
765  """get_starting_radius(PolarResamplingParameters self) -> double"""
766  return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
767 
768 
769  def get_ending_radius(self):
770  """get_ending_radius(PolarResamplingParameters self) -> double"""
771  return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
772 
773 
774  def get_radius(self, n_ring):
775  """get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
776  return _IMP_em2d.PolarResamplingParameters_get_radius(self, n_ring)
777 
778 
779  def get_number_of_rings(self):
780  """get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
781  return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
782 
783 
784  def set_estimated_number_of_angles(self, aprox_value):
785  """set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
786  return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, aprox_value)
787 
788 
789  def get_number_of_angles(self):
790  """get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
791  return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
792 
793 
794  def get_angle_step(self):
795  """get_angle_step(PolarResamplingParameters self) -> double"""
796  return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
797 
798 
799  def get_radius_step(self):
800  """get_radius_step(PolarResamplingParameters self) -> double"""
801  return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
802 
803 
804  def create_maps_for_resampling(self):
805  """create_maps_for_resampling(PolarResamplingParameters self)"""
806  return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
807 
808 
809  def get_resampling_maps(self, m1, m2):
810  """get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
811  return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, m1, m2)
812 
813 
814  def get_resampling_map(self, m1):
815  """get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
816  return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, m1)
817 
818 
819  def show(self, out):
820  """show(PolarResamplingParameters self, _ostream out)"""
821  return _IMP_em2d.PolarResamplingParameters_show(self, out)
822 
823 
824  def get_is_setup(self):
825  """get_is_setup(PolarResamplingParameters self) -> bool"""
826  return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
827 
828 
829  def __str__(self):
830  """__str__(PolarResamplingParameters self) -> std::string"""
831  return _IMP_em2d.PolarResamplingParameters___str__(self)
832 
833 
834  def __repr__(self):
835  """__repr__(PolarResamplingParameters self) -> std::string"""
836  return _IMP_em2d.PolarResamplingParameters___repr__(self)
837 
838 PolarResamplingParameters_swigregister = _IMP_em2d.PolarResamplingParameters_swigregister
839 PolarResamplingParameters_swigregister(PolarResamplingParameters)
840 
841 class SegmentationParameters(object):
842  """Proxy of C++ IMP::em2d::SegmentationParameters class."""
843 
844  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
845  image_pixel_size = _swig_property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set)
846  diffusion_beta = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set)
847  diffusion_timesteps = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set)
848  fill_holes_stddevs = _swig_property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set)
849  opening_kernel = _swig_property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set)
850  remove_sizing_percentage = _swig_property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set)
851  binary_background = _swig_property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set)
852  binary_foreground = _swig_property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set)
853  threshold = _swig_property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set)
854 
855  def __init__(self, *args):
856  """
857  __init__(IMP::em2d::SegmentationParameters self) -> SegmentationParameters
858  __init__(IMP::em2d::SegmentationParameters self, double apix, double diff_beta, unsigned int diff_timesteps, double fh_stddevs, cv::Mat const & kr, int background, int foreground) -> SegmentationParameters
859  """
860  this = _IMP_em2d.new_SegmentationParameters(*args)
861  try:
862  self.this.append(this)
863  except __builtin__.Exception:
864  self.this = this
865 
866  def show(self, *args):
867  """
868  show(SegmentationParameters self, _ostream out)
869  show(SegmentationParameters self)
870  """
871  return _IMP_em2d.SegmentationParameters_show(self, *args)
872 
873 
874  def __str__(self):
875  """__str__(SegmentationParameters self) -> std::string"""
876  return _IMP_em2d.SegmentationParameters___str__(self)
877 
878 
879  def __repr__(self):
880  """__repr__(SegmentationParameters self) -> std::string"""
881  return _IMP_em2d.SegmentationParameters___repr__(self)
882 
883  __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
884  __del__ = lambda self: None
885 SegmentationParameters_swigregister = _IMP_em2d.SegmentationParameters_swigregister
886 SegmentationParameters_swigregister(SegmentationParameters)
887 
888 class MatchTemplateResult(object):
889  """Proxy of C++ IMP::em2d::MatchTemplateResult class."""
890 
891  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
892  pair = _swig_property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set)
893  cross_correlation = _swig_property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set)
894 
895  def __init__(self, p, cc):
896  """__init__(IMP::em2d::MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
897  this = _IMP_em2d.new_MatchTemplateResult(p, cc)
898  try:
899  self.this.append(this)
900  except __builtin__.Exception:
901  self.this = this
902 
903  def show(self, *args):
904  """
905  show(MatchTemplateResult self, _ostream out)
906  show(MatchTemplateResult self)
907  """
908  return _IMP_em2d.MatchTemplateResult_show(self, *args)
909 
910 
911  def __str__(self):
912  """__str__(MatchTemplateResult self) -> std::string"""
913  return _IMP_em2d.MatchTemplateResult___str__(self)
914 
915 
916  def __repr__(self):
917  """__repr__(MatchTemplateResult self) -> std::string"""
918  return _IMP_em2d.MatchTemplateResult___repr__(self)
919 
920  __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
921  __del__ = lambda self: None
922 MatchTemplateResult_swigregister = _IMP_em2d.MatchTemplateResult_swigregister
923 MatchTemplateResult_swigregister(MatchTemplateResult)
924 
925 
926 def apply_mask(m, result, mask, val):
927  """apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
928  return _IMP_em2d.apply_mask(m, result, mask, val)
929 
930 def apply_circular_mask(mat, result, radius, value=0.0):
931  """
932  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)
933  apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius)
934  """
935  return _IMP_em2d.apply_circular_mask(mat, result, radius, value)
936 
937 def get_mean(mat, mask):
938  """get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
939  return _IMP_em2d.get_mean(mat, mask)
940 
941 def create_circular_mask(rows, cols, radius):
942  """create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
943  return _IMP_em2d.create_circular_mask(rows, cols, radius)
944 
945 def do_histogram_stretching(m, boxes, offset):
946  """do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
947  return _IMP_em2d.do_histogram_stretching(m, boxes, offset)
948 
949 def do_dilate_and_shrink_warp(m, grayscale, kernel):
950  """do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
951  return _IMP_em2d.do_dilate_and_shrink_warp(m, grayscale, kernel)
952 
953 def do_morphologic_reconstruction(mask, marker, neighbors_mode=4):
954  """
955  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)
956  do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker)
957  """
958  return _IMP_em2d.do_morphologic_reconstruction(mask, marker, neighbors_mode)
959 
960 def do_labeling(m, mat_to_label):
961  """do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
962  return _IMP_em2d.do_labeling(m, mat_to_label)
963 
964 def get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang):
965  """get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
966  return _IMP_em2d.get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang)
967 
968 def get_domes(m, result, h):
969  """get_domes(cv::Mat & m, cv::Mat & result, double h)"""
970  return _IMP_em2d.get_domes(m, result, h)
971 
972 def get_transformed(input, transformed, T):
973  """get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
974  return _IMP_em2d.get_transformed(input, transformed, T)
975 
976 def apply_threshold(m, result, threshold=0.0):
977  """
978  apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)
979  apply_threshold(cv::Mat & m, cv::Mat & result)
980  """
981  return _IMP_em2d.apply_threshold(m, result, threshold)
982 
983 def do_morphologic_contrast_enhancement(m, result, kernel, iterations):
984  """do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
985  return _IMP_em2d.do_morphologic_contrast_enhancement(m, result, kernel, iterations)
986 
987 def get_morphologic_gradient(m, result, kernel):
988  """get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
989  return _IMP_em2d.get_morphologic_gradient(m, result, kernel)
990 
991 def get_overlap_percentage(m1, m2, center):
992  """get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
993  return _IMP_em2d.get_overlap_percentage(m1, m2, center)
994 
995 def get_best_template_matches(m, templ, n):
996  """get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
997  return _IMP_em2d.get_best_template_matches(m, templ, n)
998 class Image(IMP.Object):
999  """Proxy of C++ IMP::em2d::Image class."""
1000 
1001  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1002 
1003  def __init__(self, *args):
1004  """
1005  __init__(IMP::em2d::Image self) -> Image
1006  __init__(IMP::em2d::Image self, int rows, int cols) -> Image
1007  __init__(IMP::em2d::Image self, IMP::String filename, ImageReaderWriter reader) -> Image
1008  """
1009  this = _IMP_em2d.new_Image(*args)
1010  try:
1011  self.this.append(this)
1012  except __builtin__.Exception:
1013  self.this = this
1014 
1015  def get_data(self):
1016  """get_data(Image self) -> cv::Mat &"""
1017  return _IMP_em2d.Image_get_data(self)
1018 
1019 
1020  def set_data(self, mat):
1021  """set_data(Image self, cv::Mat const & mat)"""
1022  return _IMP_em2d.Image_set_data(self, mat)
1023 
1024 
1025  def set_zeros(self):
1026  """set_zeros(Image self)"""
1027  return _IMP_em2d.Image_set_zeros(self)
1028 
1029 
1030  def set_value(self, *args):
1031  """
1032  set_value(Image self, double val)
1033  set_value(Image self, int i, int j, double val)
1034  """
1035  return _IMP_em2d.Image_set_value(self, *args)
1036 
1037 
1038  def __call__(self, i, j):
1039  """__call__(Image self, int i, int j) -> double"""
1040  return _IMP_em2d.Image___call__(self, i, j)
1041 
1042 
1043  def get_header(self):
1044  """get_header(Image self) -> ImageHeader"""
1045  return _IMP_em2d.Image_get_header(self)
1046 
1047 
1048  def set_size(self, *args):
1049  """
1050  set_size(Image self, int rows, int cols)
1051  set_size(Image self, Image img)
1052  """
1053  return _IMP_em2d.Image_set_size(self, *args)
1054 
1055 
1056  def update_header(self):
1057  """update_header(Image self)"""
1058  return _IMP_em2d.Image_update_header(self)
1059 
1060 
1061  def read(self, filename, reader):
1062  """read(Image self, IMP::String filename, ImageReaderWriter reader)"""
1063  return _IMP_em2d.Image_read(self, filename, reader)
1064 
1065 
1066  def write(self, filename, writer):
1067  """write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
1068  return _IMP_em2d.Image_write(self, filename, writer)
1069 
1070 
1071  def show(self, out):
1072  """show(Image self, _ostream out)"""
1073  return _IMP_em2d.Image_show(self, out)
1074 
1075 
1076  def get_version_info(self):
1077  """get_version_info(Image self) -> VersionInfo"""
1078  return _IMP_em2d.Image_get_version_info(self)
1079 
1080 
1081  def set_name(self, name):
1082  """set_name(Image self, IMP::String const & name)"""
1083  return _IMP_em2d.Image_set_name(self, name)
1084 
1085 
1086  def get_name(self):
1087  """get_name(Image self) -> IMP::String"""
1088  return _IMP_em2d.Image_get_name(self)
1089 
1090 
1091  def get_min_and_max_values(self):
1092  """get_min_and_max_values(Image self) -> IMP::FloatRange"""
1093  return _IMP_em2d.Image_get_min_and_max_values(self)
1094 
1095 
1096  def __str__(self):
1097  """__str__(Image self) -> std::string"""
1098  return _IMP_em2d.Image___str__(self)
1099 
1100 
1101  def __repr__(self):
1102  """__repr__(Image self) -> std::string"""
1103  return _IMP_em2d.Image___repr__(self)
1104 
1105 
1106  @staticmethod
1107  def get_from(o):
1108  return _object_cast_to_Image(o)
1109 
1110 Image_swigregister = _IMP_em2d.Image_swigregister
1111 Image_swigregister(Image)
1112 
1113 
1114 def read_images(names, rw):
1115  """read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1116  return _IMP_em2d.read_images(names, rw)
1117 
1118 def save_images(images, names, rw):
1119  """save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1120  return _IMP_em2d.save_images(images, names, rw)
1121 
1122 def do_normalize(*args):
1123  """
1124  do_normalize(cv::Mat & m)
1125  do_normalize(Image im, bool force=False)
1126  do_normalize(Image im)
1127  """
1128  return _IMP_em2d.do_normalize(*args)
1129 
1130 def get_histogram(*args):
1131  """
1132  get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1133  get_histogram(Image img, int bins) -> IMP::Floats
1134  """
1135  return _IMP_em2d.get_histogram(*args)
1136 
1137 def apply_variance_filter(*args):
1138  """
1139  apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1140  apply_variance_filter(Image input, Image filtered, int kernelsize)
1141  """
1142  return _IMP_em2d.apply_variance_filter(*args)
1143 
1144 def apply_diffusion_filter(*args):
1145  """
1146  apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1147  apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1148  """
1149  return _IMP_em2d.apply_diffusion_filter(*args)
1150 
1151 def do_fill_holes(*args):
1152  """
1153  do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1154  do_fill_holes(Image input, Image result, double n_stddevs)
1155  """
1156  return _IMP_em2d.do_fill_holes(*args)
1157 
1158 def do_combined_fill_holes_and_threshold(*args):
1159  """
1160  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1161  do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs)
1162  do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1163  """
1164  return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1165 
1166 def do_extend_borders(*args):
1167  """
1168  do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1169  do_extend_borders(Image im1, Image im2, unsigned int pix)
1170  """
1171  return _IMP_em2d.do_extend_borders(*args)
1172 
1173 def do_segmentation(*args):
1174  """
1175  do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1176  do_segmentation(Image input, Image result, SegmentationParameters params)
1177  """
1178  return _IMP_em2d.do_segmentation(*args)
1179 
1180 def do_remove_small_objects(*args):
1181  """
1182  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1183  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0)
1184  do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage)
1185  do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1186  do_remove_small_objects(Image input, double percentage, int background=0)
1187  do_remove_small_objects(Image input, double percentage)
1188  """
1189  return _IMP_em2d.do_remove_small_objects(*args)
1190 
1191 def do_subtract_images(first, second, result):
1192  """do_subtract_images(Image first, Image second, Image result)"""
1193  return _IMP_em2d.do_subtract_images(first, second, result)
1194 
1195 def add_noise(*args):
1196  """
1197  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode, double df=3)
1198  add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode)
1199  add_noise(cv::Mat & v, double op1, double op2)
1200  add_noise(Image im1, double op1, double op2, IMP::String const & mode, double df=3)
1201  add_noise(Image im1, double op1, double op2, IMP::String const & mode)
1202  add_noise(Image im1, double op1, double op2)
1203  """
1204  return _IMP_em2d.add_noise(*args)
1205 
1206 def do_resample_polar(*args):
1207  """
1208  do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1209  do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1210  """
1211  return _IMP_em2d.do_resample_polar(*args)
1212 
1213 def crop(*args):
1214  """
1215  crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1216  crop(Image img, IMP::IntPair const & center, int size)
1217  """
1218  return _IMP_em2d.crop(*args)
1219 
1220 def apply_mean_outside_mask(img, radius):
1221  """apply_mean_outside_mask(Image img, double radius)"""
1222  return _IMP_em2d.apply_mean_outside_mask(img, radius)
1223 class RegistrationResult(object):
1224  """Proxy of C++ IMP::em2d::RegistrationResult class."""
1225 
1226  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1227 
1228  def __init__(self, *args):
1229  """
1230  __init__(IMP::em2d::RegistrationResult self) -> RegistrationResult
1231  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1232  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1233  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0) -> RegistrationResult
1234  __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift) -> RegistrationResult
1235  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1236  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1237  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0) -> RegistrationResult
1238  __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift) -> RegistrationResult
1239  __init__(IMP::em2d::RegistrationResult self, Rotation3D R) -> RegistrationResult
1240  """
1241  this = _IMP_em2d.new_RegistrationResult(*args)
1242  try:
1243  self.this.append(this)
1244  except __builtin__.Exception:
1245  self.this = this
1246 
1247  def get_phi(self):
1248  """get_phi(RegistrationResult self) -> double"""
1249  return _IMP_em2d.RegistrationResult_get_phi(self)
1250 
1251 
1252  def get_theta(self):
1253  """get_theta(RegistrationResult self) -> double"""
1254  return _IMP_em2d.RegistrationResult_get_theta(self)
1255 
1256 
1257  def get_psi(self):
1258  """get_psi(RegistrationResult self) -> double"""
1259  return _IMP_em2d.RegistrationResult_get_psi(self)
1260 
1261 
1262  def get_shift(self):
1263  """get_shift(RegistrationResult self) -> Vector2D"""
1264  return _IMP_em2d.RegistrationResult_get_shift(self)
1265 
1266 
1267  def get_shift_3d(self):
1268  """get_shift_3d(RegistrationResult self) -> Vector3D"""
1269  return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1270 
1271 
1272  def get_projection_index(self):
1273  """get_projection_index(RegistrationResult self) -> int"""
1274  return _IMP_em2d.RegistrationResult_get_projection_index(self)
1275 
1276 
1277  def set_projection_index(self, index):
1278  """set_projection_index(RegistrationResult self, int index)"""
1279  return _IMP_em2d.RegistrationResult_set_projection_index(self, index)
1280 
1281 
1282  def get_image_index(self):
1283  """get_image_index(RegistrationResult self) -> int"""
1284  return _IMP_em2d.RegistrationResult_get_image_index(self)
1285 
1286 
1287  def set_image_index(self, index):
1288  """set_image_index(RegistrationResult self, int index)"""
1289  return _IMP_em2d.RegistrationResult_set_image_index(self, index)
1290 
1291 
1292  def get_name(self):
1293  """get_name(RegistrationResult self) -> IMP::String"""
1294  return _IMP_em2d.RegistrationResult_get_name(self)
1295 
1296 
1297  def get_ccc(self):
1298  """get_ccc(RegistrationResult self) -> double"""
1299  return _IMP_em2d.RegistrationResult_get_ccc(self)
1300 
1301 
1302  def set_ccc(self, ccc):
1303  """set_ccc(RegistrationResult self, double ccc)"""
1304  return _IMP_em2d.RegistrationResult_set_ccc(self, ccc)
1305 
1306 
1307  def get_score(self):
1308  """get_score(RegistrationResult self) -> double"""
1309  return _IMP_em2d.RegistrationResult_get_score(self)
1310 
1311 
1312  def set_score(self, Score):
1313  """set_score(RegistrationResult self, double Score)"""
1314  return _IMP_em2d.RegistrationResult_set_score(self, Score)
1315 
1316 
1317  def set_rotation(self, *args):
1318  """
1319  set_rotation(RegistrationResult self, double phi, double theta, double psi)
1320  set_rotation(RegistrationResult self, Rotation3D R)
1321  """
1322  return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1323 
1324 
1325  def set_shift(self, shift):
1326  """set_shift(RegistrationResult self, Vector2D shift)"""
1327  return _IMP_em2d.RegistrationResult_set_shift(self, shift)
1328 
1329 
1330  def set_name(self, name):
1331  """set_name(RegistrationResult self, IMP::String name)"""
1332  return _IMP_em2d.RegistrationResult_set_name(self, name)
1333 
1334 
1335  def add_in_plane_transformation(self, t):
1336  """add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1337  return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, t)
1338 
1339 
1340  def show(self, *args):
1341  """
1342  show(RegistrationResult self, _ostream out)
1343  show(RegistrationResult self)
1344  """
1345  return _IMP_em2d.RegistrationResult_show(self, *args)
1346 
1347 
1348  def write(self, *args):
1349  """
1350  write(RegistrationResult self, _ostream out)
1351  write(RegistrationResult self)
1352  """
1353  return _IMP_em2d.RegistrationResult_write(self, *args)
1354 
1355 
1356  def write_comment_line(self, *args):
1357  """
1358  write_comment_line(RegistrationResult self, _ostream out)
1359  write_comment_line(RegistrationResult self)
1360  """
1361  return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1362 
1363 
1364  def read(self, s):
1365  """read(RegistrationResult self, IMP::String const & s)"""
1366  return _IMP_em2d.RegistrationResult_read(self, s)
1367 
1368 
1369  def set_random_registration(self, index, maximum_shift):
1370  """set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1371  return _IMP_em2d.RegistrationResult_set_random_registration(self, index, maximum_shift)
1372 
1373 
1374  def get_rotation(self):
1375  """get_rotation(RegistrationResult self) -> Rotation3D"""
1376  return _IMP_em2d.RegistrationResult_get_rotation(self)
1377 
1378 
1379  def set_in_image(self, header):
1380  """set_in_image(RegistrationResult self, ImageHeader header)"""
1381  return _IMP_em2d.RegistrationResult_set_in_image(self, header)
1382 
1383 
1384  def read_from_image(self, header):
1385  """read_from_image(RegistrationResult self, ImageHeader header)"""
1386  return _IMP_em2d.RegistrationResult_read_from_image(self, header)
1387 
1388 
1389  def get_is_optimized_result(self):
1390  """get_is_optimized_result(RegistrationResult self) -> bool"""
1391  return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1392 
1393  __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1394  __del__ = lambda self: None
1395 
1396  def __str__(self):
1397  """__str__(RegistrationResult self) -> std::string"""
1398  return _IMP_em2d.RegistrationResult___str__(self)
1399 
1400 
1401  def __repr__(self):
1402  """__repr__(RegistrationResult self) -> std::string"""
1403  return _IMP_em2d.RegistrationResult___repr__(self)
1404 
1405 RegistrationResult_swigregister = _IMP_em2d.RegistrationResult_swigregister
1406 RegistrationResult_swigregister(RegistrationResult)
1407 
1408 
1409 def read_registration_results(filename):
1410  """read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1411  return _IMP_em2d.read_registration_results(filename)
1412 
1413 def write_registration_results(filename, results):
1414  """write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1415  return _IMP_em2d.write_registration_results(filename, results)
1416 
1417 def get_random_registration_results(n, maximum_shift=5.0):
1418  """
1419  get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults
1420  get_random_registration_results(unsigned int n) -> IMP::em2d::RegistrationResults
1421  """
1422  return _IMP_em2d.get_random_registration_results(n, maximum_shift)
1423 
1425  """get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1426  return _IMP_em2d.get_evenly_distributed_registration_results(n_projections)
1427 class SpiderImageReaderWriter(ImageReaderWriter):
1428  """Proxy of C++ IMP::em2d::SpiderImageReaderWriter class."""
1429 
1430  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1431  filename_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set)
1432  skip_type_check_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set)
1433  force_reversed_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set)
1434  skip_extra_checkings_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set)
1435 
1436  def __init__(self, *args):
1437  """
1438  __init__(IMP::em2d::SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1439  __init__(IMP::em2d::SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1440  """
1441  this = _IMP_em2d.new_SpiderImageReaderWriter(*args)
1442  try:
1443  self.this.append(this)
1444  except __builtin__.Exception:
1445  self.this = this
1446 
1447  def __str__(self):
1448  """__str__(SpiderImageReaderWriter self) -> std::string"""
1449  return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1450 
1451 
1452  def __repr__(self):
1453  """__repr__(SpiderImageReaderWriter self) -> std::string"""
1454  return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1455 
1456 
1457  @staticmethod
1458  def get_from(o):
1459  return _object_cast_to_SpiderImageReaderWriter(o)
1460 
1461 SpiderImageReaderWriter_swigregister = _IMP_em2d.SpiderImageReaderWriter_swigregister
1462 SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1463 
1464 class JPGImageReaderWriter(ImageReaderWriter):
1465  """Proxy of C++ IMP::em2d::JPGImageReaderWriter class."""
1466 
1467  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1468 
1469  def __init__(self):
1470  """__init__(IMP::em2d::JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1471  this = _IMP_em2d.new_JPGImageReaderWriter()
1472  try:
1473  self.this.append(this)
1474  except __builtin__.Exception:
1475  self.this = this
1476 
1477  def __str__(self):
1478  """__str__(JPGImageReaderWriter self) -> std::string"""
1479  return _IMP_em2d.JPGImageReaderWriter___str__(self)
1480 
1481 
1482  def __repr__(self):
1483  """__repr__(JPGImageReaderWriter self) -> std::string"""
1484  return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1485 
1486 
1487  @staticmethod
1488  def get_from(o):
1489  return _object_cast_to_JPGImageReaderWriter(o)
1490 
1491 JPGImageReaderWriter_swigregister = _IMP_em2d.JPGImageReaderWriter_swigregister
1492 JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1493 
1494 class TIFFImageReaderWriter(ImageReaderWriter):
1495  """Proxy of C++ IMP::em2d::TIFFImageReaderWriter class."""
1496 
1497  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1498 
1499  def __init__(self):
1500  """__init__(IMP::em2d::TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1501  this = _IMP_em2d.new_TIFFImageReaderWriter()
1502  try:
1503  self.this.append(this)
1504  except __builtin__.Exception:
1505  self.this = this
1506 
1507  def __str__(self):
1508  """__str__(TIFFImageReaderWriter self) -> std::string"""
1509  return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1510 
1511 
1512  def __repr__(self):
1513  """__repr__(TIFFImageReaderWriter self) -> std::string"""
1514  return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1515 
1516 
1517  @staticmethod
1518  def get_from(o):
1519  return _object_cast_to_TIFFImageReaderWriter(o)
1520 
1521 TIFFImageReaderWriter_swigregister = _IMP_em2d.TIFFImageReaderWriter_swigregister
1522 TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1523 
1524 
1526  """do_matrix_to_image_flip(cv::Mat & m)"""
1527  return _IMP_em2d.do_matrix_to_image_flip(m)
1528 
1530  """get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1531  return _IMP_em2d.get_autocorrelation2d_no_preprocessing(M, corr)
1532 
1533 def get_autocorrelation2d(*args):
1534  """
1535  get_autocorrelation2d(Image im1, Image im2)
1536  get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1537  """
1538  return _IMP_em2d.get_autocorrelation2d(*args)
1539 
1540 def get_correlation2d(*args):
1541  """
1542  get_correlation2d(Image im1, Image im2, Image corr)
1543  get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1544  """
1545  return _IMP_em2d.get_correlation2d(*args)
1546 
1547 def get_correlation2d_no_preprocessing(M1, M2, corr):
1548  """get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1549  return _IMP_em2d.get_correlation2d_no_preprocessing(M1, M2, corr)
1550 
1551 def get_fft_using_optimal_size(m, M):
1552  """get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1553  return _IMP_em2d.get_fft_using_optimal_size(m, M)
1554 
1555 def get_spectrum(m, real, imag):
1556  """get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1557  return _IMP_em2d.get_spectrum(m, real, imag)
1558 
1559 def get_rotation_error(rr1, rr2):
1560  """get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1561  return _IMP_em2d.get_rotation_error(rr1, rr2)
1562 
1563 def get_shift_error(rr1, rr2):
1564  """get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1565  return _IMP_em2d.get_shift_error(rr1, rr2)
1566 
1567 def get_average_rotation_error(correct_RRs, computed_RRs):
1568  """get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1569  return _IMP_em2d.get_average_rotation_error(correct_RRs, computed_RRs)
1570 
1571 def get_average_shift_error(correct_RRs, computed_RRs):
1572  """get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1573  return _IMP_em2d.get_average_shift_error(correct_RRs, computed_RRs)
1574 
1576  """
1577  get_cross_correlation_coefficient(Image im1, Image im2) -> double
1578  get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1579  """
1580  return _IMP_em2d.get_cross_correlation_coefficient(*args)
1581 
1582 def get_global_score(RRs):
1583  """get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1584  return _IMP_em2d.get_global_score(RRs)
1585 class ScoreFunction(IMP.Object):
1586  """Proxy of C++ IMP::em2d::ScoreFunction class."""
1587 
1588  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1589 
1590  def __init__(self, *args, **kwargs):
1591  raise AttributeError("No constructor defined - class is abstract")
1592 
1593  def get_score(self, image, projection):
1594  """get_score(ScoreFunction self, Image image, Image projection) -> double"""
1595  return _IMP_em2d.ScoreFunction_get_score(self, image, projection)
1596 
1597 
1598  def set_variance_image(self, var):
1599  """set_variance_image(ScoreFunction self, Image var)"""
1600  return _IMP_em2d.ScoreFunction_set_variance_image(self, var)
1601 
1602 
1603  def get_version_info(self):
1604  """get_version_info(ScoreFunction self) -> VersionInfo"""
1605  return _IMP_em2d.ScoreFunction_get_version_info(self)
1606 
1607 
1608  def __str__(self):
1609  """__str__(ScoreFunction self) -> std::string"""
1610  return _IMP_em2d.ScoreFunction___str__(self)
1611 
1612 
1613  def __repr__(self):
1614  """__repr__(ScoreFunction self) -> std::string"""
1615  return _IMP_em2d.ScoreFunction___repr__(self)
1616 
1617 
1618  @staticmethod
1619  def get_from(o):
1620  return _object_cast_to_ScoreFunction(o)
1621 
1622 ScoreFunction_swigregister = _IMP_em2d.ScoreFunction_swigregister
1623 ScoreFunction_swigregister(ScoreFunction)
1624 
1625 class ChiSquaredScore(ScoreFunction):
1626  """Proxy of C++ IMP::em2d::ChiSquaredScore class."""
1627 
1628  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1629 
1630  def __init__(self):
1631  """__init__(IMP::em2d::ChiSquaredScore self) -> ChiSquaredScore"""
1632  this = _IMP_em2d.new_ChiSquaredScore()
1633  try:
1634  self.this.append(this)
1635  except __builtin__.Exception:
1636  self.this = this
1637 
1638  def __str__(self):
1639  """__str__(ChiSquaredScore self) -> std::string"""
1640  return _IMP_em2d.ChiSquaredScore___str__(self)
1641 
1642 
1643  def __repr__(self):
1644  """__repr__(ChiSquaredScore self) -> std::string"""
1645  return _IMP_em2d.ChiSquaredScore___repr__(self)
1646 
1647 
1648  @staticmethod
1649  def get_from(o):
1650  return _object_cast_to_ChiSquaredScore(o)
1651 
1652  __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1653  __del__ = lambda self: None
1654 ChiSquaredScore_swigregister = _IMP_em2d.ChiSquaredScore_swigregister
1655 ChiSquaredScore_swigregister(ChiSquaredScore)
1656 
1657 class EM2DScore(ScoreFunction):
1658  """Proxy of C++ IMP::em2d::EM2DScore class."""
1659 
1660  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1661 
1662  def __init__(self):
1663  """__init__(IMP::em2d::EM2DScore self) -> EM2DScore"""
1664  this = _IMP_em2d.new_EM2DScore()
1665  try:
1666  self.this.append(this)
1667  except __builtin__.Exception:
1668  self.this = this
1669 
1670  def __str__(self):
1671  """__str__(EM2DScore self) -> std::string"""
1672  return _IMP_em2d.EM2DScore___str__(self)
1673 
1674 
1675  def __repr__(self):
1676  """__repr__(EM2DScore self) -> std::string"""
1677  return _IMP_em2d.EM2DScore___repr__(self)
1678 
1679 
1680  @staticmethod
1681  def get_from(o):
1682  return _object_cast_to_EM2DScore(o)
1683 
1684  __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1685  __del__ = lambda self: None
1686 EM2DScore_swigregister = _IMP_em2d.EM2DScore_swigregister
1687 EM2DScore_swigregister(EM2DScore)
1688 
1689 class MeanAbsoluteDifference(ScoreFunction):
1690  """Proxy of C++ IMP::em2d::MeanAbsoluteDifference class."""
1691 
1692  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1693 
1694  def __init__(self):
1695  """__init__(IMP::em2d::MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1696  this = _IMP_em2d.new_MeanAbsoluteDifference()
1697  try:
1698  self.this.append(this)
1699  except __builtin__.Exception:
1700  self.this = this
1701 
1702  def __str__(self):
1703  """__str__(MeanAbsoluteDifference self) -> std::string"""
1704  return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1705 
1706 
1707  def __repr__(self):
1708  """__repr__(MeanAbsoluteDifference self) -> std::string"""
1709  return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1710 
1711 
1712  @staticmethod
1713  def get_from(o):
1714  return _object_cast_to_MeanAbsoluteDifference(o)
1715 
1716  __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1717  __del__ = lambda self: None
1718 MeanAbsoluteDifference_swigregister = _IMP_em2d.MeanAbsoluteDifference_swigregister
1719 MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1720 
1721 
1722 def read_selection_file(fn):
1723  """read_selection_file(IMP::String fn) -> IMP::Strings"""
1724  return _IMP_em2d.read_selection_file(fn)
1725 
1726 def create_filenames(number, basic_name, extension):
1727  """create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1728  return _IMP_em2d.create_filenames(number, basic_name, extension)
1729 class ProjectionParameters(IMP.Decorator):
1730  """Proxy of C++ IMP::em2d::ProjectionParameters class."""
1731 
1732  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1733 
1734  def __init__(self, *args):
1735  """
1736  __init__(IMP::em2d::ProjectionParameters self) -> ProjectionParameters
1737  __init__(IMP::em2d::ProjectionParameters self, Model m, ParticleIndex id) -> ProjectionParameters
1738  __init__(IMP::em2d::ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1739  """
1740  this = _IMP_em2d.new_ProjectionParameters(*args)
1741  try:
1742  self.this.append(this)
1743  except __builtin__.Exception:
1744  self.this = this
1745 
1746  def show(self, *args):
1747  """
1748  show(ProjectionParameters self, _ostream out)
1749  show(ProjectionParameters self)
1750  """
1751  return _IMP_em2d.ProjectionParameters_show(self, *args)
1752 
1753 
1754  def setup_particle(*args):
1755  """
1756  setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
1757  setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1758  """
1759  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1760 
1761  setup_particle = staticmethod(setup_particle)
1762  __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1763  __del__ = lambda self: None
1764 
1765  def get_keys():
1766  """get_keys() -> IMP::FloatKeys const &"""
1767  return _IMP_em2d.ProjectionParameters_get_keys()
1768 
1769  get_keys = staticmethod(get_keys)
1770 
1771  def set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values):
1772  """set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1773  return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values)
1774 
1775 
1776  def get_is_setup(*args):
1777  """
1778  get_is_setup(_ParticleAdaptor p) -> bool
1779  get_is_setup(Model m, ParticleIndex pi) -> bool
1780  """
1781  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1782 
1783  get_is_setup = staticmethod(get_is_setup)
1784 
1785  def get_parameters_optimized(self):
1786  """get_parameters_optimized(ProjectionParameters self) -> bool"""
1787  return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1788 
1789 
1790  def get_translation(self):
1791  """get_translation(ProjectionParameters self) -> Vector3D"""
1792  return _IMP_em2d.ProjectionParameters_get_translation(self)
1793 
1794 
1795  def set_translation(self, v):
1796  """set_translation(ProjectionParameters self, Vector3D v)"""
1797  return _IMP_em2d.ProjectionParameters_set_translation(self, v)
1798 
1799 
1800  def get_rotation(self):
1801  """get_rotation(ProjectionParameters self) -> Rotation3D"""
1802  return _IMP_em2d.ProjectionParameters_get_rotation(self)
1803 
1804 
1805  def set_rotation(self, R):
1806  """set_rotation(ProjectionParameters self, Rotation3D R)"""
1807  return _IMP_em2d.ProjectionParameters_set_rotation(self, R)
1808 
1809 
1810  def set_parameters_optimized(self, tf):
1811  """set_parameters_optimized(ProjectionParameters self, bool tf)"""
1812  return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, tf)
1813 
1814 
1815  def get_quaternion_1(self):
1816  """get_quaternion_1(ProjectionParameters self) -> double"""
1817  return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1818 
1819 
1820  def set_quaternion_1(self, t):
1821  """set_quaternion_1(ProjectionParameters self, double t)"""
1822  return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, t)
1823 
1824 
1825  def get_quaternion_2(self):
1826  """get_quaternion_2(ProjectionParameters self) -> double"""
1827  return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1828 
1829 
1830  def set_quaternion_2(self, t):
1831  """set_quaternion_2(ProjectionParameters self, double t)"""
1832  return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, t)
1833 
1834 
1835  def get_quaternion_3(self):
1836  """get_quaternion_3(ProjectionParameters self) -> double"""
1837  return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1838 
1839 
1840  def set_quaternion_3(self, t):
1841  """set_quaternion_3(ProjectionParameters self, double t)"""
1842  return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, t)
1843 
1844 
1845  def get_quaternion_4(self):
1846  """get_quaternion_4(ProjectionParameters self) -> double"""
1847  return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1848 
1849 
1850  def set_quaternion_4(self, t):
1851  """set_quaternion_4(ProjectionParameters self, double t)"""
1852  return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, t)
1853 
1854 
1855  def get_translation_x(self):
1856  """get_translation_x(ProjectionParameters self) -> double"""
1857  return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1858 
1859 
1860  def set_translation_x(self, t):
1861  """set_translation_x(ProjectionParameters self, double t)"""
1862  return _IMP_em2d.ProjectionParameters_set_translation_x(self, t)
1863 
1864 
1865  def get_translation_y(self):
1866  """get_translation_y(ProjectionParameters self) -> double"""
1867  return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1868 
1869 
1870  def set_translation_y(self, t):
1871  """set_translation_y(ProjectionParameters self, double t)"""
1872  return _IMP_em2d.ProjectionParameters_set_translation_y(self, t)
1873 
1874 
1875  def add_attribute(self, *args):
1876  """
1877  add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1878  add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1879  add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1880  add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1881  add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1882  add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1883  """
1884  return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1885 
1886 
1887  def get_value(self, *args):
1888  """
1889  get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1890  get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1891  get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1892  get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1893  get_value(ProjectionParameters self, ObjectKey a0) -> Object
1894  """
1895  return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1896 
1897 
1898  def set_value(self, *args):
1899  """
1900  set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1901  set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1902  set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1903  set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1904  set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1905  """
1906  return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1907 
1908 
1909  def remove_attribute(self, *args):
1910  """
1911  remove_attribute(ProjectionParameters self, FloatKey a0)
1912  remove_attribute(ProjectionParameters self, IntKey a0)
1913  remove_attribute(ProjectionParameters self, StringKey a0)
1914  remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1915  remove_attribute(ProjectionParameters self, ObjectKey a0)
1916  """
1917  return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1918 
1919 
1920  def has_attribute(self, *args):
1921  """
1922  has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1923  has_attribute(ProjectionParameters self, IntKey a0) -> bool
1924  has_attribute(ProjectionParameters self, StringKey a0) -> bool
1925  has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
1926  has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
1927  """
1928  return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
1929 
1930 
1931  def get_derivative(self, a0):
1932  """get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
1933  return _IMP_em2d.ProjectionParameters_get_derivative(self, a0)
1934 
1935 
1936  def get_name(self):
1937  """get_name(ProjectionParameters self) -> std::string"""
1938  return _IMP_em2d.ProjectionParameters_get_name(self)
1939 
1940 
1941  def clear_caches(self):
1942  """clear_caches(ProjectionParameters self)"""
1943  return _IMP_em2d.ProjectionParameters_clear_caches(self)
1944 
1945 
1946  def set_name(self, a0):
1947  """set_name(ProjectionParameters self, std::string a0)"""
1948  return _IMP_em2d.ProjectionParameters_set_name(self, a0)
1949 
1950 
1951  def set_check_level(self, a0):
1952  """set_check_level(ProjectionParameters self, IMP::CheckLevel a0)"""
1953  return _IMP_em2d.ProjectionParameters_set_check_level(self, a0)
1954 
1955 
1956  def add_to_derivative(self, a0, a1, a2):
1957  """add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1958  return _IMP_em2d.ProjectionParameters_add_to_derivative(self, a0, a1, a2)
1959 
1960 
1961  def set_is_optimized(self, a0, a1):
1962  """set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
1963  return _IMP_em2d.ProjectionParameters_set_is_optimized(self, a0, a1)
1964 
1965 
1966  def get_is_optimized(self, a0):
1967  """get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
1968  return _IMP_em2d.ProjectionParameters_get_is_optimized(self, a0)
1969 
1970 
1971  def get_check_level(self):
1972  """get_check_level(ProjectionParameters self) -> IMP::CheckLevel"""
1973  return _IMP_em2d.ProjectionParameters_get_check_level(self)
1974 
1975 
1976  def __eq__(self, *args):
1977  """
1978  __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
1979  __eq__(ProjectionParameters self, Particle d) -> bool
1980  """
1981  return _IMP_em2d.ProjectionParameters___eq__(self, *args)
1982 
1983 
1984  def __ne__(self, *args):
1985  """
1986  __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
1987  __ne__(ProjectionParameters self, Particle d) -> bool
1988  """
1989  return _IMP_em2d.ProjectionParameters___ne__(self, *args)
1990 
1991 
1992  def __le__(self, *args):
1993  """
1994  __le__(ProjectionParameters self, ProjectionParameters o) -> bool
1995  __le__(ProjectionParameters self, Particle d) -> bool
1996  """
1997  return _IMP_em2d.ProjectionParameters___le__(self, *args)
1998 
1999 
2000  def __lt__(self, *args):
2001  """
2002  __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
2003  __lt__(ProjectionParameters self, Particle d) -> bool
2004  """
2005  return _IMP_em2d.ProjectionParameters___lt__(self, *args)
2006 
2007 
2008  def __ge__(self, *args):
2009  """
2010  __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
2011  __ge__(ProjectionParameters self, Particle d) -> bool
2012  """
2013  return _IMP_em2d.ProjectionParameters___ge__(self, *args)
2014 
2015 
2016  def __gt__(self, *args):
2017  """
2018  __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
2019  __gt__(ProjectionParameters self, Particle d) -> bool
2020  """
2021  return _IMP_em2d.ProjectionParameters___gt__(self, *args)
2022 
2023 
2024  def __hash__(self):
2025  """__hash__(ProjectionParameters self) -> std::size_t"""
2026  return _IMP_em2d.ProjectionParameters___hash__(self)
2027 
2028 
2029  def __str__(self):
2030  """__str__(ProjectionParameters self) -> std::string"""
2031  return _IMP_em2d.ProjectionParameters___str__(self)
2032 
2033 
2034  def __repr__(self):
2035  """__repr__(ProjectionParameters self) -> std::string"""
2036  return _IMP_em2d.ProjectionParameters___repr__(self)
2037 
2038 ProjectionParameters_swigregister = _IMP_em2d.ProjectionParameters_swigregister
2039 ProjectionParameters_swigregister(ProjectionParameters)
2040 
2041 def ProjectionParameters_setup_particle(*args):
2042  """
2043  setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
2044  ProjectionParameters_setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
2045  """
2046  return _IMP_em2d.ProjectionParameters_setup_particle(*args)
2047 
2048 def ProjectionParameters_get_keys():
2049  """ProjectionParameters_get_keys() -> IMP::FloatKeys const &"""
2050  return _IMP_em2d.ProjectionParameters_get_keys()
2051 
2052 def ProjectionParameters_get_is_setup(*args):
2053  """
2054  get_is_setup(_ParticleAdaptor p) -> bool
2055  ProjectionParameters_get_is_setup(Model m, ParticleIndex pi) -> bool
2056  """
2057  return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
2058 
2059 
2060 def __lshift__(out, n):
2061  """__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
2062  return _IMP_em2d.__lshift__(out, n)
2063 class ProjectionParametersScoreState(IMP.ScoreState):
2064  """Proxy of C++ IMP::em2d::ProjectionParametersScoreState class."""
2065 
2066  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2067 
2068  def __init__(self, p):
2069  """__init__(IMP::em2d::ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
2070  this = _IMP_em2d.new_ProjectionParametersScoreState(p)
2071  try:
2072  self.this.append(this)
2073  except __builtin__.Exception:
2074  self.this = this
2075 
2076  def do_before_evaluate(self):
2077  """do_before_evaluate(ProjectionParametersScoreState self)"""
2078  return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
2079 
2080 
2081  def do_after_evaluate(self, da):
2082  """do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
2083  return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, da)
2084 
2085 
2086  def do_get_inputs(self):
2087  """do_get_inputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2088  return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
2089 
2090 
2091  def do_get_outputs(self):
2092  """do_get_outputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2093  return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
2094 
2095 
2096  def get_version_info(self):
2097  """get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
2098  return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
2099 
2100 
2101  def __str__(self):
2102  """__str__(ProjectionParametersScoreState self) -> std::string"""
2103  return _IMP_em2d.ProjectionParametersScoreState___str__(self)
2104 
2105 
2106  def __repr__(self):
2107  """__repr__(ProjectionParametersScoreState self) -> std::string"""
2108  return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
2109 
2110 
2111  @staticmethod
2112  def get_from(o):
2113  return _object_cast_to_ProjectionParametersScoreState(o)
2114 
2115 ProjectionParametersScoreState_swigregister = _IMP_em2d.ProjectionParametersScoreState_swigregister
2116 ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
2117 
2118 class ProjectionMask(object):
2119  """Proxy of C++ IMP::em2d::ProjectionMask class."""
2120 
2121  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2122 
2123  def __init__(self, *args, **kwargs):
2124  raise AttributeError("No constructor defined")
2125 
2126  def apply(self, m, v):
2127  """apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
2128  return _IMP_em2d.ProjectionMask_apply(self, m, v)
2129 
2130 
2131  def show(self, *args):
2132  """
2133  show(ProjectionMask self, _ostream out)
2134  show(ProjectionMask self)
2135  """
2136  return _IMP_em2d.ProjectionMask_show(self, *args)
2137 
2138  __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
2139  __del__ = lambda self: None
2140 
2141  def __str__(self):
2142  """__str__(ProjectionMask self) -> std::string"""
2143  return _IMP_em2d.ProjectionMask___str__(self)
2144 
2145 
2146  def __repr__(self):
2147  """__repr__(ProjectionMask self) -> std::string"""
2148  return _IMP_em2d.ProjectionMask___repr__(self)
2149 
2150 ProjectionMask_swigregister = _IMP_em2d.ProjectionMask_swigregister
2151 ProjectionMask_swigregister(ProjectionMask)
2152 
2153 
2154 def do_place(mask, m, v):
2155  """do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
2156  return _IMP_em2d.do_place(mask, m, v)
2157 class MasksManager(object):
2158  """Proxy of C++ IMP::em2d::MasksManager class."""
2159 
2160  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2161 
2162  def __init__(self, *args):
2163  """
2164  __init__(IMP::em2d::MasksManager self) -> MasksManager
2165  __init__(IMP::em2d::MasksManager self, double resolution, double pixelsize) -> MasksManager
2166  """
2167  this = _IMP_em2d.new_MasksManager(*args)
2168  try:
2169  self.this.append(this)
2170  except __builtin__.Exception:
2171  self.this = this
2172 
2173  def setup_kernel(self, resolution, pixelsize):
2174  """setup_kernel(MasksManager self, double resolution, double pixelsize)"""
2175  return _IMP_em2d.MasksManager_setup_kernel(self, resolution, pixelsize)
2176 
2177 
2178  def create_masks(self, ps):
2179  """create_masks(MasksManager self, IMP::ParticlesTemp const & ps)"""
2180  return _IMP_em2d.MasksManager_create_masks(self, ps)
2181 
2182 
2183  def create_mask(self, mass):
2184  """create_mask(MasksManager self, double mass)"""
2185  return _IMP_em2d.MasksManager_create_mask(self, mass)
2186 
2187 
2188  def find_mask(self, mass):
2189  """find_mask(MasksManager self, double mass) -> IMP::em2d::ProjectionMaskPtr"""
2190  return _IMP_em2d.MasksManager_find_mask(self, mass)
2191 
2192 
2193  def show(self, *args):
2194  """
2195  show(MasksManager self, _ostream out)
2196  show(MasksManager self)
2197  """
2198  return _IMP_em2d.MasksManager_show(self, *args)
2199 
2200 
2201  def get_number_of_masks(self):
2202  """get_number_of_masks(MasksManager self) -> unsigned int"""
2203  return _IMP_em2d.MasksManager_get_number_of_masks(self)
2204 
2205  __swig_destroy__ = _IMP_em2d.delete_MasksManager
2206  __del__ = lambda self: None
2207 
2208  def __str__(self):
2209  """__str__(MasksManager self) -> std::string"""
2210  return _IMP_em2d.MasksManager___str__(self)
2211 
2212 
2213  def __repr__(self):
2214  """__repr__(MasksManager self) -> std::string"""
2215  return _IMP_em2d.MasksManager___repr__(self)
2216 
2217 MasksManager_swigregister = _IMP_em2d.MasksManager_swigregister
2218 MasksManager_swigregister(MasksManager)
2219 
2220 class ProjectingParameters(object):
2221  """Proxy of C++ IMP::em2d::ProjectingParameters class."""
2222 
2223  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2224  pixel_size = _swig_property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set)
2225  resolution = _swig_property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set)
2226 
2227  def __init__(self, *args):
2228  """
2229  __init__(IMP::em2d::ProjectingParameters self) -> ProjectingParameters
2230  __init__(IMP::em2d::ProjectingParameters self, double ps, double res) -> ProjectingParameters
2231  """
2232  this = _IMP_em2d.new_ProjectingParameters(*args)
2233  try:
2234  self.this.append(this)
2235  except __builtin__.Exception:
2236  self.this = this
2237 
2238  def show(self, *args):
2239  """
2240  show(ProjectingParameters self, _ostream out)
2241  show(ProjectingParameters self)
2242  """
2243  return _IMP_em2d.ProjectingParameters_show(self, *args)
2244 
2245 
2246  def __str__(self):
2247  """__str__(ProjectingParameters self) -> std::string"""
2248  return _IMP_em2d.ProjectingParameters___str__(self)
2249 
2250 
2251  def __repr__(self):
2252  """__repr__(ProjectingParameters self) -> std::string"""
2253  return _IMP_em2d.ProjectingParameters___repr__(self)
2254 
2255  __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2256  __del__ = lambda self: None
2257 ProjectingParameters_swigregister = _IMP_em2d.ProjectingParameters_swigregister
2258 ProjectingParameters_swigregister(ProjectingParameters)
2259 
2260 class ProjectingOptions(ProjectingParameters):
2261  """Proxy of C++ IMP::em2d::ProjectingOptions class."""
2262 
2263  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2264  save_images = _swig_property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set)
2265  normalize = _swig_property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set)
2266  clear_matrix_before_projecting = _swig_property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set)
2267 
2268  def __init__(self, *args):
2269  """
2270  __init__(IMP::em2d::ProjectingOptions self) -> ProjectingOptions
2271  __init__(IMP::em2d::ProjectingOptions self, double ps, double res) -> ProjectingOptions
2272  __init__(IMP::em2d::ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2273  """
2274  this = _IMP_em2d.new_ProjectingOptions(*args)
2275  try:
2276  self.this.append(this)
2277  except __builtin__.Exception:
2278  self.this = this
2279 
2280  def show(self, *args):
2281  """
2282  show(ProjectingOptions self, _ostream out)
2283  show(ProjectingOptions self)
2284  """
2285  return _IMP_em2d.ProjectingOptions_show(self, *args)
2286 
2287 
2288  def __str__(self):
2289  """__str__(ProjectingOptions self) -> std::string"""
2290  return _IMP_em2d.ProjectingOptions___str__(self)
2291 
2292 
2293  def __repr__(self):
2294  """__repr__(ProjectingOptions self) -> std::string"""
2295  return _IMP_em2d.ProjectingOptions___repr__(self)
2296 
2297  __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2298  __del__ = lambda self: None
2299 ProjectingOptions_swigregister = _IMP_em2d.ProjectingOptions_swigregister
2300 ProjectingOptions_swigregister(ProjectingOptions)
2301 
2302 
2303 def get_projections(*args):
2304  """
2305  get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2306  get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2307  get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2308  get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2309  """
2310  return _IMP_em2d.get_projections(*args)
2311 
2312 def get_projection(*args):
2313  """
2314  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks, IMP::String name)
2315  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)
2316  get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options)
2317  """
2318  return _IMP_em2d.get_projection(*args)
2319 
2320 def do_project_particles(ps, m2, R, translation, options, masks):
2321  """do_project_particles(IMP::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)"""
2322  return _IMP_em2d.do_project_particles(ps, m2, R, translation, options, masks)
2323 
2324 def create_evenly_distributed_projections(ps, n, options):
2325  """create_evenly_distributed_projections(IMP::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2326  return _IMP_em2d.create_evenly_distributed_projections(ps, n, options)
2327 
2328 def do_project_vectors(*args):
2329  """
2330  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2331  do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2332  """
2333  return _IMP_em2d.do_project_vectors(*args)
2334 
2335 def get_enclosing_image_size(ps, pixel_size, slack):
2336  """get_enclosing_image_size(IMP::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2337  return _IMP_em2d.get_enclosing_image_size(ps, pixel_size, slack)
2338 
2339 def get_complete_alignment(input, m_to_align, apply=False):
2340  """
2341  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2342  get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2343  """
2344  return _IMP_em2d.get_complete_alignment(input, m_to_align, apply)
2345 
2346 def get_rotational_alignment(input, m_to_align, apply=False):
2347  """
2348  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2349  get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2350  """
2351  return _IMP_em2d.get_rotational_alignment(input, m_to_align, apply)
2352 
2353 def get_translational_alignment(input, m_to_align, apply=False):
2354  """
2355  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2356  get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2357  """
2358  return _IMP_em2d.get_translational_alignment(input, m_to_align, apply)
2359 
2360 def get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply=False):
2361  """
2362  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align, cv::Mat const & POLAR2, bool apply=False) -> ResultAlign2D
2363  get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align, cv::Mat const & POLAR2) -> ResultAlign2D
2364  """
2365  return _IMP_em2d.get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply)
2366 
2367 def get_rotational_alignment_no_preprocessing(POLAR1, POLAR2):
2368  """get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2369  return _IMP_em2d.get_rotational_alignment_no_preprocessing(POLAR1, POLAR2)
2370 
2372  """get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2373  return _IMP_em2d.get_translational_alignment_no_preprocessing(M1, M2)
2374 
2375 def get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2):
2376  """get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2377  return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2)
2378 
2379 def write_vectors_as_pdb(*args):
2380  """
2381  write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2382  write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2383  """
2384  return _IMP_em2d.write_vectors_as_pdb(*args)
2385 class Em2DRestraintParameters(ProjectingParameters):
2386  """Proxy of C++ IMP::em2d::Em2DRestraintParameters class."""
2387 
2388  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2389  n_projections = _swig_property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set)
2390  coarse_registration_method = _swig_property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set)
2391  save_match_images = _swig_property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set)
2392  optimization_steps = _swig_property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set)
2393  simplex_initial_length = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set)
2394  simplex_minimum_size = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set)
2395 
2396  def __init__(self, *args):
2397  """
2398  __init__(IMP::em2d::Em2DRestraintParameters self) -> Em2DRestraintParameters
2399  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2400  __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res) -> Em2DRestraintParameters
2401  """
2402  this = _IMP_em2d.new_Em2DRestraintParameters(*args)
2403  try:
2404  self.this.append(this)
2405  except __builtin__.Exception:
2406  self.this = this
2407 
2408  def show(self, *args):
2409  """
2410  show(Em2DRestraintParameters self, _ostream out)
2411  show(Em2DRestraintParameters self)
2412  """
2413  return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2414 
2415 
2416  def __str__(self):
2417  """__str__(Em2DRestraintParameters self) -> std::string"""
2418  return _IMP_em2d.Em2DRestraintParameters___str__(self)
2419 
2420 
2421  def __repr__(self):
2422  """__repr__(Em2DRestraintParameters self) -> std::string"""
2423  return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2424 
2425  __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2426  __del__ = lambda self: None
2427 Em2DRestraintParameters_swigregister = _IMP_em2d.Em2DRestraintParameters_swigregister
2428 Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2429 cvar = _IMP_em2d.cvar
2430 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2431 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2432 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2433 
2434 class ProjectionFinder(IMP.Object):
2435  """Proxy of C++ IMP::em2d::ProjectionFinder class."""
2436 
2437  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2438 
2439  def __init__(self):
2440  """__init__(IMP::em2d::ProjectionFinder self) -> ProjectionFinder"""
2441  this = _IMP_em2d.new_ProjectionFinder()
2442  try:
2443  self.this.append(this)
2444  except __builtin__.Exception:
2445  self.this = this
2446 
2447  def setup(self, score_function, params):
2448  """setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2449  return _IMP_em2d.ProjectionFinder_setup(self, score_function, params)
2450 
2451 
2452  def set_subjects(self, subjects):
2453  """set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2454  return _IMP_em2d.ProjectionFinder_set_subjects(self, subjects)
2455 
2456 
2457  def set_projections(self, projections):
2458  """set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2459  return _IMP_em2d.ProjectionFinder_set_projections(self, projections)
2460 
2461 
2462  def set_variance_images(self, variances):
2463  """set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2464  return _IMP_em2d.ProjectionFinder_set_variance_images(self, variances)
2465 
2466 
2467  def set_model_particles(self, ps):
2468  """set_model_particles(ProjectionFinder self, IMP::ParticlesTemp const & ps)"""
2469  return _IMP_em2d.ProjectionFinder_set_model_particles(self, ps)
2470 
2471 
2472  def set_save_match_images(self, x):
2473  """set_save_match_images(ProjectionFinder self, bool x)"""
2474  return _IMP_em2d.ProjectionFinder_set_save_match_images(self, x)
2475 
2476 
2477  def get_save_match_images(self):
2478  """get_save_match_images(ProjectionFinder self) -> bool"""
2479  return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2480 
2481 
2482  def set_fast_mode(self, n):
2483  """set_fast_mode(ProjectionFinder self, unsigned int n)"""
2484  return _IMP_em2d.ProjectionFinder_set_fast_mode(self, n)
2485 
2486 
2487  def get_registration_results(self):
2488  """get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2489  return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2490 
2491 
2492  def get_coarse_registration(self):
2493  """get_coarse_registration(ProjectionFinder self)"""
2494  return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2495 
2496 
2497  def get_complete_registration(self):
2498  """get_complete_registration(ProjectionFinder self)"""
2499  return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2500 
2501 
2502  def get_global_score(self):
2503  """get_global_score(ProjectionFinder self) -> double"""
2504  return _IMP_em2d.ProjectionFinder_get_global_score(self)
2505 
2506 
2507  def show(self, out):
2508  """show(ProjectionFinder self, _ostream out)"""
2509  return _IMP_em2d.ProjectionFinder_show(self, out)
2510 
2511 
2512  def get_preprocessing_time(self):
2513  """get_preprocessing_time(ProjectionFinder self) -> double"""
2514  return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2515 
2516 
2517  def get_coarse_registration_time(self):
2518  """get_coarse_registration_time(ProjectionFinder self) -> double"""
2519  return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2520 
2521 
2522  def get_fine_registration_time(self):
2523  """get_fine_registration_time(ProjectionFinder self) -> double"""
2524  return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2525 
2526 
2527  def get_number_of_subjects(self):
2528  """get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2529  return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2530 
2531 
2532  def set_number_of_class_averages_members(self, n_members):
2533  """set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2534  return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, n_members)
2535 
2536 
2537  def get_number_of_projections(self):
2538  """get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2539  return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2540 
2541 
2542  def get_version_info(self):
2543  """get_version_info(ProjectionFinder self) -> VersionInfo"""
2544  return _IMP_em2d.ProjectionFinder_get_version_info(self)
2545 
2546 
2547  def __str__(self):
2548  """__str__(ProjectionFinder self) -> std::string"""
2549  return _IMP_em2d.ProjectionFinder___str__(self)
2550 
2551 
2552  def __repr__(self):
2553  """__repr__(ProjectionFinder self) -> std::string"""
2554  return _IMP_em2d.ProjectionFinder___repr__(self)
2555 
2556 
2557  @staticmethod
2558  def get_from(o):
2559  return _object_cast_to_ProjectionFinder(o)
2560 
2561 ProjectionFinder_swigregister = _IMP_em2d.ProjectionFinder_swigregister
2562 ProjectionFinder_swigregister(ProjectionFinder)
2563 
2564 class Em2DRestraint(IMP.Restraint):
2565  """Proxy of C++ IMP::em2d::Em2DRestraint class."""
2566 
2567  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2568 
2569  def __init__(self, m):
2570  """__init__(IMP::em2d::Em2DRestraint self, Model m) -> Em2DRestraint"""
2571  this = _IMP_em2d.new_Em2DRestraint(m)
2572  try:
2573  self.this.append(this)
2574  except __builtin__.Exception:
2575  self.this = this
2576 
2577  def setup(self, score_function, params):
2578  """setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2579  return _IMP_em2d.Em2DRestraint_setup(self, score_function, params)
2580 
2581 
2582  def set_particles(self, particles_container):
2583  """set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2584  return _IMP_em2d.Em2DRestraint_set_particles(self, particles_container)
2585 
2586 
2587  def set_images(self, em_images):
2588  """set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2589  return _IMP_em2d.Em2DRestraint_set_images(self, em_images)
2590 
2591 
2592  def set_variance_images(self, variance_images):
2593  """set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2594  return _IMP_em2d.Em2DRestraint_set_variance_images(self, variance_images)
2595 
2596 
2597  def set_fast_mode(self, n):
2598  """set_fast_mode(Em2DRestraint self, unsigned int n)"""
2599  return _IMP_em2d.Em2DRestraint_set_fast_mode(self, n)
2600 
2601 
2602  def set_coarse_registration_mode(self, opt):
2603  """set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2604  return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, opt)
2605 
2606 
2607  def get_registration_results(self):
2608  """get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2609  return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2610 
2611 
2612  def do_get_inputs(self):
2613  """do_get_inputs(Em2DRestraint self) -> IMP::ModelObjectsTemp"""
2614  return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2615 
2616 
2617  def get_version_info(self):
2618  """get_version_info(Em2DRestraint self) -> VersionInfo"""
2619  return _IMP_em2d.Em2DRestraint_get_version_info(self)
2620 
2621 
2622  def __str__(self):
2623  """__str__(Em2DRestraint self) -> std::string"""
2624  return _IMP_em2d.Em2DRestraint___str__(self)
2625 
2626 
2627  def __repr__(self):
2628  """__repr__(Em2DRestraint self) -> std::string"""
2629  return _IMP_em2d.Em2DRestraint___repr__(self)
2630 
2631 
2632  @staticmethod
2633  def get_from(o):
2634  return _object_cast_to_Em2DRestraint(o)
2635 
2636 Em2DRestraint_swigregister = _IMP_em2d.Em2DRestraint_swigregister
2637 Em2DRestraint_swigregister(Em2DRestraint)
2638 
2639 class ClusterSet(object):
2640  """Proxy of C++ IMP::em2d::ClusterSet class."""
2641 
2642  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2643 
2644  def __init__(self, N):
2645  """__init__(IMP::em2d::ClusterSet self, unsigned int N) -> ClusterSet"""
2646  this = _IMP_em2d.new_ClusterSet(N)
2647  try:
2648  self.this.append(this)
2649  except __builtin__.Exception:
2650  self.this = this
2651 
2652  def do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters):
2653  """do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2654  return _IMP_em2d.ClusterSet_do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters)
2655 
2656 
2657  def get_cluster_elements(self, id):
2658  """get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2659  return _IMP_em2d.ClusterSet_get_cluster_elements(self, id)
2660 
2661 
2662  def get_clusters_below_cutoff(self, cutoff):
2663  """get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2664  return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, cutoff)
2665 
2666 
2667  def get_cluster_formed_at_step(self, step):
2668  """get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2669  return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, step)
2670 
2671 
2672  def get_distance_at_step(self, step):
2673  """get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2674  return _IMP_em2d.ClusterSet_get_distance_at_step(self, step)
2675 
2676 
2677  def get_id_for_cluster_at_step(self, step):
2678  """get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2679  return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, step)
2680 
2681 
2682  def get_linkage_matrix(self):
2683  """get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2684  return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2685 
2686 
2687  def get_linkage_matrix_in_matlab_format(self):
2688  """get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2689  return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2690 
2691 
2692  def get_number_of_steps(self):
2693  """get_number_of_steps(ClusterSet self) -> unsigned int"""
2694  return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2695 
2696 
2697  def show(self, out):
2698  """show(ClusterSet self, _ostream out)"""
2699  return _IMP_em2d.ClusterSet_show(self, out)
2700 
2701 
2702  def __str__(self):
2703  """__str__(ClusterSet self) -> std::string"""
2704  return _IMP_em2d.ClusterSet___str__(self)
2705 
2706 
2707  def __repr__(self):
2708  """__repr__(ClusterSet self) -> std::string"""
2709  return _IMP_em2d.ClusterSet___repr__(self)
2710 
2711  __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2712  __del__ = lambda self: None
2713 ClusterSet_swigregister = _IMP_em2d.ClusterSet_swigregister
2714 ClusterSet_swigregister(ClusterSet)
2715 
2716 class SingleLinkage(object):
2717  """Proxy of C++ IMP::em2d::SingleLinkage class."""
2718 
2719  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2720 
2721  def __init__(self):
2722  """__init__(IMP::em2d::SingleLinkage self) -> SingleLinkage"""
2723  this = _IMP_em2d.new_SingleLinkage()
2724  try:
2725  self.this.append(this)
2726  except __builtin__.Exception:
2727  self.this = this
2728 
2729  def __call__(self, id1, id2, cluster_set, distances):
2730  """__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2731  return _IMP_em2d.SingleLinkage___call__(self, id1, id2, cluster_set, distances)
2732 
2733 
2734  def show(self, out):
2735  """show(SingleLinkage self, _ostream out)"""
2736  return _IMP_em2d.SingleLinkage_show(self, out)
2737 
2738 
2739  def __str__(self):
2740  """__str__(SingleLinkage self) -> std::string"""
2741  return _IMP_em2d.SingleLinkage___str__(self)
2742 
2743 
2744  def __repr__(self):
2745  """__repr__(SingleLinkage self) -> std::string"""
2746  return _IMP_em2d.SingleLinkage___repr__(self)
2747 
2748  __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2749  __del__ = lambda self: None
2750 SingleLinkage_swigregister = _IMP_em2d.SingleLinkage_swigregister
2751 SingleLinkage_swigregister(SingleLinkage)
2752 
2753 class CompleteLinkage(object):
2754  """Proxy of C++ IMP::em2d::CompleteLinkage class."""
2755 
2756  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2757 
2758  def __init__(self):
2759  """__init__(IMP::em2d::CompleteLinkage self) -> CompleteLinkage"""
2760  this = _IMP_em2d.new_CompleteLinkage()
2761  try:
2762  self.this.append(this)
2763  except __builtin__.Exception:
2764  self.this = this
2765 
2766  def __call__(self, id1, id2, cluster_set, distances):
2767  """__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2768  return _IMP_em2d.CompleteLinkage___call__(self, id1, id2, cluster_set, distances)
2769 
2770 
2771  def show(self, out):
2772  """show(CompleteLinkage self, _ostream out)"""
2773  return _IMP_em2d.CompleteLinkage_show(self, out)
2774 
2775 
2776  def __str__(self):
2777  """__str__(CompleteLinkage self) -> std::string"""
2778  return _IMP_em2d.CompleteLinkage___str__(self)
2779 
2780 
2781  def __repr__(self):
2782  """__repr__(CompleteLinkage self) -> std::string"""
2783  return _IMP_em2d.CompleteLinkage___repr__(self)
2784 
2785  __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2786  __del__ = lambda self: None
2787 CompleteLinkage_swigregister = _IMP_em2d.CompleteLinkage_swigregister
2788 CompleteLinkage_swigregister(CompleteLinkage)
2789 
2790 class AverageDistanceLinkage(object):
2791  """Proxy of C++ IMP::em2d::AverageDistanceLinkage class."""
2792 
2793  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2794 
2795  def __init__(self):
2796  """__init__(IMP::em2d::AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2797  this = _IMP_em2d.new_AverageDistanceLinkage()
2798  try:
2799  self.this.append(this)
2800  except __builtin__.Exception:
2801  self.this = this
2802 
2803  def __call__(self, id1, id2, cluster_set, distances):
2804  """__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2805  return _IMP_em2d.AverageDistanceLinkage___call__(self, id1, id2, cluster_set, distances)
2806 
2807 
2808  def show(self, out):
2809  """show(AverageDistanceLinkage self, _ostream out)"""
2810  return _IMP_em2d.AverageDistanceLinkage_show(self, out)
2811 
2812 
2813  def __str__(self):
2814  """__str__(AverageDistanceLinkage self) -> std::string"""
2815  return _IMP_em2d.AverageDistanceLinkage___str__(self)
2816 
2817 
2818  def __repr__(self):
2819  """__repr__(AverageDistanceLinkage self) -> std::string"""
2820  return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2821 
2822  __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2823  __del__ = lambda self: None
2824 AverageDistanceLinkage_swigregister = _IMP_em2d.AverageDistanceLinkage_swigregister
2825 AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2826 
2827 class CollisionCrossSection(IMP.Object):
2828  """Proxy of C++ IMP::em2d::CollisionCrossSection class."""
2829 
2830  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2831 
2832  def __init__(self, n_projections, resolution, pixel_size, projection_image_size):
2833  """__init__(IMP::em2d::CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2834  this = _IMP_em2d.new_CollisionCrossSection(n_projections, resolution, pixel_size, projection_image_size)
2835  try:
2836  self.this.append(this)
2837  except __builtin__.Exception:
2838  self.this = this
2839 
2840  def set_model_particles(self, ps):
2841  """set_model_particles(CollisionCrossSection self, IMP::ParticlesTemp const & ps)"""
2842  return _IMP_em2d.CollisionCrossSection_set_model_particles(self, ps)
2843 
2844 
2845  def get_ccs(self):
2846  """get_ccs(CollisionCrossSection self) -> double"""
2847  return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2848 
2849 
2850  def show(self, out):
2851  """show(CollisionCrossSection self, _ostream out)"""
2852  return _IMP_em2d.CollisionCrossSection_show(self, out)
2853 
2854 
2855  def get_version_info(self):
2856  """get_version_info(CollisionCrossSection self) -> VersionInfo"""
2857  return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2858 
2859 
2860  def __str__(self):
2861  """__str__(CollisionCrossSection self) -> std::string"""
2862  return _IMP_em2d.CollisionCrossSection___str__(self)
2863 
2864 
2865  def __repr__(self):
2866  """__repr__(CollisionCrossSection self) -> std::string"""
2867  return _IMP_em2d.CollisionCrossSection___repr__(self)
2868 
2869 
2870  @staticmethod
2871  def get_from(o):
2872  return _object_cast_to_CollisionCrossSection(o)
2873 
2874 CollisionCrossSection_swigregister = _IMP_em2d.CollisionCrossSection_swigregister
2875 CollisionCrossSection_swigregister(CollisionCrossSection)
2876 
2877 class GridStates(IMP.domino.ParticleStates):
2878  """Proxy of C++ IMP::em2d::GridStates class."""
2879 
2880  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2881 
2882  def __init__(self, *args):
2883  """
2884  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::String const & name) -> GridStates
2885  __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations) -> GridStates
2886  """
2887  this = _IMP_em2d.new_GridStates(*args)
2888  try:
2889  self.this.append(this)
2890  except __builtin__.Exception:
2891  self.this = this
2892 
2893  def get_position(self, i):
2894  """get_position(GridStates self, unsigned int i) -> Vector3D"""
2895  return _IMP_em2d.GridStates_get_position(self, i)
2896 
2897 
2898  def get_orientation(self, i):
2899  """get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2900  return _IMP_em2d.GridStates_get_orientation(self, i)
2901 
2902 
2903  def get_version_info(self):
2904  """get_version_info(GridStates self) -> VersionInfo"""
2905  return _IMP_em2d.GridStates_get_version_info(self)
2906 
2907 
2908  def __str__(self):
2909  """__str__(GridStates self) -> std::string"""
2910  return _IMP_em2d.GridStates___str__(self)
2911 
2912 
2913  def __repr__(self):
2914  """__repr__(GridStates self) -> std::string"""
2915  return _IMP_em2d.GridStates___repr__(self)
2916 
2917 
2918  @staticmethod
2919  def get_from(o):
2920  return _object_cast_to_GridStates(o)
2921 
2922 GridStates_swigregister = _IMP_em2d.GridStates_swigregister
2923 GridStates_swigregister(GridStates)
2924 
2925 class ProjectionStates(GridStates):
2926  """Proxy of C++ IMP::em2d::ProjectionStates class."""
2927 
2928  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2929 
2930  def __init__(self, *args):
2931  """
2932  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections, IMP::String const & name) -> ProjectionStates
2933  __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections) -> ProjectionStates
2934  """
2935  this = _IMP_em2d.new_ProjectionStates(*args)
2936  try:
2937  self.this.append(this)
2938  except __builtin__.Exception:
2939  self.this = this
2940 
2941  def get_projection(self, i):
2942  """get_projection(ProjectionStates self, unsigned int i) -> Image"""
2943  return _IMP_em2d.ProjectionStates_get_projection(self, i)
2944 
2945 
2946  def __str__(self):
2947  """__str__(ProjectionStates self) -> std::string"""
2948  return _IMP_em2d.ProjectionStates___str__(self)
2949 
2950 
2951  def __repr__(self):
2952  """__repr__(ProjectionStates self) -> std::string"""
2953  return _IMP_em2d.ProjectionStates___repr__(self)
2954 
2955 
2956  @staticmethod
2957  def get_from(o):
2958  return _object_cast_to_ProjectionStates(o)
2959 
2960 ProjectionStates_swigregister = _IMP_em2d.ProjectionStates_swigregister
2961 ProjectionStates_swigregister(ProjectionStates)
2962 
2963 class DistanceFilter(IMP.domino.SubsetFilter):
2964  """Proxy of C++ IMP::em2d::DistanceFilter class."""
2965 
2966  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
2967 
2968  def __init__(self, subset_to_act_on, subset_to_restrain, ps_table, max_distance):
2969  """__init__(IMP::em2d::DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table, double max_distance) -> DistanceFilter"""
2970  this = _IMP_em2d.new_DistanceFilter(subset_to_act_on, subset_to_restrain, ps_table, max_distance)
2971  try:
2972  self.this.append(this)
2973  except __builtin__.Exception:
2974  self.this = this
2975 
2976  def show(self, *args):
2977  """
2978  show(DistanceFilter self, _ostream out)
2979  show(DistanceFilter self)
2980  """
2981  return _IMP_em2d.DistanceFilter_show(self, *args)
2982 
2983 
2984  def get_version_info(self):
2985  """get_version_info(DistanceFilter self) -> VersionInfo"""
2986  return _IMP_em2d.DistanceFilter_get_version_info(self)
2987 
2988 
2989  def __str__(self):
2990  """__str__(DistanceFilter self) -> std::string"""
2991  return _IMP_em2d.DistanceFilter___str__(self)
2992 
2993 
2994  def __repr__(self):
2995  """__repr__(DistanceFilter self) -> std::string"""
2996  return _IMP_em2d.DistanceFilter___repr__(self)
2997 
2998 
2999  @staticmethod
3000  def get_from(o):
3001  return _object_cast_to_DistanceFilter(o)
3002 
3003 DistanceFilter_swigregister = _IMP_em2d.DistanceFilter_swigregister
3004 DistanceFilter_swigregister(DistanceFilter)
3005 
3006 class DistanceFilterTable(IMP.domino.SubsetFilterTable):
3007  """Proxy of C++ IMP::em2d::DistanceFilterTable class."""
3008 
3009  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3010 
3011  def __init__(self, subset_to_act_on, ps_table, max_distance):
3012  """__init__(IMP::em2d::DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
3013  this = _IMP_em2d.new_DistanceFilterTable(subset_to_act_on, ps_table, max_distance)
3014  try:
3015  self.this.append(this)
3016  except __builtin__.Exception:
3017  self.this = this
3018 
3019  def show(self, *args):
3020  """
3021  show(DistanceFilterTable self, _ostream out)
3022  show(DistanceFilterTable self)
3023  """
3024  return _IMP_em2d.DistanceFilterTable_show(self, *args)
3025 
3026 
3027  def get_version_info(self):
3028  """get_version_info(DistanceFilterTable self) -> VersionInfo"""
3029  return _IMP_em2d.DistanceFilterTable_get_version_info(self)
3030 
3031 
3032  def __str__(self):
3033  """__str__(DistanceFilterTable self) -> std::string"""
3034  return _IMP_em2d.DistanceFilterTable___str__(self)
3035 
3036 
3037  def __repr__(self):
3038  """__repr__(DistanceFilterTable self) -> std::string"""
3039  return _IMP_em2d.DistanceFilterTable___repr__(self)
3040 
3041 
3042  @staticmethod
3043  def get_from(o):
3044  return _object_cast_to_DistanceFilterTable(o)
3045 
3046 DistanceFilterTable_swigregister = _IMP_em2d.DistanceFilterTable_swigregister
3047 DistanceFilterTable_swigregister(DistanceFilterTable)
3048 
3049 class IntsOrder(object):
3050  """Proxy of C++ IMP::em2d::IntsOrder class."""
3051 
3052  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3053  __repr__ = _swig_repr
3054 
3055  def __call__(self, a, b):
3056  """__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
3057  return _IMP_em2d.IntsOrder___call__(self, a, b)
3058 
3059 
3060  def __init__(self):
3061  """__init__(IMP::em2d::IntsOrder self) -> IntsOrder"""
3062  this = _IMP_em2d.new_IntsOrder()
3063  try:
3064  self.this.append(this)
3065  except __builtin__.Exception:
3066  self.this = this
3067  __swig_destroy__ = _IMP_em2d.delete_IntsOrder
3068  __del__ = lambda self: None
3069 IntsOrder_swigregister = _IMP_em2d.IntsOrder_swigregister
3070 IntsOrder_swigregister(IntsOrder)
3071 
3072 class RigidBodiesImageFitRestraint(IMP.Restraint):
3073  """Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class."""
3074 
3075  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3076 
3077  def get_version_info(self):
3078  """get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
3079  return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
3080 
3081 
3082  def __init__(self, scf, rbs, img):
3083  """__init__(IMP::em2d::RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
3084  this = _IMP_em2d.new_RigidBodiesImageFitRestraint(scf, rbs, img)
3085  try:
3086  self.this.append(this)
3087  except __builtin__.Exception:
3088  self.this = this
3089 
3090  def set_projecting_parameters(self, p):
3091  """set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
3092  return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, p)
3093 
3094 
3095  def set_orientations(self, rb, rots):
3096  """set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
3097  return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, rb, rots)
3098 
3099 
3100  def get_number_of_masks(self, rb):
3101  """get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
3102  return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, rb)
3103 
3104 
3105  def __str__(self):
3106  """__str__(RigidBodiesImageFitRestraint self) -> std::string"""
3107  return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
3108 
3109 
3110  def __repr__(self):
3111  """__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
3112  return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
3113 
3114 
3115  @staticmethod
3116  def get_from(o):
3117  return _object_cast_to_RigidBodiesImageFitRestraint(o)
3118 
3119 RigidBodiesImageFitRestraint_swigregister = _IMP_em2d.RigidBodiesImageFitRestraint_swigregister
3120 RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
3121 
3122 
3123 def get_unique_index(rot):
3124  """get_unique_index(Rotation3D rot) -> IMP::Ints"""
3125  return _IMP_em2d.get_unique_index(rot)
3126 class RelativePositionMover(IMP.core.RigidBodyMover):
3127  """Proxy of C++ IMP::em2d::RelativePositionMover class."""
3128 
3129  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3130 
3131  def __init__(self, d, max_translation, max_rotation):
3132  """__init__(IMP::em2d::RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
3133  this = _IMP_em2d.new_RelativePositionMover(d, max_translation, max_rotation)
3134  try:
3135  self.this.append(this)
3136  except __builtin__.Exception:
3137  self.this = this
3138 
3139  def add_internal_transformations(self, d, transforms):
3140  """add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
3141  return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, d, transforms)
3142 
3143 
3144  def set_random_move_probability(self, p):
3145  """set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
3146  return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, p)
3147 
3148 
3149  def __str__(self):
3150  """__str__(RelativePositionMover self) -> std::string"""
3151  return _IMP_em2d.RelativePositionMover___str__(self)
3152 
3153 
3154  def __repr__(self):
3155  """__repr__(RelativePositionMover self) -> std::string"""
3156  return _IMP_em2d.RelativePositionMover___repr__(self)
3157 
3158 
3159  @staticmethod
3160  def get_from(o):
3161  return _object_cast_to_RelativePositionMover(o)
3162 
3163 RelativePositionMover_swigregister = _IMP_em2d.RelativePositionMover_swigregister
3164 RelativePositionMover_swigregister(RelativePositionMover)
3165 
3166 class DummyRestraint(IMP.Restraint):
3167  """Proxy of C++ IMP::em2d::DummyRestraint class."""
3168 
3169  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3170 
3171  def __init__(self, p, q):
3172  """__init__(IMP::em2d::DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
3173  this = _IMP_em2d.new_DummyRestraint(p, q)
3174  try:
3175  self.this.append(this)
3176  except __builtin__.Exception:
3177  self.this = this
3178 
3179  def show(self, *args):
3180  """
3181  show(DummyRestraint self, _ostream out)
3182  show(DummyRestraint self)
3183  """
3184  return _IMP_em2d.DummyRestraint_show(self, *args)
3185 
3186 
3187  def do_get_inputs(self):
3188  """do_get_inputs(DummyRestraint self) -> IMP::ModelObjectsTemp"""
3189  return _IMP_em2d.DummyRestraint_do_get_inputs(self)
3190 
3191 
3192  def get_version_info(self):
3193  """get_version_info(DummyRestraint self) -> VersionInfo"""
3194  return _IMP_em2d.DummyRestraint_get_version_info(self)
3195 
3196 
3197  def __str__(self):
3198  """__str__(DummyRestraint self) -> std::string"""
3199  return _IMP_em2d.DummyRestraint___str__(self)
3200 
3201 
3202  def __repr__(self):
3203  """__repr__(DummyRestraint self) -> std::string"""
3204  return _IMP_em2d.DummyRestraint___repr__(self)
3205 
3206 
3207  @staticmethod
3208  def get_from(o):
3209  return _object_cast_to_DummyRestraint(o)
3210 
3211 DummyRestraint_swigregister = _IMP_em2d.DummyRestraint_swigregister
3212 DummyRestraint_swigregister(DummyRestraint)
3213 
3214 class ParticlesDummyRestraint(IMP.Restraint):
3215  """Proxy of C++ IMP::em2d::ParticlesDummyRestraint class."""
3216 
3217  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3218 
3219  def __init__(self, sc):
3220  """__init__(IMP::em2d::ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
3221  this = _IMP_em2d.new_ParticlesDummyRestraint(sc)
3222  try:
3223  self.this.append(this)
3224  except __builtin__.Exception:
3225  self.this = this
3226 
3227  def show(self, *args):
3228  """
3229  show(ParticlesDummyRestraint self, _ostream out)
3230  show(ParticlesDummyRestraint self)
3231  """
3232  return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
3233 
3234 
3235  def do_get_inputs(self):
3236  """do_get_inputs(ParticlesDummyRestraint self) -> IMP::ModelObjectsTemp"""
3237  return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3238 
3239 
3240  def get_version_info(self):
3241  """get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3242  return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3243 
3244 
3245  def __str__(self):
3246  """__str__(ParticlesDummyRestraint self) -> std::string"""
3247  return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3248 
3249 
3250  def __repr__(self):
3251  """__repr__(ParticlesDummyRestraint self) -> std::string"""
3252  return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3253 
3254 
3255  @staticmethod
3256  def get_from(o):
3257  return _object_cast_to_ParticlesDummyRestraint(o)
3258 
3259 ParticlesDummyRestraint_swigregister = _IMP_em2d.ParticlesDummyRestraint_swigregister
3260 ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3261 
3262 class PCAFitRestraint(IMP.Restraint):
3263  """Proxy of C++ IMP::em2d::PCAFitRestraint class."""
3264 
3265  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3266 
3267  def __init__(self, particles, image_files, pixel_size, resolution=10.0, projection_number=100, reuse_direction=False, n_components=1):
3268  """
3269  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False, unsigned int n_components=1) -> PCAFitRestraint
3270  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False) -> PCAFitRestraint
3271  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100) -> PCAFitRestraint
3272  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0) -> PCAFitRestraint
3273  __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size) -> PCAFitRestraint
3274  """
3275  this = _IMP_em2d.new_PCAFitRestraint(particles, image_files, pixel_size, resolution, projection_number, reuse_direction, n_components)
3276  try:
3277  self.this.append(this)
3278  except __builtin__.Exception:
3279  self.this = this
3280 
3281  def get_projection_number(self):
3282  """get_projection_number(PCAFitRestraint self) -> unsigned int"""
3283  return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3284 
3285 
3286  def set_projection_number(self, n):
3287  """set_projection_number(PCAFitRestraint self, unsigned int n)"""
3288  return _IMP_em2d.PCAFitRestraint_set_projection_number(self, n)
3289 
3290 
3291  def get_transformation(self, image_number):
3292  """get_transformation(PCAFitRestraint self, unsigned int image_number) -> Transformation3D"""
3293  return _IMP_em2d.PCAFitRestraint_get_transformation(self, image_number)
3294 
3295 
3296  def get_cross_correlation_coefficient(self, image_number):
3297  """get_cross_correlation_coefficient(PCAFitRestraint self, unsigned int image_number) -> double"""
3298  return _IMP_em2d.PCAFitRestraint_get_cross_correlation_coefficient(self, image_number)
3299 
3300 
3301  def write_best_projections(self, file_name, evaluate=False):
3302  """
3303  write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)
3304  write_best_projections(PCAFitRestraint self, std::string file_name)
3305  """
3306  return _IMP_em2d.PCAFitRestraint_write_best_projections(self, file_name, evaluate)
3307 
3308 
3309  def do_get_inputs(self):
3310  """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
3311  return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3312 
3313 
3314  def get_version_info(self):
3315  """get_version_info(PCAFitRestraint self) -> VersionInfo"""
3316  return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3317 
3318 
3319  def __str__(self):
3320  """__str__(PCAFitRestraint self) -> std::string"""
3321  return _IMP_em2d.PCAFitRestraint___str__(self)
3322 
3323 
3324  def __repr__(self):
3325  """__repr__(PCAFitRestraint self) -> std::string"""
3326  return _IMP_em2d.PCAFitRestraint___repr__(self)
3327 
3328 
3329  @staticmethod
3330  def get_from(o):
3331  return _object_cast_to_em2dPCAFitRestraint(o)
3332 
3333 PCAFitRestraint_swigregister = _IMP_em2d.PCAFitRestraint_swigregister
3334 PCAFitRestraint_swigregister(PCAFitRestraint)
3335 
3336 class ResultAlign2D(object):
3337  """Proxy of C++ std::pair<(IMP::algebra::Transformation2D,double)> class."""
3338 
3339  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
3340  __repr__ = _swig_repr
3341 
3342  def __init__(self, *args):
3343  """
3344  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self) -> ResultAlign2D
3345  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, Transformation2D first, double second) -> ResultAlign2D
3346  __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, ResultAlign2D p) -> ResultAlign2D
3347  """
3348  this = _IMP_em2d.new_ResultAlign2D(*args)
3349  try:
3350  self.this.append(this)
3351  except __builtin__.Exception:
3352  self.this = this
3353  first = _swig_property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set)
3354  second = _swig_property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set)
3355  def __len__(self):
3356  return 2
3357  def __repr__(self):
3358  return str((self.first, self.second))
3359  def __getitem__(self, index):
3360  if not (index % 2):
3361  return self.first
3362  else:
3363  return self.second
3364  def __setitem__(self, index, val):
3365  if not (index % 2):
3366  self.first = val
3367  else:
3368  self.second = val
3369  __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3370  __del__ = lambda self: None
3371 ResultAlign2D_swigregister = _IMP_em2d.ResultAlign2D_swigregister
3372 ResultAlign2D_swigregister(ResultAlign2D)
3373 
3374 
3375 def _do_hierarchical_clustering_single_linkage(distances):
3376  """_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3377  return _IMP_em2d._do_hierarchical_clustering_single_linkage(distances)
3378 
3379 def _do_hierarchical_clustering_complete_linkage(distances):
3380  """_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3381  return _IMP_em2d._do_hierarchical_clustering_complete_linkage(distances)
3382 
3383 def _do_hierarchical_clustering_average_distance_linkage(distances):
3384  """_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3385  return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(distances)
3386 
3387 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3388 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3389 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3390 
3391 
3392 def get_module_version():
3393  """get_module_version() -> std::string const"""
3394  return _IMP_em2d.get_module_version()
3395 
3396 def get_example_path(fname):
3397  """get_example_path(std::string fname) -> std::string"""
3398  return _IMP_em2d.get_example_path(fname)
3399 
3400 def get_data_path(fname):
3401  """get_data_path(std::string fname) -> std::string"""
3402  return _IMP_em2d.get_data_path(fname)
3403 
3404 from . import _version_check
3405 _version_check.check_version(get_module_version())
3406 __version__ = get_module_version()
3407 
3408 
3409 
double get_shift_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Distance between the two in-plane translations.
Images create_evenly_distributed_projections(const ParticlesTemp &ps, unsigned int n, const ProjectingOptions &options)
void get_autocorrelation2d_no_preprocessing(const cv::Mat &M, cv::Mat &corr)
Autocorrelation without preprocessing.
void do_morphologic_contrast_enhancement(const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel, unsigned int iterations)
double get_mean(const cv::Mat &mat, const cvIntMat &mask)
CheckLevel get_check_level()
Get the current audit mode.
Definition: exception.h:81
setup
Definition: setup.py:1
void apply_threshold(cv::Mat &m, cv::Mat &result, double threshold=0.0)
em2d::Images get_projections(const ParticlesTemp &ps, const algebra::SphericalVector3Ds &vs, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
Generates projections from particles.
IMPEM2D_BEGIN_NAMESPACE Strings read_selection_file(String fn)
Reads a selection file.
ResultAlign2D get_complete_alignment_with_centers_no_preprocessing(const algebra::Vector2D &center1, const algebra::Vector2D &center2, const cv::Mat &AUTOC_POLAR1, const cv::Mat &AUTOC_POLAR2)
Strings create_filenames(unsigned long number, String basic_name, String extension)
Various classes to hold sets of particles.
ResultAlign2D get_translational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
Aligns two matrices translationally.
void get_correlation2d(const cv::Mat &A, const cv::Mat &B, cv::Mat &corr)
Correlation matrix between two 2D matrices using FFT.
cvIntMat create_circular_mask(int rows, int cols, int radius)
ResultAlign2D get_complete_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
void do_dilate_and_shrink_warp(cv::Mat &m, const cv::Mat &grayscale, cv::Mat &kernel)
(U. Adiga, 2005)
em2d::ResultAlign2D get_rotational_alignment(const cv::Mat &input, cv::Mat &m_to_align, bool apply=false)
RegistrationResults get_evenly_distributed_registration_results(unsigned int n_projections)
void apply_variance_filter(Image *input, Image *filtered, int kernelsize)
Definition: Image.h:266
void apply_diffusion_filter(Image *input, Image *filtered, double beta, double pixelsize, int time_steps)
Definition: Image.h:279
int do_labeling(const cvIntMat &m, cvIntMat &mat_to_label)
Labeling function for a matrix.
Make CGAL functionality available to IMP.
MatchTemplateResults get_best_template_matches(const cv::Mat &m, const cv::Mat &templ, unsigned int n)
Modify the transformation of a rigid body.
void do_project_particles(const ParticlesTemp &ps, cv::Mat &m2, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const ProjectingOptions &options, MasksManagerPtr masks)
Projects a set of particles. This is the core function that others call.
void get_autocorrelation2d(const cv::Mat &m, cv::Mat &corr)
Computes the autocorrelation matrix.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
void apply_mean_outside_mask(Image *img, double radius)
Several general purpose optimizers from the GNU Scientific Library (GSL).
double get_rotation_error(const RegistrationResult &rr1, const RegistrationResult &rr2)
Composable functors to implement scores via compile-time composition.
ResultAlign2D get_rotational_alignment_no_preprocessing(const cv::Mat &POLAR1, const cv::Mat &POLAR2)
void get_fft_using_optimal_size(const cv::Mat &m, cv::Mat &M)
Floats get_histogram(Image *img, int bins)
Definition: Image.h:255
void write_matrix(cv::Mat &m, std::string name)
Quick and dirty way of writing a OpenCV matrix to a Spider image.
void do_subtract_images(Image *first, Image *second, Image *result)
Code to compute statistical measures.
RegistrationResults get_random_registration_results(unsigned int n, double maximum_shift=5.0)
Provides a set of random registration results (or parameters)
algebra::Vector2Ds do_project_vectors(const algebra::Vector3Ds &ps, const algebra::Rotation3D &R, const algebra::Vector3D &translation)
Project the points contained in Vector3Ds to gen vectors in 2D.
void write_vectors_as_pdb(const algebra::Vector2Ds vs, const String filename)
Common base class for heavy weight IMP objects.
Definition: Object.h:106
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:53
void apply_circular_mask(const cv::Mat &mat, cv::Mat &result, int radius, double value=0.0)
Images read_images(const Strings &names, const ImageReaderWriter *rw)
void write_registration_results(String filename, const RegistrationResults &results)
Writes a set of registration results.
Basic utilities for handling cryo-electron microscopy 3D density maps.
void crop(Image *img, const IntPair &center, int size)
void get_morphologic_gradient(const cv::Mat &m, cv::Mat &result, const cv::Mat &kernel)
void apply_mask(const cv::Mat &m, cv::Mat &result, const cvIntMat &mask, double val)
Applies a binary mask to an image.
double get_cross_correlation_coefficient(Image *im1, Image *im2)
Cross correlation between two images.
void save_images(Images images, const Strings &names, const ImageReaderWriter *rw)
void get_domes(cv::Mat &m, cv::Mat &result, double h)
Gets the domes of m with height h.
void do_normalize(Image *im, bool force=false)
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:118
void do_matrix_to_image_flip(cv::Mat &m)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
ResultAlign2D get_translational_alignment_no_preprocessing(const cv::Mat &M1, const cv::Mat &M2)
void get_correlation2d_no_preprocessing(const cv::Mat &M1, const cv::Mat &M2, cv::Mat &corr)
Correlation without preprocessing.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
unsigned int get_enclosing_image_size(const ParticlesTemp &ps, double pixel_size, unsigned int slack)
Get an automatic size for an image that contains the particles.
std::pair< algebra::Transformation2D, double > ResultAlign2D
Definition: align2D.h:22
void do_resample_polar(Image *im1, Image *im2, const PolarResamplingParameters &polar_params)
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
em2d::ResultAlign2D get_complete_alignment_no_preprocessing(const cv::Mat &input, const cv::Mat &INPUT, const cv::Mat &POLAR1, cv::Mat &m_to_align, const cv::Mat &POLAR2, bool apply=false)
double get_overlap_percentage(cv::Mat &m1, cv::Mat &m2, const IntPair &center)
RegistrationResults read_registration_results(const String &filename)
Reads a set of registration results.
void get_diffusion_filtering_partial_derivative(const cv::Mat &m, cv::Mat &der, double dx, double dy, double ang)
Ints get_unique_index(const algebra::Rotation3D &rot)
Map a rotation to a list of 4 "unique" integers.
double get_global_score(const RegistrationResults &RRs)
void do_place(cv::Mat &mask, cv::Mat &m, const algebra::Vector2D &v)
void do_morphologic_reconstruction(const cv::Mat &mask, cv::Mat &marker, int neighbors_mode=4)
morphologic grayscale reconstruction (L Vincent, 1993)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Definition: exception.h:73
void get_projection(em2d::Image *img, const ParticlesTemp &ps, const RegistrationResult &reg, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="")
Generates a projection from particles.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54
void get_spectrum(const cv::Mat &m, cv::Mat &real, cv::Mat &imag)
Computes the fft of a matrix and returns the real and imaginary matrices.