11 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
19 import builtins
as __builtin__
25 strthis =
"proxy of " + self.this.__repr__()
26 except __builtin__.Exception:
28 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
31 def _swig_setattr_nondynamic_instance_variable(set):
32 def set_instance_attr(self, name, value):
34 set(self, name, value)
35 elif name ==
"thisown":
37 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
38 set(self, name, value)
40 raise AttributeError(
"You cannot add instance attributes to %s" % self)
41 return set_instance_attr
44 def _swig_setattr_nondynamic_class_variable(set):
45 def set_class_attr(cls, name, value):
46 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
49 raise AttributeError(
"You cannot add class attributes to %s" % cls)
53 def _swig_add_metaclass(metaclass):
54 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
56 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
60 class _SwigNonDynamicMeta(type):
61 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
67 class IMP_EM2D_SwigPyIterator(object):
68 r"""Proxy of C++ swig::IMP_EM2D_SwigPyIterator class."""
70 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
72 def __init__(self, *args, **kwargs):
73 raise AttributeError(
"No constructor defined - class is abstract")
75 __swig_destroy__ = _IMP_em2d.delete_IMP_EM2D_SwigPyIterator
78 r"""value(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
79 return _IMP_em2d.IMP_EM2D_SwigPyIterator_value(self)
82 r"""incr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator"""
83 return _IMP_em2d.IMP_EM2D_SwigPyIterator_incr(self, n)
86 r"""decr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator"""
87 return _IMP_em2d.IMP_EM2D_SwigPyIterator_decr(self, n)
89 def distance(self, x):
90 r"""distance(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t"""
91 return _IMP_em2d.IMP_EM2D_SwigPyIterator_distance(self, x)
94 r"""equal(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
95 return _IMP_em2d.IMP_EM2D_SwigPyIterator_equal(self, x)
98 r"""copy(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator"""
99 return _IMP_em2d.IMP_EM2D_SwigPyIterator_copy(self)
102 r"""next(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
103 return _IMP_em2d.IMP_EM2D_SwigPyIterator_next(self)
106 r"""__next__(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
107 return _IMP_em2d.IMP_EM2D_SwigPyIterator___next__(self)
110 r"""previous(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
111 return _IMP_em2d.IMP_EM2D_SwigPyIterator_previous(self)
113 def advance(self, n):
114 r"""advance(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
115 return _IMP_em2d.IMP_EM2D_SwigPyIterator_advance(self, n)
118 r"""__eq__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
119 return _IMP_em2d.IMP_EM2D_SwigPyIterator___eq__(self, x)
122 r"""__ne__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
123 return _IMP_em2d.IMP_EM2D_SwigPyIterator___ne__(self, x)
125 def __iadd__(self, n):
126 r"""__iadd__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
127 return _IMP_em2d.IMP_EM2D_SwigPyIterator___iadd__(self, n)
129 def __isub__(self, n):
130 r"""__isub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
131 return _IMP_em2d.IMP_EM2D_SwigPyIterator___isub__(self, n)
133 def __add__(self, n):
134 r"""__add__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
135 return _IMP_em2d.IMP_EM2D_SwigPyIterator___add__(self, n)
137 def __sub__(self, *args):
139 __sub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator
140 __sub__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t
142 return _IMP_em2d.IMP_EM2D_SwigPyIterator___sub__(self, *args)
147 _IMP_em2d.IMP_EM2D_SwigPyIterator_swigregister(IMP_EM2D_SwigPyIterator)
154 IMP_DEBUG = _IMP_em2d.IMP_DEBUG
156 IMP_RELEASE = _IMP_em2d.IMP_RELEASE
158 IMP_SILENT = _IMP_em2d.IMP_SILENT
160 IMP_PROGRESS = _IMP_em2d.IMP_PROGRESS
162 IMP_TERSE = _IMP_em2d.IMP_TERSE
164 IMP_VERBOSE = _IMP_em2d.IMP_VERBOSE
166 IMP_MEMORY = _IMP_em2d.IMP_MEMORY
168 IMP_NONE = _IMP_em2d.IMP_NONE
170 IMP_USAGE = _IMP_em2d.IMP_USAGE
172 IMP_INTERNAL = _IMP_em2d.IMP_INTERNAL
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_em2d.IMP_KERNEL_HAS_LOG4CXX
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_em2d.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em2d.IMP_COMPILER_HAS_DEBUG_VECTOR
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_em2d.IMP_COMPILER_HAS_RANDOM_SHUFFLE
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_em2d.IMP_COMPILER_HAS_THREE_WAY
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_KERNEL_HAS_BOOST_RANDOM
186 IMP_KERNEL_HAS_NUMPY = _IMP_em2d.IMP_KERNEL_HAS_NUMPY
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em2d.IMP_KERNEL_HAS_GPERFTOOLS
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
194 IMPKERNEL_SHOW_WARNINGS = _IMP_em2d.IMPKERNEL_SHOW_WARNINGS
198 class _DirectorObjects(object):
199 """@internal Simple class to keep references to director objects
200 to prevent premature deletion."""
203 def register(self, obj):
204 """Take a reference to a director object; will only work for
205 refcounted C++ classes"""
206 if hasattr(obj,
'get_ref_count'):
207 self._objects.append(obj)
209 """Only drop our reference and allow cleanup by Python if no other
210 Python references exist (we hold 3 references: one in self._objects,
211 one in x, and one in the argument list for getrefcount) *and* no
212 other C++ references exist (the Python object always holds one)"""
213 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
214 or x.get_ref_count() > 1]
218 def get_object_count(self):
219 """Get number of director objects (useful for testing only)"""
220 return len(self._objects)
221 _director_objects = _DirectorObjects()
223 class _ostream(object):
224 r"""Proxy of C++ std::ostream class."""
226 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
228 def __init__(self, *args, **kwargs):
229 raise AttributeError(
"No constructor defined")
230 __repr__ = _swig_repr
232 def write(self, osa_buf):
233 r"""write(_ostream self, char const * osa_buf)"""
234 return _IMP_em2d._ostream_write(self, osa_buf)
237 _IMP_em2d._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_em2d.IMP_C_OPEN_BINARY
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_FILESYSTEM
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CGAL_HAS_BOOST_RANDOM
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_SYSTEM
249 IMP_CGAL_HAS_NUMPY = _IMP_em2d.IMP_CGAL_HAS_NUMPY
251 IMPCGAL_SHOW_WARNINGS = _IMP_em2d.IMPCGAL_SHOW_WARNINGS
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_IMP_CGAL
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_RANDOM
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_SYSTEM
264 IMP_ALGEBRA_HAS_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_CGAL
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_em2d.IMP_ALGEBRA_HAS_NUMPY
268 IMP_ALGEBRA_HAS_ANN = _IMP_em2d.IMP_ALGEBRA_HAS_ANN
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_em2d.IMPALGEBRA_SHOW_WARNINGS
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_IMP_CGAL
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_RANDOM
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_SYSTEM
283 IMP_DISPLAY_HAS_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_CGAL
285 IMP_DISPLAY_HAS_NUMPY = _IMP_em2d.IMP_DISPLAY_HAS_NUMPY
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_em2d.IMPDISPLAY_SHOW_WARNINGS
290 IMP_GSL_HAS_IMP_CGAL = _IMP_em2d.IMP_GSL_HAS_IMP_CGAL
292 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_FILESYSTEM
294 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
296 IMP_GSL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_GSL_HAS_BOOST_RANDOM
298 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_SYSTEM
300 IMP_GSL_HAS_CGAL = _IMP_em2d.IMP_GSL_HAS_CGAL
302 IMP_GSL_HAS_NUMPY = _IMP_em2d.IMP_GSL_HAS_NUMPY
304 IMPGSL_SHOW_WARNINGS = _IMP_em2d.IMPGSL_SHOW_WARNINGS
307 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
309 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
311 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
313 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
315 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_CGAL
319 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_HDF5
321 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_NUMPY
323 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em2d.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
330 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
332 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_RANDOM
334 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_SYSTEM
336 IMP_STATISTICS_HAS_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_CGAL
338 IMP_STATISTICS_HAS_NUMPY = _IMP_em2d.IMP_STATISTICS_HAS_NUMPY
340 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em2d.IMPSTATISTICS_SHOW_WARNINGS
343 IMP_CORE_HAS_IMP_CGAL = _IMP_em2d.IMP_CORE_HAS_IMP_CGAL
345 IMP_CORE_HAS_IMP_KERNEL = _IMP_em2d.IMP_CORE_HAS_IMP_KERNEL
347 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_FILESYSTEM
349 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
351 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CORE_HAS_BOOST_RANDOM
353 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_SYSTEM
355 IMP_CORE_HAS_CGAL = _IMP_em2d.IMP_CORE_HAS_CGAL
357 IMP_CORE_HAS_HDF5 = _IMP_em2d.IMP_CORE_HAS_HDF5
359 IMP_CORE_HAS_NUMPY = _IMP_em2d.IMP_CORE_HAS_NUMPY
361 IMPCORE_SHOW_WARNINGS = _IMP_em2d.IMPCORE_SHOW_WARNINGS
364 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em2d.IMP_CONTAINER_HAS_IMP_ALGEBRA
366 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_CGAL
368 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em2d.IMP_CONTAINER_HAS_IMP_DISPLAY
370 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_KERNEL
372 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
374 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
376 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
378 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_RANDOM
380 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_SYSTEM
382 IMP_CONTAINER_HAS_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_CGAL
384 IMP_CONTAINER_HAS_HDF5 = _IMP_em2d.IMP_CONTAINER_HAS_HDF5
386 IMP_CONTAINER_HAS_NUMPY = _IMP_em2d.IMP_CONTAINER_HAS_NUMPY
388 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em2d.IMP_CONTAINER_HAS_PYTHON_IHM
390 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em2d.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
392 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em2d.IMP_CONTAINER_HAS_ROBIN_MAP
394 IMPCONTAINER_SHOW_WARNINGS = _IMP_em2d.IMPCONTAINER_SHOW_WARNINGS
397 IMP_ATOM_HAS_IMP_CGAL = _IMP_em2d.IMP_ATOM_HAS_IMP_CGAL
399 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em2d.IMP_ATOM_HAS_IMP_KERNEL
401 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
403 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
405 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ATOM_HAS_BOOST_RANDOM
407 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em2d.IMP_ATOM_HAS_BOOST_REGEX
409 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ATOM_HAS_BOOST_SYSTEM
411 IMP_ATOM_HAS_CGAL = _IMP_em2d.IMP_ATOM_HAS_CGAL
413 IMP_ATOM_HAS_HDF5 = _IMP_em2d.IMP_ATOM_HAS_HDF5
415 IMP_ATOM_HAS_NUMPY = _IMP_em2d.IMP_ATOM_HAS_NUMPY
417 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em2d.IMP_ATOM_HAS_PYTHON_IHM
419 IMPATOM_SHOW_WARNINGS = _IMP_em2d.IMPATOM_SHOW_WARNINGS
421 IMP_ATOM_TYPE_INDEX = _IMP_em2d.IMP_ATOM_TYPE_INDEX
423 IMP_RESIDUE_TYPE_INDEX = _IMP_em2d.IMP_RESIDUE_TYPE_INDEX
425 IMP_HIERARCHY_TYPE_INDEX = _IMP_em2d.IMP_HIERARCHY_TYPE_INDEX
427 IMP_CHAIN_TYPE_INDEX = _IMP_em2d.IMP_CHAIN_TYPE_INDEX
430 IMP_EM_HAS_IMP_CGAL = _IMP_em2d.IMP_EM_HAS_IMP_CGAL
432 IMP_EM_HAS_IMP_CONTAINER = _IMP_em2d.IMP_EM_HAS_IMP_CONTAINER
434 IMP_EM_HAS_IMP_DISPLAY = _IMP_em2d.IMP_EM_HAS_IMP_DISPLAY
436 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM_HAS_IMP_SCORE_FUNCTOR
438 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_FILESYSTEM
440 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
442 IMP_EM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM_HAS_BOOST_RANDOM
444 IMP_EM_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM_HAS_BOOST_REGEX
446 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_SYSTEM
448 IMP_EM_HAS_CGAL = _IMP_em2d.IMP_EM_HAS_CGAL
450 IMP_EM_HAS_HDF5 = _IMP_em2d.IMP_EM_HAS_HDF5
452 IMP_EM_HAS_NUMPY = _IMP_em2d.IMP_EM_HAS_NUMPY
454 IMP_EM_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM_HAS_PYTHON_IHM
456 IMPEM_SHOW_WARNINGS = _IMP_em2d.IMPEM_SHOW_WARNINGS
459 IMP_SAXS_HAS_IMP_CGAL = _IMP_em2d.IMP_SAXS_HAS_IMP_CGAL
461 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_em2d.IMP_SAXS_HAS_IMP_CONTAINER
463 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_em2d.IMP_SAXS_HAS_IMP_DISPLAY
465 IMP_SAXS_HAS_IMP_KERNEL = _IMP_em2d.IMP_SAXS_HAS_IMP_KERNEL
467 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
469 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SAXS_HAS_BOOST_FILESYSTEM
471 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
473 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SAXS_HAS_BOOST_RANDOM
475 IMP_SAXS_HAS_BOOST_REGEX = _IMP_em2d.IMP_SAXS_HAS_BOOST_REGEX
477 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SAXS_HAS_BOOST_SYSTEM
479 IMP_SAXS_HAS_CGAL = _IMP_em2d.IMP_SAXS_HAS_CGAL
481 IMP_SAXS_HAS_HDF5 = _IMP_em2d.IMP_SAXS_HAS_HDF5
483 IMP_SAXS_HAS_NUMPY = _IMP_em2d.IMP_SAXS_HAS_NUMPY
485 IMP_SAXS_HAS_PYTHON_IHM = _IMP_em2d.IMP_SAXS_HAS_PYTHON_IHM
487 IMPSAXS_SHOW_WARNINGS = _IMP_em2d.IMPSAXS_SHOW_WARNINGS
490 IMP_ISD_HAS_IMP_CGAL = _IMP_em2d.IMP_ISD_HAS_IMP_CGAL
492 IMP_ISD_HAS_IMP_DISPLAY = _IMP_em2d.IMP_ISD_HAS_IMP_DISPLAY
494 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
496 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ISD_HAS_BOOST_FILESYSTEM
498 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
500 IMP_ISD_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ISD_HAS_BOOST_RANDOM
502 IMP_ISD_HAS_BOOST_REGEX = _IMP_em2d.IMP_ISD_HAS_BOOST_REGEX
504 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ISD_HAS_BOOST_SYSTEM
506 IMP_ISD_HAS_CGAL = _IMP_em2d.IMP_ISD_HAS_CGAL
508 IMP_ISD_HAS_HDF5 = _IMP_em2d.IMP_ISD_HAS_HDF5
510 IMP_ISD_HAS_NUMPY = _IMP_em2d.IMP_ISD_HAS_NUMPY
512 IMP_ISD_HAS_PYTHON_IHM = _IMP_em2d.IMP_ISD_HAS_PYTHON_IHM
514 IMPISD_SHOW_WARNINGS = _IMP_em2d.IMPISD_SHOW_WARNINGS
517 IMP_RMF_HAS_IMP_CGAL = _IMP_em2d.IMP_RMF_HAS_IMP_CGAL
519 IMP_RMF_HAS_IMP_EM = _IMP_em2d.IMP_RMF_HAS_IMP_EM
521 IMP_RMF_HAS_IMP_SAXS = _IMP_em2d.IMP_RMF_HAS_IMP_SAXS
523 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
525 IMP_RMF_HAS_IMP_STATISTICS = _IMP_em2d.IMP_RMF_HAS_IMP_STATISTICS
527 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_FILESYSTEM
529 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
531 IMP_RMF_HAS_BOOST_RANDOM = _IMP_em2d.IMP_RMF_HAS_BOOST_RANDOM
533 IMP_RMF_HAS_BOOST_REGEX = _IMP_em2d.IMP_RMF_HAS_BOOST_REGEX
535 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_SYSTEM
537 IMP_RMF_HAS_CGAL = _IMP_em2d.IMP_RMF_HAS_CGAL
539 IMP_RMF_HAS_HDF5 = _IMP_em2d.IMP_RMF_HAS_HDF5
541 IMP_RMF_HAS_NUMPY = _IMP_em2d.IMP_RMF_HAS_NUMPY
543 IMP_RMF_HAS_PYTHON_IHM = _IMP_em2d.IMP_RMF_HAS_PYTHON_IHM
545 IMPRMF_SHOW_WARNINGS = _IMP_em2d.IMPRMF_SHOW_WARNINGS
549 IMP_DOMINO_HAS_IMP_ATOM = _IMP_em2d.IMP_DOMINO_HAS_IMP_ATOM
551 IMP_DOMINO_HAS_IMP_CGAL = _IMP_em2d.IMP_DOMINO_HAS_IMP_CGAL
553 IMP_DOMINO_HAS_IMP_EM = _IMP_em2d.IMP_DOMINO_HAS_IMP_EM
555 IMP_DOMINO_HAS_IMP_ISD = _IMP_em2d.IMP_DOMINO_HAS_IMP_ISD
557 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_em2d.IMP_DOMINO_HAS_IMP_KERNEL
559 IMP_DOMINO_HAS_IMP_RMF = _IMP_em2d.IMP_DOMINO_HAS_IMP_RMF
561 IMP_DOMINO_HAS_IMP_SAXS = _IMP_em2d.IMP_DOMINO_HAS_IMP_SAXS
563 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
565 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_FILESYSTEM
567 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
569 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_RANDOM
571 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_em2d.IMP_DOMINO_HAS_BOOST_REGEX
573 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_SYSTEM
575 IMP_DOMINO_HAS_CGAL = _IMP_em2d.IMP_DOMINO_HAS_CGAL
577 IMP_DOMINO_HAS_HDF5 = _IMP_em2d.IMP_DOMINO_HAS_HDF5
579 IMP_DOMINO_HAS_NUMPY = _IMP_em2d.IMP_DOMINO_HAS_NUMPY
581 IMP_DOMINO_HAS_RMF = _IMP_em2d.IMP_DOMINO_HAS_RMF
583 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_em2d.IMP_DOMINO_HAS_PYTHON_IHM
585 IMPDOMINO_SHOW_WARNINGS = _IMP_em2d.IMPDOMINO_SHOW_WARNINGS
589 IMP_EM2D_HAS_IMP_CGAL = _IMP_em2d.IMP_EM2D_HAS_IMP_CGAL
591 IMP_EM2D_HAS_IMP_ISD = _IMP_em2d.IMP_EM2D_HAS_IMP_ISD
593 IMP_EM2D_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM2D_HAS_IMP_KERNEL
595 IMP_EM2D_HAS_IMP_RMF = _IMP_em2d.IMP_EM2D_HAS_IMP_RMF
597 IMP_EM2D_HAS_IMP_SAXS = _IMP_em2d.IMP_EM2D_HAS_IMP_SAXS
599 IMP_EM2D_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM2D_HAS_IMP_SCORE_FUNCTOR
601 IMP_EM2D_HAS_IMP_STATISTICS = _IMP_em2d.IMP_EM2D_HAS_IMP_STATISTICS
603 IMP_EM2D_HAS_BOOST_GRAPH = _IMP_em2d.IMP_EM2D_HAS_BOOST_GRAPH
605 IMP_EM2D_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM2D_HAS_BOOST_RANDOM
607 IMP_EM2D_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM2D_HAS_BOOST_REGEX
609 IMP_EM2D_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM2D_HAS_BOOST_SYSTEM
611 IMP_EM2D_HAS_CGAL = _IMP_em2d.IMP_EM2D_HAS_CGAL
613 IMP_EM2D_HAS_GSL = _IMP_em2d.IMP_EM2D_HAS_GSL
615 IMP_EM2D_HAS_HDF5 = _IMP_em2d.IMP_EM2D_HAS_HDF5
617 IMP_EM2D_HAS_NUMPY = _IMP_em2d.IMP_EM2D_HAS_NUMPY
619 IMP_EM2D_HAS_OPENCV3 = _IMP_em2d.IMP_EM2D_HAS_OPENCV3
621 IMP_EM2D_HAS_RMF = _IMP_em2d.IMP_EM2D_HAS_RMF
623 IMP_EM2D_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM2D_HAS_PYTHON_IHM
625 IMP_EM2D_HAS_OPENCV21 = _IMP_em2d.IMP_EM2D_HAS_OPENCV21
627 IMP_EM2D_HAS_OPENCV22 = _IMP_em2d.IMP_EM2D_HAS_OPENCV22
629 IMPEM2D_SHOW_WARNINGS = _IMP_em2d.IMPEM2D_SHOW_WARNINGS
632 PolarResamplingParametersList=list
633 _plural_types.append(
"PolarResamplingParametersList")
634 _value_types.append(
"PolarResamplingParameters")
638 _plural_types.append(
"ProjectionMasks")
639 _value_types.append(
"ProjectionMask")
643 _plural_types.append(
"MasksManagers")
644 _value_types.append(
"MasksManager")
647 RegistrationResults=list
648 _plural_types.append(
"RegistrationResults")
649 _value_types.append(
"RegistrationResult")
653 _plural_types.append(
"ClusterSets")
654 _value_types.append(
"ClusterSet")
658 _plural_types.append(
"SingleLinkages")
659 _value_types.append(
"SingleLinkage")
662 CompleteLinkages=list
663 _plural_types.append(
"CompleteLinkages")
664 _value_types.append(
"CompleteLinkage")
667 AverageDistanceLinkages=list
668 _plural_types.append(
"AverageDistanceLinkages")
669 _value_types.append(
"AverageDistanceLinkage")
672 SegmentationParametersList=list
673 _plural_types.append(
"SegmentationParametersList")
674 _value_types.append(
"SegmentationParameters")
677 MatchTemplateResults=list
678 _plural_types.append(
"MatchTemplateResults")
679 _value_types.append(
"MatchTemplateResult")
682 ProjectingParametersList=list
683 _plural_types.append(
"ProjectingParametersList")
684 _value_types.append(
"ProjectingParameters")
687 ProjectingOptionsList=list
688 _plural_types.append(
"ProjectingOptionsList")
689 _value_types.append(
"ProjectingOptions")
692 Em2DRestraintParametersList=list
693 _plural_types.append(
"Em2DRestraintParametersList")
694 _value_types.append(
"Em2DRestraintParameters")
697 _object_types.append(
"ProjectionFinder")
700 def _object_cast_to_ProjectionFinder(o):
701 r"""_object_cast_to_ProjectionFinder(Object o) -> ProjectionFinder"""
702 return _IMP_em2d._object_cast_to_ProjectionFinder(o)
704 _object_types.append(
"ScoreFunction")
707 def _object_cast_to_ScoreFunction(o):
708 r"""_object_cast_to_ScoreFunction(Object o) -> ScoreFunction"""
709 return _IMP_em2d._object_cast_to_ScoreFunction(o)
711 _object_types.append(
"ChiSquaredScore")
714 def _object_cast_to_ChiSquaredScore(o):
715 r"""_object_cast_to_ChiSquaredScore(Object o) -> ChiSquaredScore"""
716 return _IMP_em2d._object_cast_to_ChiSquaredScore(o)
718 _object_types.append(
"EM2DScore")
721 def _object_cast_to_EM2DScore(o):
722 r"""_object_cast_to_EM2DScore(Object o) -> EM2DScore"""
723 return _IMP_em2d._object_cast_to_EM2DScore(o)
725 _object_types.append(
"MeanAbsoluteDifference")
728 def _object_cast_to_MeanAbsoluteDifference(o):
729 r"""_object_cast_to_MeanAbsoluteDifference(Object o) -> MeanAbsoluteDifference"""
730 return _IMP_em2d._object_cast_to_MeanAbsoluteDifference(o)
732 _object_types.append(
"ProjectionParametersScoreState")
735 def _object_cast_to_ProjectionParametersScoreState(o):
736 r"""_object_cast_to_ProjectionParametersScoreState(Object o) -> ProjectionParametersScoreState"""
737 return _IMP_em2d._object_cast_to_ProjectionParametersScoreState(o)
739 _object_types.append(
"Em2DRestraint")
742 def _object_cast_to_Em2DRestraint(o):
743 r"""_object_cast_to_Em2DRestraint(Object o) -> Em2DRestraint"""
744 return _IMP_em2d._object_cast_to_Em2DRestraint(o)
746 _object_types.append(
"Image")
749 def _object_cast_to_Image(o):
750 r"""_object_cast_to_Image(Object o) -> Image"""
751 return _IMP_em2d._object_cast_to_Image(o)
753 _object_types.append(
"ImageReaderWriter")
756 def _object_cast_to_ImageReaderWriter(o):
757 r"""_object_cast_to_ImageReaderWriter(Object o) -> ImageReaderWriter"""
758 return _IMP_em2d._object_cast_to_ImageReaderWriter(o)
760 _object_types.append(
"JPGImageReaderWriter")
763 def _object_cast_to_JPGImageReaderWriter(o):
764 r"""_object_cast_to_JPGImageReaderWriter(Object o) -> JPGImageReaderWriter"""
765 return _IMP_em2d._object_cast_to_JPGImageReaderWriter(o)
767 _object_types.append(
"TIFFImageReaderWriter")
770 def _object_cast_to_TIFFImageReaderWriter(o):
771 r"""_object_cast_to_TIFFImageReaderWriter(Object o) -> TIFFImageReaderWriter"""
772 return _IMP_em2d._object_cast_to_TIFFImageReaderWriter(o)
774 _object_types.append(
"SpiderImageReaderWriter")
777 def _object_cast_to_SpiderImageReaderWriter(o):
778 r"""_object_cast_to_SpiderImageReaderWriter(Object o) -> SpiderImageReaderWriter"""
779 return _IMP_em2d._object_cast_to_SpiderImageReaderWriter(o)
781 _object_types.append(
"CollisionCrossSection")
784 def _object_cast_to_CollisionCrossSection(o):
785 r"""_object_cast_to_CollisionCrossSection(Object o) -> CollisionCrossSection"""
786 return _IMP_em2d._object_cast_to_CollisionCrossSection(o)
788 _object_types.append(
"GridStates")
791 def _object_cast_to_GridStates(o):
792 r"""_object_cast_to_GridStates(Object o) -> GridStates"""
793 return _IMP_em2d._object_cast_to_GridStates(o)
795 _object_types.append(
"ProjectionStates")
798 def _object_cast_to_ProjectionStates(o):
799 r"""_object_cast_to_ProjectionStates(Object o) -> ProjectionStates"""
800 return _IMP_em2d._object_cast_to_ProjectionStates(o)
802 _object_types.append(
"DistanceFilter")
805 def _object_cast_to_DistanceFilter(o):
806 r"""_object_cast_to_DistanceFilter(Object o) -> DistanceFilter"""
807 return _IMP_em2d._object_cast_to_DistanceFilter(o)
809 _object_types.append(
"DistanceFilterTable")
812 def _object_cast_to_DistanceFilterTable(o):
813 r"""_object_cast_to_DistanceFilterTable(Object o) -> DistanceFilterTable"""
814 return _IMP_em2d._object_cast_to_DistanceFilterTable(o)
816 _object_types.append(
"RigidBodiesImageFitRestraint")
819 def _object_cast_to_RigidBodiesImageFitRestraint(o):
820 r"""_object_cast_to_RigidBodiesImageFitRestraint(Object o) -> RigidBodiesImageFitRestraint"""
821 return _IMP_em2d._object_cast_to_RigidBodiesImageFitRestraint(o)
823 _object_types.append(
"DummyRestraint")
826 def _object_cast_to_DummyRestraint(o):
827 r"""_object_cast_to_DummyRestraint(Object o) -> DummyRestraint"""
828 return _IMP_em2d._object_cast_to_DummyRestraint(o)
830 _object_types.append(
"ParticlesDummyRestraint")
833 def _object_cast_to_ParticlesDummyRestraint(o):
834 r"""_object_cast_to_ParticlesDummyRestraint(Object o) -> ParticlesDummyRestraint"""
835 return _IMP_em2d._object_cast_to_ParticlesDummyRestraint(o)
837 _object_types.append(
"RelativePositionMover")
840 def _object_cast_to_RelativePositionMover(o):
841 r"""_object_cast_to_RelativePositionMover(Object o) -> RelativePositionMover"""
842 return _IMP_em2d._object_cast_to_RelativePositionMover(o)
844 _object_types.append(
"PCAFitRestraint")
847 def _object_cast_to_em2dPCAFitRestraint(o):
848 r"""_object_cast_to_em2dPCAFitRestraint(Object o) -> PCAFitRestraint"""
849 return _IMP_em2d._object_cast_to_em2dPCAFitRestraint(o)
851 def ProjectionParametersList(l=[]):
852 return [ProjectionParameters(x)
for x
in l]
853 _plural_types.append(
"ProjectionParametersList")
856 _value_types.append(
"ProjectionParameters")
860 r"""show(cv::Mat const & m, _ostream out=std::cout)"""
861 return _IMP_em2d.show(*args)
864 r"""write_matrix(cv::Mat & m, std::string name)"""
865 return _IMP_em2d.write_matrix(m, name)
867 r"""Proxy of C++ IMP::em2d::ImageReaderWriter class."""
869 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
871 def __init__(self, *args, **kwargs):
872 raise AttributeError(
"No constructor defined - class is abstract")
874 def read(self, filename, header, data):
875 r"""read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
876 return _IMP_em2d.ImageReaderWriter_read(self, filename, header, data)
878 def read_from_floats(self, filename, header, data):
879 r"""read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
880 return _IMP_em2d.ImageReaderWriter_read_from_floats(self, filename, header, data)
882 def read_from_ints(self, filename, header, data):
883 r"""read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
884 return _IMP_em2d.ImageReaderWriter_read_from_ints(self, filename, header, data)
886 def write(self, filename, header, data):
887 r"""write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
888 return _IMP_em2d.ImageReaderWriter_write(self, filename, header, data)
890 def write_to_floats(self, filename, header, data):
891 r"""write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
892 return _IMP_em2d.ImageReaderWriter_write_to_floats(self, filename, header, data)
894 def write_to_ints(self, filename, header, data):
895 r"""write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
896 return _IMP_em2d.ImageReaderWriter_write_to_ints(self, filename, header, data)
898 def get_version_info(self):
899 r"""get_version_info(ImageReaderWriter self) -> VersionInfo"""
900 return _IMP_em2d.ImageReaderWriter_get_version_info(self)
901 __swig_destroy__ = _IMP_em2d.delete_ImageReaderWriter
904 r"""__str__(ImageReaderWriter self) -> std::string"""
905 return _IMP_em2d.ImageReaderWriter___str__(self)
908 r"""__repr__(ImageReaderWriter self) -> std::string"""
909 return _IMP_em2d.ImageReaderWriter___repr__(self)
913 return _object_cast_to_ImageReaderWriter(o)
917 _IMP_em2d.ImageReaderWriter_swigregister(ImageReaderWriter)
918 class PolarResamplingParameters(object):
919 r"""Proxy of C++ IMP::em2d::PolarResamplingParameters class."""
921 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
923 def __init__(self, *args):
925 __init__(PolarResamplingParameters self) -> PolarResamplingParameters
926 __init__(PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
927 __init__(PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
929 _IMP_em2d.PolarResamplingParameters_swiginit(self, _IMP_em2d.new_PolarResamplingParameters(*args))
930 __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
932 def setup(self, rows, cols):
933 r"""setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
934 return _IMP_em2d.PolarResamplingParameters_setup(self, rows, cols)
936 def get_starting_radius(self):
937 r"""get_starting_radius(PolarResamplingParameters self) -> double"""
938 return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
940 def get_ending_radius(self):
941 r"""get_ending_radius(PolarResamplingParameters self) -> double"""
942 return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
944 def get_radius(self, n_ring):
945 r"""get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
946 return _IMP_em2d.PolarResamplingParameters_get_radius(self, n_ring)
948 def get_number_of_rings(self):
949 r"""get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
950 return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
952 def set_estimated_number_of_angles(self, aprox_value):
953 r"""set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
954 return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, aprox_value)
956 def get_number_of_angles(self):
957 r"""get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
958 return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
960 def get_angle_step(self):
961 r"""get_angle_step(PolarResamplingParameters self) -> double"""
962 return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
964 def get_radius_step(self):
965 r"""get_radius_step(PolarResamplingParameters self) -> double"""
966 return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
968 def create_maps_for_resampling(self):
969 r"""create_maps_for_resampling(PolarResamplingParameters self)"""
970 return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
972 def get_resampling_maps(self, m1, m2):
973 r"""get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
974 return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, m1, m2)
976 def get_resampling_map(self, m1):
977 r"""get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
978 return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, m1)
981 r"""show(PolarResamplingParameters self, _ostream out)"""
982 return _IMP_em2d.PolarResamplingParameters_show(self, out)
984 def get_is_setup(self):
985 r"""get_is_setup(PolarResamplingParameters self) -> bool"""
986 return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
989 r"""__str__(PolarResamplingParameters self) -> std::string"""
990 return _IMP_em2d.PolarResamplingParameters___str__(self)
993 r"""__repr__(PolarResamplingParameters self) -> std::string"""
994 return _IMP_em2d.PolarResamplingParameters___repr__(self)
996 def _get_as_binary(self):
997 r"""_get_as_binary(PolarResamplingParameters self) -> PyObject *"""
998 return _IMP_em2d.PolarResamplingParameters__get_as_binary(self)
1000 def _set_from_binary(self, p):
1001 r"""_set_from_binary(PolarResamplingParameters self, PyObject * p)"""
1002 return _IMP_em2d.PolarResamplingParameters__set_from_binary(self, p)
1004 def __getstate__(self):
1005 p = self._get_as_binary()
1006 if len(self.__dict__) > 1:
1007 d = self.__dict__.copy()
1012 def __setstate__(self, p):
1013 if not hasattr(self,
'this'):
1015 if isinstance(p, tuple):
1017 self.__dict__.update(d)
1018 return self._set_from_binary(p)
1022 _IMP_em2d.PolarResamplingParameters_swigregister(PolarResamplingParameters)
1023 class SegmentationParameters(object):
1024 r"""Proxy of C++ IMP::em2d::SegmentationParameters class."""
1026 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1027 image_pixel_size = property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set, doc=
r"""image_pixel_size : double""")
1028 diffusion_beta = property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set, doc=
r"""diffusion_beta : double""")
1029 diffusion_timesteps = property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set, doc=
r"""diffusion_timesteps : double""")
1030 fill_holes_stddevs = property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set, doc=
r"""fill_holes_stddevs : double""")
1031 opening_kernel = property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set, doc=
r"""opening_kernel : cv::Mat""")
1032 remove_sizing_percentage = property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set, doc=
r"""remove_sizing_percentage : double""")
1033 binary_background = property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set, doc=
r"""binary_background : int""")
1034 binary_foreground = property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set, doc=
r"""binary_foreground : int""")
1035 threshold = property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set, doc=
r"""threshold : double""")
1037 def __init__(self, *args):
1039 __init__(SegmentationParameters self) -> SegmentationParameters
1040 __init__(SegmentationParameters self, double apix, double diff_beta, unsigned int diff_timesteps, double fh_stddevs, cv::Mat const & kr, int background, int foreground) -> SegmentationParameters
1042 _IMP_em2d.SegmentationParameters_swiginit(self, _IMP_em2d.new_SegmentationParameters(*args))
1044 def show(self, *args):
1045 r"""show(SegmentationParameters self, _ostream out=std::cout)"""
1046 return _IMP_em2d.SegmentationParameters_show(self, *args)
1049 r"""__str__(SegmentationParameters self) -> std::string"""
1050 return _IMP_em2d.SegmentationParameters___str__(self)
1053 r"""__repr__(SegmentationParameters self) -> std::string"""
1054 return _IMP_em2d.SegmentationParameters___repr__(self)
1056 def _get_as_binary(self):
1057 r"""_get_as_binary(SegmentationParameters self) -> PyObject *"""
1058 return _IMP_em2d.SegmentationParameters__get_as_binary(self)
1060 def _set_from_binary(self, p):
1061 r"""_set_from_binary(SegmentationParameters self, PyObject * p)"""
1062 return _IMP_em2d.SegmentationParameters__set_from_binary(self, p)
1064 def __getstate__(self):
1065 p = self._get_as_binary()
1066 if len(self.__dict__) > 1:
1067 d = self.__dict__.copy()
1072 def __setstate__(self, p):
1073 if not hasattr(self,
'this'):
1075 if isinstance(p, tuple):
1077 self.__dict__.update(d)
1078 return self._set_from_binary(p)
1080 __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
1083 _IMP_em2d.SegmentationParameters_swigregister(SegmentationParameters)
1084 class MatchTemplateResult(object):
1085 r"""Proxy of C++ IMP::em2d::MatchTemplateResult class."""
1087 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1088 pair = property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set, doc=
r"""pair : IMP::IntPair""")
1089 cross_correlation = property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set, doc=
r"""cross_correlation : double""")
1091 def __init__(self, p, cc):
1092 r"""__init__(MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
1093 _IMP_em2d.MatchTemplateResult_swiginit(self, _IMP_em2d.new_MatchTemplateResult(p, cc))
1095 def show(self, *args):
1096 r"""show(MatchTemplateResult self, _ostream out=std::cout)"""
1097 return _IMP_em2d.MatchTemplateResult_show(self, *args)
1100 r"""__str__(MatchTemplateResult self) -> std::string"""
1101 return _IMP_em2d.MatchTemplateResult___str__(self)
1104 r"""__repr__(MatchTemplateResult self) -> std::string"""
1105 return _IMP_em2d.MatchTemplateResult___repr__(self)
1107 def _get_as_binary(self):
1108 r"""_get_as_binary(MatchTemplateResult self) -> PyObject *"""
1109 return _IMP_em2d.MatchTemplateResult__get_as_binary(self)
1111 def _set_from_binary(self, p):
1112 r"""_set_from_binary(MatchTemplateResult self, PyObject * p)"""
1113 return _IMP_em2d.MatchTemplateResult__set_from_binary(self, p)
1115 def __getstate__(self):
1116 p = self._get_as_binary()
1117 if len(self.__dict__) > 1:
1118 d = self.__dict__.copy()
1123 def __setstate__(self, p):
1124 if not hasattr(self,
'this'):
1126 if isinstance(p, tuple):
1128 self.__dict__.update(d)
1129 return self._set_from_binary(p)
1131 __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
1134 _IMP_em2d.MatchTemplateResult_swigregister(MatchTemplateResult)
1137 r"""apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
1138 return _IMP_em2d.apply_mask(m, result, mask, val)
1141 r"""apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)"""
1142 return _IMP_em2d.apply_circular_mask(mat, result, radius, value)
1145 r"""get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
1146 return _IMP_em2d.get_mean(mat, mask)
1149 r"""create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
1150 return _IMP_em2d.create_circular_mask(rows, cols, radius)
1152 def do_histogram_stretching(m, boxes, offset):
1153 r"""do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
1154 return _IMP_em2d.do_histogram_stretching(m, boxes, offset)
1157 r"""do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
1158 return _IMP_em2d.do_dilate_and_shrink_warp(m, grayscale, kernel)
1161 r"""do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)"""
1162 return _IMP_em2d.do_morphologic_reconstruction(mask, marker, neighbors_mode)
1165 r"""do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
1166 return _IMP_em2d.do_labeling(m, mat_to_label)
1169 r"""get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
1170 return _IMP_em2d.get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang)
1173 r"""get_domes(cv::Mat & m, cv::Mat & result, double h)"""
1174 return _IMP_em2d.get_domes(m, result, h)
1176 def get_transformed(input, transformed, T):
1177 r"""get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
1178 return _IMP_em2d.get_transformed(input, transformed, T)
1181 r"""apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)"""
1182 return _IMP_em2d.apply_threshold(m, result, threshold)
1185 r"""do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
1186 return _IMP_em2d.do_morphologic_contrast_enhancement(m, result, kernel, iterations)
1189 r"""get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
1190 return _IMP_em2d.get_morphologic_gradient(m, result, kernel)
1193 r"""get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
1194 return _IMP_em2d.get_overlap_percentage(m1, m2, center)
1197 r"""get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
1198 return _IMP_em2d.get_best_template_matches(m, templ, n)
1200 r"""Proxy of C++ IMP::em2d::Image class."""
1202 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1204 def __init__(self, *args):
1206 __init__(Image self) -> Image
1207 __init__(Image self, int rows, int cols) -> Image
1208 __init__(Image self, IMP::String filename, ImageReaderWriter reader) -> Image
1210 _IMP_em2d.Image_swiginit(self, _IMP_em2d.new_Image(*args))
1213 r"""get_data(Image self) -> cv::Mat &"""
1214 return _IMP_em2d.Image_get_data(self)
1216 def set_data(self, mat):
1217 r"""set_data(Image self, cv::Mat const & mat)"""
1218 return _IMP_em2d.Image_set_data(self, mat)
1220 def set_zeros(self):
1221 r"""set_zeros(Image self)"""
1222 return _IMP_em2d.Image_set_zeros(self)
1224 def set_value(self, *args):
1226 set_value(Image self, double val)
1227 set_value(Image self, int i, int j, double val)
1229 return _IMP_em2d.Image_set_value(self, *args)
1231 def __call__(self, i, j):
1232 r"""__call__(Image self, int i, int j) -> double"""
1233 return _IMP_em2d.Image___call__(self, i, j)
1235 def get_header(self):
1236 r"""get_header(Image self) -> ImageHeader"""
1237 return _IMP_em2d.Image_get_header(self)
1239 def set_size(self, *args):
1241 set_size(Image self, int rows, int cols)
1242 set_size(Image self, Image img)
1244 return _IMP_em2d.Image_set_size(self, *args)
1246 def update_header(self):
1247 r"""update_header(Image self)"""
1248 return _IMP_em2d.Image_update_header(self)
1250 def read(self, filename, reader):
1251 r"""read(Image self, IMP::String filename, ImageReaderWriter reader)"""
1252 return _IMP_em2d.Image_read(self, filename, reader)
1254 def write(self, filename, writer):
1255 r"""write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
1256 return _IMP_em2d.Image_write(self, filename, writer)
1258 def show(self, out):
1259 r"""show(Image self, _ostream out)"""
1260 return _IMP_em2d.Image_show(self, out)
1262 def get_version_info(self):
1263 r"""get_version_info(Image self) -> VersionInfo"""
1264 return _IMP_em2d.Image_get_version_info(self)
1265 __swig_destroy__ = _IMP_em2d.delete_Image
1267 def set_name(self, name):
1268 r"""set_name(Image self, IMP::String const & name)"""
1269 return _IMP_em2d.Image_set_name(self, name)
1272 r"""get_name(Image self) -> IMP::String"""
1273 return _IMP_em2d.Image_get_name(self)
1275 def get_min_and_max_values(self):
1276 r"""get_min_and_max_values(Image self) -> IMP::FloatRange"""
1277 return _IMP_em2d.Image_get_min_and_max_values(self)
1280 r"""__str__(Image self) -> std::string"""
1281 return _IMP_em2d.Image___str__(self)
1284 r"""__repr__(Image self) -> std::string"""
1285 return _IMP_em2d.Image___repr__(self)
1289 return _object_cast_to_Image(o)
1293 _IMP_em2d.Image_swigregister(Image)
1296 r"""read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1297 return _IMP_em2d.read_images(names, rw)
1300 r"""save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1301 return _IMP_em2d.save_images(images, names, rw)
1305 do_normalize(cv::Mat & m)
1306 do_normalize(Image im, bool force=False)
1308 return _IMP_em2d.do_normalize(*args)
1312 get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1313 get_histogram(Image img, int bins) -> IMP::Floats
1315 return _IMP_em2d.get_histogram(*args)
1319 apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1320 apply_variance_filter(Image input, Image filtered, int kernelsize)
1322 return _IMP_em2d.apply_variance_filter(*args)
1326 apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1327 apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1329 return _IMP_em2d.apply_diffusion_filter(*args)
1331 def do_fill_holes(*args):
1333 do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1334 do_fill_holes(Image input, Image result, double n_stddevs)
1336 return _IMP_em2d.do_fill_holes(*args)
1338 def do_combined_fill_holes_and_threshold(*args):
1340 do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1341 do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1343 return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1345 def do_extend_borders(*args):
1347 do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1348 do_extend_borders(Image im1, Image im2, unsigned int pix)
1350 return _IMP_em2d.do_extend_borders(*args)
1352 def do_segmentation(*args):
1354 do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1355 do_segmentation(Image input, Image result, SegmentationParameters params)
1357 return _IMP_em2d.do_segmentation(*args)
1359 def do_remove_small_objects(*args):
1361 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1362 do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1364 return _IMP_em2d.do_remove_small_objects(*args)
1367 r"""do_subtract_images(Image first, Image second, Image result)"""
1368 return _IMP_em2d.do_subtract_images(first, second, result)
1370 def add_noise(*args):
1372 add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode="uniform", double df=3)
1373 add_noise(Image im1, double op1, double op2, IMP::String const & mode="uniform", double df=3)
1375 return _IMP_em2d.add_noise(*args)
1379 do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1380 do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1382 return _IMP_em2d.do_resample_polar(*args)
1386 crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1387 crop(Image img, IMP::IntPair const & center, int size)
1389 return _IMP_em2d.crop(*args)
1392 r"""apply_mean_outside_mask(Image img, double radius)"""
1393 return _IMP_em2d.apply_mean_outside_mask(img, radius)
1394 class RegistrationResult(object):
1395 r"""Proxy of C++ IMP::em2d::RegistrationResult class."""
1397 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1399 def __init__(self, *args):
1401 __init__(RegistrationResult self) -> RegistrationResult
1402 __init__(RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name="") -> RegistrationResult
1403 __init__(RegistrationResult self, Rotation3D R, Vector2D shift=IMP::algebra::Vector2D(0., 0.), int projection_index=0, int image_index=0, IMP::String name="") -> RegistrationResult
1405 _IMP_em2d.RegistrationResult_swiginit(self, _IMP_em2d.new_RegistrationResult(*args))
1408 r"""get_phi(RegistrationResult self) -> double"""
1409 return _IMP_em2d.RegistrationResult_get_phi(self)
1411 def get_theta(self):
1412 r"""get_theta(RegistrationResult self) -> double"""
1413 return _IMP_em2d.RegistrationResult_get_theta(self)
1416 r"""get_psi(RegistrationResult self) -> double"""
1417 return _IMP_em2d.RegistrationResult_get_psi(self)
1419 def get_shift(self):
1420 r"""get_shift(RegistrationResult self) -> Vector2D"""
1421 return _IMP_em2d.RegistrationResult_get_shift(self)
1423 def get_shift_3d(self):
1424 r"""get_shift_3d(RegistrationResult self) -> Vector3D"""
1425 return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1427 def get_projection_index(self):
1428 r"""get_projection_index(RegistrationResult self) -> int"""
1429 return _IMP_em2d.RegistrationResult_get_projection_index(self)
1431 def set_projection_index(self, index):
1432 r"""set_projection_index(RegistrationResult self, int index)"""
1433 return _IMP_em2d.RegistrationResult_set_projection_index(self, index)
1435 def get_image_index(self):
1436 r"""get_image_index(RegistrationResult self) -> int"""
1437 return _IMP_em2d.RegistrationResult_get_image_index(self)
1439 def set_image_index(self, index):
1440 r"""set_image_index(RegistrationResult self, int index)"""
1441 return _IMP_em2d.RegistrationResult_set_image_index(self, index)
1444 r"""get_name(RegistrationResult self) -> IMP::String"""
1445 return _IMP_em2d.RegistrationResult_get_name(self)
1448 r"""get_ccc(RegistrationResult self) -> double"""
1449 return _IMP_em2d.RegistrationResult_get_ccc(self)
1451 def set_ccc(self, ccc):
1452 r"""set_ccc(RegistrationResult self, double ccc)"""
1453 return _IMP_em2d.RegistrationResult_set_ccc(self, ccc)
1455 def get_score(self):
1456 r"""get_score(RegistrationResult self) -> double"""
1457 return _IMP_em2d.RegistrationResult_get_score(self)
1459 def set_score(self, Score):
1460 r"""set_score(RegistrationResult self, double Score)"""
1461 return _IMP_em2d.RegistrationResult_set_score(self, Score)
1463 def set_rotation(self, *args):
1465 set_rotation(RegistrationResult self, double phi, double theta, double psi)
1466 set_rotation(RegistrationResult self, Rotation3D R)
1468 return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1470 def set_shift(self, shift):
1471 r"""set_shift(RegistrationResult self, Vector2D shift)"""
1472 return _IMP_em2d.RegistrationResult_set_shift(self, shift)
1474 def set_name(self, name):
1475 r"""set_name(RegistrationResult self, IMP::String name)"""
1476 return _IMP_em2d.RegistrationResult_set_name(self, name)
1478 def add_in_plane_transformation(self, t):
1479 r"""add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1480 return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, t)
1482 def show(self, *args):
1483 r"""show(RegistrationResult self, _ostream out=std::cout)"""
1484 return _IMP_em2d.RegistrationResult_show(self, *args)
1486 def write(self, *args):
1487 r"""write(RegistrationResult self, _ostream out=std::cout)"""
1488 return _IMP_em2d.RegistrationResult_write(self, *args)
1490 def write_comment_line(self, *args):
1491 r"""write_comment_line(RegistrationResult self, _ostream out=std::cout)"""
1492 return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1495 r"""read(RegistrationResult self, IMP::String const & s)"""
1496 return _IMP_em2d.RegistrationResult_read(self, s)
1498 def set_random_registration(self, index, maximum_shift):
1499 r"""set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1500 return _IMP_em2d.RegistrationResult_set_random_registration(self, index, maximum_shift)
1502 def get_rotation(self):
1503 r"""get_rotation(RegistrationResult self) -> Rotation3D"""
1504 return _IMP_em2d.RegistrationResult_get_rotation(self)
1506 def set_in_image(self, header):
1507 r"""set_in_image(RegistrationResult self, ImageHeader header)"""
1508 return _IMP_em2d.RegistrationResult_set_in_image(self, header)
1510 def read_from_image(self, header):
1511 r"""read_from_image(RegistrationResult self, ImageHeader header)"""
1512 return _IMP_em2d.RegistrationResult_read_from_image(self, header)
1514 def get_is_optimized_result(self):
1515 r"""get_is_optimized_result(RegistrationResult self) -> bool"""
1516 return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1517 __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1520 r"""__str__(RegistrationResult self) -> std::string"""
1521 return _IMP_em2d.RegistrationResult___str__(self)
1524 r"""__repr__(RegistrationResult self) -> std::string"""
1525 return _IMP_em2d.RegistrationResult___repr__(self)
1527 def _get_as_binary(self):
1528 r"""_get_as_binary(RegistrationResult self) -> PyObject *"""
1529 return _IMP_em2d.RegistrationResult__get_as_binary(self)
1531 def _set_from_binary(self, p):
1532 r"""_set_from_binary(RegistrationResult self, PyObject * p)"""
1533 return _IMP_em2d.RegistrationResult__set_from_binary(self, p)
1535 def __getstate__(self):
1536 p = self._get_as_binary()
1537 if len(self.__dict__) > 1:
1538 d = self.__dict__.copy()
1543 def __setstate__(self, p):
1544 if not hasattr(self,
'this'):
1546 if isinstance(p, tuple):
1548 self.__dict__.update(d)
1549 return self._set_from_binary(p)
1553 _IMP_em2d.RegistrationResult_swigregister(RegistrationResult)
1556 r"""read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1557 return _IMP_em2d.read_registration_results(filename)
1560 r"""write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1561 return _IMP_em2d.write_registration_results(filename, results)
1564 r"""get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults"""
1565 return _IMP_em2d.get_random_registration_results(n, maximum_shift)
1568 r"""get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1569 return _IMP_em2d.get_evenly_distributed_registration_results(n_projections)
1570 class SpiderImageReaderWriter(ImageReaderWriter):
1571 r"""Proxy of C++ IMP::em2d::SpiderImageReaderWriter class."""
1573 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1574 filename_ = property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set, doc=
r"""filename_ : IMP::String""")
1575 skip_type_check_ = property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set, doc=
r"""skip_type_check_ : bool""")
1576 force_reversed_ = property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set, doc=
r"""force_reversed_ : bool""")
1577 skip_extra_checkings_ = property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set, doc=
r"""skip_extra_checkings_ : bool""")
1579 def __init__(self, *args):
1581 __init__(SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1582 __init__(SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1584 _IMP_em2d.SpiderImageReaderWriter_swiginit(self, _IMP_em2d.new_SpiderImageReaderWriter(*args))
1585 __swig_destroy__ = _IMP_em2d.delete_SpiderImageReaderWriter
1588 r"""__str__(SpiderImageReaderWriter self) -> std::string"""
1589 return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1592 r"""__repr__(SpiderImageReaderWriter self) -> std::string"""
1593 return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1597 return _object_cast_to_SpiderImageReaderWriter(o)
1601 _IMP_em2d.SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1602 class JPGImageReaderWriter(ImageReaderWriter):
1603 r"""Proxy of C++ IMP::em2d::JPGImageReaderWriter class."""
1605 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1608 r"""__init__(JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1609 _IMP_em2d.JPGImageReaderWriter_swiginit(self, _IMP_em2d.new_JPGImageReaderWriter())
1610 __swig_destroy__ = _IMP_em2d.delete_JPGImageReaderWriter
1613 r"""__str__(JPGImageReaderWriter self) -> std::string"""
1614 return _IMP_em2d.JPGImageReaderWriter___str__(self)
1617 r"""__repr__(JPGImageReaderWriter self) -> std::string"""
1618 return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1622 return _object_cast_to_JPGImageReaderWriter(o)
1626 _IMP_em2d.JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1627 class TIFFImageReaderWriter(ImageReaderWriter):
1628 r"""Proxy of C++ IMP::em2d::TIFFImageReaderWriter class."""
1630 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1633 r"""__init__(TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1634 _IMP_em2d.TIFFImageReaderWriter_swiginit(self, _IMP_em2d.new_TIFFImageReaderWriter())
1635 __swig_destroy__ = _IMP_em2d.delete_TIFFImageReaderWriter
1638 r"""__str__(TIFFImageReaderWriter self) -> std::string"""
1639 return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1642 r"""__repr__(TIFFImageReaderWriter self) -> std::string"""
1643 return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1647 return _object_cast_to_TIFFImageReaderWriter(o)
1651 _IMP_em2d.TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1654 r"""do_matrix_to_image_flip(cv::Mat & m)"""
1655 return _IMP_em2d.do_matrix_to_image_flip(m)
1658 r"""get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1659 return _IMP_em2d.get_autocorrelation2d_no_preprocessing(M, corr)
1663 get_autocorrelation2d(Image im1, Image im2)
1664 get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1666 return _IMP_em2d.get_autocorrelation2d(*args)
1670 get_correlation2d(Image im1, Image im2, Image corr)
1671 get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1673 return _IMP_em2d.get_correlation2d(*args)
1676 r"""get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1677 return _IMP_em2d.get_correlation2d_no_preprocessing(M1, M2, corr)
1680 r"""get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1681 return _IMP_em2d.get_fft_using_optimal_size(m, M)
1684 r"""get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1685 return _IMP_em2d.get_spectrum(m, real, imag)
1688 r"""get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1689 return _IMP_em2d.get_rotation_error(rr1, rr2)
1692 r"""get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1693 return _IMP_em2d.get_shift_error(rr1, rr2)
1695 def get_average_rotation_error(correct_RRs, computed_RRs):
1696 r"""get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1697 return _IMP_em2d.get_average_rotation_error(correct_RRs, computed_RRs)
1699 def get_average_shift_error(correct_RRs, computed_RRs):
1700 r"""get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1701 return _IMP_em2d.get_average_shift_error(correct_RRs, computed_RRs)
1705 get_cross_correlation_coefficient(Image im1, Image im2) -> double
1706 get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1708 return _IMP_em2d.get_cross_correlation_coefficient(*args)
1711 r"""get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1712 return _IMP_em2d.get_global_score(RRs)
1714 r"""Proxy of C++ IMP::em2d::ScoreFunction class."""
1716 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1718 def __init__(self, *args, **kwargs):
1719 raise AttributeError(
"No constructor defined - class is abstract")
1721 def get_score(self, image, projection):
1722 r"""get_score(ScoreFunction self, Image image, Image projection) -> double"""
1723 return _IMP_em2d.ScoreFunction_get_score(self, image, projection)
1725 def set_variance_image(self, var):
1726 r"""set_variance_image(ScoreFunction self, Image var)"""
1727 return _IMP_em2d.ScoreFunction_set_variance_image(self, var)
1729 def get_version_info(self):
1730 r"""get_version_info(ScoreFunction self) -> VersionInfo"""
1731 return _IMP_em2d.ScoreFunction_get_version_info(self)
1732 __swig_destroy__ = _IMP_em2d.delete_ScoreFunction
1735 r"""__str__(ScoreFunction self) -> std::string"""
1736 return _IMP_em2d.ScoreFunction___str__(self)
1739 r"""__repr__(ScoreFunction self) -> std::string"""
1740 return _IMP_em2d.ScoreFunction___repr__(self)
1744 return _object_cast_to_ScoreFunction(o)
1748 _IMP_em2d.ScoreFunction_swigregister(ScoreFunction)
1749 class ChiSquaredScore(ScoreFunction):
1750 r"""Proxy of C++ IMP::em2d::ChiSquaredScore class."""
1752 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1755 r"""__init__(ChiSquaredScore self) -> ChiSquaredScore"""
1756 _IMP_em2d.ChiSquaredScore_swiginit(self, _IMP_em2d.new_ChiSquaredScore())
1759 r"""__str__(ChiSquaredScore self) -> std::string"""
1760 return _IMP_em2d.ChiSquaredScore___str__(self)
1763 r"""__repr__(ChiSquaredScore self) -> std::string"""
1764 return _IMP_em2d.ChiSquaredScore___repr__(self)
1768 return _object_cast_to_ChiSquaredScore(o)
1770 __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1773 _IMP_em2d.ChiSquaredScore_swigregister(ChiSquaredScore)
1774 class EM2DScore(ScoreFunction):
1775 r"""Proxy of C++ IMP::em2d::EM2DScore class."""
1777 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1780 r"""__init__(EM2DScore self) -> EM2DScore"""
1781 _IMP_em2d.EM2DScore_swiginit(self, _IMP_em2d.new_EM2DScore())
1784 r"""__str__(EM2DScore self) -> std::string"""
1785 return _IMP_em2d.EM2DScore___str__(self)
1788 r"""__repr__(EM2DScore self) -> std::string"""
1789 return _IMP_em2d.EM2DScore___repr__(self)
1793 return _object_cast_to_EM2DScore(o)
1795 __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1798 _IMP_em2d.EM2DScore_swigregister(EM2DScore)
1799 class MeanAbsoluteDifference(ScoreFunction):
1800 r"""Proxy of C++ IMP::em2d::MeanAbsoluteDifference class."""
1802 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1805 r"""__init__(MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1806 _IMP_em2d.MeanAbsoluteDifference_swiginit(self, _IMP_em2d.new_MeanAbsoluteDifference())
1809 r"""__str__(MeanAbsoluteDifference self) -> std::string"""
1810 return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1813 r"""__repr__(MeanAbsoluteDifference self) -> std::string"""
1814 return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1818 return _object_cast_to_MeanAbsoluteDifference(o)
1820 __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1823 _IMP_em2d.MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1826 r"""read_selection_file(IMP::String fn) -> IMP::Strings"""
1827 return _IMP_em2d.read_selection_file(fn)
1830 r"""create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1831 return _IMP_em2d.create_filenames(number, basic_name, extension)
1833 r"""Proxy of C++ IMP::em2d::ProjectionParameters class."""
1835 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1837 def __init__(self, *args):
1839 __init__(ProjectionParameters self) -> ProjectionParameters
1840 __init__(ProjectionParameters self, Model m, ParticleIndex id) -> ProjectionParameters
1841 __init__(ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1843 _IMP_em2d.ProjectionParameters_swiginit(self, _IMP_em2d.new_ProjectionParameters(*args))
1845 def show(self, *args):
1846 r"""show(ProjectionParameters self, _ostream out=std::cout)"""
1847 return _IMP_em2d.ProjectionParameters_show(self, *args)
1850 def setup_particle(*args):
1852 setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
1853 setup_particle(_ParticleAdaptor pa) -> ProjectionParameters
1855 return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1856 __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1860 r"""get_keys() -> IMP::FloatKeys const &"""
1861 return _IMP_em2d.ProjectionParameters_get_keys()
1863 def set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values):
1864 r"""set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1865 return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values)
1868 def get_is_setup(*args):
1870 get_is_setup(_ParticleAdaptor p) -> bool
1871 get_is_setup(Model m, ParticleIndex pi) -> bool
1873 return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1875 def get_parameters_optimized(self):
1876 r"""get_parameters_optimized(ProjectionParameters self) -> bool"""
1877 return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1879 def get_translation(self):
1880 r"""get_translation(ProjectionParameters self) -> Vector3D"""
1881 return _IMP_em2d.ProjectionParameters_get_translation(self)
1883 def set_translation(self, v):
1884 r"""set_translation(ProjectionParameters self, Vector3D v)"""
1885 return _IMP_em2d.ProjectionParameters_set_translation(self, v)
1887 def get_rotation(self):
1888 r"""get_rotation(ProjectionParameters self) -> Rotation3D"""
1889 return _IMP_em2d.ProjectionParameters_get_rotation(self)
1891 def set_rotation(self, R):
1892 r"""set_rotation(ProjectionParameters self, Rotation3D R)"""
1893 return _IMP_em2d.ProjectionParameters_set_rotation(self, R)
1895 def set_parameters_optimized(self, tf):
1896 r"""set_parameters_optimized(ProjectionParameters self, bool tf)"""
1897 return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, tf)
1899 def get_quaternion_1(self):
1900 r"""get_quaternion_1(ProjectionParameters self) -> double"""
1901 return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1903 def set_quaternion_1(self, t):
1904 r"""set_quaternion_1(ProjectionParameters self, double t)"""
1905 return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, t)
1907 def get_quaternion_2(self):
1908 r"""get_quaternion_2(ProjectionParameters self) -> double"""
1909 return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1911 def set_quaternion_2(self, t):
1912 r"""set_quaternion_2(ProjectionParameters self, double t)"""
1913 return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, t)
1915 def get_quaternion_3(self):
1916 r"""get_quaternion_3(ProjectionParameters self) -> double"""
1917 return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1919 def set_quaternion_3(self, t):
1920 r"""set_quaternion_3(ProjectionParameters self, double t)"""
1921 return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, t)
1923 def get_quaternion_4(self):
1924 r"""get_quaternion_4(ProjectionParameters self) -> double"""
1925 return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1927 def set_quaternion_4(self, t):
1928 r"""set_quaternion_4(ProjectionParameters self, double t)"""
1929 return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, t)
1931 def get_translation_x(self):
1932 r"""get_translation_x(ProjectionParameters self) -> double"""
1933 return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1935 def set_translation_x(self, t):
1936 r"""set_translation_x(ProjectionParameters self, double t)"""
1937 return _IMP_em2d.ProjectionParameters_set_translation_x(self, t)
1939 def get_translation_y(self):
1940 r"""get_translation_y(ProjectionParameters self) -> double"""
1941 return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1943 def set_translation_y(self, t):
1944 r"""set_translation_y(ProjectionParameters self, double t)"""
1945 return _IMP_em2d.ProjectionParameters_set_translation_y(self, t)
1947 def add_attribute(self, *args):
1949 add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1950 add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1951 add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1952 add_attribute(ProjectionParameters self, FloatsKey a0, IMP::Floats a1)
1953 add_attribute(ProjectionParameters self, IntsKey a0, IMP::Ints a1)
1954 add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1955 add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1956 add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1958 return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1960 def get_value(self, *args):
1962 get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1963 get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1964 get_value(ProjectionParameters self, FloatsKey a0) -> IMP::Floats
1965 get_value(ProjectionParameters self, IntsKey a0) -> IMP::Ints
1966 get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1967 get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1968 get_value(ProjectionParameters self, ObjectKey a0) -> Object
1970 return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1972 def set_value(self, *args):
1974 set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1975 set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1976 set_value(ProjectionParameters self, FloatsKey a0, IMP::Floats a1)
1977 set_value(ProjectionParameters self, IntsKey a0, IMP::Ints a1)
1978 set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1979 set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1980 set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1982 return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1984 def remove_attribute(self, *args):
1986 remove_attribute(ProjectionParameters self, FloatKey a0)
1987 remove_attribute(ProjectionParameters self, IntKey a0)
1988 remove_attribute(ProjectionParameters self, FloatsKey a0)
1989 remove_attribute(ProjectionParameters self, IntsKey a0)
1990 remove_attribute(ProjectionParameters self, StringKey a0)
1991 remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1992 remove_attribute(ProjectionParameters self, ObjectKey a0)
1994 return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1996 def has_attribute(self, *args):
1998 has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1999 has_attribute(ProjectionParameters self, IntKey a0) -> bool
2000 has_attribute(ProjectionParameters self, FloatsKey a0) -> bool
2001 has_attribute(ProjectionParameters self, IntsKey a0) -> bool
2002 has_attribute(ProjectionParameters self, StringKey a0) -> bool
2003 has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
2004 has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
2006 return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
2008 def get_derivative(self, a0):
2009 r"""get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
2010 return _IMP_em2d.ProjectionParameters_get_derivative(self, a0)
2013 r"""get_name(ProjectionParameters self) -> std::string"""
2014 return _IMP_em2d.ProjectionParameters_get_name(self)
2016 def clear_caches(self):
2017 r"""clear_caches(ProjectionParameters self)"""
2018 return _IMP_em2d.ProjectionParameters_clear_caches(self)
2020 def set_name(self, a0):
2021 r"""set_name(ProjectionParameters self, std::string a0)"""
2022 return _IMP_em2d.ProjectionParameters_set_name(self, a0)
2025 r"""set_check_level(ProjectionParameters self, IMP::CheckLevel a0)"""
2026 return _IMP_em2d.ProjectionParameters_set_check_level(self, a0)
2028 def add_to_derivative(self, a0, a1, a2):
2029 r"""add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
2030 return _IMP_em2d.ProjectionParameters_add_to_derivative(self, a0, a1, a2)
2032 def set_is_optimized(self, a0, a1):
2033 r"""set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
2034 return _IMP_em2d.ProjectionParameters_set_is_optimized(self, a0, a1)
2036 def get_is_optimized(self, a0):
2037 r"""get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
2038 return _IMP_em2d.ProjectionParameters_get_is_optimized(self, a0)
2041 r"""get_check_level(ProjectionParameters self) -> IMP::CheckLevel"""
2042 return _IMP_em2d.ProjectionParameters_get_check_level(self)
2044 def __eq__(self, *args):
2046 __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
2047 __eq__(ProjectionParameters self, Particle d) -> bool
2049 return _IMP_em2d.ProjectionParameters___eq__(self, *args)
2051 def __ne__(self, *args):
2053 __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
2054 __ne__(ProjectionParameters self, Particle d) -> bool
2056 return _IMP_em2d.ProjectionParameters___ne__(self, *args)
2058 def __le__(self, *args):
2060 __le__(ProjectionParameters self, ProjectionParameters o) -> bool
2061 __le__(ProjectionParameters self, Particle d) -> bool
2063 return _IMP_em2d.ProjectionParameters___le__(self, *args)
2065 def __lt__(self, *args):
2067 __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
2068 __lt__(ProjectionParameters self, Particle d) -> bool
2070 return _IMP_em2d.ProjectionParameters___lt__(self, *args)
2072 def __ge__(self, *args):
2074 __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
2075 __ge__(ProjectionParameters self, Particle d) -> bool
2077 return _IMP_em2d.ProjectionParameters___ge__(self, *args)
2079 def __gt__(self, *args):
2081 __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
2082 __gt__(ProjectionParameters self, Particle d) -> bool
2084 return _IMP_em2d.ProjectionParameters___gt__(self, *args)
2087 r"""__hash__(ProjectionParameters self) -> std::size_t"""
2088 return _IMP_em2d.ProjectionParameters___hash__(self)
2091 r"""__str__(ProjectionParameters self) -> std::string"""
2092 return _IMP_em2d.ProjectionParameters___str__(self)
2095 r"""__repr__(ProjectionParameters self) -> std::string"""
2096 return _IMP_em2d.ProjectionParameters___repr__(self)
2098 def _get_as_binary(self):
2099 r"""_get_as_binary(ProjectionParameters self) -> PyObject *"""
2100 return _IMP_em2d.ProjectionParameters__get_as_binary(self)
2102 def _set_from_binary(self, p):
2103 r"""_set_from_binary(ProjectionParameters self, PyObject * p)"""
2104 return _IMP_em2d.ProjectionParameters__set_from_binary(self, p)
2106 def __getstate__(self):
2107 p = self._get_as_binary()
2108 if len(self.__dict__) > 1:
2109 d = self.__dict__.copy()
2114 def __setstate__(self, p):
2115 if not hasattr(self,
'this'):
2117 if isinstance(p, tuple):
2119 self.__dict__.update(d)
2120 return self._set_from_binary(p)
2124 _IMP_em2d.ProjectionParameters_swigregister(ProjectionParameters)
2126 def __lshift__(out, n):
2127 r"""__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
2128 return _IMP_em2d.__lshift__(out, n)
2130 r"""Proxy of C++ IMP::em2d::ProjectionParametersScoreState class."""
2132 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2134 def __init__(self, p):
2135 r"""__init__(ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
2136 _IMP_em2d.ProjectionParametersScoreState_swiginit(self, _IMP_em2d.new_ProjectionParametersScoreState(p))
2138 def do_before_evaluate(self):
2139 r"""do_before_evaluate(ProjectionParametersScoreState self)"""
2140 return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
2142 def do_after_evaluate(self, da):
2143 r"""do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
2144 return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, da)
2146 def do_get_inputs(self):
2147 r"""do_get_inputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2148 return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
2150 def do_get_outputs(self):
2151 r"""do_get_outputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2152 return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
2154 def get_version_info(self):
2155 r"""get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
2156 return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
2157 __swig_destroy__ = _IMP_em2d.delete_ProjectionParametersScoreState
2160 r"""__str__(ProjectionParametersScoreState self) -> std::string"""
2161 return _IMP_em2d.ProjectionParametersScoreState___str__(self)
2164 r"""__repr__(ProjectionParametersScoreState self) -> std::string"""
2165 return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
2169 return _object_cast_to_ProjectionParametersScoreState(o)
2173 _IMP_em2d.ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
2174 class ProjectionMask(object):
2175 r"""Proxy of C++ IMP::em2d::ProjectionMask class."""
2177 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2180 r"""__init__(ProjectionMask self) -> ProjectionMask"""
2181 _IMP_em2d.ProjectionMask_swiginit(self, _IMP_em2d.new_ProjectionMask())
2183 def apply(self, m, v):
2184 r"""apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
2185 return _IMP_em2d.ProjectionMask_apply(self, m, v)
2187 def show(self, *args):
2188 r"""show(ProjectionMask self, _ostream out=std::cout)"""
2189 return _IMP_em2d.ProjectionMask_show(self, *args)
2190 __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
2193 r"""__str__(ProjectionMask self) -> std::string"""
2194 return _IMP_em2d.ProjectionMask___str__(self)
2197 r"""__repr__(ProjectionMask self) -> std::string"""
2198 return _IMP_em2d.ProjectionMask___repr__(self)
2200 def _get_as_binary(self):
2201 r"""_get_as_binary(ProjectionMask self) -> PyObject *"""
2202 return _IMP_em2d.ProjectionMask__get_as_binary(self)
2204 def _set_from_binary(self, p):
2205 r"""_set_from_binary(ProjectionMask self, PyObject * p)"""
2206 return _IMP_em2d.ProjectionMask__set_from_binary(self, p)
2208 def __getstate__(self):
2209 p = self._get_as_binary()
2210 if len(self.__dict__) > 1:
2211 d = self.__dict__.copy()
2216 def __setstate__(self, p):
2217 if not hasattr(self,
'this'):
2219 if isinstance(p, tuple):
2221 self.__dict__.update(d)
2222 return self._set_from_binary(p)
2226 _IMP_em2d.ProjectionMask_swigregister(ProjectionMask)
2229 r"""do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
2230 return _IMP_em2d.do_place(mask, m, v)
2231 class MasksManager(object):
2232 r"""Proxy of C++ IMP::em2d::MasksManager class."""
2234 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2236 def __init__(self, *args):
2238 __init__(MasksManager self) -> MasksManager
2239 __init__(MasksManager self, double resolution, double pixelsize) -> MasksManager
2241 _IMP_em2d.MasksManager_swiginit(self, _IMP_em2d.new_MasksManager(*args))
2243 def setup_kernel(self, resolution, pixelsize):
2244 r"""setup_kernel(MasksManager self, double resolution, double pixelsize)"""
2245 return _IMP_em2d.MasksManager_setup_kernel(self, resolution, pixelsize)
2247 def create_masks(self, ps):
2248 r"""create_masks(MasksManager self, IMP::ParticlesTemp const & ps)"""
2249 return _IMP_em2d.MasksManager_create_masks(self, ps)
2251 def create_mask(self, mass):
2252 r"""create_mask(MasksManager self, double mass)"""
2253 return _IMP_em2d.MasksManager_create_mask(self, mass)
2255 def find_mask(self, mass):
2256 r"""find_mask(MasksManager self, double mass) -> IMP::em2d::ProjectionMaskPtr"""
2257 return _IMP_em2d.MasksManager_find_mask(self, mass)
2259 def show(self, *args):
2260 r"""show(MasksManager self, _ostream out=std::cout)"""
2261 return _IMP_em2d.MasksManager_show(self, *args)
2263 def get_number_of_masks(self):
2264 r"""get_number_of_masks(MasksManager self) -> unsigned int"""
2265 return _IMP_em2d.MasksManager_get_number_of_masks(self)
2266 __swig_destroy__ = _IMP_em2d.delete_MasksManager
2269 r"""__str__(MasksManager self) -> std::string"""
2270 return _IMP_em2d.MasksManager___str__(self)
2273 r"""__repr__(MasksManager self) -> std::string"""
2274 return _IMP_em2d.MasksManager___repr__(self)
2276 def _get_as_binary(self):
2277 r"""_get_as_binary(MasksManager self) -> PyObject *"""
2278 return _IMP_em2d.MasksManager__get_as_binary(self)
2280 def _set_from_binary(self, p):
2281 r"""_set_from_binary(MasksManager self, PyObject * p)"""
2282 return _IMP_em2d.MasksManager__set_from_binary(self, p)
2284 def __getstate__(self):
2285 p = self._get_as_binary()
2286 if len(self.__dict__) > 1:
2287 d = self.__dict__.copy()
2292 def __setstate__(self, p):
2293 if not hasattr(self,
'this'):
2295 if isinstance(p, tuple):
2297 self.__dict__.update(d)
2298 return self._set_from_binary(p)
2302 _IMP_em2d.MasksManager_swigregister(MasksManager)
2303 class ProjectingParameters(object):
2304 r"""Proxy of C++ IMP::em2d::ProjectingParameters class."""
2306 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2307 pixel_size = property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set, doc=
r"""pixel_size : double""")
2308 resolution = property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set, doc=
r"""resolution : double""")
2310 def __init__(self, *args):
2312 __init__(ProjectingParameters self) -> ProjectingParameters
2313 __init__(ProjectingParameters self, double ps, double res) -> ProjectingParameters
2315 _IMP_em2d.ProjectingParameters_swiginit(self, _IMP_em2d.new_ProjectingParameters(*args))
2317 def show(self, *args):
2318 r"""show(ProjectingParameters self, _ostream out=std::cout)"""
2319 return _IMP_em2d.ProjectingParameters_show(self, *args)
2322 r"""__str__(ProjectingParameters self) -> std::string"""
2323 return _IMP_em2d.ProjectingParameters___str__(self)
2326 r"""__repr__(ProjectingParameters self) -> std::string"""
2327 return _IMP_em2d.ProjectingParameters___repr__(self)
2329 def _get_as_binary(self):
2330 r"""_get_as_binary(ProjectingParameters self) -> PyObject *"""
2331 return _IMP_em2d.ProjectingParameters__get_as_binary(self)
2333 def _set_from_binary(self, p):
2334 r"""_set_from_binary(ProjectingParameters self, PyObject * p)"""
2335 return _IMP_em2d.ProjectingParameters__set_from_binary(self, p)
2337 def __getstate__(self):
2338 p = self._get_as_binary()
2339 if len(self.__dict__) > 1:
2340 d = self.__dict__.copy()
2345 def __setstate__(self, p):
2346 if not hasattr(self,
'this'):
2348 if isinstance(p, tuple):
2350 self.__dict__.update(d)
2351 return self._set_from_binary(p)
2353 __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2356 _IMP_em2d.ProjectingParameters_swigregister(ProjectingParameters)
2357 class ProjectingOptions(ProjectingParameters):
2358 r"""Proxy of C++ IMP::em2d::ProjectingOptions class."""
2360 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2361 save_images = property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set, doc=
r"""save_images : bool""")
2362 normalize = property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set, doc=
r"""normalize : bool""")
2363 clear_matrix_before_projecting = property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set, doc=
r"""clear_matrix_before_projecting : bool""")
2365 def __init__(self, *args):
2367 __init__(ProjectingOptions self) -> ProjectingOptions
2368 __init__(ProjectingOptions self, double ps, double res) -> ProjectingOptions
2369 __init__(ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2371 _IMP_em2d.ProjectingOptions_swiginit(self, _IMP_em2d.new_ProjectingOptions(*args))
2373 def show(self, *args):
2374 r"""show(ProjectingOptions self, _ostream out=std::cout)"""
2375 return _IMP_em2d.ProjectingOptions_show(self, *args)
2378 r"""__str__(ProjectingOptions self) -> std::string"""
2379 return _IMP_em2d.ProjectingOptions___str__(self)
2382 r"""__repr__(ProjectingOptions self) -> std::string"""
2383 return _IMP_em2d.ProjectingOptions___repr__(self)
2384 __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2387 _IMP_em2d.ProjectingOptions_swigregister(ProjectingOptions)
2391 get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options, IMP::Strings names=IMP::Strings()) -> IMP::em2d::Images
2392 get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options, IMP::Strings names=IMP::Strings()) -> IMP::em2d::Images
2394 return _IMP_em2d.get_projections(*args)
2397 r"""get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks=IMP::em2d::MasksManagerPtr(), IMP::String name="")"""
2398 return _IMP_em2d.get_projection(*args)
2401 r"""do_project_particles(IMP::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)"""
2402 return _IMP_em2d.do_project_particles(ps, m2, R, translation, options, masks)
2405 r"""create_evenly_distributed_projections(IMP::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2406 return _IMP_em2d.create_evenly_distributed_projections(ps, n, options)
2410 do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2411 do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2413 return _IMP_em2d.do_project_vectors(*args)
2416 r"""get_enclosing_image_size(IMP::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2417 return _IMP_em2d.get_enclosing_image_size(ps, pixel_size, slack)
2420 r"""get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D"""
2421 return _IMP_em2d.get_complete_alignment(input, m_to_align, apply)
2424 r"""get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D"""
2425 return _IMP_em2d.get_rotational_alignment(input, m_to_align, apply)
2428 r"""get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D"""
2429 return _IMP_em2d.get_translational_alignment(input, m_to_align, apply)
2432 r"""get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align, cv::Mat const & POLAR2, bool apply=False) -> ResultAlign2D"""
2433 return _IMP_em2d.get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply)
2436 r"""get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2437 return _IMP_em2d.get_rotational_alignment_no_preprocessing(POLAR1, POLAR2)
2440 r"""get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2441 return _IMP_em2d.get_translational_alignment_no_preprocessing(M1, M2)
2444 r"""get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2445 return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2)
2449 write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2450 write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2452 return _IMP_em2d.write_vectors_as_pdb(*args)
2453 class Em2DRestraintParameters(ProjectingParameters):
2454 r"""Proxy of C++ IMP::em2d::Em2DRestraintParameters class."""
2456 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2457 n_projections = property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set, doc=
r"""n_projections : unsigned int""")
2458 coarse_registration_method = property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set, doc=
r"""coarse_registration_method : unsigned int""")
2459 save_match_images = property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set, doc=
r"""save_match_images : bool""")
2460 optimization_steps = property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set, doc=
r"""optimization_steps : unsigned int""")
2461 simplex_initial_length = property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set, doc=
r"""simplex_initial_length : double""")
2462 simplex_minimum_size = property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set, doc=
r"""simplex_minimum_size : double""")
2464 def __init__(self, *args):
2466 __init__(Em2DRestraintParameters self) -> Em2DRestraintParameters
2467 __init__(Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2469 _IMP_em2d.Em2DRestraintParameters_swiginit(self, _IMP_em2d.new_Em2DRestraintParameters(*args))
2471 def show(self, *args):
2472 r"""show(Em2DRestraintParameters self, _ostream out=std::cout)"""
2473 return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2476 r"""__str__(Em2DRestraintParameters self) -> std::string"""
2477 return _IMP_em2d.Em2DRestraintParameters___str__(self)
2480 r"""__repr__(Em2DRestraintParameters self) -> std::string"""
2481 return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2483 def _get_as_binary(self):
2484 r"""_get_as_binary(Em2DRestraintParameters self) -> PyObject *"""
2485 return _IMP_em2d.Em2DRestraintParameters__get_as_binary(self)
2487 def _set_from_binary(self, p):
2488 r"""_set_from_binary(Em2DRestraintParameters self, PyObject * p)"""
2489 return _IMP_em2d.Em2DRestraintParameters__set_from_binary(self, p)
2491 def __getstate__(self):
2492 p = self._get_as_binary()
2493 if len(self.__dict__) > 1:
2494 d = self.__dict__.copy()
2499 def __setstate__(self, p):
2500 if not hasattr(self,
'this'):
2502 if isinstance(p, tuple):
2504 self.__dict__.update(d)
2505 return self._set_from_binary(p)
2507 __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2510 _IMP_em2d.Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2511 cvar = _IMP_em2d.cvar
2512 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2513 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2514 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2517 r"""Proxy of C++ IMP::em2d::ProjectionFinder class."""
2519 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2522 r"""__init__(ProjectionFinder self) -> ProjectionFinder"""
2523 _IMP_em2d.ProjectionFinder_swiginit(self, _IMP_em2d.new_ProjectionFinder())
2525 def setup(self, score_function, params):
2526 r"""setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2527 return _IMP_em2d.ProjectionFinder_setup(self, score_function, params)
2529 def set_subjects(self, subjects):
2530 r"""set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2531 return _IMP_em2d.ProjectionFinder_set_subjects(self, subjects)
2533 def set_projections(self, projections):
2534 r"""set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2535 return _IMP_em2d.ProjectionFinder_set_projections(self, projections)
2537 def set_variance_images(self, variances):
2538 r"""set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2539 return _IMP_em2d.ProjectionFinder_set_variance_images(self, variances)
2541 def set_model_particles(self, ps):
2542 r"""set_model_particles(ProjectionFinder self, IMP::ParticlesTemp const & ps)"""
2543 return _IMP_em2d.ProjectionFinder_set_model_particles(self, ps)
2545 def set_save_match_images(self, x):
2546 r"""set_save_match_images(ProjectionFinder self, bool x)"""
2547 return _IMP_em2d.ProjectionFinder_set_save_match_images(self, x)
2549 def get_save_match_images(self):
2550 r"""get_save_match_images(ProjectionFinder self) -> bool"""
2551 return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2553 def set_fast_mode(self, n):
2554 r"""set_fast_mode(ProjectionFinder self, unsigned int n)"""
2555 return _IMP_em2d.ProjectionFinder_set_fast_mode(self, n)
2557 def get_registration_results(self):
2558 r"""get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2559 return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2561 def get_coarse_registration(self):
2562 r"""get_coarse_registration(ProjectionFinder self)"""
2563 return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2565 def get_complete_registration(self):
2566 r"""get_complete_registration(ProjectionFinder self)"""
2567 return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2570 r"""get_global_score(ProjectionFinder self) -> double"""
2571 return _IMP_em2d.ProjectionFinder_get_global_score(self)
2573 def show(self, out):
2574 r"""show(ProjectionFinder self, _ostream out)"""
2575 return _IMP_em2d.ProjectionFinder_show(self, out)
2577 def get_preprocessing_time(self):
2578 r"""get_preprocessing_time(ProjectionFinder self) -> double"""
2579 return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2581 def get_coarse_registration_time(self):
2582 r"""get_coarse_registration_time(ProjectionFinder self) -> double"""
2583 return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2585 def get_fine_registration_time(self):
2586 r"""get_fine_registration_time(ProjectionFinder self) -> double"""
2587 return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2589 def get_number_of_subjects(self):
2590 r"""get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2591 return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2593 def set_number_of_class_averages_members(self, n_members):
2594 r"""set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2595 return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, n_members)
2597 def get_number_of_projections(self):
2598 r"""get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2599 return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2601 def get_version_info(self):
2602 r"""get_version_info(ProjectionFinder self) -> VersionInfo"""
2603 return _IMP_em2d.ProjectionFinder_get_version_info(self)
2604 __swig_destroy__ = _IMP_em2d.delete_ProjectionFinder
2607 r"""__str__(ProjectionFinder self) -> std::string"""
2608 return _IMP_em2d.ProjectionFinder___str__(self)
2611 r"""__repr__(ProjectionFinder self) -> std::string"""
2612 return _IMP_em2d.ProjectionFinder___repr__(self)
2616 return _object_cast_to_ProjectionFinder(o)
2620 _IMP_em2d.ProjectionFinder_swigregister(ProjectionFinder)
2622 r"""Proxy of C++ IMP::em2d::Em2DRestraint class."""
2624 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2626 def __init__(self, m):
2627 r"""__init__(Em2DRestraint self, Model m) -> Em2DRestraint"""
2628 _IMP_em2d.Em2DRestraint_swiginit(self, _IMP_em2d.new_Em2DRestraint(m))
2630 def setup(self, score_function, params):
2631 r"""setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2632 return _IMP_em2d.Em2DRestraint_setup(self, score_function, params)
2634 def set_particles(self, particles_container):
2635 r"""set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2636 return _IMP_em2d.Em2DRestraint_set_particles(self, particles_container)
2638 def set_images(self, em_images):
2639 r"""set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2640 return _IMP_em2d.Em2DRestraint_set_images(self, em_images)
2642 def set_variance_images(self, variance_images):
2643 r"""set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2644 return _IMP_em2d.Em2DRestraint_set_variance_images(self, variance_images)
2646 def set_fast_mode(self, n):
2647 r"""set_fast_mode(Em2DRestraint self, unsigned int n)"""
2648 return _IMP_em2d.Em2DRestraint_set_fast_mode(self, n)
2650 def set_coarse_registration_mode(self, opt):
2651 r"""set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2652 return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, opt)
2654 def get_registration_results(self):
2655 r"""get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2656 return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2658 def do_get_inputs(self):
2659 r"""do_get_inputs(Em2DRestraint self) -> IMP::ModelObjectsTemp"""
2660 return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2662 def get_version_info(self):
2663 r"""get_version_info(Em2DRestraint self) -> VersionInfo"""
2664 return _IMP_em2d.Em2DRestraint_get_version_info(self)
2665 __swig_destroy__ = _IMP_em2d.delete_Em2DRestraint
2668 r"""__str__(Em2DRestraint self) -> std::string"""
2669 return _IMP_em2d.Em2DRestraint___str__(self)
2672 r"""__repr__(Em2DRestraint self) -> std::string"""
2673 return _IMP_em2d.Em2DRestraint___repr__(self)
2677 return _object_cast_to_Em2DRestraint(o)
2681 _IMP_em2d.Em2DRestraint_swigregister(Em2DRestraint)
2682 class ClusterSet(object):
2683 r"""Proxy of C++ IMP::em2d::ClusterSet class."""
2685 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2687 def __init__(self, *args):
2689 __init__(ClusterSet self) -> ClusterSet
2690 __init__(ClusterSet self, unsigned int N) -> ClusterSet
2692 _IMP_em2d.ClusterSet_swiginit(self, _IMP_em2d.new_ClusterSet(*args))
2694 def do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters):
2695 r"""do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2696 return _IMP_em2d.ClusterSet_do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters)
2698 def get_cluster_elements(self, id):
2699 r"""get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2700 return _IMP_em2d.ClusterSet_get_cluster_elements(self, id)
2702 def get_clusters_below_cutoff(self, cutoff):
2703 r"""get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2704 return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, cutoff)
2706 def get_cluster_formed_at_step(self, step):
2707 r"""get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2708 return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, step)
2710 def get_distance_at_step(self, step):
2711 r"""get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2712 return _IMP_em2d.ClusterSet_get_distance_at_step(self, step)
2714 def get_id_for_cluster_at_step(self, step):
2715 r"""get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2716 return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, step)
2718 def get_linkage_matrix(self):
2719 r"""get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2720 return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2722 def get_linkage_matrix_in_matlab_format(self):
2723 r"""get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2724 return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2726 def get_number_of_steps(self):
2727 r"""get_number_of_steps(ClusterSet self) -> unsigned int"""
2728 return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2730 def show(self, out):
2731 r"""show(ClusterSet self, _ostream out)"""
2732 return _IMP_em2d.ClusterSet_show(self, out)
2735 r"""__str__(ClusterSet self) -> std::string"""
2736 return _IMP_em2d.ClusterSet___str__(self)
2739 r"""__repr__(ClusterSet self) -> std::string"""
2740 return _IMP_em2d.ClusterSet___repr__(self)
2742 def _get_as_binary(self):
2743 r"""_get_as_binary(ClusterSet self) -> PyObject *"""
2744 return _IMP_em2d.ClusterSet__get_as_binary(self)
2746 def _set_from_binary(self, p):
2747 r"""_set_from_binary(ClusterSet self, PyObject * p)"""
2748 return _IMP_em2d.ClusterSet__set_from_binary(self, p)
2750 def __getstate__(self):
2751 p = self._get_as_binary()
2752 if len(self.__dict__) > 1:
2753 d = self.__dict__.copy()
2758 def __setstate__(self, p):
2759 if not hasattr(self,
'this'):
2761 if isinstance(p, tuple):
2763 self.__dict__.update(d)
2764 return self._set_from_binary(p)
2766 __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2769 _IMP_em2d.ClusterSet_swigregister(ClusterSet)
2770 class SingleLinkage(object):
2771 r"""Proxy of C++ IMP::em2d::SingleLinkage class."""
2773 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2776 r"""__init__(SingleLinkage self) -> SingleLinkage"""
2777 _IMP_em2d.SingleLinkage_swiginit(self, _IMP_em2d.new_SingleLinkage())
2779 def __call__(self, id1, id2, cluster_set, distances):
2780 r"""__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2781 return _IMP_em2d.SingleLinkage___call__(self, id1, id2, cluster_set, distances)
2783 def show(self, out):
2784 r"""show(SingleLinkage self, _ostream out)"""
2785 return _IMP_em2d.SingleLinkage_show(self, out)
2788 r"""__str__(SingleLinkage self) -> std::string"""
2789 return _IMP_em2d.SingleLinkage___str__(self)
2792 r"""__repr__(SingleLinkage self) -> std::string"""
2793 return _IMP_em2d.SingleLinkage___repr__(self)
2795 def _get_as_binary(self):
2796 r"""_get_as_binary(SingleLinkage self) -> PyObject *"""
2797 return _IMP_em2d.SingleLinkage__get_as_binary(self)
2799 def _set_from_binary(self, p):
2800 r"""_set_from_binary(SingleLinkage self, PyObject * p)"""
2801 return _IMP_em2d.SingleLinkage__set_from_binary(self, p)
2803 def __getstate__(self):
2804 p = self._get_as_binary()
2805 if len(self.__dict__) > 1:
2806 d = self.__dict__.copy()
2811 def __setstate__(self, p):
2812 if not hasattr(self,
'this'):
2814 if isinstance(p, tuple):
2816 self.__dict__.update(d)
2817 return self._set_from_binary(p)
2819 __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2822 _IMP_em2d.SingleLinkage_swigregister(SingleLinkage)
2823 class CompleteLinkage(object):
2824 r"""Proxy of C++ IMP::em2d::CompleteLinkage class."""
2826 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2829 r"""__init__(CompleteLinkage self) -> CompleteLinkage"""
2830 _IMP_em2d.CompleteLinkage_swiginit(self, _IMP_em2d.new_CompleteLinkage())
2832 def __call__(self, id1, id2, cluster_set, distances):
2833 r"""__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2834 return _IMP_em2d.CompleteLinkage___call__(self, id1, id2, cluster_set, distances)
2836 def show(self, out):
2837 r"""show(CompleteLinkage self, _ostream out)"""
2838 return _IMP_em2d.CompleteLinkage_show(self, out)
2841 r"""__str__(CompleteLinkage self) -> std::string"""
2842 return _IMP_em2d.CompleteLinkage___str__(self)
2845 r"""__repr__(CompleteLinkage self) -> std::string"""
2846 return _IMP_em2d.CompleteLinkage___repr__(self)
2848 def _get_as_binary(self):
2849 r"""_get_as_binary(CompleteLinkage self) -> PyObject *"""
2850 return _IMP_em2d.CompleteLinkage__get_as_binary(self)
2852 def _set_from_binary(self, p):
2853 r"""_set_from_binary(CompleteLinkage self, PyObject * p)"""
2854 return _IMP_em2d.CompleteLinkage__set_from_binary(self, p)
2856 def __getstate__(self):
2857 p = self._get_as_binary()
2858 if len(self.__dict__) > 1:
2859 d = self.__dict__.copy()
2864 def __setstate__(self, p):
2865 if not hasattr(self,
'this'):
2867 if isinstance(p, tuple):
2869 self.__dict__.update(d)
2870 return self._set_from_binary(p)
2872 __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2875 _IMP_em2d.CompleteLinkage_swigregister(CompleteLinkage)
2876 class AverageDistanceLinkage(object):
2877 r"""Proxy of C++ IMP::em2d::AverageDistanceLinkage class."""
2879 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2882 r"""__init__(AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2883 _IMP_em2d.AverageDistanceLinkage_swiginit(self, _IMP_em2d.new_AverageDistanceLinkage())
2885 def __call__(self, id1, id2, cluster_set, distances):
2886 r"""__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2887 return _IMP_em2d.AverageDistanceLinkage___call__(self, id1, id2, cluster_set, distances)
2889 def show(self, out):
2890 r"""show(AverageDistanceLinkage self, _ostream out)"""
2891 return _IMP_em2d.AverageDistanceLinkage_show(self, out)
2894 r"""__str__(AverageDistanceLinkage self) -> std::string"""
2895 return _IMP_em2d.AverageDistanceLinkage___str__(self)
2898 r"""__repr__(AverageDistanceLinkage self) -> std::string"""
2899 return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2901 def _get_as_binary(self):
2902 r"""_get_as_binary(AverageDistanceLinkage self) -> PyObject *"""
2903 return _IMP_em2d.AverageDistanceLinkage__get_as_binary(self)
2905 def _set_from_binary(self, p):
2906 r"""_set_from_binary(AverageDistanceLinkage self, PyObject * p)"""
2907 return _IMP_em2d.AverageDistanceLinkage__set_from_binary(self, p)
2909 def __getstate__(self):
2910 p = self._get_as_binary()
2911 if len(self.__dict__) > 1:
2912 d = self.__dict__.copy()
2917 def __setstate__(self, p):
2918 if not hasattr(self,
'this'):
2920 if isinstance(p, tuple):
2922 self.__dict__.update(d)
2923 return self._set_from_binary(p)
2925 __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2928 _IMP_em2d.AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2930 r"""Proxy of C++ IMP::em2d::CollisionCrossSection class."""
2932 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2934 def __init__(self, n_projections, resolution, pixel_size, projection_image_size):
2935 r"""__init__(CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2936 _IMP_em2d.CollisionCrossSection_swiginit(self, _IMP_em2d.new_CollisionCrossSection(n_projections, resolution, pixel_size, projection_image_size))
2938 def set_model_particles(self, ps):
2939 r"""set_model_particles(CollisionCrossSection self, IMP::ParticlesTemp const & ps)"""
2940 return _IMP_em2d.CollisionCrossSection_set_model_particles(self, ps)
2943 r"""get_ccs(CollisionCrossSection self) -> double"""
2944 return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2946 def show(self, out):
2947 r"""show(CollisionCrossSection self, _ostream out)"""
2948 return _IMP_em2d.CollisionCrossSection_show(self, out)
2950 def get_version_info(self):
2951 r"""get_version_info(CollisionCrossSection self) -> VersionInfo"""
2952 return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2953 __swig_destroy__ = _IMP_em2d.delete_CollisionCrossSection
2956 r"""__str__(CollisionCrossSection self) -> std::string"""
2957 return _IMP_em2d.CollisionCrossSection___str__(self)
2960 r"""__repr__(CollisionCrossSection self) -> std::string"""
2961 return _IMP_em2d.CollisionCrossSection___repr__(self)
2965 return _object_cast_to_CollisionCrossSection(o)
2969 _IMP_em2d.CollisionCrossSection_swigregister(CollisionCrossSection)
2971 r"""Proxy of C++ IMP::em2d::GridStates class."""
2973 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2975 def __init__(self, *args):
2976 r"""__init__(GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::String const & name="GridStates") -> GridStates"""
2977 _IMP_em2d.GridStates_swiginit(self, _IMP_em2d.new_GridStates(*args))
2979 def get_position(self, i):
2980 r"""get_position(GridStates self, unsigned int i) -> Vector3D"""
2981 return _IMP_em2d.GridStates_get_position(self, i)
2983 def get_orientation(self, i):
2984 r"""get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2985 return _IMP_em2d.GridStates_get_orientation(self, i)
2987 def get_version_info(self):
2988 r"""get_version_info(GridStates self) -> VersionInfo"""
2989 return _IMP_em2d.GridStates_get_version_info(self)
2990 __swig_destroy__ = _IMP_em2d.delete_GridStates
2993 r"""__str__(GridStates self) -> std::string"""
2994 return _IMP_em2d.GridStates___str__(self)
2997 r"""__repr__(GridStates self) -> std::string"""
2998 return _IMP_em2d.GridStates___repr__(self)
3002 return _object_cast_to_GridStates(o)
3006 _IMP_em2d.GridStates_swigregister(GridStates)
3007 class ProjectionStates(GridStates):
3008 r"""Proxy of C++ IMP::em2d::ProjectionStates class."""
3010 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3012 def __init__(self, *args):
3013 r"""__init__(ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections, IMP::String const & name="ProjectionStates") -> ProjectionStates"""
3014 _IMP_em2d.ProjectionStates_swiginit(self, _IMP_em2d.new_ProjectionStates(*args))
3017 r"""get_projection(ProjectionStates self, unsigned int i) -> Image"""
3018 return _IMP_em2d.ProjectionStates_get_projection(self, i)
3019 __swig_destroy__ = _IMP_em2d.delete_ProjectionStates
3022 r"""__str__(ProjectionStates self) -> std::string"""
3023 return _IMP_em2d.ProjectionStates___str__(self)
3026 r"""__repr__(ProjectionStates self) -> std::string"""
3027 return _IMP_em2d.ProjectionStates___repr__(self)
3031 return _object_cast_to_ProjectionStates(o)
3035 _IMP_em2d.ProjectionStates_swigregister(ProjectionStates)
3037 r"""Proxy of C++ IMP::em2d::DistanceFilter class."""
3039 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3041 def __init__(self, subset_to_act_on, subset_to_restrain, ps_table, max_distance):
3042 r"""__init__(DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table, double max_distance) -> DistanceFilter"""
3043 _IMP_em2d.DistanceFilter_swiginit(self, _IMP_em2d.new_DistanceFilter(subset_to_act_on, subset_to_restrain, ps_table, max_distance))
3045 def show(self, *args):
3046 r"""show(DistanceFilter self, _ostream out=std::cout)"""
3047 return _IMP_em2d.DistanceFilter_show(self, *args)
3049 def get_version_info(self):
3050 r"""get_version_info(DistanceFilter self) -> VersionInfo"""
3051 return _IMP_em2d.DistanceFilter_get_version_info(self)
3052 __swig_destroy__ = _IMP_em2d.delete_DistanceFilter
3055 r"""__str__(DistanceFilter self) -> std::string"""
3056 return _IMP_em2d.DistanceFilter___str__(self)
3059 r"""__repr__(DistanceFilter self) -> std::string"""
3060 return _IMP_em2d.DistanceFilter___repr__(self)
3064 return _object_cast_to_DistanceFilter(o)
3068 _IMP_em2d.DistanceFilter_swigregister(DistanceFilter)
3070 r"""Proxy of C++ IMP::em2d::DistanceFilterTable class."""
3072 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3074 def __init__(self, subset_to_act_on, ps_table, max_distance):
3075 r"""__init__(DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
3076 _IMP_em2d.DistanceFilterTable_swiginit(self, _IMP_em2d.new_DistanceFilterTable(subset_to_act_on, ps_table, max_distance))
3078 def show(self, *args):
3079 r"""show(DistanceFilterTable self, _ostream out=std::cout)"""
3080 return _IMP_em2d.DistanceFilterTable_show(self, *args)
3082 def get_version_info(self):
3083 r"""get_version_info(DistanceFilterTable self) -> VersionInfo"""
3084 return _IMP_em2d.DistanceFilterTable_get_version_info(self)
3085 __swig_destroy__ = _IMP_em2d.delete_DistanceFilterTable
3088 r"""__str__(DistanceFilterTable self) -> std::string"""
3089 return _IMP_em2d.DistanceFilterTable___str__(self)
3092 r"""__repr__(DistanceFilterTable self) -> std::string"""
3093 return _IMP_em2d.DistanceFilterTable___repr__(self)
3097 return _object_cast_to_DistanceFilterTable(o)
3101 _IMP_em2d.DistanceFilterTable_swigregister(DistanceFilterTable)
3102 class IntsOrder(object):
3103 r"""Proxy of C++ IMP::em2d::IntsOrder class."""
3105 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3106 __repr__ = _swig_repr
3108 def __call__(self, a, b):
3109 r"""__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
3110 return _IMP_em2d.IntsOrder___call__(self, a, b)
3113 r"""__init__(IntsOrder self) -> IntsOrder"""
3114 _IMP_em2d.IntsOrder_swiginit(self, _IMP_em2d.new_IntsOrder())
3115 __swig_destroy__ = _IMP_em2d.delete_IntsOrder
3118 _IMP_em2d.IntsOrder_swigregister(IntsOrder)
3120 r"""Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class."""
3122 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3124 def get_version_info(self):
3125 r"""get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
3126 return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
3127 __swig_destroy__ = _IMP_em2d.delete_RigidBodiesImageFitRestraint
3129 def __init__(self, scf, rbs, img):
3130 r"""__init__(RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
3131 _IMP_em2d.RigidBodiesImageFitRestraint_swiginit(self, _IMP_em2d.new_RigidBodiesImageFitRestraint(scf, rbs, img))
3133 def set_projecting_parameters(self, p):
3134 r"""set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
3135 return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, p)
3137 def set_orientations(self, rb, rots):
3138 r"""set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
3139 return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, rb, rots)
3141 def get_number_of_masks(self, rb):
3142 r"""get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
3143 return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, rb)
3146 r"""__str__(RigidBodiesImageFitRestraint self) -> std::string"""
3147 return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
3150 r"""__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
3151 return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
3155 return _object_cast_to_RigidBodiesImageFitRestraint(o)
3159 _IMP_em2d.RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
3162 r"""get_unique_index(Rotation3D rot) -> IMP::Ints"""
3163 return _IMP_em2d.get_unique_index(rot)
3165 r"""Proxy of C++ IMP::em2d::RelativePositionMover class."""
3167 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3169 def __init__(self, d, max_translation, max_rotation):
3170 r"""__init__(RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
3171 _IMP_em2d.RelativePositionMover_swiginit(self, _IMP_em2d.new_RelativePositionMover(d, max_translation, max_rotation))
3173 def add_internal_transformations(self, d, transforms):
3174 r"""add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
3175 return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, d, transforms)
3177 def set_random_move_probability(self, p):
3178 r"""set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
3179 return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, p)
3180 __swig_destroy__ = _IMP_em2d.delete_RelativePositionMover
3183 r"""__str__(RelativePositionMover self) -> std::string"""
3184 return _IMP_em2d.RelativePositionMover___str__(self)
3187 r"""__repr__(RelativePositionMover self) -> std::string"""
3188 return _IMP_em2d.RelativePositionMover___repr__(self)
3192 return _object_cast_to_RelativePositionMover(o)
3196 _IMP_em2d.RelativePositionMover_swigregister(RelativePositionMover)
3198 r"""Proxy of C++ IMP::em2d::DummyRestraint class."""
3200 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3202 def __init__(self, p, q):
3203 r"""__init__(DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
3204 _IMP_em2d.DummyRestraint_swiginit(self, _IMP_em2d.new_DummyRestraint(p, q))
3206 def show(self, *args):
3207 r"""show(DummyRestraint self, _ostream out=std::cout)"""
3208 return _IMP_em2d.DummyRestraint_show(self, *args)
3210 def do_get_inputs(self):
3211 r"""do_get_inputs(DummyRestraint self) -> IMP::ModelObjectsTemp"""
3212 return _IMP_em2d.DummyRestraint_do_get_inputs(self)
3214 def get_version_info(self):
3215 r"""get_version_info(DummyRestraint self) -> VersionInfo"""
3216 return _IMP_em2d.DummyRestraint_get_version_info(self)
3217 __swig_destroy__ = _IMP_em2d.delete_DummyRestraint
3220 r"""__str__(DummyRestraint self) -> std::string"""
3221 return _IMP_em2d.DummyRestraint___str__(self)
3224 r"""__repr__(DummyRestraint self) -> std::string"""
3225 return _IMP_em2d.DummyRestraint___repr__(self)
3229 return _object_cast_to_DummyRestraint(o)
3233 _IMP_em2d.DummyRestraint_swigregister(DummyRestraint)
3235 r"""Proxy of C++ IMP::em2d::ParticlesDummyRestraint class."""
3237 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3239 def __init__(self, sc):
3240 r"""__init__(ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
3241 _IMP_em2d.ParticlesDummyRestraint_swiginit(self, _IMP_em2d.new_ParticlesDummyRestraint(sc))
3243 def show(self, *args):
3244 r"""show(ParticlesDummyRestraint self, _ostream out=std::cout)"""
3245 return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
3247 def do_get_inputs(self):
3248 r"""do_get_inputs(ParticlesDummyRestraint self) -> IMP::ModelObjectsTemp"""
3249 return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3251 def get_version_info(self):
3252 r"""get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3253 return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3254 __swig_destroy__ = _IMP_em2d.delete_ParticlesDummyRestraint
3257 r"""__str__(ParticlesDummyRestraint self) -> std::string"""
3258 return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3261 r"""__repr__(ParticlesDummyRestraint self) -> std::string"""
3262 return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3266 return _object_cast_to_ParticlesDummyRestraint(o)
3270 _IMP_em2d.ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3272 r"""Proxy of C++ IMP::em2d::PCAFitRestraint class."""
3274 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3276 def __init__(self, particles, image_files, pixel_size, resolution=10.0, projection_number=100, reuse_direction=False, n_components=1, micrographs_number=0):
3277 r"""__init__(PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False, unsigned int n_components=1, unsigned int micrographs_number=0) -> PCAFitRestraint"""
3278 _IMP_em2d.PCAFitRestraint_swiginit(self, _IMP_em2d.new_PCAFitRestraint(particles, image_files, pixel_size, resolution, projection_number, reuse_direction, n_components, micrographs_number))
3280 def get_projection_number(self):
3281 r"""get_projection_number(PCAFitRestraint self) -> unsigned int"""
3282 return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3284 def set_projection_number(self, n):
3285 r"""set_projection_number(PCAFitRestraint self, unsigned int n)"""
3286 return _IMP_em2d.PCAFitRestraint_set_projection_number(self, n)
3288 def get_micrographs_number(self):
3289 r"""get_micrographs_number(PCAFitRestraint self) -> unsigned int"""
3290 return _IMP_em2d.PCAFitRestraint_get_micrographs_number(self)
3292 def set_micrographs_number(self, n):
3293 r"""set_micrographs_number(PCAFitRestraint self, unsigned int n)"""
3294 return _IMP_em2d.PCAFitRestraint_set_micrographs_number(self, n)
3296 def get_transformation(self, image_number):
3297 r"""get_transformation(PCAFitRestraint self, unsigned int image_number) -> Transformation3D"""
3298 return _IMP_em2d.PCAFitRestraint_get_transformation(self, image_number)
3301 r"""get_cross_correlation_coefficient(PCAFitRestraint self, unsigned int image_number) -> double"""
3302 return _IMP_em2d.PCAFitRestraint_get_cross_correlation_coefficient(self, image_number)
3304 def write_best_projections(self, file_name, evaluate=False):
3305 r"""write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)"""
3306 return _IMP_em2d.PCAFitRestraint_write_best_projections(self, file_name, evaluate)
3308 def do_get_inputs(self):
3309 r"""do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
3310 return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3312 def get_version_info(self):
3313 r"""get_version_info(PCAFitRestraint self) -> VersionInfo"""
3314 return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3315 __swig_destroy__ = _IMP_em2d.delete_PCAFitRestraint
3318 r"""__str__(PCAFitRestraint self) -> std::string"""
3319 return _IMP_em2d.PCAFitRestraint___str__(self)
3322 r"""__repr__(PCAFitRestraint self) -> std::string"""
3323 return _IMP_em2d.PCAFitRestraint___repr__(self)
3327 return _object_cast_to_em2dPCAFitRestraint(o)
3331 _IMP_em2d.PCAFitRestraint_swigregister(PCAFitRestraint)
3333 r"""Proxy of C++ std::pair< IMP::algebra::Transformation2D,double > class."""
3335 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3336 __repr__ = _swig_repr
3338 def __init__(self, *args):
3340 __init__(ResultAlign2D self) -> ResultAlign2D
3341 __init__(ResultAlign2D self, Transformation2D first, double second) -> ResultAlign2D
3342 __init__(ResultAlign2D self, ResultAlign2D other) -> ResultAlign2D
3344 _IMP_em2d.ResultAlign2D_swiginit(self, _IMP_em2d.new_ResultAlign2D(*args))
3345 first = property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set, doc=
r"""first : IMP::algebra::Transformation2D""")
3346 second = property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set, doc=
r"""second : double""")
3350 return str((self.first, self.second))
3351 def __getitem__(self, index):
3356 def __setitem__(self, index, val):
3361 __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3364 _IMP_em2d.ResultAlign2D_swigregister(ResultAlign2D)
3366 def _do_hierarchical_clustering_single_linkage(distances):
3367 r"""_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3368 return _IMP_em2d._do_hierarchical_clustering_single_linkage(distances)
3370 def _do_hierarchical_clustering_complete_linkage(distances):
3371 r"""_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3372 return _IMP_em2d._do_hierarchical_clustering_complete_linkage(distances)
3374 def _do_hierarchical_clustering_average_distance_linkage(distances):
3375 r"""_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3376 return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(distances)
3378 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3379 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3380 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3384 r"""get_module_version() -> std::string const"""
3385 return _IMP_em2d.get_module_version()
3388 r"""get_example_path(std::string fname) -> std::string"""
3389 return _IMP_em2d.get_example_path(fname)
3392 r"""get_data_path(std::string fname) -> std::string"""
3393 return _IMP_em2d.get_data_path(fname)
3395 from .
import _version_check
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.
void apply_threshold(cv::Mat &m, cv::Mat &result, double threshold=0.0)
em2d::Images get_projections(const ParticlesTemp &ps, const algebra::SphericalVector3Ds &vs, int rows, int cols, const ProjectingOptions &options, Strings names=Strings())
Generates projections from particles.
std::string get_module_version()
Return the version of this module, as a string.
IMPEM2D_BEGIN_NAMESPACE Strings read_selection_file(String fn)
Reads a selection file.
ResultAlign2D get_complete_alignment_with_centers_no_preprocessing(const algebra::Vector2D ¢er1, const algebra::Vector2D ¢er2, 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)
void apply_diffusion_filter(Image *input, Image *filtered, double beta, double pixelsize, int time_steps)
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)
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.
ScoreStates maintain invariants in the Model.
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 ¢er, 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)
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
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 ¢er)
RegistrationResults read_registration_results(const String &filename)
Reads a set of registration results.
void get_diffusion_filtering_partial_derivative(const cv::Mat &m, cv::Mat &der, double dx, double dy, double ang)
Ints get_unique_index(const algebra::Rotation3D &rot)
Map a rotation to a list of 4 "unique" integers.
double get_global_score(const RegistrationResults &RRs)
void do_place(cv::Mat &mask, cv::Mat &m, const algebra::Vector2D &v)
void do_morphologic_reconstruction(const cv::Mat &mask, cv::Mat &marker, int neighbors_mode=4)
morphologic grayscale reconstruction (L Vincent, 1993)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for the RMF file format for storing hierarchical molecular data and markup.
Divide-and-conquer inferential optimization in discrete space.
Support for small angle X-ray scattering (SAXS) data.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
void get_projection(em2d::Image *img, const ParticlesTemp &ps, const RegistrationResult ®, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="")
Generates a projection from particles.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.
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.