10 from __future__
import print_function, division, absolute_import
15 from sys
import version_info
as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17 def swig_import_helper():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_em2d')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_em2d')
25 _IMP_em2d = swig_import_helper()
26 del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28 def swig_import_helper():
29 from os.path
import dirname
33 fp, pathname, description = imp.find_module(
'_IMP_em2d', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_em2d', fp, pathname, description)
43 _IMP_em2d = swig_import_helper()
44 del swig_import_helper
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
78 def _swig_getattr(self, class_type, name):
79 if (name ==
"thisown"):
80 return self.this.own()
81 method = class_type.__swig_getmethods__.get(name,
None)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
95 def _swig_setattr_nondynamic_method(set):
96 def set_attr(self, name, value):
97 if (name ==
"thisown"):
98 return self.this.own(value)
99 if hasattr(self, name)
or (name ==
"this"):
100 set(self, name, value)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_EM2D_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_EM2D_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_em2d.delete_IMP_EM2D_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
126 return _IMP_em2d.IMP_EM2D_SwigPyIterator_value(self)
131 incr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
132 incr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
134 return _IMP_em2d.IMP_EM2D_SwigPyIterator_incr(self, n)
139 decr(IMP_EM2D_SwigPyIterator self, size_t n=1) -> IMP_EM2D_SwigPyIterator
140 decr(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator
142 return _IMP_em2d.IMP_EM2D_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_em2d.IMP_EM2D_SwigPyIterator_distance(self, x)
151 """equal(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
152 return _IMP_em2d.IMP_EM2D_SwigPyIterator_equal(self, x)
156 """copy(IMP_EM2D_SwigPyIterator self) -> IMP_EM2D_SwigPyIterator"""
157 return _IMP_em2d.IMP_EM2D_SwigPyIterator_copy(self)
161 """next(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
162 return _IMP_em2d.IMP_EM2D_SwigPyIterator_next(self)
166 """__next__(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
167 return _IMP_em2d.IMP_EM2D_SwigPyIterator___next__(self)
171 """previous(IMP_EM2D_SwigPyIterator self) -> PyObject *"""
172 return _IMP_em2d.IMP_EM2D_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
177 return _IMP_em2d.IMP_EM2D_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
182 return _IMP_em2d.IMP_EM2D_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> bool"""
187 return _IMP_em2d.IMP_EM2D_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
192 return _IMP_em2d.IMP_EM2D_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
197 return _IMP_em2d.IMP_EM2D_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator"""
202 return _IMP_em2d.IMP_EM2D_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_EM2D_SwigPyIterator self, ptrdiff_t n) -> IMP_EM2D_SwigPyIterator
208 __sub__(IMP_EM2D_SwigPyIterator self, IMP_EM2D_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_em2d.IMP_EM2D_SwigPyIterator___sub__(self, *args)
214 IMP_EM2D_SwigPyIterator_swigregister = _IMP_em2d.IMP_EM2D_SwigPyIterator_swigregister
215 IMP_EM2D_SwigPyIterator_swigregister(IMP_EM2D_SwigPyIterator)
223 IMP_DEBUG = _IMP_em2d.IMP_DEBUG
224 IMP_RELEASE = _IMP_em2d.IMP_RELEASE
225 IMP_SILENT = _IMP_em2d.IMP_SILENT
226 IMP_PROGRESS = _IMP_em2d.IMP_PROGRESS
227 IMP_TERSE = _IMP_em2d.IMP_TERSE
228 IMP_VERBOSE = _IMP_em2d.IMP_VERBOSE
229 IMP_MEMORY = _IMP_em2d.IMP_MEMORY
230 IMP_NONE = _IMP_em2d.IMP_NONE
231 IMP_USAGE = _IMP_em2d.IMP_USAGE
232 IMP_INTERNAL = _IMP_em2d.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_em2d.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_em2d.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_em2d.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_em2d.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_em2d.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_em2d.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_em2d.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_em2d._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_em2d._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_em2d.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_em2d.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_em2d.IMP_HAS_NOEXCEPT
288 IMP_C_OPEN_BINARY = _IMP_em2d.IMP_C_OPEN_BINARY
290 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_FILESYSTEM
291 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
292 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CGAL_HAS_BOOST_RANDOM
293 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CGAL_HAS_BOOST_SYSTEM
294 IMPCGAL_SHOW_WARNINGS = _IMP_em2d.IMPCGAL_SHOW_WARNINGS
296 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_IMP_CGAL
297 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
298 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
299 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_RANDOM
300 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ALGEBRA_HAS_BOOST_SYSTEM
301 IMP_ALGEBRA_HAS_CGAL = _IMP_em2d.IMP_ALGEBRA_HAS_CGAL
302 IMP_ALGEBRA_HAS_ANN = _IMP_em2d.IMP_ALGEBRA_HAS_ANN
303 IMPALGEBRA_SHOW_WARNINGS = _IMP_em2d.IMPALGEBRA_SHOW_WARNINGS
305 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_IMP_CGAL
306 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
307 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
308 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_RANDOM
309 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DISPLAY_HAS_BOOST_SYSTEM
310 IMP_DISPLAY_HAS_CGAL = _IMP_em2d.IMP_DISPLAY_HAS_CGAL
311 IMPDISPLAY_SHOW_WARNINGS = _IMP_em2d.IMPDISPLAY_SHOW_WARNINGS
313 IMP_GSL_HAS_IMP_CGAL = _IMP_em2d.IMP_GSL_HAS_IMP_CGAL
314 IMP_GSL_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_FILESYSTEM
315 IMP_GSL_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_GSL_HAS_BOOST_PROGRAMOPTIONS
316 IMP_GSL_HAS_BOOST_RANDOM = _IMP_em2d.IMP_GSL_HAS_BOOST_RANDOM
317 IMP_GSL_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_GSL_HAS_BOOST_SYSTEM
318 IMP_GSL_HAS_CGAL = _IMP_em2d.IMP_GSL_HAS_CGAL
319 IMPGSL_SHOW_WARNINGS = _IMP_em2d.IMPGSL_SHOW_WARNINGS
321 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
322 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
323 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
324 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
325 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
326 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_CGAL
327 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_em2d.IMP_SCORE_FUNCTOR_HAS_HDF5
328 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_em2d.IMPSCOREFUNCTOR_SHOW_WARNINGS
330 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_IMP_CGAL
331 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
332 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
333 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_RANDOM
334 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_STATISTICS_HAS_BOOST_SYSTEM
335 IMP_STATISTICS_HAS_CGAL = _IMP_em2d.IMP_STATISTICS_HAS_CGAL
336 IMPSTATISTICS_SHOW_WARNINGS = _IMP_em2d.IMPSTATISTICS_SHOW_WARNINGS
338 IMP_CORE_HAS_IMP_CGAL = _IMP_em2d.IMP_CORE_HAS_IMP_CGAL
339 IMP_CORE_HAS_IMP_KERNEL = _IMP_em2d.IMP_CORE_HAS_IMP_KERNEL
340 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_FILESYSTEM
341 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
342 IMP_CORE_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CORE_HAS_BOOST_RANDOM
343 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CORE_HAS_BOOST_SYSTEM
344 IMP_CORE_HAS_CGAL = _IMP_em2d.IMP_CORE_HAS_CGAL
345 IMP_CORE_HAS_HDF5 = _IMP_em2d.IMP_CORE_HAS_HDF5
346 IMPCORE_SHOW_WARNINGS = _IMP_em2d.IMPCORE_SHOW_WARNINGS
348 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_em2d.IMP_CONTAINER_HAS_IMP_ALGEBRA
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_CGAL
350 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_em2d.IMP_CONTAINER_HAS_IMP_DISPLAY
351 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_em2d.IMP_CONTAINER_HAS_IMP_KERNEL
352 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
353 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
354 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
355 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_RANDOM
356 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_CONTAINER_HAS_BOOST_SYSTEM
357 IMP_CONTAINER_HAS_CGAL = _IMP_em2d.IMP_CONTAINER_HAS_CGAL
358 IMP_CONTAINER_HAS_HDF5 = _IMP_em2d.IMP_CONTAINER_HAS_HDF5
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_em2d.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_em2d.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_em2d.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_em2d.IMPCONTAINER_SHOW_WARNINGS
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_em2d.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_em2d.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_em2d.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_em2d.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_em2d.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_PYTHON_IHM = _IMP_em2d.IMP_ATOM_HAS_PYTHON_IHM
374 IMPATOM_SHOW_WARNINGS = _IMP_em2d.IMPATOM_SHOW_WARNINGS
375 IMP_ATOM_TYPE_INDEX = _IMP_em2d.IMP_ATOM_TYPE_INDEX
376 IMP_RESIDUE_TYPE_INDEX = _IMP_em2d.IMP_RESIDUE_TYPE_INDEX
377 IMP_HIERARCHY_TYPE_INDEX = _IMP_em2d.IMP_HIERARCHY_TYPE_INDEX
378 IMP_CHAIN_TYPE_INDEX = _IMP_em2d.IMP_CHAIN_TYPE_INDEX
380 IMP_EM_HAS_IMP_CGAL = _IMP_em2d.IMP_EM_HAS_IMP_CGAL
381 IMP_EM_HAS_IMP_CONTAINER = _IMP_em2d.IMP_EM_HAS_IMP_CONTAINER
382 IMP_EM_HAS_IMP_DISPLAY = _IMP_em2d.IMP_EM_HAS_IMP_DISPLAY
383 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM_HAS_IMP_SCORE_FUNCTOR
384 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_FILESYSTEM
385 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
386 IMP_EM_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM_HAS_BOOST_RANDOM
387 IMP_EM_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM_HAS_BOOST_REGEX
388 IMP_EM_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM_HAS_BOOST_SYSTEM
389 IMP_EM_HAS_CGAL = _IMP_em2d.IMP_EM_HAS_CGAL
390 IMP_EM_HAS_HDF5 = _IMP_em2d.IMP_EM_HAS_HDF5
391 IMP_EM_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM_HAS_PYTHON_IHM
392 IMPEM_SHOW_WARNINGS = _IMP_em2d.IMPEM_SHOW_WARNINGS
394 IMP_RMF_HAS_IMP_CGAL = _IMP_em2d.IMP_RMF_HAS_IMP_CGAL
395 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
396 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_FILESYSTEM
397 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
398 IMP_RMF_HAS_BOOST_RANDOM = _IMP_em2d.IMP_RMF_HAS_BOOST_RANDOM
399 IMP_RMF_HAS_BOOST_REGEX = _IMP_em2d.IMP_RMF_HAS_BOOST_REGEX
400 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_RMF_HAS_BOOST_SYSTEM
401 IMP_RMF_HAS_CGAL = _IMP_em2d.IMP_RMF_HAS_CGAL
402 IMP_RMF_HAS_HDF5 = _IMP_em2d.IMP_RMF_HAS_HDF5
403 IMP_RMF_HAS_PYTHON_IHM = _IMP_em2d.IMP_RMF_HAS_PYTHON_IHM
404 IMPRMF_SHOW_WARNINGS = _IMP_em2d.IMPRMF_SHOW_WARNINGS
407 IMP_DOMINO_HAS_IMP_ATOM = _IMP_em2d.IMP_DOMINO_HAS_IMP_ATOM
408 IMP_DOMINO_HAS_IMP_CGAL = _IMP_em2d.IMP_DOMINO_HAS_IMP_CGAL
409 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_em2d.IMP_DOMINO_HAS_IMP_KERNEL
410 IMP_DOMINO_HAS_IMP_RMF = _IMP_em2d.IMP_DOMINO_HAS_IMP_RMF
411 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
412 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_FILESYSTEM
413 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_em2d.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
414 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_RANDOM
415 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_em2d.IMP_DOMINO_HAS_BOOST_REGEX
416 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_DOMINO_HAS_BOOST_SYSTEM
417 IMP_DOMINO_HAS_CGAL = _IMP_em2d.IMP_DOMINO_HAS_CGAL
418 IMP_DOMINO_HAS_HDF5 = _IMP_em2d.IMP_DOMINO_HAS_HDF5
419 IMP_DOMINO_HAS_RMF = _IMP_em2d.IMP_DOMINO_HAS_RMF
420 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_em2d.IMP_DOMINO_HAS_PYTHON_IHM
421 IMPDOMINO_SHOW_WARNINGS = _IMP_em2d.IMPDOMINO_SHOW_WARNINGS
424 IMP_EM2D_HAS_IMP_CGAL = _IMP_em2d.IMP_EM2D_HAS_IMP_CGAL
425 IMP_EM2D_HAS_IMP_KERNEL = _IMP_em2d.IMP_EM2D_HAS_IMP_KERNEL
426 IMP_EM2D_HAS_IMP_RMF = _IMP_em2d.IMP_EM2D_HAS_IMP_RMF
427 IMP_EM2D_HAS_IMP_SCORE_FUNCTOR = _IMP_em2d.IMP_EM2D_HAS_IMP_SCORE_FUNCTOR
428 IMP_EM2D_HAS_IMP_STATISTICS = _IMP_em2d.IMP_EM2D_HAS_IMP_STATISTICS
429 IMP_EM2D_HAS_BOOST_GRAPH = _IMP_em2d.IMP_EM2D_HAS_BOOST_GRAPH
430 IMP_EM2D_HAS_BOOST_RANDOM = _IMP_em2d.IMP_EM2D_HAS_BOOST_RANDOM
431 IMP_EM2D_HAS_BOOST_REGEX = _IMP_em2d.IMP_EM2D_HAS_BOOST_REGEX
432 IMP_EM2D_HAS_BOOST_SYSTEM = _IMP_em2d.IMP_EM2D_HAS_BOOST_SYSTEM
433 IMP_EM2D_HAS_CGAL = _IMP_em2d.IMP_EM2D_HAS_CGAL
434 IMP_EM2D_HAS_GSL = _IMP_em2d.IMP_EM2D_HAS_GSL
435 IMP_EM2D_HAS_HDF5 = _IMP_em2d.IMP_EM2D_HAS_HDF5
436 IMP_EM2D_HAS_OPENCV22 = _IMP_em2d.IMP_EM2D_HAS_OPENCV22
437 IMP_EM2D_HAS_RMF = _IMP_em2d.IMP_EM2D_HAS_RMF
438 IMP_EM2D_HAS_PYTHON_IHM = _IMP_em2d.IMP_EM2D_HAS_PYTHON_IHM
439 IMP_EM2D_HAS_OPENCV21 = _IMP_em2d.IMP_EM2D_HAS_OPENCV21
440 IMP_EM2D_HAS_OPENCV3 = _IMP_em2d.IMP_EM2D_HAS_OPENCV3
441 IMPEM2D_SHOW_WARNINGS = _IMP_em2d.IMPEM2D_SHOW_WARNINGS
443 PolarResamplingParametersList=list
444 _plural_types.append(
"PolarResamplingParametersList")
445 _value_types.append(
"PolarResamplingParameters")
449 _plural_types.append(
"ProjectionMasks")
450 _value_types.append(
"ProjectionMask")
454 _plural_types.append(
"MasksManagers")
455 _value_types.append(
"MasksManager")
458 RegistrationResults=list
459 _plural_types.append(
"RegistrationResults")
460 _value_types.append(
"RegistrationResult")
464 _plural_types.append(
"ClusterSets")
465 _value_types.append(
"ClusterSet")
469 _plural_types.append(
"SingleLinkages")
470 _value_types.append(
"SingleLinkage")
473 CompleteLinkages=list
474 _plural_types.append(
"CompleteLinkages")
475 _value_types.append(
"CompleteLinkage")
478 AverageDistanceLinkages=list
479 _plural_types.append(
"AverageDistanceLinkages")
480 _value_types.append(
"AverageDistanceLinkage")
483 SegmentationParametersList=list
484 _plural_types.append(
"SegmentationParametersList")
485 _value_types.append(
"SegmentationParameters")
488 MatchTemplateResults=list
489 _plural_types.append(
"MatchTemplateResults")
490 _value_types.append(
"MatchTemplateResult")
493 ProjectingParametersList=list
494 _plural_types.append(
"ProjectingParametersList")
495 _value_types.append(
"ProjectingParameters")
498 ProjectingOptionsList=list
499 _plural_types.append(
"ProjectingOptionsList")
500 _value_types.append(
"ProjectingOptions")
503 Em2DRestraintParametersList=list
504 _plural_types.append(
"Em2DRestraintParametersList")
505 _value_types.append(
"Em2DRestraintParameters")
508 _object_types.append(
"ProjectionFinder")
511 def _object_cast_to_ProjectionFinder(o):
512 """_object_cast_to_ProjectionFinder(Object o) -> ProjectionFinder"""
513 return _IMP_em2d._object_cast_to_ProjectionFinder(o)
515 _object_types.append(
"ScoreFunction")
518 def _object_cast_to_ScoreFunction(o):
519 """_object_cast_to_ScoreFunction(Object o) -> ScoreFunction"""
520 return _IMP_em2d._object_cast_to_ScoreFunction(o)
522 _object_types.append(
"ChiSquaredScore")
525 def _object_cast_to_ChiSquaredScore(o):
526 """_object_cast_to_ChiSquaredScore(Object o) -> ChiSquaredScore"""
527 return _IMP_em2d._object_cast_to_ChiSquaredScore(o)
529 _object_types.append(
"EM2DScore")
532 def _object_cast_to_EM2DScore(o):
533 """_object_cast_to_EM2DScore(Object o) -> EM2DScore"""
534 return _IMP_em2d._object_cast_to_EM2DScore(o)
536 _object_types.append(
"MeanAbsoluteDifference")
539 def _object_cast_to_MeanAbsoluteDifference(o):
540 """_object_cast_to_MeanAbsoluteDifference(Object o) -> MeanAbsoluteDifference"""
541 return _IMP_em2d._object_cast_to_MeanAbsoluteDifference(o)
543 _object_types.append(
"ProjectionParametersScoreState")
546 def _object_cast_to_ProjectionParametersScoreState(o):
547 """_object_cast_to_ProjectionParametersScoreState(Object o) -> ProjectionParametersScoreState"""
548 return _IMP_em2d._object_cast_to_ProjectionParametersScoreState(o)
550 _object_types.append(
"Em2DRestraint")
553 def _object_cast_to_Em2DRestraint(o):
554 """_object_cast_to_Em2DRestraint(Object o) -> Em2DRestraint"""
555 return _IMP_em2d._object_cast_to_Em2DRestraint(o)
557 _object_types.append(
"Image")
560 def _object_cast_to_Image(o):
561 """_object_cast_to_Image(Object o) -> Image"""
562 return _IMP_em2d._object_cast_to_Image(o)
564 _object_types.append(
"ImageReaderWriter")
567 def _object_cast_to_ImageReaderWriter(o):
568 """_object_cast_to_ImageReaderWriter(Object o) -> ImageReaderWriter"""
569 return _IMP_em2d._object_cast_to_ImageReaderWriter(o)
571 _object_types.append(
"JPGImageReaderWriter")
574 def _object_cast_to_JPGImageReaderWriter(o):
575 """_object_cast_to_JPGImageReaderWriter(Object o) -> JPGImageReaderWriter"""
576 return _IMP_em2d._object_cast_to_JPGImageReaderWriter(o)
578 _object_types.append(
"TIFFImageReaderWriter")
581 def _object_cast_to_TIFFImageReaderWriter(o):
582 """_object_cast_to_TIFFImageReaderWriter(Object o) -> TIFFImageReaderWriter"""
583 return _IMP_em2d._object_cast_to_TIFFImageReaderWriter(o)
585 _object_types.append(
"SpiderImageReaderWriter")
588 def _object_cast_to_SpiderImageReaderWriter(o):
589 """_object_cast_to_SpiderImageReaderWriter(Object o) -> SpiderImageReaderWriter"""
590 return _IMP_em2d._object_cast_to_SpiderImageReaderWriter(o)
592 _object_types.append(
"CollisionCrossSection")
595 def _object_cast_to_CollisionCrossSection(o):
596 """_object_cast_to_CollisionCrossSection(Object o) -> CollisionCrossSection"""
597 return _IMP_em2d._object_cast_to_CollisionCrossSection(o)
599 _object_types.append(
"GridStates")
602 def _object_cast_to_GridStates(o):
603 """_object_cast_to_GridStates(Object o) -> GridStates"""
604 return _IMP_em2d._object_cast_to_GridStates(o)
606 _object_types.append(
"ProjectionStates")
609 def _object_cast_to_ProjectionStates(o):
610 """_object_cast_to_ProjectionStates(Object o) -> ProjectionStates"""
611 return _IMP_em2d._object_cast_to_ProjectionStates(o)
613 _object_types.append(
"DistanceFilter")
616 def _object_cast_to_DistanceFilter(o):
617 """_object_cast_to_DistanceFilter(Object o) -> DistanceFilter"""
618 return _IMP_em2d._object_cast_to_DistanceFilter(o)
620 _object_types.append(
"DistanceFilterTable")
623 def _object_cast_to_DistanceFilterTable(o):
624 """_object_cast_to_DistanceFilterTable(Object o) -> DistanceFilterTable"""
625 return _IMP_em2d._object_cast_to_DistanceFilterTable(o)
627 _object_types.append(
"RigidBodiesImageFitRestraint")
630 def _object_cast_to_RigidBodiesImageFitRestraint(o):
631 """_object_cast_to_RigidBodiesImageFitRestraint(Object o) -> RigidBodiesImageFitRestraint"""
632 return _IMP_em2d._object_cast_to_RigidBodiesImageFitRestraint(o)
634 _object_types.append(
"DummyRestraint")
637 def _object_cast_to_DummyRestraint(o):
638 """_object_cast_to_DummyRestraint(Object o) -> DummyRestraint"""
639 return _IMP_em2d._object_cast_to_DummyRestraint(o)
641 _object_types.append(
"ParticlesDummyRestraint")
644 def _object_cast_to_ParticlesDummyRestraint(o):
645 """_object_cast_to_ParticlesDummyRestraint(Object o) -> ParticlesDummyRestraint"""
646 return _IMP_em2d._object_cast_to_ParticlesDummyRestraint(o)
648 _object_types.append(
"RelativePositionMover")
651 def _object_cast_to_RelativePositionMover(o):
652 """_object_cast_to_RelativePositionMover(Object o) -> RelativePositionMover"""
653 return _IMP_em2d._object_cast_to_RelativePositionMover(o)
655 _object_types.append(
"PCAFitRestraint")
658 def _object_cast_to_em2dPCAFitRestraint(o):
659 """_object_cast_to_em2dPCAFitRestraint(Object o) -> PCAFitRestraint"""
660 return _IMP_em2d._object_cast_to_em2dPCAFitRestraint(o)
662 def ProjectionParametersList(l=[]):
663 return [ProjectionParameters(x)
for x
in l]
664 _plural_types.append(
"ProjectionParametersList")
667 _value_types.append(
"ProjectionParameters")
672 show(cv::Mat const & m, _ostream out)
673 show(cv::Mat const & m)
675 return _IMP_em2d.show(*args)
678 """write_matrix(cv::Mat & m, std::string name)"""
679 return _IMP_em2d.write_matrix(m, name)
681 """Proxy of C++ IMP::em2d::ImageReaderWriter class."""
683 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
685 def __init__(self, *args, **kwargs):
686 raise AttributeError(
"No constructor defined - class is abstract")
688 def read(self, filename, header, data):
689 """read(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
690 return _IMP_em2d.ImageReaderWriter_read(self, filename, header, data)
693 def read_from_floats(self, filename, header, data):
694 """read_from_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
695 return _IMP_em2d.ImageReaderWriter_read_from_floats(self, filename, header, data)
698 def read_from_ints(self, filename, header, data):
699 """read_from_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat & data)"""
700 return _IMP_em2d.ImageReaderWriter_read_from_ints(self, filename, header, data)
703 def write(self, filename, header, data):
704 """write(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
705 return _IMP_em2d.ImageReaderWriter_write(self, filename, header, data)
708 def write_to_floats(self, filename, header, data):
709 """write_to_floats(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
710 return _IMP_em2d.ImageReaderWriter_write_to_floats(self, filename, header, data)
713 def write_to_ints(self, filename, header, data):
714 """write_to_ints(ImageReaderWriter self, IMP::String const & filename, ImageHeader header, cv::Mat const & data)"""
715 return _IMP_em2d.ImageReaderWriter_write_to_ints(self, filename, header, data)
718 def get_version_info(self):
719 """get_version_info(ImageReaderWriter self) -> VersionInfo"""
720 return _IMP_em2d.ImageReaderWriter_get_version_info(self)
724 """__str__(ImageReaderWriter self) -> std::string"""
725 return _IMP_em2d.ImageReaderWriter___str__(self)
729 """__repr__(ImageReaderWriter self) -> std::string"""
730 return _IMP_em2d.ImageReaderWriter___repr__(self)
735 return _object_cast_to_ImageReaderWriter(o)
737 ImageReaderWriter_swigregister = _IMP_em2d.ImageReaderWriter_swigregister
738 ImageReaderWriter_swigregister(ImageReaderWriter)
740 class PolarResamplingParameters(object):
741 """Proxy of C++ IMP::em2d::PolarResamplingParameters class."""
743 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
745 def __init__(self, *args):
747 __init__(IMP::em2d::PolarResamplingParameters self) -> PolarResamplingParameters
748 __init__(IMP::em2d::PolarResamplingParameters self, unsigned int rows, unsigned int cols) -> PolarResamplingParameters
749 __init__(IMP::em2d::PolarResamplingParameters self, cv::Mat const & m) -> PolarResamplingParameters
751 this = _IMP_em2d.new_PolarResamplingParameters(*args)
753 self.this.append(this)
754 except __builtin__.Exception:
756 __swig_destroy__ = _IMP_em2d.delete_PolarResamplingParameters
757 __del__ =
lambda self:
None
759 def setup(self, rows, cols):
760 """setup(PolarResamplingParameters self, unsigned int rows, unsigned int cols)"""
761 return _IMP_em2d.PolarResamplingParameters_setup(self, rows, cols)
764 def get_starting_radius(self):
765 """get_starting_radius(PolarResamplingParameters self) -> double"""
766 return _IMP_em2d.PolarResamplingParameters_get_starting_radius(self)
769 def get_ending_radius(self):
770 """get_ending_radius(PolarResamplingParameters self) -> double"""
771 return _IMP_em2d.PolarResamplingParameters_get_ending_radius(self)
774 def get_radius(self, n_ring):
775 """get_radius(PolarResamplingParameters self, unsigned int n_ring) -> double"""
776 return _IMP_em2d.PolarResamplingParameters_get_radius(self, n_ring)
779 def get_number_of_rings(self):
780 """get_number_of_rings(PolarResamplingParameters self) -> unsigned int"""
781 return _IMP_em2d.PolarResamplingParameters_get_number_of_rings(self)
784 def set_estimated_number_of_angles(self, aprox_value):
785 """set_estimated_number_of_angles(PolarResamplingParameters self, unsigned int aprox_value)"""
786 return _IMP_em2d.PolarResamplingParameters_set_estimated_number_of_angles(self, aprox_value)
789 def get_number_of_angles(self):
790 """get_number_of_angles(PolarResamplingParameters self) -> unsigned int"""
791 return _IMP_em2d.PolarResamplingParameters_get_number_of_angles(self)
794 def get_angle_step(self):
795 """get_angle_step(PolarResamplingParameters self) -> double"""
796 return _IMP_em2d.PolarResamplingParameters_get_angle_step(self)
799 def get_radius_step(self):
800 """get_radius_step(PolarResamplingParameters self) -> double"""
801 return _IMP_em2d.PolarResamplingParameters_get_radius_step(self)
804 def create_maps_for_resampling(self):
805 """create_maps_for_resampling(PolarResamplingParameters self)"""
806 return _IMP_em2d.PolarResamplingParameters_create_maps_for_resampling(self)
809 def get_resampling_maps(self, m1, m2):
810 """get_resampling_maps(PolarResamplingParameters self, cv::Mat & m1, cv::Mat & m2)"""
811 return _IMP_em2d.PolarResamplingParameters_get_resampling_maps(self, m1, m2)
814 def get_resampling_map(self, m1):
815 """get_resampling_map(PolarResamplingParameters self, cv::Mat & m1)"""
816 return _IMP_em2d.PolarResamplingParameters_get_resampling_map(self, m1)
820 """show(PolarResamplingParameters self, _ostream out)"""
821 return _IMP_em2d.PolarResamplingParameters_show(self, out)
824 def get_is_setup(self):
825 """get_is_setup(PolarResamplingParameters self) -> bool"""
826 return _IMP_em2d.PolarResamplingParameters_get_is_setup(self)
830 """__str__(PolarResamplingParameters self) -> std::string"""
831 return _IMP_em2d.PolarResamplingParameters___str__(self)
835 """__repr__(PolarResamplingParameters self) -> std::string"""
836 return _IMP_em2d.PolarResamplingParameters___repr__(self)
838 PolarResamplingParameters_swigregister = _IMP_em2d.PolarResamplingParameters_swigregister
839 PolarResamplingParameters_swigregister(PolarResamplingParameters)
841 class SegmentationParameters(object):
842 """Proxy of C++ IMP::em2d::SegmentationParameters class."""
844 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
845 image_pixel_size = _swig_property(_IMP_em2d.SegmentationParameters_image_pixel_size_get, _IMP_em2d.SegmentationParameters_image_pixel_size_set)
846 diffusion_beta = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_beta_get, _IMP_em2d.SegmentationParameters_diffusion_beta_set)
847 diffusion_timesteps = _swig_property(_IMP_em2d.SegmentationParameters_diffusion_timesteps_get, _IMP_em2d.SegmentationParameters_diffusion_timesteps_set)
848 fill_holes_stddevs = _swig_property(_IMP_em2d.SegmentationParameters_fill_holes_stddevs_get, _IMP_em2d.SegmentationParameters_fill_holes_stddevs_set)
849 opening_kernel = _swig_property(_IMP_em2d.SegmentationParameters_opening_kernel_get, _IMP_em2d.SegmentationParameters_opening_kernel_set)
850 remove_sizing_percentage = _swig_property(_IMP_em2d.SegmentationParameters_remove_sizing_percentage_get, _IMP_em2d.SegmentationParameters_remove_sizing_percentage_set)
851 binary_background = _swig_property(_IMP_em2d.SegmentationParameters_binary_background_get, _IMP_em2d.SegmentationParameters_binary_background_set)
852 binary_foreground = _swig_property(_IMP_em2d.SegmentationParameters_binary_foreground_get, _IMP_em2d.SegmentationParameters_binary_foreground_set)
853 threshold = _swig_property(_IMP_em2d.SegmentationParameters_threshold_get, _IMP_em2d.SegmentationParameters_threshold_set)
855 def __init__(self, *args):
857 __init__(IMP::em2d::SegmentationParameters self) -> SegmentationParameters
858 __init__(IMP::em2d::SegmentationParameters self, double apix, double diff_beta, unsigned int diff_timesteps, double fh_stddevs, cv::Mat const & kr, int background, int foreground) -> SegmentationParameters
860 this = _IMP_em2d.new_SegmentationParameters(*args)
862 self.this.append(this)
863 except __builtin__.Exception:
866 def show(self, *args):
868 show(SegmentationParameters self, _ostream out)
869 show(SegmentationParameters self)
871 return _IMP_em2d.SegmentationParameters_show(self, *args)
875 """__str__(SegmentationParameters self) -> std::string"""
876 return _IMP_em2d.SegmentationParameters___str__(self)
880 """__repr__(SegmentationParameters self) -> std::string"""
881 return _IMP_em2d.SegmentationParameters___repr__(self)
883 __swig_destroy__ = _IMP_em2d.delete_SegmentationParameters
884 __del__ =
lambda self:
None
885 SegmentationParameters_swigregister = _IMP_em2d.SegmentationParameters_swigregister
886 SegmentationParameters_swigregister(SegmentationParameters)
888 class MatchTemplateResult(object):
889 """Proxy of C++ IMP::em2d::MatchTemplateResult class."""
891 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
892 pair = _swig_property(_IMP_em2d.MatchTemplateResult_pair_get, _IMP_em2d.MatchTemplateResult_pair_set)
893 cross_correlation = _swig_property(_IMP_em2d.MatchTemplateResult_cross_correlation_get, _IMP_em2d.MatchTemplateResult_cross_correlation_set)
895 def __init__(self, p, cc):
896 """__init__(IMP::em2d::MatchTemplateResult self, IMP::IntPair p, double cc) -> MatchTemplateResult"""
897 this = _IMP_em2d.new_MatchTemplateResult(p, cc)
899 self.this.append(this)
900 except __builtin__.Exception:
903 def show(self, *args):
905 show(MatchTemplateResult self, _ostream out)
906 show(MatchTemplateResult self)
908 return _IMP_em2d.MatchTemplateResult_show(self, *args)
912 """__str__(MatchTemplateResult self) -> std::string"""
913 return _IMP_em2d.MatchTemplateResult___str__(self)
917 """__repr__(MatchTemplateResult self) -> std::string"""
918 return _IMP_em2d.MatchTemplateResult___repr__(self)
920 __swig_destroy__ = _IMP_em2d.delete_MatchTemplateResult
921 __del__ =
lambda self:
None
922 MatchTemplateResult_swigregister = _IMP_em2d.MatchTemplateResult_swigregister
923 MatchTemplateResult_swigregister(MatchTemplateResult)
927 """apply_mask(cv::Mat const & m, cv::Mat & result, IMP::em2d::cvIntMat const & mask, double val)"""
928 return _IMP_em2d.apply_mask(m, result, mask, val)
932 apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius, double value=0.0)
933 apply_circular_mask(cv::Mat const & mat, cv::Mat & result, int radius)
935 return _IMP_em2d.apply_circular_mask(mat, result, radius, value)
938 """get_mean(cv::Mat const & mat, IMP::em2d::cvIntMat const & mask) -> double"""
939 return _IMP_em2d.get_mean(mat, mask)
942 """create_circular_mask(int rows, int cols, int radius) -> IMP::em2d::cvIntMat"""
943 return _IMP_em2d.create_circular_mask(rows, cols, radius)
945 def do_histogram_stretching(m, boxes, offset):
946 """do_histogram_stretching(cv::Mat & m, int boxes, int offset)"""
947 return _IMP_em2d.do_histogram_stretching(m, boxes, offset)
950 """do_dilate_and_shrink_warp(cv::Mat & m, cv::Mat const & grayscale, cv::Mat & kernel)"""
951 return _IMP_em2d.do_dilate_and_shrink_warp(m, grayscale, kernel)
955 do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker, int neighbors_mode=4)
956 do_morphologic_reconstruction(cv::Mat const & mask, cv::Mat & marker)
958 return _IMP_em2d.do_morphologic_reconstruction(mask, marker, neighbors_mode)
961 """do_labeling(IMP::em2d::cvIntMat const & m, IMP::em2d::cvIntMat & mat_to_label) -> int"""
962 return _IMP_em2d.do_labeling(m, mat_to_label)
965 """get_diffusion_filtering_partial_derivative(cv::Mat const & m, cv::Mat & der, double dx, double dy, double ang)"""
966 return _IMP_em2d.get_diffusion_filtering_partial_derivative(m, der, dx, dy, ang)
969 """get_domes(cv::Mat & m, cv::Mat & result, double h)"""
970 return _IMP_em2d.get_domes(m, result, h)
972 def get_transformed(input, transformed, T):
973 """get_transformed(cv::Mat const & input, cv::Mat & transformed, Transformation2D T)"""
974 return _IMP_em2d.get_transformed(input, transformed, T)
978 apply_threshold(cv::Mat & m, cv::Mat & result, double threshold=0.0)
979 apply_threshold(cv::Mat & m, cv::Mat & result)
981 return _IMP_em2d.apply_threshold(m, result, threshold)
984 """do_morphologic_contrast_enhancement(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel, unsigned int iterations)"""
985 return _IMP_em2d.do_morphologic_contrast_enhancement(m, result, kernel, iterations)
988 """get_morphologic_gradient(cv::Mat const & m, cv::Mat & result, cv::Mat const & kernel)"""
989 return _IMP_em2d.get_morphologic_gradient(m, result, kernel)
992 """get_overlap_percentage(cv::Mat & m1, cv::Mat & m2, IMP::IntPair const & center) -> double"""
993 return _IMP_em2d.get_overlap_percentage(m1, m2, center)
996 """get_best_template_matches(cv::Mat const & m, cv::Mat const & templ, unsigned int n) -> IMP::em2d::MatchTemplateResults"""
997 return _IMP_em2d.get_best_template_matches(m, templ, n)
999 """Proxy of C++ IMP::em2d::Image class."""
1001 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1003 def __init__(self, *args):
1005 __init__(IMP::em2d::Image self) -> Image
1006 __init__(IMP::em2d::Image self, int rows, int cols) -> Image
1007 __init__(IMP::em2d::Image self, IMP::String filename, ImageReaderWriter reader) -> Image
1009 this = _IMP_em2d.new_Image(*args)
1011 self.this.append(this)
1012 except __builtin__.Exception:
1016 """get_data(Image self) -> cv::Mat &"""
1017 return _IMP_em2d.Image_get_data(self)
1020 def set_data(self, mat):
1021 """set_data(Image self, cv::Mat const & mat)"""
1022 return _IMP_em2d.Image_set_data(self, mat)
1025 def set_zeros(self):
1026 """set_zeros(Image self)"""
1027 return _IMP_em2d.Image_set_zeros(self)
1030 def set_value(self, *args):
1032 set_value(Image self, double val)
1033 set_value(Image self, int i, int j, double val)
1035 return _IMP_em2d.Image_set_value(self, *args)
1038 def __call__(self, i, j):
1039 """__call__(Image self, int i, int j) -> double"""
1040 return _IMP_em2d.Image___call__(self, i, j)
1043 def get_header(self):
1044 """get_header(Image self) -> ImageHeader"""
1045 return _IMP_em2d.Image_get_header(self)
1048 def set_size(self, *args):
1050 set_size(Image self, int rows, int cols)
1051 set_size(Image self, Image img)
1053 return _IMP_em2d.Image_set_size(self, *args)
1056 def update_header(self):
1057 """update_header(Image self)"""
1058 return _IMP_em2d.Image_update_header(self)
1061 def read(self, filename, reader):
1062 """read(Image self, IMP::String filename, ImageReaderWriter reader)"""
1063 return _IMP_em2d.Image_read(self, filename, reader)
1066 def write(self, filename, writer):
1067 """write(Image self, IMP::String const & filename, ImageReaderWriter writer)"""
1068 return _IMP_em2d.Image_write(self, filename, writer)
1071 def show(self, out):
1072 """show(Image self, _ostream out)"""
1073 return _IMP_em2d.Image_show(self, out)
1076 def get_version_info(self):
1077 """get_version_info(Image self) -> VersionInfo"""
1078 return _IMP_em2d.Image_get_version_info(self)
1081 def set_name(self, name):
1082 """set_name(Image self, IMP::String const & name)"""
1083 return _IMP_em2d.Image_set_name(self, name)
1087 """get_name(Image self) -> IMP::String"""
1088 return _IMP_em2d.Image_get_name(self)
1091 def get_min_and_max_values(self):
1092 """get_min_and_max_values(Image self) -> IMP::FloatRange"""
1093 return _IMP_em2d.Image_get_min_and_max_values(self)
1097 """__str__(Image self) -> std::string"""
1098 return _IMP_em2d.Image___str__(self)
1102 """__repr__(Image self) -> std::string"""
1103 return _IMP_em2d.Image___repr__(self)
1108 return _object_cast_to_Image(o)
1110 Image_swigregister = _IMP_em2d.Image_swigregister
1111 Image_swigregister(Image)
1115 """read_images(IMP::Strings const & names, ImageReaderWriter rw) -> IMP::em2d::Images"""
1116 return _IMP_em2d.read_images(names, rw)
1119 """save_images(IMP::em2d::Images images, IMP::Strings const & names, ImageReaderWriter rw)"""
1120 return _IMP_em2d.save_images(images, names, rw)
1124 do_normalize(cv::Mat & m)
1125 do_normalize(Image im, bool force=False)
1126 do_normalize(Image im)
1128 return _IMP_em2d.do_normalize(*args)
1132 get_histogram(cv::Mat const & m, int bins) -> IMP::Floats
1133 get_histogram(Image img, int bins) -> IMP::Floats
1135 return _IMP_em2d.get_histogram(*args)
1139 apply_variance_filter(cv::Mat const & input, cv::Mat & filtered, int kernelsize)
1140 apply_variance_filter(Image input, Image filtered, int kernelsize)
1142 return _IMP_em2d.apply_variance_filter(*args)
1146 apply_diffusion_filter(cv::Mat const & m, cv::Mat & result, double beta, double pixelsize, unsigned int time_steps)
1147 apply_diffusion_filter(Image input, Image filtered, double beta, double pixelsize, int time_steps)
1149 return _IMP_em2d.apply_diffusion_filter(*args)
1151 def do_fill_holes(*args):
1153 do_fill_holes(cv::Mat const & m, cv::Mat & result, double h)
1154 do_fill_holes(Image input, Image result, double n_stddevs)
1156 return _IMP_em2d.do_fill_holes(*args)
1158 def do_combined_fill_holes_and_threshold(*args):
1160 do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs, double threshold=0.0)
1161 do_combined_fill_holes_and_threshold(cv::Mat & m, cv::Mat & result, double n_stddevs)
1162 do_combined_fill_holes_and_threshold(Image input, Image result, double n_stddevs)
1164 return _IMP_em2d.do_combined_fill_holes_and_threshold(*args)
1166 def do_extend_borders(*args):
1168 do_extend_borders(cv::Mat & orig, cv::Mat & dst, unsigned int pix)
1169 do_extend_borders(Image im1, Image im2, unsigned int pix)
1171 return _IMP_em2d.do_extend_borders(*args)
1173 def do_segmentation(*args):
1175 do_segmentation(cv::Mat const & m, cv::Mat & result, SegmentationParameters params)
1176 do_segmentation(Image input, Image result, SegmentationParameters params)
1178 return _IMP_em2d.do_segmentation(*args)
1180 def do_remove_small_objects(*args):
1182 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0, int foreground=1)
1183 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage, int background=0)
1184 do_remove_small_objects(IMP::em2d::cvIntMat & m, double percentage)
1185 do_remove_small_objects(Image input, double percentage, int background=0, int foreground=1)
1186 do_remove_small_objects(Image input, double percentage, int background=0)
1187 do_remove_small_objects(Image input, double percentage)
1189 return _IMP_em2d.do_remove_small_objects(*args)
1192 """do_subtract_images(Image first, Image second, Image result)"""
1193 return _IMP_em2d.do_subtract_images(first, second, result)
1195 def add_noise(*args):
1197 add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode, double df=3)
1198 add_noise(cv::Mat & v, double op1, double op2, IMP::String const & mode)
1199 add_noise(cv::Mat & v, double op1, double op2)
1200 add_noise(Image im1, double op1, double op2, IMP::String const & mode, double df=3)
1201 add_noise(Image im1, double op1, double op2, IMP::String const & mode)
1202 add_noise(Image im1, double op1, double op2)
1204 return _IMP_em2d.add_noise(*args)
1208 do_resample_polar(cv::Mat const & input, cv::Mat & resampled, PolarResamplingParameters polar_params)
1209 do_resample_polar(Image im1, Image im2, PolarResamplingParameters polar_params)
1211 return _IMP_em2d.do_resample_polar(*args)
1215 crop(cv::Mat const & m, IMP::IntPair const & center, int size) -> cv::Mat
1216 crop(Image img, IMP::IntPair const & center, int size)
1218 return _IMP_em2d.crop(*args)
1221 """apply_mean_outside_mask(Image img, double radius)"""
1222 return _IMP_em2d.apply_mean_outside_mask(img, radius)
1223 class RegistrationResult(object):
1224 """Proxy of C++ IMP::em2d::RegistrationResult class."""
1226 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1228 def __init__(self, *args):
1230 __init__(IMP::em2d::RegistrationResult self) -> RegistrationResult
1231 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1232 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1233 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift, int projection_index=0) -> RegistrationResult
1234 __init__(IMP::em2d::RegistrationResult self, double phi, double theta, double psi, Vector2D shift) -> RegistrationResult
1235 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0, IMP::String name) -> RegistrationResult
1236 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0, int image_index=0) -> RegistrationResult
1237 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift, int projection_index=0) -> RegistrationResult
1238 __init__(IMP::em2d::RegistrationResult self, Rotation3D R, Vector2D shift) -> RegistrationResult
1239 __init__(IMP::em2d::RegistrationResult self, Rotation3D R) -> RegistrationResult
1241 this = _IMP_em2d.new_RegistrationResult(*args)
1243 self.this.append(this)
1244 except __builtin__.Exception:
1248 """get_phi(RegistrationResult self) -> double"""
1249 return _IMP_em2d.RegistrationResult_get_phi(self)
1252 def get_theta(self):
1253 """get_theta(RegistrationResult self) -> double"""
1254 return _IMP_em2d.RegistrationResult_get_theta(self)
1258 """get_psi(RegistrationResult self) -> double"""
1259 return _IMP_em2d.RegistrationResult_get_psi(self)
1262 def get_shift(self):
1263 """get_shift(RegistrationResult self) -> Vector2D"""
1264 return _IMP_em2d.RegistrationResult_get_shift(self)
1267 def get_shift_3d(self):
1268 """get_shift_3d(RegistrationResult self) -> Vector3D"""
1269 return _IMP_em2d.RegistrationResult_get_shift_3d(self)
1272 def get_projection_index(self):
1273 """get_projection_index(RegistrationResult self) -> int"""
1274 return _IMP_em2d.RegistrationResult_get_projection_index(self)
1277 def set_projection_index(self, index):
1278 """set_projection_index(RegistrationResult self, int index)"""
1279 return _IMP_em2d.RegistrationResult_set_projection_index(self, index)
1282 def get_image_index(self):
1283 """get_image_index(RegistrationResult self) -> int"""
1284 return _IMP_em2d.RegistrationResult_get_image_index(self)
1287 def set_image_index(self, index):
1288 """set_image_index(RegistrationResult self, int index)"""
1289 return _IMP_em2d.RegistrationResult_set_image_index(self, index)
1293 """get_name(RegistrationResult self) -> IMP::String"""
1294 return _IMP_em2d.RegistrationResult_get_name(self)
1298 """get_ccc(RegistrationResult self) -> double"""
1299 return _IMP_em2d.RegistrationResult_get_ccc(self)
1302 def set_ccc(self, ccc):
1303 """set_ccc(RegistrationResult self, double ccc)"""
1304 return _IMP_em2d.RegistrationResult_set_ccc(self, ccc)
1307 def get_score(self):
1308 """get_score(RegistrationResult self) -> double"""
1309 return _IMP_em2d.RegistrationResult_get_score(self)
1312 def set_score(self, Score):
1313 """set_score(RegistrationResult self, double Score)"""
1314 return _IMP_em2d.RegistrationResult_set_score(self, Score)
1317 def set_rotation(self, *args):
1319 set_rotation(RegistrationResult self, double phi, double theta, double psi)
1320 set_rotation(RegistrationResult self, Rotation3D R)
1322 return _IMP_em2d.RegistrationResult_set_rotation(self, *args)
1325 def set_shift(self, shift):
1326 """set_shift(RegistrationResult self, Vector2D shift)"""
1327 return _IMP_em2d.RegistrationResult_set_shift(self, shift)
1330 def set_name(self, name):
1331 """set_name(RegistrationResult self, IMP::String name)"""
1332 return _IMP_em2d.RegistrationResult_set_name(self, name)
1335 def add_in_plane_transformation(self, t):
1336 """add_in_plane_transformation(RegistrationResult self, Transformation2D t)"""
1337 return _IMP_em2d.RegistrationResult_add_in_plane_transformation(self, t)
1340 def show(self, *args):
1342 show(RegistrationResult self, _ostream out)
1343 show(RegistrationResult self)
1345 return _IMP_em2d.RegistrationResult_show(self, *args)
1348 def write(self, *args):
1350 write(RegistrationResult self, _ostream out)
1351 write(RegistrationResult self)
1353 return _IMP_em2d.RegistrationResult_write(self, *args)
1356 def write_comment_line(self, *args):
1358 write_comment_line(RegistrationResult self, _ostream out)
1359 write_comment_line(RegistrationResult self)
1361 return _IMP_em2d.RegistrationResult_write_comment_line(self, *args)
1365 """read(RegistrationResult self, IMP::String const & s)"""
1366 return _IMP_em2d.RegistrationResult_read(self, s)
1369 def set_random_registration(self, index, maximum_shift):
1370 """set_random_registration(RegistrationResult self, unsigned int index, double maximum_shift)"""
1371 return _IMP_em2d.RegistrationResult_set_random_registration(self, index, maximum_shift)
1374 def get_rotation(self):
1375 """get_rotation(RegistrationResult self) -> Rotation3D"""
1376 return _IMP_em2d.RegistrationResult_get_rotation(self)
1379 def set_in_image(self, header):
1380 """set_in_image(RegistrationResult self, ImageHeader header)"""
1381 return _IMP_em2d.RegistrationResult_set_in_image(self, header)
1384 def read_from_image(self, header):
1385 """read_from_image(RegistrationResult self, ImageHeader header)"""
1386 return _IMP_em2d.RegistrationResult_read_from_image(self, header)
1389 def get_is_optimized_result(self):
1390 """get_is_optimized_result(RegistrationResult self) -> bool"""
1391 return _IMP_em2d.RegistrationResult_get_is_optimized_result(self)
1393 __swig_destroy__ = _IMP_em2d.delete_RegistrationResult
1394 __del__ =
lambda self:
None
1397 """__str__(RegistrationResult self) -> std::string"""
1398 return _IMP_em2d.RegistrationResult___str__(self)
1402 """__repr__(RegistrationResult self) -> std::string"""
1403 return _IMP_em2d.RegistrationResult___repr__(self)
1405 RegistrationResult_swigregister = _IMP_em2d.RegistrationResult_swigregister
1406 RegistrationResult_swigregister(RegistrationResult)
1410 """read_registration_results(IMP::String const & filename) -> IMP::em2d::RegistrationResults"""
1411 return _IMP_em2d.read_registration_results(filename)
1414 """write_registration_results(IMP::String filename, IMP::em2d::RegistrationResults const & results)"""
1415 return _IMP_em2d.write_registration_results(filename, results)
1419 get_random_registration_results(unsigned int n, double maximum_shift=5.0) -> IMP::em2d::RegistrationResults
1420 get_random_registration_results(unsigned int n) -> IMP::em2d::RegistrationResults
1422 return _IMP_em2d.get_random_registration_results(n, maximum_shift)
1425 """get_evenly_distributed_registration_results(unsigned int n_projections) -> IMP::em2d::RegistrationResults"""
1426 return _IMP_em2d.get_evenly_distributed_registration_results(n_projections)
1427 class SpiderImageReaderWriter(ImageReaderWriter):
1428 """Proxy of C++ IMP::em2d::SpiderImageReaderWriter class."""
1430 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1431 filename_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_filename__get, _IMP_em2d.SpiderImageReaderWriter_filename__set)
1432 skip_type_check_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_type_check__get, _IMP_em2d.SpiderImageReaderWriter_skip_type_check__set)
1433 force_reversed_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_force_reversed__get, _IMP_em2d.SpiderImageReaderWriter_force_reversed__set)
1434 skip_extra_checkings_ = _swig_property(_IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__get, _IMP_em2d.SpiderImageReaderWriter_skip_extra_checkings__set)
1436 def __init__(self, *args):
1438 __init__(IMP::em2d::SpiderImageReaderWriter self) -> SpiderImageReaderWriter
1439 __init__(IMP::em2d::SpiderImageReaderWriter self, IMP::String const & filename, bool skip_type_check, bool force_reversed, bool skip_extra_checkings) -> SpiderImageReaderWriter
1441 this = _IMP_em2d.new_SpiderImageReaderWriter(*args)
1443 self.this.append(this)
1444 except __builtin__.Exception:
1448 """__str__(SpiderImageReaderWriter self) -> std::string"""
1449 return _IMP_em2d.SpiderImageReaderWriter___str__(self)
1453 """__repr__(SpiderImageReaderWriter self) -> std::string"""
1454 return _IMP_em2d.SpiderImageReaderWriter___repr__(self)
1459 return _object_cast_to_SpiderImageReaderWriter(o)
1461 SpiderImageReaderWriter_swigregister = _IMP_em2d.SpiderImageReaderWriter_swigregister
1462 SpiderImageReaderWriter_swigregister(SpiderImageReaderWriter)
1464 class JPGImageReaderWriter(ImageReaderWriter):
1465 """Proxy of C++ IMP::em2d::JPGImageReaderWriter class."""
1467 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1470 """__init__(IMP::em2d::JPGImageReaderWriter self) -> JPGImageReaderWriter"""
1471 this = _IMP_em2d.new_JPGImageReaderWriter()
1473 self.this.append(this)
1474 except __builtin__.Exception:
1478 """__str__(JPGImageReaderWriter self) -> std::string"""
1479 return _IMP_em2d.JPGImageReaderWriter___str__(self)
1483 """__repr__(JPGImageReaderWriter self) -> std::string"""
1484 return _IMP_em2d.JPGImageReaderWriter___repr__(self)
1489 return _object_cast_to_JPGImageReaderWriter(o)
1491 JPGImageReaderWriter_swigregister = _IMP_em2d.JPGImageReaderWriter_swigregister
1492 JPGImageReaderWriter_swigregister(JPGImageReaderWriter)
1494 class TIFFImageReaderWriter(ImageReaderWriter):
1495 """Proxy of C++ IMP::em2d::TIFFImageReaderWriter class."""
1497 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1500 """__init__(IMP::em2d::TIFFImageReaderWriter self) -> TIFFImageReaderWriter"""
1501 this = _IMP_em2d.new_TIFFImageReaderWriter()
1503 self.this.append(this)
1504 except __builtin__.Exception:
1508 """__str__(TIFFImageReaderWriter self) -> std::string"""
1509 return _IMP_em2d.TIFFImageReaderWriter___str__(self)
1513 """__repr__(TIFFImageReaderWriter self) -> std::string"""
1514 return _IMP_em2d.TIFFImageReaderWriter___repr__(self)
1519 return _object_cast_to_TIFFImageReaderWriter(o)
1521 TIFFImageReaderWriter_swigregister = _IMP_em2d.TIFFImageReaderWriter_swigregister
1522 TIFFImageReaderWriter_swigregister(TIFFImageReaderWriter)
1526 """do_matrix_to_image_flip(cv::Mat & m)"""
1527 return _IMP_em2d.do_matrix_to_image_flip(m)
1530 """get_autocorrelation2d_no_preprocessing(cv::Mat const & M, cv::Mat & corr)"""
1531 return _IMP_em2d.get_autocorrelation2d_no_preprocessing(M, corr)
1535 get_autocorrelation2d(Image im1, Image im2)
1536 get_autocorrelation2d(cv::Mat const & m, cv::Mat & corr)
1538 return _IMP_em2d.get_autocorrelation2d(*args)
1542 get_correlation2d(Image im1, Image im2, Image corr)
1543 get_correlation2d(cv::Mat const & A, cv::Mat const & B, cv::Mat & corr)
1545 return _IMP_em2d.get_correlation2d(*args)
1548 """get_correlation2d_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2, cv::Mat & corr)"""
1549 return _IMP_em2d.get_correlation2d_no_preprocessing(M1, M2, corr)
1552 """get_fft_using_optimal_size(cv::Mat const & m, cv::Mat & M)"""
1553 return _IMP_em2d.get_fft_using_optimal_size(m, M)
1556 """get_spectrum(cv::Mat const & m, cv::Mat & real, cv::Mat & imag)"""
1557 return _IMP_em2d.get_spectrum(m, real, imag)
1560 """get_rotation_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1561 return _IMP_em2d.get_rotation_error(rr1, rr2)
1564 """get_shift_error(RegistrationResult rr1, RegistrationResult rr2) -> double"""
1565 return _IMP_em2d.get_shift_error(rr1, rr2)
1567 def get_average_rotation_error(correct_RRs, computed_RRs):
1568 """get_average_rotation_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1569 return _IMP_em2d.get_average_rotation_error(correct_RRs, computed_RRs)
1571 def get_average_shift_error(correct_RRs, computed_RRs):
1572 """get_average_shift_error(IMP::em2d::RegistrationResults const & correct_RRs, IMP::em2d::RegistrationResults const & computed_RRs) -> double"""
1573 return _IMP_em2d.get_average_shift_error(correct_RRs, computed_RRs)
1577 get_cross_correlation_coefficient(Image im1, Image im2) -> double
1578 get_cross_correlation_coefficient(cv::Mat const & m1, cv::Mat const & m2) -> double
1580 return _IMP_em2d.get_cross_correlation_coefficient(*args)
1583 """get_global_score(IMP::em2d::RegistrationResults const & RRs) -> double"""
1584 return _IMP_em2d.get_global_score(RRs)
1586 """Proxy of C++ IMP::em2d::ScoreFunction class."""
1588 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1590 def __init__(self, *args, **kwargs):
1591 raise AttributeError(
"No constructor defined - class is abstract")
1593 def get_score(self, image, projection):
1594 """get_score(ScoreFunction self, Image image, Image projection) -> double"""
1595 return _IMP_em2d.ScoreFunction_get_score(self, image, projection)
1598 def set_variance_image(self, var):
1599 """set_variance_image(ScoreFunction self, Image var)"""
1600 return _IMP_em2d.ScoreFunction_set_variance_image(self, var)
1603 def get_version_info(self):
1604 """get_version_info(ScoreFunction self) -> VersionInfo"""
1605 return _IMP_em2d.ScoreFunction_get_version_info(self)
1609 """__str__(ScoreFunction self) -> std::string"""
1610 return _IMP_em2d.ScoreFunction___str__(self)
1614 """__repr__(ScoreFunction self) -> std::string"""
1615 return _IMP_em2d.ScoreFunction___repr__(self)
1620 return _object_cast_to_ScoreFunction(o)
1622 ScoreFunction_swigregister = _IMP_em2d.ScoreFunction_swigregister
1623 ScoreFunction_swigregister(ScoreFunction)
1625 class ChiSquaredScore(ScoreFunction):
1626 """Proxy of C++ IMP::em2d::ChiSquaredScore class."""
1628 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1631 """__init__(IMP::em2d::ChiSquaredScore self) -> ChiSquaredScore"""
1632 this = _IMP_em2d.new_ChiSquaredScore()
1634 self.this.append(this)
1635 except __builtin__.Exception:
1639 """__str__(ChiSquaredScore self) -> std::string"""
1640 return _IMP_em2d.ChiSquaredScore___str__(self)
1644 """__repr__(ChiSquaredScore self) -> std::string"""
1645 return _IMP_em2d.ChiSquaredScore___repr__(self)
1650 return _object_cast_to_ChiSquaredScore(o)
1652 __swig_destroy__ = _IMP_em2d.delete_ChiSquaredScore
1653 __del__ =
lambda self:
None
1654 ChiSquaredScore_swigregister = _IMP_em2d.ChiSquaredScore_swigregister
1655 ChiSquaredScore_swigregister(ChiSquaredScore)
1657 class EM2DScore(ScoreFunction):
1658 """Proxy of C++ IMP::em2d::EM2DScore class."""
1660 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1663 """__init__(IMP::em2d::EM2DScore self) -> EM2DScore"""
1664 this = _IMP_em2d.new_EM2DScore()
1666 self.this.append(this)
1667 except __builtin__.Exception:
1671 """__str__(EM2DScore self) -> std::string"""
1672 return _IMP_em2d.EM2DScore___str__(self)
1676 """__repr__(EM2DScore self) -> std::string"""
1677 return _IMP_em2d.EM2DScore___repr__(self)
1682 return _object_cast_to_EM2DScore(o)
1684 __swig_destroy__ = _IMP_em2d.delete_EM2DScore
1685 __del__ =
lambda self:
None
1686 EM2DScore_swigregister = _IMP_em2d.EM2DScore_swigregister
1687 EM2DScore_swigregister(EM2DScore)
1689 class MeanAbsoluteDifference(ScoreFunction):
1690 """Proxy of C++ IMP::em2d::MeanAbsoluteDifference class."""
1692 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1695 """__init__(IMP::em2d::MeanAbsoluteDifference self) -> MeanAbsoluteDifference"""
1696 this = _IMP_em2d.new_MeanAbsoluteDifference()
1698 self.this.append(this)
1699 except __builtin__.Exception:
1703 """__str__(MeanAbsoluteDifference self) -> std::string"""
1704 return _IMP_em2d.MeanAbsoluteDifference___str__(self)
1708 """__repr__(MeanAbsoluteDifference self) -> std::string"""
1709 return _IMP_em2d.MeanAbsoluteDifference___repr__(self)
1714 return _object_cast_to_MeanAbsoluteDifference(o)
1716 __swig_destroy__ = _IMP_em2d.delete_MeanAbsoluteDifference
1717 __del__ =
lambda self:
None
1718 MeanAbsoluteDifference_swigregister = _IMP_em2d.MeanAbsoluteDifference_swigregister
1719 MeanAbsoluteDifference_swigregister(MeanAbsoluteDifference)
1723 """read_selection_file(IMP::String fn) -> IMP::Strings"""
1724 return _IMP_em2d.read_selection_file(fn)
1727 """create_filenames(unsigned long number, IMP::String basic_name, IMP::String extension) -> IMP::Strings"""
1728 return _IMP_em2d.create_filenames(number, basic_name, extension)
1730 """Proxy of C++ IMP::em2d::ProjectionParameters class."""
1732 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1734 def __init__(self, *args):
1736 __init__(IMP::em2d::ProjectionParameters self) -> ProjectionParameters
1737 __init__(IMP::em2d::ProjectionParameters self, Model m, ParticleIndex id) -> ProjectionParameters
1738 __init__(IMP::em2d::ProjectionParameters self, _ParticleAdaptor d) -> ProjectionParameters
1740 this = _IMP_em2d.new_ProjectionParameters(*args)
1742 self.this.append(this)
1743 except __builtin__.Exception:
1746 def show(self, *args):
1748 show(ProjectionParameters self, _ostream out)
1749 show(ProjectionParameters self)
1751 return _IMP_em2d.ProjectionParameters_show(self, *args)
1754 def setup_particle(*args):
1756 setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
1757 setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
1759 return _IMP_em2d.ProjectionParameters_setup_particle(*args)
1761 setup_particle = staticmethod(setup_particle)
1762 __swig_destroy__ = _IMP_em2d.delete_ProjectionParameters
1763 __del__ =
lambda self:
None
1766 """get_keys() -> IMP::FloatKeys const &"""
1767 return _IMP_em2d.ProjectionParameters_get_keys()
1769 get_keys = staticmethod(get_keys)
1771 def set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values):
1772 """set_proper_ranges_for_keys(ProjectionParameters self, Model m, Vector3D min_translation_values, Vector3D max_translation_values)"""
1773 return _IMP_em2d.ProjectionParameters_set_proper_ranges_for_keys(self, m, min_translation_values, max_translation_values)
1776 def get_is_setup(*args):
1778 get_is_setup(_ParticleAdaptor p) -> bool
1779 get_is_setup(Model m, ParticleIndex pi) -> bool
1781 return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
1783 get_is_setup = staticmethod(get_is_setup)
1785 def get_parameters_optimized(self):
1786 """get_parameters_optimized(ProjectionParameters self) -> bool"""
1787 return _IMP_em2d.ProjectionParameters_get_parameters_optimized(self)
1790 def get_translation(self):
1791 """get_translation(ProjectionParameters self) -> Vector3D"""
1792 return _IMP_em2d.ProjectionParameters_get_translation(self)
1795 def set_translation(self, v):
1796 """set_translation(ProjectionParameters self, Vector3D v)"""
1797 return _IMP_em2d.ProjectionParameters_set_translation(self, v)
1800 def get_rotation(self):
1801 """get_rotation(ProjectionParameters self) -> Rotation3D"""
1802 return _IMP_em2d.ProjectionParameters_get_rotation(self)
1805 def set_rotation(self, R):
1806 """set_rotation(ProjectionParameters self, Rotation3D R)"""
1807 return _IMP_em2d.ProjectionParameters_set_rotation(self, R)
1810 def set_parameters_optimized(self, tf):
1811 """set_parameters_optimized(ProjectionParameters self, bool tf)"""
1812 return _IMP_em2d.ProjectionParameters_set_parameters_optimized(self, tf)
1815 def get_quaternion_1(self):
1816 """get_quaternion_1(ProjectionParameters self) -> double"""
1817 return _IMP_em2d.ProjectionParameters_get_quaternion_1(self)
1820 def set_quaternion_1(self, t):
1821 """set_quaternion_1(ProjectionParameters self, double t)"""
1822 return _IMP_em2d.ProjectionParameters_set_quaternion_1(self, t)
1825 def get_quaternion_2(self):
1826 """get_quaternion_2(ProjectionParameters self) -> double"""
1827 return _IMP_em2d.ProjectionParameters_get_quaternion_2(self)
1830 def set_quaternion_2(self, t):
1831 """set_quaternion_2(ProjectionParameters self, double t)"""
1832 return _IMP_em2d.ProjectionParameters_set_quaternion_2(self, t)
1835 def get_quaternion_3(self):
1836 """get_quaternion_3(ProjectionParameters self) -> double"""
1837 return _IMP_em2d.ProjectionParameters_get_quaternion_3(self)
1840 def set_quaternion_3(self, t):
1841 """set_quaternion_3(ProjectionParameters self, double t)"""
1842 return _IMP_em2d.ProjectionParameters_set_quaternion_3(self, t)
1845 def get_quaternion_4(self):
1846 """get_quaternion_4(ProjectionParameters self) -> double"""
1847 return _IMP_em2d.ProjectionParameters_get_quaternion_4(self)
1850 def set_quaternion_4(self, t):
1851 """set_quaternion_4(ProjectionParameters self, double t)"""
1852 return _IMP_em2d.ProjectionParameters_set_quaternion_4(self, t)
1855 def get_translation_x(self):
1856 """get_translation_x(ProjectionParameters self) -> double"""
1857 return _IMP_em2d.ProjectionParameters_get_translation_x(self)
1860 def set_translation_x(self, t):
1861 """set_translation_x(ProjectionParameters self, double t)"""
1862 return _IMP_em2d.ProjectionParameters_set_translation_x(self, t)
1865 def get_translation_y(self):
1866 """get_translation_y(ProjectionParameters self) -> double"""
1867 return _IMP_em2d.ProjectionParameters_get_translation_y(self)
1870 def set_translation_y(self, t):
1871 """set_translation_y(ProjectionParameters self, double t)"""
1872 return _IMP_em2d.ProjectionParameters_set_translation_y(self, t)
1875 def add_attribute(self, *args):
1877 add_attribute(ProjectionParameters self, FloatKey k, IMP::Float v, bool opt)
1878 add_attribute(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1879 add_attribute(ProjectionParameters self, IntKey a0, IMP::Int a1)
1880 add_attribute(ProjectionParameters self, StringKey a0, IMP::String a1)
1881 add_attribute(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1882 add_attribute(ProjectionParameters self, ObjectKey a0, Object a1)
1884 return _IMP_em2d.ProjectionParameters_add_attribute(self, *args)
1887 def get_value(self, *args):
1889 get_value(ProjectionParameters self, FloatKey a0) -> IMP::Float
1890 get_value(ProjectionParameters self, IntKey a0) -> IMP::Int
1891 get_value(ProjectionParameters self, StringKey a0) -> IMP::String
1892 get_value(ProjectionParameters self, ParticleIndexKey a0) -> Particle
1893 get_value(ProjectionParameters self, ObjectKey a0) -> Object
1895 return _IMP_em2d.ProjectionParameters_get_value(self, *args)
1898 def set_value(self, *args):
1900 set_value(ProjectionParameters self, FloatKey a0, IMP::Float a1)
1901 set_value(ProjectionParameters self, IntKey a0, IMP::Int a1)
1902 set_value(ProjectionParameters self, StringKey a0, IMP::String a1)
1903 set_value(ProjectionParameters self, ParticleIndexKey a0, Particle a1)
1904 set_value(ProjectionParameters self, ObjectKey a0, Object a1)
1906 return _IMP_em2d.ProjectionParameters_set_value(self, *args)
1909 def remove_attribute(self, *args):
1911 remove_attribute(ProjectionParameters self, FloatKey a0)
1912 remove_attribute(ProjectionParameters self, IntKey a0)
1913 remove_attribute(ProjectionParameters self, StringKey a0)
1914 remove_attribute(ProjectionParameters self, ParticleIndexKey a0)
1915 remove_attribute(ProjectionParameters self, ObjectKey a0)
1917 return _IMP_em2d.ProjectionParameters_remove_attribute(self, *args)
1920 def has_attribute(self, *args):
1922 has_attribute(ProjectionParameters self, FloatKey a0) -> bool
1923 has_attribute(ProjectionParameters self, IntKey a0) -> bool
1924 has_attribute(ProjectionParameters self, StringKey a0) -> bool
1925 has_attribute(ProjectionParameters self, ParticleIndexKey a0) -> bool
1926 has_attribute(ProjectionParameters self, ObjectKey a0) -> bool
1928 return _IMP_em2d.ProjectionParameters_has_attribute(self, *args)
1931 def get_derivative(self, a0):
1932 """get_derivative(ProjectionParameters self, FloatKey a0) -> double"""
1933 return _IMP_em2d.ProjectionParameters_get_derivative(self, a0)
1937 """get_name(ProjectionParameters self) -> std::string"""
1938 return _IMP_em2d.ProjectionParameters_get_name(self)
1941 def clear_caches(self):
1942 """clear_caches(ProjectionParameters self)"""
1943 return _IMP_em2d.ProjectionParameters_clear_caches(self)
1946 def set_name(self, a0):
1947 """set_name(ProjectionParameters self, std::string a0)"""
1948 return _IMP_em2d.ProjectionParameters_set_name(self, a0)
1952 """set_check_level(ProjectionParameters self, IMP::CheckLevel a0)"""
1953 return _IMP_em2d.ProjectionParameters_set_check_level(self, a0)
1956 def add_to_derivative(self, a0, a1, a2):
1957 """add_to_derivative(ProjectionParameters self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1958 return _IMP_em2d.ProjectionParameters_add_to_derivative(self, a0, a1, a2)
1961 def set_is_optimized(self, a0, a1):
1962 """set_is_optimized(ProjectionParameters self, FloatKey a0, bool a1)"""
1963 return _IMP_em2d.ProjectionParameters_set_is_optimized(self, a0, a1)
1966 def get_is_optimized(self, a0):
1967 """get_is_optimized(ProjectionParameters self, FloatKey a0) -> bool"""
1968 return _IMP_em2d.ProjectionParameters_get_is_optimized(self, a0)
1972 """get_check_level(ProjectionParameters self) -> IMP::CheckLevel"""
1973 return _IMP_em2d.ProjectionParameters_get_check_level(self)
1976 def __eq__(self, *args):
1978 __eq__(ProjectionParameters self, ProjectionParameters o) -> bool
1979 __eq__(ProjectionParameters self, Particle d) -> bool
1981 return _IMP_em2d.ProjectionParameters___eq__(self, *args)
1984 def __ne__(self, *args):
1986 __ne__(ProjectionParameters self, ProjectionParameters o) -> bool
1987 __ne__(ProjectionParameters self, Particle d) -> bool
1989 return _IMP_em2d.ProjectionParameters___ne__(self, *args)
1992 def __le__(self, *args):
1994 __le__(ProjectionParameters self, ProjectionParameters o) -> bool
1995 __le__(ProjectionParameters self, Particle d) -> bool
1997 return _IMP_em2d.ProjectionParameters___le__(self, *args)
2000 def __lt__(self, *args):
2002 __lt__(ProjectionParameters self, ProjectionParameters o) -> bool
2003 __lt__(ProjectionParameters self, Particle d) -> bool
2005 return _IMP_em2d.ProjectionParameters___lt__(self, *args)
2008 def __ge__(self, *args):
2010 __ge__(ProjectionParameters self, ProjectionParameters o) -> bool
2011 __ge__(ProjectionParameters self, Particle d) -> bool
2013 return _IMP_em2d.ProjectionParameters___ge__(self, *args)
2016 def __gt__(self, *args):
2018 __gt__(ProjectionParameters self, ProjectionParameters o) -> bool
2019 __gt__(ProjectionParameters self, Particle d) -> bool
2021 return _IMP_em2d.ProjectionParameters___gt__(self, *args)
2025 """__hash__(ProjectionParameters self) -> std::size_t"""
2026 return _IMP_em2d.ProjectionParameters___hash__(self)
2030 """__str__(ProjectionParameters self) -> std::string"""
2031 return _IMP_em2d.ProjectionParameters___str__(self)
2035 """__repr__(ProjectionParameters self) -> std::string"""
2036 return _IMP_em2d.ProjectionParameters___repr__(self)
2038 ProjectionParameters_swigregister = _IMP_em2d.ProjectionParameters_swigregister
2039 ProjectionParameters_swigregister(ProjectionParameters)
2041 def ProjectionParameters_setup_particle(*args):
2043 setup_particle(Model m, ParticleIndex pi) -> ProjectionParameters
2044 ProjectionParameters_setup_particle(_ParticleAdaptor decorator) -> ProjectionParameters
2046 return _IMP_em2d.ProjectionParameters_setup_particle(*args)
2048 def ProjectionParameters_get_keys():
2049 """ProjectionParameters_get_keys() -> IMP::FloatKeys const &"""
2050 return _IMP_em2d.ProjectionParameters_get_keys()
2052 def ProjectionParameters_get_is_setup(*args):
2054 get_is_setup(_ParticleAdaptor p) -> bool
2055 ProjectionParameters_get_is_setup(Model m, ParticleIndex pi) -> bool
2057 return _IMP_em2d.ProjectionParameters_get_is_setup(*args)
2060 def __lshift__(out, n):
2061 """__lshift__(_ostream out, ProjectionParameters n) -> _ostream"""
2062 return _IMP_em2d.__lshift__(out, n)
2064 """Proxy of C++ IMP::em2d::ProjectionParametersScoreState class."""
2066 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2068 def __init__(self, p):
2069 """__init__(IMP::em2d::ProjectionParametersScoreState self, Particle p) -> ProjectionParametersScoreState"""
2070 this = _IMP_em2d.new_ProjectionParametersScoreState(p)
2072 self.this.append(this)
2073 except __builtin__.Exception:
2076 def do_before_evaluate(self):
2077 """do_before_evaluate(ProjectionParametersScoreState self)"""
2078 return _IMP_em2d.ProjectionParametersScoreState_do_before_evaluate(self)
2081 def do_after_evaluate(self, da):
2082 """do_after_evaluate(ProjectionParametersScoreState self, DerivativeAccumulator da)"""
2083 return _IMP_em2d.ProjectionParametersScoreState_do_after_evaluate(self, da)
2086 def do_get_inputs(self):
2087 """do_get_inputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2088 return _IMP_em2d.ProjectionParametersScoreState_do_get_inputs(self)
2091 def do_get_outputs(self):
2092 """do_get_outputs(ProjectionParametersScoreState self) -> IMP::ModelObjectsTemp"""
2093 return _IMP_em2d.ProjectionParametersScoreState_do_get_outputs(self)
2096 def get_version_info(self):
2097 """get_version_info(ProjectionParametersScoreState self) -> VersionInfo"""
2098 return _IMP_em2d.ProjectionParametersScoreState_get_version_info(self)
2102 """__str__(ProjectionParametersScoreState self) -> std::string"""
2103 return _IMP_em2d.ProjectionParametersScoreState___str__(self)
2107 """__repr__(ProjectionParametersScoreState self) -> std::string"""
2108 return _IMP_em2d.ProjectionParametersScoreState___repr__(self)
2113 return _object_cast_to_ProjectionParametersScoreState(o)
2115 ProjectionParametersScoreState_swigregister = _IMP_em2d.ProjectionParametersScoreState_swigregister
2116 ProjectionParametersScoreState_swigregister(ProjectionParametersScoreState)
2118 class ProjectionMask(object):
2119 """Proxy of C++ IMP::em2d::ProjectionMask class."""
2121 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2123 def __init__(self, *args, **kwargs):
2124 raise AttributeError(
"No constructor defined")
2126 def apply(self, m, v):
2127 """apply(ProjectionMask self, cv::Mat & m, Vector2D v)"""
2128 return _IMP_em2d.ProjectionMask_apply(self, m, v)
2131 def show(self, *args):
2133 show(ProjectionMask self, _ostream out)
2134 show(ProjectionMask self)
2136 return _IMP_em2d.ProjectionMask_show(self, *args)
2138 __swig_destroy__ = _IMP_em2d.delete_ProjectionMask
2139 __del__ =
lambda self:
None
2142 """__str__(ProjectionMask self) -> std::string"""
2143 return _IMP_em2d.ProjectionMask___str__(self)
2147 """__repr__(ProjectionMask self) -> std::string"""
2148 return _IMP_em2d.ProjectionMask___repr__(self)
2150 ProjectionMask_swigregister = _IMP_em2d.ProjectionMask_swigregister
2151 ProjectionMask_swigregister(ProjectionMask)
2155 """do_place(cv::Mat & mask, cv::Mat & m, Vector2D v)"""
2156 return _IMP_em2d.do_place(mask, m, v)
2157 class MasksManager(object):
2158 """Proxy of C++ IMP::em2d::MasksManager class."""
2160 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2162 def __init__(self, *args):
2164 __init__(IMP::em2d::MasksManager self) -> MasksManager
2165 __init__(IMP::em2d::MasksManager self, double resolution, double pixelsize) -> MasksManager
2167 this = _IMP_em2d.new_MasksManager(*args)
2169 self.this.append(this)
2170 except __builtin__.Exception:
2173 def setup_kernel(self, resolution, pixelsize):
2174 """setup_kernel(MasksManager self, double resolution, double pixelsize)"""
2175 return _IMP_em2d.MasksManager_setup_kernel(self, resolution, pixelsize)
2178 def create_masks(self, ps):
2179 """create_masks(MasksManager self, IMP::ParticlesTemp const & ps)"""
2180 return _IMP_em2d.MasksManager_create_masks(self, ps)
2183 def create_mask(self, mass):
2184 """create_mask(MasksManager self, double mass)"""
2185 return _IMP_em2d.MasksManager_create_mask(self, mass)
2188 def find_mask(self, mass):
2189 """find_mask(MasksManager self, double mass) -> IMP::em2d::ProjectionMaskPtr"""
2190 return _IMP_em2d.MasksManager_find_mask(self, mass)
2193 def show(self, *args):
2195 show(MasksManager self, _ostream out)
2196 show(MasksManager self)
2198 return _IMP_em2d.MasksManager_show(self, *args)
2201 def get_number_of_masks(self):
2202 """get_number_of_masks(MasksManager self) -> unsigned int"""
2203 return _IMP_em2d.MasksManager_get_number_of_masks(self)
2205 __swig_destroy__ = _IMP_em2d.delete_MasksManager
2206 __del__ =
lambda self:
None
2209 """__str__(MasksManager self) -> std::string"""
2210 return _IMP_em2d.MasksManager___str__(self)
2214 """__repr__(MasksManager self) -> std::string"""
2215 return _IMP_em2d.MasksManager___repr__(self)
2217 MasksManager_swigregister = _IMP_em2d.MasksManager_swigregister
2218 MasksManager_swigregister(MasksManager)
2220 class ProjectingParameters(object):
2221 """Proxy of C++ IMP::em2d::ProjectingParameters class."""
2223 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2224 pixel_size = _swig_property(_IMP_em2d.ProjectingParameters_pixel_size_get, _IMP_em2d.ProjectingParameters_pixel_size_set)
2225 resolution = _swig_property(_IMP_em2d.ProjectingParameters_resolution_get, _IMP_em2d.ProjectingParameters_resolution_set)
2227 def __init__(self, *args):
2229 __init__(IMP::em2d::ProjectingParameters self) -> ProjectingParameters
2230 __init__(IMP::em2d::ProjectingParameters self, double ps, double res) -> ProjectingParameters
2232 this = _IMP_em2d.new_ProjectingParameters(*args)
2234 self.this.append(this)
2235 except __builtin__.Exception:
2238 def show(self, *args):
2240 show(ProjectingParameters self, _ostream out)
2241 show(ProjectingParameters self)
2243 return _IMP_em2d.ProjectingParameters_show(self, *args)
2247 """__str__(ProjectingParameters self) -> std::string"""
2248 return _IMP_em2d.ProjectingParameters___str__(self)
2252 """__repr__(ProjectingParameters self) -> std::string"""
2253 return _IMP_em2d.ProjectingParameters___repr__(self)
2255 __swig_destroy__ = _IMP_em2d.delete_ProjectingParameters
2256 __del__ =
lambda self:
None
2257 ProjectingParameters_swigregister = _IMP_em2d.ProjectingParameters_swigregister
2258 ProjectingParameters_swigregister(ProjectingParameters)
2260 class ProjectingOptions(ProjectingParameters):
2261 """Proxy of C++ IMP::em2d::ProjectingOptions class."""
2263 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2264 save_images = _swig_property(_IMP_em2d.ProjectingOptions_save_images_get, _IMP_em2d.ProjectingOptions_save_images_set)
2265 normalize = _swig_property(_IMP_em2d.ProjectingOptions_normalize_get, _IMP_em2d.ProjectingOptions_normalize_set)
2266 clear_matrix_before_projecting = _swig_property(_IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_get, _IMP_em2d.ProjectingOptions_clear_matrix_before_projecting_set)
2268 def __init__(self, *args):
2270 __init__(IMP::em2d::ProjectingOptions self) -> ProjectingOptions
2271 __init__(IMP::em2d::ProjectingOptions self, double ps, double res) -> ProjectingOptions
2272 __init__(IMP::em2d::ProjectingOptions self, double ps, double res, ImageReaderWriter irw) -> ProjectingOptions
2274 this = _IMP_em2d.new_ProjectingOptions(*args)
2276 self.this.append(this)
2277 except __builtin__.Exception:
2280 def show(self, *args):
2282 show(ProjectingOptions self, _ostream out)
2283 show(ProjectingOptions self)
2285 return _IMP_em2d.ProjectingOptions_show(self, *args)
2289 """__str__(ProjectingOptions self) -> std::string"""
2290 return _IMP_em2d.ProjectingOptions___str__(self)
2294 """__repr__(ProjectingOptions self) -> std::string"""
2295 return _IMP_em2d.ProjectingOptions___repr__(self)
2297 __swig_destroy__ = _IMP_em2d.delete_ProjectingOptions
2298 __del__ =
lambda self:
None
2299 ProjectingOptions_swigregister = _IMP_em2d.ProjectingOptions_swigregister
2300 ProjectingOptions_swigregister(ProjectingOptions)
2305 get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2306 get_projections(IMP::ParticlesTemp const & ps, IMP::algebra::SphericalVector3Ds const & vs, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2307 get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options, IMP::Strings names) -> IMP::em2d::Images
2308 get_projections(IMP::ParticlesTemp const & ps, IMP::em2d::RegistrationResults const & registration_values, int rows, int cols, ProjectingOptions options) -> IMP::em2d::Images
2310 return _IMP_em2d.get_projections(*args)
2314 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks, IMP::String name)
2315 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)
2316 get_projection(Image img, IMP::ParticlesTemp const & ps, RegistrationResult reg, ProjectingOptions options)
2318 return _IMP_em2d.get_projection(*args)
2321 """do_project_particles(IMP::ParticlesTemp const & ps, cv::Mat & m2, Rotation3D R, Vector3D translation, ProjectingOptions options, IMP::em2d::MasksManagerPtr masks)"""
2322 return _IMP_em2d.do_project_particles(ps, m2, R, translation, options, masks)
2325 """create_evenly_distributed_projections(IMP::ParticlesTemp const & ps, unsigned int n, ProjectingOptions options) -> IMP::em2d::Images"""
2326 return _IMP_em2d.create_evenly_distributed_projections(ps, n, options)
2330 do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation) -> IMP::algebra::Vector2Ds
2331 do_project_vectors(IMP::algebra::Vector3Ds const & ps, Rotation3D R, Vector3D translation, Vector3D center) -> IMP::algebra::Vector2Ds
2333 return _IMP_em2d.do_project_vectors(*args)
2336 """get_enclosing_image_size(IMP::ParticlesTemp const & ps, double pixel_size, unsigned int slack) -> unsigned int"""
2337 return _IMP_em2d.get_enclosing_image_size(ps, pixel_size, slack)
2341 get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2342 get_complete_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2344 return _IMP_em2d.get_complete_alignment(input, m_to_align, apply)
2348 get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2349 get_rotational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2351 return _IMP_em2d.get_rotational_alignment(input, m_to_align, apply)
2355 get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align, bool apply=False) -> ResultAlign2D
2356 get_translational_alignment(cv::Mat const & input, cv::Mat & m_to_align) -> ResultAlign2D
2358 return _IMP_em2d.get_translational_alignment(input, m_to_align, apply)
2362 get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align, cv::Mat const & POLAR2, bool apply=False) -> ResultAlign2D
2363 get_complete_alignment_no_preprocessing(cv::Mat const & input, cv::Mat const & INPUT, cv::Mat const & POLAR1, cv::Mat & m_to_align, cv::Mat const & POLAR2) -> ResultAlign2D
2365 return _IMP_em2d.get_complete_alignment_no_preprocessing(input, INPUT, POLAR1, m_to_align, POLAR2, apply)
2368 """get_rotational_alignment_no_preprocessing(cv::Mat const & POLAR1, cv::Mat const & POLAR2) -> ResultAlign2D"""
2369 return _IMP_em2d.get_rotational_alignment_no_preprocessing(POLAR1, POLAR2)
2372 """get_translational_alignment_no_preprocessing(cv::Mat const & M1, cv::Mat const & M2) -> ResultAlign2D"""
2373 return _IMP_em2d.get_translational_alignment_no_preprocessing(M1, M2)
2376 """get_complete_alignment_with_centers_no_preprocessing(Vector2D center1, Vector2D center2, cv::Mat const & AUTOC_POLAR1, cv::Mat const & AUTOC_POLAR2) -> ResultAlign2D"""
2377 return _IMP_em2d.get_complete_alignment_with_centers_no_preprocessing(center1, center2, AUTOC_POLAR1, AUTOC_POLAR2)
2381 write_vectors_as_pdb(IMP::algebra::Vector2Ds const vs, IMP::String const filename)
2382 write_vectors_as_pdb(IMP::algebra::Vector3Ds const vs, IMP::String const filename)
2384 return _IMP_em2d.write_vectors_as_pdb(*args)
2385 class Em2DRestraintParameters(ProjectingParameters):
2386 """Proxy of C++ IMP::em2d::Em2DRestraintParameters class."""
2388 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2389 n_projections = _swig_property(_IMP_em2d.Em2DRestraintParameters_n_projections_get, _IMP_em2d.Em2DRestraintParameters_n_projections_set)
2390 coarse_registration_method = _swig_property(_IMP_em2d.Em2DRestraintParameters_coarse_registration_method_get, _IMP_em2d.Em2DRestraintParameters_coarse_registration_method_set)
2391 save_match_images = _swig_property(_IMP_em2d.Em2DRestraintParameters_save_match_images_get, _IMP_em2d.Em2DRestraintParameters_save_match_images_set)
2392 optimization_steps = _swig_property(_IMP_em2d.Em2DRestraintParameters_optimization_steps_get, _IMP_em2d.Em2DRestraintParameters_optimization_steps_set)
2393 simplex_initial_length = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_initial_length_get, _IMP_em2d.Em2DRestraintParameters_simplex_initial_length_set)
2394 simplex_minimum_size = _swig_property(_IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_get, _IMP_em2d.Em2DRestraintParameters_simplex_minimum_size_set)
2396 def __init__(self, *args):
2398 __init__(IMP::em2d::Em2DRestraintParameters self) -> Em2DRestraintParameters
2399 __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res, unsigned int n_proj=20) -> Em2DRestraintParameters
2400 __init__(IMP::em2d::Em2DRestraintParameters self, double ps, double res) -> Em2DRestraintParameters
2402 this = _IMP_em2d.new_Em2DRestraintParameters(*args)
2404 self.this.append(this)
2405 except __builtin__.Exception:
2408 def show(self, *args):
2410 show(Em2DRestraintParameters self, _ostream out)
2411 show(Em2DRestraintParameters self)
2413 return _IMP_em2d.Em2DRestraintParameters_show(self, *args)
2417 """__str__(Em2DRestraintParameters self) -> std::string"""
2418 return _IMP_em2d.Em2DRestraintParameters___str__(self)
2422 """__repr__(Em2DRestraintParameters self) -> std::string"""
2423 return _IMP_em2d.Em2DRestraintParameters___repr__(self)
2425 __swig_destroy__ = _IMP_em2d.delete_Em2DRestraintParameters
2426 __del__ =
lambda self:
None
2427 Em2DRestraintParameters_swigregister = _IMP_em2d.Em2DRestraintParameters_swigregister
2428 Em2DRestraintParameters_swigregister(Em2DRestraintParameters)
2429 cvar = _IMP_em2d.cvar
2430 ALIGN2D_NO_PREPROCESSING = cvar.ALIGN2D_NO_PREPROCESSING
2431 ALIGN2D_PREPROCESSING = cvar.ALIGN2D_PREPROCESSING
2432 ALIGN2D_WITH_CENTERS = cvar.ALIGN2D_WITH_CENTERS
2435 """Proxy of C++ IMP::em2d::ProjectionFinder class."""
2437 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2440 """__init__(IMP::em2d::ProjectionFinder self) -> ProjectionFinder"""
2441 this = _IMP_em2d.new_ProjectionFinder()
2443 self.this.append(this)
2444 except __builtin__.Exception:
2447 def setup(self, score_function, params):
2448 """setup(ProjectionFinder self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2449 return _IMP_em2d.ProjectionFinder_setup(self, score_function, params)
2452 def set_subjects(self, subjects):
2453 """set_subjects(ProjectionFinder self, IMP::em2d::Images const & subjects)"""
2454 return _IMP_em2d.ProjectionFinder_set_subjects(self, subjects)
2457 def set_projections(self, projections):
2458 """set_projections(ProjectionFinder self, IMP::em2d::Images const & projections)"""
2459 return _IMP_em2d.ProjectionFinder_set_projections(self, projections)
2462 def set_variance_images(self, variances):
2463 """set_variance_images(ProjectionFinder self, IMP::em2d::Images const & variances)"""
2464 return _IMP_em2d.ProjectionFinder_set_variance_images(self, variances)
2467 def set_model_particles(self, ps):
2468 """set_model_particles(ProjectionFinder self, IMP::ParticlesTemp const & ps)"""
2469 return _IMP_em2d.ProjectionFinder_set_model_particles(self, ps)
2472 def set_save_match_images(self, x):
2473 """set_save_match_images(ProjectionFinder self, bool x)"""
2474 return _IMP_em2d.ProjectionFinder_set_save_match_images(self, x)
2477 def get_save_match_images(self):
2478 """get_save_match_images(ProjectionFinder self) -> bool"""
2479 return _IMP_em2d.ProjectionFinder_get_save_match_images(self)
2482 def set_fast_mode(self, n):
2483 """set_fast_mode(ProjectionFinder self, unsigned int n)"""
2484 return _IMP_em2d.ProjectionFinder_set_fast_mode(self, n)
2487 def get_registration_results(self):
2488 """get_registration_results(ProjectionFinder self) -> IMP::em2d::RegistrationResults"""
2489 return _IMP_em2d.ProjectionFinder_get_registration_results(self)
2492 def get_coarse_registration(self):
2493 """get_coarse_registration(ProjectionFinder self)"""
2494 return _IMP_em2d.ProjectionFinder_get_coarse_registration(self)
2497 def get_complete_registration(self):
2498 """get_complete_registration(ProjectionFinder self)"""
2499 return _IMP_em2d.ProjectionFinder_get_complete_registration(self)
2503 """get_global_score(ProjectionFinder self) -> double"""
2504 return _IMP_em2d.ProjectionFinder_get_global_score(self)
2507 def show(self, out):
2508 """show(ProjectionFinder self, _ostream out)"""
2509 return _IMP_em2d.ProjectionFinder_show(self, out)
2512 def get_preprocessing_time(self):
2513 """get_preprocessing_time(ProjectionFinder self) -> double"""
2514 return _IMP_em2d.ProjectionFinder_get_preprocessing_time(self)
2517 def get_coarse_registration_time(self):
2518 """get_coarse_registration_time(ProjectionFinder self) -> double"""
2519 return _IMP_em2d.ProjectionFinder_get_coarse_registration_time(self)
2522 def get_fine_registration_time(self):
2523 """get_fine_registration_time(ProjectionFinder self) -> double"""
2524 return _IMP_em2d.ProjectionFinder_get_fine_registration_time(self)
2527 def get_number_of_subjects(self):
2528 """get_number_of_subjects(ProjectionFinder self) -> unsigned int"""
2529 return _IMP_em2d.ProjectionFinder_get_number_of_subjects(self)
2532 def set_number_of_class_averages_members(self, n_members):
2533 """set_number_of_class_averages_members(ProjectionFinder self, IMP::Ints n_members)"""
2534 return _IMP_em2d.ProjectionFinder_set_number_of_class_averages_members(self, n_members)
2537 def get_number_of_projections(self):
2538 """get_number_of_projections(ProjectionFinder self) -> unsigned int"""
2539 return _IMP_em2d.ProjectionFinder_get_number_of_projections(self)
2542 def get_version_info(self):
2543 """get_version_info(ProjectionFinder self) -> VersionInfo"""
2544 return _IMP_em2d.ProjectionFinder_get_version_info(self)
2548 """__str__(ProjectionFinder self) -> std::string"""
2549 return _IMP_em2d.ProjectionFinder___str__(self)
2553 """__repr__(ProjectionFinder self) -> std::string"""
2554 return _IMP_em2d.ProjectionFinder___repr__(self)
2559 return _object_cast_to_ProjectionFinder(o)
2561 ProjectionFinder_swigregister = _IMP_em2d.ProjectionFinder_swigregister
2562 ProjectionFinder_swigregister(ProjectionFinder)
2565 """Proxy of C++ IMP::em2d::Em2DRestraint class."""
2567 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2569 def __init__(self, m):
2570 """__init__(IMP::em2d::Em2DRestraint self, Model m) -> Em2DRestraint"""
2571 this = _IMP_em2d.new_Em2DRestraint(m)
2573 self.this.append(this)
2574 except __builtin__.Exception:
2577 def setup(self, score_function, params):
2578 """setup(Em2DRestraint self, ScoreFunction score_function, Em2DRestraintParameters params)"""
2579 return _IMP_em2d.Em2DRestraint_setup(self, score_function, params)
2582 def set_particles(self, particles_container):
2583 """set_particles(Em2DRestraint self, SingletonContainer particles_container)"""
2584 return _IMP_em2d.Em2DRestraint_set_particles(self, particles_container)
2587 def set_images(self, em_images):
2588 """set_images(Em2DRestraint self, IMP::em2d::Images const em_images)"""
2589 return _IMP_em2d.Em2DRestraint_set_images(self, em_images)
2592 def set_variance_images(self, variance_images):
2593 """set_variance_images(Em2DRestraint self, IMP::em2d::Images const variance_images)"""
2594 return _IMP_em2d.Em2DRestraint_set_variance_images(self, variance_images)
2597 def set_fast_mode(self, n):
2598 """set_fast_mode(Em2DRestraint self, unsigned int n)"""
2599 return _IMP_em2d.Em2DRestraint_set_fast_mode(self, n)
2602 def set_coarse_registration_mode(self, opt):
2603 """set_coarse_registration_mode(Em2DRestraint self, bool opt)"""
2604 return _IMP_em2d.Em2DRestraint_set_coarse_registration_mode(self, opt)
2607 def get_registration_results(self):
2608 """get_registration_results(Em2DRestraint self) -> IMP::em2d::RegistrationResults"""
2609 return _IMP_em2d.Em2DRestraint_get_registration_results(self)
2612 def do_get_inputs(self):
2613 """do_get_inputs(Em2DRestraint self) -> IMP::ModelObjectsTemp"""
2614 return _IMP_em2d.Em2DRestraint_do_get_inputs(self)
2617 def get_version_info(self):
2618 """get_version_info(Em2DRestraint self) -> VersionInfo"""
2619 return _IMP_em2d.Em2DRestraint_get_version_info(self)
2623 """__str__(Em2DRestraint self) -> std::string"""
2624 return _IMP_em2d.Em2DRestraint___str__(self)
2628 """__repr__(Em2DRestraint self) -> std::string"""
2629 return _IMP_em2d.Em2DRestraint___repr__(self)
2634 return _object_cast_to_Em2DRestraint(o)
2636 Em2DRestraint_swigregister = _IMP_em2d.Em2DRestraint_swigregister
2637 Em2DRestraint_swigregister(Em2DRestraint)
2639 class ClusterSet(object):
2640 """Proxy of C++ IMP::em2d::ClusterSet class."""
2642 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2644 def __init__(self, N):
2645 """__init__(IMP::em2d::ClusterSet self, unsigned int N) -> ClusterSet"""
2646 this = _IMP_em2d.new_ClusterSet(N)
2648 self.this.append(this)
2649 except __builtin__.Exception:
2652 def do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters):
2653 """do_join_clusters(ClusterSet self, unsigned int cluster_id1, unsigned int cluster_id2, double distance_between_clusters)"""
2654 return _IMP_em2d.ClusterSet_do_join_clusters(self, cluster_id1, cluster_id2, distance_between_clusters)
2657 def get_cluster_elements(self, id):
2658 """get_cluster_elements(ClusterSet self, unsigned int id) -> IMP::Ints"""
2659 return _IMP_em2d.ClusterSet_get_cluster_elements(self, id)
2662 def get_clusters_below_cutoff(self, cutoff):
2663 """get_clusters_below_cutoff(ClusterSet self, double cutoff) -> IMP::Ints"""
2664 return _IMP_em2d.ClusterSet_get_clusters_below_cutoff(self, cutoff)
2667 def get_cluster_formed_at_step(self, step):
2668 """get_cluster_formed_at_step(ClusterSet self, unsigned int step) -> IMP::Ints"""
2669 return _IMP_em2d.ClusterSet_get_cluster_formed_at_step(self, step)
2672 def get_distance_at_step(self, step):
2673 """get_distance_at_step(ClusterSet self, unsigned int step) -> double"""
2674 return _IMP_em2d.ClusterSet_get_distance_at_step(self, step)
2677 def get_id_for_cluster_at_step(self, step):
2678 """get_id_for_cluster_at_step(ClusterSet self, unsigned int step) -> unsigned int"""
2679 return _IMP_em2d.ClusterSet_get_id_for_cluster_at_step(self, step)
2682 def get_linkage_matrix(self):
2683 """get_linkage_matrix(ClusterSet self) -> IMP::FloatsList"""
2684 return _IMP_em2d.ClusterSet_get_linkage_matrix(self)
2687 def get_linkage_matrix_in_matlab_format(self):
2688 """get_linkage_matrix_in_matlab_format(ClusterSet self) -> IMP::FloatsList"""
2689 return _IMP_em2d.ClusterSet_get_linkage_matrix_in_matlab_format(self)
2692 def get_number_of_steps(self):
2693 """get_number_of_steps(ClusterSet self) -> unsigned int"""
2694 return _IMP_em2d.ClusterSet_get_number_of_steps(self)
2697 def show(self, out):
2698 """show(ClusterSet self, _ostream out)"""
2699 return _IMP_em2d.ClusterSet_show(self, out)
2703 """__str__(ClusterSet self) -> std::string"""
2704 return _IMP_em2d.ClusterSet___str__(self)
2708 """__repr__(ClusterSet self) -> std::string"""
2709 return _IMP_em2d.ClusterSet___repr__(self)
2711 __swig_destroy__ = _IMP_em2d.delete_ClusterSet
2712 __del__ =
lambda self:
None
2713 ClusterSet_swigregister = _IMP_em2d.ClusterSet_swigregister
2714 ClusterSet_swigregister(ClusterSet)
2716 class SingleLinkage(object):
2717 """Proxy of C++ IMP::em2d::SingleLinkage class."""
2719 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2722 """__init__(IMP::em2d::SingleLinkage self) -> SingleLinkage"""
2723 this = _IMP_em2d.new_SingleLinkage()
2725 self.this.append(this)
2726 except __builtin__.Exception:
2729 def __call__(self, id1, id2, cluster_set, distances):
2730 """__call__(SingleLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2731 return _IMP_em2d.SingleLinkage___call__(self, id1, id2, cluster_set, distances)
2734 def show(self, out):
2735 """show(SingleLinkage self, _ostream out)"""
2736 return _IMP_em2d.SingleLinkage_show(self, out)
2740 """__str__(SingleLinkage self) -> std::string"""
2741 return _IMP_em2d.SingleLinkage___str__(self)
2745 """__repr__(SingleLinkage self) -> std::string"""
2746 return _IMP_em2d.SingleLinkage___repr__(self)
2748 __swig_destroy__ = _IMP_em2d.delete_SingleLinkage
2749 __del__ =
lambda self:
None
2750 SingleLinkage_swigregister = _IMP_em2d.SingleLinkage_swigregister
2751 SingleLinkage_swigregister(SingleLinkage)
2753 class CompleteLinkage(object):
2754 """Proxy of C++ IMP::em2d::CompleteLinkage class."""
2756 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2759 """__init__(IMP::em2d::CompleteLinkage self) -> CompleteLinkage"""
2760 this = _IMP_em2d.new_CompleteLinkage()
2762 self.this.append(this)
2763 except __builtin__.Exception:
2766 def __call__(self, id1, id2, cluster_set, distances):
2767 """__call__(CompleteLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2768 return _IMP_em2d.CompleteLinkage___call__(self, id1, id2, cluster_set, distances)
2771 def show(self, out):
2772 """show(CompleteLinkage self, _ostream out)"""
2773 return _IMP_em2d.CompleteLinkage_show(self, out)
2777 """__str__(CompleteLinkage self) -> std::string"""
2778 return _IMP_em2d.CompleteLinkage___str__(self)
2782 """__repr__(CompleteLinkage self) -> std::string"""
2783 return _IMP_em2d.CompleteLinkage___repr__(self)
2785 __swig_destroy__ = _IMP_em2d.delete_CompleteLinkage
2786 __del__ =
lambda self:
None
2787 CompleteLinkage_swigregister = _IMP_em2d.CompleteLinkage_swigregister
2788 CompleteLinkage_swigregister(CompleteLinkage)
2790 class AverageDistanceLinkage(object):
2791 """Proxy of C++ IMP::em2d::AverageDistanceLinkage class."""
2793 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2796 """__init__(IMP::em2d::AverageDistanceLinkage self) -> AverageDistanceLinkage"""
2797 this = _IMP_em2d.new_AverageDistanceLinkage()
2799 self.this.append(this)
2800 except __builtin__.Exception:
2803 def __call__(self, id1, id2, cluster_set, distances):
2804 """__call__(AverageDistanceLinkage self, unsigned int id1, unsigned int id2, ClusterSet cluster_set, IMP::FloatsList const & distances) -> double"""
2805 return _IMP_em2d.AverageDistanceLinkage___call__(self, id1, id2, cluster_set, distances)
2808 def show(self, out):
2809 """show(AverageDistanceLinkage self, _ostream out)"""
2810 return _IMP_em2d.AverageDistanceLinkage_show(self, out)
2814 """__str__(AverageDistanceLinkage self) -> std::string"""
2815 return _IMP_em2d.AverageDistanceLinkage___str__(self)
2819 """__repr__(AverageDistanceLinkage self) -> std::string"""
2820 return _IMP_em2d.AverageDistanceLinkage___repr__(self)
2822 __swig_destroy__ = _IMP_em2d.delete_AverageDistanceLinkage
2823 __del__ =
lambda self:
None
2824 AverageDistanceLinkage_swigregister = _IMP_em2d.AverageDistanceLinkage_swigregister
2825 AverageDistanceLinkage_swigregister(AverageDistanceLinkage)
2828 """Proxy of C++ IMP::em2d::CollisionCrossSection class."""
2830 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2832 def __init__(self, n_projections, resolution, pixel_size, projection_image_size):
2833 """__init__(IMP::em2d::CollisionCrossSection self, unsigned int n_projections, double resolution, double pixel_size, double projection_image_size) -> CollisionCrossSection"""
2834 this = _IMP_em2d.new_CollisionCrossSection(n_projections, resolution, pixel_size, projection_image_size)
2836 self.this.append(this)
2837 except __builtin__.Exception:
2840 def set_model_particles(self, ps):
2841 """set_model_particles(CollisionCrossSection self, IMP::ParticlesTemp const & ps)"""
2842 return _IMP_em2d.CollisionCrossSection_set_model_particles(self, ps)
2846 """get_ccs(CollisionCrossSection self) -> double"""
2847 return _IMP_em2d.CollisionCrossSection_get_ccs(self)
2850 def show(self, out):
2851 """show(CollisionCrossSection self, _ostream out)"""
2852 return _IMP_em2d.CollisionCrossSection_show(self, out)
2855 def get_version_info(self):
2856 """get_version_info(CollisionCrossSection self) -> VersionInfo"""
2857 return _IMP_em2d.CollisionCrossSection_get_version_info(self)
2861 """__str__(CollisionCrossSection self) -> std::string"""
2862 return _IMP_em2d.CollisionCrossSection___str__(self)
2866 """__repr__(CollisionCrossSection self) -> std::string"""
2867 return _IMP_em2d.CollisionCrossSection___repr__(self)
2872 return _object_cast_to_CollisionCrossSection(o)
2874 CollisionCrossSection_swigregister = _IMP_em2d.CollisionCrossSection_swigregister
2875 CollisionCrossSection_swigregister(CollisionCrossSection)
2878 """Proxy of C++ IMP::em2d::GridStates class."""
2880 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2882 def __init__(self, *args):
2884 __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::String const & name) -> GridStates
2885 __init__(IMP::em2d::GridStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations) -> GridStates
2887 this = _IMP_em2d.new_GridStates(*args)
2889 self.this.append(this)
2890 except __builtin__.Exception:
2893 def get_position(self, i):
2894 """get_position(GridStates self, unsigned int i) -> Vector3D"""
2895 return _IMP_em2d.GridStates_get_position(self, i)
2898 def get_orientation(self, i):
2899 """get_orientation(GridStates self, unsigned int i) -> Rotation3D"""
2900 return _IMP_em2d.GridStates_get_orientation(self, i)
2903 def get_version_info(self):
2904 """get_version_info(GridStates self) -> VersionInfo"""
2905 return _IMP_em2d.GridStates_get_version_info(self)
2909 """__str__(GridStates self) -> std::string"""
2910 return _IMP_em2d.GridStates___str__(self)
2914 """__repr__(GridStates self) -> std::string"""
2915 return _IMP_em2d.GridStates___repr__(self)
2920 return _object_cast_to_GridStates(o)
2922 GridStates_swigregister = _IMP_em2d.GridStates_swigregister
2923 GridStates_swigregister(GridStates)
2925 class ProjectionStates(GridStates):
2926 """Proxy of C++ IMP::em2d::ProjectionStates class."""
2928 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2930 def __init__(self, *args):
2932 __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections, IMP::String const & name) -> ProjectionStates
2933 __init__(IMP::em2d::ProjectionStates self, IMP::algebra::Vector3Ds const & positions, IMP::algebra::Rotation3Ds const & orientations, IMP::em2d::Images const & projections) -> ProjectionStates
2935 this = _IMP_em2d.new_ProjectionStates(*args)
2937 self.this.append(this)
2938 except __builtin__.Exception:
2942 """get_projection(ProjectionStates self, unsigned int i) -> Image"""
2943 return _IMP_em2d.ProjectionStates_get_projection(self, i)
2947 """__str__(ProjectionStates self) -> std::string"""
2948 return _IMP_em2d.ProjectionStates___str__(self)
2952 """__repr__(ProjectionStates self) -> std::string"""
2953 return _IMP_em2d.ProjectionStates___repr__(self)
2958 return _object_cast_to_ProjectionStates(o)
2960 ProjectionStates_swigregister = _IMP_em2d.ProjectionStates_swigregister
2961 ProjectionStates_swigregister(ProjectionStates)
2964 """Proxy of C++ IMP::em2d::DistanceFilter class."""
2966 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2968 def __init__(self, subset_to_act_on, subset_to_restrain, ps_table, max_distance):
2969 """__init__(IMP::em2d::DistanceFilter self, Subset subset_to_act_on, Subset subset_to_restrain, ParticleStatesTable ps_table, double max_distance) -> DistanceFilter"""
2970 this = _IMP_em2d.new_DistanceFilter(subset_to_act_on, subset_to_restrain, ps_table, max_distance)
2972 self.this.append(this)
2973 except __builtin__.Exception:
2976 def show(self, *args):
2978 show(DistanceFilter self, _ostream out)
2979 show(DistanceFilter self)
2981 return _IMP_em2d.DistanceFilter_show(self, *args)
2984 def get_version_info(self):
2985 """get_version_info(DistanceFilter self) -> VersionInfo"""
2986 return _IMP_em2d.DistanceFilter_get_version_info(self)
2990 """__str__(DistanceFilter self) -> std::string"""
2991 return _IMP_em2d.DistanceFilter___str__(self)
2995 """__repr__(DistanceFilter self) -> std::string"""
2996 return _IMP_em2d.DistanceFilter___repr__(self)
3001 return _object_cast_to_DistanceFilter(o)
3003 DistanceFilter_swigregister = _IMP_em2d.DistanceFilter_swigregister
3004 DistanceFilter_swigregister(DistanceFilter)
3007 """Proxy of C++ IMP::em2d::DistanceFilterTable class."""
3009 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3011 def __init__(self, subset_to_act_on, ps_table, max_distance):
3012 """__init__(IMP::em2d::DistanceFilterTable self, Subset subset_to_act_on, ParticleStatesTable ps_table, double max_distance) -> DistanceFilterTable"""
3013 this = _IMP_em2d.new_DistanceFilterTable(subset_to_act_on, ps_table, max_distance)
3015 self.this.append(this)
3016 except __builtin__.Exception:
3019 def show(self, *args):
3021 show(DistanceFilterTable self, _ostream out)
3022 show(DistanceFilterTable self)
3024 return _IMP_em2d.DistanceFilterTable_show(self, *args)
3027 def get_version_info(self):
3028 """get_version_info(DistanceFilterTable self) -> VersionInfo"""
3029 return _IMP_em2d.DistanceFilterTable_get_version_info(self)
3033 """__str__(DistanceFilterTable self) -> std::string"""
3034 return _IMP_em2d.DistanceFilterTable___str__(self)
3038 """__repr__(DistanceFilterTable self) -> std::string"""
3039 return _IMP_em2d.DistanceFilterTable___repr__(self)
3044 return _object_cast_to_DistanceFilterTable(o)
3046 DistanceFilterTable_swigregister = _IMP_em2d.DistanceFilterTable_swigregister
3047 DistanceFilterTable_swigregister(DistanceFilterTable)
3049 class IntsOrder(object):
3050 """Proxy of C++ IMP::em2d::IntsOrder class."""
3052 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3053 __repr__ = _swig_repr
3055 def __call__(self, a, b):
3056 """__call__(IntsOrder self, IMP::Ints const & a, IMP::Ints const & b) -> bool"""
3057 return _IMP_em2d.IntsOrder___call__(self, a, b)
3061 """__init__(IMP::em2d::IntsOrder self) -> IntsOrder"""
3062 this = _IMP_em2d.new_IntsOrder()
3064 self.this.append(this)
3065 except __builtin__.Exception:
3067 __swig_destroy__ = _IMP_em2d.delete_IntsOrder
3068 __del__ =
lambda self:
None
3069 IntsOrder_swigregister = _IMP_em2d.IntsOrder_swigregister
3070 IntsOrder_swigregister(IntsOrder)
3073 """Proxy of C++ IMP::em2d::RigidBodiesImageFitRestraint class."""
3075 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3077 def get_version_info(self):
3078 """get_version_info(RigidBodiesImageFitRestraint self) -> VersionInfo"""
3079 return _IMP_em2d.RigidBodiesImageFitRestraint_get_version_info(self)
3082 def __init__(self, scf, rbs, img):
3083 """__init__(IMP::em2d::RigidBodiesImageFitRestraint self, ScoreFunction scf, IMP::core::RigidBodies const & rbs, Image img) -> RigidBodiesImageFitRestraint"""
3084 this = _IMP_em2d.new_RigidBodiesImageFitRestraint(scf, rbs, img)
3086 self.this.append(this)
3087 except __builtin__.Exception:
3090 def set_projecting_parameters(self, p):
3091 """set_projecting_parameters(RigidBodiesImageFitRestraint self, ProjectingParameters p)"""
3092 return _IMP_em2d.RigidBodiesImageFitRestraint_set_projecting_parameters(self, p)
3095 def set_orientations(self, rb, rots):
3096 """set_orientations(RigidBodiesImageFitRestraint self, RigidBody rb, IMP::algebra::Rotation3Ds const & rots)"""
3097 return _IMP_em2d.RigidBodiesImageFitRestraint_set_orientations(self, rb, rots)
3100 def get_number_of_masks(self, rb):
3101 """get_number_of_masks(RigidBodiesImageFitRestraint self, RigidBody rb) -> unsigned int"""
3102 return _IMP_em2d.RigidBodiesImageFitRestraint_get_number_of_masks(self, rb)
3106 """__str__(RigidBodiesImageFitRestraint self) -> std::string"""
3107 return _IMP_em2d.RigidBodiesImageFitRestraint___str__(self)
3111 """__repr__(RigidBodiesImageFitRestraint self) -> std::string"""
3112 return _IMP_em2d.RigidBodiesImageFitRestraint___repr__(self)
3117 return _object_cast_to_RigidBodiesImageFitRestraint(o)
3119 RigidBodiesImageFitRestraint_swigregister = _IMP_em2d.RigidBodiesImageFitRestraint_swigregister
3120 RigidBodiesImageFitRestraint_swigregister(RigidBodiesImageFitRestraint)
3124 """get_unique_index(Rotation3D rot) -> IMP::Ints"""
3125 return _IMP_em2d.get_unique_index(rot)
3127 """Proxy of C++ IMP::em2d::RelativePositionMover class."""
3129 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3131 def __init__(self, d, max_translation, max_rotation):
3132 """__init__(IMP::em2d::RelativePositionMover self, RigidBody d, IMP::Float max_translation, IMP::Float max_rotation) -> RelativePositionMover"""
3133 this = _IMP_em2d.new_RelativePositionMover(d, max_translation, max_rotation)
3135 self.this.append(this)
3136 except __builtin__.Exception:
3139 def add_internal_transformations(self, d, transforms):
3140 """add_internal_transformations(RelativePositionMover self, RigidBody d, IMP::algebra::Transformation3Ds transforms)"""
3141 return _IMP_em2d.RelativePositionMover_add_internal_transformations(self, d, transforms)
3144 def set_random_move_probability(self, p):
3145 """set_random_move_probability(RelativePositionMover self, IMP::Float p)"""
3146 return _IMP_em2d.RelativePositionMover_set_random_move_probability(self, p)
3150 """__str__(RelativePositionMover self) -> std::string"""
3151 return _IMP_em2d.RelativePositionMover___str__(self)
3155 """__repr__(RelativePositionMover self) -> std::string"""
3156 return _IMP_em2d.RelativePositionMover___repr__(self)
3161 return _object_cast_to_RelativePositionMover(o)
3163 RelativePositionMover_swigregister = _IMP_em2d.RelativePositionMover_swigregister
3164 RelativePositionMover_swigregister(RelativePositionMover)
3167 """Proxy of C++ IMP::em2d::DummyRestraint class."""
3169 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3171 def __init__(self, p, q):
3172 """__init__(IMP::em2d::DummyRestraint self, Particle p, Particle q) -> DummyRestraint"""
3173 this = _IMP_em2d.new_DummyRestraint(p, q)
3175 self.this.append(this)
3176 except __builtin__.Exception:
3179 def show(self, *args):
3181 show(DummyRestraint self, _ostream out)
3182 show(DummyRestraint self)
3184 return _IMP_em2d.DummyRestraint_show(self, *args)
3187 def do_get_inputs(self):
3188 """do_get_inputs(DummyRestraint self) -> IMP::ModelObjectsTemp"""
3189 return _IMP_em2d.DummyRestraint_do_get_inputs(self)
3192 def get_version_info(self):
3193 """get_version_info(DummyRestraint self) -> VersionInfo"""
3194 return _IMP_em2d.DummyRestraint_get_version_info(self)
3198 """__str__(DummyRestraint self) -> std::string"""
3199 return _IMP_em2d.DummyRestraint___str__(self)
3203 """__repr__(DummyRestraint self) -> std::string"""
3204 return _IMP_em2d.DummyRestraint___repr__(self)
3209 return _object_cast_to_DummyRestraint(o)
3211 DummyRestraint_swigregister = _IMP_em2d.DummyRestraint_swigregister
3212 DummyRestraint_swigregister(DummyRestraint)
3215 """Proxy of C++ IMP::em2d::ParticlesDummyRestraint class."""
3217 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3219 def __init__(self, sc):
3220 """__init__(IMP::em2d::ParticlesDummyRestraint self, SingletonContainer sc) -> ParticlesDummyRestraint"""
3221 this = _IMP_em2d.new_ParticlesDummyRestraint(sc)
3223 self.this.append(this)
3224 except __builtin__.Exception:
3227 def show(self, *args):
3229 show(ParticlesDummyRestraint self, _ostream out)
3230 show(ParticlesDummyRestraint self)
3232 return _IMP_em2d.ParticlesDummyRestraint_show(self, *args)
3235 def do_get_inputs(self):
3236 """do_get_inputs(ParticlesDummyRestraint self) -> IMP::ModelObjectsTemp"""
3237 return _IMP_em2d.ParticlesDummyRestraint_do_get_inputs(self)
3240 def get_version_info(self):
3241 """get_version_info(ParticlesDummyRestraint self) -> VersionInfo"""
3242 return _IMP_em2d.ParticlesDummyRestraint_get_version_info(self)
3246 """__str__(ParticlesDummyRestraint self) -> std::string"""
3247 return _IMP_em2d.ParticlesDummyRestraint___str__(self)
3251 """__repr__(ParticlesDummyRestraint self) -> std::string"""
3252 return _IMP_em2d.ParticlesDummyRestraint___repr__(self)
3257 return _object_cast_to_ParticlesDummyRestraint(o)
3259 ParticlesDummyRestraint_swigregister = _IMP_em2d.ParticlesDummyRestraint_swigregister
3260 ParticlesDummyRestraint_swigregister(ParticlesDummyRestraint)
3263 """Proxy of C++ IMP::em2d::PCAFitRestraint class."""
3265 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3267 def __init__(self, particles, image_files, pixel_size, resolution=10.0, projection_number=100, reuse_direction=False, n_components=1):
3269 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False, unsigned int n_components=1) -> PCAFitRestraint
3270 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100, bool reuse_direction=False) -> PCAFitRestraint
3271 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0, unsigned int projection_number=100) -> PCAFitRestraint
3272 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size, double resolution=10.0) -> PCAFitRestraint
3273 __init__(IMP::em2d::PCAFitRestraint self, IMP::Particles particles, Strings image_files, double pixel_size) -> PCAFitRestraint
3275 this = _IMP_em2d.new_PCAFitRestraint(particles, image_files, pixel_size, resolution, projection_number, reuse_direction, n_components)
3277 self.this.append(this)
3278 except __builtin__.Exception:
3281 def get_projection_number(self):
3282 """get_projection_number(PCAFitRestraint self) -> unsigned int"""
3283 return _IMP_em2d.PCAFitRestraint_get_projection_number(self)
3286 def set_projection_number(self, n):
3287 """set_projection_number(PCAFitRestraint self, unsigned int n)"""
3288 return _IMP_em2d.PCAFitRestraint_set_projection_number(self, n)
3291 def get_transformation(self, image_number):
3292 """get_transformation(PCAFitRestraint self, unsigned int image_number) -> Transformation3D"""
3293 return _IMP_em2d.PCAFitRestraint_get_transformation(self, image_number)
3297 """get_cross_correlation_coefficient(PCAFitRestraint self, unsigned int image_number) -> double"""
3298 return _IMP_em2d.PCAFitRestraint_get_cross_correlation_coefficient(self, image_number)
3301 def write_best_projections(self, file_name, evaluate=False):
3303 write_best_projections(PCAFitRestraint self, std::string file_name, bool evaluate=False)
3304 write_best_projections(PCAFitRestraint self, std::string file_name)
3306 return _IMP_em2d.PCAFitRestraint_write_best_projections(self, file_name, evaluate)
3309 def do_get_inputs(self):
3310 """do_get_inputs(PCAFitRestraint self) -> IMP::ModelObjectsTemp"""
3311 return _IMP_em2d.PCAFitRestraint_do_get_inputs(self)
3314 def get_version_info(self):
3315 """get_version_info(PCAFitRestraint self) -> VersionInfo"""
3316 return _IMP_em2d.PCAFitRestraint_get_version_info(self)
3320 """__str__(PCAFitRestraint self) -> std::string"""
3321 return _IMP_em2d.PCAFitRestraint___str__(self)
3325 """__repr__(PCAFitRestraint self) -> std::string"""
3326 return _IMP_em2d.PCAFitRestraint___repr__(self)
3331 return _object_cast_to_em2dPCAFitRestraint(o)
3333 PCAFitRestraint_swigregister = _IMP_em2d.PCAFitRestraint_swigregister
3334 PCAFitRestraint_swigregister(PCAFitRestraint)
3337 """Proxy of C++ std::pair<(IMP::algebra::Transformation2D,double)> class."""
3339 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3340 __repr__ = _swig_repr
3342 def __init__(self, *args):
3344 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self) -> ResultAlign2D
3345 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, Transformation2D first, double second) -> ResultAlign2D
3346 __init__(std::pair<(IMP::algebra::Transformation2D,double)> self, ResultAlign2D p) -> ResultAlign2D
3348 this = _IMP_em2d.new_ResultAlign2D(*args)
3350 self.this.append(this)
3351 except __builtin__.Exception:
3353 first = _swig_property(_IMP_em2d.ResultAlign2D_first_get, _IMP_em2d.ResultAlign2D_first_set)
3354 second = _swig_property(_IMP_em2d.ResultAlign2D_second_get, _IMP_em2d.ResultAlign2D_second_set)
3358 return str((self.first, self.second))
3359 def __getitem__(self, index):
3364 def __setitem__(self, index, val):
3369 __swig_destroy__ = _IMP_em2d.delete_ResultAlign2D
3370 __del__ =
lambda self:
None
3371 ResultAlign2D_swigregister = _IMP_em2d.ResultAlign2D_swigregister
3372 ResultAlign2D_swigregister(ResultAlign2D)
3375 def _do_hierarchical_clustering_single_linkage(distances):
3376 """_do_hierarchical_clustering_single_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3377 return _IMP_em2d._do_hierarchical_clustering_single_linkage(distances)
3379 def _do_hierarchical_clustering_complete_linkage(distances):
3380 """_do_hierarchical_clustering_complete_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3381 return _IMP_em2d._do_hierarchical_clustering_complete_linkage(distances)
3383 def _do_hierarchical_clustering_average_distance_linkage(distances):
3384 """_do_hierarchical_clustering_average_distance_linkage(IMP::FloatsList const & distances) -> ClusterSet"""
3385 return _IMP_em2d._do_hierarchical_clustering_average_distance_linkage(distances)
3387 do_hierarchical_clustering_single_linkage = _do_hierarchical_clustering_single_linkage
3388 do_hierarchical_clustering_complete_linkage = _do_hierarchical_clustering_complete_linkage
3389 do_hierarchical_clustering_average_distance_linkage = _do_hierarchical_clustering_average_distance_linkage
3392 def get_module_version():
3393 """get_module_version() -> std::string const"""
3394 return _IMP_em2d.get_module_version()
3397 """get_example_path(std::string fname) -> std::string"""
3398 return _IMP_em2d.get_example_path(fname)
3401 """get_data_path(std::string fname) -> std::string"""
3402 return _IMP_em2d.get_data_path(fname)
3404 from .
import _version_check
3405 _version_check.check_version(get_module_version())
3406 __version__ = get_module_version()
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.
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.
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.
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.